ALBERT

Beschreibung: Background: Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci. Results: The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations. Conclusions: This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian/non-riparian lineages showed contrasting patterns of gene flow and genetic differentiation, implying that each lineage showed different degrees of reproductive isolation and that they had experienced unique evolutionary and demographic histories in the process of adaptive divergence.

Beschreibung: Background: The sequencing of the genome of the pea aphid Acyrthosiphon pisum revealed an unusual expansion of the miRNA machinery, with two argonaute-1, two dicer-1 and four pasha gene copies. In this report, we have undertaken a deeper evolutionary analysis of the phylogenetic timing of these gene duplications and of the associated selective pressures by sequencing the two copies of ago-1 and dcr-1 in different aphid species of the subfamily Aphidinae. We have also carried out an analysis of the expression of both copies of ago-1 and dcr-1 by semi-quantitative PCR in different morphs of the pea aphid life cycle. Results: The analysis has shown that the duplication of ago-1 occurred in an ancestor of the subfamily Aphidinae while the duplication of dcr-1 appears to be more recent. Besides, it has confirmed a pattern of one conserved copy and one accelerated copy for both genes, and has revealed the action of positive selection on several regions of the fast-evolving ago-1b. On the other hand, the semi-quantitative PCR experiments have revealed a differential expression of these genes between the morphs of the parthenogenetic and the sexual phases of Acyrthosiphon pisum. Conclusions: The discovery of these gene duplications in the miRNA machinery of aphids opens new perspectives of research about the regulation of gene expression in these insects. Accelerated evolution, positive selection and differential expression affecting some of the copies of these genes suggests the possibility of a neofunctionalization of these duplicates, which might play a role in the display of the striking phenotypic plasticity of aphids.

Beschreibung: Background: While search costs have long been understood to affect the evolution of female preference, other costs associated with mating have been the focus of much less attention. Here I consider a novel mate choice cost: female-female intrasexual competition, that is, when females compete with each other for mates. This competition results in cost to female fecundity, such as a reduction in fertility due to decreased direct benefits, sperm limitation, or time and resources spent competing for a mate. I asked if female-female competition affects the evolution of preferences, and further, if the presence of multiple, different, preferences in a population can reduce competitive costs. Results: Using population genetic models of preference and trait evolution, I found that intrasexual competition leads to direct selection against female preferences, and restricts the parameter space under which preference may evolve. I also examined how multiple, different, preferences affected preference evolution with female intrasexual competition. Conclusions: Multiple preferences primarily serve to increase competitive costs and decrease the range of parameters under which preferences may evolve.

Beschreibung: Background: Zona pellucida domain-containing proteins (ZP proteins) have been identified as the principle constituents of the egg coat (EC) of diverse metazoan taxa, including jawed vertebrates, urochordates and molluscs that span hundreds of millions of years of evolutionary divergence. Although ZP proteins generally contain the zona pellucida (ZP) structural modules to fulfill sperm recognition and EC polymerization functions during fertilization, the primary sequences of the ZP proteins from the above-mentioned animal classes are drastically different, which makes it difficult to assess the evolutionary relationships of ZP proteins. To understand the origin of vertebrate ZP proteins, we characterized the egg coat components of Branchiostoma belcheri, an invertebrate species that belongs to the chordate subphylum Cephalochordata. Results: Five ZP proteins (BbZP1-5) were identified by mass spectrometry analyses using the egg coat extracts from both unfertilized and fertilized eggs. In addition to the C-terminal ZP module in each of the BbZPs, the majority contain a low-density lipoprotein receptor domain and a von Willebrand factor type A (vWFA) domain, but none possess an EGF-like domain that is frequently observed in the ZP proteins of urochordates. Fluorescence in situ hybridization and immuno-histochemical analyses of B. belcheri ovaries showed that the five BbZPs are synthesized predominantly in developing eggs and deposited around the extracellular space of the egg, which indicates that they are bona fide egg coat ZP proteins. BbZP1, BbZP3 and BbZP4 are significantly more abundant than BbZP2 and BbZP5 in terms of gene expression levels and the amount of mature proteins present on the egg coats. The major ZP proteins showed high polymorphism because multiple variants are present with different molecular weights. Sequence comparison and phylogenetic analysis between the ZP proteins from cephalochordates, urochordates and vertebrates showed that BbZP1-5 form a monophyletic group and share no significant sequence similarities with the ZP proteins of urochordates and the ZP3 subtype of jawed vertebrates. By contrast, small regions of homology were identifiable between the BbZP and ZP proteins of the non-jawed vertebrate, the sea lamprey Petromyzon marinus. The lamprey ZP proteins were highly similar to the ZP1 and ZP2 subtypes of the jawed vertebrates, which suggests that the ZP proteins of basal chordates most likely shared a recent common ancestor with vertebrate ZP1/2 subtypes and lamprey ZP proteins. Conclusions: The results document the spectra of zona pellucida domain-containing proteins of the egg coat of basal chordates. Particularly, the study provides solid evidence for an invertebrate origin of vertebrate ZP proteins and indicates that there are diverse domain architectures in ZP proteins of various metazoan groups.

Beschreibung: Although the simulation data as well as the conclusion on the proportionality between Vip(i) and Vg(i) in the work[1] is correct, interpretation of some data therein should be corrected.

Beschreibung: Background: Over the last ten years we have seen great efforts focused on revising amphibian systematics. Phylogenetic reconstructions derived from DNA sequence data have played a central role in these revisionary studies but have typically under-sampled the diverse frog family Microhylidae. Here, we present a detailed phylogenetic study focused on expanding previous hypotheses of relationships within this cosmopolitan family. Specifically, we placed an emphasis on assessing relationships among New World genera and those taxa with uncertain phylogenetic affinities (i.e., incertae sedis). Results: One mitochondrial and three nuclear genes (about 2.8 kb) were sequenced to assess phylogenetic relationships. We utilized an unprecedented sampling of 200 microhylid taxa representing 91% of currently recognized subfamilies and 95% of New World genera. Our analyses do not fully resolve relationships among subfamilies supporting previous studies that have suggested a rapid early diversification of this clade. We observed a close relationship between Synapturanus and Otophryne of the subfamily Otophryninae. Within the subfamily Gastrophryninae relationships between genera were well resolved. Conclusion: Otophryninae is distantly related to all other New World microhylids that were recovered as a monophyletic group, Gastrophryninae. Within Gastrophryninae, five genera were recovered as non-monophyletic; we propose taxonomic re-arrangements to render all genera monophyletic. This hypothesis of relationships and updated classification for New World microhylids may serve as a guide to better understand the evolutionary history of this group that is apparently subject to convergent morphological evolution and chromosome reduction. Based on a divergence analysis calibrated with hypotheses from previous studies and fossil data, it appears that microhylid genera inhabiting the New World originated during a period of gradual cooling from the late Oligocene to mid Miocene.

Beschreibung: Background: Delimiting genetic units is useful to enhance taxonomic discovery and is often the first step toward understanding evolutionary mechanisms generating diversification. The six species within the Rhinella crucifer group of toads were defined under morphological criteria alone. Previous data suggest limited correspondence of these species to mitochondrial lineages, and morphological intergradation at transitions between forms suggests hybridization. Here we extensively sampled populations throughout the geographic distribution of the group and analyzed mitochondrial and nuclear sequence data to delimit genetic units using tree--based and allele frequency--based approaches. Results: These approaches yielded complementary results, with allele frequency-based methods performing unexpectedly well given the limited number of loci examined. Both mitochondrial and nuclear markers supported a genetic structure of five units within the group, with three of the inferred units distributed within its main range, while two other units occur in separate isolates. The inferred units are mostly discordant with currently described forms: unequivocal association exists for only two of the six species in the group. Genetic evidence for hybridization exists for two pairs of units, with clear cyto--nuclear allele mixing observed in one case. Conclusions: Our results confirmed that current taxonomy does not represent evolutionary units in the Rhinella crucifer group. Correspondence between genetically distinguishable units and the currently recognized species is only possible for Rhinella henseli and R. inopina. The recognition of other species relies on the reassessment of the geographic range of R. crucifer, the examination of the type series of R. ornata for hybrids, and on the use of additional markers to verify the genetic distinctiveness of R. abei. We state that R. pombali should not remain a valid species since its description appears to be based on hybrids, and that the name R. pombali should be considered a synonym of both R. crucifer and R. ornata. The fifth inferred but undescribed genetic unit may represent a new species. Our results underscore the potential of the R. crucifer species group to contribute to a better understanding of diversification processes and hybridization patterns in the Neotropics, and provide the basis for future evolutionary and taxonomic studies.

Beschreibung: Background: Climatic oscillations throughout the Quaternary had profound effects on temperate biodiversity, but the extent of Quaternary climate change was more severe in temperate regions of the northern hemisphere than in the southern hemisphere. We sought to determine whether this geographic disparity differentially influenced the timing of intraspecific diversification events within ectothermic and endothermic vertebrate species. Using published phylogenetic hypotheses, we gathered data on the oldest intraspecific diversification event within mammal, bird, freshwater fish, amphibian, and reptile species from temperate-zone areas. We then tested whether the timing of diversification events differed between hemispheres. Results: Our analyses provide strong evidence that vertebrates from temperate regions of the northern hemisphere are younger than those from the southern hemisphere. However, we find little evidence to suggest that this relationship differs between endotherms versus ectotherms, or that it varies widely across the five classes of vertebrates that we considered. In addition, we find that on average, endothermic species are much younger than ectothermic species. Conclusion: Our findings suggest that geographic variation in the magnitude of climatic oscillations during the Quaternary led to substantial disparity in the timing of intraspecific diversification events between northern and southern hemisphere vertebrates, and that the magnitude of this divergence is largely congruent across vertebrate taxa.

Beschreibung: Background: Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies. Results: Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication. Conclusions: This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.

Beschreibung: Background: Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities. Results: We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits. Conclusion: Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors' websites.

Beschreibung: Background: Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. Results: We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions: Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South--north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.

Beschreibung: Background: The exponential growth of the number of fully sequenced genomes at varying taxonomic closeness allows one to characterize transcriptional regulation using comparative-genomics analysis instead of time-consuming experimental methods. A transcriptional regulatory unit consists of a transcription factor, its binding site and a regulated gene. These units constitute a graph which contains so-called "network motifs", subgraphs of a given structure. Here we consider genomes of closely related Enterobacteriales and estimate the fraction of conserved network motifs and sites as well as positions under selection in various types of non-coding regions. Results: Using a newly developed technique, we found that the highest fraction of positions under selection, approximately 50%, was observed in synvergon spacers (between consecutive genes from the same strand), followed by ~45% in divergon spacers (common 5'-regions), and ~10% in convergon spacers (common 3'-regions). The fraction of selected positions in functional regions was higher, 60% in transcription factor-binding sites and ~45% in terminators and promoters. Small, but significant differences were observed between Escherichia coli and Salmonella enterica. This fraction is similar to the one observed in eukaryotes.The conservation of binding sites demonstrated some differences between types of regulatory units. In E. coli, strains the interactions of the type "local transcriptional factor gene" turned out to be more conserved in feed-forward loops (FFLs) compared to non-motif interactions. The coherent FFLs tend to be less conserved than the incoherent FFLs. A natural explanation is that the former imply functional redundancy. Conclusions: A naive hypothesis that FFL would be highly conserved turned out to be not entirely true: its conservation depends on its status in the transcriptional network and also from its usage. The fraction of positions under selection in intergenic regions of bacterial genomes is roughly similar to that of eukaryotes. Known regulatory sites explain 20+/-5% of selected positions.

Beschreibung: Background: Phenotypic plasticity, i.e. the capacity to change the phenotype in response to changes in theenvironment without alteration of the genotype, is important for coping with unstableenvironments. In spite of the ample evidence that microorganisms are a major environmentalcomponent playing a significant role in eukaryotic organisms health and disease, there is notmuch information about the effect of microorganism-induced developmental phenotypicplasticity on an adult animals' stress resistance and longevity. Results: We examined the consequences of development of Caenorhabditis elegans larvae fed withdifferent bacterial strains on stress resistance and lifespan of adult nematodes. Bacterialstrains used in this study were either pathogenic or innocuous to nematodes. Exposure to thepathogen during development did not affect larval survival. However, the development ofnematodes on the pathogenic bacterial strains increased lifespan of adult nematodes exposedto the same or a different pathogen. A longer nematode lifespan, developed on pathogens andexposed to pathogens as adults, did not result from an enhanced capacity to kill bacteria, butis likely due to an increased tolerance to the damage inflicted by the pathogenic bacteria. Weobserved that adult nematodes developed on a pathogen induce higher level of expression ofthe hsp-16.2 gene and have higher resistance to heat shock than nematodes developed on aninnocuous strain. Therefore, the increased resistance to pathogens could be, at least partially,due to the early induction of the heat-shock response in nematodes developed on pathogens.The lifespan increase is controlled by the DBL-1 transforming growth factor beta-like, DAF-2/DAF-16 insulin-like, and p38 MAP kinase pathways. Therefore, the observed modulationof adult nematode lifespans by developmental exposure to a pathogen is likely a geneticallycontrolled response. Conclusions: Our study shows that development on pathogens has a hormetic effect on adult nematodes, asit results in increased resistance to different pathogens and to heat shock. Such developmentalplasticity of C. elegans nematodes, which are self-fertilizing homozygous animals producingoffspring with negligible genetic variation, could increase the probability of survival inchanging environments.

Beschreibung: Background: The cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity. Results: Phylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions from other populations (one from a xeric population at Mitzpe Ramon and one from the xeric 'African Slope' of "Evolution Canyon") formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number transcription factor binding sites: 121--128 and 121--134 sites in the two southern arid populations, and 123--128,125--128, and 123--125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light. Conclusions: Drought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticle in plants under stresses.

Beschreibung: Background: Red deer (Cervus elaphus) have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. Results: We obtained mtDNA (D-loop) sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. Conclusions: Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.

Beschreibung: Background: Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. Results: The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. Conclusions: The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for understanding the organization of repeated sequences in the genome.

Beschreibung: Background: The maintenance of biological systems requires plasticity and robustness. The function of the ecdysone receptor, a heterodimer composed of the nuclear receptors ECR (NR1H1) and USP (NR2B4), was maintained in insects despite a dramatic divergence that occurred during the emergence of Mecopterida. This receptor is therefore a good model to study the evolution of plasticity. We tested the hypothesis that selection has shaped the Ligand-Binding Domain (LBD) of USP during evolution of Mecopterida. Results: We isolated usp and cox1 in several species of Drosophilidae, Tenebrionidae and Blattaria and estimated non-synonymous/synonymous rate ratios using maximum-likelihood methods and codon-based substitution models. Although the usp sequences were mainly under negative selection, we detected relaxation at residues located on the surface of the LBD within Mecopterida families. Using branch-site models, we also detected changes in selective constraints along three successive branches of the Mecopterida evolution. Residues located at the bottom of the ligand-binding pocket (LBP) underwent strong positive selection during the emergence of Mecopterida. This change is correlated with the acquisition of a large LBP filled by phospholipids that probably allowed the stabilisation of the new Mecopterida structure. Later, when the two subgroups of Mecopterida (Amphiesmenoptera: Lepidoptera, Trichoptera; Antliophora: Diptera, Mecoptera, Siphonaptera) diverged, the same positions became under purifying selection. Similarly, several positions of the heterodimerisation interface experienced positive selection during the emergence of Mecopterida, rapidly followed by a phase of constrained evolution. An enlargement of the heterodimerisation surface is specific for Mecopterida and was associated with a reinforcement of the obligatory partnership between ECR and USP, at the expense of homodimerisation. Conclusions: In order to explain the episodic mode of evolution of USP, we propose a model in which the molecular adaptation of this protein is seen as a process of resilience for the maintenance of the ecdysone receptor functionality.

Beschreibung: Background: Hybridization, genetic mixture of distinct populations, gives rise to myriad recombinant genotypes. Characterizing the genomic composition of hybrids is critical for studies of hybrid zone dynamics, inheritance of traits, and consequences of hybridization for evolution and conservation. Hybrid genomes are often summarized either by an estimate of the proportion of alleles coming from each ancestral population or classification into discrete categories like F1, F2, backcross, or merely ``hybrid'' vs. ``pure''. In most cases, it is not realistic to classify individuals into the restricted set of classes produced in the first two generations of admixture. However, the continuous ancestry index misses an important dimension of the genotype. Joint consideration of ancestry together with interclass heterozygosity (proportion of loci with alleles from both ancestral populations) captures all of the information in the discrete classification without the unrealistic assumption that only two generations of admixture have transpired. Here I describe a maximum likelihood method for joint estimation of ancestry and interclass heterozygosity. Results: I present two worked examples illustrating the value of the approach for describing variation among hybrid populations and evaluating the validity of the assumption underlying discrete classification. Naively classifying natural hybrids into the standard six line cross categories can be misleading, and false classification can be a serious problem for datasets with few molecular markers. Conclusions: My analysis underscores previous work showing that many (50 or more) ancestry informative markers are needed to avoid erroneous classification. However, valuable inferences can be obtained by focusing directly on distributions of ancestry and heterozygosity. Estimating and visualizing the joint distribution of ancestry and interclass heterozygosity is an effective way to compare the genetic structure of hybrid populations and these estimates can be used in classic quantitative genetic methods for assessing additive, dominant, and epistatic genetic effects on hybrid phenotypes and fitness. The methods are implemented in a freely available package ``HIest'' for the R statistical software (http://cran.r-project.org/web/packages/HIest/index.html).

Beschreibung: Background: Myosin II (or Myosin Heavy Chain II, MHCII) is a family of molecular motors involved inthe contractile activity of animal muscle cells but also in various other cellular processes innon-muscle cells. Previous phylogenetic analyses of bilaterian MHCII genes identified twomain clades associated respectively with smooth/non-muscle cells (MHCIIa) and striatedmuscle cells (MHCIIb). Muscle cells are generally thought to have originated only once inancient animal history, and decisive insights about their early evolution are expected to comefrom expression studies of Myosin II genes in the two non-bilaterian phyla that possessmuscles, the Cnidaria and Ctenophora. Results: We have uncovered three MHCII paralogues in the ctenophore species Pleurobrachia pileus.Phylogenetic analyses indicate that the MHCIIa / MHCIIb duplication is more ancient thanthe divergence between extant metazoan lineages. The ctenophore MHCIIa gene(PpiMHCIIa) has an expression pattern akin to that of "stem cell markers" (Piwi, Vasa...)and is expressed in proliferating cells. We identified two MHCIIb genes that originated froma ctenophore-specific duplication. PpiMHCIIb1 represents the exclusively muscular form ofmyosin II in ctenophore, while PpiMHCIIb2 is expressed in non-muscle cells of varioustypes. In parallel, our phalloidin staining and TEM observations highlight the structuralcomplexity of ctenophore musculature and emphasize the experimental interest of thectenophore tentacle root, in which myogenesis is spatially ordered and strikingly similar tostriated muscle formation in vertebrates. Conclusion: MHCIIa expression in putative stem cells/proliferating cells probably represents an ancestraltrait, while specific involvement of some MHCIIa genes in smooth muscle fibres is auniquely derived feature of the vertebrates. That one ctenophore MHCIIb paralogue(PpiMHCIIb2) has retained MHCIIa-like expression features furthermore suggests thatmuscular expression of the other paralogue, PpiMHCIIb1, was the result ofneofunctionalisation within the ctenophore lineage, making independent origin of ctenophoremuscle cells a likely option.

Beschreibung: Background: Mutualistic interactions are wide-spread but the mechanisms underlying their evolutionarystability and ecological dynamics remain poorly understood. Cultivation mutualisms in whichhosts consume symbionts occur in phylogenetically diverse groups, but often have symbiontmonocultures for each host. This is consistent with the prediction that symbionts should avoidcoexistence with other strains so that host services continue to benefit relatives, but it is lessclear whether hosts should always favor monocultures and what mechanisms they might haveto manipulate symbiont diversity. Few mutualisms have been studied in sufficient geneticdetail to address these issues, so we decided to characterize symbiont diversity in thecomplex mutualism between multiple root aphid species and Lasius flavus ants. Aftershowing elsewhere that three of these aphid species have low dispersal and mostly if notexclusively asexual reproduction, we here investigate aphid diversity within and between antnest mounds. Results: The three focal species (Geoica utricularia, Forda marginata and Tetraneura ulmi) hadconsiderable clonal diversity at the population level. Yet more than half of the ant moundscontained just a single aphid species, a significantly higher percentage than expected from arandom distribution. Over 60% of these single-species mounds had a single aphid clone, andclones tended to persist across subsequent years. Whenever multiple species/clones cooccurredin the same mound, they were spatially separated with more than 95% of the aphidchambers containing individuals of a single clone. Conclusions: L. flavus "husbandry" is characterized by low aphid "livestock" diversity per colony,especially at the nest-chamber level, but it lacks the exclusive monocultures known fromother cultivation mutualisms. The ants appear to eat most of the early instar aphids, so thatadult aphids are unlikely to face limited phloem resources and scramble competition withother aphids. We suggest that such culling of carbohydrate-providing symbionts for proteiningestion may maintain maximal host yield per aphid while also benefitting the domesticatedaphids as long as their clone-mates reproduce successfully. The cost-benefit logic of this typeof polyculture husbandry has striking analogies with human farming practices based onslaughtering young animals for meat to maximize milk-production by a carefully regulatedadult livestock population.

Beschreibung: Background: The evolutionary relationships of closely related species have long been of interest to biologists since these species experienced different evolutionary processes in a relatively short period of time. Comparison of phylogenies inferred from DNA sequences with differing inheritance patterns, such as mitochondrial, autosomal, and X and Y chromosomal loci, can provide more comprehensive inferences of the evolutionary histories of species. Gibbons, especially the genus Hylobates, are particularly intriguing as they consist of multiple closely related species which emerged rapidly and live in close geographic proximity. Our current understanding of relationships among Hylobates species is largely based on data from the maternally-inherited mitochondrial DNAs (mtDNAs). Results: To infer the paternal histories of gibbon taxa, we sequenced multiple Y chromosomal loci from 26 gibbons representing 10 species. As expected, we find levels of sequence variation some five times lower than observed for the mitochondrial genome (mtgenome). Although our Y chromosome phylogenetic tree shows relatively low resolution compared to the mtgenome tree, our results are consistent with the monophyly of gibbon genera suggested by the mtgenome tree. In a comparison of the molecular dating of divergences and on the branching patterns of phylogeny trees between mtgenome and Y chromosome data, we found: 1) the inferred divergence estimates were more recent for the Y chromosome than for the mtgenome, 2) the species H. lar and H. pileatus are reciprocally monophyletic in the mtgenome phylogeny but a H. pileatus individual falls into the H. lar Y chromosome clade. Conclusions: Based on the ~6.4 kb of Y chromosomal DNA sequence data generated for each of the 26 individuals in this study, we provide molecular inferences on gibbon and particularly on Hylobates evolution complementary to those from mtDNA data. Overall, our results illustrate the utility of comparative studies of loci with different inheritance patterns for investigating potential sex specific processes on the evolutionary histories of closely related taxa, and emphasize the need for further sampling of gibbons of known provenance.

Beschreibung: Background: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. Results: We sequenced psbA, which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. Conclusions: The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA, in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others.

Beschreibung: Background: Viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. However, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. We used the segmented RNA bacteriophage [GREEK PHI SYMBOL]6 as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. To do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this 'known phylogeny'. The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts). Results: We observed that RNA segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the Small and Medium RNA chromosomes of the virus, and not on the Large segment. Our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. Using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments. Conclusions: Our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. The imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the RNA viruses that evolved in our study.

Beschreibung: Background: Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Results: Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters corresponding to the four recognised species with the additional division of T. speciosissima into populations north and south of the Shoalhaven River valley. Unexpectedly, the northern disjunct population of T. oreades grouped with T. mongaensis and was identified as a hybrid swarm by the Bayesian assignment test implemented in NewHybrids. Present day and LGM environmental niche models differed dramatically, suggesting that distributions of all species had repeatedly expanded and contracted in response to Pleistocene climatic oscillations and confirming strongly marked historical distributional gaps among taxes. Conclusions: Genetic structure and bio-climatic modeling results are more consistent with a history of allopatric speciation followed by repeated episodes of secondary contact and localised hybridisation, rather than with parapatric speciation. This study on Telopea shows that the evidence for temporal exclusion of gene flow can be found even outside obvious geographical contexts, and that it is possible to make significant progress towards excluding parapatric speciation as a contributing evolutionary process.

Beschreibung: Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in ~ 600 base pairs (bp) of the mitochondrial control region I and at 12--19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.

Beschreibung: Background: The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results: The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions: Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade.

Beschreibung: Background: Opsins are key proteins in animal photoreception. Together with a light-sensitive group, the chromophore, they form visual pigments which initiate the visual transduction cascade when photoactivated. The spectral absorption properties of visual pigments are mainly determined by their opsins, and thus opsins are crucial to understand the adaptations of animal eyes. Studies on the phylogeny and expression pattern of opsins have received considerable attention, but our knowledge about insect visual opsins is still limited. Up to now, researchers have focused on holometabolous insects, while general conclusions require sampling from a broader range of taxa. We have therefore investigated visual opsins in the ocelli and compound eyes of the two-spotted cricket Gryllus bimaculatus, a hemimetabolous insect. Results: Phylogenetic analyses place all identified cricket sequences within the three main visual opsin clades of insects. We assign three of these opsins to visual pigments found in the compound eyes with peak absorbances in the green (515 nm), blue (445 nm) and UV (332 nm) spectral range. Their expression pattern divides the retina into distinct regions: (1) the polarization-sensitive dorsal rim area with blue- and UV-opsin, (2) a newly-discovered ventral band of ommatidia with blue- and green-opsin and (3) the remainder of the compound eye with UV- and green-opsin. In addition, we provide evidence for two ocellar photopigments with peak absorbances in the green (511 nm) and UV (350 nm) spectral range, and with opsins that differ from those expressed in the compound eyes. Conclusions: Our data show that cricket eyes are spectrally more specialized than has previously been assumed, suggesting that similar adaptations in other insect species might have been overlooked. The arrangement of spectral receptor types within some ommatidia of the cricket compound eyes differs from the generally accepted pattern found in holometabolous insect taxa and awaits a functional explanation. From the opsin phylogeny, we conclude that gene duplications, which permitted differential opsin expression in insect ocelli and compound eyes, occurred independently in several insect lineages and are recent compared to the origin of the eyes themselves.

Beschreibung: Background: In addition to selection, the process of evolution is accompanied by stochastic effects, such as changingenvironmental conditions, genetic drift and mutations. Commonly it is believed that without genetic drift,advantageous mutations quickly fixate in a halpoid population due to strong selection and lead to a continuousincrease of the average fitness. This conclusion is based on the assumption of constant fitness. However, forfrequency dependent fitness, where the fitness of an individual depends on the interactions with otherindividuals in the population, this does not hold. Results: We propose a mathematical model that allows to understand the consequences of random frequency dependentmutations on the dynamics of an infinite large population. The frequencies of different types change accordingto the replicator equations and the fitness of a mutant is random and frequency dependent. To capture theinteractions of different types, we employ a payoff matrix of variable size and thus are able to accommodate anarbitrary number of mutations. We assume that at most one mutant type arises at a time. The payoff entries todescribe the mutant type are random variables obeying a probability distribution which is related to the fitnessof the parent type. Conclusions: We show that a random mutant can decrease the average fitness under frequency dependent selection, based onanalytical results for two types, and on simulations for n types. Interestingly, in the case of at most two typesthe probabilities to increase or decrease the average fitness are independent of the concrete probability densityfunction. Instead, they only depend on the probability that the payoff entries of the mutant are larger than thepayoff entries of the parent type.

Beschreibung: Background: Leanchoilia superlata is one of the best known arthropods from the middle Cambrian Burgess Shale of British Columbia. Here we re-describe the morphology of L. superlata and discuss its possible autecology. The re-description follows a standardized scheme, the descriptive matrix approach, designed to provide a template for descriptions of other megacheiran species. Results: Our findings differ in several respects from previous interpretations. Examples include a more slender body; a possible hypostome; a small specialised second appendage, bringing the number of pairs of head appendages to four; a further sub-division of the great appendage, making it more similar to that of other megacheirans; and a complex joint of the exopod reflecting the arthropod's swimming capabilities. Conclusions: Different aspects of the morphology, for example, the morphology of the great appendage and the presence of a basipod with strong median armature on the biramous appendages indicate that L. superlata was an active and agile necto-benthic predator (not a scavenger or deposit feeder as previously interpreted).

Beschreibung: Background: The amount of transcription factor binding sites (TFBS) in an organism's genome positively correlates with the complexity of the regulatory network of the organism. However, the manner by which TFBS arise and accumulate in genomes and the effects of regulatory network complexity on the organism's fitness are far from being known. The availability of TFBS data from many organisms provides an opportunity to explore these issues, particularly from an evolutionary perspective. Results: We analyzed TFBS data from five model organisms - E. coli K12, S. cerevisiae, C. elegans, D. melanogaster, A. thaliana - and found a positive correlation between the amount of non-coding DNA (ncDNA) in the organism's genome and regulatory complexity. Based on this finding, we hypothesize that the amount of ncDNA, combined with the population size, can explain the patterns of regulatory complexity across organisms. To test this hypothesis, we devised a genome-based regulatory pathway model and subjected it to the forces of evolution through population genetic simulations. The results support our hypothesis, showing neutral evolutionary forces alone can explain TFBS patterns, and that selection on the regulatory network function does not alter this finding. Conclusions: The cis-regulome is not a clean functional network crafted by adaptive forces alone, but instead a data source filled with the noise of non-adaptive forces. From a regulatory perspective, this evolutionary noise manifests as complexity on both the binding site and pathway level, which has significant implications on many directions in microbiology, genetics, and synthetic biology.

Beschreibung: Background: Remipedia, a group of homonomously segmented, cave-dwelling, eyeless arthropods have been regarded as basal crustaceans in most early morphological and taxonomic studies. However, molecular sequence information together with the discovery of a highly differentiated brain led to a reconsideration of their phylogenetic position. Various conflicting hypotheses have been proposed including the claim for a basal position of Remipedia up to a close relationship with Malacostraca or Hexapoda. To provide new morphological characters that may allow phylogenetic insights, we have analyzed the architecture of the remipede brain in more detail using immunocytochemistry (serotonin, acetylated alpha-tubulin, synapsin) combined with confocal laser-scanning microscopy and image reconstruction techniques. This approach allows for a comprehensive neuroanatomical comparison with other crustacean and hexapod taxa. Results: The dominant structures of the brain are the deutocerebral olfactory neuropils, which are linked by the olfactory globular tracts to the protocerebral hemiellipsoid bodies. The olfactory globular tracts form a characteristic chiasm in the center of the brain. In Speleonectes tulumensis, each brain hemisphere contains about 120 serotonin immunoreactive neurons, which are distributed in distinct cell groups supplying fine, profusely branching neurites to 16 neuropilar domains. The olfactory neuropil comprises more than 300 spherical olfactory glomeruli arranged in sublobes. Eight serotonin immunoreactive neurons homogeneously innervate the olfactory glomeruli. In the protocerebrum, serotonin immunoreactivity revealed several structures, which, based on their position and connectivity resemble a central complex comprising a central body, a protocerebral bridge, W-, X-, Y-, Z-tracts, and lateral accessory lobes. Conclusions: The brain of Remipedia shows several plesiomorphic features shared with other Mandibulata, such as deutocerebral olfactory neuropils with a glomerular organization, innervations by serotonin immunoreactive interneurons, and connections to protocerebral neuropils. Also, we provided tentative evidence for W-, X-, Y-, Z-tracts in the remipedian central complex like in the brain of Malacostraca, and Hexapoda. Furthermore, Remipedia display several synapomorphies with Malacostraca supporting a sister group relationship between both taxa. These homologies include a chiasm of the olfactory globular tract, which connects the olfactory neuropils with the lateral protocerebrum and the presence of hemiellipsoid bodies. Even though a growing number of molecular investigations unites Remipedia and Cephalocarida, our neuroanatomical comparison does not provide support for such a sister group relationship.

Beschreibung: Background: Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly contribute to increase protein sequence space and generate novel protein functions. However, little is known about the global impact of LCRs on protein evolution. Results: We have traced back the evolutionary history of 2,802 LCRs from a large set of homologous protein families from H.sapiens, M.musculus, G.gallus, D.rerio and C.intestinalis. Transcriptional factors and other regulatory functions are overrepresented in proteins containing LCRs. We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. This dichotomy results in net protein sequence gain over time. We have detected a significant increase in the rate of accumulation of novel LCRs in the ancestral Amniota and mammalian branches, and a reduction in the chicken branch. Alanine and/or glycine-rich LCRs are overrepresented in recently emerged LCR sets from all branches, suggesting that their expansion is better tolerated than for other LCR types. LCRs enriched in positively charged amino acids show the contrary pattern, indicating an important effect of purifying selection in their maintenance. Conclusion: We have performed the first large-scale study on the evolutionary dynamics of LCRs in protein families. The study has shown that the composition of an LCR is an important determinant of its evolutionary pattern.

Beschreibung: Background: Indehiscent sporangia are reported for only a few of derived leptosporangiate ferns. Their evolution has been likely caused by conditions in which promotion of self-fertilization is an evolutionary advantageous strategy such as the colonization of isolated regions and responds to stressful habitat conditions. The Lepisorus clathratus complex provides the opportunity to test this hypothesis because these derived ferns include specimens with regular dehiscent and irregular indehiscent sporangia. The latter occurs preferably in well-defined regions in the Himalaya. Previous studies have shown evidence for multiple origins of indehiscent sporangia and the persistence of populations with indehiscent sporangia at extreme altitudinal ranges of the Qinghai-Tibetan Plateau (QTP). Results: Independent phylogenetic relationships reconstructed using DNA sequences of the uniparentally inherited chloroplast genome and two low-copy nuclear genes confirmed the hypothesis of multiple origins of indehiscent sporangia and the restriction of particular haplotypes to indehiscent sporangia populations in the Lhasa and Nyingchi regions of the QTP. In contrast, the Hengduan Mountains were characterized by high haplotype diversity and the occurrence of accessions with and without indehiscent sporangia. Evidence was found for polyploidy and reticulate evolution in this complex. The putative case of chloroplast capture in the Nyingchi populations provided further evidence for the promotion of isolated but persistent populations by indehiscent sporangia. Conclusions: The presented results confirmed the hypothesis that indehiscent sporangia promote the establishment of persistent population in different regions of the QTP. These results are consistent with the expectations of reproductive reassurance by promotion of self-fertilization that played a critical role in the assembly of populations in isolated locations and/or extreme habitats.

Beschreibung: Background: If the geographical displacement of one species by another is accompanied by hybridization,mitochondrial DNA can introgress asymmetrically, from the outcompeted species into theinvading species, over a large area. We explore this phenomenon using the two parapatriccrested newt species, Triturus macedonicus and T. karelinii, distributed on the BalkanPeninsula in south-eastern Europe, as a model. Results: We first delimit a ca. 54,000 km2 area in which T. macedonicus contains T. kareliniimitochondrial DNA. This introgression zone bisects the range of T. karelinii, cutting off a T.karelinii enclave. The high similarity of introgressed mitochondrial DNA haplotypes withthose found in T. karelinii suggests a recent transfer across the species boundary. We then useecological niche modeling to explore habitat suitability of the location of the present dayintrogression zone under current, mid-Holocene and Last Glacial Maximum conditions. Thisarea was inhospitable during the Last Glacial Maximum for both species, but would havebeen habitable at the mid-Holocene. Since the mid-Holocene, habitat suitability generallyincreased for T. macedonicus, whereas it decreased for T. karelinii. Conclusion: The presence of a T. karelinii enclave suggests that T. karelinii was the first to colonize thearea where the present day introgression zone is positioned after the Last Glacial Maximum.Subsequently, we propose T. karelinii was outcompeted by T. macedonicus, which capturedT. karelinii mitochondrial DNA via introgressive hybridization in the process. Ecologicalniche modeling suggests that this replacement was likely facilitated by a shift in climate sincethe mid-Holocene. We suggest that the northwestern part of the current introgression zonewas probably never inhabited by T. karelinii itself, and that T. karelinii mitochondrial DNAspread there through T. macedonicus exclusively. Considering the spatial distribution of theintrogressed mitochondrial DNA and the signal derived from ecological niche modeling, wedo not favor the hypothesis that foreign mitochondrial DNA was pulled into the T.macedonicus range by natural selection.

Beschreibung: Background: Several studies in Drosophila have shown excessive movement of retrogenes from the X chromosome to autosomes, and that these genes are frequently expressed in the testis. This phenomenon has led to several hypotheses invoking natural selection as the process driving male-biased genes to the autosomes. Metta and Schlotterer (BMC Evol Biol 2010, 10:114) analyzed a set of retrogenes where the parental gene has been subsequently lost. They assumed that this class of retrogenes replaced the ancestral functions of the parental gene, and reported that these retrogenes, although mostly originating from movement out of the X chromosome, showed female-biased or unbiased expression. These observations led the authors to suggest that selective forces (such as meiotic sex chromosome inactivation and sexual antagonism) were not responsible for the observed pattern of retrogene movement out of the X chromosome. Results: We reanalyzed the dataset published by Metta and Schlotterer and found several issues that led us to a different conclusion. In particular, Metta and Schlotterer used a dataset combined with expression data in which significant sex-biased expression is not detectable. First, the authors used a segmental dataset where the genes selected for analysis were less testis-biased in expression than those that were excluded from the study. Second, sex-biased expression was defined by comparing male and female whole-body data and not the expression of these genes in gonadal tissues. This approach significantly reduces the probability of detecting sex-biased expressed genes, which explains why the vast majority of the genes analyzed (parental and retrogenes) were equally expressed in both males and females. Third, the female-biased expression observed by Metta and Schlotterer is mostly found for parental genes located on the X chromosome, which is known to be enriched with genes with female-biased expression. Fourth, using additional gonad expression data, we found that autosomal genes analyzed by Metta and Schlotterer are less up regulated in ovaries and have higher chance to be expressed in meiotic cells of spermatogenesis when compared to X-linked genes. Conclusions: The criteria used to select retrogenes and the sex-biased expression data based on whole adult flies generated a segmental dataset of female-biased and unbiased expressed genes that was unable to detect the higher propensity of autosomal retrogenes to be expressed in males. Thus, there is no support for the authors' view that the movement of new retrogenes, which originated from X-linked parental genes, was not driven by selection. Therefore, selection-based genetic models remain the most parsimonious explanations for the observed chromosomal distribution of retrogenes.

Beschreibung: Background: The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life. Results: Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a 'fourth supergroup' along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity. Conclusions: Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet's biosphere.

Beschreibung: Background: The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. Results: Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. Conclusions: We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.

Beschreibung: Background: The basic helix-loop-helix (bHLH) transcription factors and their homologs form a superfamily that plays essential roles in transcriptional networks of multiple developmental processes. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, human and mouse.ResultIn this study, we conducted a genome-wide survey for bHLH sequences, and identified 57 bHLH sequences encoded in complete genome sequence of the ponerine ant, Harpegnathos saltator. Phylogenetic analysis of the bHLH domain sequences classified these genes into 38 bHLH families with 23, 14, 10, 1, 8 and 1 members in group A, B, C, D, E and F, respectively. The number of PabHLHs (ponerine ant bHLHs) with introns is higher than many other insect species, and they are found to have introns with average lengths only inferior to those of pea aphid. In addition, two H. saltator bHLHs named PaCrp1 and PaSide locate on two separate contigs in the genome. Conclusions: A putative full set of PabHLH genes is comparable with other insect species and genes encoding Oligo, MyoRb and Figalpha were not found in genomes of all insect species of which bHLH family members have been identified. Moreover, in-family phylogenetic analyses indicate that the PabHLH genes are more closely related with Apis mellifera than others. The present study will serve as a solid foundation for further investigations into the structure and function of bHLH proteins in the regulation of H. saltator development.

Beschreibung: Background: Physarales represents the largest taxonomic order among the plasmodial slime molds (myxomycetes). Physarales is of particular interest since the two best-studied myxomycete species, Physarum polycephalum and Didymium iridis, belong to this order and are currently subjected to whole genome and transcriptome analyses. Here we report molecular phylogeny based on ribosomal DNA (rDNA) sequences that includes 57 Physarales isolates. Results: The Physarales nuclear rDNA sequences were found to be loaded with 222 autocatalytic group I introns, which may complicate correct alignments and subsequent phylogenetic tree constructions. Phylogenetic analysis of rDNA sequences depleted of introns confirmed monophyly of the Physarales families Didymiaceae and Physaraceae. Whereas good correlation was noted between phylogeny and taxonomy among the Didymiaceae isolates, significant deviations were seen in Physaraceae. The largest genus, Physarum, was found to be polyphyletic consisting of at least three well supported clades. A synapomorphy, located at the highly conserved G-binding site of L2449 group I intron ribozymes further supported the Physarum clades. Conclusions: Our results provide molecular relationship of Physarales genera, species, and isolates. This information is important in further interpretations of comparative genomics and transcriptomics. In addition, the result supports a polyphyletic origin of the genus Physarum and calls for a reevaluation of current taxonomy.

Beschreibung: Background: Genetic divergence during speciation with gene flow is heterogeneous across the genome, with some regions exhibiting stronger differentiation than others. Exceptionally differentiated regions are often assumed to experience reduced introgression, i.e., reduced flow of alleles from one population into another because such regions are affected by divergent selection or cause reproductive isolation. In contrast, the remainder of the genome can be homogenized by high introgression. Although many studies have documented variation across the genome in genetic differentiation, there are few tests of this hypothesis that explicitly quantify introgression. Here, we provide such a test using 38,304 SNPs in populations of Timema cristinae stick insects. We quantify whether loci that are highly divergent between geographically separated ('allopatric') populations exhibit unusual patterns of introgression in admixed populations. To the extent this is true, highly divergent loci between allopatric populations contribute to reproductive isolation in admixed populations. Results: As predicted, we find a substantial association between locus-specific divergence between allopatric populations and locus-specific introgression in admixed populations. However, many loci depart from this relationship, sometimes strongly so. We also report evidence for selection against foreign alleles due to local adaptation. Conclusions: Loci that are strongly differentiated between allopatric populations sometimes contribute to reproductive isolation in admixed populations. However, geographic variation in selection and local adaptation, in aspects of genetic architecture (such as organization of genes, recombination rate variation, number and effect size of variants contributing to adaptation, etc.), and in stochastic evolutionary processes such as drift can cause strong differentiation of loci that do not always contribute to reproductive isolation. The results have implications for the theory of 'genomic islands of speciation'.

Beschreibung: Background: Geographic variation in the thermal environment impacts a broad range of biochemical andphysiological processes and can be a major selective force leading to local populationadaptation. In the intertidal copepod Tigriopus californicus, populations along the coast ofCalifornia show differences in thermal tolerance that are consistent with adaptation, i.e.,southern populations withstand thermal stresses that are lethal to northern populations. Tounderstand the genetic basis of these physiological differences, we use an RNA-seq approachto compare genome-wide patterns of gene expression in two populations known to differ inthermal tolerance. Results: Observed differences in gene expression between the southern (San Diego) and the northern(Santa Cruz) populations included both the number of affected loci as well as the identity ofthese loci. However, the most pronounced differences concerned the amplitude of upregulationof genes producing heat shock proteins (Hsps) and genes involved inubiquitination and proteolysis. Among the hsp genes, orthologous pairs show markedlydifferent thermal responses as the amplitude of hsp response was greatly elevated in the SanDiego population, most notably in members of the hsp70 gene family. There was no evidenceof accelerated evolution at the sequence level for hsp genes. Among other sets of genes,cuticle genes were up-regulated in SD but down-regulated in SC, and mitochondrial geneswere down-regulated in both populations. Conclusions: Marked changes in gene expression were observed in response to acute sub-lethal thermalstress in the copepod T. californicus. Although some qualitative differences were observedbetween populations, the most pronounced differences involved the magnitude of inductionof numerous hsp and ubiquitin genes. These differences in gene expression suggest thatevolutionary divergence in the regulatory pathway(s) involved in acute temperature stressmay offer at least a partial explanation of population differences in thermal toleranceobserved in Tigriopus.

Beschreibung: Background: Atlantolacerta andreanskyi is an enigmatic lacertid lizard that, according to the most recent molecular analyses, belongs to the tribe Eremiadini, family Lacertidae. It is a mountain specialist, restricted to areas above 2400 m of the High Atlas Mountains of Morocco with apparently no connection between the different populations. In order to investigate its phylogeography, 92 specimens of A. andreanskyi were analyzed from eight different populations across the distribution range of the species for up to 1108 base pairs of mitochondrial DNA (12S, ND4 and flanking tRNA-His) and 2585 base pairs of nuclear DNA including five loci (PDC, ACM4, C-MOS, RAG1, MC1R). Results: The results obtained with both concatenated and coalescent approaches and clustering methods, clearly show that all the populations analyzed present a very high level of genetic differentiation for the mitochondrial markers used and are also generally differentiated at the nuclear level. Conclusions: These results indicate that A. andreanskyi is an additional example of a montane species complex.

Beschreibung: Background: Population bottlenecks can lead to a loss of variation at disease resistance loci, which could have important consequences for the ability of populations to adapt to pathogen pressure. Alternatively, current or past balancing selection could maintain high diversity, creating a strong heterogeneity in the retention of polymorphism across the genome of bottlenecked populations. We sequenced part of the LRR region of 9 NBS-LRR disease resistance genes in the outcrossing Capsella grandiflora and the recently derived, bottlenecked selfing species Capsella rubella, and compared levels and patterns of nucleotide diversity and divergence with genome-wide reference loci. Results: In strong contrast with reference loci, average diversity at resistance loci was comparable between C. rubella and C. grandiflora, primarily due to two loci with highly elevated diversity indicative of past or present balancing selection. Average between-species differentiation was also reduced at the set of R-genes compared with reference loci, which is consistent with the maintenance of ancestral polymorphism. Conclusions: Historical or ongoing balancing selection on plant disease resistance genes is a likely contributor to the retention of ancestral polymorphism in some regions of the bottlenecked Capella rubella genome.

Beschreibung: Background: Specialization for ecological niches is a balance of evolutionary adaptation and its accompanying tradeoffs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same, defined seasonal environment for 50,000 generations. Over this time, much adaptation and specialization to the environment has occurred. The presence of citrate in the growth media selected one lineage to gain the novel ability to utilize citrate as a carbon source after 31,000 generations. Here we test whether other strains have specialized to rely on citrate after 50,000 generations. Results: We show that in addition to the citrate-catabolizing strain, three other lineages evolving in parallel have acquired a dependence on citrate for optimal growth on glucose. None of these strains were stimulated indirectly by the sodium present in disodium citrate, nor exhibited even partial utilization of citrate as a carbon source. Instead, all three of these citrate-stimulated populations appear to rely on it as a chelator of iron. Conclusions: The strains we examine here have evolved specialization to their environment through apparent loss of function. Our results are most consistent with the accumulation of mutations in iron transport genes that were obviated by abundant citrate. The results present another example where a subtle decision in the design of an evolution experiment led to unexpected evolutionary outcomes.

Beschreibung: Background: The range of potential morphologies resulting from evolution is limited by complex interacting processes, ranging from development to function. Quantifying these interactions is important for understanding adaptation and convergent evolution. Using three-dimensional reconstructions of carnivoran and dasyuromorph tooth rows, we compared statistical models of the relationship between tooth row shape and the opposing tooth row, a static feature, as well as measures of mandibular motion during chewing (occlusion), which are kinetic features. This is a new approach to quantifying functional integration because we use measures of movement and displacement, such as the amount the mandible translates laterally during occlusion, as opposed to conventional morphological measures, such as mandible length and geometric landmarks. By sampling two distantly related groups of ecologically similar mammals, we study carnivorous mammals in general rather than a specific group of mammals. Results: Statistical model comparisons demonstrate that the best performing models always include some measure of mandibular motion, indicating that functional and statistical models of tooth shape as purely a function of the opposing tooth row are too simple and that increased model complexity provides a better understanding of tooth form. The predictors of the best performing models always included the opposing tooth row shape and a relative linear measure of mandibular motion. Conclusions: Our results provide quantitative support of long-standing hypotheses of tooth row shape as being influenced by mandibular motion in addition to the opposing tooth row. Additionally, this study illustrates the utility and necessity of including kinetic features in analyses of morphological integration.

Beschreibung: Background: A number of studies have measured selection in nature to understand how populations adapt to their environment; however, the temporal dynamics of selection is rarely investigated. The aim of this study was to assess the temporal variation in selection by comparing the mode, direction and strength of selection on fitness related traits between two cohorts of coho salmon (Oncorhynchus kisutch). Specifically, we quantified individual reproductive success and examined selection on date of return and body length in a wild population at Big Beef Creek, Washington (USA). Results: Reproductive success and the mode, direction and strength of selection on date of return and body length differed between two cohorts sampled in 2006 and 2007. Adults of the first brood year had greater success over those of the second. In 2006, disruptive selection favored early and late returning individuals in 2-year-old males, and earlier returning 3-year-old males had higher fitness. No evidence of selection on date of return was detected in females. In 2007, selection on date of return was not observed in males of either age class, but stabilizing selection on date of return was observed in females. No selection on body length was detected in males of both age classes in 2006, and large size was associated with higher fitness in females. In 2007, selection favored larger size in 3-year-old males and intermediate size in females. Correlational selection between date of return and body length was observed only in 2-year-old males in 2006. Conclusions: We found evidence of selection on body length and date of return to the spawning ground, both of which are important fitness-related traits in salmonid species, but this selection varied over time. Fluctuation in the mode, direction and strength of selection between two cohorts are likely to be due to factors such as changes in precipitation, occurrence of catastrophic events (flooding), the proportion of younger- versus older-maturing males, and sex ratio and densities of spawners.

Beschreibung: Background: Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA (hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate.Result: Electron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/ fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b. Conclusion: Some duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.

Beschreibung: Background: Previous studies have proposed that mammalian toll like receptors (TLRs) have evolvedunder diversifying selection due to their role in pathogen detection. To determine if this is thecase, we examined the extent of adaptive evolution in the TLR5 gene in both individualspecies and defined clades of the mammalia. Results: In support of previous studies, we find evidence of adaptive evolution of mammalian TLR5.However, we also show that TLR5 genes of domestic livestock have a concentration of singlenucleotide polymorphisms suggesting a specific signature of adaptation. Using codon modelsof evolution we have identified a concentration of rapidly evolving codons within the TLR5extracellular domain a site of interaction between host and the bacterial surface proteinflagellin. Conclusions: The results suggest that interactions between pathogen and host may be driving adaptivechange in TLR5 by competition between species. In support of this, we have identified singlenucleotide polymorphisms (SNP) in sheep and cattle TLR5 genes that are co-localised andco-incident with the predicted adaptive codons suggesting that adaptation in this region of theTLR5 gene is on-going in domestic species.

Beschreibung: Background: Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times. Results: A total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons and C. rufilatus), consistent with their recent divergence and/or possible hybridization with each other. Conclusions: Molecular phylogenetic analyses suggest that Pleistocene-era climatic oscillations have played an important role in the speciation of this largely forest-dwelling group. Our results also reveal the most well supported species phylogeny for the subfamily to date, but also highlight several areas of inconsistency between our current understanding of duiker taxonomy and the evolutionary relationships depicted here. These findings may therefore prove particularly relevant to future conservation efforts, given that many species are presently regulated under the Convention for Trade in Endangered Species.

Beschreibung: Background: The Neotropical catfish family Loricariidae contains over 830 species that displayextraordinary variation in jaw morphologies but nonetheless reveal little interspecificvariation from a generalized diet of detritus and algae. To investigate this paradox, wecollected delta13C and delta15N stable isotope signatures from 649 specimens representing 32loricariid genera (82 species) from 19 local assemblages distributed across South America.We calculated vectors representing the distance and direction of each specimen relative to thedelta15N/delta13C centroid for its local assemblage, and then examined the evolutionarydiversification of loricariids across assemblage isotope niche space by regressing the meanvector for each genus in each assemblage onto a phylogeny reconstructed from osteologicalcharacters. Results: Loricariids displayed a total range of delta15N assemblage centroid deviation spanning 4.9per thousand,which is within the tissue-diet discrimination range known for Loricariidae, indicating thatthey feed at a similar trophic level and that delta15N largely reflects differences in their dietaryprotein content. Total range of delta13C deviation spanned 7.4per thousand, which is less than the minimumrange reported for neotropical river fish communities, suggesting that loricariids selectivelyassimilate a restricted subset of the full basal resource spectrum available to fishes.Phylogenetic regression of assemblage centroid-standardized vectors for delta15N and delta13Crevealed that loricariid genera with allopatric distributions in disjunct river basins partitionbasal resources in an evolutionarily conserved manner concordant with patterns of jawmorphological specialization and with evolutionary diversification via ecological radiation. Conclusions: Trophic partitioning along elemental/nutritional gradients may provide an importantmechanism of dietary segregation and evolutionary diversification among loricariids andperhaps other taxonomic groups of apparently generalist detritivores and herbivores.Evolutionary patterns among the Loricariidae show a high degree of trophic nicheconservatism, indicating that evolutionary lineage affiliation can be a strong predictor of howbasal consumers segregate trophic niche space.

Beschreibung: Background: The temporal and geographical diversification of Neotropical insects remains poorlyunderstood because of the complex changes in geological and climatic conditions thatoccurred during the Cenozoic. To better understand extant patterns in Neotropicalbiodiversity, we investigated the evolutionary history of three Neotropical swallowtailTroidini genera (Papilionidae). First, DNA-based species delimitation analyses wereconducted to assess species boundaries within Neotropical Troidini using an enlargedfragment of the standard barcode gene. Molecularly delineated species were then used toinfer a time-calibrated species-level phylogeny based on a three-gene dataset and Bayesiandating analyses. The corresponding chronogram was used to explore their temporal andgeographical diversification through distinct likelihood-based methods. Results: The phylogeny for Neotropical Troidini was well resolved and strongly supported. Moleculardating and biogeographic analyses indicate that the extant lineages of Neotropical Troidinihave a late Eocene (33-42 Ma) origin in North America. Two independent lineages (Battusand Euryades + Parides) reached South America via the GAARlandia temporary connection,and later became extinct in North America. They only began substantive diversificationduring the early Miocene in Amazonia. Macroevolutionary analysis supports the "museummodel" of diversification, rather than Pleistocene refugia, as the best explanation for thediversification of these lineages. Conclusions: This study demonstrates that: (i) current Neotropical biodiversity may have originated ex situ;(ii) the GAARlandia bridge was important in facilitating invasions of South America; (iii)colonization of Amazonia initiated the crown diversification of these swallowtails; and (iv)Amazonia is not only a species-rich region but also acted as a sanctuary for the dynamics ofthis diversity. In particular, Amazonia probably allowed the persistence of old lineages andcontributed to the steady accumulation of diversity over time with constant net diversificationrates, a result that contrasts with previous studies on other South American butterflies.

Beschreibung: Background: Horizontal gene transfer (HGT) has greatly impacted the genealogical history of manylineages, particularly for prokaryotes, with genes frequently moving in and out of a line ofdescent. Many genes that were acquired by a lineage in the past likely originated fromancestral relatives that have since gone extinct. During the course of evolution, HGT hasplayed an essential role in the origin and dissemination of genetic and metabolic novelty. Results: Three divergent forms of leucyl-tRNA synthetase (LeuRS) exist in the archaeal orderHalobacteriales, commonly known as haloarchaea. Few haloarchaeal genomes have thetypical archaeal form of this enzyme and phylogenetic analysis indicates it clusters within theEuryarchaeota as expected. The majority of sequenced halobacterial genomes possess abacterial form of LeuRS. Phylogenetic reconstruction puts this larger group of haloarchaea atthe base of the bacterial domain. The most parsimonious explanation is that an ancienttransfer of LeuRS took place from an organism related to the ancestor of the bacterial domainto the haloarchaea. The bacterial form of LeuRS further underwent gene duplications and/orgene transfers within the haloarchaea, with some genomes possessing two distinct types ofbacterial LeuRS. The cognate tRNALeu also reveals two distinct clusters for the haloarchaea;however, these tRNALeu clusters do not coincide with the groupings found in the LeuRS tree,revealing that LeuRS evolved independently of its cognate tRNA. Conclusions: The study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of genetransfer originating in lineages that went extinct since the transfer occurred. The haloarchaealLeuRS and tRNALeu did not co-evolve.

Beschreibung: Background: Patterns of genetic divergence between populations of facultative metallophytes have beeninvestigated extensively. However, most previous investigations have focused on a singleplant species making it unclear if genetic divergence shows common patterns or, conversely,is species-specific. The herbs Rumex acetosa L. and Commelina communis L. are twopseudo-metallophytes thriving in both normal and cupriferous soils along the middle andlower reaches of the Yangtze River in China. Their non-metallicolous and metallicolouspopulations are often sympatric thus providing an ideal opportunity for comparativeestimation of genetic structures and divergence under the selective pressure derived fromcopper toxicity. Results: In the present study, patterns of genetic divergence of R. acetosa and C. communis, includingmetal tolerance, genetic structure and genetic relationships between populations, wereinvestigated and compared using hydroponic experiments, AFLP, ISSR and chloroplastgenetic markers. Our results show a significant reduction in genetic diversity in metallicolouspopulations of C. communis but not in R. acetosa. Moreover, genetic differentiation is less inR. acetosa than in C. communis, the latter species also shows a clustering of its metallicolouspopulations. Conclusions: We propose that the genetic divergences apparent in R. acetosa and C. communis, and thecontrasting responses of the two species to copper contamination, might be attributed to thedifferences in their intrinsic physiological and ecological properties. No simple andgeneralised conclusions on genetic divergence in pseudo-metallophytes can thus be drawn.

Beschreibung: Background: A-Kinase Anchoring Proteins (AKAPs) are molecular scaffolding proteins mediating theassembly of multi-protein complexes containing cAMP-dependent protein kinase A (PKA),directing the kinase in discrete subcellular locations. Splice variants from the AKAP7 gene(AKAP15/18) are vital components of neuronal and cardiac phosphatase complexes, ionchannels, cardiac Ca2+ handling and renal water transport. Results: Shown in evolutionary analyses, the formation of the AKAP7-RI/RII binding domain(required for AKAP/PKA-R interaction) corresponds to vertebrate-specific gene duplicationevents in the PKA-RI/RII subunits. Species analyses of AKAP7 splice variants shows theancestral AKAP7 splice variant is AKAP7alpha, while the ancestral long form AKAP7 splicevariant is AKAP7gamma. Multi-species AKAP7 gene alignments, show the recent formation ofAKAP7delta occurs with the loss of native AKAP7gamma in rats and basal primates. AKAP7 genealignments and two dimensional Western analyses indicate that AKAP7gamma is produced from aninternal translation-start site that is present in the AKAP7delta cDNA of mice and humans butabsent in rats. Immunofluorescence analysis of AKAP7 protein localization in both rat andmouse heart suggests AKAP7gamma replaces AKAP7delta at the cardiac sarcoplasmic reticulum inspecies other than rat. DNA sequencing identified Human AKAP7delta insertion-deletions(indels) that promote the production of AKAP7gamma instead of AKAP7delta. Conclusions: This AKAP7 molecular evolution study shows that these vital scaffolding proteins developedin ancestral vertebrates and that independent mutations in the AKAP7 genes of rodents andearly primates has resulted in the recent formation of AKAP7delta, a splice variant of likelylesser importance in humans than currently described.

Beschreibung: Background: During the evolutionary history of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches. Results: The maximum likelihood (ML) phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion. Conclusions: We showed that an ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.

Beschreibung: Background: Even with well-known sampling biases, the fossil record is key to understanding macroevolutionarypatterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossilrecord of scleractinian corals shows a remarkable period of rapid diversification followed bymassive extinction. Here we combine a time-calibrated molecular phylogeny based on threenuclear introns with an updated fossil stratigraphy to examine patterns of radiation andextinction in Caribbean corals within the traditional family Faviidae. Results: Concatenated phylogenetic analysis showed most species of Caribbean faviids weremonophyletic, with the exception of two Manicina species. The time-calibrated tree revealedthe stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genusManicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation andproductivity may have favored free-living, heterotrophic species. Reef and shallow waterspecialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 -6 Ma) as the Isthmus of Panama shoaled and regional productivity declined. Conclusions: Later origination of the stem group than predicted from the fossil record corroborates thehypothesis of morphological convergence in Diploria and Favia genera. Our data support therapid evolution of morphological and life-history traits among faviid corals that can be linkedto Mio-Pliocene environmental changes.

Beschreibung: After publication of our work (Lombard et al, BMC Evol Biol, 2011, 11:232), we noticed several major mistakes in the figure images provided for final publication: although the main text and the legends are correct, Figure 3 has been replaced by an image present in the Addition File 1 and Figures 4, 5 and 6 are displaced with regard to their correct numbers and legends. Please, accept our apologies and refer to the correct corresponding Figures 3, 4, 5 and 6 that we provide in this erratum. Legends are the same as in the original article.

Beschreibung: Background: Inferences concerning the evolution of invertebrate nervous systems are often hampered bythe lack of a solid data base for little known but phylogenetically crucial taxa. In order tocontribute to the discussion concerning the ancestral neural pattern of the Lophotrochozoa (amajor clade that includes a number of phyla that exhibit a ciliated larva in their life cycle), weinvestigated neurogenesis in Phoronopsis harmeri, a member of the poorly studiedPhoronida, by using antibody staining against serotonin and FMRFamide in combination withconfocal microscopy and 3D reconstruction software.Results and conclusionsThe larva of Phoronopsis harmeri exhibits a highly complex nervous system, including anapical organ that consists of four different neural cell types, such as numerous serotonin-likeimmunoreactive flask-shaped cells. Such cells are found in the majority of lophotrochozoanlarvae and therefore most likely belong to the ground pattern of the last commonlophotrochozoan ancestor (LCLA). The finding of a transitory paired ventral neurite bundlewith serially repeated commissures that disappears during metamorphosis suggests that sucha structure was part of the "ur-phoronid" nervous system, but was lost in the adult, probablydue to its acquired sessile benthic lifestyle.

Beschreibung: Background: Maternal effects are environmental influences on the phenotype of one individual that are due to the expression of genes in its mother, and are expected to evolve whenever females are better capable of assessing the environmental conditions that their offspring will experience than the offspring themselves. In the dung beetle Onthophagus taurus, conditional male dimorphism is associated with alternative reproductive tactics: majors fight and guard females whereas minors sneak copulations. Furthermore, variation in dung beetle population density has different fitness consequences for each male morph, and theory predicts that higher population density might select for a higher frequency of minors and/or greater expenditure on weaponry in majors. Because adult dung beetles provide offspring with all the nutritional resources for their development, maternal effects strongly influence male phenotype. Results: Here we tested whether female O. taurus are capable of perceiving population density, and responding by changing the phenotype of their offspring. We found that mothers who were reared with other conspecifics in their pre-mating period produced major offspring that had longer horns across a wider range of body sizes than the major offspring of females that were reared in isolation in their pre-mating period. Moreover, our results indicate that this maternal effect on male weaponry does not operate through the amount of dung provided by females to their offspring, but is rather transmitted through egg or brood mass composition. Finally, although theory predicts that females experiencing higher density might produce more minor males, we found no support for this, rather the best fitting models were equivocal as to whether fewer or the same proportions of minors were produced. Conclusions: Our study describes a new type of maternal effect in dung beetles, which probably allows females to respond to population density adaptively, preparing at least their major offspring for the sexual competition they will face in the future. This new type of maternal effect in dung beetles represents a novel transgenerational response of alternative reproductive tactics to population density.

Beschreibung: Background: Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Results: Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio omega that varies linearly with RSA provides a better model fit than an RSA-independent omega or an omega that is estimated separately in individual RSA bins. We further show that the branch length t and the transition--transverion ratio kappa also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between omega and RSA, and gene expression level affects both the intercept and the slope. Conclusions: Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between omega and RSA implies that genes are better characterized by their omega slope and intercept than by just their mean omega.

Beschreibung: Background: In food-deceptive orchids of the genera Anacamptis, Neotinea and Orchis floral isolation has been shown to be weak, whereas late-acting reproductive barriers are mostly strong, often restricting hybridization to the F1 generation. Only in a few species hybridization extends beyond the F1 generation, giving rise to hybrid swarms. However, little is known about the abundance of later-generation hybrids and what factors drive their occurrence in hybrid populations. In this study, molecular analyses were combined with detailed morphological measurements in a hybrid population of two closely related Orchis species (Orchis militaris and O. purpurea) to investigate the hypothesis that the abundance of later-generation hybrids is driven by changes in floral characters after hybridization that exert selective pressures that in turn affect hybridization. Results: Both the molecular and morphological data point to extensive genetic and morphological homogenization and asymmetric introgression. Estimating genomic clines from the multi-locus genotype data and testing for deviation from neutrality revealed that 30 out of 113 (27%) AFLP markers significantly deviated from neutral expectations. Plants with large floral displays or plant with flowers that resembled more O. purpurea had higher female fitness than plants with small floral displays or plants with flowers resembling more O. militaris, suggesting that directional selection may have contributed to the observed patterns of introgression. Conclusions: These results indicate that in closely related orchid species hybridization and gene introgression may be partly driven by selection for floral traits of one of the parental types. However, because some pure individuals were still present in the studied population, the parental species appeared to be sufficiently isolated to survive the challenge of sympatry.

Beschreibung: Background: The fern genus Dryopteris (Dryopteridaceae) is among the most common and species rich fern genera in temperate forests in the northern hemisphere containing 225--300 species worldwide. The circumscription of Dryopteris has been controversial and various related genera have, over the time, been included in and excluded from Dryopteris. The infrageneric phylogeny has largely remained unclear, and the placement of the majority of the supraspecific taxa of Dryopteris has never been tested using molecular data. Results: In this study, DNA sequences of four plastid loci (rbcL gene, rps4-trnS spacer, trnL intron, trnL-F spacer) were used to reconstruct the phylogeny of Dryopteris. A total of 122 accessions are sampled in our analysis and they represent 100 species of the expanded Dryopteris including Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema. All four subgenera and 19 sections currently recognized in Dryopteris s.s. are included. One species each of Arachniodes, Leptorumohra, and Lithostegia of Dryopteridaceae are used as outgroups. Our study confirms the paraphyly of Dryopteris and provides the first strong molecular evidence on the monophyly of Acrophorus, Diacalpe, Dryopsis, Nothoperanema, and Peranema. However, all these monophyletic groups together with the paraphyletic Acrorumohra are suggested to be merged into Dryopteris based on both molecular and morphological evidence. Our analysis identified 13 well-supported monophyletic groups. Each of the 13 clades is additionally supported by morphological synapomophies and is inferred to represent a major evolutionary lineage in Dryopteris. In contrast, monophyly of the four subgenera and 15 out of 19 sections currently recognized in Dryopteris s.s is not supported by plastid data Conclusions: The genera, Acrophorus, Acrorumohra, Diacalpe, Dryopsis, Nothoperanema, and Peranema, should all be merged into Dryopteris. Most species of these genera share a short rhizome and catadromic arrangement of frond segments, unlike the sister genus of Dryopteris s.l., Arachniodes, which has anadromic arrangement of frond segments. The non-monophyly of the 19 out of the 21 supraspecific taxa (sections, subgenera) in Dryopteris strongly suggests that the current taxonomy of this genus is in need of revision. The disagreement between the previous taxonomy and molecular results in Dryopteris may be due partly to interspecific hybridization and polyplodization. More morphological studies and molecular data, especially from the nuclear genome, are needed to thoroughly elucidate the evolutionary history of Dryopteris. The 13 well-supported clades identified based on our data represent 13 major evolutionary lineages in Dryopteris that are also supported by morphological synapomophies.

Beschreibung: Background: Transitions in habitats and feeding behaviors were fundamental to the diversification of lifeon Earth. There is ongoing debate regarding the typical directionality of transitions betweenaquatic and terrestrial habitats and the mechanisms responsible for the preponderance ofterrestrial to aquatic transitions. Snail-killing flies (Diptera: Sciomyzidae) represent anexcellent model system to study such transitions because their larvae display a range offeeding behaviors, being predators, parasitoids or saprophages of a variety of mollusks infreshwater, shoreline and dry terrestrial habitats. The remarkable genus Tetanocera(Tetanocerini) occupies five larval feeding groups and all of the habitat types mentionedabove. This study has four principal objectives: (i) construct a robust estimate of phylogenyfor Tetanocera and Tetanocerini, (ii) estimate the evolutionary transitions in larval feedingbehaviors and habitats, (iii) test the monophyly of feeding groups and (iv) identifymechanisms underlying sciomyzid habitat and feeding behavior evolution. Results: Bayesian inference and maximum likelihood analyses of molecular data provided strongsupport that the Sciomyzini, Tetanocerini and Tetanocera are monophyletic. However, themonophyly of many behavioral groupings was rejected via phylogenetic constraint analyses.We determined that (i) the ancestral sciomyzid lineage was terrestrial, (ii) there was a singleterrestrial to aquatic habitat transition early in the evolution of the Tetanocerini and (iii) therewere at least 10 independent aquatic to terrestrial habitat transitions and at least 15 feedingbehavior transitions during tetanocerine phylogenesis. The ancestor of Tetanocera wasaquatic with five lineages making independent transitions to terrestrial habitats and sevenmaking independent transitions in feeding behaviors. Conclusions: The preponderance of aquatic to terrestrial transitions in sciomyzids goes against the trendgenerally observed across eukaryotes. Damp shoreline habitats are likely transitional wherelarvae can change habitat but still have similar prey available. Transitioning from aquatic toterrestrial habitats is likely easier than the reverse for sciomyzids because morphologicalcharacters associated with air-breathing while under the water's surface are lost rather thangained, and sciomyzids originated and diversified during a general drying period in Earth'shistory. Our results imply that any animal lineage having aquatic and terrestrial members,respiring the same way in both habitats and having the same type of food available in bothhabitats could show a similar pattern of multiple independent habitat transitions coincidentwith changes in behavioral and morphological traits.

Beschreibung: Background: The New Zealand (NZ) cicada fauna contains two co-distributed lineages that independently colonized the isolated continental fragment in the Miocene. One extensively studied lineage includes 90% of the extant species (Kikihia + Maoricicada + Rhodopsalta; ca 51 spp.), while the other contains just four extant species (Amphipsalta -- 3 spp. + Notopsalta -- 1 sp.) and has been little studied. We examined mitochondrial and nuclear-gene phylogenies and phylogeography, Bayesian relaxed-clock divergence timing (incorporating literature-based uncertainty of molecular clock estimates) and ecological niche models of the species from the smaller radiation. Results: Mitochondrial and nuclear-gene trees supported the monophyly of Amphipsalta. Most interspecific diversification within Amphipsalta-Notopsalta occurred from the mid-Miocene to the Pliocene. However, interspecific divergence time estimates had large confidence intervals and were highly dependent on the assumed tree prior, and comparisons of uncorrected and patristic distances suggested difficulty in estimation of branch lengths. In contrast, intraspecific divergence times varied little across analyses, and all appear to have occurred during the Pleistocene. Two large-bodied forest taxa (A. cingulata, A. zelandica) showed minimal phylogeographic structure, with intraspecific diversification dating to ca. 0.16 and 0.37 Ma, respectively. Mid-Pleistocene-age phylogeographic structure was found within two smaller-bodied species (A. strepitans -- 1.16 Ma, N. sericea -- 1.36 Ma] inhabiting dry open habitats. Branches separating independently evolving species were long compared to intraspecific branches. Ecological niche models hindcast to the Last Glacial Maximum (LGM) matched expectations from the genetic datasets for A. zelandica and A. strepitans, suggesting that the range of A. zelandica was greatly reduced while A. strepitans refugia were more extensive. However, no LGM habitat could be reconstructed for A. cingulata and N. sericea, suggesting survival in microhabitats not detectable with our downscaled climate data. Conclusions: Unlike the large and continuous diversification exhibited by the Kikihia-Maoricicada-Rhodopsalta clade, the contemporaneous Amphipsalta-Notopsalta lineage contains four comparatively old (early branching) species that show only recent diversification. This indicates either a long period of stasis with no speciation, or one or more bouts of extinction that have pruned the radiation. Within Amphipsalta-Notopsalta, greater population structure is found in dry-open-habitat species versus forest specialists. We attribute this difference to the fact that NZ lowland forests were repeatedly reduced in extent during glacial periods, while steep, open habitats likely became more available during late Pleistocene uplift.

Beschreibung: Background: Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescence-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results: We found that divergence estimates, from both concatenated gene tree and coalescence-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions: Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.

Beschreibung: Background: It has been reported that the modularity of metabolic networks of bacteria is closely relatedto the variability of their living habitats. However, given the dependency of the modularityscore on the community structure, it remains unknown whether organisms achieve certainmodularity via similar or different community structures. Results: In this work, we studied the relationship between similarities in modularity scores andsimilarities in community structures of the metabolic networks of 1021 species. Bothsimilarities are then compared against the genetic distances. We revisited the associationbetween modularity and variability of the microbial living environments and extended theanalysis to other aspects of their life style such as temperature and oxygen requirements. Wealso tested both topological and biological intuition of the community structures identifiedand investigated the extent of their conservation with respect to the taxomony. Conclusions: We find that similar modularities are realized by different community structures. We findthat such convergent evolution of modularity is closely associated with the number of(distinct) enzymes in the organism's metabolome, a consequence of different life styles ofthe species. We find that the order of modularity is the same as the order of the number ofthe enzymes under the classification based on the temperature preference but not on theoxygen requirement. Besides, inspection of modularity-based communities reveals thatthese communities are graph-theoretically meaningful yet not reflective of specificbiological functions. From an evolutionary perspective, we find that the communitystructures are conserved only at the level of kingdoms. Our results call for moreinvestigation into the interplay between evolution and modularity: how evolution shapesmodularity, and how modularity affects evolution (mainly in terms of fitness andevolvability). Further, our results call for exploring new measures of modularity andnetwork communities that better correspond to functional categorizations.

Beschreibung: Background: The observation that females mate multiply when males provide nothing but sperm - which sexual selection theory suggests is unlikely to be limiting - continues to puzzle evolutionary biologists. Here we test the hypothesis that multiple mating is prevalent under such circumstances because it enhances female fitness. We do this by allowing female Trinidadian guppies to mate with either a single male or with multiple males, and then tracking the consequences of these matings across two generations. Results: Overall, multiply mated females produced 67% more F2 grand-offspring than singly mated females. These offspring, however, did not achieve greater net fitness, grow or mature faster, nor were they larger at birth, than the offspring of singly mated females. The higher fecundity among multiply mated mothers was driven by greater production of sons but not daughters. Contrary to expectation, multiple mating did not affect F1 growth, time to sexual maturation, or viability. Our results show that multiple mating yields benefits to females in the form of an increase in the production of F1. However, they also show that, individually, the offspring of multiply mated females do not grow at different rates than offspring of singly mated females, nor do any indirect fitness benefits or costs accrue to second-generation offspring. Conclusions: The study provides strong evidence that multiple mating is advantageous to females, even when males contribute only sperm. This benefit is achieved through an increase in fecundity in the first generation, rather than through other fitness correlates such as size at birth, growth rate, time to sexual maturation and survival. Considered alongside previous work that female guppies can choose to mate with multiple partners, our results provide compelling evidence that direct fitness benefits underpin these mating decisions.

Beschreibung: On the 4th September 2012 the International Commission on Zoological Nomenclature announced an amendment to the International Code of Zoological Nomenclature allowing for electronic publication of the scientific names of animals. In this interview Frank-T. Krell discusses the implications of this amendment for authors wishing to publish descriptions of newly identified animal species in online and open access journals, and for the future of taxonomic science.

Beschreibung: Background: The Escherichia coli species contains a variety of commensal and pathogenic strains, and itsintraspecific diversity is extraordinarily high. With the availability of an increasing number ofE. coli strain genomes, a more comprehensive concept of their evolutionary history andecological adaptation can be developed using phylogenomic analyses. In this study, weconstructed two types of whole-genome phylogenies based on 34 E. coli strains usingcollinear genomic segments. The first phylogeny was based on the concatenated collinearregions shared by all of the studied genomes, and the second phylogeny was based on thevariable collinear regions that are absent from at least one genome. Intuitively, the firstphylogeny is likely to reveal the lineal evolutionary history among these strains (i.e., anevolutionary phylogeny), whereas the latter phylogeny is likely to reflect the whole-genomesimilarities of extant strains (i.e., a similarity phylogeny). Results: Within the evolutionary phylogeny, the strains were clustered in accordance with knownphylogenetic groups and phenotypes. When comparing evolutionary and similarityphylogenies, a concept emerges that Shigella may have originated from at least three distinctancestors and evolved into a single clade. By scrutinizing the properties that are sharedamongst Shigella strains but missing in other E. coli genomes, we found that the commonregions of the Shigella genomes were mainly influenced by mobile genetic elements,implying that they may have experienced convergent evolution via horizontal gene transfer.Based on an inspection of certain key branches of interest, we identified several collinearregions that may be associated with the pathogenicity of specific strains. Moreover, byexamining the annotated genes within these regions, further detailed evidence associated withpathogenicity was revealed. Conclusions: Collinear regions are reliable genomic features used for phylogenomic analysis amongclosely related genomes while linking the genomic diversity with phenotypic differences in ameaningful way. The pathogenicity of a strain may be associated with both the arrival ofvirulence factors and the modification of genomes via mutations. Such phylogenomic studiesthat compare collinear regions of whole genomes will help to better understand the evolutionand adaptation of closely related microbes and E. coli in particular.

Beschreibung: Background: During evolution, plants and other organisms have developed a diversity of chemicaldefences, leading to the evolution of various groups of specialized metabolites selected fortheir endogenous biological function. A correlation between phylogeny and biosyntheticpathways could offer a predictive approach enabling more efficient selection of plants for thedevelopment of traditional medicine and lead discovery. However, this relationship has rarelybeen rigorously tested and the potential predictive power is consequently unknown. Results: We produced a phylogenetic hypothesis for the medicinally important plant subfamilyAmaryllidoideae (Amaryllidaceae) based on parsimony and Bayesian analysis of nuclear,plastid, and mitochondrial DNA sequences of over 100 species. We tested if alkaloiddiversity and activity in bioassays related to the central nervous system are significantlycorrelated with phylogeny and found evidence for a significant phylogenetic signal in thesetraits, although the effect is not strong. Conclusions: Several genera are non-monophyletic emphasizing the importance of using phylogeny forinterpretation of character distribution. Alkaloid diversity and in vitro inhibition ofacetylcholinesterase (AChE) and binding to the serotonin reuptake transporter (SERT) aresignificantly correlated with phylogeny. This has implications for the use of phylogenies tointerpret chemical evolution and biosynthetic pathways, to select candidate taxa for leaddiscovery, and to make recommendations for policies regarding traditional use andconservation priorities.

Beschreibung: Background: Small nucleolar (sno)RNAs are required for posttranscriptional processing and modification of ribosomal, spliceosomal and messenger RNAs. Their presence in both eukaryotes and archaea indicates that snoRNAs are evolutionarily ancient. The location of some snoRNAs within the introns of ribosomal protein genes has been suggested to belie an RNA world origin, with the exons of the earliest protein-coding genes having evolved around snoRNAs after the advent of templated protein synthesis. Alternatively, this intronic location may reflect more recent selection for coexpression of snoRNAs and ribosomal components, ensuring rRNA modification by snoRNAs during ribosome synthesis. To gain insight into the evolutionary origins of this genetic organization, we examined the antiquity of snoRNA families and the stability of their genomic location across 44 eukaryote genomes. Results: We report that dozens of snoRNA families are traceable to the Last Eukaryotic Common Ancestor (LECA), but find only weak similarities between the oldest eukaryotic snoRNAs and archaeal snoRNA-like genes. Moreover, many of these LECA snoRNAs are located within the introns of host genes independently traceable to the LECA. Comparative genomic analyses reveal the intronic location of LECA snoRNAs is not ancestral however, suggesting the pattern we observe is the result of ongoing intragenomic mobility. Analysis of human transcriptome data indicates that the primary requirement for hosting intronic snoRNAs is a broad expression profile. Consistent with ongoing mobility across broadly-expressed genes, we report a case of recent migration of a non-LECA snoRNA from the intron of a ubiquitously expressed non-LECA host gene into the introns of two LECA genes during the evolution of primates. Conclusions: Our analyses show that snoRNAs were a well-established family of RNAs at the time when eukaryotes began to diversify. While many are intronic, this association is not evolutionarily stable across the eukaryote tree; ongoing intragenomic mobility has erased signal of their ancestral gene organization, and neither introns-first nor evolved co-expression adequately explain our results. We therefore present a third model --- constrained drift --- whereby individual snoRNAs are intragenomically mobile and may occupy any genomic location from which expression satisfies phenotype.

Beschreibung: Background: Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. The SDR196C family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (SDH), which are of great industrial interest. In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed. Results: The distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria. Six different bacterial families were found, encompassing alpha-, beta- and gamma-proteobacteria. This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life. A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators.According to the obtained trees, six different lineages and three sublineages can be discerned. The phylogenetic analysis also suggested two different origins for SDH in beta-proteobacteria and four origins for gamma-proteobacteria.Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages. Conclusion: SDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy. The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure. This suggests that SDH are very old and emerged early during the evolution. This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.

Beschreibung: Background: The highly improved cognitive function is the most significant change in human evolutionaryhistory. Recently, several large-scale studies reported the evolutionary roles of DNAmethylation; however, the role of DNA methylation on brain evolution is largely unknown. Results: To test if DNA methylation has contributed to the evolution of human brain, with the use ofMeDIP-Chip and SEQUENOM MassARRAY, we conducted a genome-wide analysis toidentify differentially methylated regions (DMRs) in the brain between humans and rhesusmacaques. We first identified a total of 150 candidate DMRs by the MeDIP-Chip method,among which 4DMRs were confirmed by the MassARRAY analysis. All 4 DMRs are withinor close to the CpG islands, and a MIR3 repeat element was identified in one DMR, but norepeat sequence was observed in the other 3 DMRs. For the 4 DMR genes, their proteins tendto be conserved and two genes have neural related functions. Bisulfite sequencing andphylogenetic comparison among human, chimpanzee, rhesus macaque and rat suggestedseveral regions of lineage specific DNA methylation, including a human specifichypomethylated region in the promoter of K6IRS2 gene. Conclusions: Our study provides a new angle of studying human brain evolution and understanding theevolutionary role of DNA methylation in the central nervous system. The results suggest thatthe patterns of DNA methylation in the brain are in general similar between humans and nonhumanprimates, and only a few DMRs were identified.

Beschreibung: Background: Bdelloid rotifers are microscopic animals that have apparently survived without sex for millions of years and are able to survive desiccation at all life stages through a process called anhydrobiosis. Both of these characteristics are believed to have played a role in shaping several unusual features of bdelloid genomes discovered in recent years. Studies into the impact of asexuality and anhydrobiosis on bdelloid genomes have focused on understanding gene copy number. Here we investigate copy number and sequence divergence in alpha tubulin. Alpha tubulin is conserved and normally present in low copy numbers in animals, but multiplication of alpha tubulin copies has occurred in animals adapted to extreme environments, such as cold-adapted Antarctic fish. Using cloning and sequencing we compared alpha tubulin copy variation in four species of bdelloid rotifers and four species of monogonont rotifers, which are facultatively sexual and cannot survive desiccation as adults. Results were verified using transcriptome data from one species, Adineta ricciae. Results: In common with the typical pattern for animals, monogonont rotifers contain either one or two copies of alpha tubulin, but bdelloid species contain between 11 and 13 different copies, distributed across five classes. Approximately half of the copies form a highly conserved group that vary by only 1.1 % amino acid pairwise divergence with each other and with the monogonont copies. The other copies have divergent amino acid sequences that evolved significantly faster between classes than within them, relative to synonymous changes, and vary in predicted biochemical properties. Copies of each class were expressed under the laboratory conditions used to construct the transcriptome. Conclusions: Our findings are consistent with recent evidence that bdelloids are degenerate tetraploids and that functional divergence of ancestral copies of genes has occurred, but show how further duplication events in the ancestor of bdelloids led to proliferation in both conserved and functionally divergent copies of this gene.

Beschreibung: Background: Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellulareukaryotes such as animals. Recently, many genes of miscellaneous algal origins werediscovered in choanoflagellates. Considering that choanoflagellates are the existing closestrelatives of animals, we speculated that ancient HGT might have occurred in the unicellularancestor of animals and affected the long-term evolution of animals. Results: Through genome screening, phylogenetic and domain analyses, we identified 14 genefamilies, including 92 genes, in the tunicate Ciona intestinalis that are likely derived frommiscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed indiverse animals, suggesting that they were mostly acquired by the common ancestor ofanimals. Their miscellaneous origins also suggest that these genes are not derived from aparticular algal endosymbiont. In addition, most genes identified in our analyses arefunctionally related to molecule transport, cellular regulation and methylation signaling,suggesting that the acquisition of these genes might have facilitated the intercellularcommunication in the ancestral animal. Conclusions: Our findings provide additional evidence that algal genes in aplastidic eukaryotes are notexclusively derived from historical plastids and thus important for interpreting the evolutionof eukaryotic photosynthesis. Most importantly, our data represent the first evidence thatmore anciently acquired genes might exist in animals and that ancient HGT events haveplayed an important role in animal evolution.

Beschreibung: Background: The nuclear receptors (NRs) are an important class of transcription factors that are conservedacross animal phyla. Canonical NRs consist of a DNA-binding domain (DBD) and ligandbindingdomain (LBD). While most animals have 20-40 NRs, nematodes of the genusCaenorhabditis have experienced a spectacular proliferation and divergence of NR genes.The LBDs of evolutionarily-conserved Caenorhabditis NRs have diverged sharply from theirDrosophila and vertebrate orthologs, while the DBDs have been strongly conserved. TheNR2E family of NRs play critical roles in development, especially in the nervous system. Inthis study, we explore the phylogenetics and function of the NR2E family of Caenorhabditiselegans, using an in vivo assay to test LBD function. Results: Phylogenetic analysis reveals that the NR2E family of NRs consists of three broadlyconservedclades of orthologous NRs. In C. elegans, these clades are defined by nhr-67, fax-1and nhr-239. The vertebrate orthologs of nhr-67 and fax-1 are Tlx and PNR, respectively.While the nhr-239 clade includes orthologs in insects (Hr83), an echinoderm, and ahemichordate, the gene appears to have been lost from vertebrate lineages. The C. elegansand C. briggsae nhr-239 genes have an apparently-truncated and highly-diverged LBDregion. An additional C. elegans NR2E gene, nhr-111, appears to be a recently-evolvedparalog of fax-1; it is present in C. elegans, but not C. briggsae or other animals withcompletely-sequenced genomes. Analysis of the relatively unstudied nhr-111 and nhr-239genes demonstrates that they are both expressed--nhr-111 very broadly and nhr-239 in asmall subset of neurons. Analysis of the FAX-1 LBD in an in vivo assay revealed that it is notrequired for at least some developmental functions. Conclusions: Our analysis supports three conserved clades of NR2E receptors, only two of which arerepresented in vertebrates, indicating three ancestral NR2E genes in the urbilateria. The lackof a requirement for a FAX-1 LBD suggests that the relatively high level of sequencedivergence for Caenorhabditis LBDs reflects relaxed selection on the primary sequence asopposed to divergent positive selection. This observation is consistent with a model in whichdivergence of some Caenorhabditis LBDs is allowed, at least in part, by the absence of aligand requirement.

Beschreibung: Background: Female signals of fertility have evolved in diverse taxa. Among the most interesting study systems are those of multimale multifemale group-living primates, where females signal fertility to males through multiple signals, and in which there is substantial inter-specific variation in the composition and reliability of such signals. Among the macaques, some species display reliable behavioural and/or anogenital signals while others do not. One cause of this variation may be differences in male competitive regimes: some species show marked sexual dimorphism and reproductive skew, with males fighting for dominance, while others show low dimorphism and skew, with males queuing for dominance. As such, there is variation in the extent to which rank is a reliable proxy for male competitiveness, which may affect the extent to which it is in females' interest to signal ovulation reliably. However, data on ovulatory signals are absent from species at one end of the macaque continuum, where selection has led to high sexual dimorphism and male reproductive skew. Here we present data from 31 cycles of 19 wild female crested macaques, a highly sexually dimorphic species with strong mating skew. We collected measures of ovarian hormone data from faeces, sexual swelling size from digital images, and male and female behaviour. Results: We show that both sexual swelling size and female proceptivity are graded-signals, but relatively reliable indicators of ovulation, with swelling size largest and female proceptive behaviours most frequent around ovulation. Sexual swelling size was also larger in conceptive cycles. Male mating behaviour was well timed to female ovulation, suggesting that males had accurate information about this. Conclusion: Though probabilistic, crested macaque ovulatory signals are relatively reliable. We argue that in species where males fight over dominance, male dominance rank is surrogate for competitiveness. Under these circumstances it is in the interest of females to increase paternity concentration and assurance in dominants beyond levels seen in species where such competition is less marked. As such, we suggest that it may be variation in male competitive regimes that leads to the evolution of fertility signalling systems of different reliability.

Beschreibung: Background: Polyamine oxidase enzymes catalyze the oxidation of polyamines and acetylpolyamines. Since polyamines are basic regulators of cell growth and proliferation, their homeostasis is crucial for cell life. Members of the polyamine oxidase gene family have been identified in a wide variety of animals, including vertebrates, arthropodes, nematodes, placozoa, as well as in plants and fungi. Polyamine oxidases (PAOs) from yeast can oxidize spermine, N1-acetylspermine, and N1-acetylspermidine, however, in vertebrates two different enzymes, namely spermine oxidase (SMO) and acetylpolyamine oxidase (APAO), specifically catalyze the oxidation of spermine, and N1-acetylspermine/N1-acetylspermidine, respectively. Little is known about the molecular evolutionary history of these enzymes. However, since the yeast PAO is able to catalyze the oxidation of both acetylated and non acetylated polyamines, and in vertebrates these functions are addressed by two specialized polyamine oxidase subfamilies (APAO and SMO), it can be hypothesized an ancestral reference for the former enzyme from which the latter would have been derived. Results: We analysed 36 SMO, 26 APAO and 14 PAO homologue protein sequences from 54 taxa including various vertebrates and invertebrates. The analysis of the full-length sequences and the principal domains of vertebrate and invertebrate PAOs yielded consensus primary protein sequences for vertebrate SMOs and APAOs, and invertebrate PAOs.This analysis, coupled to molecular modeling techniques, also unveiled sequence regions that confer specific structural and functional properties, including substrate specificity, by the different PAO subfamilies. Molecular phylogenetic trees revealed a basal position of all the invertebrates PAO enzymes relative to vertebrate SMOs and APAOs. PAOs from insects constitute a monophyletic clade. Two PAO variants sampled in the amphioxus are basal to the dichotomy between two well supported monophyletic clades including, respectively, all the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS) mechanism. Conclusions: In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO) and orthologous genes related by speciation events (PAOs, SMOs/APAOs). Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies.

Beschreibung: Background: The parathyroid hormone (PTH)-family consists of a group of structurally related factors thatregulate calcium and bone homeostasis and are also involved in development of organs suchas the heart, mammary gland and immune system. They interact with specific members offamily 2 B1 G-protein coupled receptors (GPCRs), which have been characterised in teleostsand mammals. Two PTH/PTHrP receptors, PTH1R and PTH2R exist in mammals and inteleost fish a further receptor PTH3R has also been identified. Recently in chicken, PTHfamilymembers involved in calcium transport were characterized and specific PTHRs aresuggested to exist although they have not yet been isolated or functionally characterized. Theaim of this study is to further explore the evolution and function of the vertebratePTH/PTHrP system through the isolation, phylogenetic analysis and functionalcharacterization of the chicken receptors. Results: Two PTHRs were isolated in chicken and sequence comparison and phylogenetic analysisindicate that the chicken receptors correspond to PTH1R and PTH3R, which emerged prior tothe teleost/tetrapod divergence since they are present in cartilaginous fish. The vertebratePTH2R receptor and its ligand TIP39 have been lost from bird genomes. Chicken PTH1Rand PTH3R have a divergent and widespread tissue expression and are also evident in veryearly embryonic stages of development. Receptor stimulation studies using HEK293 cellsstably expressing the chicken PTH1R and PTH3R and monitoring cAMP production revealedthey are activated by chicken 1-34 N-terminal PTH-family peptides in a dose dependentmanner. PTH-L and PTHrP were the most effective peptides in activating PTH1R (EC50 = 7.7nM and EC50 = 22.7 nM, respectively). In contrast, PTH-L (100 nM) produced a small cAMPaccumulation on activation of PTH3R but PTHrP and PTH (EC50 = 2.5 nM and EC50 = 22.1nM, respectively) readily activated the receptor. PTHrP also stimulated intracellular Ca2+accumulation on activation of PTH1R but not PTH3R. Conclusion: Two PTHR homologues of the vertebrate PTH1R and PTH3R were isolated and functionallycharacterized in chicken. Their distinct pattern of expression during embryo development andin adult tissues, together with their ligand preference, suggests that they have acquiredspecific functions, which have contributed to their maintenance in the genome. PTH2R andits activating ligand, TIP39, are absent from bird genomes. Nonetheless identification ofputative PTH2R and TIP39 in the genome of an ancient agnathan, lamprey, suggests thePTH/PTHrP ligand and receptor family was already present in an early basal paraphyleticgroup of vertebrates and during the vertebrate radiation diverged via gene/genomeduplication and deletion events. Knowledge of the role PTH/PTHrP system in earlyvertebrates will help to establish evolution of function.

Beschreibung: Background: The Cucurbitaceae genus Trichosanthes comprises 90-100 species that occur from India toJapan and southeast to Australia and Fiji. Most species have large white or pale yellow petalswith conspicuously fringed margins, the fringes sometimes several cm long. Pollination isusually by hawkmoths. Previous molecular data for a small number of species suggested thata monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species,lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we testthese groups' relationships using a species sampling of c. 60% and 4759 nucleotides ofnuclear and plastid DNA. To infer the time and direction of the geographic expansion of theTrichosanthes clade we employ molecular clock dating and statistical biogeographicreconstruction, and we also address the gain or loss of petal fringes. Results: Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself ispolyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa,while Hodgsonia is more distantly related. Of six morphology-based sections inTrichosanthes with more than one species, three are supported by the molecular results; twonew sections appear warranted. Molecular dating and biogeographic analyses suggest anOligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification andspread throughout the Malesian biogeographic region and into the Australian continent. Conclusions: Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed bytwo losses in the latter coincident with shifts to other pollinators but not with long-distancedispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyosand the tropical African Telfairia, these cucurbit lineages represent an ideal system for moredetailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

Beschreibung: Background: Cancer, much like most human disease, is routinely studied by utilizing model organisms. Ofthese model organisms, mice are often dominant. However, our assumptions of functionalequivalence fail to consider the opportunity for divergence conferred by ~180 Million Years(MY) of independent evolution between these species. For a given set of human diseaserelated genes, it is therefore important to determine if functional equivalency has beenretained between species. In this study we test the hypothesis that cancer associated geneshave different patterns of substitution akin to adaptive evolution in different mammallineages. Results: Our analysis of the current literature and colon cancer databases identified 22 genesexhibiting colon cancer associated germline mutations. We identified orthologs for these 22genes across a set of high coverage (〉6X) vertebrate genomes. Analysis of these orthologousdatasets revealed significant levels of positive selection. Evidence of lineage-specific positiveselection was identified in 14 genes in both ancestral and extant lineages. Lineage-specificpositive selection was detected in the ancestral Euarchontoglires and Hominidae lineages forSTK11, in the ancestral primate lineage for CDH1, in the ancestral Murinae lineage for bothSDHC and MSH6 genes and the ancestral Muridae lineage for TSC1. Conclusion: Identifying positive selection in the primate, Hominidae, Muridae and Murinae lineagessuggest an ancestral functional shift in these genes between the rodent and primate lineages.Analyses such as this, combining evolutionary theory and predictions - along with medicallyrelevant data, can thus provide us with important clues for modeling human diseases.

Beschreibung: Background: Bacterial growth in well-mixed culture is often assumed to be an autonomous process only depending upon the external conditions under control of the investigator. However, increasingly there is awareness that interactions between cells in culture can lead to surprising phenomena such as density-dependence in the initiation of growth. Results: Here I report the unexpected discovery of a density threshold for growth of a strain of Methylobacterium extorquens AM1 used to inoculate eight replicate populations that were evolved in methanol. Six of these populations failed to grow to the expected full density during the first couple transfers. Remarkably, the final cell number of six populations crashed to levels 60- to 400-fold smaller than their cohorts. Five of these populations recovered to full density soon after, but one population remained an order of magnitude smaller for over one hundred generations. These variable dynamics appeared to be due to a density threshold for growth that was specific to both this particular ancestral strain and to growth on methanol: when tested at full density, this population had become less fit than its ancestor. Simply increasing the initial dilution just 16-fold reversed this result, revealing that this population had more than a 3-fold advantage when tested at this lower density. As this population evolved and ultimately recovered to the same final density range as the other populations this low-density advantage waned. Conclusions: These results demonstrate surprisingly strong tradeoffs for adaptation to growth at low absolute densities that manifest over just a 16-fold change in density. Capturing laboratory examples of transitions to and from growth at low density may help us understand the physiological and evolutionary forces that have led to the unusual properties of natural bacteria that have specialized to low-density environments such as the open ocean.

Beschreibung: Background: Force, Lynch and Conery proposed the duplication-degeneration-complementation (DDC) model in which partitioning of ancestral functions (subfunctionalization) and acquisition of novel functions (neofunctionalization) were the two primary mechanisms for the retention of duplicated genes. The DDC model was tested by analyzing the transcriptional induction of the duplicated fatty acid-binding protein (fabp) genes by clofibrate in zebrafish. Clofibrate is a specific ligand of the peroxisome proliferator-activated receptor (PPAR); it activates PPAR which then binds to a peroxisome proliferator response element (PPRE) to induce the transcriptional initiation of genes primarily involved in lipid homeostasis. Zebrafish was chosen as our model organism as it has many duplicated genes owing to a whole genome duplication (WGD) event that occurred ~230-400 million years ago in the teleost fish lineage. We assayed the steady-state levels of fabp mRNA and heterogeneous nuclear RNA (hnRNA) transcripts in liver, intestine, muscle, brain and heart for four sets of duplicated fabp genes, fabp1a/fabp1b.1/fabp1b.2, fabp7a/fabp7b, fabp10a/fabp10b and fabp11a/fabp11b in zebrafish fed different concentrations of clofibrate.Result: Electron microscopy showed an increase in the number of peroxisomes and mitochondria in liver and heart, respectively, in zebrafish fed clofibrate. Clofibrate also increased the steady-state level of acox1 mRNA and hnRNA transcripts in different tissues, a gene with a functional PPRE. These results demonstrate that zebrafish is responsive to clofibrate, unlike some other fishes. The levels of fabp mRNA and hnRNA transcripts for the four sets of duplicated fabp genes was determined by reverse transcription, quantitative polymerase chain reaction (RT-qPCR). The level of hnRNA coded by a gene is an indirect estimate of the rate of transcriptional initiation of that gene. Clofibrate increased the steady-state level of fabp mRNAs and hnRNAs for both the duplicated copies of fabp1a/ fabp1b.1, and fabp7a/fabp7b, but in different tissues. Clofibrate also increased the steady-state level of fabp10a and fabp11a mRNAs and hnRNAs in liver, but not for fabp10b and fabp11b. Conclusion: Some duplicated fabp genes have, most likely, retained PPREs, but induction by clofibrate is over-ridden by an, as yet, unknown tissue-specific mechanism(s). Regardless of the tissue-specific mechanism(s), transcriptional control of duplicated zebrafish fabp genes by clofibrate has markedly diverged since the WGD event.

Beschreibung: Background: Fluctuating asymmetry (FA), defined as small random deviations from the ideal bilateralsymmetry, has been hypothesized to increase in response to both genetic and environmentalstress experienced by a population. We compared levels of FA in 12 bilateral meristic traits(viz. lateral-line system neuromasts and lateral plates), and heterozygosity in 23 microsatelliteloci, among four marine (high piscine predation risk) and four pond (zero piscine predationrisk) populations of nine-spined sticklebacks (Pungitius pungitius). Results: Pond sticklebacks had on average three times higher levels of FA than marine fish and thisdifference was highly significant. Heterozygosity in microsatellite markers was on averagetwo times lower in pond (HE [almost equal to] 0.3) than in marine (HE [almost equal to] 0.6) populations, and levels of FAand heterozygosity were negatively correlated across populations. However, after controllingfor habitat effect on heterozygosity, levels of FA and heterozygosity were uncorrelated. Conclusions: The fact that levels of FA in traits likely to be important in the context of predator evasionwere elevated in ponds compared to marine populations suggests that relaxed selection forhomeostasis in ponds lacking predatory fish may be responsible for the observed habitatdifference in levels of FA. This inference also aligns with the observation that the levels ofgenetic variability across the populations did not explain population differences in levels ofFA after correcting for habitat effect. Hence, while differences in strength of selection, ratherthan in the degree of genetic stress could be argued to explain habitat differences in levels ofFA, the hypothesis that increased FA in ponds is caused by genetic stress cannot be rejected.

Beschreibung: Background: Ommatidae is arguably the "most ancestral" extant beetle family. Recent species of this group are only found in South America and Australia, but the fossil record reveals a much broader geographical distribution in the Mesozoic. Up to now, thirteen fossil genera with more than 100 species of ommatids have been described. However, the systematic relationships of the extant and extinct Ommatidae have remained obscure. Results: In this study, four new species, Pareuryomma ancistrodonta sp. nov., Pareuryomma cardiobasis sp. nov., Omma delicata sp. nov., and Tetraphalerus decorosus sp. nov., are described. Based on well-preserved fossil specimens and previously published data the phylogenetic relationships of extant and extinct lineages of Ommatidae were analyzed for the first time cladistically. Based on the results we propose a new classification with six tribes of Ommatidae: Pronotocupedini, Notocupedini, Lithocupedini, Brochocoleini, Ommatini and Tetraphalerini. These taxa replace the traditional four subfamilies. Conclusion: There is good support for the monophyly of the ingroup. Notocupedini, as defined by Ponomarenko, are paraphyletic. Notocupoides + Eurydictyon are the sister group of the remaining fossil and extant ommatids. Together they form the clade Pronotocupedini. Notocupedini and Lithocupedini are the next two branches. The tribe Brochocoleini is the sister group of a clade comprising Tetraphalerini and Ommatini.

Beschreibung: Background Gene duplication and subsequent functional divergence especially expression divergence have been widely considered as main sources for evolutionary innovations. Many studies evidenced that genetic regulatory network evolved rapidly shortly after gene duplication, thus leading to accelerated expression divergence and diversification. However, little is known whether epigenetic factors have mediated the evolution of expression regulation since gene duplication. In this study, we conducted detailed analyses on yeast histone modification (HM), the major epigenetics type in this organism, as well as other available functional genomics data to address this issue.Results Duplicate genes, on average, share more common HM-code patterns than random singleton pairs in their promoters and open reading frames (ORF). Though HM-code divergence between duplicates in both promoter and ORF regions increase with their sequence divergence, the HM-code in ORF region evolves slower than that in promoter region, probably owing to the functional constraints imposed on protein sequences. After excluding the confounding effect of sequence divergence (or evolutionary time), we found the evidence supporting the notion that in yeast, the HM-code may co-evolve with cis- and trans-regulatory factors. Moreover, we observed that deletion of some yeast HM-related enzymes increases the expression divergence between duplicate genes, yet the effect is lower than the case of transcription factor (TF) deletion or environmental stresses.Conclusions Our analyses demonstrate that after gene duplication, yeast histone modification profile between duplicates diverged with evolutionary time, similar to genetic regulatory elements. Moreover, we found the evidence of the co-evolution between genetic and epigenetic elements since gene duplication, together contributing to the expression divergence between duplicate genes.

Beschreibung: Background: Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the eld of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversication patterns of organisms, no synthesis has addressed the case of the most diversied mammalian clade: the Rodentia. Results: Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56 % and 81 % of the known specic and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversication rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identied a number of shifts in diversication rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversication factors that might have shaped the rodents radiation. Conclusions: The present glimpse on the diversication pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversication rates than any other 1rodent group. Different topological signatures suggest distinct diversication processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversication rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversication signal for most of the Paleogene nodes.

Beschreibung: Background: Gene presence/absence (P/A) polymorphisms are commonly observed in plants and are important in individual adaptation and species differentiation. Detecting their abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms in a given species. The recently sequenced 80 Arabidopsis genomes provide an opportunity to address these questions. Results: By systematically investigating these accessions, we identified 2,407 P/A genes (or 8.9%) absent in one or more genomes, averaging 444 absent genes per accession. 50.6% of P/A genes belonged to multi-copy gene families, or 31.0% to clustered genes. However, the highest proportion of P/A genes, outnumbered in singleton genes, was observed in the regions near centromeres. In addition, a significant correlation was observed between the P/Agene frequency among the 80 accessions and the diversity level at P/A loci. Furthermore, the proportion of P/A genes was different among functional gene categories. Finally, a P/A gene tree showed a diversified population structure in the worldwide Arabidopsis accessions. Conclusions: An estimate of P/A genes and their frequency distribution in the worldwide Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes, by which individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.

Beschreibung: Background: Antagonistic species interactions can lead to coevolutionary genotype or phenotypefrequency oscillations, with important implications for ecological and evolutionaryprocesses. However, direct empirical evidence of such oscillations is rare. The rarity ofobservations is generally attributed to inherent difficulties of ecological and evolutionarylong-term studies, to weak or absent interaction between species, or to the absence ofnegative frequency-dependence. Results: Here, we show that another factor - non-genetic inheritance, mediated for example byepigenetic mechanisms - can completely eliminate oscillations even if only a smallfraction of offspring are affected. We analytically derive the threshold value of thisfraction at which the dynamics change from oscillatory to stable, and investigate howselection, mutation and generation times differences between the two species affect thethreshold value. These results strongly suggest that the lack of phenotype frequencyoscillations should not be attributed to the lack of strong interactions between antagonisticspecies. Conclusions: Given increasing evidence of non-genetic effects on the outcomes of antagonistic speciesinteractions, we suggest that these effects should be incorporated into ecological andevolutionary models of interacting species.

Beschreibung: Background: As one of the most important but seriously endangered wild relatives of the cultivated tea,Camellia taliensis harbors valuable gene resources for tea tree improvement in the future.The knowledge of genetic variation and population structure may provide insights intoevolutionary history and germplasm conservation of the species. Results: Here, we sampled 21 natural populations from the species' range in China and performed thephylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplastrpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detectedat rpl32-trnL (h = 0.841; pi = 0.00314) were almost as high as at PAL (h = 0.836; pi = 0.00417).Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989),suggesting fairly high genetic differentiation and low levels of recurrent gene flow throughseeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests thatpopulation genetic structure in C. taliensis has been affected by habitat fragmentation in thepast. However, the detection of a moderate nrDNA population subdivision (GST = 0.222;NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populationsand significant phylogeographical structure (NST 〉 GST; P 〈 0.01). The analysis of PALhaplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused byrestricted gene flow with isolation by distance, which was also supported by Mantel's test ofnrDNA haplotypes (r = 0.234, P 〈 0.001). We found that chlorotype C1 was fixed in sevenpopulations of Lancang River Region, implying that the Lancang River might have provideda corridor for the long-distance dispersal of the species. Conclusions: We found that C. taliensis showed fairly high genetic differentiation resulting from restrictedgene flow and habitat fragmentation. This phylogeographical study gives us deep insightsinto population structure of the species and conservation strategies for germplasm samplingand developing in situ conservation of natural populations.

Beschreibung: Background: Members of the hemipteran suborder Auchenorrhyncha (commonly known as planthoppers,tree- and leafhoppers, spittlebugs, and cicadas) are unusual among insects known to harborendosymbiotic bacteria in that they are associated with diverse assemblages of bacterialendosymbionts. Early light microscopic surveys of species representing the two majorlineages of Auchenorrhyncha (the planthopper superfamily Fulgoroidea; and Cicadomorpha,comprising Membracoidea [tree- and leafhoppers], Cercopoidea [spittlebugs], and Cicadoidea[cicadas]), found that most examined species harbored at least two morphologically distinctbacterial endosymbionts, and some harbored as many as six. Recent investigations usingmolecular techniques have identified multiple obligate bacterial endosymbionts inCicadomorpha; however, much less is known about endosymbionts of Fulgoroidea. In thisstudy, we present the initial findings of an ongoing PCR-based survey (sequencing 16SrDNA) of planthopper-associated bacteria to document endosymbionts with a long-termhistory of codiversification with their fulgoroid hosts. Results: Results of PCR surveys and phylogenetic analyses of 16S rDNA recovered a monophyleticclade of Betaproteobacteria associated with planthoppers; this clade included Vidaniafulgoroideae, a recently described bacterium identified in exemplars of the planthopperfamily Cixiidae. We surveyed 77 planthopper species representing 18 fulgoroid families, anddetected Vidania in 40 species (representing 13 families). Further, we detected the Sulciaendosymbiont (identified as an obligate endosymbiont of Auchenorrhyncha in previousstudies) in 30 of the 40 species harboring Vidania. Concordance of the Vidania phylogenywith the phylogeny of the planthopper hosts (reconstructed based on sequence data from fivegenes generated from the same insect specimens from which the bacterial sequences wereobtained) was supported by statistical tests of codiversification. Codiversification tests alsosupported concordance of the Sulcia phylogeny with the phylogeny of the planthopper hosts,as well as concordance of planthopper-associated Vidania and Sulcia phylogenies. Conclusions: Our results indicate that the Betaproteobacterium Vidania is an ancient endosymbiont thatinfected the common ancestor of Fulgoroidea at least 130 million years ago. Comparison ofour findings with the early light-microscopic surveys conducted by Muller suggests thatVidania is Muller's x-symbiont, which he hypothesized to have codiversified with mostlineages of planthoppers and with the Sulcia endosymbiont.

Beschreibung: Background: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses. Results: In this study, we report the molecular properties of two novel dsRNA mycoviruses that were isolated from a field strain of Sclerotinia sclerotiorum, Sunf-M: one is a large monopartite virus representing a distinct evolutionary lineage of dsRNA viruses; the other is a new member of the family Partitiviridae. Comprehensive phylogenetic analysis and genome comparison revealed that there are at least ten monopartite, three bipartite, one tripartite and three quadripartite lineages in the known dsRNA mycoviruses and that the multipartite lineages have possibly evolved from different monopartite dsRNA viruses. Moreover, we found that homologs of the S7 Domain, characteristic of members of the genus phytoreovirus in family Reoviridae are widely distributed in diverse dsRNA viral lineages, including chrysoviruses, endornaviruses and some unclassified dsRNA mycoviruses. We further provided evidence that multiple HGT events may have occurred among these dsRNA viruses from different families. Conclusions: Our study provides an insight into the phylogeny and evolution of mycovirus-related dsRNA viruses and reveals that the occurrence of HGT between different virus species and the development of multipartite genomes during evolution are important macroevolutionary mechanisms in dsRNA viruses.

Beschreibung: Background: Dynactin is a large multisubunit protein complex that enhances the processivity of cytoplasmic dynein and acts as an adapter between dynein and the cargo. It is composed of eleven different polypeptides of which eight are unique to this complex, namely dynactin1 (p150Glued), dynactin2 (p50 or dynamitin), dynactin3 (p24), dynactin4 (p62), dynactin5 (p25), dynactin6 (p27), and the actin-related proteins Arp1 and Arp10 (Arp11). Results: To reveal the evolution of dynactin across the eukaryotic tree the presence or absence of all dynactin subunits was determined in most of the available eukaryotic genome assemblies. Altogether, 3061 dynactin sequences from 478 organisms have been annotated. Phylogenetic trees of the various subunit sequences were used to reveal sub-family relationships and to reconstruct gene duplication events. Especially in the metazoan lineage, several of the dynactin subunits were duplicated independently in different branches. The largest subunit repertoire is found in vertebrates. Dynactin diversity in vertebrates is further increased by alternative splicing of several subunits. The most prominent example is the dynactin1 gene, which may code for up to 36 different isoforms due to three different transcription start sites and four exons that are spliced as differentially included exons. Conclusions: The dynactin complex is a very ancient complex that most likely included all subunits in the last common ancestor of extant eukaryotes. The absence of dynactin in certain species coincides with that of the cytoplasmic dynein heavy chain: Organisms that do not encode cytoplasmic dynein like plants and diplomonads also do not encode the unique dynactin subunits. The conserved core of dynactin consists of dynactin1, dynactin2, dynactin4, dynactin5, Arp1, and the heterodimeric actin capping protein. The evolution of the remaining subunits dynactin3, dynactin6, and Arp10 is characterized by many branch- and species-specific gene loss events.

Beschreibung: Background: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC). Results: We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but more of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression. Conclusions: Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.

Beschreibung: Background: With the establishment of high-throughput sequencing technologies and new methods for rapid and extensive single nucleotide (SNP) discovery, marker-based genome scans in search of signatures of divergent selection between populations occupying ecologically distinct environments are becoming increasingly popular. Results: On the basis of genome-wide SNP marker data generated by RAD sequencing of lake and stream stickleback populations, we show that the outcome of such studies can be systematically biased if markers with a very low minor allele frequency are included in the analysis. The reason is that these 'uninformative' polymorphisms lack the adequate potential to capture signatures of drift and hitchhiking, the focal processes in ecological genome scans. Bias associated with uninformative polymorphisms is not eliminated by just avoiding technical artefacts in the data (sequencing and PCR errors), as a high proportion of SNPs with a low minor allele frequency is a general biological feature of natural populations. Conclusions: We suggest that uninformative markers should be excluded from genome scans based on empirical criteria derived from careful inspection of the data, and that these criteria should be reported explicitly. Together, this should increase the quality and comparability of genome scans, and hence promote our understanding of the processes driving genomic differentiation.

Beschreibung: Background: The Chilean shoreline, a nearly strait line of coast expanding across 35 latitudinal degrees,represents an interesting region to assess historical processes using phylogeographic analyses.Stretching along the temperate section of the East Pacific margin, the region is characterizedby intense geologic activity and has experienced drastic geomorphological transformationslinked to eustatic and isostatic changes during the Quaternary. In this study, we used twomolecular markers to evaluate the existence of phylogeographic discontinuities and detect thegenetic footprints of Pleistocene glaciations among Patagonian populations of Mazzaellalaminarioides, a low-dispersal benthic intertidal red seaweed that inhabits along ~3,700 kmof the Chilean coastal rocky shore. Results: Three main genetic lineages were found within M. laminarioides. They are distributed alongthe Chilean coast in strict parapatry. The deep divergence among lineages suggests that theycould be considered putative genetic sibling species. Unexpectedly, genetic breaks were notstrictly concordant with the biogeographic breaks described in the region. A Northern lineagewas restricted to a broad transition zone located between 30degreesS and 33degreesS and showed signalsof a recent bottleneck. The reduction of population size could be related to warm eventslinked to El Nino Southern Oscillation, which is known to cause massive seaweed mortalityin this region. To the south, we propose that transient habitat discontinuities driven byepisodic tectonic uplifting of the shoreline around the Arauco region (37degreesS-38degreesS); one of themost active forearc-basins in the South East Pacific; could be at the origin of theCentral/South genetic break. The large beaches, located around 38degreesS, are likely to contributeto the lineages' integrity by limiting present gene flow. Finally, the Southern lineage,occupies an area affected by ice-cover during the last glaciations. Phylogeny suggested it is aderived clade and demographic analyses showed the lineage has a typical signature ofpostglacial recolonization from a northern glacial refugium area. Conclusions: Even if environmental adaptation could have strengthened divergence among lineages in M.laminarioides, low dispersal capacity and small population size are sufficient to generatephylogeographic discontinuities determined by genetic drift alone. Interestingly, our resultsconfirm that seaweed population connectivity over large geographic scales does not rely onlyon dispersal capacity but also seem to depend highly on substratum availability andpopulation density of the receiving locality.

Beschreibung: Background: Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Results: We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions: Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses, particularly for modelling in the face of phylogenetic uncertainty and accounting for measurement error or individual variation in explanatory variables. Code for all models is provided in the BUGS model description language.

Beschreibung: Background: The loss of phenotypic characters is a common feature of evolution. Cave organisms provideexcellent models for investigating the underlying patterns and processes governing theevolutionary loss of phenotypic traits. The blind Mexican cavefish, Astyanax mexicanus,represents a particularly strong model for both developmental and genetic analyses as thesefish can be raised in the laboratory and hybridized with conspecific surface form counterpartsto produce large F2 pedigrees. As studies have begun to illuminate the genetic bases for traitevolution in these cavefish, it has become increasingly important to understand thesephenotypic changes within the context of cavefish origins. Understanding these origins is achallenge. For instance, widespread convergence on similar features renders morphologicalcharacters less informative. In addition, current and past gene flow between surface and caveforms have complicated the delineation of particular cave populations. Results: Past population-level analyses have sought to: 1) estimate at what time in the geological pastcave forms became isolated from surface-dwelling ancestors, 2) define the extent to whichcave form populations originated from a common invasion (single origin hypothesis) orseveral invasions (multiple origin hypothesis), and 3) clarify the role of geological andclimatic events in Astyanax cavefish evolution. In recent years, thanks to the combined use ofmorphological and genetic data, a much clearer picture has emerged regarding the origins ofAstyanax cavefish. Conclusions: The consensus view, based on several recent studies, is that cave forms originated from atleast two distinct ancestral surface-dwelling stocks over the past several million years. Inaddition, each stock gave rise to multiple invasions of the subterranean biotope. The olderstock is believed to have invaded the El Abra caves at least three times while the new stockseparately invaded the northern Guatemala and western Micos caves. This renewed picture ofAstyanax cavefish origins will help investigators draw conclusions regarding the evolution ofphenotypic traits through parallelism versus convergence. Additionally, it will help usunderstand how the presence of cave-associated traits in old versus young cave populationsmay be influenced by the time since isolation in the cave environment. This will, in turn, helpto inform our broader understanding of the forces that govern the evolution of phenotypicloss.

Beschreibung: Background: The thirteen species of Dryopteris in North America have long been suspected of havingundergone a complicated history of reticulate evolution via allopolyploid hybridization.Various explanations for the origins of the allopolyploid taxa have been suggested, andthough most lines of evidence have supported the so-called "semicristata" hypothesis,contention over the group's history has continued in several recent, conflicting studies. Results: Sequence data from nine plastid and two nuclear markers were collected from 73 accessionsrepresenting 35 species of Dryopteris. Sequences from each of the allopolyploids are mostclosely related to their progenitor species as predicted by the "semicristata" hypothesis.Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D.expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D.carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D.ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D.cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, basedon divergence time analyses, were within the last 6 Ma. We found no evidence for recurrentformation of any of the allopolyploids. The sexual allopolyploid taxa are derived fromcrosses between parents that show intermediate levels of genetic divergence relative to allpairs of potential progenitors. In addition, the four allotetraploids are transgressive withrespect to geographic range relative to one or both of their parents (their ranges extendbeyond those of the parents), suggesting that ecological advantages in novel habitats orregions may promote long-term regional coexistence of the hybrid taxa with theirprogenitors. Conclusions: This study provides the first thorough evaluation of the North American complex ofwoodferns using extensive sampling of taxa and genetic markers. Phylogenies produced fromeach of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis,including the existence of a missing diploid progenitor, and allowed us to reject all competinghypotheses. This study demonstrates the value of using multiple, biparentally inheritedmarkers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization,and determine the relative importance of introgression vs. hybridization in shaping thehistories of such groups.

Beschreibung: Background: The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easilyrecognizable based on its vegetative morphology, which shows one to several spiralchloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra iscommonly excluded from phylogenetic analyses because the genus is known as a long-branchtaxon caused by a high evolutionary rate. Results: We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclearribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequenceswere used for phylogenetic analyses using complex evolutionary models (posteriorprobability, maximum likelihood, neighbor joining, and maximum parsimony methods). Thesequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53individual clones, but our results still support monophyly of the genus. Our data set did notcontain a single slow-evolving taxon that would have been placed on a shorter branchcompared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a