There are currently 0 users and 32 guests online.
April 24, 2015
Extending the Conserved Phylogenetic Core of Archaea Disentangles the Evolution of the Third Domain of Life
Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new superclasses within the Euryarchaeota: Methanomada and Diaforarchaea.
Malaria parasites are highly virulent pathogens which infect a wide range of vertebrates. Despite their importance, the way different hosts control and suppress malaria infections remains poorly understood. With recent developments in next-generation sequencing techniques, however, it is now possible to quantify the response of the entire transcriptome to infections. We experimentally infected Eurasian siskins (Carduelis spinus) with avian malaria parasites (Plasmodium ashfordi), and used high-throughput RNA-sequencing to measure the avian transcriptome in blood collected before infection (day 0), during peak parasitemia (day 21 postinfection), and when parasitemia was decreasing (day 31). We found considerable differences in the transcriptomes of infected and uninfected individuals, with a large number of genes differentially expressed during both peak and decreasing parasitemia stages. These genes were overrepresented among functions involved in the immune system, stress response, cell death regulation, metabolism, and telomerase activity. Comparative analyses of the differentially expressed genes in our study to those found in other hosts of malaria (human and mouse) revealed a set of genes that are potentially involved in highly conserved evolutionary responses to malaria infection. By using RNA-sequencing we gained a more complete view of the host response, and were able to pinpoint not only well-documented host genes but also unannotated genes with clear significance during infection, such as microRNAs. This study shows how the avian blood transcriptome shifts in response to malaria infection, and we believe that it will facilitate further research into the diversity of molecular mechanisms that hosts utilize to fight malaria infections.
Evolutionary Histories of Transposable Elements in the Genome of the Largest Living Marsupial Carnivore, the Tasmanian Devil
The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba
Utricularia gibba is an aquatic carnivorous plant with highly specialized morphology, featuring fibrous floating networks of branches and leaf-like organs, no recognizable roots, and bladder traps that capture and digest prey. We recently described the compressed genome of U. gibba as sufficient to control the development and reproduction of a complex organism. We hypothesized intense deletion pressure as a mechanism whereby most noncoding DNA was deleted, despite evidence for three independent whole-genome duplications (WGDs). Here, we explore the impact of intense genome fractionation in the evolutionary dynamics of U. gibba’s functional gene space. We analyze U. gibba gene family turnover by modeling gene gain/death rates under a maximum-likelihood statistical framework. In accord with our deletion pressure hypothesis, we show that the U. gibba gene death rate is significantly higher than those of four other eudicot species. Interestingly, the gene gain rate is also significantly higher, likely reflecting the occurrence of multiple WGDs and possibly also small-scale genome duplications. Gene ontology enrichment analyses of U. gibba-specific two-gene orthogroups, multigene orthogroups, and singletons highlight functions that may represent adaptations in an aquatic carnivorous plant. We further discuss two homeodomain transcription factor gene families (WOX and HDG/HDZIP-IV) showing conspicuous differential expansions and contractions in U. gibba. Our results 1) reconcile the compactness of the U. gibba genome with its accommodation of a typical number of genes for a plant genome, and 2) highlight the role of high gene family turnover in the evolutionary diversification of U. gibba’s functional gene space and adaptations to its unique lifestyle and highly specialized body plan.
Restriction Site-Associated DNA Sequencing (RAD-seq) Reveals an Extraordinary Number of Transitions among Gecko Sex-Determining Systems
Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from 12 gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately one-half to two-thirds of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery.
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages toward the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
Evolution of the Telomere-Associated Protein POT1a in Arabidopsis thaliana Is Characterized by Positive Selection to Reinforce Protein-Protein Interaction
Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana encodes two divergent POT1 paralogs termed AtPOT1a and AtPOT1b. AtPOT1a positively regulates telomerase activity, whereas AtPOT1b is proposed to negatively regulate telomerase and promote chromosome end protection. Phylogenetic analysis uncovered two independent POT1 duplication events in the plant kingdom, including one at the base of Brassicaceae. Tests for positive selection implemented in PAML revealed that the Brassicaceae POT1a lineage experienced positive selection postduplication and identified three amino acid residues with signatures of positive selection. A sensitive and quantitative genetic complementation assay was developed to assess POT1a function in A. thaliana. The assay showed that AtPOT1a is functionally distinct from single-copy POT1 genes in other plants. Moreover, for two of the sites with a strong signature of positive selection, substitutions that swap the amino acids in AtPOT1a for residues found in AtPOT1b dramatically compromised AtPOT1a function in vivo. In vitro-binding studies demonstrated that all three sites under positive selection specifically enhance the AtPOT1a interaction with CTC1, a core component of the highly conserved CST (CTC1/STN1/TEN1) telomere protein complex. Our results reveal a molecular mechanism for the role of these positively selected sites in AtPOT1a. The data also provide an important empirical example to refine theories of duplicate gene retention, as the outcome of positive selection here appears to be reinforcement of an ancestral function, rather than neofunctionalization. We propose that this outcome may not be unusual when the duplicated protein is a component of a multisubunit complex whose function is in part specified by other members.
Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection
Over the past two decades, comparative sequence analysis using codon-substitution models has been honed into a powerful and popular approach for detecting signatures of natural selection from molecular data. A substantial body of work has focused on developing a class of "branch-site" models which permit selective pressures on sequences, quantified by the ratio, to vary among both codon sites and individual branches in the phylogeny. We develop and present a method in this class, adaptive branch-site random effects likelihood (aBSREL), whose key innovation is variable parametric complexity chosen with an information theoretic criterion. By applying models of different complexity to different branches in the phylogeny, aBSREL delivers statistical performance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster. Based on simulated data analysis, we offer guidelines for what extent and strength of diversifying positive selection can be detected reliably and suggest that there is a natural limit on the optimal parametric complexity for "branch-site" models. An aBSREL analysis of 8,893 Euteleostomes gene alignments demonstrates that over 80% of branches in typical gene phylogenies can be adequately modeled with a single ratio model, that is, current models are unnecessarily complicated. However, there are a relatively small number of key branches, whose identities are derived from the data using a model selection procedure, for which it is essential to accurately model evolutionary complexity.
A New Method for Estimating Species Age Supports the Coexistence of Malaria Parasites and Their Mammalian Hosts
Species in the genus Plasmodium cause malaria in humans and infect a variety of mammals and other vertebrates. Currently, estimated ages for several mammalian Plasmodium parasites differ by as much as one order of magnitude, an inaccuracy that frustrates reliable estimation of evolutionary rates of disease-related traits. We developed a novel statistical approach to dating the relative age of evolutionary lineages, based on Total Least Squares regression. We validated this lineage dating approach by applying it to the genus Drosophila. Using data from the Drosophila 12 Genomes project, our approach accurately reconstructs the age of well-established Drosophila clades, including the speciation event that led to the subgenera Drosophila and Sophophora, and age of the melanogaster species subgroup. We applied this approach to hundreds of loci from seven mammalian Plasmodium species. We demonstrate the existence of a molecular clock specific to individual Plasmodium proteins, and estimate the relative age of mammalian-infecting Plasmodium. These analyses indicate that: 1) the split between the human parasite Plasmodium vivax and P. knowlesi, from Old World monkeys, occurred 6.1 times earlier than that between P. falciparum and P. reichenowi, parasites of humans and chimpanzees, respectively; and 2) mammalian Plasmodium parasites originated 22 times earlier than the split between P. falciparum and P. reichenowi. Calibrating the absolute divergence times for Plasmodium with eukaryotic substitution rates, we show that the split between P. falciparum and P. reichenowi occurred 3.0–5.5 Ma, and that mammalian Plasmodium parasites originated over 64 Ma. Our results indicate that mammalian-infecting Plasmodium evolved contemporaneously with their hosts, with little evidence for parasite host-switching on an evolutionary scale, and provide a solid timeframe within which to place the evolution of new Plasmodium species.
We present BUSTED, a new approach to identifying gene-wide evidence of episodic positive selection, where the non-synonymous substitution rate is transiently greater than the synonymous rate. BUSTED can be used either on an entire phylogeny (without requiring an a priori hypothesis regarding which branches are under positive selection) or on a pre-specified subset of foreground lineages (if a suitable a priori hypothesis is available). Selection is modeled as varying stochastically over branches and sites, and we propose a computationally inexpensive evidence metric for identifying sites subject to episodic positive selection on any foreground branches. We compare BUSTED with existing models on simulated and empirical data. An implementation is available on www.datamonkey.org/busted, with a widget allowing the interactive specification of foreground branches.
April 23, 2015
The identification and explanation of long-term evolutionary trends in higher taxa and biological communities is an important goal of biological research. Body size is the single most important ecological characteristic of metazoa and the variable most easily applied to analysis of evolutionary trends across distantly related taxa. The proposed working group will bring together paleobiologists studying body size evolution in deep time and across higher taxa with biologists studying the distribution of body sizes in living organisms from the community to global scale. The working group will initiate a community-wide database of body sizes through the Phanerozoic, an effort that requires standardized data on body size across higher taxa. The working group will also catalyze collaborations between paleobiologists and biologists to develop the theory necessary to investigate long-term dynamics in body-size evolution across diverse living and extinct metazoan lineages. The workshop will provide a venue for members to address the relationships between the pattern of body size evolution and the distribution of body sizes in extant organisms. How well can macroevolutionary patterns be inferred from macroecological ones? How well do those patterns reflect evolutionary mechanisms, whether driven or passive? Ultimately, the resulting database will become a broadly applicable and dynamic resource for macroevolutionary research, with real potential to help future workers shed light on the forces that have shaped the evolutionary trajectory of animal life on Earth.
Background: Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a third distinct group of previously unclassified perennial ryegrass-associated endophytes was identified as belonging to a putative novel taxon (or taxa) (PNT) in a previous analysis based on simple sequence repeat (SSR) marker diversity. As well as genotypic differences, distinctive alkaloid production profiles were observed for members of the PNT group. Results: A detailed phylogenetic analysis of perennial ryegrass-associated endophytes using components of whole genome sequence data was performed using complete sequences of 7 nuclear protein-encoding genes. Three independently selected genes (encoding a DEAD/DEAH box helicase [Sbp4], a glycosyl hydrolase [family 92 protein] and a MEAB protein), none of which have been previously used for taxonomic studies of endophytes, were selected together with the frequently used ‘house-keeping’ genes tefA and tubB (encoding translation elongation factor 1-α and β-tubulin, respectively). In addition, an endophyte-specific gene (perA for peramine biosynthesis) and the fungal-specific MT genes for mating-type control were included. The results supported previous phylogenomic inferences for the known species, but revealed distinctive patterns of diversity for the previously unclassified endophyte strains, which were further proposed to belong not one but two distinct novel taxa. Potential progenitor genomes for the asexual endophytes among contemporary teleomorphic (sexual Epichloë) species were also identified from the phylogenetic analysis. Conclusions: Unique taxonomic status for the PNT was confirmed through comparison of multiple nuclear gene sequences, and also supported by evidence from chemotypic diversity. Analysis of MT gene idiomorphs further supported a predicted independent origin of two distinct perennial ryegrass-associated novel taxa, designated LpTG-3 and LpTG-4, from different members of a similar founder population related to contemporary E. festucae. The analysis also provided higher resolution to the known progenitor contributions of previously characterised perennial ryegrass-associated endophyte taxa.
Source: BMC Evolutionary Biology
Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa
Background: This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. Results: The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. Crocidura somalica is part of the complex. Conclusions: Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex.
Source: BMC Evolutionary Biology
reminder: upcoming deadline PhD positions in Population Genetics Over the past years, Vienna has developed into one of the leading centres of population genetics. The Vienna Graduate School of Population Genetics has been founded to provide a training opportunity for PhD students to build on this excellent on site expertise. We invite applications from highly motivated and outstanding students with a background in one of the following disciplines: bioinformatics, statistics, evolutionary genetics, functional genetics, theoretical and experimental population genetics. Students from related disciplines, such as physics or mathematics are also welcome to apply. Topics include: via Gmail
–_004_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: multipart/alternative; boundary=“_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_” –_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable Dear Brian, Would you please post the attached Graduate position ad on EvolDir? Sincerely, Kristina Sefc –_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: text/html; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable
–_000_D15DD1EC43A49lg8beservicesvirginiaedu_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable The Department of Biology at the University of Virginia invites applications for a postdoctoral Research Associate position in the lab of Dr. Laura Galloway. The position is supported by an NSF-funded project to explore the relationship between biogeography and mating system evolution in American bellflower (Campanulastrum americanum). Mating systems are evolutionarily labile and variation is often explained by hypotheses focusing on the context-dependent benefits of selfing (e.g. reproductive assurance). However, mating system evolution may be driven by historical changes in genetic load. In particular, colonization from glacial refugia to current distributions often entailed bottlenecks and small population sizes that shape population genetic structure and hence potential for mating system evolution. Our goal is to integrate studies of biogeography and mating system using Campanulastrum americanum, a North American herb in which preliminary data indicate reduced inbreeding depression and greater autogamy in sites where phylogeographic data suggest recent colonization. The Research Associate will work with the PI, our collaborator Jeremiah Busch (Washington State Univ), and lab personnel to design and lead research in the lab and field. The Research Associate will conduct greenhouse studies of genetic load and mechanisms of autogamy, field studies of factors that underlie pollen limitation, estimate population selfing rate and interact with collaborators determining population genetic structure. The position also involves data management and dissemination, preparing manuscripts, and mentoring graduate and undergraduate students. The ideal candidate will enjoy working both in a team and independently, and may use the appointment to develop and pursue additional related studies. Finally, this position will coordinate outreach activities at Mountain Lake Biological Station and an Environmental Studies Academy at a local high school. Demonstrated expertise in ecological genetics including field and greenhouse work and strong written and oral communication skills are required. Experience in evolutionary genetics is desirable. The completion of a PhD degree in Biology or related field by the appointment start date is required. Preferred appointment start date is Summer 2015. This is a two-year appointment; the appointment may be renewed for an additional year, contingent upon availability of funds and satisfactory performance. To apply, please submit a candidate profile through Jobs@UVA (http://bit.ly/1ccxWRu) and electronically attach: curriculum vitae with list of publications, a cover letter that summarizes research interests and professional goals, and contact information for three (3) references; search on posting number 0616239. Review of applications will begin May 9, 2015; however, the position will remain open until filled. Questions regarding this position should be directed to: Dr. Laura Galloway (firstname.lastname@example.org) Questions regarding the Candidate Profile process or Jobs@UVA should be directed to: Rich Haverstrom (email@example.com) The University will perform background checks on all new hires prior to making a final offer of employment. The University of Virginia is an Equal Opportunity/Affirmative Action Employer. Women, minorities, veterans and persons with disabilities are encouraged to apply. –_000_D15DD1EC43A49lg8beservicesvirginiaedu_ Content-Type: text/html; charset=“us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable The Department of Biology at the University of Virginia invites applications for a postdoctoral Research Associate position in the lab of Dr. Laura Galloway. The position is supported by an NSF-funded project to explore the relationship between biogeography and mating system evolution in American bellflower (Campanulastrum americanum). Mating systems are evolutionarily labile and variation is often explained by hypotheses focusing on the context-dependent benefits of selfing (e.g. reproductive assurance). However, mating system evolution may be driven by historical changes in genetic load. In particular, colonization from glacial refugia to current distributions often entailed bottlenecks and small population sizes that shape population genetic structure and hence potential for mating system evolution. Our goal is to integrate studies of biogeography and mating system using Campanulastrum americanum, a North American herb in which preliminary data indicate reduced inbreeding depression and greater autogamy in sites where phylogeographic data suggest recent colonization. The Research Associate will work with the PI, our collaborator Jeremiah Busch (Washington State Univ), and lab personnel to design and lead research in the lab and field. The Research Associate will conduct greenhouse studies of genetic load and mechanisms of autogamy, field studies of factors that underlie pollen limitation, estimate population selfing rate and interact with collaborators determining population genetic structure. The position also involves data management and dissemination, preparing manuscripts, and mentoring graduate and undergraduate students. The ideal candidate will enjoy working both in a team and independently, and may use the appointment to develop and pursue additional related studies. Finally, this position will coordinate outreach activities at Mountain Lake Biological Station and an Environmental Studies Academy at a local high school. Demonstrated expertise in ecological genetics including field and greenhouse work and strong written and oral communication skills are required. Experience in evolutionary genetics is desirable. The completion of a PhD degree in Biology or related field by the appointment start date is required. Preferred appointment start date is Summer 2015. This is a two-year appointment; the appointment may be renewed for an additional year, contingent upon availability of funds and satisfactory performance. To apply, please submit a candidate profile through Jobs@UVA (http://bit.ly/1ccxWRu) and electronically attach: curriculum vitae with list of publications, a cover letter that summarizes research interests and professional goals, and contact information for three (3) references; search on posting number 0616239. Review of applications will begin May 9, 2015; however, the position will remain open until filled. Questions regarding this position should be directed to: Dr. Laura Galloway (firstname.lastname@example.org) Questions regarding the Candidate Profile process or Jobs@UVA should be directed to: Rich Haverstrom (email@example.com) The University will perform background checks on all new hires prior to making a final offer of employment. The University of Virginia is an Equal Opportunity/Affirmative Action Employer. Women, minorities, veterans and persons with disabilities are encouraged to apply. –_000_D15DD1EC43A49lg8beservicesvirginiaedu via Gmail
Category: Course Topic: AMUPoznan.Poland.Bioinformatics.RNA.July6-10 Dear colleagues, We are extremely happy to announce 11th edition of Poznan Summer School of Bioinformatics. This meeting takes place at Adam Mickiewicz University in Poznan (Poland) from 6th to 10th July 2015. This year’s course will cover modern approaches to RNA analyses, including subjects like: 1. Introduction to RNA biology 2. Applications of next-generation sequencing in RNA studies 3. Transcriptome sequencing, assembly and gene expression estimation 4. Identification and analysis of microRNAs and other small RNAs 5. long non-coding RNAs 6. Secondary and tertiary structures of RNAs The course is suitable both for beginners and for those who already have some basic knowledge in computational biology and find it necessary and interesting to learn more about bioinformatic applications in RNA studies. Our school consists of lectures and hands-on - this combination should fit best your needs as you have a chance to try out the discussed methods yourself. For further information please visit our website: http://bit.ly/1DDxbdc Please forward this announcement to anyone who might be interested. Best regards, PSSB Organizing Committee Contact: firstname.lastname@example.org Bioinfo School via Gmail
PhD scholarship opportunity Subject title: “Epigenetic inheritance of physiological flexibility in a primate species, the grey mouse lemur” Location: UMR CNRS/MNHN 7179 (MECADEV) 1 avenue du petit château, 91800 Brunoy (France) Main PhD supervisor: Dr Fabienne Aujard Secondary PhD supervisors: Drs Pierre-Yves Henry and Jérémy Terrien The French research unit UMR 7179 is offering an opportunity to defend a PhD scholarship to be attributed by the Museum National d'Histoire Naturelle. The applicant will defend a subject treating on the “Epigenetic inheritance of physiological flexibility in a primate species, the grey mouse lemur”. Briefly, exhibiting high phenotypic flexibility requires fine tuning of all mechanisms involved in the control of metabolism, including regulation of gene expression through epigenetic changes. Epigenetic modifications are a mechanism of regulating gene expression that is reversible, heritable and particularly sensitive to environmental conditions. The role of epigenetic modifications as a way of adjusting phenotypic flexibility in response to environmental change has gained much interest since epigenetic inheritance has been described as a potential mechanism for a specimen to benefit from its parents history. In this project, we propose to evaluate the potential of epigenetic inheritance in a primate species, the grey mouse lemur (Microcebus murinus), characterized by its great phenotypic flexibility adapted to the unpredictability of Madagascar climate. Using the in-house breeding colony resource (~400 individuals), we will mimic periods of food scarcity during key periods of reproduction (spermatogenesis for males and gestation, lactation for females) and evaluate the impacts of such treatment in juveniles and their ability to respond to the same energetic challenge. The student will have to conduct experiments to answer 2 main questions: 1) Which are the epigenetic modifications induced by an energetic challenge in the adult grey mouse lemur, and can we link these changes to metabolic phenotyping characteristics? 2) Can we estimate the epigenetic inheritance in such context, and evaluate the potential of parental history on juvenile physiological capacities? Applicants must be highly motivated and have a strong interest in our scientific area (for more information, please visit our website at http://bit.ly/1yVcfmq). A strong background of basic molecular research methodology (knowledge of epigenetic mechanisms would be highly appreciated) is highly recommended. Given the scope of this subject, a good background in physiology and biology of adaptation would be appreciated. Applications should contain a CV, a short statement of your research interests as well as a recommendation letter. Please send your application to email@example.com before May 20, 2015. Jrmy TERRIEN via Gmail
*Call for candidates to apply for an FCT * *We are looking for* candidates to apply for an FCT (Portuguese Foundation for Science and Technology) doctoral fellowship for a mixed Ph.D at the Centre for Functional Ecology of the University of Coimbra (cfe.uc.pt), and Durham University (http://bit.ly/1DDnOu0). *The successful candidate* will be expected to develop a research project to investigate evolution and adaptation of the invasive weed *Centaurea solstitialis* across broad biogeographical ranges. The research involves laboratory and field-based work and involves the interaction with an international network of collaborators from the USA, Chile, Argentina, Australia, Turkey, Spain, and the UK. The candidate is expected to spend half of the time in Portugal and half in the UK. *The candidate* should have a good scientific background, with an interest into reproductive and evolutionary ecology, and genetics of invasive weeds. A good knowledge of the English language, of ecological statistics, or molecular biology is highly desirable. Candidates should be European or permanent residents, and comply with the conditions to be a candidate for the FCT Doctoral Grants ( http://bit.ly/1EfKF3q). *The doctoral fellowship includes* a monthly payment of 980 euros (tax-free), plus an accident insurance and a monthly contribution to the Portuguese Social Security system (full healthcare and retirement, but no unemployment benefits). During stages in the UK, the scholarship will be topped up to 1710 euros monthly to compensate for differences in the cost of living. The scholarship is renewable for up to four years, at the end of which the candidate is expected to defend his or her PhD. dissertation thesis. *A call for fellowship applications* will open during July and be open until May 11, 2015 (http://bit.ly/VgqPC8), but contacts should be made before *May 1*, at 6pm Greenwich time. Interested candidates should send a one page cover letter describing their research interests and experience, a CV (explicitly including average scores for B.Sc. and/or M.Sc.), and the contact information for up to two referees to Daniel Montesinos (firstname.lastname@example.org) and Adrian Brennan (email@example.com). Informal inquiries are welcome. More information about the groups can be found here: http://bit.ly/1EfKF3u http://bit.ly/1DDnRpD http://bit.ly/VgqMWI Daniel Montesinos Researcher (IF) Centre for Functional Ecology DCV - FCTUC - Universidade de Coimbra Calada Martim de Freitas 3000-456 Coimbra, Portugal T: (+351) 239 855 223 (ext. 156) http://bit.ly/1EfKF3u Editor-in-Chief Web Ecology www.web-ecology.net Daniel Montesinos via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology