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June 28, 2015

00:20

–_000_D1B48D7EE0BEdb60standrewsacuk_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable Dear Evoldir, 4273pi is for those wishing to teach, learn or use research-grade bioinformatics on the low-cost Raspberry Pi computer. 4273pi includes Open Access teaching material and a customised Linux operating system for the Raspberry Pi. Coverage of particular interest to Evoldir includes: delimiting gene/protein families; multiple alignment and phylogeny; gene family evolution; looking at species differences; and function and evolution of enzymes. We are happy to announce 4273pi version 1.31. This has the best software and teaching material yet, and may be downloaded at: http://bit.ly/16toIJY For further details on 4273pi, see also: http://bit.ly/1aY6gRa and http://bit.ly/1Nn9QU3 - Daniel via Gmail

June 27, 2015

23:54

POSITION TITLE: Clinical Genomics Scientist, AncestryHealth LOCATION: San Francisco, CA AncestryHealth (http://bit.ly/1KicYAJ) is seeking a motivated, collaborative and talented computational biologist with experience in the analysis of clinical and genomic data. Working with a nimble team of geneticists, statisticians, computer scientists and epidemiologists, the Clinical Genomics Scientist will invent algorithms and methods to interpret our singular data set of genotypes, pedigrees and phenotypes. We are seeking applicants who are eager to develop novel ways to extract actionable and accurate clinical genomics discoveries for consumers. Requirements/Qualifications: * The successful candidate for the position will have an M.D. or Ph.D. in Computational Biology, Genetics, Statistics, Computer Science (or a related field). * The candidate must have a passion for using genomic data to advance healthcare, population health, and wellness. * Demonstrated excellence in algorithm development using “- omics” data in clinical applications is important. * The successful applicant will have a strong working knowledge of statistics and proficiency in one or more of Python, Java, C/C++ or R. * Excellent verbal and written communication skills are required. * Strong organizational and interpersonal skills will be needed in our fast-paced team. Interested? Here’s how to apply: Begin your online application http://bit.ly/1ICCZq1 or if you have any problems please submit your CV/resume to careers@ancestryhealth.com Please reference CLINICAL GENOMICS SCIENTIST in the subject field of your e-mail. Ancestry (www.ancestry.com) is a private equity owned company with large US offices in Provo, Utah, and San Francisco, as well as several international offices including London, Dublin, Munich, Toronto, and Sydney. Ancestry is the world’s largest online resource for family history with an extensive collection of over 13 billion historical records that have been digitized, indexed, and made available online over the past 15 years. These digital records and documents enabled Ancestry’s 2.7 million plus paying subscribers and over 12 million registrants to create nearly 60 million family trees. While most of Ancestry’s subscribers are in the US, the company has a strong presence in the UK, Canada, and Australia, and is in the process of a large international expansion into Eastern Europe and Mexico. In 2014, Ancestry had non-GAAP revenue of $619.5 million (up 10.3% YOY) and adjusted EBITDA of $214.8 million. AncestryDNA (www.ancestryDNA.com ) has become the fastest growing direct-to-consumer genomic company by providing consumers insights into their ancestral origins. A team of scientists leverages pedigrees, documents, demographics, and genomes to conduct innovative research in population – via Gmail

23:27

Dear All We have recently released the R package LEA that enables users to run genome-wide ecological association studies from the R command line. Genome-wide ecological association studies aim at detecting allele frequencies that exhibit significant statistical association with ecological gradients. Ecological association studies can provide lists of genetic polymorphisms that are potentially involved in local adaptation to environmental conditions through natural selection. The package LEA runs (very fast) STRUCTURE-like analyses of population structure, and performs genome scans for selection from large genomic data sets. It derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results. The package is available from the Bioconductor resource repository http://bit.ly/1TWf0Ld. Online documentations and tutorials are available from the authors’ webpages http://bit.ly/1NoZ277. See also the application note here: http://bit.ly/1TWeZXK If you have any questions or want to send feedback, do not hesitate to contact us at: olivier.francois@imag.fr Best regards, Olivier via Gmail

June 20, 2015

02:32

Graduate Position: CarletonU. (Ottawa, Canada): Evolution of Sex If interested in pursing an MSc or PhD in evolution of sex with Root Gorelick at Carleton University in Ottawa, please send the following information, preferably in a single e-mail attachment: (1) a thoughtful and passionate 1-2 page essay on why you would like to pursue this degree and your vision of what the research might entail (2) your CV (3) a scanned copy of your university transcript (4) contact information for at least two faculty members who could recommend you Tentative, less formal inquires are also welcomed. Funding is currently only available for citizens and permanent residents of Canada. My current interests in evolution of sex are in origins of meiosis and in differences between females and males. However, I am open to research projects in other areas of evolution of sex. I am especially interested in sex of organisms other than plants and animals, such as chromalveolates. Root Gorelick Carleton University Ottawa, Ontario, Canada Root.Gorelick@carleton.ca http://bit.ly/1TCUjDX Root.Gorelick@carleton.ca via Gmail

01:44
Hi, I m teaching Evolution for Biology students and now we are working about variation, genetic drift, gene flow and natural selection. When searching for videos in the internet about evolutionary mechanisms I saw many examples with incomplete explanations and also presenting the mechanisms in a way my students dont understand how they act together. I would like to know if some in the list have a good suggestion about an animation or video to be used in classroom. Thanks for any help! Prof. Dr. J. C. VOLTOLINI Grupo de Pesquisa e Ensino em Biologia da Conservação - ECOTROP Universidade de Taubaté, Departamento de Biologia Taubaté, SP. 12030-010. E-Mail: jcvoltol@uol.com.br * Grupo de pesquisa ECOTROP CNPq: http://bit.ly/1IUKFXt 35 * Currculo Lattes: http://bit.ly/1huRkbE * Assessoria Estatstica: http://bit.ly/OrqJnN * Fotos de Cursos e Projetos: http://on.fb.me/1K5JT9b VOLTOLINI via Gmail
01:44
INSTITUTO DE CIENCIASDEL MAR YLIMNOLOGÍA The Marine Science and Limnology Institute of the National Autonomous University of Mexico (UNAM) is opening a position as Full Time Associate Researcher level Cto be filled as fixed-term contract as described in Article 51 but with possibility of yearly renewals. SPECIALTY AREA: Genomics of Aquatic Organisms REQUIREMENTS: ·This position will be made available as part of the University’s Program for Renovating the Academic Staff, Subprogram for the Incorporation of Young Career Academics. The Program’s requirements specify that the candidates must be younger than 39 years of age for women and younger than 37 for men at the date of approval by the corresponding Technical Committee. ·Availability to settle in Mazatlán, Sinaloa (México). ·Minimal Academic Level: Ph. D., with two years of postdoctoral experience. ·A research project addressing national problems related to aquatic organisms using a Genomics approach must be proposed ·Proponent’s curriculum vitae without original documents, which should include 10 or more scientific papers published with SCI and IF, teaching experience and graduate and undergraduate theses directed BASE SALARY: $MXN 16,651.16 DEADLINE TO RECEIVE SUBMISSIONS: 27 July2015. Contact person: Dr. María Adela Monreal Gómez Academic Secretary ICML Phone number: (+52) (55) 5622-5772 E-mail:icmlsa@cmarl.unam.mx Samuel Gomez via Gmail
01:28
The University of Maryland Applications are invited for a Postdoctoral Associate position at the University of Maryland Institute for Bioscience and Biotechnology Research (IBBR). Position Summary Because species phylogenies (trees) are so widely used in the life sciences, there has been a major worldwide effort to determine trees for various groups and assemble them into a grand “Tree of Life” or ToL. While experts continue improving the ToL, our focus is on getting this knowledge into the hands of scientists, educators, and the general public, so that they can get online species trees as easily as they get online driving directions. In preliminary work, we organized community hackathons at which participants prototyped a web-services system, called “Phylotastic” (www.phylotastic.org), that aims to provide an open, distributed, community-owned system for efficient delivery of ToL knowledge. NSF recently funded a 3-year collaborative project to develop production system based on this prototype. Responsibilities will include participating in the design process, developing tools for specific use-cases (including educational ones), and playing a key role in software evaluation. The successful applicant will be part of a distributed, collaborative team including key personnel from IBBR, NMSU, UTK, OpenTree and GlobalNames. Qualifications: A Ph.D. in a relevant discipline is required. Understanding how and why scientists use phylogenies is critical. Typically this knowledge will come from research experience using phylogenies. Experience in scientific software programming is strongly preferred. Experience programming with phylogenies, or with web services, is desirable. Salary: Commensurate with qualifications. Applications: Applicants should send a (1) cover letter (include skills, suggested start date, and expected PhD date as needed); a (2) CV; (3) a short research statement; (4) Contact information for two references; and (5) link(s) to repositories with examples of code you have written or attachments including such code to: http://bit.ly/1d7dEvEwww.phylotastic.org), that aims to provide an open, distributed, community-owned system for efficient delivery of ToL knowledge. NSF recently funded a 3-year collaborative project to develop production system based on this prototype. Responsibilities will include participating in the design process, developing tools for specific use-cases (including educational ones), and playing a key role in software evaluation. The successful applicant will be part of a distributed, collaborative team including key personnel from IBBR, NMSU, UTK, OpenTree and GlobalNames. Qualifications: A Ph.D. in a relevant discipline is required. Understanding how and why scientists use phylogenies is critical. Typically this knowledge will come from research experience using phylogenies. Experience in scientific software programming is strongly preferred. Experience programming with phylogenies, or with web services, is desirable. Salary: Commensurate with qualifications. Applications: Applicants should send a (1) cover letter (include skills, suggested start date, and expected PhD date as needed); a (2) CV; (3) a short research statement; (4) Contact information for two references; and (5) link(s) to repositories with examples of code you have written or attachments including such code to: http://bit.ly/1d7dEvE Pre-submission inquiries are encouraged Closing Date: Review of candidates will begin on 06/20/2015 and will continue until the position is filled. The University of Maryland, College Park, actively subscribes to a policy of equal employment opportunity, and will not discriminate against any employee or applicant because of race, age, sex, color, sexual orientation, physical or mental disability, religion, ancestry or national origin, marital status, genetic information, political affiliation, and gender identity or expression. Minorities and women are encouraged to apply. Rita Varela via Gmail
00:56

Graduate Position: CarletonU. (Ottawa, Canada): Indigenous/Aboriginal perspectives in evolution and ecology If interested in pursing an MSc or PhD in Indigenous/Aboriginal perspectives in evolution and ecology with Root Gorelick at Carleton University in Ottawa, please send the following information, preferably in a single e-mail attachment: (1) a thoughtful and passionate 1-2 page essay on why you would like to pursue this degree and your vision of what the research might entail (2) your CV (3) a scanned copy of your university transcript (4) contact information for at least two faculty members who could recommend you. Tentative, less formal inquires are also welcomed. Funding is currently only available for citizens and permanent residents of Canada. Root Gorelick Carleton University Ottawa, Ontario, Canada Root.Gorelick@carleton.ca http://bit.ly/1TCUjDX Root.Gorelick@carleton.ca via Gmail

June 19, 2015

01:29

–001a113cf01edeeb8e0518ce7c47 Content-Type: text/plain; charset=UTF-8 Postdoc ad below. I’ll be at Evolution (Brazil), ESA (Baltimore), & Plant Genome Evolution (Amsterdam in September) this summer for anyone interested in meeting in person. A postdoc position is available in the lab of Jesse R. Lasky (laskylab.org) in the Department of Biology at The Pennsylvania State University, University Park, PA. Lab goals are to understand the processes that generate and maintain biodiversity, with a focus on spatiotemporal variation in high-dimensional systems. In particular, the lab studies genetic and ecological mechanisms of local adaptation to environment. Furthermore, the lab will pursue connections between local adaptation and community ecology, conservation, and agriculture. The primary study organisms are plants; currently including forest trees, Arabidopsis, and sorghum. Penn State University has research strengths in genomics ( http://bit.ly/1GUGZ8F and Genomics), plant biology ( http://bit.ly/1LmTtWg Biology), and ecology ( http://bit.ly/1GUH1xf) across departments and colleges. The postdoc will have freedom to develop new projects in the lab and to build collaborations with other labs.The position requires a PhD in Ecology, Evolution, Genetics, Plant Biology, Statistics, or a related field. The ideal candidate will have experience including population/landscape genomics, analysis of sequence data, GWAS methods, statistics, and computation (R, python, shell, HPC cluster). Complementary expertise in molecular biology, ecophysiology, and ecology is also of interest, but not required. Excellent communication skills, including writing, are required, as is a strong publication record. Applications must be submitted electronically at http://bit.ly/1LmTtWi and include a cover letter detailing experience and research interests, a current CV, and contact information for three professional references. The position is initially funded for one year, with possibility of refunding. Anticipated start date is Fall 2015, but this is flexible. Review of applications will begin on June 15, and continue until the position is filled. CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://bit.ly/1uz49No, which will also provide you with detail on how to request a hard copy of the Annual Security Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status. Job URL: http://bit.ly/1LmTtWi –001a113cf01edeeb8e0518ce7c47 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Postdoc ad below. I’ll be at Evolution (Brazil), ESA (Baltimore), & Plant Genome Evolution (Amsterdam in September) this summer for anyone interested in meeting in person.A postdoc position is available in the lab of Jesse R. Lasky (laskylab.org) in the Department of Biology at The Pennsylvania State University, University Park, PA. Lab goals are to understand the processes that generate and maintain biodiversity, with a focus on spatiotemporal variation in high-dimensional systems. In particular, the lab studies genetic and ecological mechanisms of local adaptation to environment. Furthermore, the lab will pursue connections between local adaptation and community ecology, conservation, and agriculture. The primary study organisms are plants; currently including forest trees, Arabidopsis, and sorghum. Penn State University has research strengths in genomics (http://bit.ly/1GUGZ8F and Genomics), plant biology (http://bit.ly/1LmTtWg Biology), and ecology (http://bit.ly/1GUH1xf) across departments and colleges. The postdoc will have freedom to develop new projects in the lab and to build collaborations with other labs.The position requires a PhD in Ecology, Evolution, Genetics, Plant Biology, Statistics, or a related field. The ideal candidate will have experience including population/landscape genomics, analysis of sequence data, GWAS methods, statistics, and computation (R, python, shell, HPC cluster). Complementary expertise in molecular biology, ecophysiology, and ecology is also of interest, but not require d. Excellent communication skills, including writing, are required, as is a strong publication record. Applications must be submitted electronically at http://bit.ly/1LmTtWi and include a cover letter detailing experience and research interests, a current CV, and contact information for three professional references. The position is initially funded for one year, with possibility of refunding. Anticipated start date is Fall 2015, but this is flexible. Review of applications will begin on June 15, and continue until the position is filled.CAMPUS SECURITY CRIME STATISTICS: For more about safety at Penn State, and to review the Annual Security Report which contains information about crime statistics and other safety and security matters, please go to http://bit.ly/1uz49No, which will also provide you with detail on how to request a hard copy of theAnnual Secur ity Report. Penn State is an equal opportunity, affirmative action employer, and is committed to providing employment opportunities to all qualified applicants without regard to race, color, religion, age, sex, sexual orientation, gender identity, national origin, disability or protected veteran status.Job URL: http://bit.ly/1LmTtWi –001a113cf01edeeb8e0518ce7c4 via Gmail
01:29
Computational Biologist - Population Genetics 23andMe Mountain View, CA, United States We are looking for a colleague with training and experience in computational biology to join our highly productive Research Team. This person will be involved in the analysis of human genetic data and the development of computational methods, which requires a mix of computational skills, statistical knowledge, creativity and biological insight. Who we are Since 2006, 23andMes mission has been to help people access, understand, and benefit from the human genome. We are a group of passionate individuals pushing the boundaries of whats possible to help turn genetic insight into better health and personal understanding. Our Research Team 23andMes Research Team prides itself on driving cutting edge, industrial-scale science that makes an impact which belies the teams size, in an environment and culture that fosters creativity, innovation, collaboration and fun. Our science has garnered the respect of many members of the broader scientific community. As 23andMe continues to grow, we are looking for people who are excited by the potential discoveries we can make with our innovative research framework. Who you are You have a medley of mathematical, statistical and computation skills and a passion for understanding evolution. You get motivated when working on something that feels valuable. You appreciate the power of statistics and believe in the value of accessing ones genetic information. You enjoy working as part of a team, are goal-driven and are excited to contribute to something that truly impacts peoples lives. What youll contribute to - Developing methods and performing genetic analyses that will advance the understanding of human genetics and shape 23andMes consumer product. - Long term R&D projects that bring research advances into 23andMes consumer product. - Providing scientific support to a variety of teams across the company, including communications and public relations, making scientific knowledge accessible to the average person. We hope you have - PhD in Computational Biology or related field such as Genetics, Computer Science, Engineering, Physics, Math, or Bioinformatics. - Strong bioinformatics and biostatistics background, with experience in algorithm development and machine learning approaches. - Evolutionary or population genetics research experience. - Track record of applying innovative methods to drive project success. - Strong programming skills, especially in scripting languages such as Python and R. - At ease in a Linux environment. - Familiarity with the fundamentals of human genetics. - Enthusiasm for working in a highly collaborative environment. - The ability to be proactive, thorough and independent, but also to work effectively within a dynamic, fast-paced and interdisciplinary team. Other skills we are looking for - Demonstrated record of developing and distributing tools for the analysis and visualization of genomics data. - Experience with C/C++, Django, HTML, Git. Apply online: http://bit.ly/1LmTrO1 ABOUT US 23andMe, Inc. is the leading personal genetics company. Founded in 2006, the mission of the company is to help people access, understand and benefit from the human genome. 23andMe has over 900,000 customers worldwide with over 80 percent consented to participate in research. 23andMe, Inc. is located in Mountain View, CA. More information is available at www.23andMe.com. Kasia Bryc via Gmail
01:29
The Research Programmer will develop and extend high performance software, manage data, and perform analyses to further computational genetics research. The lab does interdisciplinary research at the interface of computer science, genetics (primarily human genetics), and statistics, with a key emphasis on developing novel computational methods that can analyze massively sized datasets (tens to hundreds of thousands of samples). Responsibilities of the position include but are not limited to: * Development, maintenance, and support of high performance software packages for analysis of genetic data in order to infer relationships of samples to one another, the population of origin of regions of a sample’s genome, and other related genetic properties of samples. Includes implementing novel algorithms using data structures designed for efficient processing of huge datasets; providing documentation for users; and responding to occasional user questions and bug reports. * Assisting in genome-wide analyses. Includes developing scripts to parse, convert, and otherwise process large data sets; running analysis programs in parallel on large compute clusters; and integrating, organizing, and analyzing program output. * Development and maintenance of general software and data storage infrastructure of the lab. Includes organizing large data sets, software tools, and web resources, and supporting lab members and close collaborators in tool development and data analysis. Research in the Williams Lab aims to elucidate human genetic history, evolution, and the genetic basis of human disease, with a focus on uncovering population and individual relationships from the past several thousand years. The algorithms under development utilize machine learning techniques, including hidden Markov models (HMMs) and expectation-maximization (EM) approaches, and utilize specialized data structures to achieve high efficiency that scale to very large datasets. This work depends critically on the development and maintenance of efficient, reliable software tools, and the organization and management of large data sets. For more information on the lab’s research, see http://bit.ly/1makgwW. Qualifications: Required: * Bachelor’s degree in computer science, engineering or related field, and 3-5 years of experience in software development. * Experience with C/C++, high performance programming, and machine learning. Knowledge of algorithms, data structures, and object-oriented programming, and a familiarity with probability and statistics. * Experience in a Unix/Linux environment, including proficiency in shell scripting, and scripting in a language such as Perl or Python. * Strong interpersonal skills and ability to work as part of a diverse team, while contributing to a high-quality and respectful work environment. * Excellent oral and written communication skills, with the ability to communicate effectively to colleagues and staff across multi-disciplinary areas. * Ability to manage multiple projects in a dynamic environment with changing priorities. * Ability to help establish realistic goals and deliver work on schedule. * Ability to work independently and solve problems as they arise. * Interest in genetics, bioinformatics, and evolution, and willingness to learn concepts and terminology from these fields as needed. Preferred: * Master’s degree. * Some experience or training in bioinformatics. * Experience working with very large data sets and compute clusters. * Basic knowledge of statistics. * Experience with R and/or Matlab. * Coursework or job experience in genetics, molecular biology, or evolutionary biology. * Strong judgment, organization, and leadership skills, and a high capacity for critical, creative thinking. Amy Williams via Gmail
00:47

Multi-scale microbial dynamics in health and disease. The Brown lab is recruiting, with new postdoc and grad student positions available as part of an August move to the Georgia Institute of Technology (biology.gatech.edu). I am interested in candidates with experience in either computational and/or experimental approaches that are relevant to the study of microbial dynamics: Computational I am particularly interested in candidates with experience in statistical modeling and bio-informatics in an ecological/evolutionary context. Simulation and analytical approaches are also of interest, if coupled with experience of biological applications V ideally in microbiology/ecology/evolution. Experimental I am interested in candidates with strong backgrounds spanning molecular microbiology and ecology/evolution. Experience with Pseudomonas aeruginosa, quorum-sensing, regulatory evolution or mobile genetic elements is a plus. Research themes Bacterial sociality, cooperation, decision-making, quorum-sensing, biofilms, microbiomes, HGT, pathogen emergence, virulence, resistance, novel therapeuticsK (and ecology/evolution of all the above). To learn more, take a look at our website (http://bit.ly/1BncuHW) and recent relevant publications: Estrela S, Whiteley M, Brown SP. 2015. The demographic determinants of human microbiome health. Trends Microbiology 23, 134-141. McNally L, Viana M, Brown SP 2014. Cooperative secretions facilitate host range expansion in bacteria. Nature Communications. 5, 4594. Cornforth D, Popat R, McNally L, Gurney J, Scott-Phillips T, Ivens A, Diggle SP, Brown SP 2014 Combinatorial quorum sensing allows bacteria to resolve their social and physical environment. PNAS 111, 4280-4284. Allen R, Popat R, Diggle SP, Brown SP 2014 Targeting virulence: can we make evolution-proof drugs? Nature Reviews Microbiology 12, 300-308. To apply, please email a CV, brief description of research interests and how they relate to Brown lab themes (1 page) and the names and contact info for at least 3 references to Sam Brown (sam.brown@ed.ac.uk). Review of applications will begin on July 6th and continue until positions are filled. Start dates are flexible, with preference for early 2016. via Gmail

00:25

Dear Member, *Postdoctoral Position in plant breeding methodology to optimise selection schemes and selection indices for the improvement of grassland species mixtures at INRA URP3F (France)* _POSITION DESCRIPTION._ The INRA URP3F research unit is seeking for a post-doctoral researcher to contribute to a collaborative research project (PRAISE) granted by the ANR 2013 call Bioadapt. PRAISE is a pluridisciplinary project at the crossroad of Quantitative and Population Genetics, Ecophysiology and Functional Ecology. It aims to identify the best genetic composition of sown grassland mixtures and to provide the bases of innovative selection methods of grassland species for their use in mixture. This post-doctoral research will develop a theoretical analyse of selection schemes designed to improve grassland species for their use in mixture and will set up a new selection index method to reach optimal compromise between directional selection on some traits and conservation of diversity on others. Theoretical analyse of selection schemes for the use of grassland species in mixtures. The usual selection scheme of grassland species is a recurrent selection scheme based on the agronomic assessment of half-sib progenies. Half-sib progenies are usually tested in pure mono-specific stands although grassland species are commonly sown in mixtures of several grass and legume species. However, previous results obtained at INRA UR P3F suggest that the agronomic value of genotypes in pure stands correlates quite poorly with their value in mixtures of two or more species. It is thus necessary to conceive selection schemes in which half-sib progenies of a species would be tested in micro-assemblages with other species. Such selection schemes can be considered as multi-species selection schemes in which several species would be simultaneously improved. At each selection cycle, half-sib progenies of a given species would be tested in factorial micro-assemblages with other species. Different factorial micro-assemblage designs can be conceived with different emphasis on the general and specific abilities for association in pluri-specific mixtures (GAA and SAA, respectively). The post-doctoral research will aim to define the relative efficiency of several factorial micro-assemblage designs according to values of GAA and SAA on the basis of theoretical expectations of genetic gains. These expected genetic gains will also be compared to the correlative response of mixture performance obtained with parallel classical selection schemes based on the test of pure stands of half-sib progenies, according to the value of the correlation of pure stand performances with GAA and SAA. Finally, field assays from INRA UR P3F will provide experimental values of GAA, SAA and of their correlation with pure stand performances to practically identify the best selection design. Optimisation of selection indices. The selection methods used in plant breeding are inherently directional and reduce genetic variability. They allow maintenance of variability only for traits genetically unrelated to traits submitted to selection. Usually, the control of selection on several traits is obtained by choosing candidates to selection based on the value of an index, i.e. a linear combination of the estimated breeding values of candidates for traits being selected. The coefficients of the index are determined using a constraint system based on expectations of genetic gains. The post-doctoral fellow will complete this constraint system by applying additional constraints to maintain sufficient genetic variance of some traits and will set up an operational research script to solve this constraint system. This improved index selection method will enable to deal with the trade-off between selection on some traits and conservation of diversity on others, which is of primary importance to release improved populations of grassland species for creating species mixtures able to cope with various environmental conditions. _REQUIREMENTS._ The post-doctoral fellow is expected to have a background in quantitative genetics, statistics, applied mathematics and agronomic sciences. _CONDITIONS._ The post-doctoral fellow will be hosted at the INRA URP3F research unit in Lusignan (France) where he will get support from Jean-Paul Sampoux (responsible of work-package about selection methodology of PRAISE) and Isabelle Litrico (coordinator of PRAISE). The appointment is for one year duration; starting date is wished between October 1st 2015 and January 1st 2016. _HOW TO APPLY._ Candidates can apply by sending a copy of their CV and a cover letter to J.P. Sampoux and I. Litrico (jean-paul.sampoux@lusignan.inra.fr; isabelle.litrico@lusignan.inra.fr) best regards, via Gmail

June 16, 2015

02:24

A 3 year post-doctoral position, including a 25% teaching component, is available at the University of Turku, Finland to work in Prof. Craig Primmer’s research group (http://bit.ly/1GJxNWk). The research component of the position is a part of a research consortium that aims at integrating evolutionary genetics, ecological modelling and environmental sociology to understand the external drivers of life history changes in a heavily fished Atlantic salmon population complex and to advance sustainable use of these aquatic natural resources. This project has been recently funded as a part of the Finnish Academy Arctic Research program (http://bit.ly/1cXXPXY) The post-doc will be responsible for conducting and co-supervising research investigating the genetic basis of life-history traits such as age at maturity (e.g. Johnston et al. 2014) and repeat spawning, as well as conducting genome scans for identifying genes involved in adaptation to local environmental conditions. Teaching will involve giving lectures and computer classes on topics related to the position. Suitable candidates will have a strong background in evolutionary genetics/genomics and/or quantitative genetics research (in any species). Experience with the methodologies for analysis of large-scale SNP and high-throughput sequencing data is an advantage, as is an interest in conservation genetics and fisheries management. Undergraduate teaching experience is also advantageous. Informal inquiries should be directed to Prof. Craig Primmer (craig.primmer@utu.fi). Formal applications should include a CV (with names and contact details of at least two referees), a publication list, an academic portfolio and a max. 2 page letter of motivation and can be submitted at http://bit.ly/1GJxNWm. The deadline for applications is August 3, with the preferred starting date being January 2016 or earlier. The position is available until the end of 2018. The starting salary is approx. 3140 - 3500 EUR per month, depending on the previous relevant research and teaching experience of the candidate. Turku, Finland’s 5th largest city (176 000 people), is located in the southwestern Finland. It has a rich cultural history and is the gateway to a beautiful archipelago. The University of Turku is one of the major multidisciplinary universities in Finland and is ranked in the top 5% of universities in the world. Johnston et al. (2014) Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar). Molecular Ecology 23: 3452-3468 via Gmail

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ANNOUNCEMENT / REMINDER Dear EVOLdir subscriber Applications are open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: June 28th 2015 Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://bit.ly/1BjCdko Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro via Gmail

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**LAST CALL - LIMITED SPACES AVAILABLE** THIRD INTERNATIONAL ENVIRONMENTAL ‘OMICS SYNTHESIS CONFERENCE - IEOS2015 University of St Andrews 6-8 July 2015 http://bit.ly/1HHj0eI DEADLINE for registration and abstract submission (posters only): EXTENDED to 19 June 2015 DEADLINE for application for postgraduate student bursaries: EXTENDED to 19 June 2015 STUDENT BURSARIES: Postgraduate students who submit abstracts are eligible for a bursary, covering 100% of the registration fee. When submitting an abstract, students should indicate they wish to be considered for a bursary. Successful applicants will receive a code for FREE registration. KEYNOTE SPEAKERS: Professor ELIZABETH THOMPSON, University of Washington http://bit.ly/1GJFnOS Professor MARK BLAXTER, University of Edinburgh http://bit.ly/1AG0jpq Professor BARBARA METHE, J Craig Venter Institute http://bit.ly/1R3mPud INVITED SPEAKERS: Dr LOGAN KISTLER, University of Warwick http://bit.ly/1GJFkm9 Dr UMER ZEESHAN IJAZ, University of Glasgow http://bit.ly/1R3mPuf Professor JIANQUAN LIU, Lanzhou University http://bit.ly/1R3mPuh Dr NATHAN BAILEY, University of St Andrews http://bit.ly/1GJFkmd Professor C-H CHRISTINA CHENG, University of Illinois at Urbana-Champaign http://bit.ly/1R3mPuj Dr DAVID MARSHALL, James Hutton Institute http://bit.ly/1GJFnOW Professor DAVID WALLOM, Oxford University http://bit.ly/1R3mPup Professor DANNIE DURAND, Carnegie Mellon University http://bit.ly/1GJFnP1 IEOS2015: The aim of this conference is to bring together researchers and organisations from a range of disciplines with shared interests in the development of new approaches for data handling, generation and analysis in environmental omics. Science areas of interest include bioinformatics, DNA-barcoding, genomics, metagenomics, metabarcoding, transcriptomics, proteomics, metabolomics, epigenetics, evolutionary and ecological omics, phylogenetics, study of ancient DNA and anthropology, new tools, resources and training, and beyond as applied to the study of the natural environmental and environmentally relevant organisms and systems. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the consolidation of a wider integrated environmental 'omics community. EOS and this conference are supported by Natural Environmental Research Council (NERC) through its Mathematics and Informatics for Environmental 'Omics Data Synthesis programme and the UK Science and Technology Facilities Council (STFC) Global Challenges programme. PRE- and POST- MEETING WORKSHOPS http://bit.ly/1R3mPur 6 July - training workshops provided by the NERC Biomolecular Analysis Facility Gene expression analysis Metabolomics workshop Restriction-site Associated DNA (RAD) Data Analysis eDNA & metabarcoding 9 July Analyzing environmental DNA: Bio-Linux on the EOS Cloud (T. Booth, CEH Wallingford) >From reads to genes, a NGS analysis (Dr M. Pinheiro, University of St Andrews) SUMMER OF V’S IEOS2015 attendees are also welcome at a separate meeting on Data Science, The Summer of V’s, immediately preceding the main registration event for IEOS. Separate registration is required for the Summer of V’s: http://bit.ly/1R3mRT6 IEOS2015: http://bit.ly/1HHj0eI With best wishes, Professor Thomas Meagher, Chair The IEOS Conference Organising Committee http://bit.ly/1R3mPus The University of St Andrews is a charity registered in Scotland : No SC013532 Professor Thomas R. Meagher School of Biology, Sir Harold Mitchell Building University of St Andrews St Andrews KY16 9TH UK +44(0)1334 463364 office +44(0)7793356889 mobile +44(0)1334 463366 fax http://bit.ly/1IUL9NW Thomas Meagher via Gmail
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We will welcome and give full support to postdoc applications for a Marie Curie fellowship (deadline 10 september 2015) in the fields of evolutionary ecology, infectious disease ecology and conservation biology. We particularly welcome applications related to evolutionary ecology of host-parasite interactions, ecology of infectious diseases, movement ecology (dispersal, connectivity, invasive species) and landscape genomics. We are a dynamic and internationally oriented research group with three Faculty members (Herwig Leirs, Erik Matthysen, Stefan Van Dongen), several postdocs and 10-15 PhD students. Our main model systems are birds and mammals, including their parasites and infectious diseases, in both temperate and tropical systems. We combine field research with state-of-the-art modelling and molecular approaches. We are core members of two of the nine currently recognized Excellence Consortia in the University of Antwerp (Global Change Ecology and Infectious Diseases). We will be happy to discuss possible projects and assist candidates with applications for Marie Curie funding, as well as other funding options such as FWO postdoctoral fellowships. For more information on our projects and job opportunities, see our website at http://bit.ly/1GJr26P. Erik Prof. Dr. Erik Matthysen Evolutionary Ecology Group University of Antwerp Groenenborgerlaan 171, B-2020 Antwerpen 03 265 3464 Matthysen Erik via Gmail
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A postdoctoral position in evolutionary genomics is available in the Vicoso group at the Institute of Science and Technology, Austria. The general focus of the lab is the evolution of sex chromosomes, which we investigate using a combination of experimental and computational approaches. Questions that motivate our research include: why do some Y/W chromosomes degenerate while other remain homomorphic? What forces drive some species to acquire global dosage compensation, while others only compensate specific genes? What are the frequency and molecular dynamics of sex-chromosome turnover? The successful applicant will apply comparative genomics analyses to a wide variety of species, and combine them with population DNA and gene expression data, to achieve a better understanding of the evolutionary and molecular forces driving sex chromosome differentiation. Candidates wishing to work on a specific project in sex chromosome evolution are also encouraged to apply. Applicants should have obtained, or anticipate obtaining by the start date, a PhD in biology, genetics, bioinformatics, or a related field. A strong background in one or more the following areas is highly desired: • comparative genomics • molecular evolution • population genetics • bioinformatics The initial appointment is for two years, with the possibility of extension and a minimum salary of 49,070 Euros per year (gross). IST Austria (www.ist.ac.at) is a young and vibrant institute dedicated to basic research, with a strong focus on evolutionary biology (other EB groups include those of Nick Barton, Jonathan Bollback, and Sylvia Cremer) and ties to several evolutionary groups in the area (http://bit.ly/1pSDzd6). We are located on the outskirts of Vienna, and the official language of the institute is English. To apply, send a short summary of research interests, a CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (bvicoso@ist.ac.at). The review of applications will start on July 1st and continue until the position is filled. The start date is flexible, but an earlier start would be preferable. More information on the lab is available at: http://bit.ly/1QAnLvawww.ist.ac.at) is a young and vibrant institute dedicated to basic research, with a strong focus on evolutionary biology (other EB groups include those of Nick Barton, Jonathan Bollback, and Sylvia Cremer) and ties to several evolutionary groups in the area (http://bit.ly/1pSDzd6). We are located on the outskirts of Vienna, and the official language of the institute is English. To apply, send a short summary of research interests, a CV, up to three relevant publications/manuscripts, and the names and contact information for three references to Beatriz Vicoso (bvicoso@ist.ac.at). The review of applications will start on July 1st and continue until the position is filled. The start date is flexible, but an earlier start would be preferable. More information on the lab is available at: http://bit.ly/1QAnLva Beatriz Vicoso via Gmail

June 15, 2015

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*Laboratory technician in population genomics* *Louis Calder Center, Fordham University* *Armonk, NY 10504* *DUTIES & RESPONSIBILITIES* The Munshi-South Lab at the Louis Calder Center, Fordham Universitys biological field station, is looking for a lab technician to join a dynamic research group and contribute to a number of projects that use population genomic tools to address fundamental questions about the evolution of urban wildlife. The research technician will be involved in collecting and analyzing molecular datasets, with a particular emphasis on RAD-Seq and whole genome resequencing. Particular molecular techniques will include DNA extraction, DNA quantification, restriction digests, ligations, and gel electrophoresis. Running and maintenance of a liquid handling robotic platform will also be part of the technicians duties. The technician will share responsibility for day-to-day lab operations including laboratory administration, sample and data organization, and mentoring undergraduate researchers. The position may also include occasional assistance with field work, including trapping and sample collection from mammals, amphibians, and insects. More information about research activities in the Munshi-South Lab is available at http://bit.ly/1Ca7jGg *QUALIFICATIONS:* *Required:* Bachelor’s degree in Biology (or related field) with at least six months of experience with molecular wet-lab research, and excellent organizational skills. Ability to communicate clearly, work independently, and interact collaboratively is essential. *Preferred: *Experience with RADSeq or SNP genotyping; familiarity with Geneious, R, or programming languages (e.g. Python / PERL). *SALARY & APPOINTMENT INFORMATION* The initial term of appointment is for one year, with renewal for a second year contingent on satisfactory progress. The pay rate is $17.50 / hour for up to 35 hours / week (i.e. $32,000 annually). The Calder Center is located 25 miles north of New York City, and has the advantages of an idyllic, forested setting and potential for subsidized housing. *APPLICATION PROCEDURES* To apply for this position, please send application materials as a single PDF to Jason Munshi-South at jmunshisouth@fordham.edu. A complete application will include a cover letter explaining your research interests and qualifications for the position, a CV, and contact information for up to three professional references. Full consideration will be given to complete applications received by *13 July 2015*. Jason Munshi-South, Ph.D. Associate Professor Louis Calder Center & Dept of Biological Sciences Fordham University Armonk, NY 10504 jmunshisouth@fordham.edu (914) 273-3078 ext 20 http://bit.ly/1Ca7jGg jason.munshisouth@gmail.com via Gmail