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January 15, 2015

01:18

—Apple-Mail=_7A189FCE-5B01-4E19-88A5-24E51CFD6EAE Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Job title: Postdoctoral position in computational evolutionary biology / phylogenetics A postdoctoral position in computational evolutionary biology / phylogenetics is available in Dan Rabosky’s lab at the University of Michigan, Ann Arbor. The postdoctoral researcher will be involved the development and application of methods for studying evolutionary dynamics (speciation, extinction, phenotypic evolution) across phylogenetic trees that potentially include many thousands of taxa. The project will involve extensions of the BAMM / BAMMtools software platform developed by the Rabosky lab (see http://bit.ly/1prr2sZ for more information). BAMM is a Bayesian framework for modeling complex mixtures of dynamic evolutionary processes on phylogenetic trees. The postdoctoral researcher will be involved with development and implementation of new methods for modeling evolutionary dynamics from phylogenetic and/or paleontological data. An area of particular interest involves combined analyses of paleontological and neontological data with BAMM. An additional objective involves development of BAMMtools, our R package for analyzing and visualizing evolutionary dynamics from BAMM output. The ideal candidate will have a background in computational biology and/or quantitative methods in evolutionary biology. Programming experience in C/C++ and/or R is required. Previous experience studying macroevolution dynamics is helpful, but we welcome applications from any area of computational biology, including population genetics, theoretical ecology, and applied mathematics. The position offers exceptional opportunities for independent research, career development, and quantitative skills training. We have an outstanding group of researchers in quantitative/computational evolutionary biology and biodiversity science in the Department of Ecology and Evolutionary Biology, the UM Museum of Zoology, and the UM Museum of Paleontology. Applications should be sent to drabosky at umich.edu. Please include a cover letter describing your research interests and background, a C.V., evidence of programming experience, and contact information for three references. Any questions about the position can be directed to Dan Rabosky. _____________________ Dan Rabosky Assistant Professor & Curator of Herpetology Museum of Zoology & Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor, MI 48109-1079 USA drabosky@umich.edu http://bit.ly/1prr2sZ —Apple-Mail=_7A189FCE-5B01-4E19-88A5-24E51CFD6EAE Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii

Job title: Postdoctoral position in computational evolutionary biology / phylogeneticsA postdoctoral position in computational evolutionary biology / phylogenetics is available in Dan Rabosky’s lab at the University of Michigan, Ann Arbor.  The postdoctoral researcher will be involved the development and application of methods for studying evolutionary dynamics (speciation, extinction, phenotypic evolution) across phylogenetic trees that potentially include many thousands of taxa. The project will involve extensions of the BAMM / BAMMtools software platform developed by the Rabosky lab (see http://bit.ly/1prr2sZ for more information). BAMM is a Bayesian framework for modeling complex mixtures of dynamic evolutionary processes on ph ylogenetic trees. The postdoctoral researcher will be involved with development and implementation of new methods for modeling evolutionary dynamics from phylogenetic and/or paleontological data. An area of particular interest involves combined analyses of paleontological and neontological data with BAMM. An additional objective involves development of BAMMtools, our R package for analyzing and visualizing evolutionary dynamics from BAMM output.The ideal candidate will have a background in computational biology and/or quantitative methods in evolutionary biology. Programming experience in C/C++ and/or R is required. Previous experience studying macroevolution dynamics is helpful, but we welcome applications from any area of computational biology, including population genetics, theoretical ecology, and applied mathematics.The position offers exceptional opportunities for independent research, career development, and quantita tive skills training. We have an outstanding group of researchers in quantitative/computational evolutionary biology and biodiversity science in the Department of Ecology and Evolutionary Biology, the UM Museum of Zoology, and the UM Museum of Paleontology.Applications should be sent to drabosky at umich.edu. Please include a cover letter describing your research interests and background, a C.V., evidence of programming experience, and contact information for three references. Any questions about the position can be directed to Dan Rabosky. _____________________Dan RaboskyAssistant Professor & Curator of HerpetologyMuseum of Zoology &Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn Arbor, MI 48109-1079 USAdrabosky@umich.eduhttp://bit.ly/1prr2sZ —Apple-Mail=_7A189FCE-5B01-4E19-88A5-24E51CFD6EA via Gmail
Source: EVOLDIR
01:18
A postdoc position (funded up to 4 years) and a PhD student position (funded up to 5 years) are available in the Moran lab at Department of Ecology, Evolution and Behavior at the Hebrew University of Jerusalem, Israel (HUJI). These positions will be funded by a new European Research Council (ERC) project aimed to shed new light on the evolution of post-transcriptional regulation by microRNAs. In our lab we use the sea anemone *Nematostella vectensis* as a model and employ various biochemical, genetic, microscopic and computational approaches to answer our questions. The fellowships associated with the project are at the very high end of Israeli standards and the successful candidates will also receive funds for attending relevant international workshops and conferences. The Hebrew University of Jerusalem (HUJI) is Israel’s premier university. HUJI has been ranked among the top universities in the world in two comprehensive surveys conducted by The Times Higher Education Supplement of London and Shanghai University. The host lab is located at the Natural Sciences campus, where a wide range of available technical services and facilities enable the cutting-edge research in various fields of Life Sciences. Our department is highly international and the lab working language is English. The suitable candidate should have experience in standard biochemical and molecular biology techniques. Having prior experience in microscopy and/or computational analysis of HiSeq data is an advantage. More details about our research group can be found online at yehumoran.com Interested candidates are welcome to contact Yehu Moran (yehu.moran@mail.huji.ac.il). Please send a CV, list of publications and contact details of 2-3 referees. Yehu Moran Yehu Moran via Gmail
Source: EVOLDIR
00:59
A postdoc position (funded up to 4 years) and a PhD student position (funded up to 5 years) are available in the Moran lab at Department of Ecology, Evolution and Behavior at the Hebrew University of Jerusalem, Israel (HUJI). These positions will be funded by a new European Research Council (ERC) project aimed to shed new light on the evolution of post-transcriptional regulation by microRNAs. In our lab we use the sea anemone *Nematostella vectensis* as a model and employ various biochemical, genetic, microscopic and computational approaches to answer our questions. The fellowships associated with the project are at the very high end of Israeli standards and the successful candidates will also receive funds for attending relevant international workshops and conferences. The Hebrew University of Jerusalem (HUJI) is Israel’s premier university. HUJI has been ranked among the top universities in the world in two comprehensive surveys conducted by The Times Higher Education Supplement of London and Shanghai University. The host lab is located at the Natural Sciences campus, where a wide range of available technical services and facilities enable the cutting-edge research in various fields of Life Sciences. Our department is highly international and the lab working language is English. The suitable candidate should have experience in standard biochemical and molecular biology techniques. Having prior experience in microscopy and/or computational analysis of HiSeq data is an advantage. More details about our research group can be found online at yehumoran.com Interested candidates are welcome to contact Yehu Moran (yehu.moran@mail.huji.ac.il). Please send a CV, list of publications and contact details of 2-3 referees. Yehu Moran via Gmail
Source: EVOLDIR
00:44
Dear Evoldir members, I am pleased to announce that three fully-funded PhD studentships are available in the Evolutionary Biology Group at the University of Hull, UK, starting September 2015. The studentships are as follows (please follow the links for more information or contact the first supervisors for informal enquiries): 1. Untangling molecular food webs to investigate the impact of invasive predators on whole communities and ecosystem services Supervisors: Dr Lori Lawson Handley (l.lawson-handley@hull.ac.uk), Dr Bernd Haenfling, Dr Darren Evans (Hull), Dr Helen Roy (Centre for Ecology & Hydrology), Prof Neil Boonham (FERA) 2. Rapid biodiversity monitoring of freshwater pond diversity using environmental DNA: Supervisors: Developing state-of-the-art tools to inform wetland management Dr Bernd Hnfling (b.haenfling@hull.ac.uk), Dr Lori Lawson Handley, Dr Phil Wheeler (Hull), Prof Neil Boonham (FERA) 3. Discovering and monitoring endangered Triops cancriformis populations in ephemeral ponds Supervisors: Dr Africa Gmez (a.gomez@hull.ac.uk), Dr Bernd Hnfling, (Hull) Dr Larry Griffin (Wildfowl & Wetlands Trust), Prof Neil Boonham (FERA) Please note the closing date is ***2nd February***, so please forward this advert to anyone you think might be interested or contact us and apply as soon as possible Many thanks and best wishes for the new year Lori Dr Lori Lawson Handley School of Biological, Biomedical and Environmental Sciences University of Hull Cottingham Rd, Hull, HU6 7RX U.K. Tel 0044 1482 462061 Email l.lawson-handley@hull.ac.uk http://bit.ly/1x3ZUFv Twitter: @Calvia14 L.Lawson-Handley@hull.ac.uk via Gmail
Source: EVOLDIR

January 14, 2015

23:42

Two separate PhD projects are available with my group in the School Biology, University of Leeds, UK, for UK and EU students. 1. Ecological Genomics of UK and European Bats. NERC-DTP funded project, closing date 2nd Feb 2015. More details here: http://bit.ly/1u5NEZv 2. Emerging infectious diseases (flexible topic disease ecology/evolutionary genomics of disease vectors). University of Leeds 110 Anniversary Research Scholarships. Closing date 29th January 2015. More details here: http://bit.ly/1u5NH7P Dr Simon Goodman ===========================================================Dr Simon Goodman School of Biology Manton Building University of Leeds Clarendon Way Leeds, LS2 9JT, UK Tel: +44-(0)113-3432561, Fax: +44-(0)113-3432835 Email: s.j.goodman@leeds.ac.uk Skype: simon.j.goodman Twitter: @DrSimon_Goodman =========================================================== via Gmail

Source: EVOLDIR
22:00
When a seed germinates determines the seasonal environment experienced by a plant throughout its life, and germination phenology is one of the very first phenotypes expressed by plants during ontogeny. As such, germination phenology is subject to extremely strong natural selection, especially during early stages of adaptation. Moreover, germination co-evolves with seed dispersal, mating system, and reproductive strategy to determine plant life cycles and demographic dynamics of plant populations. This working group will test the importance of germination adaptations in delimiting species niche and range limits, both in the past and in response to changed environments. More generally, this topic pertains to the identification of key traits associated with adaptation to environmental change, and the role that early life-stage traits and traits associated with habitat selection contribute to these dynamics. The focus on germination provides a clear and tractable system for addressing general evolutionary and ecological questions concerning the interactions between ontogeny and adaptation, trait coevolution, and the roles of habitat selection and organismal responses to their environment in niche evolution. It also will contribute tangibly to efforts to predict plant responses to environmental change. The group will compile and analyze a comprehensive data set on germination and dormancy, combined with data on niche breadth, geographic range, and life history, in order to test hypotheses concerning trait coevolution and species range limits. The group will also theoretically explore interactions between ontogeny and adaptation, theoretically model trait coevolution via habitat selection and bet hedging, and develop phenological models of integrated life histories that include germination in order to predict plant responses to environmental change.
Source: NESCent
03:43

NERC-funded PhD studentship available for anthropological genetics at Imperial College London. Attention students looking to do a PhD in human evolutionary genetics. We are currently accepting applications for a PhD student to be co-supervised by Dr. Jason Hodgson and Prof. Miguel Araujo. The title of the project is “Understanding the relationship between tsetse flies, trypanosomiasis, and humans in rural Africa using population genomics and ecological niche modelling.” Details can be found at: http://bit.ly/1sxm6Lx The project will require a fun mix of fieldwork, lab work, and an integrated analytical approach employing population genomics and ecological niche modelling. Applications need to be received by January 25th, 2015. Directions for how to apply can be found at: http://bit.ly/1GOsKy8 Please contact me with any queries: j.hodgson@imperial.ac.uk Eligibility for the studentship is limited to those with ‘settled status’ in the UK (i.e. no restrictions on how long you can stay in the UK, you have been ordinarily resident in the UK for three years prior to the start of the studentship, for non EU-nationals you have not been residing in the UK wholly for educational purposes). jason.a.hodgson@gmail.com via Gmail

Source: EVOLDIR
03:25
Postdoctoral Researcher in Fish Genomics and Genetics Great Lakes Genetics/Genomics Laboratory, University of Toledo Lake Erie Center, Toledo, OH Closing Date: February 28, 2015 Web Address: http://bit.ly/1seQy6U Description The research project is to help develop, test, and publish a Next-generation sequence assay for detecting and identifying all Great Lakes native and invasive fish species, including those anticipated to invade, from environmental DNA and plankton samples. The postdoctoral research associate will organize large DNA sequence databases, train and co-supervise students and technicians, and be thoroughly competent and experienced in bioinformatics, DNA extraction, PCR, DNA sequencing, and population genetic and systematic evolutionary data analyses. Qualifications Ph.D. degree required in hand. Publication of Ph.D. results in peer-reviewed journals required. Excellent recommendation from former advisors required. Teaching and supervisory experience preferred. Grant funding record preferred. Data management experience, bioinformatics, and data analysis experience in molecular phylogenetics and population genetics required. DNA extraction, PCR, DNA Sequencing (both Sanger and Illumina MiSeq), sequence alignment and GenBank experience required. Familiarity with QIIME, Unix/Linux operating systems and writing script in Perl is a plus. Strong communication (written, oral) skills required. Experience in working with fishes strongly preferred. Strong personnel interaction skills and experience in training others required. Oral research presentation experience at national or international scientific conferences required. Fish specimen collection experience Vstrongly preferred. How to Apply Send (1) cover letter, (2) CV, (3) 2 letters of reference, (4) copies of graduate and undergraduate transcripts via .pdf to Dr. Stepien at carol.stepien@utoledo.edu. Competitive salary, full benefits. Beautiful well-funded lab (by NSF, USEPA, ARS, Sea Grant) on Lake Erie (with view) at Lake Erie Center field station 20-25 minutes from main University of Toledo campus. The Great Lakes Genetics Laboratory currently has another post-doc, 3 Ph.D. students, a full-time technician, and 2 undergraduate researchers. The University of Toledo is an Equal Access, Equal Opportunity, Affirmative Action Employer and Educator and is committed to increasing the diversity of our campus. Contact Carol Stepien Distinguished University Professor and Director Lake Erie Center and Dept. Environmental Sciences 6200 Bayshore Rd. Toledo, OH 43615 Phone: 4195308362 Fax: 4195308399 carol.stepien@utoledo.edu “Klymus, Katy Elizabeth” via Gmail
Source: EVOLDIR
03:25
SMBE SYMPOSIUM ON MICRO-EVO-DEVO – VIENNA JULY 12-16TH 2015. Title: ‘Micro-evo-devo: using natural variation to explain the how and why of phenotypic evolution’ Invited Speaker: Marie Anne-Felix (Institute of Biology of the Ecole Normale Supérieure, Paris) Dear colleagues, we would like to welcome you to submit your abstract to our symposium on Micro- Evo- Devo. Micro-evo-devo synthesises population genetics and evolutionary developmental biology to take advantage of natural variation to explain the genetic and developmental bases, and fitness consequence of phenotypic change, as well as the evolutionary forces that have shaped it. Therefore, this symposium will highlight how the integrative framework of micro-evo-devo has great potential to explain how and why phenotypic diversity among populations has evolved. This symposium will provide a platform for the most recent advances using established models and attract researchers using recent advances in sequencing and genome editing technologies to investigate phenotypic evolution in emerging models. We expect that our proposed symposium will serve to consolidate this growing community and help the field to realise its full potential to enhance our understanding of the evolution of biological diversity. Registration and abstract submission deadline is Feb 8, 2015 (http://bit.ly/1FUHrVk). Please feel free to contact us directly in case you have any question. Looking forward to seeing you in Vienna! Luisa Pallares (pallares@evolbio.mpg.de) Daniela Nunes (msantos-nunes@brookes.ac.uk) Alistair McGregor (amcgregor@brookes.ac.uk) Daniela Santos Nunes via Gmail
Source: EVOLDIR
03:05

—Boundary_(ID_N9myiXleYvkwr809UZflcA) Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: QUOTED-PRINTABLE Field Assistants Required-North American red squirrels Kluane, Yukon, Canada We are looking for 3 volunteers to assist with fieldwork for the period of February 20 to the end of May, 2015, and a further 5 volunteers from May through August (please note: there is the exciting possibility of linking this position with a sister study’ on Columbian ground squirrels in Alberta. See below). The positions are part of a long-term study of red squirrel population dynamics. As a member of the study, assistants will be involved with monitoring the reproduction and survival of individuals. Fieldwork will involve live-trapping and handling of animals, radio-telemetry, behavioural observation, and climbing trees to find young in nests. This is an excellent opportunity to gain experience working with a collaborative research team on a long-term study of a wild mammal. All fieldwork is carried out in the beautiful backdrop of southwestern Yukon, Canada. We will be staying at a rustic field station two hours from Whitehorse. Food and accommodation are provided. Volunteers are required to provide for their own travel to Edmonton, Alberta; however, travel from Edmonton to the field station (and back again!) is provided. Training will be provided and no experience is necessary, but candidates should have an interest in a number of the following: ecology, evolutionary biology, wildlife, field biology, and animal behaviour. The field camp is remote and low tech (no showers, cell phone service, or internet), so successful applicants must enjoy the outdoors and be able to remain a positive and responsible team member under relatively isolated and demanding conditions. Candidates must be in good physical condition, be willing to climb trees, and have an enthusiasm for learning. We work on squirrel time’, which often involves long work days; as such, applicants must have a strong work ethic. That said, the atmosphere at squirrel camp is friendly and inclusive, and this area is one of the most beautiful in Canada. Columbian ground squirrel study: We are also involved with a similar long-term study on Columbian ground squirrels in Kananaskis, Alberta. We are thus able to provide the opportunity for interested applicants to be involved with both programs. Volunteers would begin work on red squirrels in February and switch to ground squirrels for May to August 31. Both projects use a similar approach (lifetime monitoring using live-trapping and observation), but are conducted in two different landscapes and on species differing in natural history (e.g., winter-active vs. hibernating). If you are interested in this joint opportunity, please see our advertisement on this webpage and mention it in your application. If you wish to apply for one of these posts then please send a CV with a cover letter and contact details for three references (with e-mail addresses), by email to Ainsley Sykes (contact info below), by January 30, 2015. Contact: Ainsley Sykes via email: asykes@ualberta.ca Department of Biological Sciences, University of Alberta Twitter: @KluaneSquirrels —Boundary_(ID_N9myiXleYvkwr809UZflcA) Content-type: text/html; charset=Windows-1252 Content-transfer-encoding: QUOTED-PRINTABLE

Source: EVOLDIR
02:46

Research Associate Position in Single Cell Phylogenomics University of British Columbia Vancouver, Canada The Department of Botany seeks a well-trained highly motivated and enthusiastic individual interested in exploring the evolutionary biology of complex microbial life and their organelles using single cell genomics methods coupled with phylogenomic analyses as a Research Associate. The applicant must have a PhD or equivalent and at least three additional years of research experience. Expertise in eukaryotic biodiversity and evolutionary history, and the application of single cell genomics methods (genomic and transcriptomic datasets) and phylogenic analyses are essential. The applicant must have excellent written and oral communication skills and be highly organised. Basic molecular biology and analyses techniques are also highly desirable. The candidate must have a proven record of publication in significant journals in the field.The position is available starting May 15 2015 for an initial period of one year with a possibility for extension subject to a satisfactory performance and funding. To apply, please send a cover letter outlining research experience and interest, a curriculum vitae and the names and contact information for 3 referees to Patrick Keeling, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, B. C. V6T 1Z4, Canada. Email pkeeling@mail.ubc.ca. Fax (604) 822-6089. Closing date is Feb. 16, 2015. UBC hires on the basis of merit and is strongly committed to equity and diversity within its community. We especially welcome applications from visible minority group members, women, Aboriginal persons, persons with disabilities, persons of minority sexual orientations and gender identities, and others with the skills and knowledge to productively engage with diverse communities. Canadians and permanent residents of Canada will be given priority. via Gmail

Source: EVOLDIR
02:07

SMBE SYMPOSIUM ON DETECTING SELECTION USING ANCIENT GENOMES - VIENNA JULY 12-16TH 2015. We are pleased to invite you to participate in the symposium “Ancient genomes: A time machine for investigating natural selection”, which will take place at the annual meeting of the Society for Molecular Biology and Evolution (Vienna, July 12-16th 2015). Symposium abstract: ‘Detecting natural selection and processes underlying genetic adaptations are core objectives of evolutionary biology and ecology. A number of statistical approaches have been developed in recent years to detect signatures of natural selection in modern genetic data. However, they all have poor temporal resolution, most are confounded by past demographic processes, and many are insensitive to selection acting on standing variation. Ancient genomics has gained considerable momentum in recent years but its application to selection studies is still in its infancy. Sequencing ancient genomes from fossil material provides a unique snapshot of past genetic variation, thus providing a powerful tool for investigating adaptation hypotheses directly, and the only means of assessing temporal heterogeneity in natural selection. In this Symposium we will explore new methods and the potentials of using heterochronic data to study natural selection, whether comparing ancient genomes to modern variation and/or ancient genomes from different time periods. We will discuss the principles, examples and potential limitations of detecting selection in any organism for which ancient genomes are available, including prokaryotes, plants, animals, and humans.’ Confirmed keynote speakers: Johannes Krause (http://bit.ly/1yaI7lQ) and Ludovic Orlando (http://bit.ly/1qXj1Qw). Submit your abstracts for oral presentations (ABSTRACT SUBMISSION DEADLINE: 8TH OF FEBRUARY 2015 – Check submission details on SMBE’s annual meeting webpage http://smbe2015.at/). Other important dates: Abstract submission for poster presentations, March 29, 2015 - Early bird registration, March 1, 2015. See you in Vienna! Zuzana Faltyskova, Yoan Diekmann, David Díez-del-Molino, Pascale Gerbault and Mark Thomas. Research Department of Genetics, Evolution and Environment, University College London, London, UK. via Gmail

Source: EVOLDIR
01:47

—Boundary_(ID_hCtak77prCoV3ghvM4XS0g) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Field Assistants Required - Black-tailed prairie dogs Grasslands National Park, Saskatchewan, Canada I am looking for 3 volunteers to assist with fieldwork beginning March 10 and continuing until July 10 (with a possibility of extension to Oct 10 for at least 1 of the positions). The project investigates the ecology of Black-tailed prairie dogs and will involve live-trapping, handling and monitoring of individuals. Prairie dog towns are home to (among others): burrowing owls, swift fox and, the recently reintroduced, black-footed ferret. Assistants will have the opportunity of seeing all of these iconic grassland species, plus the many more resident in the Park. This is an excellent opportunity to gain experience working with a population of wild mammals in a spectacular setting and in collaboration with university, park and zoo researchers. All fieldwork is carried out in Grasslands National Park, southern Saskatchewan, one of the largest remaining tracts of native prairie in Canada. We will be staying in Parks Canada housing in the heart of the park. Food and accommodation are provided. Volunteers are required to provide for their own travel to Saskatoon, Saskatchewan. Travel between the field station and Saskatoon is provided. Training will be provided and no experience is necessary, but candidates should have an interest in the following (the more the better!): ecology, evolutionary biology, wildlife, field biology, and conservation biology. The field house and study population is isolated (the nearest town is approx. 45 min away) and, as such, successful applicants need to be able to cope under these conditions, enjoy the outdoors, be up-beat, positive, responsible and work well as a member of a team. If you wish to apply for one of these posts then please send a CV with a cover letter and contact details for three references (with e-mail addresses), by email to Jeff Lane (contact info below) by January 31, 2015. Contact: Dr. Jeff Lane Department of Biology University of Saskatchewan jeffrey.lane@usask.ca www.lanelab.ca —Boundary_(ID_hCtak77prCoV3ghvM4XS0g) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE

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Source: EVOLDIR
01:26
A two-year postdoc position in ancient DNA is currently available at Stockholm University and the Science for Life Laboratory. The successful candidate will join the collaborative research project “Testing the utility of massively parallel sequencing on ancient sediments”. This project is aimed at retrieving and analyzing metagenomic data sets from environmental DNA from 11,000-16,000-year old lake sediments. The postdoctoral position is shared between the groups of Barbara Wohlfarth (Department of Geological Sciences, Stockholm University), Tanja Slotte (Department of Ecology, Environment and Plant Sciences, Stockholm University, and Science for Life Laboratory) and Laura Parducci (Department of Plant Ecology and Evolution, Uppsala University). The postdoctoral fellow will be employed by the Department of Geological Sciences, but will have his/her main working place at the Science for Life Laboratory in Stockholm. Link to the full ad on Stockholm University’s website: http://bit.ly/1yifWOP Project Ancient lake sediments store a wealth of biological, chemical and physical information that allow reconstructing past climatic and environmental conditions in great detail. Although a wealth of paleoclimatic and paleoenvironmental information has been obtained, it is clear that the analysed microscopic and macroscopic fossil assemblages only represent a tiny fraction of the organisms that had existed at a certain time in the past and that each of the analytical methods employed has its specific limitation. Recent advances in environmental DNA analyses that make use of new large-scale sequencing technologies now offer the unprecedented opportunity to unravel a complementary spectrum of ancient faunal and floral remains than those identified by micro- or macrofossil analyses. As such, aDNA analysis can provide a completely new understanding of how ecosystems responded to dramatic climatic changes. The postdoctoral fellow will work in close collaboration with molecular ecologists, paleoecologists, paleoclimatologists and bioinformaticians and will utilize state-of-the-art approaches to retrieve and analyze the metagenomic data sets and to lead hypothesis-driven genomic analyses in an evolutionary context. He/she will also be involved in fieldwork (coring lake sediments), lab-work to sub-sample the sediment cores and DNA extraction in facilities specifically dedicated to ancient DNA extraction. Bioinformatics work will be done in collaboration with the Bioinformatic Service (https://www.bils.se) available at the Science for Life Laboratory in Stockholm. Terms of employment This is a full-time position for two years, financed by the Faculty of Science at Stockholm University. Salaries at Stockholm University are set on an individual basis. The preferred starting date is May 2015. Qualification requirements The applicant must hold a doctoral degree from an accredited college/university in a subject area relevant to the project. The ideal candidate must have very good experience in molecular biology, genetics, and bioinformatic analyses or equivalent. Candidates with a strong record in genetics/genomics, and previous experience in the field of ancient DNA will be preferred. Experience beyond the doctoral degree is not required. However the successful candidate must be highly motivated, creatively thinking and have a record of high quality scientific publications. He/she must demonstrate independency in working and be able to collaborate with scientists from different disciplines (biology, paleoscience, bioinformatics). Excellent English language skills, both written and spoken, are required. Selection criteria The successful applicant will be selected based on the qualifications specified above. References and interviews will be used during the selection process to assess the qualifications of the applicants. Infrastructure and environment Stockholm University is a leading European university offering a multicultural environment in one of the world’s most dynamic capital cities. With more than 60,000 students and 5,000 staff, the University facilitates individual and societal development by providing top quality education that is tightly linked to its internationally recognized research programs. The Department of Geological Sciences (http://bit.ly/1zaiAJD) is located in the Frescati Campus of Stockholm University. Our research combines classical geology with geochemistry, marine geology and paleoclimate and is strongly integrated with the interests of the Bolin Centre for Climate Research (http://bit.ly/1zaiAJF). Science for Life Laboratory (SciLifeLab, http://bit.ly/17a7QLt) is a collaboration between Stockholm University, the Karolinska Institute, the Royal Institute of Technology, and Uppsala University, is a national centre for large-scale biosciences with a focus on health and environmental research. The centre combines advanced technical know-how and state-of-the-art equipment with a broad knowledge in translational medicine and molecular biosciences. The postdoctoral researcher will be employed by the Department of Geological Sciences and will be integrated into SciLifeLab in Stockholm. He/she will frequently visit the Department of Plant Ecology and Evolution, Uppsala University to perform laboratory work. The environment is international with English as the working language. More information Further information about the position can be requested from Barbara Wohlfarth (barbara.wohlfarth@geo.su.se), tel. +46(0)8-16 48 83; Tanja Slotte (tanja.slotte@su.se); and Laura Parducci (laura.parducci@ebc.uu.se), tel. +46(0)18-471 64 14. Trade union representatives Anqi Lindblom-Ahlm (SACO-S), Lisbeth Häggberg (Fackförbundet ST), tel. 08-16 20 00 (switchboard), and Gunnar Stenberg (SEKO), tel. +46 70 316 43 41. Application Applications marked with reference number SU FV-0064-15 should be submitted electronically as a single PDF file. Applications should comprise the following: 1. CV, including full contact information, date of birth and date of PhD degree 2. Personal statement describing research interests (1-2 paragraphs), research experience (1-2 paragraphs) and career goals (1-2 paragraphs). 3. List of publications. 4. List of 2-3 references; please include name, e-mail address and telephone number. 5. Relevant documents: the applicants are encouraged to provide copies of documents that substantiate their qualifications Welcome with your complete application, labeled with reference number SU FV-0064-15 no later than March 15, 2015 to: registrator@su.se. Stockholm University strives to be a workplace, which is free from discrimination and offers equal opportunities to everyone. Tanja Slotte via Gmail
Source: EVOLDIR
00:30
*Biodiversity and Metagenomics of the Herbivore Microbiome* The Dearing lab at the University of Utah invites applications for a postdoctoral fellow to participate in a collaborative study to understand the gut microbiome of mammalian herbivores with respect to detoxification of plant defensive compounds. Our investigations suggest 1) the microbiome in the foregut of woodrats is critical for the ingestion of dietary toxins, 2) microbial biodiversity is important in this process and 3) previous exposure to toxins shapes the microbiome. For more information on previous research, see: http://bit.ly/1BnDPqK This postdoctoral position will focus on the influences of host evolutionary history and diet in sculpting the diversity and function of the mammalian microbiome. One component of this will be a broad survey of microbiomes and phylogeny across the woodrat genus (*Neotoma). *The ideal candidate will have a strong interest and experience in microbial ecology and metagenomics, with experience in gut systems preferably of vertebrates. Basic bioinformatic and molecular skills are required. Fieldwork for small mammal collection will be necessary; prior experience preferred but not required. The candidate should have a demonstrated record of publication with at least one first authored publication in press, and will be expected to work well in a collaborative environment. The Dearing lab provides a strong training and career development environment for candidates interested in academic positions. *Applications will be reviewed as they are received through January 30, 2015*. The preferred start date is March 15, 2015. Please send a C.V., statement of research experience and interests that includes career goals (1-2 pgs), pdfs of papers, and contact information (emails, phone numbers and professional relationship) for at least 3 professional references to Dr. Denise Dearing, care of Dr. Jael Malenke ; please put $B!H(BMicrobiome Postdoctoral Applicant$B!I(B in the Subject Line. jaelmalenke@gmail.com via Gmail
Source: EVOLDIR
00:30
Responses to sexual environments modelled as neural networks. Norwich Research Park Doctoral Training Partnership PI: T Chapman (http://bit.ly/1BnDPaq) Co-Is: Tamas Dalmay, Irina Mohorianu. The ability to respond appropriately to the environment (e.g. temperature, day length, presence of females or same-sex rivals) is crucially important. Therefore the detection of environmental cues, and integration of information from them, are vital. Recently, there has been much interest in modelling the underlying biological mechanisms responsible, using ‘neural networks’. Our recent work suggests that the response of male fruitflies to conspecific mating rivals can be modelled via this type of network. The aim is to test this idea and identify the alternative pathways involved. This will be done via the analysis of RNA sequencing data of the transcriptomes of males with manipulated sensory systems. http://bit.ly/1AOJ0hT Contact for more information: tracey.chapman@uea.ac.uk Application Deadline: 06/03/2015 “Tracey Chapman (BIO)” via Gmail
Source: EVOLDIR

January 13, 2015

23:32

[corrected version] Dear colleagues, it is our pleasure to invite you to submit abstracts to our symposium on the **Origins and Evolution of Molecular Innovation** ! Our guest invited speaker is Prof. M. Mar Albà from the UPF in Barcelona. This symposium will be a part of the 2015 Society for Molecular Biology and Evolution Meeting (http://smbe2015.at/). The meeting will be held in the Hofburg Palace in Vienna, Austria, from July 12 to 16. Further about the destination can be found here: http://bit.ly/1BORVzD The deadline for registration is Feb. 8, 2015. You may find registration information and a link to the registration portal here: http://bit.ly/1Hs3vnD Symposium description: Generally, the field of molecular evolution is dominated by studies of descent with accumulation of slight modifications. However, larger changes are also possible, in which entirely new molecular features originate for the first time. We will consider rapid or spontaneous molecular innovations of diverse kinds (structures, functions, interactions, networks), with a preference for the most dramatic leaps between the absence and the presence of the molecular traits or features in question. Timely examples of great interest in the community include (i) de novo emergence of new genes, protein domains, regulatory regions and (ii) neo-functionalization, e.g. via the acquisition of new and adaptive binding activities. The symposium will not only address well-documented examples of spontaneous emergence of novel molecular traits, but also cover findings relevant to the processes of innovation and its aftermath. These include (but are not limited to) the roles of promiscuity (e.g. in the emergence of novel enzymatic functions) and stochasticity across different organization levels. We look forward to seeing you in Vienna! Joanna Masel (masel@u.arizona.edu) Rafik Neme (rneme@evolbio.mpg.de) Erich Bornberg-Bauer (ebb@wwu.de) via Gmail

Source: EVOLDIR
22:30

BLAST is a computer program that searches a database for similarity matches to a given query sequence, either DNA or amino acid. It is most commonly used to search the GenBank database for matches to any new sequence that we might happen to have, in the hope that we will find one or more homologous sequences.

To most of us BLAST is a black box, in the sense that we have little idea about the details of how it does what it does. So, maybe we should at least look at what it does, just in case we ever need to know.

About 10 years ago I was working with some EST data. For those of you not old enough to know, ESTs consist of short DNA reads from arbitrary primers. In the hope of identifying the coding gene represented by each EST, BLASTX is used to search the GenBank protein database using each translated nucleotide query (in all six possible reading frames). BLASTX produces an E-value for each matching sequence, representing the strength of the match to the query. An E-value is not a probability (as they can vary from 0 to infinity), but at p=0.050 the expected E-value happens to be E=0.051. There is no consensus for what E-value should serve as indicating a "significant" match.

I decided to find out what happens if a DNA query sequence varies in either length or GC content. I used both random sequences (which were thus not in GenBank) as well as real sequences (which were in GenBank). The short answer is that the BLASTX results vary a lot. I never published these results because I figured the first thing a referee would do is ask me to explain BLASTX's behaviour, and I did not have an explanation (and still don't).

I present the results here for what they are still worth. Obviously, the results are not restricted to EST data, but apply any time that we use BLASTX.

Experimentation

The content of GenBank is quite different today to what it was back in late 2003, and so maybe the results will vary if the work was to be repeated. For reference, the first graph shows the GC content of the GenBank protein-coding sequences at the time of my work. Also, it is possible that BLASTX is different as well — I used v. 2.2.6 with default parameters (BLOSUM62, edge correction, length correction, SEG filtering, universal genetic code, gap penalty 11+k). Maybe some intrepid soul will be inspired to find out what happens nowadays.


Random sequences

I generated sets of 1,000 replicate "ESTs" using the perl script Randseq by M. Raymer (5/27/2003). These sets varied in DNA length (100–1,000 nt) and in GC content (0–94%), but were otherwise random sequences of nucleotides. These sequences are not expected to be homologous to anything already in GenBank, and should thus form BLASTX matches only by random chance.

The results for varying the sequence length are shown in the next graph, with each point representing the mean E-value observed. The lines represent four somewhat different GC contents; and the anticipated E-value for random data (0.051) is also shown. Clearly, very few points are near the expected value. The lines all show the same shape, with a minimum E-value near 450 nt, and rising slowly with longer lengths and rising rapidly with shorter lengths.


A more detailed assessment of the results for varying the GC content is shown in the third graph. The lines represent two somewhat different sequence lengths; and the anticipated E-value for random data (0.051) is also shown. It is clear that the E-value is capable of varying by up to seven orders of magnitude in response to variation in the GC content of the sequence.


Real sequences

I used the sequences contained in the Poxvirux Orthologous Clusters database (POCs), which used to be available at: http://athena.bioc.uvic.ca/pbr/POCs/pocs.html. This has since been replaced by the Viral Orthologous Clusters database (VOCs). These virus protein sequences are expected to already be in GenBank, and they should thus form good BLASTX matches.

The POCs database could be queried by both sequence length and GC content, and it was the only such database that I could find at the time. For each combination of length (in 50-nt bands) and GC-value (in 10% bands) I gathered a minimum of 20 sequences. There were few sequences for the shortest lengths, so I chopped up the longest sequences (longer then needed) to increase the sample size. There were also few sequences at the greatest GC values, so I used sequence AE004437.1 from GenBank (a Halobacterium sp.) to increase the sample size.

The results are shown in the final graph, with each point representing the mean E-value observed. The E-values are all small, since they represent actual database matches. Clearly, variation in sequence length can lead to orders of magnitude variation in E-value, while variation in GC content has an effect only at longer sequence lengths.


Conclusions

For a program that is supposed to produce comparable results, no matter what the sequence, these BLASTX results are disquieting. After all, BLAST is one of the most cited programs ever (see Massive citations of bioinformatics in biology papers), and yet I suspect that most people do not realize that it behaves like this.

The random sequences assess the effect of false positives. That they vary so much in E-value is amazing. Clearly, BLASTX E-values are not comparable between sequences. It is interesting that GC content seems to have a bigger effect than sequence length — for any given GC content the effect of length is relatively small for sequences longer than c. 600 nt. However, variation in GC content can produce orders of magnitude of effect at any given sequence length.

The real sequences assess the effect of true positives. That they vary in E-value is also not good — the E-values all represent true database matches (and presumably exact ones). Nevertheless, the effect of variation in sequence length and GC content is repeated for these real sequences. However, variation in GC content only has a large effect for the longer sequences, and instead it is the sequence length that produces the orders of magnitude variation in E-value.

You can make of this what you will.

22:00
Humans are vulnerable to a number of unique musculoskeletal maladies as a consequence of our evolutionary history. Although walking on our extended hind limbs is the hallmark adaptation characterizing our species it nevertheless makes us vulnerable to a wide range of serious joint and soft tissue problems. When viewed from an evolutionary perspective many of these medical issues become understandable and, indeed, novel methods of diagnosis and treatment can emerge. The proposed collaborative, a working group of paleoanthropologists, comparative anatomists, biomechanical engineers, and physicians will create new analytical approaches and new ways of viewing the disorders that uniquely plague our species. The results of this work include the development and implementation of a model curriculum, the creation of a website, and the publication of an edited volume. The disorders directly related to our way of walking include chronically sprained ankles, hernias, osteoporotic fractures of the hip, spine, and forearm, obstetric problems, knee problems, foot disorders, fatigue fractures, and many others. By understanding how our anatomy changed in order to walk upright, and why these changes occurred, we gain a better understanding of why these adaptations sometimes go awry resulting in disorders and pain.
Source: NESCent
09:10

Erick Matsen wrote:

I had no idea that this was coming down the pipe, but was excited to see a paper come out describing Phycas (http://www.phycas.org) from its authors, including @mtholder. Code is at https://github.com/plewis/phycas.

www.ncbi.nlm.nih.gov Phycas: Software for Bayesian Phylogenetic Analysis. PO Lewis, MT Holder and DL Swofford, Systematic biology, Jan 9 2015

Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using newer methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used harmonic mean estimator. In addition, Phycas supports two posterior predictive approaches to model selection: Gelfand-Ghosh and Conditional Predictive Ordinates. The GTR family of substitution models, as well as a codon model, are available, and data can be partitioned with all parameters unlinked except tree topology and edge lengths. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length.

I haven't played with Phycas, but I can describe what I think of as its "killer feature," which is the ability to use a prior incorporating polytomous trees. That means that the software can return trees that look like this:

where I've put an arrow pointing at the polytomy. In this case, the polytomy shows three descendants of a given lineage.

I would argue that such a representation is a more honest one (a "shrunken" estimate for @nicolas_lartill and friends). That is, if there is not information to resolve an internal node, then an unresolved tree is returned. One often sees such nodes when people collapse nodes in ML trees that have low bootstrap support. However, I think that it's better than that because it's rolled into the actual inference, meaning that the overall likelihoods are properly estimated. In a field where we are already in statistically tenuous territory with the number of discrete parameters being on the order of the number of independent data points (to say nothing of the discrete estimation part) having fewer parameters when appropriate is refreshing.

In the Bayesian phylogenetics world, not allowing such multifurcations can cause some trouble, as was the subject of some research in the mid-2000's. A good culmination of that work is this paper by Z Yang:

www.ncbi.nlm.nih.gov Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. Z Yang, Molecular biology and evolution, Aug 2007

The star-tree paradox refers to the conjecture that the posterior probabilities for the three unrooted trees for four species (or the three rooted trees for three species if the molecular clock is assumed) do not approach 1/3 when the data are generated using the star tree and when the amount of data approaches infinity. It reflects the more general phenomenon of high and presumably spurious posterior probabilities for trees or clades produced by the Bayesian method of phylogenetic reconstruction, and it is perceived to be a manifestation of the deeper problem of the extreme sensitivity of Bayesian model selection to the prior on parameters. Analysis of the star-tree paradox has been hampered by the intractability of the integrals involved. In this article, I use Laplacian expansion to approximate the posterior probabilities for the three rooted trees for three species using binary characters evolving at a constant rate. The approximation enables calculation of posterior tree probabilities for arbitrarily large data sets. Both theoretical analysis of the analogous fair-coin and fair-balance problems and computer simulation for the tree problem confirmed the existence of the star-tree paradox. When the data size n --> infinity, the posterior tree probabilities do not converge to 1/3 each, but they vary among data sets according to a statistical distribution. This distribution is characterized. Two strategies for resolving the star-tree paradox are explored: (1) a nonzero prior probability for the degenerate star tree and (2) an increasingly informative prior forcing the internal branch length toward zero. Both appear to be effective in resolving the paradox, but the latter is simpler to implement. The posterior tree probabilities are found to be very sensitive to the prior.

The point of this work is that if the data truly doesn't have any signal concerning an unresolved node, and we use a Bayesian phylogenetic inference package that doesn't allow multifurcations (every one except for Phycas as far as I know) the data set may (with non-vanishing probability) give very high confidence that one of the resolutions is correct. This is shown in this figure from Yang's paper (click to expand):

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See the deep red in the corners? That's showing that in replicate data sets there is a substantial probability that one of the resolutions will be very highly supported.

So, I can't comment on Phycas' usability, runtimes, etc, and Conditional Predictive Ordinates sound nice, but for me, proper support for polytomies is the headlining feature of Phycas. If anyone tries it out, please post here!

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