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April 19, 2014

02:43

—_000_E4951CD6BF594C45AA32F057668E3ABE27391F31UFEXCHMBXN02adu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Postdoctoral Researcher position in butterfly evolutionary ecology at University of Florida A Postdoctoral Researcher position is available at the Florida Museum of Natural History’s McGuire Center for Lepidoptera and Biodiversity, University of Florida. The postdoc will form an integral part of the multi-institution team working on the NSF-funded project “Dimensions: Collaborative Research: Connecting the proximate mechanisms responsible for organismal diversity to the ultimate causes of latitudinal gradients in species richness”. In particular, the postdoc will be responsible for conducting and coordinating ecological studies of Adelpha butterfly communities in several Neotropical field sites. The deadline for applications is May 16th, 2014, with the position available from January 2015 (or earlier) for three years. Information on the position and application instructions are available here: http://bit.ly/1jhpnnl Please contact me (kwillmott@flmnh.ufl.edu) with any questions. Keith Willmott Associate Curator for Lepidoptera McGuire Center for Lepidoptera and Biodiversity Florida Museum of Natural History 3215 Hull Road, Powell Hall PO Box 112710 Gainesville, FL 32611 (USA) Tel: ( 1 352) 273 2012 Fax: (1 352) 392 0479 —_000_E4951CD6BF594C45AA32F057668E3ABE27391F31UFEXCHMBXN02adu_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable

Source: EVOLDIR
02:28
Graduate research opportunity to study ectoparasite population genetics and metapopulation dynamics. Department of Biological Sciences - University of Tulsa A graduate student at the M.S. or Ph.D level is sought to work with Drs. Charles Brown and Warren Booth in the Department of Biological Sciences at The University of Tulsa, Oklahoma. The successful applicant will develop a thesis research project focused on the metapopulation dynamics and population structure of swallow bugs (Oeciacus vicarius: Cimicidae), a disease vectoring ectoparasite of cliff swallows (Petrochelidon pyrrhonota). The PIs have amassed a large collection of swallow bugs from cliff swallow colonies varying in size, geographic location, and patterns of occupation, and have recently identified hundreds of microsatellite markers specifically for swallow bugs using next-generation sequencing. The work will draw on a long-term (32-year) study on social behavior and reproductive ecology of cliff swallows in western Nebraska. The study aims to examine the following objectives: nest fidelity and dispersal patterns, inbreeding dynamics, metapopulation structure and population differentiation; relationships between host and parasite genetic structure and diversity; and the potential of blood-fed bugs as indirect indicators of cliff swallow demography and social structure. Additionally, the student may explore the evolution of extreme phenotypes exhibited by the study species through comparative transcriptomic methods. Applicants for this position should have a strong background in population genetics, molecular ecology, evolutionary biology, or ecology, be willing to undertake seasonal field research at the study site in western Nebraska, and meet the admission requirements for the Department of Biological Sciences graduate program. (http://bit.ly/1aOtTdZ) Applications should include the following: 1) A letter of interest (not exceeding two pages). 2) A curriculum vitae. 3) Names and email addresses for at least three academics/researchers willing to provide a letter of recommendation 4) Copies of undergraduate/post-graduate transcripts 5) Electronic copies of published manuscripts, if any. For more information about this opportunity, contact Drs. Brown (charles-brown@utulsa.edu) or Booth (warren-booth@utulsa.edu). Anticipated start date is mid-August 2014. Additional information regarding our research can be found at our current departmental webpages: Brown - http://bit.ly/1jhmPWr Booth - www.booth-lab.org Dr. Warren Booth Assistant Professor of Molecular Ecology Department of Biological Sciences University of Tulsa 315 Oliphant Hall Tulsa, OK 74104 Tel. (918) 631-3421 - Office (918) 631-3136 - Lab Web site - TU academic Lab website “Booth, Warren” via Gmail
Source: EVOLDIR
02:14
*Postdoctoral Research Associate Position: Examining Microbial Interactions in Marine Plankton* The Rynearson lab at the University of Rhode Island, Graduate School of Oceanography invites applications for a Postdoctoral Research Associate. The research project, funded by the Gordon and Betty Moore Foundation, will examine microscale interactions between marine diatoms and bacteria and is a collaboration with Professor D. Hunt, Duke University. *Responsibilities and Duties*: The postdoctoral associate will be primarily responsible for analysis of the gene expression component of the project and will be working with high-throughput transcriptomic data and physiological data to tease apart diatom-bacteria interactions. Responsibilities include dissemination of results in publications and presentations, contributions to the functioning of the lab, and assistance with graduate and undergraduate student mentoring. The successful applicant will have the opportunity to design follow-on controlled laboratory experiments and with future proposal preparation. *Qualifications*: Candidates are required to have a Ph.D. degree by August 2014 in Computer Sciences, Oceanography, Biology or a related field. Excellent command of the English language (written and verbal) and quantitative analytical skills are essential. Candidates should possess demonstrable experience with either the analysis of high throughput sequencing data including programming knowledge or with experimental marine microbiology. *Appointment*: The position is for 12 months initially, commencing July or August 2014 and renewable for an additional 12 months depending on performance. The successful candidate will receive training in research collaboration, presentation and publication of results, and outreach and mentoring. There will be opportunities for development of additional research projects and proposals. *To Apply*: Applications must include (1) a statement of experience,**career goals, research vision and interests; (2) curriculum vitae, (3) reprints of relevant publications and (4) names and addresses of three referees willing to write confidential letters of recommendation. All materials should be emailed as a single pdf document to: rynearson@mail.uri.edu with ‘PostDoc Application’ in the subject line. Candidates will be selected based on overall excellence, including academic qualifications, letters of recommendation, and prior skills, experience, and research goals that are compatible with the goals of the funded research. The position is compensated through a competitive salary and excellent benefits package. *Closing date*: For full consideration, applications should be received by May 5, 2014.Further information: Rynearson lab: http://bit.ly/1liWo9T URI Graduate School of Oceanography: http://bit.ly/1f6QRec Hunt Lab: http://bit.ly/1f6QRed Tatiana Rynearson via Gmail
Source: EVOLDIR
01:36

A postdoctoral position is available in Artyom Kopps lab starting in the summer of 2014. Our work focuses on the evolution of developmental pathways, especially with regard to evolutionary innovations and convergent evolution. By focusing on closely related species of Drosophila, we integrate molecular-genetic approaches with phylogenetic, quantitative-genetic, and population-genetic analyses. The main postdoctoral project would involve the identification of genes responsible for convergent evolution of sex-specific color patterns in different (non-model) Drosophila species. Additional projects may focus on the evolution of sex- and tissue-specific transcriptomes. Postdocs will be encouraged to develop independent research reflecting their own interests, within the broad field of developmental evolution and evolutionary genomics. Initial appointment is for one year, extendable by mutual agreement. Candidates should have demonstrated expertise in genomics and bioinformatics/computational biology. Experience in eukaryotic genome assembly, resequencing, GWAS, RNA-seq, and ChIP-seq is highly desirable. Our lab provides a relaxed and supportive atmosphere. The broader research environment at UC - Davis offers postdoctoral fellows an excellent chance to interact and collaborate with many other people working in the fields of evolutionary genetics and comparative genomics. Northern California, where Davis is located, provides outstanding recreational opportunities. Interested applicants should contact Artyom Kopp (akopp@ucdavis.edu) with a CV, a brief statement of research interests, and the names of three references. via Gmail

Source: EVOLDIR
01:20

Dear all I propose a post-doctoralfelllowship (6 - 24 months) Marine comparative population genetics and community ecology. We obtained funds for 24 months of fellowships. The fellowship is financed by a FP7 European program (DEVOTES: Development of innovative tools for monitoring and assessing the good environmental status of the marine environment). *We seek candidates who proved their autonomy in data analyses and in writing international scientific papers.* A solid experience in population genetics is also required. Expertise in community ecology, benthic coastal marine biodiversity, marine currentology, modelisation, as well as scuba-diving is not compulsory but considered as a “plus”. Our goal (IMBE) is to evaluate the interest and the limits of intra-specific genetic diversity (of a set of species) as an indicator of the good environment status of a locality. For this, we compare local diversity among species, with species diversity (Shannon or other indices) when possible, and we aim at correcting for (or taking into account) genetic connectivity and physical connectivity. The post-doc will at first benefit from an already available data set (partly published) of population genetic data from 6-10 invertebrate species (eventually a red alga may also be available) with contrasted dispersal abilities in a common set of localities along the French Mediterranean coast. His first goal will be to combine those data in a global comparative analysis, integrating physical data and models (by collaborations with physical oceanographers), biological data on life history traits(duration and season of dispersal stage), and disentangle factors linked to physics, life history traits. The post-doc is expected to write and submit one scientific article (at least) within the 6 months period with the data that were already available. A fellowship of 18 months will then be proposed for a combined study comparing community composition and intra-species genetic diversity, focusing on coralligenous habitats. Coralligenous habitats are typically Mediterranean; they are highly complex habitats, based on a biogenic substratum composed of a variety of red algae. Community composition will be obtained from metabarcoding (with controls by classical taxonomy and photo-quadrats). Population genetics will be studied for a few species of the coralligenous habitat: at least one red alga (or a full species complex, providing natural replicates), a bryozoan, etc. (NGS genotyping will be obtained for some species). Samplings are finely contextualized by contrasted ecological parameters (orientation, depths, slope, rugosity, temperature…) within each locality (islets), allowing estimating the relative parts of adaptation and neutrality at both the intra-specific and the community levels (local adaptation, neutral theory of biodiversity). This sampling and ecological study is a strong part of the European ANR “CIGESMED” (an ERANET project of the Seas-ERA call). Do not hesitate to contact us for more details on the scientific project and the contract. Contact: anne.chenuil@imbe.fr *www.imbe.fr* *http://bit.ly/1qXWsei *http://bit.ly/1mhqIRD via Gmail

Source: EVOLDIR
01:05

The lab of Dr. Scott Pitnick at Syracuse University in central New York is looking for a mature, motivated undergraduate for NSF REU (Research Experience for Undergraduates) research in sexual selection and speciation biology. The successful candidate will work with the PI, a technician, postdoctoral fellows and PhD students to conduct experiments on three different model dipteran study systems: (1) the fruit fly Drosophila melanogaster and related species, (2) the yellow dung fly Scathophaga stercoraria and (3) the dung fly Sepsis punctum. Investigations will be conducted in the laboratory, with artificial pastures in a greenhouse and at local cattle and sheep pastures. The successful candidate will potentially participate in projects conceptually related to postcopulatory sexual selection, rapid evolutionary diversification, mechanisms of reproductive isolation between sibling species, mechanisms of ejaculate-female interaction, and alternative male reproductive tactics. She/he will receive training and experience in many to all of the following skills: rearing, maintaining and handling fly cultures; collecting virgins and setting up mating crosses; dissecting male and female reproductive tissues; preparing and staining sperm slides; microscopy and use of camera software to quantify sperm quantity, quality, performance and fate within the female reproductive tract. The student will be on campus from May 26-Aug. 15 (some flexibility allowed) and will receive a summer stipend of $4950. Only US citizens or permanent residents who are fully enrolled in undergraduate institutions are eligible. Please send an official transcript, a brief essay (no longer than one page) on your research interests, career goals and what you seek to gain from an REU experience, and provide contact information for two references to Dr. Pitnick at sspitnic@syr.edu. Deadline for application is April 30. Dr. Scott Pitnick Professor of Biology Syracuse University Syracuse, NY 13244 USA (315) 443-5128 sspitnic@syr.edu http://bit.ly/1gSUloG via Gmail

Source: EVOLDIR
00:50

Bastien Boussau Universit de Lyon Gene tree-species tree methods for comparative genomics Tuesday, April 22, 2014 9:00 AM PDT In this second talk of our series on genome-scale phylogeny, I build upon Gergely’s introduction and present the modelling assumptions and algorithmic details behind some of the methods we and others have developed. There will be two parts to this talk. I start with the model of gene duplications and losses implemented in PHYLDOG. I present the assumptions we make and the shortcuts we take to improve the program’s efficiency, and show some results on real and simulated sequence data. I notably show problems that arise when the program is confronted with data generated with a model of incomplete lineage sorting (Rasmussen and Kellis, 2012), and present avenues of research to find solutions to these problems. In the second part, I present our current efforts to use our model of gene duplication, loss, and transfer (Szllosi et al, 2013) to infer a species tree in which speciation nodes are ordered in time. I briefly remind the forgetful viewer of what this model does and how it works, and I then explain how we devise a new MCMC algorithm to use it on data sets containing dozens of species and thousands of gene families. I finish with some perspectives of our plans uniting gene tree-species tree models and databases of gene families and phylogenetic trees. For more details, see http://bit.ly/16UKCta. Frederick “Erick” Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://bit.ly/18kRSvK ematsen@gmail.com via Gmail

Source: EVOLDIR
00:34

A 3-year PhD position for the mathematical modelling of the evolutionary ecology of host-parasite interactions is available immediately in the group of Jacob Koella at the University of Neuchatel, Switzerland. The general research of the group is to integrate evolutionary and ecological thinking into the epidemiology and control of infectious diseases. We develop the theoretical basis of this integration and test empirically assumptions and predictions of the theory, using malaria, microsporidians and their mosquito hosts as experimental systems. The PhD-project will develop mathematical models to integrate resource ecology with the within-host dynamics of parasite to obtain a better picture of the evolution of the host-parasite interaction. This approach explicitly takes into account a fundamental, yet largely neglected, aspect of parasites: that they steal resources from their host to support their own development. Resource ecology thus gives a mechanistic basis of the host’s and the parasite’s development. The project will be done in close contact with an experimental project on the same topic, which uses the microsporidian Vavraia culicis and its host, the mosquito Aedes aegypti as an experimental system The position requires an independent, enthusiastic, and scientifically curious person with a strong background (at the level of an MSc) in theoretical evolutionary biology or applied mathematics and an interest in parasitology. The position requires some teaching of undergraduate and graduate biology labs. The generous salary is in accordance with the standards of the Swiss National Science Foundation. Neuchatel is located in the French part of Switzerland and is an attractive city with a high quality of life. The city is situated on the shore of Lake Neuchtel with the Jura Mountains to the North and a view of the Bernese Alps to the South. For outdoors enthusiasts, this is an excellent area for outdoor activities such as hiking, climbing or skiing. To apply, send a 1-2 page cover letter (in English) indicating research interests, your CV, and the names and email addresses of two referees by email to: jkoella@gmail.com Applications will be considered until the position is filled. Jacob Koella Institut de Biologie Universit de Neuchtel rue Emile-Argand 11 2000 Neuchtel Switzerland jkoella@gmail.com via Gmail

Source: EVOLDIR
00:20

Graduate position in mathematical and population genetics Graduate student positions in mathematical and population genetics are available in Simon Gravel’s group at McGill University in Montreal, Canada. The group focuses on creating mathematical and statistical methods to understand human history and evolution through the analysis of high-throughput genomic data. Students will be involved in conceptual methods development, implementation, and applications to exciting datasets. This is unique opportunity to be involved in work that is relevant and interesting from a mathematical, biological, and historical perspectives. We welcome applications from qualified candidates from diverse backgrounds, including biology, anthropology, mathematics, physics, computer science, and related fields. The position offers an exceptional opportunity for collaborative research in a quantitative and theoretical lab with access to cutting-edge data. McGills Department of Human Genetics, the Genome Quebec Innovation Center, and the numerous nearby institutes in downtown Montreal provide a thriving research environment. Applications and queries should be sent to gravellab@gmail.com. Please include a statement of interest (1 page), a CV with a list of publications, contact information for three references, and a low-resolution scan of official transcripts. simon.gravel@gmail.com via Gmail

Source: EVOLDIR
00:03

4-year PhD studentship, Microbial Evolution and Ecology Institute of Biology, University of Leiden, The Netherlands A 4-year PhD position in microbial evolution and ecology is available at the University of Leiden in The Netherlands. This NWO funded project, run jointly by Daniel Rozen and Gilles van Wezel, will study the evolution and ecology of antibiotic production and resistance in the soil, with the broad aim of understanding the role of antibiotics in nature. Focusing on the prolific antibiotic producing genus, Streptomyces, the student will test the idea that the control of antibiotic production and resistance is tied to competitive and social interactions between coexisting bacteria. The project will integrate methods from microbial and chemical ecology and use high-end mass spectrometry to identify compounds that modify antibiotic production or resistance. Interested applicants should ideally have experience in microbial ecology and a strong background in evolutionary biology. Experience with molecular genetics and an interest in chemical ecology is also desirable. Applications will reviewed until the position is filled. Informal enquiries can be addressed to: Daniel Rozen, Tel: +31 (0)71 527 7990, Email: d.e.rozen@biology.leidenuniv.nl d.e.rozen@biology.leidenuniv.nl via Gmail

Source: EVOLDIR

April 18, 2014

01:57

—Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429B Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Call for Symposia for 2015 Annual Meeting The 2015 annual meeting of the Society for the Study of Evolution is planned for June 26-30, 2015 in Guaruja, Brazil. The SSE Council invites proposals for the two Society-sponsored symposia to be held in conjunction with the meeting. Symposium proposals should include: (1) a synopsis of the symposium theme (about one page); (2) a tentative list of speakers, including institutional affiliations, and topics; (3) a rationale for the symposium explaining why this topic and this group of speakers are particularly appropriate for a Society-sponsored symposium; and (4) a statement that all potential speakers have been contacted and agree to participate in the symposium. In evaluating proposals, SSE Council seriously considers the diversity of participants as a major qualification. Symposium organizers are expected to take into account gender, seniority, nationality, and other aspects traditionally underrepresented in Society symposia when preparing proposals. In addition, Council will favor those proposals whose topics concern newly emerging fields, fields ripe for syntheses, and fields different from those that have been included in recent Society symposia. The Council will select two proposals for half-day symposia at the annual meeting in June 2014. All applicants will be notified of the Council’s decision in August. The Society provides travel support for organizers and participants in sponsored symposia. Details are available on request. To be assured of full consideration, proposals must be received by midnight Eastern Standard Time on June 6, 2014: Proposals should be sent by email (bbrodie@virginia.edu) as a single attachment in PDF format (under subject heading: SSE Symposia Proposal). Please expect and request confirmation of receipt of the proposal. Butch Brodie Executive Vice President, SSE —Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429B Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

Call for Symposia for 2015 Annual Meeting

The 2015 annual meeting of the Society for the Study of Evolution is planned for June 26-30, 2015 in Guaruja, Brazil. The SSE Council invites proposals for the two Society-sponsored symposia to be held in conjunction with the meeting. Symposium proposals should include: (1) a synopsis of the symposium theme (about one page); (2) a tentative list of speakers, including institutional affiliations, and topics; (3) a rationale for the symposium explaining why this topic and this group of speakers are particularly appropriate for a Society-sponsored symposium; and (4) a statement that all potential speakers have been contacted and agree to participate in the symposium.

In evaluating proposals, SSE Council seriously considers the diversity of participants as a major qualification. Symposium organizers are expected to take into account gender, seniority, nationality, and other aspects traditionally underrepresented in Society symposia when preparing proposals. In addition, Council will favor those proposals whose topics concern newly emerging fields, fields ripe for syntheses, and fields different from those that have been included in recent Society symposia.

The Council will select two proposals for half-day symposia at the annual meeting in June 2014. All applicants will be notified of the Council’s decision in August. The Society provides travel support for organizers and participants in sponsored symposia. Details are available on request. To be assured of full consideration, proposals must be received by midnight Eastern Standard Time on June 6, 2014: 

Proposals should be sent by email (bbrodie@virginia.edu) as a single attachment in PDF format (under subject heading: SSE Symposia Proposal). Please expect and request confirmation of receipt of the proposal.

Butch Brodie

Executive Vice President, SSE

—Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429 via Gmail
Source: EVOLDIR
01:24
—_000_ea828d69bb414cd4a4c6c9b66b2038ceBLUPR07MB513namprd07pro_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Hello all, I am working on a study of the evolutionary genetics of house mice (Mus musculus), and I am looking for fresh tissue samples from populations of house mice specifically from the eastern shore of Maryland and anywhere in Delaware. Because the tissue must be relatively fresh, I am specifically looking for anyone who is currently, or will soon be, doing small mammal trapping (whether for research purposes or to remove a nuisance species), and who might be willing to collect some tissue from any house mice collected. I can provide a sampling kit and pay for shipping, so the commitment would mostly be in terms of time (which should be minimal if part of an established trap line or while trying to remove a mouse infestation from a home or farm). If you are interested in helping out with this study, please email me at achunco@gmail.com and I’d be happy to provide more details about this study. Thank you in advance, Amanda Amanda Chunco Environmental Studies Elon University achunco@gmail.com —_000_ea828d69bb414cd4a4c6c9b66b2038ceBLUPR07MB513namprd07pro_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
Source: EVOLDIR
01:08
MULTIPLE POSTDOCTORAL POSITIONS are available in Dr. Adam Siepel’s research group in its new location at the Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory, starting in September, 2014. The Siepel group specializes in the development of probabilistic models, algorithms for inference, prediction methods, and application of these methods in large-scale genomic data analysis. Of particular interest is research relevant to existing, NIH-supported projects in (1) human population genomics, including demography inference using Bayesian coalescent-based methods, inference of natural selection on regulatory and other noncoding sequences, and prediction of fitness consequences for noncoding mutations; and (2) transcriptional regulation in mammals and Drosophila, including the estimation of rates and patterns of transcriptional elongation from the GRO-seq data, prediction of transcription factor binding sites from DNase-seq data, and regulatory network inference based on joint patterns of transcription and binding in inducible systems. The research on transcriptional regulation will continue to be carried out in close collaboration with Dr. John Lis at Cornell University. Relevant recent papers including the following: 1. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. Genome-wide inference of ancestral recombination graphs. PLOS Genet., in press. 2. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, et al. (30 co-authors). Genome sequencing highlights the dynamic early history of dogs. PLOS Genet.10(1):e1004016, 2014. 3. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLOS Genet. 9(8):e1003684, 2013. 4. Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nature Genetics 45(7):723- 729, 2013. 5. Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell50(2):212- 222, 2013. 6. Gronau I, Arbiza L, Mohammed J, Siepel A. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol. Biol. Evol. 30(5):1159-1171, 2013. 7. Guertin MJ, Martins AL, Siepel A, Lis JT. Accurate prediction of inducible transcription factor binding intensities in vivo. PLOS Genetics, 8(3):e1002610, 2012. 8. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43(10):1031-1034, 2011. The ideal candidate will be enthusiastic, highly motivated, and independent, will have a strong background in comparative genomics, population genomics, or transcriptional regulation, a serious interest in molecular biology and genetics combined with good skills in mathematics and computer science, and a strong record of accomplishment in research. Postdoctoral associates in the group are expected to participate in both methods development and data analysis, to be comfortable in a fast-moving, interactive, and collaborative research environment, and to actively publish and present results. Required Qualifications 1. Ph.D. in bioinformatics, computer science, statistics, genetics, molecular biology, applied mathematics, or a related field. 2. Research experience (with first-author publications) in computational genomics or a closely related field. 3. Fluency in probabilistic modeling and computational statistics. 4. Proficiency in programming, ideally in C or C++ as well as in scripting languages such as python, perl, matlab, or R. Should be comfortable in a linux environment, with large data sets, computer clusters, and databases. Term The term for this position is flexible but most likely will be 2-3 years. The proposed start date is September 2014. As many as 4 positions may be filled, depending on the quality of the applicants. To Apply Submit a CV, a short description of research interests and experience, and contact information for three references by e-mail to acs4 at cornell dot edu. Informal inquiries are welcome. Adam Siepel 102E Weill Hall Cornell University Ithaca, NY 14853 Adam Charles Siepel via Gmail
Source: EVOLDIR
01:08
Postdoctoral Position in modeling the genetics of adaptation of invasive populations We seek to hire a post-doctoral research associate for a Grand Federative Project funded by the French Agropolis Fondation1 called BIOFIS “Bioagressors and invasive species: from individual to population to species”. The project is dedicated to develop, coordinate and communicate research actions on bioagressors in Europe (insects, mites, trees, fungi and virus) and on their associated natural enemies. Term and location: The position should start in December 2014 at the latest. Support is for one year. This position is co-supervised by E. Klein (INRA – BIOSP, Avignon France) and V. Ravigné (CIRAD – BGPI, Montpellier, France). We encourage the postdoctoral fellow to be based in Montpellier but being hosted in Avignon is also possible. Eligibility: Agropolis Fondation typically considers applications from candidates that have not resided or carried out their main activity (work, studies, etc) in France for more than 12 months in the 3 years immediately prior to the date of submission of the proposal and that have obtained their PhD degree for no more than 3 years upon the date of application. However, we encourage excellent candidates not entirely fulfilling these conditions to contact us, as these might be funded if no other eligible candidate satisfies scientific requirements for the job. Project: Bioinvasions have long been considered as purely ecological processes until researchers recognize that evolutionary processes such as drift and selection may play a substantial role in their success. Recently particular attention has been paid to evolutionary processes occurring during spatial expansions. Selection for different life-history strategies at the source and front of invasions is expected to affect the speed of spatial spread. The strong effects of genetic drift associated to the specific demography of an expansion (in particular successive funding effects distributed in space) may as well shape the neutral and selected diversity along invasion waves. To better understand the interaction between drift, selection, and dispersal, we wish to design and analyze spatially explicit simulation models allowing studying the spatial spread of beneficial/neutral/deleterious mutations during a colonization process. We are particularly interested in studying the effect of i) environmental heterogeneity and ii) non-standard mating systems (e.g., mixing sexual and asexual reproduction) on the process. In the end, these theoretical results may be confronted to population genetics data in different species. This work is mainly theoretical in its present shape but it is expected to produce useful results for approaches aiming at detecting traces of selection during bioinvasions from the analysis of the spatial genetic structure of populations at a large number of loci (genome scan). We seek a young researcher who combines with a strong conceptual background in evolutionary biology and some modeling skills (mathematics and computer science). Experience with programming, bioinformatics and theoretical population genetics is required. Skills in data analysis are not necessary but will be considered positively. Facility in writing is important. The post-doc will benefit by working as a member of the BIOFIS project team with an extent network of collaborators interested in dispersal, invasion biology, plant pathology, evolutionary biology and population genetics. Contact: Virginie Ravigné. Virginie.ravigne@cirad.fr 1 Agropolis Fondation: http://bit.ly/18BZkTN Virginie Ravigné Chercheuse CIRAD - Département BIOS - UMR BGPI UMR PVBMT Station de Ligne-Paradis Pôle de protection des plantes 7 chemin de l’IRAT 97410 Saint-Pierre - Réunion Tel : 0262 49 92 24 /06 92 32 04 97 Mail : Virginie.Ravigne@cirad.fr http://bit.ly/1aqgmda Virginie Ravigné via Gmail
Source: EVOLDIR
00:27

Master studies in Ecology and Evolution EcoEvo is a two year Master of Science programme for students interested in the functionning and evolution of the biosphere offered by the Institute of Environmental Sciences at Jagiellonian University in Krakow,Poland. The participants will investigate the mechanisms underlying ecological and evolutionary processes and will develop practical skills related to carrying out research and conservation projects. They will undertake a range of multidisciplinary courses (consisting of lectures, seminars, laboratory work and field classes) as well as carry out group and individual research projects. Starting date: October 2014 Admission: the application for the programme is a continuous process; additional application rounds start until there are no more places available or the last application round is over. The dates of application rounds for 2014 are: 19 March V 6 May, 7 May V 24 June, 25 June V 19 August and 20 August V 17 September. Tuition fees: (1) EU citizens and non-EU citizens with documented Polish background - no tuition fee; (2) non-EU citizens V 1st year: 2200, 2nd year: 2000. For more information see: www.ecoevo.uj.edu.pl — via Gmail

Source: EVOLDIR
00:09
Attention! The deadline is approaching for the 1st Greifswald Phylogenetics Meeting, which will be held in July 2014!!!! I herewith want to announce the 1st Greifswald Phylogenetics Meeting, which will be held in Greifswald (north eastern Germany) from the 14th till the 16th of July 2014. Registration is now open and the deadline (both for registration as well as for abstract submission) is the 30th of April. There are still a few free slots, so please register asap! Our conference poster can be found here: http://bit.ly/1lbEJkk Feel free to print it and forward it to anybody who might be interested! For more details, please visit the conference website: http://bit.ly/1eAnepX This meeting will have a particular focus on mathematical (e.g. graph theoretical, combinatorial, probabilistic and algebraic) aspects of evolutionary tree or network reconstruction, but it will also bring together scientists from different disciplines in order to provide the opportunity of close collaboration. Scope: Phylogenetics is an interdisciplinary research area that aims at reconstructing the evolutionary history of biological systems such as, for example, collections of species, populations or groups of bio-molecules. To achieve this, biologists work closely together with mathematicians and computer scientists. The conference will provide researchers from all three involved disciplines an opportunity to present their recent work and exchange ideas. Location: Greifswald is a beautiful little town located directly at the Baltic Sea in close proximity to the famous islands Rgen and Usedom. Greifswald university was founded in 1496 and has therefore a long tradition and history. Being a former Hanse town, Greifswald is famous for its historic market square, its cathedral and the museum harbor. Other famous towns like Stralsund with the Oceaneum or the world cultural heritage city of Wismar are nearby, as well as the city of Rostock with its newly established Darwineum. The region is a holiday region but not too crowded by tourists. In July the weather is most likely to be great and we hope that if you can come to our meeting, you will find the time to stay longer and enjoy this unique area. There is a direct and regular train connection to and from Berlin, and the nearest international airports are Hamburg and Berlin. Please note that the meeting starts early on the 14th with one of our highlight talks and ends in the evening of the 16th with another highlight talk - so if possible, please plan your stay from the 13th till the 17th of July. The registration fee is 150 Euros (100 Euros for students). Organizers: Mareike Fischer, Andreas Spillner, Martin Haase Invited speakers: Olaf Bininda-Emonds, Mike Steel, Olivier Gascuel, Vince Moulton, Allen Rodrigo For more details, visit our website http://bit.ly/1eAnepX or contact Mareike Fischer: email@mareikefischer.de Mareike Fischer via Gmail
Source: EVOLDIR

April 17, 2014

23:53
Job description: The laboratories Mathmatique Informatique et Gnome (MIG) and Gntique Animale et Biologie Intgrative (GABI) at INRA research center in Jouy-en-Josas, (30 km south of Paris) have an open post-doctoral position funded by the Domestichick ANR grant. Project description: The objective of the project is to study the evolutionary dynamics of chicken domestication, using a comparative genomics approach. The Gallus genus comprises 4 species. G. gallus is considered as the ancestral species of the domestic chicken. Previous work demonstrated the genomic contribution of G. sonneratii and it is considered that other species may also have contributed to the genomic make-up of the domestic chicken. Our approach relies on (1) deep-sequencing of a representative sample of wild Gallus species (n) and (2) deep re-sequencing of birds from various domestic breeds, to identify the genomic structure of the domestic chicken genome and to detect introgression or other evolutionary events fixed during domestication. The study is three-pronged: 1. The first step deals with genome assembly, using the domestic chicken reference genome, and variant detection (SNPs, indels, structural variants). 2. In the second step, we will build a hidden markov model (HMM) to represent the evolutionary history of both wild and domestic birds and infer local ancestry of domestic birds along the genome. 3. The third step is devoted to the evolutionary dynamics that shaped the Gallus genome at the genus level. We will more specifically develop and implement an Approximate Bayesian Computation by Population Monte-Carlo (ABC-PMC) method to test different demographic scenarios and identify the complex events underlying the current diversity: bottleneck, gene flow, selection. The post-doctoral fellow will be involved in all steps of the studies but his/her work will focus on the modeling, implementation and use of the statistical models mentioned in steps 2 and 3. Research Environment: The work will take place in MIG laboratory, an interdisciplinary laboratory that hosts around 40 people in addition to a bioinformatics platform. The work involves close collaboration with MIG and GABI researchers. The candidate will benefit from the bioinformatics expertise of both laboratories, the expert knowledge of GABI researchers about the domestic chicken and the MIGALE computation facility hosted by MIG. On a broader scale, the candidate will also benefit from the scientific environment of the INRA research center of Jouy-en-Josas, which hosts several research teams working on animal genetics, and the collaboration network of both partners, known for their skills in statistical genetics. Qualifications: The candidate should hold a PhD in bioinformatics, biostatistics or applied mathematics with applications in molecular biology. (1) Skills and/or knowledge in computational or Bayesian statistics and (2) skills with NGS data analysis would be a plus but not required. The candidate should have a strong interest in data analysis, especially in comparative genomics, and a taste for collaborative work. Funding: 21 months post-doctoral fellowship, starting as soon as possible and financed by ANR grant Domestichick. Salary will depend on the candidate’s background and experience. Additional financial compensation through the AgreenSkills program will be sought for eligible candidate (http://bit.ly/1mbR0EZ). The job will be located at the INRA research center of Jouy-en-Josas, in the South-West of Paris. Application: Send a detailed CV, a short motivation letter and references to Frdric Hospital and Mahendra Mariadassou . Applications should be submitted before June 1st, 2014 via Gmail
Source: EVOLDIR
18:00
Background: Plasticity, i.e. non-heritable morphological variation, enables organisms to modify the shape of their skeletal tissues in response to varying environmental stimuli. Plastic variation may also allow individuals to survive in the face of new environmental conditions, enabling the evolution of heritable adaptive traits. However, it is uncertain whether such a plastic response of morphology constitutes an evolutionary adaption itself. Here we investigate whether shape differences due to plastic bone remodelling have functionally advantageous biomechanical consequences in mouse mandibles. Shape characteristics of mandibles from two groups of inbred laboratory mice fed either rodent pellets or ground pellets mixed with jelly were assessed using geometric morphometrics and mechanical advantage measurements of jaw adductor musculature. Results: Mandibles raised on diets with differing food consistency showed significant differences in shape, which in turn altered their biomechanical profile. Mice raised on a soft food diet show a reduction in mechanical advantage relative to mice of the same inbred strain raised on a typical hard food diet. Further, the soft food eaters showed lower levels of integration between jaw regions, particularly between the molar and angular region relative to hard food eaters. Conclusions: Bone remodelling in mouse mandibles allows for significant shifts in biomechanical ability. Food consistency significantly influences this process in an adaptive direction, as mice raised on hard food develop jaws better suited to handle hard foods. This remodelling also affects the organisation of the mandible, as mice raised on soft food appear to be released from developmental constraints showing less overall integration than those raised on hard foods, but with a shift of integration towards the most solicited regions of the mandible facing such a food, namely the incisors. Our results illustrate how environmentally driven plasticity can lead to adaptive functional changes that increase biomechanical efficiency of food processing in the face of an increased solicitation. In contrast, decreased demand in terms of food processing seems to release developmental interactions between jaw parts involved in mastication, and may generate new patterns of co-variation, possibly opening new directions to subsequent selection. Overall, our results emphasize that mandible shape and integration evolved as parts of a complex system including mechanical loading food resource utilization and possibly foraging behaviour.
18:00
Background: Raphidioptera (snakeflies) is a holometabolous order of the superorder Neuropterida characterized by the narrowly elongate adult prothorax and the long female ovipositor. Mesozoic snakeflies were markedly more diverse than the modern ones are. However, the evolutionary history of Raphidioptera is largely unexplored, as a result of the poorly studied phylogeny among fossil and extant lineages within the order. Results: In this paper, we report a new snakefly family, Juroraphidiidae fam. nov., based on exquisitely preserved fossils, attributed to a new species Juroraphidia longicollum gen. et sp. nov., from the Jiulongshan Formation (Middle Jurassic) in Inner Mongolia, China. The new family is characterized by an unexpected combination of plesiomorphic and apomorphic characters of Raphidioptera. Based on our phylogenetic analysis, Juroraphidiidae fam. nov. together with Raphidiomorpha form a monophyletic clade, which is the sister to Priscaenigmatomorpha. The snakefly affinity of Priscaenigmatomorpha is confirmed and another new family, Chrysoraphidiidae fam. nov., is erected in this suborder. Conclusions: Juroraphidiidae fam. nov. is determined to be a transitional lineage between Priscaenigmatomorpha and Raphidiomorpha. Diversification of higher snakefly taxa had occurred by the Early Jurassic, suggesting that these insects had already had a long but undocumented history by this time.
07:19

Erick Matsen wrote:

In the paper describing MrBayes 3.2, there is the following phrase:

MrBayes 3.2 further includes a completely new type of tree proposal that is guided using parsimony scores. The details of the parsimony-biased proposals will be presented elsewhere; however, tentative empirical results show that they can improve the speed of convergence by an order of magnitude on some problems (see also Höhna and Drummond 2012).

Can someone point me to this paper? I'd like to read about them! (@Alexis_RAxML, I'm assuming that you learned about then from just reading the MB source?)

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