ALBERT

Description: Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture ( Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.

Description: Cellular Ca 2+ homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP 3 Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca 2+ release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms, an appreciation of their evolution and the biology of orthologs in unicellular organisms is largely lacking. Extensive phylogenetic analyses reveal that the IP 3 R gene superfamily is ancient and diverged into two subfamilies, IP 3 R-A and IP 3 R-B/RyR, at the dawn of Opisthokonta. IP 3 R-B/RyR further diversified into IP 3 R-B and RyR at the stem of Filozoa. Subsequent evolution and speciation of Holozoa is associated with duplication of IP 3 R-A and RyR genes, and loss of IP 3 R-B in the vertebrate lineages. To gain insight into the properties of IP 3 R important for the challenges of multicellularity, the IP 3 R-A and IP 3 R-B family orthologs were cloned from Capsaspora owczarzaki, a close unicellular relative to Metazoa (designated as CO.IP 3 R-A and CO.IP 3 R-B). Both proteins were targeted to the endoplasmic reticulum. However, CO.IP 3 R-A, but strikingly not CO.IP 3 R-B, bound IP 3 , exhibited robust Ca 2+ release activity and associated with mammalian IP 3 Rs. These data indicate strongly that CO.IP 3 R-A as an exemplar of ancestral IP 3 R-A orthologs forms bona fide IP 3 -gated channels. Notably, however, CO.IP 3 R-A appears not to be regulated by Ca 2+ , ATP or Protein kinase A-phosphorylation. Collectively, our findings explore the origin, conservation, and diversification of IP 3 R gene families and provide insight into the functionality of ancestral IP 3 Rs and the added specialization of these proteins in Metazoa.

Description: Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.

Description: The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13–29 °C). Gene expression is highly plastic with 83.3% of the genes being differentially expressed. We distinguished three components of plasticity: 1) Dynamics of gene expression intensity (sum of change), 2) direction of change, and 3) curvature of the reaction norm (linear vs. quadratic). Studying their regulatory architecture we found that all three plasticity components were most strongly affected by the number of different transcription factors (TFs) binding to the target gene. More TFs were found in genes with less expression changes across temperatures. Although the effect of microRNAs was weaker, we consistently noted a trend in the opposite direction. The most plastic genes were regulated by fewer TFs and more microRNAs than less plastic genes. Different patterns of plasticity were also reflected by their functional characterization based on gene ontology. Our results suggest that reaction norms provide an important key to understand the functional requirements of natural populations exposed to variable environmental conditions.

Description: Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops , which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.

Description: Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of the interactome. It is assumed that observed patterns of covariation are caused by molecular coevolution, where substitutions at one site affect the evolutionary forces acting at neighboring sites. Our theoretical and empirical results cast doubt on this assumption. We demonstrate that the strongest coevolutionary signal is a decrease in evolutionary rate and that unfeasibly long times are required to produce coordinated substitutions. We find that covarying substitutions are mostly found on different branches of the phylogenetic tree, indicating that they are independent events that may or may not be attributable to coevolution. These observations undermine the hypothesis that molecular coevolution is the primary cause of the covariation signal. In contrast, we find that the pairs of residues with the strongest covariation signal tend to have low evolutionary rates, and that it is this low rate that gives rise to the covariation signal. Slowly evolving residue pairs are disproportionately located in the protein’s core, which explains covariation methods’ ability to detect pairs of residues that are close in three dimensions. These observations lead us to propose the "coevolution paradox": The strength of coevolution required to cause coordinated changes means the evolutionary rate is so low that such changes are highly unlikely to occur. As modern covariation methods may lead to breakthroughs in structural genomics, it is critical to recognize their biases and limitations.

Description: We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC) 3 (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC) 3 to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/ .

Description: Understanding the genetic and molecular bases of the ability to distinguish self from nonself (allorecognition) and mechanisms underlying evolution of allorecognition systems is an important endeavor for understanding cases where it becomes dysfunctional, such as in autoimmune disorders. In filamentous fungi, allorecognition can result in vegetative or heterokaryon incompatibility, which is a type of programmed cell death that occurs following fusion of genetically different cells. Allorecognition is genetically controlled by het loci, with coexpression of any combination of incompatible alleles triggering vegetative incompatibility. Herein, we identified, characterized, and inferred the evolutionary history of candidate het loci in the filamentous fungus Neurospora crassa . As characterized het loci encode proteins carrying an HET domain, we annotated HET domain genes in 25 isolates from a natural population along with the N. crassa reference genome using resequencing data. Because allorecognition systems can be affected by frequency-dependent selection favoring rare alleles (i.e., balancing selection), we mined resequencing data for HET domain loci whose alleles displayed elevated levels of variability, excess of intermediate frequency alleles, and deep gene genealogies. From these analyses, 34 HET domain loci were identified as likely to be under balancing selection. Using transformation, incompatibility assays and genetic analyses, we determined that one of these candidates functioned as a het locus ( het-e ). The het-e locus has three divergent allelic groups that showed signatures of positive selection, intra- and intergroup recombination, and trans-species polymorphism. Our findings represent a compelling case of balancing selection functioning on multiple alleles across multiple loci potentially involved in allorecognition.

Description: Scoring the impact of noncoding variation on the function of cis -regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here, we examine the use of the Ornstein–Uhlenbeck (OU) model to infer selection at the level of predicted cis -regulatory modules (CRMs), and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-Seq and STARR-Seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence.

Description: How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1 , a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

Description: Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714–5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1–44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG ( Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013 . Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323–330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540–1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/ .

Description: Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.

Description: Environmental control of flowering allows plant reproduction to occur under optimal conditions and facilitates adaptation to different locations. At high latitude, flowering of many plants is controlled by seasonal changes in day length. The photoperiodic flowering pathway confers this response in the Brassicaceae, which colonized temperate latitudes after divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO) transcription factor of Arabidopsis thaliana , a member of the Brassicaceae, is central to the photoperiodic flowering response and shows characteristic patterns of transcription required for day-length sensing. CO is believed to be widely conserved among flowering plants; however, we show that it arose after gene duplication at the root of the Brassicaceae followed by divergence of transcriptional regulation and protein function. CO has two close homologs, CONSTANS-LIKE1 ( COL1 ) and COL2 , which are related to CO by tandem duplication and whole-genome duplication, respectively. The single CO homolog present in the Cleomaceae shows transcriptional and functional features similar to those of COL1 and COL2 , suggesting that these were ancestral. We detect cis -regulatory and codon changes characteristic of CO and use transgenic assays to demonstrate their significance in the day-length-dependent activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The origin of CO may have contributed to the range expansion of the Brassicaceae and suggests that in other families CO genes involved in photoperiodic flowering arose by convergent evolution.

Description: The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contains LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

Description: Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears ( Ursus americanus ) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species.

Description: Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E. coli , but differs in mutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A:T-〉G:C transitions and 82 A:T-〉C:G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G:C-〉A:T transitions and 33 G:C-〉T:A transversions). We propose that this unique spectrum is shaped mainly by the abundant uracil DNA glycosylases reducing G:C-〉A:T transitions, adenine methylation elevating A:T-〉C:G transversions, and absence of cytosine methylation decreasing G:C-〉A:T transitions. As opposed to the greater than 100 x elevation of the mutation rate in MMR – (DNA Mismatch Repair deficient) strains of most other organisms, MMR – D. radiodurans only exhibits a 4-fold elevation, raising the possibility that other DNA repair mechanisms compensate for a relatively low-efficiency DNA MMR pathway. As D. radiodurans has plentiful insertion sequence (IS) elements in the genome and the activities of IS elements are rarely directly explored, we also estimated the insertion (transposition) rate of the IS elements to be 2.50 x 10 –3 per genome per generation in the wild-type strain; knocking out MMR did not elevate the IS element insertion rate in this organism.

Description: Because mating systems affect population genetics and ecology, they are expected to impact the molecular evolution of species. Self-fertilizing species experience reduced effective population size, recombination rates, and heterozygosity, which in turn should decrease the efficacy of natural selection, both adaptive and purifying, and the strength of meiotic drive processes such as GC-biased gene conversion. The empirical evidence is only partly congruent with these predictions, depending on the analyzed species, some, but not all, of the expected effects have been observed. One possible reason is that self-fertilization is an evolutionary dead-end, so that most current selfers recently evolved self-fertilization, and their genome has not yet been strongly impacted by selfing. Here, we investigate the molecular evolution of two groups of freshwater snails in which mating systems have likely been stable for several millions of years. Analyzing coding sequence polymorphism, divergence, and expression levels, we report a strongly reduced genetic diversity, decreased efficacy of purifying selection, slower rate of adaptive evolution, and weakened codon usage bias/GC-biased gene conversion in the selfer Galba compared with the outcrosser Physa , in full agreement with theoretical expectations. Our results demonstrate that self-fertilization, when effective in the long run, is a major driver of population genomic and molecular evolutionary processes. Despite the genomic effects of selfing, Galba truncatula seems to escape the demographic consequences of the genetic load. We suggest that the particular ecology of the species may buffer the negative consequences of selfing, shedding new light on the dead-end hypothesis.

Description: We compute the algebraic $K$ -theory of the non-commutative ring $k\langle x_1,\ldots ,x_n \rangle /(m^a)$ when $k$ is a perfect field of positive characteristic and $m=(x_1,\ldots ,x_n)$ . We express the answer in terms of the truncation poset Witt vectors developed in Angeltveit [‘Witt vectors and truncation posets’, Preprint, 2014, arXiv:1409.4156].

Description: In this paper, we investigate the exactness of the Grassmannian Bernstein-Gel’fand-Gel’fand complexes introduced in a previous work of the author, and obtain some inequalities between some Hodge numbers of some irregular varieties. In particular, we obtain sharp lower bounds for the Hodge numbers of smooth subvarieties of Abelian varieties, as well as some improvements of results of Lazarsfeld-Popa and Lombardi concerning threefolds and fourfolds.

Description: We prove that every finitely presented group with positive first $\ell ^2$ -Betti number that virtually surjects onto $\mathbb Z$ is acylindrically hyperbolic. In particular, this implies acylindrical hyperbolicity of finitely presented residually finite groups with positive first $\ell ^2$ -Betti number as well as groups of deficiency at least $2$ .

Description: We give an elementary proof of Iyama–Yoshino's classification of rigid maximal Cohen-Macaulay modules on Veronese embeddings in $\mathbb P ^9$ .

Description: The virtual dimensions of both framed and unframed SU(2) magnetic monopoles on asymptotically conic 3-manifolds are obtained by computing the index of a Fredholm extension of the associated deformation complex. The unframed dimension coincides with the one obtained by Braam for conformally compact 3-manifolds. The computation follows from the application of a Callias-type index theorem.

Description: Let $f : (\mathbb {C}^n, 0) \rightarrow (\mathbb {C}, 0)$ be a semiquasihomogeneous function. We give a formula for the local Łojasiewicz exponent ${\mathcal L}_0 (f)$ of $f$ , in terms of weights of $f$ . In particular, in the case of a quasihomogeneous (QH) isolated singularity $f$ , we generalize a formula for ${\mathcal L}_0 (f)$ of Krasiłski, Oleksik and Płoski from 3 to $n$ dimensions. This was previously announced in the paper [ 19 ] of Tan, Yau and Zuo [Łojasiewicz inequality for weighted homogeneous polynomial with isolated singularity, Proc. Amer. Math. Soc. 138 (2010) 3975–3984], but as a matter of fact it was not proved correctly there, as noted by the AMS reviewer Tadeusz Krasiłski. As a consequence of our result, we obtain that the Łojasiewicz exponent is invariant in topologically trivial families of singularities coming from a QH germ. This is an affirmative partial answer to Teissier's conjecture.

Description: We show that the complement of the closure of the coamoeba of a variety of codimension $k + 1$ is $k$ -convex, in the sense of Gromov and Henriques. This generalizes a result of Nisse for hypersurface coamoebas. We use this to show that the complement of the nonarchimedean coamoeba of a variety of codimension $k + 1$ is $k$ -convex.

Description: We prove an analog of Lagrange's theorem for continued fractions on the Heisenberg group: points with an eventually periodic continued fraction expansion are those that satisfy a particular type of quadratic form, and vice-versa.

Description: Let $(M^n, g)$ be a compact $n$ -dimensional ( $n\geq 2$ ) manifold with nonnegative Ricci curvature, and if $n\geq 3,$ then we assume that $(M^n, g)\times \mathbb {R}$ has nonnegative isotropic curvature. The lower bound of the Ricci flow's existence time on $(M^n, g)$ is proved. This provides an alternative proof for the uniform lower bound of a family of closed Ricci flows' maximal existence times, which was first proved by E. Cabezas-Rivas and B. Wilking. We also get an interior curvature estimate for $n= 3$ under ${\rm Rc}\geq 0$ assumption among others. Combining these results, we proved the short-time existence of the Ricci flow on a large class of three-dimensional open manifolds, which admit some suitable exhaustion covering and have nonnegative Ricci curvature.

Description: Given any $\varepsilon 〉 0$ , we construct an orthonormal system of $n_k$ uniformly bounded polynomials of degree at most $k$ on the unit sphere in $\mathbb {R}^{m+1}$ where $n_k$ is bigger than $1-\varepsilon $ times the dimension of the space of polynomials of degree at most $k$ . Similarly, we construct an orthonormal system of sections of powers $A^k$ of a positive holomorphic line bundle on a compact Kähler manifold with cardinality bigger than $1-\varepsilon $ times the dimension of the space of global holomorphic sections to $A^k$ .

Description: We prove that if $\mu $ is a Radon measure on the Heisenberg group $\mathbb {H}^n$ such that the density $\Theta ^s(\mu ,\cdot )$ , computed with respect to the Korányi metric $d_H$ , exists and is positive and finite on a set of positive $\mu $ measure, then $s$ is an integer. The proof relies on an analysis of uniformly distributed measures on $(\mathbb {H}^n,d_H)$ . We provide a number of examples of such measures, illustrating both the similarities and the striking differences of this sub-Riemannian setting from its Euclidean counterpart.

Description: Let $d 〉 1$ be an integer. In 1986, Shen defined a class of weight modules $F^\alpha _b(V)$ over the Witt algebra $\mathcal {W}_d$ for $\alpha \in {\mathbb C} ^d$ , $b\in {{\mathbb C}}$ , and an irreducible module $V$ over the general linear Lie algebra $\mathfrak {gl} _d$ on which the identity matrix acts as multiplication by $b$ . In 1996, Eswara Rao determined necessary and sufficient conditions for these modules to be irreducible when $V$ is finite-dimensional. In this note, we will determine necessary and sufficient conditions for all these modules $F^\alpha _b(V)$ to be irreducible where $V$ is not necessarily finite-dimensional. In this way, we obtain a large new family of irreducible $\mathcal {W}_d$ -modules with infinite-dimensional weight spaces.

Description: Using the Bockstein spectral sequence developed previously by the authors, we compute the ring $ER(n)^\ast (BO(q))$ explicitly. We then use this calculation to show that the ring spectrum $MO[2^{n+1}]$ is $ER(n)$ -orientable (but not $ER(n+1)$ -orientable), where $MO[2^{n+1}]$ is defined as the Thom spectrum for the self-map of $BO$ given by multiplication by $2^{n+1}$ .

Description: The commuting probability of a finite group is defined to be the probability that two randomly chosen group elements commute. Let ${{\mathcal P}}\subset (0,1]$ be the set of commuting probabilities of all finite groups. We prove that every point of ${{\mathcal P}}$ is nearly an Egyptian fraction of bounded complexity. As a corollary, we deduce two conjectures of Keith Joseph from 1977: all limit points of ${{\mathcal P}}$ are rational, and ${{\mathcal P}}$ is well ordered by $ 〉 $ . We also prove analogous theorems for bilinear maps of abelian groups.

Description: Although copepods have been considered tolerant against the direct influence of the ocean acidification (OA) projected for the end of the century, some recent studies have challenged this view. Here, we have examined the direct impact of short-term exposure to a pCO 2 / pH level relevant for the year 2100 ( pH NBS , control: 8.18, low pH : 7.78), on the physiological performance of two representative marine copepods: the calanoid Acartia grani and the cyclopoid Oithona davisae . Adults of both species, from laboratory cultures, were preconditioned for four consecutive days in algal suspensions ( Akashiwo sanguinea ) prepared with filtered sea water pre-adjusted to the targeted pH values via CO 2 bubbling. We measured the feeding and respiratory activity and reproductive output of those pre-conditioned females. The largely unaffected fatty acid composition of the prey offered between OA treatments and controls supports the absence in the study of indirect OA effects (i.e. changes of food nutritional quality). Our results show no direct effect of acidification on the vital rates examined in either copepod species. Our findings are compared with results from previous short- and long-term manipulative experiments on other copepod species.

Description: We analyzed the genetic structure of the radiolarian morphospecies Larcopyle buetschlii from the surface to deep waters (up to 2000 m) in the Japan Sea using the internal transcribed spacer (ITS) regions of ribosomal RNA genes. Each individual had several ITS variants, but these polymorphisms show no vertical phylogeographic structure, suggesting a single biological species. Its rapid clonal reproduction suggested by high ITS variation likely plays a pivotal role in maintaining its wide vertical distribution.

Description: Phronima sedentaria is a hyperiid amphipod that diel migrates into a pronounced oxygen minimum zone (OMZ) in the Eastern Tropical North Pacific. In this study, oxygen consumption and lactate production were measured in P. sedentaria to estimate the aerobic and anaerobic contributions to total metabolism under conditions that mimic its day- (1% oxygen, 10°C) and night-time (20% oxygen, 20°C) habitat. When exposed to hypoxia and low temperature, the total metabolism of P. sedentaria was depressed by 78% compared with normoxic conditions. The metabolic enzymes citrate synthase (CS) and lactate dehydrogenase (LDH) were also measured as indicators of aerobic and anaerobic metabolism, and compared with specimens collected from the California Current and the North Atlantic to assess potential adaptations to low oxygen. LDH activity was not significantly different between regions. Significant differences in CS activity may be due to variation in food availability. Climate change is predicted to increase surface temperatures and cause the expansion of OMZs. This will result in vertical compression of the night-time range for P. sedentaria and is likely to have the same impact on other diel migrators. Habitat compression will reduce zooplankton contribution to carbon cycling and alter oceanic ecology, including predator–prey interactions.

Description: Many phytoplankton exploit phosphorus (P) from organic sources when dissolved inorganic P (DIP) is depleted. This process is, however, rarely considered in ecological and biogeochemical models. We present a mechanistic model describing explicitly the ability of phytoplankton to use dissolved organic P (DOP) when DIP is limiting, by synthesizing alkaline phosphatase (AP) that releases DIP from DOP. This model, applicable to any phytoplankton species expressing AP, is here specifically developed for the colony-forming Phaeocystis globosa. It describes the main processes related to P metabolism, including DIP transport, intracellular accumulation and assimilation. Model behaviour is explored in DIP-limiting batch-type conditions for different DOP ranging between 0 and 1.5 mmol P m –3 . Simulations show that the DOP-derived DIP increases the maximum biomass reached and extends the period of net growth. The magnitude of the enhanced biomass production is controlled by the DOP initially present as well as the released DOP, the latter being recycled by lysis of P. globosa cells. We also present a simplified model version derived from the mechanistic model, which involves fewer state variables and parameters. The latter is directly usable in both variable (quota-type) and fixed stoichiometry descriptions of phytoplankton growth.

Description: Zooplankton diel vertical migration (DVM) is often explained as a balance between predator avoidance and resource acquisition. However, recent studies suggest that ultraviolet radiation (UV) may also be important in driving zooplankton DVM in some systems. Williamson et al. ( Williamson et al ., 2011 ) proposed the "transparency-regulator hypothesis," which integrates UV into our current understanding of the drivers of DVM and predicts that the relative roles of UV and visual predation pressure will vary systematically across a gradient of lake transparency. To assess this hypothesis, we conducted in situ mesocosm experiments in five different lakes: two lakes without fish and three lakes with fish that spanned a range of UV and visible light transparency. We used an open-bottomed mesocosm design that allowed for the direct manipulation of UV that did not constrain visual predators or the amplitude or timing of natural migrations. Consistent with the transparency-regulator hypothesis, we found that UV is an important driver of Daphnia DVM in highly UV transparent lakes with and without fish but not in low transparency systems. Our results also suggest that UV and visual predation pressure may interact in systems of intermediate transparency.

Description: Competition for resources can lead to species exclusion. However, this exclusion may be avoided if species show differential adaptation to physical environment. Empirical studies on competition are difficult when species are phylogenetically close and have complex life cycles. This is the case of B. plicatilis and B. manjavacas , two cryptic rotifer species differing in their salinity niches and in life-history traits related to sex and diapause. These differences have been suggested to promote the stable co-occurrence observed in natural populations of these species. However, in a previous empirical study, the outcome of competition between both species was always exclusion. Here, we theoretically explored the effect of complex life-history traits and salinity fluctuations on the long-term competitive outcome of B. plicatilis and B. manjavacas . We developed a model and simulated ecological scenarios combining different growing period lengths, levels of crossed induction of sex between species and salinity regimes. Results show that a fluctuating salinity regime, an intermediate length of growing season and a low level of crossed induction of sex are essential conditions to take into account to explain coexistence.

Description: Colonization of new habitats through dispersal of phytoplankton cysts might be limited, if resident populations outcompete invaders during germination. We reciprocally transferred Gonyostomum semen (Raphidophyceae) cysts from three lakes into native and foreign waters originating from the respective habitats. Germination rate and germling growth were impacted by water origin, but there was no preference for native water. Gonyostomum semen 's ability to germinate in different conditions might explain its expansion in northern Europe.

Description: Measuring zooplankton biomass and physiological rates is of paramount importance in biological oceanography in order to assess the role of this community in, e.g. carbon fluxes. Classical methods (incubations) are very time-consuming and cannot match the frequency of physical and chemical measurements. Attempting to solve this, a variety of methods (e.g. egg production, RNA/DNA ratio or enzyme activities) have been developed over the last decades. These methods also show uncertainties and hitherto only incubation methods have been widely accepted. Predictive equations relating physiological processes and body weight (bw) and temperature are a rough alternative, normally used to ascertain the role of these organisms in the oceanic ecosystem. However, using imaging systems and empirical relationships to determine bw allows the application of physiological models to each individual, obtaining reliable estimates for taxonomic groups and size classes. In this study, we developed predictive equations suitable for growth and respiration estimations in subtropical regions. In addition, biomass and physiological rates assessed from empirical equations in combination with an image-based system (ZooImage) were compared with standard and enzymatic methods, respectively. We observed a consistent agreement between methodologies, the former resulting in an inexpensive and faster procedure for the appraisal of biomass and community carbon fluxes at large spatial and temporal scales.

Description: Carbon-specific prey clearance and ingestion rates of 1.5-mm tentaculate larvae of the ctenophore Mnemiopsis leidyi increased linearly between 6 and 25°C but declined between 25 and 30°C. Both absolute (length) and carbon-specific growth rate increased linearly with increasing temperature. The latter was 0.87 d –1 at 25°C. Extremely low or negative growth rates observed at 6 and 30°C help define the thermal limits to population growth of this successful biological invader.

Description: We have supplemented available, concurrent measurements of fresh weight ( W , g) and body carbon (C, g) (46 individuals, 14 species) and nitrogen (N, g) (11 individuals, 9 species) of marine gelatinous animals with data obtained during the global ocean MALASPINA 2010 Expedition (totalling 267 individuals and 33 species for the W versus C data; totalling 232 individuals and 31 species for the N versus C data). We then used those data to test the allometric properties of the W versus C and N versus C relationships. Overall, gelatinous organisms contain 1.13 ± 1.57% of C (by weight, mean ± SD) in their bodies and show a C:N of 4.56 ± 2.46, respectively, although estimations can be improved by using separate conversion coefficients for the carnivores and the filter feeders. Reduced major axis regression indicates that W increases isometrically with C in the carnivores (cnidarians and ctenophores), implying that their water content can be described by a single conversion coefficient of 173.78 gW(g C) –1 , or a C content of 1.17 ± 1.90% by weight, although there is much variability due to the existence of carbon-dense species. In contrast, W increases more rapidly than C in the filter feeders (salps and doliolids), according to a power relationship W = 446.68C 1.54 . This exponent is not significantly different from 1.2, which is consistent with the idea that the watery bodies of gelatinous animals represent an evolutionary response towards increasing food capture surfaces, i.e. a bottom-up rather than a top-down mechanism. Thus, the available evidence negates a bottom-up mechanism in the carnivores, but supports it in the filter feeders. Last, N increases isometrically with C in both carnivores and filter feeders with C:N ratios of 3.89 ± 1.34 and 4.38 ± 1.21, respectively. These values are similar to those of compact, non-gelatinous organisms and reflect a predominantly herbivorous diet in the filter feeders, which is confirmed by a difference of one trophic level between filter feeders and carnivores, according to stable N isotope enrichment data.

Description: I explored mortality estimation for stage-structured populations, building on previous work that applied vertical life-table methods to populations of copepods. A new Bayesian approach for estimating mortality rates accounts for uncertainties in stage duration and number counted by stage, which have not been fully incorporated into previous analyses. This method assumes that mortality is similar among similar life stages. Results using simulated data show that realistic values of the standard deviation of stage duration and number of individuals counted result in reliable mortality estimates, though with wide confidence intervals. This uncertainty obscures variation in estimated mortality between successive stages and can also obscure bias due to violation of underlying assumptions such as that of a stable stage distribution. More importantly, the uncertainty calls into question many previous mortality estimates across pairs of life stages that do not account for these sources of uncertainty. The method was applied to an introduced population of the brackish-water cyclopoid copepod Limnoithona tetraspina in the San Francisco Estuary. Despite the uncertainties, results were interpretable: mortality was highest in nauplii and lowest in adults, probably because of high vulnerability of nauplii to invertebrate predators and low vulnerability of adults to fish predation.

Description: The strong La Niña of 2010–2011 provided an opportunity to investigate the ecological impacts of El Niño-Southern Oscillation on coastal plankton communities using the nine national reference stations around Australia. Based on remote sensing and across the entire Australian region 2011 (La Niña) was only modestly different from 2010 (El Niño) with the average temperature declining 0.2%, surface chlorophyll a up 3% and modelled primary production down 14%. Other changes included a poleward shift in Prochlorococcus and Synechococcus . Along the east coast, there was a reduction in salinity, increase in nutrients, Chlorophytes and Prasinophytes (taxa with chlorophyll b , neoxanthin and prasinoxanthin). The southwest region had a rise in the proportion of 19-hexoyloxyfucoxanthin; possibly coccolithophorids in eddies of the Leeuwin Current and along the sub-tropical front. Pennate diatoms increased, Ceratium spp. decreased and Scrippsiella spp. increased in 2011. Zooplankton biomass declined significantly in 2011. There was a reduction in the abundance of Calocalanus pavo and Temora turbinata and increases in Clausocalanus farrani , Oncaea scottodicarloi and Macrosetella gracilis in 2011. The changes in the plankton community during the strong La Niña of 2011 suggest that this climatic oscillation exacerbates the tropicalization of Australia.

Description: Jellyfish are effective predators on mesozooplankton and release large amounts of dissolved organic matter. Nevertheless, jellyfish initiated trophic cascades and bottom-up influences impacting lower trophic levels have received limited attention. We conducted a mesocosm experiment to quantify simultaneous top-down and bottom-up effects of a common jellyfish, Cyanea capillata , in a natural plankton community during autumn. Treatments were 0, 2 or 5 jellyfish per 2.5 m 3 mesocosm, four replicates each, with initial additions of inorganic nutrients. Primary and bacterial production, species abundance and composition of several trophic levels and nutrient and carbon dynamics were followed during the 8-day experiment. Multivariate statistics and generalized additive mixed modelling were applied to test whether jellyfish carbon concentration (0–1.26 mg jellyC L –1 ) in the mesocosms affected the variables monitored. Unexpected negligible predatory impact of jellyfish on mesozooplankton was observed, potentially related to jellyfish senescence. Community compositions of bacteria, phytoplankton and mesozooplankton changed with time, but did not differ between treatments. However, nutrient regeneration by jellyfish was evident, and jellyfish had a positive impact on total and specific bacterial production, total primary production and the 〉10 µm chlorophyll a fraction. Bottom-up influences from abundant jellyfish could thus stimulate productivity in nutrient depleted autumnal surface waters.

Description: The feeding ecology of Blackfordia virginica was evaluated concurrently with their ecophysiological condition in a temperate estuary. The diet of B. virginica is composed not only of metazooplankton, as commonly observed for other jellyfish species, but also of phytoplankton, ciliates and detritus. This feeding behavior might explain their good nutritional condition and sustainable growth during bloom peaks, when zooplankton abundance has already decreased significantly.

Description: The pelagic dynamics of the cosmopolitan scyphozoan Aurelia sp . was investigated in three French Mediterranean lagoons, Thau, Berre and Bages-Sigean, which harbour resident populations. The annual cycles showed a common univoltine pattern in all lagoons where the presence of pelagic stages in the water column lasted ~8 months. Field observations showed a release of ephyrae in winter time followed by pronounced growth between April and July, when individuals reached the largest sizes, before disappearing from the water column. Maximum abundance of ephyrae and medusae were registered in Thau. Medusae abundance attained a maximum of 331 ind 100 m –3 in Thau, 18 ind 100 m –3 in Berre and 7 ind 100 m –3 in Bages-Sigean lagoons. Temperature and zooplankton abundance appeared as leading factors of growth, where Bages-Sigean showed the population with higher growth rates (2.66 mm day –1 ) and maximum size (32 cm), followed by Thau (0.57–2.56 mm day –1 ; 22.4 cm) and Berre (1.57–2.22 mm day –1 ; 17 cm). The quantification of environmental windows used by the species showed wider ranges than previously reported in the Mediterranean Sea, which suggests a wide ecological plasticity of Aurelia spp. populations in north-western Mediterranean lagoons.

Description: Two lobate ctenophores, Bolinopsis infundibulum and Mnemiopsis leidyi , occur in the North Sea. Stomach contents of field-collected B. infundibulum were recorded and clearance rates for cladocerans and copepods calculated. In starvation experiments, daily body carbon losses of 2.2 and 1.2% and total carbon content losses of 76 and 63% were observed for B. infundibulum (after 68 days) and M. leidyi (after 67 days), respectively.

Description: The ctenophore Mnemiopsis leidyi is characterized by high growth rates and a large reproductive capacity. However, reproductive dynamics are not yet well understood. Here, we present laboratory data on food-dependent egg production in M. leidyi and egg hatching time and success. Further, we report on the reproduction of laboratory-reared and field-caught animals during starvation. Our results show that the half-saturation zooplankton prey concentration for egg production is reached at food levels of 12–23 µgC L –1 , which is below the average summer food concentration encountered in invaded areas of northern Europe. Furthermore, starved animals continue to produce eggs for up to 12 days after cessation of feeding with high overall hatching success of 65–90%. These life history traits allow M. leidyi to thrive and reproduce in environments with varying food conditions and give it a competitive advantage under unfavourable conditions. This may explain why recurrent population blooms are observed and sustained in localized areas in invaded northern Europe, where water exchange is limited and zooplankton food resources are quickly depleted by M. leidyi . We suggest that these reproductive life history traits are key to its invasion success.

Description: Surface-dwelling colonies of Velella velella occur throughout tropical to cold-temperate oceans of the world and sometimes are stranded in masses along hundreds of kilometers of beaches. Large-scale blooms in the Western Mediterranean Sea in 2013 and 2014 allowed the study of diet, prey digestion times and predation rates. Gastrozooid content analyses showed that 59% of the 769 identified prey were euphausiid larvae (calytopsis and furcilia) captured at night. Copepods (41%), fish eggs (2.2%) and larvae (0.5%) were captured both at day and night. Digestion times at ambient temperature (~17°C) of calytopsis, furcilia and copepods were estimated to be 〉6.5, 4.4 and 3.9 h, respectively. Estimated prey consumption was substantially lower in 2014 than in 2013 (41 vs. 75 prey day –1 colony –1 ). Velella velella and other gelatinous species bloomed in the Mediterranean Sea and the northeastern Atlantic and Pacific oceans in 2013 and 2014. Because of the wide distribution of V. velella colonies, their mass occurrences, potential importance as predators and competitors of fish, additional production from symbiotic zooxanthellae and stranding on beaches, they could be important in open-ocean carbon cycling and in transport of pelagic production to landmasses.

Description: The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis- regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella , which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis- regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis- regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora . We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis -regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.

Description: The phenomenon of male sterility in interspecies hybrids has been observed for over a century, however, few genes influencing this recurrent phenotype have been identified. Genetic investigations have been primarily limited to a small number of model organisms, thus limiting our understanding of the underlying molecular basis of this well-documented "rule of speciation." We utilized two interspecies hybrid cat breeds in a genome-wide association study employing the Illumina 63 K single-nucleotide polymorphism array. Collectively, we identified eight autosomal genes/gene regions underlying associations with hybrid male sterility (HMS) involved in the function of the blood-testis barrier, gamete structural development, and transcriptional regulation. We also identified several candidate hybrid sterility regions on the X chromosome, with most residing in close proximity to complex duplicated regions. Differential gene expression analyses revealed significant chromosome-wide upregulation of X chromosome transcripts in testes of sterile hybrids, which were enriched for genes involved in chromatin regulation of gene expression. Our expression results parallel those reported in Mus hybrids, supporting the "Large X-Effect" in mammalian HMS and the potential epigenetic basis for this phenomenon. These results support the value of the interspecies feline model as a powerful tool for comparison to rodent models of HMS, demonstrating unique aspects and potential commonalities that underpin mammalian reproductive isolation.

Description: Horizontal gene transfer threatens the therapeutic success of antibiotics by facilitating the rapid dissemination of resistance alleles among bacterial species. The conjugative mobile element Tn916 provides an excellent context for examining the role of adaptive parasexuality as it carries the tetracycline-resistance allele tetM and has been identified in a wide range of pathogens. We have used a combination of experimental evolution and allelic frequency measurements to gain insights into the adaptive trajectories leading to tigecycline resistance in a hospital strain of Enterococcus faecalis and predict what mechanisms of resistance are most likely to appear in the clinical setting. Here, we show that antibiotic selection led to the near fixation of adaptive alleles that simultaneously altered TetM expression and produced remarkably increased levels of Tn916 horizontal gene transfer. In the absence of drug, approximately 1 in 120,000 of the nonadapted E. faecalis S613 cells had an excised copy of Tn916, whereas nearly 1 in 50 cells had an excised copy of Tn916 upon selection for resistance resulting in a more than 1,000-fold increase in conjugation rates. We also show that tigecycline, a translation inhibitor, selected for a mutation in the ribosomal S10 protein. Our results show the first example of mutations that concurrently confer resistance to an antibiotic and lead to constitutive conjugal-transfer of the resistance allele. Selection created a highly parasexual phenotype and high frequency of Tn916 jumping demonstrating how the use of antibiotics can lead directly to the proliferation of resistance in, and potentially among, pathogens.

Description: Organisms with nonphotosynthetic plastids often retain genomes; their gene contents provide clues as to the functions of these organelles. Yet the functional roles of some retained genes—such as those coding for ATP synthase—remain mysterious. In this study, we report the complete plastid genome and transcriptome data of a nonphotosynthetic diatom and propose that its ATP synthase genes may function in ATP hydrolysis to maintain a proton gradient between thylakoids and stroma, required by the twin arginine translocator (Tat) system for translocation of particular proteins into thylakoids. Given the correlated retention of ATP synthase genes and genes for the Tat system in distantly related nonphotosynthetic plastids, we suggest that this Tat-related role for ATP synthase was a key constraint during parallel loss of photosynthesis in multiple independent lineages of algae/plants.

Description: The brown rat, Rattus norvegicus , is both a notorious pest and a frequently used model in biomedical research. By analyzing genome sequences of 12 wild-caught brown rats from their presumed ancestral range in NE China, along with the sequence of a black rat, Rattus rattus , we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size ( N e ) of this species = 1.24 x 105 , based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse ( Mus musculus castaneus ), which has a much larger N e . This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements. This leads to negative estimates of the rate of adaptive evolution ( α ) in proteins and conserved noncoding elements, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.

Description: Despite much attention, history of sheep ( Ovis aries ) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences ( n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637–0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (~8–11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20–60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5–6.8 ka (lineages A and B: ~6.4–6.8 ka; C: ~4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West–East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.

Description: The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.

Description: Shared host cells can serve as melting pots for viral genomes, giving many phylogenies a web-like appearance due to horizontal gene transfer. However, not all virus families exhibit web-like phylogenies. Microviruses form three distinct clades, represented by X174, G4, and α3. Here, we investigate protein-based barriers to horizontal gene transfer between clades. We transferred gene G, which encodes a structural protein, between X174 and G4, and monitored the evolutionary recovery of the resulting chimeras. In both cases, particle assembly was the major barrier after gene transfer. The G4XG chimera displayed a temperature-sensitive assembly defect that could easily be corrected through single mutations that promote productive assembly. Gene transfer in the other direction was more problematic. The initial XG4G chimera required an exogenous supply of both the X174 major spike G and DNA pilot H proteins. Elevated DNA pilot protein levels may be required to compensate for off-pathway reactions that may have become thermodynamically and/or kinetically favored when the foreign spike protein was present. After three targeted genetic selections, the foreign spike protein was productively integrated into the X174 background. The first adaption involved a global decrease in gene expression. This was followed by modifications affecting key protein–protein interactions that govern assembly. Finally, gene expression was re-elevated. Although the first selection suppresses nonproductive reactions, subsequent selections promote productive assembly and ultimately viability. However, viable chimeric strains exhibited reduced fitness compared with wild-type. This chimera’s path to recovery may partially explain how unusual recombinant viruses could persist long enough to naturally emerge.

Description: Head crests are important display structures in wild bird species and are also common in domesticated lineages. Many breeds of domestic rock pigeon ( Columba livia ) have crests of reversed occipital feathers, and this recessive trait is associated with a nonsynonymous coding mutation in the intracellular kinase domain of EphB2 (Ephrin receptor B2). The domestic ringneck dove ( Streptopelia risoria ) also has a recessive crested morph with reversed occipital feathers, and interspecific crosses between crested doves and pigeons produce crested offspring, suggesting a similar genetic basis for this trait in both species. We therefore investigated EphB2 as a candidate for the head crest phenotype of ringneck doves and identified a nonsynonymous coding mutation in the intracellular kinase domain that is significantly associated with the crested morph. This mutation is over 100 amino acid positions away from the crest mutation found in rock pigeons, yet both mutations are predicted to negatively affect the function of ATP-binding pocket. Furthermore, bacterial toxicity assays suggest that "crest" mutations in both species severely impact kinase activity. We conclude that head crests are associated with different mutations in the same functional domain of the same gene in two different columbid species, thereby representing striking evolutionary convergence in morphology and molecules.

Description: The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish ( Sebastes ). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.

Description: Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size.

Description: Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide single nucleotide polymorphism data from 2,493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.

Description: Evidence is mounting that epistasis is widespread among mutations. The cost of carrying two deleterious mutations, or the advantage of acquiring two beneficial alleles, is typically lower that the sum of their individual effects. Much less is known on epistasis between beneficial and deleterious mutations, even though this is key to the amount of genetic hitchhiking that may occur during evolution. This is particularly important in the context of antibiotic resistance: Most resistances are deleterious, but some can be beneficial and remarkably rifampicin resistance can emerge de novo in populations evolving without antibiotics. Here we show pervasive positive pairwise epistasis on Escherichia coli fitness between beneficial mutations, which confer resistance to rifampicin, and deleterious mutations, which confer resistance to streptomycin. We find that 65% of double resistant strains outcompete sensitive bacteria in an environment devoid of antibiotics. Weak beneficial mutations may therefore overcome strong deleterious mutations and can even render double mutants strong competitors.

Description: There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here, we used liquid chromatography–tandem mass spectrometry to detect and quantify expressed levels of more than 2,400 proteins in ten different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to 1 in males and lower than 1 in females, consistent with partly reduced Z chromosome expression in females. Although our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared with the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to 2-fold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution.

Description: Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 ( HD1 ), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

Description: The fundamental asymmetry of female meiosis creates an arena for genetic elements to compete for inclusion in the egg, promoting the selfish evolution of centromere variants that maximize their transmission to the future egg. Such "female meiotic drive" has been hypothesized to explain the paradoxically complex and rapidly evolving nature of centromeric DNA and proteins. Although theoretically widespread, few cases of active drive have been observed, thereby limiting the opportunities to directly assess the impact of centromeric drive on molecular variation at centromeres and binding proteins. Here, we characterize the molecular evolutionary patterns of CENH3 , the centromere-defining histone variant, in Mimulus monkeyflowers, a genus with one of the few known cases of active centromere-associated female meiotic drive. First, we identify a novel duplication of CENH3 in diploid Mimulus , including in lineages with actively driving centromeres. Second, we demonstrate long-term adaptive evolution at several sites in the N-terminus of CENH3 , a region with some meiosis-specific functions that putatively interacts with centromeric DNA. Finally, we infer that the paralogs evolve under different selective regimes; some sites in the N-terminus evolve under positive selection in the pro-orthologs or only one paralog ( CENH3_B ) and the paralogs exhibit significantly different patterns of polymorphism within populations. Our finding of long-term, adaptive evolution at CENH3 in the context of centromere-associated meiotic drive supports an antagonistic, coevolutionary battle for evolutionary dominance between centromeric DNA and binding proteins.

Description: The genomic G+C content of ocean bacteria varies from below 30% to over 60%. This broad range of base composition is likely shaped by distinct mutational processes, recombination, effective population size, and selection driven by environmental factors. A number of studies have hypothesized that depletion of G/C in genomes of marine bacterioplankton cells is an adaptation to the nitrogen-poor pelagic oceans, but they failed to disentangle environmental factors from mutational biases and population history. Here, we reconstructed the evolutionary changes of bases at synonymous sites in genomes of two marine SAR11 populations and a freshwater counterpart with its evolutionary origin rooted in the marine lineage. Although they all have similar genome sizes, DNA repair gene repertoire, and base compositions, there is a stronger bias toward A/T changes, a reduced frequency of nitrogenous amino acids, and an exclusive occurrence of polyamine, opine, and taurine transport systems in the ocean populations, consistent with a greater nitrogen stress in surface oceans compared with freshwater lakes. Furthermore, the ratio of nonsynoymous to synonymous nucleotide diversity is not statistically distinguishable among these populations, suggesting that population history has a limited effect. Taken together, the ecological transition of SAR11 from ocean to freshwater habitats makes nitrogen more available to these organisms, and thus relaxation of purifying selection drove a genome-wide reduction in the frequency of G/C to A/T changes in the freshwater population.

Description: The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection.

Description: In species with a heterogametic sex, population genetics theory predicts that DNA sequences on the X chromosome can evolve faster than comparable sequences on autosomes. Both neutral and nonneutral evolutionary processes can generate this pattern. Complex traits like gene expression are not predicted to have accelerated evolution by these theories, yet a "faster-X" pattern of gene expression divergence has recently been reported for both Drosophila and mammals. Here, we test the hypothesis that accelerated adaptive evolution of cis -regulatory sequences on the X chromosome is responsible for this pattern by comparing the relative contributions of cis - and trans -regulatory changes to patterns of faster-X expression divergence observed between strains and species of Drosophila with a range of divergence times. We find support for this hypothesis, especially among male-biased genes, when comparing different species. However, we also find evidence that trans -regulatory differences contribute to a faster-X pattern of expression divergence both within and between species. This contribution is surprising because trans -acting regulators of X-linked genes are generally assumed to be randomly distributed throughout the genome. We found, however, that X-linked transcription factors appear to preferentially regulate expression of X-linked genes, providing a potential mechanistic explanation for this result. The contribution of trans -regulatory variation to faster-X expression divergence was larger within than between species, suggesting that it is more likely to result from neutral processes than positive selection. These data show how accelerated evolution of both coding and noncoding sequences on the X chromosome can lead to accelerated expression divergence on the X chromosome relative to autosomes.

Description: Molecular chaperones fold many proteins and their mutated versions in a cell and can sometimes buffer the phenotypic effect of mutations that affect protein folding. Unanswered questions about this buffering include the nature of its mechanism, its influence on the genetic variation of a population, the fitness trade-offs constraining this mechanism, and its role in expediting evolution. Answering these questions is fundamental to understand the contribution of buffering to increase genetic variation and ecological diversification. Here, we performed experimental evolution, genome resequencing, and computational analyses to determine the trade-offs and evolutionary trajectories of Escherichia coli expressing high levels of the essential chaperonin GroEL. GroEL is abundantly present in bacteria, particularly in bacteria with large loads of deleterious mutations, suggesting its role in mutational buffering. We show that groEL overexpression is costly to large populations evolving in the laboratory, leading to groE expression decline within 66 generations. In contrast, populations evolving under the strong genetic drift characteristic of endosymbiotic bacteria avoid extinction or can be rescued in the presence of abundant GroEL. Genomes resequenced from cells evolved under strong genetic drift exhibited significantly higher tolerance to deleterious mutations at high GroEL levels than at native levels, revealing that GroEL is buffering mutations in these cells. GroEL buffered mutations in a highly diverse set of proteins that interact with the environment, including substrate and ion membrane transporters, hinting at its role in ecological diversification. Our results reveal the fitness trade-offs of mutational buffering and how genetic variation is maintained in populations.

Description: Natural selection inference methods often target one mode of selection of a particular age and strength. However, detecting multiple modes simultaneously, or with atypical representations, would be advantageous for understanding a population’s evolutionary history. We have developed an anomaly detection algorithm using distributions of pairwise time to most recent common ancestor (TMRCA) to simultaneously detect multiple modes of natural selection in whole-genome sequences. As natural selection distorts local genealogies in distinct ways, the method uses pairwise TMRCA distributions, which approximate genealogies at a nonrecombining locus, to detect distortions without targeting a specific mode of selection. We evaluate the performance of our method, TSel, for both positive and balancing selection over different time-scales and selection strengths and compare TSel’s performance with that of other methods. We then apply TSel to the Complete Genomics diversity panel, a set of human whole-genome sequences, and recover loci previously inferred to be under positive or balancing selection.

Description: Most studies on the evolution of antibiotic resistance are focused on selection for resistance at lethal antibiotic concentrations, which has allowed the detection of mutant strains that show strong phenotypic traits. However, solely focusing on lethal concentrations of antibiotics narrowly limits our perspective of antibiotic resistance evolution. New high-resolution competition assays have shown that resistant bacteria are selected at relatively low concentrations of antibiotics. This finding is important because sublethal concentrations of antibiotics are found widely in patients undergoing antibiotic therapies, and in nonmedical conditions such as wastewater treatment plants, and food and water used in agriculture and farming. To understand the impacts of sublethal concentrations on selection, we measured 30 adaptive landscapes for a set of TEM β-lactamases containing all combinations of the four amino acid substitutions that exist in TEM-50 for 15 β-lactam antibiotics at multiple concentrations. We found that there are many evolutionary pathways within this collection of landscapes that lead to nearly every TEM-genotype that we studied . While it is known that the pathways change depending on the type of β-lactam, this study demonstrates that the landscapes including fitness optima also change dramatically as the concentrations of antibiotics change. Based on these results we conclude that the presence of multiple concentrations of β-lactams in an environment result in many different adaptive landscapes through which pathways to nearly every genotype are available. Ultimately this may increase the diversity of genotypes in microbial populations.

Description: The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution.

Description: We present a motivated construction of large graphs not containing a given complete bipartite subgraph. The key insight is that the algebraic constructions yield very non-smooth probability distributions.

Description: In this paper, we give the first examples of connected Polish groups that have ample generics, answering a question of Kechris and Rosendal. We show that any Polish group with ample generics embeds into a connected Polish group with ample generics and that full groups of type III hyperfinite ergodic equivalence relations have ample generics. We also sketch a proof of the following result: the full group of any type III ergodic equivalence relation has topological rank 2.

Description: We establish an essentially optimal estimate for the ninth moment of the exponential sum having argument $\alpha x^3+\beta x$ . The first substantial advance in this topic for over 60 years, this leads to improvements in Heath-Brown's variant of Weyl's inequality, and other applications of Diophantine type.

Description: Recently it was shown by H. Guenancia and M. Păun that a singular metric satisfying the conical Kähler–Einstein equation with a simple normal crossing divisor is quasi-isometric to a conical metric along that divisor. In this article, we present an alternative proof of their theorem.

Description: We describe the spectrum of certain integration operators acting on generalized Fock spaces.

Description: One of the main results of a recent paper by Gross–Tosatti–Zhang establishes estimates on the collapsing of Ricci-flat Kähler metrics on holomorphic torus fibrations. We remove a projectivity assumption from these estimates and simplify some of the underlying analysis.

Description: A coregulated module of genes ("regulon") can have evolutionarily conserved expression patterns and yet have diverged upstream regulators across species. For instance, the ribosomal genes regulon is regulated by the transcription factor (TF) TBF1 in Candida albicans , while in Saccharomyces cerevisiae it is regulated by RAP1 . Only a handful of such rewiring events have been established, and the prevalence or conditions conducive to such events are not well known. Here, we develop a novel probabilistic scoring method to comprehensively screen for regulatory rewiring within regulons across 23 yeast species. Investigation of 1,713 regulons and 176 TFs yielded 5,353 significant rewiring events at 5% false discovery rate (FDR). Besides successfully recapitulating known rewiring events, our analyses also suggest TF candidates for certain processes reported to be under distinct regulatory controls in S. cerevisiae and C. albicans , for which the implied regulators are not known: 1) Oxidative stress response (Sc- MSN2 to Ca- FKH2 ) and 2) nutrient modulation (Sc- RTG1 to Ca- GCN4 /Ca- UME6 ). Furthermore, a stringent screen to detect TF rewiring at individual genes identified 1,446 events at 10% FDR. Overall, these events are supported by strong coexpression between the predicted regulator and its target gene(s) in a species-specific fashion (〉50-fold). Independent functional analyses of rewiring TF pairs revealed greater functional interactions and shared biological processes between them ( P = 1 x 10 –3 ). Our study represents the first comprehensive assessment of regulatory rewiring; with a novel approach that has generated a unique high-confidence resource of several specific events, suggesting that evolutionary rewiring is relatively frequent and may be a significant mechanism of regulatory innovation.

Description: Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. Although the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex biphasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted coregulatory networks, which unveiled genus- and family-specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored.

Description: Mobile genetic elements such as plasmids are important for the evolution of prokaryotes. It has been suggested that there are differences between functions coded for by mobile genes and those in the "core" genome and that these differences can be seen between plasmids and chromosomes. In particular, it has been suggested that essential genes, such as those involved in the formation of structural proteins or in basic metabolic functions, are rarely located on plasmids. We model competition between genotypically varying bacteria within a single population to investigate whether selection favors a chromosomal location for essential genes. We find that in general, chromosomal locations for essential genes are indeed favored. This is because the inheritance of chromosomes is more stable than that for plasmids. We define the "degradation" rate as the rate at which chance genetic processes, for example, mutation, deletion, or translocation, render essential genes nonfunctioning. The only way in which plasmids can be a location for functioning essential genes is if chromosomal genes degrade faster than plasmid genes. If the two degradation rates are equal, or if plasmid genes degrade faster than chromosomal genes, functioning essential genes will be found only on chromosomes.

Description: During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.

Description: Viviparity (live birth) has evolved more than 150 times in vertebrates, and represents an excellent model system for studying the evolution of complex traits. There are at least 23 independent origins of viviparity in fishes, with syngnathid fishes (seahorses and pipefish) unique in exhibiting male pregnancy. Male seahorses and pipefish have evolved specialized brooding pouches that provide protection, gas exchange, osmoregulation, and limited nutrient provisioning to developing embryos. Pouch structures differ widely across the Syngnathidae, offering an ideal opportunity to study the evolution of reproductive complexity. However, the physiological and genetic changes facilitating male pregnancy are largely unknown. We used transcriptome profiling to examine pouch gene expression at successive gestational stages in a syngnathid with the most complex brood pouch morphology, the seahorse Hippocampus abdominalis. Using a unique time-calibrated RNA-seq data set including brood pouch at key stages of embryonic development, we identified transcriptional changes associated with brood pouch remodeling, nutrient and waste transport, gas exchange, osmoregulation, and immunological protection of developing embryos at conception, development and parturition. Key seahorse transcripts share homology with genes of reproductive function in pregnant mammals, reptiles, and other live-bearing fish, suggesting a common toolkit of genes regulating pregnancy in divergent evolutionary lineages.

Description: The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.

Description: Although millions of RNA editing events have been reported to modify hereditary information across the primate transcriptome, evidence for their functional significance remains largely elusive, particularly for the vast majority of editing sites in noncoding regions. Here, we report a new mechanism for the functionality of RNA editing—a crosstalk with PIWI-interacting RNA (piRNA) biogenesis. Exploiting rhesus macaque as an emerging model organism closely related to human, in combination with extensive genome and transcriptome sequencing in seven tissues of the same animal, we deciphered accurate RNA editome across both long transcripts and the piRNA species. Superimposing and comparing these two distinct RNA editome profiles revealed 4,170 editing-bearing piRNA variants, or epiRNAs, that primarily derived from edited long transcripts. These epiRNAs represent distinct entities that evidence an intersection between RNA editing regulations and piRNA biogenesis. Population genetics analyses in a macaque population of 31 independent animals further demonstrated that the epiRNA-associated RNA editing is maintained by purifying selection, lending support to the functional significance of this crosstalk in rhesus macaque. Correspondingly, these findings are consistent in human, supporting the conservation of this mechanism during the primate evolution. Overall, our study reports the earliest lines of evidence for a crosstalk between selectively constrained RNA editing regulation and piRNA biogenesis, and further illustrates that such an interaction may contribute substantially to the diversification of the piRNA repertoire in primates.

Description: Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase zeta (pol ), an essential error-prone polymerase biased toward transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol is strongly biased toward GC-〉AA/TT DNMs. Using primate divergence data, we show that the GC-〉AA/TT pol mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of approximately 10. Unlike the overall rate of DNMs, the pol signature drastically increases with the replication time in the human genome. Finally, the pol signature is enriched in transcribed regions, and there is a strong prevalence of GC-〉TT over GC-〉AA DNMs on the nontemplate strand, indicating association with transcription. A recurrently occurring GC-〉TT DNM in HRAS and SOD1 genes causes the Costello syndrome and amyotrophic lateral sclerosis correspondently; we observe an approximately 1 kb long mutation hotspot enriched by transversions near these DNMs in both cases, suggesting a link between these diseases and pol activity. This study uncovers the genomic preferences of pol , shedding light on a novel cause of mutational heterogeneity along the genome.

Description: In this study, we present an analysis of Neanderthal introgression at the dipeptidase 1 gene, DPEP1 . A Neanderthal origin for the putative introgressive haplotypes was demonstrated using an established three-step approach. This introgression was under positive natural selection, reached a frequency of 〉50%, and introduced a homocysteine level- and pigmentation-associated allele (rs460879-T) into East Asians. However, the same allele was also found in non-East Asians, but not from Neanderthal introgression. It is likely that rs460879-T was lost in East Asians and was reintroduced subsequently through Neanderthal introgression. Our findings suggest that Neanderthal introgression could reintroduce an important previously existing allele into populations where the allele had been lost. This study sheds new light on understanding the contribution of Neanderthal introgression to the adaptation of non-Africans.