ALBERT

Description: Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally . This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.

Description: Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola . BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae . The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea .

Description: Gene expression evolution occurs through changes in cis - or trans -regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus ) and within species (comparing two closely related S. cerevisiae strains).

Description: Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (~7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (~10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.

Description: Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.

Description: Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria ) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu.

Description: Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium ) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we report the discovery of a novel family of small nonautonomous long terminal repeat retrotransposons (also known as terminal-repeat retrotransposons in miniature, TRIMs) which we have named ta-TRIM (taeniid TRIM). ta-TRIM s are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. These elements originated at the base of the taeniid tree and have expanded during taeniid diversification, including after the divergence of closely related species such as Echinococcus multilocularis and Echinococcus granulosus . They are massively expressed in larval stages, from a small proportion of full-length copies and from isolated terminal repeats that show transcriptional read-through into downstream regions, generating novel noncoding RNAs and transcriptional fusions to coding genes. In E. multilocularis , ta-TRIM s are specifically expressed in the germinative cells (the somatic stem cells) during asexual reproduction of metacestode larvae. This would provide a developmental mechanism for insertion of ta-TRIM s into cells that will eventually generate the adult germ line. Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes.

Description: Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (~326 kb) of the dinoflagellate, Symbiodinium minutum , is AT-rich (~64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum . Gene map comparisons show that gene order is only slightly conserved between S. minutu m and P. falciparum . However, small RNAs and intergenic sequences share sequence similarities with P. falciparum , suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures.

Description: Evolutionary studies usually use a two-step process to investigate sequence data. Step one estimates a multiple sequence alignment (MSA) and step two applies phylogenetic methods to ask evolutionary questions of that MSA. Modern phylogenetic methods infer evolutionary parameters using maximum likelihood or Bayesian inference, mediated by a probabilistic substitution model that describes sequence change over a tree. The statistical properties of these methods mean that more data directly translates to an increased confidence in downstream results, providing the substitution model is adequate and the MSA is correct. Many studies have investigated the robustness of phylogenetic methods in the presence of substitution model misspecification, but few have examined the statistical properties of those methods when the MSA is unknown. This simulation study examines the statistical properties of the complete two-step process when inferring sequence divergence and the phylogenetic tree topology. Both nucleotide and amino acid analyses are negatively affected by the alignment step, both through inaccurate guide tree estimates and through overfitting to that guide tree. For many alignment tools these effects become more pronounced when additional sequences are added to the analysis. Nucleotide sequences are particularly susceptible, with MSA errors leading to statistical support for long-branch attraction artifacts, which are usually associated with gross substitution model misspecification. Amino acid MSAs are more robust, but do tend to arbitrarily resolve multifurcations in favor of the guide tree. No inference strategies produce consistently accurate estimates of divergence between sequences, although amino acid MSAs are again more accurate than their nucleotide counterparts. We conclude with some practical suggestions about how to limit the effect of MSA uncertainty on evolutionary inference.

Description: The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the α-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNA Ile lysidine synthetase, and RNase P. Our results support the observation that the fate of nuclear-encoded mitochondrial proteins is influenced by the evolution of molecules encoded in mitochondrial DNA, but in a more complex manner than appreciated previously. The data also suggest that relaxed selection on mitochondrial translation rather than coevolution between mitochondrial and nuclear subunits is responsible for elevated rates of evolution in mitochondrial translational proteins.

Description: The expansion of DUF1220 domain copy number during human evolution is a dramatic example of rapid and repeated domain duplication. Although patterns of expression, homology, and disease associations suggest a role in cortical development, this hypothesis has not been robustly tested using phylogenetic methods. Here, we estimate DUF1220 domain counts across 12 primate genomes using a nucleotide Hidden Markov Model. We then test a series of hypotheses designed to examine the potential evolutionary significance of DUF1220 copy number expansion. Our results suggest a robust association with brain size, and more specifically neocortex volume. In contradiction to previous hypotheses, we find a strong association with postnatal brain development but not with prenatal brain development. Our results provide further evidence of a conserved association between specific loci and brain size across primates, suggesting that human brain evolution may have occurred through a continuation of existing processes.

Description: Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

Description: There is widespread interest today in understanding enhancers, which are regulatory elements typically harboring several transcription factor binding sites and mediating the combinatorial effect of transcription factors on gene expression. The evolution of enhancers poses interesting unanswered questions, for example, the evolutionary time taken for a typical enhancer to emerge or the factors shaping its evolution. Existing approaches to cis -regulatory evolution have often ignored the combinatorial nature and varied biochemical mechanisms of gene regulation encoded in enhancers. We report on our investigation of enhancer evolution through the use of PEBCRES, a framework for evolutionary simulation of enhancers that employs a mechanistic and well-supported sequence-to-expression model to assign fitness to the evolving enhancer genotype. We estimated the time necessary to evolve, from genomic background, enhancers capable of driving complex gene expression patterns similar to those involved in early development in Drosophila. We found the time-to-evolve to range between 0.5 and 10 Myr, and to vary greatly with the target expression pattern, complexity of the real enhancer known to encode that pattern, and the strength of input from specific transcription factors. To our knowledge, this is the first estimate of waiting times for realistic enhancers to evolve. The in silico evolved enhancers had, with a few interesting exceptions, site compositions similar to those seen in real enhancers for the same patterns. Our simulations also revealed that certain features of an enhancer might evolve not due to their biological function but as aids to the evolutionary process itself.

Description: Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.

Description: Organisms can adapt to local environmental conditions as a plastic response or become adapted through natural selection on genetic variation. The ability to adapt to increased water temperatures will be of paramount importance for many fish species as the climate continues to warm and water resources become limited. Because increased water temperatures will reduce the dissolved oxygen available for fish, we hypothesized that adaptation to low oxygen environments would involve improved respiration through oxidative phosphorylation (OXPHOS). To test this hypothesis, we subjected individuals from two ecologically divergent populations of inland (redband) rainbow trout ( Oncorhynchus mykiss gairdneri ) with historically different temperature regimes (desert and montane) and their F1 progeny to diel cycles of temperature stress and then examined gene expression data for 80 nuclear- and mitochondrial-encoded OXPHOS subunits that participate in respiration. Of the 80 transcripts, 7 showed ≥ 2-fold difference in expression levels in gill tissue from desert fish under heat stress whereas the montane fish had none and the F1 only had one differentially expressed gene. A structural analysis of the proteins encoded by those genes suggests that the response could coordinate the formation of supercomplexes and oligomers. Supercomplexes may increase the efficiency of respiration because complexes I, III, and IV are brought into close proximity and oligomerization of complex V alters the macrostructure of mitochondria to improve respiration. Significant differences in gene expression patterns in response to heat stress in a common environment indicate that the response was not due to plasticity but had a genetic basis.

Description: The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata , a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae–Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.

Description: We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis . These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling.

Description: Most sequenced eukaryotic genomes show a large excess of recent duplicates. As duplicates age, both the population genetic process of failed fixation and the mutation-driven process of nonfunctionalization act to reduce the observed number of duplicates. Understanding the processes generating the age distributions of recent duplicates is important to also understand the role of duplicate genes in the functional divergence of genomes. To date, mechanistic models for duplicate gene retention only account for the mutation-driven nonfunctionalization process. Here, a neutral model for the distribution of synonymous substitutions in duplicated genes which are segregating and expected to never fix in a population is introduced. This model enables differentiation of neutral loss due to failed fixation from loss due to mutation-driven nonfunctionalization. The model has been validated on simulated data and subsequent analysis with the model on genomic data from human and mouse shows that conclusions about the underlying mechanisms for duplicate gene retention can be sensitive to consideration of population genetic processes.

Description: Stenotrophomonas maltophilia , a ubiquitous Gram-negative -proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain’s phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance–nodulation–division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.

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: The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the "non-Bantu" genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.

Description: Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders.

Description: Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (~0.4X to 2X) for six fern species from the Polypodiales ( Ceratopteris , Pteridium , Polypodium , Cystopteris ), Cyatheales ( Plagiogyria ), and Gleicheniales ( Dipteris ). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

Description: The evolution of heterogametic sex chromosomes is often—but not always—accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) species but not in female-heterogametic (ZW) species, which will consequently exhibit "incomplete" sex chromosome dosage compensation. However, recent results suggest that at least some Lepidoptera (moths and butterflies) may prove to be an exception to this prediction. Studies in bombycoid moths indicate the presence of a chromosome-wide epigenetic mechanism that effectively balances Z chromosome gene expression between the sexes by reducing Z-linked expression in males. In contrast, strong sex chromosome dosage effects without any reduction in male Z-linked expression were previously reported in a pyralid moth, suggesting a lack of any such dosage compensating mechanism. Here we report an analysis of sex chromosome dosage compensation in Heliconius butterflies, sampling multiple individuals for several different adult tissues (head, abdomen, leg, mouth, and antennae). Methodologically, we introduce a novel application of linear mixed-effects models to assess dosage compensation, offering a unified statistical framework that can estimate effects specific to chromosome, to sex, and their interactions (i.e., a dosage effect). Our results show substantially reduced Z-linked expression relative to autosomes in both sexes, as previously observed in bombycoid moths. This observation is consistent with an increasing body of evidence that some lepidopteran species possess an epigenetic dosage compensating mechanism that reduces Z chromosome expression in males to levels comparable with females. However, this mechanism appears to be imperfect in Heliconius , resulting in a modest dosage effect that produces an average 5–20% increase in male expression relative to females on the Z chromosome, depending on the tissue. Thus our results in Heliconius reflect a mixture of previous patterns reported for Lepidoptera. In Heliconius, a moderate pattern of incomplete dosage compensation persists apparently despite the presence of an epigenetic dosage compensating mechanism. The chromosomal distributions of sex-biased genes show an excess of male-biased and a dearth of female-biased genes on the Z chromosome relative to autosomes, consistent with predictions of sexually antagonistic evolution.

Description: Mycobacterium avium ( M. a. ) subsp. paratuberculosis (MAP)—the etiologic agent of Johne’s disease—affects cattle, sheep, and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III], respectively, MAP-C [Type-II]), comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. This study presents the so far best assembled genome of a MAP-S-strain: Sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from the United States and Australia, and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI (National Center for Biotechnology Information) annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined by either NCBI or BacProt. A new Shine–Dalgarno sequence motif (5'-AGCTGG-3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 noncoding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four of ten assumed MAP-S-specific large sequence polymorphism regions (LSP S s) are still present in MAP-C strains; new LSP S s were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirms the strong similarity of MAP-C strains and shows higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to Mycobacterium intracellulare .

Description: Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals’ digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.

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: A number of sap-sucking insects harbor endosymbionts, which are thought to play an important role in the development of their hosts. One of the most important rice pests, the brown planthopper (BPH), Nilaparvata lugens (Stål), harbors an obligatory yeast-like symbiont (YLS) that cannot be cultured in vitro. Genomic information on this YLS would be useful to better understand its evolution. In this study, we performed genome sequencing of the YLS using both 454 and Illumina approaches, generating a draft genome that shows a slightly smaller genome size and relatively higher GC content than most ascomycete fungi. A phylogenomic analysis of the YLS supported its close relationship with insect pathogens. We analyzed YLS-specific genes and the categories of genes that are likely to have changed in the YLS during its evolution. The loss of mating type locus demonstrated in the YLS sheds light on the evolution of eukaryotic symbionts. This information about the YLS genome provides a helpful guide for further understanding endosymbiotic associations in hemiptera and the symbiotic replacement of ancient bacteria with a multifunctional YLS seems to have been a successful change.

Description: The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica , a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis . The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon , and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.

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: Comparisons of draft genome sequences of three geographically distinct isolates of Fusarium fujikuroi with two recently published genome sequences from the same species suggest diverse profiles of secondary metabolite production within F. fujikuroi . Species- and lineage-specific genes, many of which appear to exhibit expression profiles that are consistent with roles in host–pathogen interactions and adaptation to environmental changes, are concentrated in subtelomeric regions. These genomic compartments also exhibit distinct gene densities and compositional characteristics with respect to other genomic partitions, and likely play a role in the generation of molecular diversity. Our data provide additional evidence that gene duplication, divergence, and differential loss play important roles in F. fujikuroi genome evolution and suggest that hundreds of lineage-specific genes might have been acquired through horizontal gene transfer.

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: Passerines are the largest avian order, and the 6,000 species comprise more than half of all extant bird species. This successful radiation probably had its origin in the Australasian region, but dating this origin has been difficult due to a scarce fossil record and poor biogeographic assumptions. Many of New Zealand’s endemic passerines fall within the deeper branches of the passerine radiation, and a well resolved phylogeny for the modern New Zealand element in the deeper branches of the oscine lineage will help us understand both oscine and passerine biogeography. To this end we present complete mitochondrial genomes representing all families of New Zealand passerines in a phylogenetic framework of over 100 passerine species. Dating analyses of this robust phylogeny suggest Passeriformes originated in the early Paleocene, with the major lineages of oscines "escaping" from Australasia about 30 Ma, and radiating throughout the world during the Oligocene. This independently derived conclusion is consistent with the passerine fossil record.

Description: Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides , Triplophysa scleroptera , and Triplophysa dalaica , and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish ( Astyanax mexicanus ), zebrafish ( Danio rerio ), large-scale loach ( Paramisgurnus dabryanus ), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa -specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa -specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.

Description: Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response . The genome also harbored a large number of mobile elements (~5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.

Description: Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton, or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of nonsynonymous to synonymous substitution rate ratios (d N /d S ) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits—suggesting an important role for NC network architecture during the diversification in vertebrates.

Description: Cymbomonas tetramitiformis —a marine prasinophyte—is one of only a few green algae that still retain an ancestral particulate-feeding mechanism while harvesting energy through photosynthesis. The genome of the alga is estimated to be 850 Mb–1.2 Gb in size—the bulk of which is filled with repetitive sequences—and is annotated with 37,366 protein-coding gene models. A number of unusual metabolic pathways (for the Chloroplastida) are predicted for C. tetramitiformis , including pathways for Lipid-A and peptidoglycan metabolism. Comparative analyses of the predicted peptides of C. tetramitiformis to sets of other eukaryotes revealed that nonphagocytes are depleted in a number of genes, a proportion of which have known function in feeding. In addition, our analysis suggests that obligatory phagotrophy is associated with the loss of genes that function in biosynthesis of small molecules (e.g., amino acids). Further, C. tetramitiformis and at least one other phago-mixotrophic alga are thus unique, compared with obligatory heterotrophs and nonphagocytes, in that both feeding and small molecule synthesis-related genes are retained in their genomes. These results suggest that early, ancestral host eukaryotes that gave rise to phototrophs had the capacity to assimilate building block molecules from inorganic substances (i.e., prototrophy). The loss of biosynthesis genes, thus, may at least partially explain the apparent lack of instances of permanent incorporation of photosynthetic endosymbionts in later-divergent, auxotrophic eukaryotic lineages, such as metazoans and ciliates.

Description: Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. Identification of new species since 1989 and emergence of zoonotic infections, including abortion in women, underscore the need for genome sequencing of multiple strains of each species to advance our knowledge of evolutionary dynamics across Chlamydiaceae . Here, we genome sequenced isolates from avian, lower mammalian and human hosts. Based on core gene phylogeny, five isolates previously classified as Chlamydia abortus were identified as members of Chlamydia psittaci and Chlamydia pecorum. Chlamydia abortus is the most recently emerged species and is a highly monomorphic group that lacks the conserved virulence-associated plasmid. Low-level recombination and evidence for adaptation to the placenta echo evolutionary processes seen in recently emerged, highly virulent niche-restricted pathogens, such as Bacillus anthracis . In contrast, gene flow occurred within C. psittaci and other Chlamydiaceae species. The C. psittaci strain RTH, isolated from a red-tailed hawk ( Buteo jamaicensis ), is an outlying strain with admixture of C. abortus , C. psittaci , and its own population markers. An average nucleotide identity of less than 94% compared with other Chlamydiaceae species suggests that RTH belongs to a new species intermediary between C. psittaci and C. abortus . Hawks, as scavengers and predators, have extensive opportunities to acquire multiple species in their intestinal tract. This could facilitate transformation and homologous recombination with the potential for new species emergence. Our findings indicate that incubator hosts such as birds-of-prey likely promote Chlamydiaceae evolution resulting in novel pathogenic lineages.

Description: The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences—which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.

Description: Zagier's well-known work on traces of singular moduli relates the coefficients of certain weakly holomorphic modular forms of weight $\frac {1}{2}$ to traces of values of the modular $j$ -function at imaginary quadratic points. A real quadratic analogue was recently studied by Duke, Imamoglu, and Tóth. They showed that the coefficients of certain weight $\frac {1}{2}$ mock modular forms \[f_D = \sum _{d 〉 0} a(d,D) q^d, \quad D 〉 0\] are given in terms of traces of cycle integrals of the $j$ -function. Their result applies to those coefficients $a(d,D)$ for which $dD$ is not a square. Recently, Bruinier, Funke, and Imamoglu employed a regularized theta lift to show that the coefficients $a(d,D)$ for square $dD$ are traces of regularized integrals of the $j$ -function. In the present paper, we provide an alternate approach to this problem. We introduce functions $j_{m,Q}$ (for $Q$ a quadratic form) which are related to the $j$ -function and show, by modifying the method of Duke, Imamoglu, and Tóth, that the coefficients for which $dD$ is a square are traces of cycle integrals of the functions $j_{m,Q}$ .

Description: For $q$ an odd prime power with $q 〉 169,$ we prove that there are always three consecutive primitive elements in the finite field $\mathbb {F}_{q}$ . Indeed, there are precisely eleven values of $q \leq 169$ for which this is false. For $4\leq n \leq 8,$ we present conjectures on the size of $q_{0}(n)$ such that $q 〉 q_{0}(n)$ guarantees the existence of $n$ consecutive primitive elements in $\mathbb {F}_{q}$ , provided that $\mathbb {F}_{q}$ has characteristic at least $n$ . Finally, we improve the upper bound on $q_{0}(n)$ for all $n\geq 3$ .

Description: Let ${{{\bf{G}}}}$ be a connected reductive group with connected center defined over ${{\mathbb {F}}}_q$ , with Frobenius morphism $F$ . We parameterize all of the real-valued irreducible complex characters of ${{{\bf{G}}}}^F$ using the Jordan decomposition of characters.

Description: By a 35-year-old theorem of Shelah, $\square _\lambda + \diamondsuit (\lambda ^+ )$ does not imply for regular uncountable cardinals $\lambda$ . Here, it is proved that $\square _\lambda + \diamondsuit (\lambda ^+ )$ is equivalent to for every singular cardinal $\lambda$ .

Description: Let $E = (E^0, E^1, r, s)$ be a topological graph with no sinks such that $E^0$ and $E^1$ are compact. We show that when $C^* (E)$ is finite, there is a natural isomorphism $C^* (E) \cong C(E^\infty ) \rtimes \mathbb {Z}$ , where $E^\infty$ is the infinite path space of $E$ and the action is given by the backwards shift on $E^\infty$ . Combining this with a result of Pimsner, we show the properties of being approximately finite-dimensional-embeddable, quasidiagonal, stably finite, and finite are equivalent for $C^* (E)$ and can be characterized by a natural ‘combinatorial’ condition on $E$ .

Description: We prove partial regularity of minimizers $u$ for $p(x)$ -energy functionals of the following type: \[{\mathcal E}(u)=\int _\Omega (A^{\alpha \beta }_{ij}(x,u)D_{\alpha }u^i D_{\beta }u^j)^{p(x)/2}\,d x,\] assuming that $A^{\alpha \beta }_{ij}(x,u)$ and $p(x)$ are sufficiently smooth and that $p(x)$ is subquadratic. We prove that $u\in C^{0,\alpha }(\Omega _0)$ for some $\alpha \in (0,1)$ and an open set $\Omega _0 \subset \Omega$ with ${\mathcal H}^{m-\gamma _1}(\Omega -\Omega _0)=0$ , where ${\mathcal H}^s$ denotes the $s$ -dimensional Hausdorff measure and $\gamma _1=\inf _{\Omega } p(x)$ .

Description: By adopting a new approach to the analysis of the density of $p$ -adic solutions arising in applications of the circle method, we show that under modest conditions the existence of non-trivial $p$ -adic solutions suffices to establish positivity of the singular series. This improves on earlier approaches due to Davenport, Schmidt and others, and allows us to establish an asymptotic formula for the number of simultaneous zeros of non-singular pairs of cubic forms in at least $131$ variables. As a by-product, we obtain a version of Hensel's lemma for linear spaces.

Description: Let $\{\phi _t\}_{t\geq 0}$ be a semigroup of holomorphic self-maps of the unit disk. We assume that the Denjoy–Wolff point of the semigroup is the point $1$ ; so $1$ is the unique attractive boundary fixed point of the semigroup. We further assume that for all $t 〉 0$ , $\phi _t^\prime (1)\lt 1$ (angular derivative), namely the semigroup is hyperbolic. We prove then that the rate of convergence of the semigroup to the point $1$ , as $t\to + \infty$ , is exponential with exponent arbitrarily close to $-\pi t/\nu (\Omega )$ , where $\nu (\Omega )$ is the width of the smallest strip containing the associated planar domain $\Omega$ . We also prove that the trajectories of the semigroup approach the point $1$ in a monotonic way.

Description: The McCool group, denoted $P\Sigma _n$ , is the group of pure symmetric automorphisms of a free group of rank $n$ . A presentation of the cohomology algebra $H^* (P\Sigma _n, {{\mathbb Q}})$ was determined by Jensen, McCammond, and Meier. We prove that $H^* (P\Sigma _n, {{\mathbb Q}})$ is a non-Koszul algebra for $n \geq 4$ , which answers a question of Cohen and Pruidze. We also study the enveloping algebra of the graded Lie algebra associated to the lower central series of $P\Sigma _n$ , and prove that it has two natural decompositions as a smash product of algebras.

Description: Let ${\mathcal {H}ol}({\mathbb D})$ denote the space of holomorphic functions on the unit disk ${\mathbb D}$ . We characterize those radial weights ${w}$ on ${\mathbb D}$ for which there exist functions $f, g\in {\mathcal {H}ol}({\mathbb D})$ such that the sum $|f| + |g|$ is equivalent to ${w}$ . Also, we obtain similar results in several complex variables for circular, strictly convex domains with smooth boundary.

Description: We use the Dandelin–Gallucci theorem to give a proof of Wedderburn's little theorem that every finite division ring is commutative, and the proof is geometric in the sense that the non-geometric concepts employed are of an elementary nature. As a consequence, we obtain a geometric proof that a finite Desarguesian projective space is Pappian.

Description: We study the stability of the standing wave solutions of a Gross–Pitaevskii equation describing Bose–Einstein condensation of dipolar quantum gases and characterize their orbit. As an intermediate step, we consider the corresponding constrained minimization problem and establish existence, symmetry and uniqueness of the ground state solutions.

Description: Brachiopods are a lineage of invertebrates well known for the breadth and depth of their fossil record. Although the quality of this fossil record attracts the attention of paleontologists, geochemists, and paleoclimatologists, modern day brachiopods are also of interest to evolutionary biologists due to their potential to address a variety of questions ranging from developmental biology to biomineralization. The brachiopod shell is a composite material primarily composed of either calcite or calcium phosphate in close association with proteins and polysaccharides which give these composite structures their material properties. The information content of these biomolecules, sequestered within the shell during its construction, has the potential to inform hypotheses focused on describing how brachiopod shell formation evolved. Here, using high throughput proteomic approaches and next generation sequencing, we have surveyed and characterized the first shell-proteome and shell-forming transcriptome of any brachiopod, the South American Magellania venosa (Rhynchonelliformea: Terebratulida) . We find that the seven most abundant proteins present in the shell are unique to M. venosa , but that these proteins display biochemical features found in other metazoan biomineralization proteins. We can also detect some M. venosa proteins that display significant sequence similarity to other metazoan biomineralization proteins, suggesting that some elements of the brachiopod shell-forming proteome are deeply evolutionarily conserved. We also employed a variety of preparation methods to isolate shell proteins and find that in comparison to the shells of other spiralian invertebrates (such as mollusks) the shell ultrastructure of M. venosa may explain the effects these preparation strategies have on our results.

Description: Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipid metabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genes encoding paralogs of FFAR2 in the chicken, considered as a model organism for developmental biology and biomedical research. By estimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencing data, we showed the existence of 23 ± 1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared an identity from 87.2% up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities between these genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/synonymous substitution ratios on some amino acids within or in close-vicinity of the ligand-binding groove suggest that positive selection may have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function of some FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes were expressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, and lung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specific events along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species.

Description: Several hypotheses exist that describe phytoplankton spring blooms in temperate and subpolar oceans: the critical depth, shoaling mixed layer (ML), critical turbulence, onset of stratification and disturbance-recovery hypotheses. These theories appear to be mutually exclusive and none of them describe the annual cycle of phytoplankton biomass. Here, we present a model of the annual cycle in phytoplankton that recognizes that phytoplankton are not always mixed throughout the so-called ML, and that it is important to distinguish between the surface biomass and depth-integrated phytoplankton. Once these important distinctions are made, the annual cycles and blooms in surface and depth-integrated phytoplankton can be described straightforwardly in terms of the physical drivers and biotic responses.