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June 19, 2015
Multi-scale microbial dynamics in health and disease. The Brown lab is recruiting, with new postdoc and grad student positions available as part of an August move to the Georgia Institute of Technology (biology.gatech.edu). I am interested in candidates with experience in either computational and/or experimental approaches that are relevant to the study of microbial dynamics: Computational I am particularly interested in candidates with experience in statistical modeling and bio-informatics in an ecological/evolutionary context. Simulation and analytical approaches are also of interest, if coupled with experience of biological applications V ideally in microbiology/ecology/evolution. Experimental I am interested in candidates with strong backgrounds spanning molecular microbiology and ecology/evolution. Experience with Pseudomonas aeruginosa, quorum-sensing, regulatory evolution or mobile genetic elements is a plus. Research themes Bacterial sociality, cooperation, decision-making, quorum-sensing, biofilms, microbiomes, HGT, pathogen emergence, virulence, resistance, novel therapeuticsK (and ecology/evolution of all the above). To learn more, take a look at our website (http://bit.ly/1BncuHW) and recent relevant publications: Estrela S, Whiteley M, Brown SP. 2015. The demographic determinants of human microbiome health. Trends Microbiology 23, 134-141. McNally L, Viana M, Brown SP 2014. Cooperative secretions facilitate host range expansion in bacteria. Nature Communications. 5, 4594. Cornforth D, Popat R, McNally L, Gurney J, Scott-Phillips T, Ivens A, Diggle SP, Brown SP 2014 Combinatorial quorum sensing allows bacteria to resolve their social and physical environment. PNAS 111, 4280-4284. Allen R, Popat R, Diggle SP, Brown SP 2014 Targeting virulence: can we make evolution-proof drugs? Nature Reviews Microbiology 12, 300-308. To apply, please email a CV, brief description of research interests and how they relate to Brown lab themes (1 page) and the names and contact info for at least 3 references to Sam Brown (firstname.lastname@example.org). Review of applications will begin on July 6th and continue until positions are filled. Start dates are flexible, with preference for early 2016. via Gmail
Dear Member, *Postdoctoral Position in plant breeding methodology to optimise selection schemes and selection indices for the improvement of grassland species mixtures at INRA URP3F (France)* _POSITION DESCRIPTION._ The INRA URP3F research unit is seeking for a post-doctoral researcher to contribute to a collaborative research project (PRAISE) granted by the ANR 2013 call Bioadapt. PRAISE is a pluridisciplinary project at the crossroad of Quantitative and Population Genetics, Ecophysiology and Functional Ecology. It aims to identify the best genetic composition of sown grassland mixtures and to provide the bases of innovative selection methods of grassland species for their use in mixture. This post-doctoral research will develop a theoretical analyse of selection schemes designed to improve grassland species for their use in mixture and will set up a new selection index method to reach optimal compromise between directional selection on some traits and conservation of diversity on others. Theoretical analyse of selection schemes for the use of grassland species in mixtures. The usual selection scheme of grassland species is a recurrent selection scheme based on the agronomic assessment of half-sib progenies. Half-sib progenies are usually tested in pure mono-specific stands although grassland species are commonly sown in mixtures of several grass and legume species. However, previous results obtained at INRA UR P3F suggest that the agronomic value of genotypes in pure stands correlates quite poorly with their value in mixtures of two or more species. It is thus necessary to conceive selection schemes in which half-sib progenies of a species would be tested in micro-assemblages with other species. Such selection schemes can be considered as multi-species selection schemes in which several species would be simultaneously improved. At each selection cycle, half-sib progenies of a given species would be tested in factorial micro-assemblages with other species. Different factorial micro-assemblage designs can be conceived with different emphasis on the general and specific abilities for association in pluri-specific mixtures (GAA and SAA, respectively). The post-doctoral research will aim to define the relative efficiency of several factorial micro-assemblage designs according to values of GAA and SAA on the basis of theoretical expectations of genetic gains. These expected genetic gains will also be compared to the correlative response of mixture performance obtained with parallel classical selection schemes based on the test of pure stands of half-sib progenies, according to the value of the correlation of pure stand performances with GAA and SAA. Finally, field assays from INRA UR P3F will provide experimental values of GAA, SAA and of their correlation with pure stand performances to practically identify the best selection design. Optimisation of selection indices. The selection methods used in plant breeding are inherently directional and reduce genetic variability. They allow maintenance of variability only for traits genetically unrelated to traits submitted to selection. Usually, the control of selection on several traits is obtained by choosing candidates to selection based on the value of an index, i.e. a linear combination of the estimated breeding values of candidates for traits being selected. The coefficients of the index are determined using a constraint system based on expectations of genetic gains. The post-doctoral fellow will complete this constraint system by applying additional constraints to maintain sufficient genetic variance of some traits and will set up an operational research script to solve this constraint system. This improved index selection method will enable to deal with the trade-off between selection on some traits and conservation of diversity on others, which is of primary importance to release improved populations of grassland species for creating species mixtures able to cope with various environmental conditions. _REQUIREMENTS._ The post-doctoral fellow is expected to have a background in quantitative genetics, statistics, applied mathematics and agronomic sciences. _CONDITIONS._ The post-doctoral fellow will be hosted at the INRA URP3F research unit in Lusignan (France) where he will get support from Jean-Paul Sampoux (responsible of work-package about selection methodology of PRAISE) and Isabelle Litrico (coordinator of PRAISE). The appointment is for one year duration; starting date is wished between October 1st 2015 and January 1st 2016. _HOW TO APPLY._ Candidates can apply by sending a copy of their CV and a cover letter to J.P. Sampoux and I. Litrico (email@example.com; firstname.lastname@example.org) best regards, via Gmail
June 18, 2015
Background: Cuticular specialisations such as joints and membranes play an important role in the function of arthropod limbs. This includes sclerotisations and mineral incrustations of cuticular areas to achieve either more rigidity or flexibility. The anterior eight thoracopods of Malacostraca have limb stems comprising a coxa and a basipod, which carries the two rami. Their pleopods, the limbs of the posterior trunk part, have for long been regarded to lack a coxa. Several calcitic sclerites occur in the area between ventral body and limb stem. This raises the questions: do these elements represent specialisations of the membrane due to functional requirements, and do they originate from an originally larger limb portion, i.e., the coxa, or in fact represent it. Results: We investigated 16 species of selected malacostracan taxa from all major in-groups. Calcitic sclerites occur in constant numbers and position within a species (no individual variation, and independent of specific modification such as in genital appendages). These are even constant within a supra-specific taxon, which facilitates comparisons. In general the sclerites connect via two pivot joints to the sternite medially and the tergopleura laterally, and two more to the limb stem. Based on this, we reconstructed putative ground-pattern conditions for the sclerites of the examined taxa of Malacostraca. Conclusions: The pattern of sclerites is characteristic for each monophyletic malacostracan taxon. The highest number of sclerites most likely represents the plesiomorphic state. Reduction of sclerite numbers occurs in Caridoida and its in-groups. Sclerite arrangement in these taxa provides an important character complex for phylogenetic studies. The presence of pivot joints to the body proximally and basipod distally demonstrates the existence of a coxa, which is just slightly less sclerotised, particularly on its posterior side. This can be explained by enhanced flexibility of the pleopods evolved in the course to their major role as swimming devices. Both the pivot joints and the proximal and distal extension of the calcitic sclerites demarcate the minimum area of the coxa. With this, sclerites appear as very valuable also in shedding more light on the putative relationships between Malacostraca, Myriapoda, Insecta, and Remipedia.
Hi everyone. One of the consequences of NESCent closing is that its mailing lists will be going away in the coming months. I was part of 2 working groups that maintained email lists. The 2 lists include pretty much everyone who has attended a hackathon at NESCent (wg-phyloinformatics, which began in 2006, and hip, which began in 2011).
We considered just migrating to a new non-NESCent email list, but an alternative would be to encourage current list members to sign up on phylobabble. If we could start a topic on phyloinformatics, then presumably users could set up a feed and it would have the same immediacy as an email list.
What do you think? I welcome your thoughts on that idea.
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications
Background: The genus Flaveria has been extensively used as a model to study the evolution of C 4 photosynthesis as it contains C 3 and C 4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F). Results: Here we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a “F. pringlei” genotype recently used in a number of labs may be a hybrid between F. pringlei (C 3 ) and F. angustifolia (C 3 -C 4 ). Conclusions: We propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C 4 photosynthesis in the Flavaria clade.
Background: Sexual ornamentation may be related to the degree of paternal care and the ‘good-parent’ model predicts that male secondary characters honestly advertise paternal investment. In most birds, males are involved in bringing up the young and successful reproduction highly depends on male contribution during breeding. In passerines, male song is indicative of male attributes and for few species it has been shown that song features also signal paternal investment to females. Males of nightingales Luscinia megarhynchos are famous for their elaborate singing but so far there is only little knowledge on the role of male song in intersexual communication, and it is unknown whether male song predicts male parenting abilities. Results: Using RFID technology to record male feeding visits to the nest, we found that nightingale males substantially contribute to chick feeding. Also, we analyzed male nocturnal song with focus on song features that have been shown to signal male quality before. We found that several song features, namely measures of song complexity and song sequencing, were correlated with male feeding rates. Moreover, the combination of these song features had strong predictive power for male contribution to nestling feeding. Conclusions: Since male nightingales are involved in chick rearing, paternal investment might be a crucial variable for female mate choice in this species. Females may assess future paternal care on the basis of song features identified in our study and thus these features may have evolved to signal direct benefits to females. Additionally we underline the importance of multiple acoustic cues for female mating decisions especially in species with complex song such as the nightingale.
Evolution Is an Experiment: Assessing Parallelism in Crop Domestication and Experimental Evolution: (Nei Lecture, SMBE 2014, Puerto Rico)
In this commentary, I make inferences about the level of repeatability and constraint in the evolutionary process, based on two sets of replicated experiments. The first experiment is crop domestication, which has been replicated across many different species. I focus on results of whole-genome scans for genes selected during domestication and ask whether genes are, in fact, selected in parallel across different domestication events. If genes are selected in parallel, it implies that the number of genetic solutions to the challenge of domestication is constrained. However, I find no evidence for parallel selection events either between species (maize vs. rice) or within species (two domestication events within beans). These results suggest that there are few constraints on genetic adaptation, but conclusions must be tempered by several complicating factors, particularly the lack of explicit design standards for selection screens. The second experiment involves the evolution of Escherichia coli to thermal stress. Unlike domestication, this highly replicated experiment detected a limited set of genes that appear prone to modification during adaptation to thermal stress. However, the number of potentially beneficial mutations within these genes is large, such that adaptation is constrained at the genic level but much less so at the nucleotide level. Based on these two experiments, I make the general conclusion that evolution is remarkably flexible, despite the presence of epistatic interactions that constrain evolutionary trajectories. I also posit that evolution is so rapid that we should establish a Speciation Prize, to be awarded to the first researcher who demonstrates speciation with a sexual organism in the laboratory.
Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR–) mutation–accumulation (MA) lines of the gram-positive model organism Bacillus subtilis. We then analyzed>7,500 spontaneous base-substitution mutations across B. subtilis, Escherichia coli, and Mesoplasma florum WT and MMR– MA lines, finding a context-dependent mutation pattern that is asymmetric around the origin of replication. Different neighboring nucleotides can alter site-specific mutation rates by as much as 75-fold, with sites neighboring G:C base pairs or dimers involving alternating pyrimidine–purine and purine–pyrimidine nucleotides having significantly elevated mutation rates. The influence of context-dependent mutation on genome architecture is strongest in M. florum, consistent with the reduced efficiency of selection in organisms with low effective population size. If not properly accounted for, the disparities arising from patterns of context-dependent mutation can significantly influence interpretations of positive and purifying selection.
Ancient Duplications and Expression Divergence in the Globin Gene Superfamily of Vertebrates: Insights from the Elephant Shark Genome and Transcriptome
Comparative analyses of vertebrate genomes continue to uncover a surprising diversity of genes in the globin gene superfamily, some of which have very restricted phyletic distributions despite their antiquity. Genomic analysis of the globin gene repertoire of cartilaginous fish (Chondrichthyes) should be especially informative about the duplicative origins and ancestral functions of vertebrate globins, as divergence between Chondrichthyes and bony vertebrates represents the most basal split within the jawed vertebrates. Here, we report a comparative genomic analysis of the vertebrate globin gene family that includes the complete globin gene repertoire of the elephant shark (Callorhinchus milii). Using genomic sequence data from representatives of all major vertebrate classes, integrated analyses of conserved synteny and phylogenetic relationships revealed that the last common ancestor of vertebrates possessed a repertoire of at least seven globin genes: single copies of androglobin and neuroglobin, four paralogous copies of globin X, and the single-copy progenitor of the entire set of vertebrate-specific globins. Combined with expression data, the genomic inventory of elephant shark globins yielded four especially surprising findings: 1) there is no trace of the neuroglobin gene (a highly conserved gene that is present in all other jawed vertebrates that have been examined to date), 2) myoglobin is highly expressed in heart, but not in skeletal muscle (reflecting a possible ancestral condition in vertebrates with single-circuit circulatory systems), 3) elephant shark possesses two highly divergent globin X paralogs, one of which is preferentially expressed in gonads, and 4) elephant shark possesses two structurally distinct α-globin paralogs, one of which is preferentially expressed in the brain. Expression profiles of elephant shark globin genes reveal distinct specializations of function relative to orthologs in bony vertebrates and suggest hypotheses about ancestral functions of vertebrate globins.
Although an increasing number of horizontal gene transfers have been reported in eukaryotes, experimental evidence for their adaptive value is lacking. Here, we report the recent transfer of a 158-kb genomic region between Torulaspora microellipsoides and Saccharomyces cerevisiae wine yeasts or closely related strains. This genomic region has undergone several rearrangements in S. cerevisiae strains, including gene loss and gene conversion between two tandemly duplicated FOT genes encoding oligopeptide transporters. We show that FOT genes confer a strong competitive advantage during grape must fermentation by increasing the number and diversity of oligopeptides that yeast can utilize as a source of nitrogen, thereby improving biomass formation, fermentation efficiency, and cell viability. Thus, the acquisition of FOT genes has favored yeast adaptation to the nitrogen-limited wine fermentation environment. This finding indicates that anthropic environments offer substantial ecological opportunity for evolutionary diversification through gene exchange between distant yeast species.
Homologous recombination promotes genetic diversity by facilitating the integration of foreign DNA and intrachromosomal gene shuffling. It has been hypothesized that if recombination is variable among strains, selection should favor higher recombination rates among pathogens, as they face additional selection pressures from host defenses. To test this hypothesis we have developed a plasmid-based method for estimating the rate of recombination independently of other factors such as DNA transfer, selective processes, and mutational interference. Our results with 160 human commensal and extraintestinal pathogenic Escherichia coli (ExPEC) isolates show that the recombinant frequencies are extremely diverse (ranging 9 orders of magnitude) and plastic (they are profoundly affected by growth in urine, a condition commonly encountered by ExPEC). We find that the frequency of recombination is biased by strain lifestyle, as ExPEC isolates display strikingly higher recombination rates than their commensal counterparts. Furthermore, the presence of virulence factors is positively associated with higher recombination frequencies. These results suggest selection for high homologous recombination capacity, which may result in a higher evolvability for pathogens compared with commensals.
It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes.
Multispecies Analysis of Expression Pattern Diversification in the Recently Expanded Insect Ly6 Gene Family
Gene families often consist of members with diverse expression domains reflecting their functions in a wide variety of tissues. However, how the expression of individual members, and thus their tissue-specific functions, diversified during the course of gene family expansion is not well understood. In this study, we approached this question through the analysis of the duplication history and transcriptional evolution of a rapidly expanding subfamily of insect Ly6 genes. We analyzed different insect genomes and identified seven Ly6 genes that have originated from a single ancestor through sequential duplication within the higher Diptera. We then determined how the original embryonic expression pattern of the founding gene diversified by characterizing its tissue-specific expression in the beetle Tribolium castaneum, the butterfly Bicyclus anynana, and the mosquito Anopheles stephensi and those of its duplicates in three higher dipteran species, representing various stages of the duplication history (Megaselia abdita, Ceratitis capitata, and Drosophila melanogaster). Our results revealed that frequent neofunctionalization episodes contributed to the increased expression breadth of this subfamily and that these events occurred after duplication and speciation events at comparable frequencies. In addition, at each duplication node, we consistently found asymmetric expression divergence. One paralog inherited most of the tissue-specificities of the founder gene, whereas the other paralog evolved drastically reduced expression domains. Our approach attests to the power of combining a well-established duplication history with a comprehensive coverage of representative species in acquiring unequivocal information about the dynamics of gene expression evolution in gene families.
When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (
An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors
Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms.
Understanding the driving forces behind protein evolution requires the ability to correlate the molecular impact of mutations with organismal fitness. To address this issue, we employ here metallo-β-lactamases as a model system, which are Zn(II) dependent enzymes that mediate antibiotic resistance. We present a study of all the possible evolutionary pathways leading to a metallo-β-lactamase variant optimized by directed evolution. By studying the activity, stability and Zn(II) binding capabilities of all mutants in the preferred evolutionary pathways, we show that this local fitness landscape is strongly conditioned by epistatic interactions arising from the pleiotropic effect of mutations in the different molecular features of the enzyme. Activity and stability assays in purified enzymes do not provide explanatory power. Instead, measurement of these molecular features in an environment resembling the native one provides an accurate description of the observed antibiotic resistance profile. We report that optimization of Zn(II) binding abilities of metallo-β-lactamases during evolution is more critical than stabilization of the protein to enhance fitness. A global analysis of these parameters allows us to connect genotype with fitness based on quantitative biochemical and biophysical parameters.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology