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November 25, 2014
Conference: Lausanne.ESEB2015_VariationInNaturalSelection.Aug10-14 Dear evoldir members, You have probably noticed that you can now register for the XVth ESEB Meeting which will be held in Lausanne on August 10th-14th 2015. If you are interested in how natural and sexual selection vary in time and space, from an evolutionary or ecological perspective, using theoretical or empirical tools, please check out our symposium n28: Variation in natural selection: patterns, causes, and consequences A more detailed abstract for this symposium can be found below and on the ESEB website: http://bit.ly/1AEbj5O (n28) ** Our invited speakers: Dr Christina Caruso (University of Guelph, http://bit.ly/15kDJE4) Dr Luis-Miguel Chevin (CNRS, Montpellier, http://bit.ly/1v8ILMh) ** Deadline for abstract submission (for contributed talks and posters): 10th January 2015. http://bit.ly/11NqzxR submission/. We look forward to receiving your contributions and discussing this subject in Lausanne, Anne Charmantier & Michael Morrissey Dr Anne Charmantier CNRS, Montpellier, France email@example.com Dr Michael Morrissey University of St Andrews, UK firstname.lastname@example.org Symposium Title : Variation in natural selection: patterns, causes, and consequences Despite longstanding interest in the dynamics of selection in space and time and its impact on adaptive evolution, the topic has been remarkably resistant to general empirical progress. This symposium will gather contributions that address the following fundamental questions using theoretical, empirical and experimental approaches: How much does natural/sexual selection vary in time and space? What is the evolutionary importance of fluctuating selection? In particular, can variation in selection explain evolutionary stasis, that is, the absence of microevolution in traits that are heritable and appear under strong directional selection? What are causes (ecological drivers) of variation in selection? Under what conditions does spatial variation in selection lead to local adaptation? These long-standing questions may remain unresolved in part because of a lack of a conceptual framework to guide empirical studies. Recent theoretical and synthetic studies have begun to provide such a framework. We will bring together theoreticians and empiricists, and people who have recently been developing methods specific to understanding variation in selection. The symposium with therefore be particularly timely in moving this topic forward. CHARMANTIER Anne via Gmail
WHERE: Weggis, Switzerland WHAT: Winter School “Bioinformatics for Adaptation Genomics: Adaptation genomics in the realm of Next-Generation Sequencing data analysis” WHEN: 1 – 7 March 2015 The rapid development of next-generation sequencing technologies and their application to adaptation genomics research holds great promise to increase our understanding of genotype-phenotype-environment interactions, and the pioneering findings of recent years have inspired the launching of genome-scale projects in an ever-increasing number of organisms. A great effort has been made to develop software that can handle the large datasets that typically characterise ecological genomics studies, while still providing robust analytical platforms for supporting their application in non-model systems. However, due to the sheer number and complexity of available packages, it is often difficult for investigators to assess the potential and limitations of alternative methods, and determine which are best suited for their particular question and dataset. This winter school aims at providing an opportunity for investigators to gain insight into the rationale behind some of the established analytical pipelines in adaptation genomics research and acquire knowledge on the best practice to perform analyses and experimental design. The School aims to address primarily evolutionary biologists and bioinformaticians who want to gain deeper knowledge on state-of-the-art methods to detect adaptive patterns from genome-wide nucleotide data. Applications from early career researchers (PhD and post-doctoral level) as well as faculty with a background in ecology, genetics, or bioinformatics will be considered. The workshop is particularly aimed at candidates with experience of the Unix environment and with previous practice on analytical pipelines for genomic data. Participants will be requested to bring their own laptop with which to connect to the server for the practical sessions. The school will have a limited number of participants (ca. 30) and lecturers (5). AIM & OBJECTIVES The Winter School provides an opportunity for investigators to penetrate the ‘black box’ behind the complex approaches available for investigating adaptation genomics throughout the analytical pipeline; from the assumptions and requirements necessary to produce a high quality SNP dataset from raw next-generation sequence data, to the in-depth interpretation of methods designed to detect signature of selection, demographic patterns and associations between genotypes and environment, and/or phenotypes. Specifically, the following objectives will be addressed: •the rationale and assumptions intrinsic to different available analytical approaches •comparison of the implementation and results of alternative analytical methods as applied on the same or similar datasets •interpretation of the outputs from the programs at different stages in the analysis •best practice to implement the available packages when addressing different evolutionary questions, and how this conditions experimental design Lessons will include initial lectures on the theoretical background of the programs and practical demonstrations given by the instructor followed by hands-on exercises performed by the participants under guided supervision. Computing activity will rely on individual connections to the Genetic Diversity Centre (GDC, ETH Zurich) server that will provide resources for demonstrations and practical training. Emphasis will be given to interpretation of the output of the programs, with slots of discussion time allowed to facilitate interactions between the instructor and the audience. VENUE The school will be hosted at the Alexander & Gerbi Hotel in Weggis, Switzerland (http://bit.ly/1rmxTqb). Weggis is a scenic town located on the shore of Lake Lucerne in central Switzerland. The location was chosen to provide a friendly and stimulating work environment. The area is known for its relaxing character in a peaceful mountain scenery. Full board (Breakfast, Lunch, Dinner and coffee breaks) and lodging in double rooms will be provided at the Alexander & Gerbi Hotel during the workshop, and is paid by ESF and ACE. REGISTRATION We ask that all interested participants submit a cover letter (1 page max) detailing their research interests, their level of bioinformatics experience, and motivation for attending the workshop, as well as their CV (2 pages max) to BioinfAdapt@env.ethz.ch by December 15th 2014. Participants will be notified of the outcome of the selection process by December 23rd 2014. For competing applications, priority will be given first to applicants from the contributing member countries of the congenomics network, then to candidates from ESF member and ESF non-member countries in Europe. Member countries of the congenomics network are: Belgium, Denmark, Finland, Germany, Greece, Italy, Luxembourg, Netherlands, Norway, Portugal, Spain, Sweden and Switzerland. ESF member countries: http://bit.ly/1rmxTqe The workshop is supported by the ESF and ACE programmes. Registration is free and all accommodation and meals are sponsored by these grants. Travel costs will be reimbursed up to a maximum of CHF200 after the School. The reimbursement of travel costs (train, bus, and plane) is subject to receipt of the original travel tickets (or electronic tickets with indication of price). Updated information is available here: http://bit.ly/1rmxTqg Registration deadline: December 15th 2014 // Notification of acceptance: December 23rd 2014 “Vergeer, Philippine” via Gmail
*A PhD position *is available. In**the Max Planck Research Group “Environmental genomics”headed by Pr. Dr. Eva H. Stukenbrock and affiliated with the Christian-Albrechts University of Kiel and the Max Planck Institute for Evolutionary Biology, Plön, Germany. This position at payment class TV-L 13 (dependent on qualifications) is at 65% level and includes teaching. Start of the position is February 2015. The dual affiliation of the group provides a unique opportunity to benefit from two distinct environments and develop relationships with departments from both institutes. The candidate will have a contract with the Christian-Albrechts University of Kiel. /Background/ The group works on adaptation of parasites to their host and host driven speciation using different plant pathogenic fungi. A main goal of our research is to understand the underlying molecular mechanism of species divergence and adaptive processes in host-pathogen systems. To this end, we combine molecular biology, microscopic and bioinformatic approaches. A recent topic in the group is the importance of histone modifications in host-pathogen interactions as well as genome dynamics. /Relevant papers/ Soyer JL et al., PLoS Genet., 2014 Giraldo MC & Valent B, Nat. Rev. Microbiol., 2013 Stukenbrock EH et al., Genome Res., 2011 de Jonge et al., 2011 Curr. Opinion Plant Biology, 2011 /Objectives/ This PhD project will focus on the characterization of effector candidate genes in the fungal wheat pathogen /Zymoseptoria tritici/. The PhD student will select promising candidate effector genes by combined analysis of “omics” datasets (transcriptomes, genomes and genome wide histone maps) generated in the team. A functional characterization of these candidate genes will be the main objective of the PhD project. This work will include gene deletions, in-vitro and in-planta assays, expression analyses and protein characterization. The project will further aim to understand the role of the particular candidate genes in host specialization by analyses of orthologs of the candidate genes in closely related species of /Z. tritici/. /Prerequisites/ We are looking for a highly motivated and autonomous candidate, with good communication skills. The daily language in the group is mainly English. Candidates with solid knowledge in molecular biology, molecular evolution and phytopathology are strongly encouraged to apply. Interests for epigenetics and / or experience for analyses of high-throughput “omics” data will be an advantage. The PhD candidate is expected to become a member of the International Max Planck Research School for Evolutionary Biology (see _http://www.evolbio.mpg.de/6269/aboutIMPRS_). Kiel University is an equal opportunity employer and is committed to increasing the proportion of female scientists in research and teaching, and strongly encourages female applicants. Women will be given preference in case of equal suitability, competence, and professional performance. The University is also committed to the employment of disabled persons, and such individuals will be accorded preference if suitable. Applications by people with a migration background are particularly welcomed. Please refrain from submitting application photos. /Contact/ Application should be sent as a single pdf file by e-mail to Pr. Dr. Eva H. Stukenbrock email@example.com _, cc. Dr. Jessica L. Soyer firstname.lastname@example.org _ before December 15th. The position will however remain open until filled. The application should include a short CV, names and contact information of two referees, report of previous research (4 pages max.) and results of the Master degree. “Jessica L. Soyer” via Gmail
November 24, 2014
Dear evoldir members, We would like to announce the symposium “Groups versus individuals: levels of selection in microbial systems” at the upcoming ESEB 2015 conference and would like to invite abstract submissions. This symposium focuses on how different levels of selection shape the link between genotype and phenotype in microbial systems. A number of recent discoveries have revolutionized our understanding of the molecular mechanisms that govern the expression of microbial phenotypes as well as the selective conditions that determine their evolution in the long-run. For example, microbes combine stochastic molecular processes with signals they receive from their environment and from conspecifics to produce phenotypic diversity in clonal populations, and to engage in behaviours that have selective consequences for themselves as well as for the group. Moreover, by combining metabolic functions among microorganisms of the same or different species, new group-level phenotypes can emerge that drastically impact selection acting on individual cells. The aim of this symposium is to discuss how selection at different levels of biological organization affects the expression of phenotypes as well as to analyse how cell-level phenotypes can promote functionality at the level of groups. By drawing together empirical and theoretical contributions from evolutionary and quantitative biology, this interdisciplinary symposium will facilitate discussions among scientists that otherwise would not meet and help to identify future research avenues. * Invited speakers: Thierry Emonet (Yale University) http://bit.ly/1yatD2Y Martin Polz (Massachusetts Institute of Technology) http://bit.ly/1FmvfXO * Organisers: Christian Kost (Max Planck Institute for Chemical Ecology) http://bit.ly/1yatD32 Martin Ackermann (ETH Zürich) http://bit.ly/1FmvfXQ * Deadline for submission for abstracts for contributed talks and posters is 10th January 2015. More information can be found at http://bit.ly/11NqzxR submission/ . We look forward to receiving your submissions and to seeing you at the conference and our symposium. *Dr. Christian Kost* VW Research group leader Experimental Ecology and Evolution Group Department of Bioorganic Chemistry Max Planck Institute for Chemical Ecology Beutenberg Campus Hans-Knöll-Straße 8 D-07745 Jena Germany Tel.: ++49 (0)3641 57 1212 Fax.: ++49 (0)3641 57 1202 Email: email@example.com http://bit.ly/1FmvfXU http://bit.ly/1yatBZ1 firstname.lastname@example.org via Gmail
Dear colleagues, We are pleased to invite submissions for the ESEB 2015 symposium: HOST DEFENSE IN A PARASITIZED WORLD: SELECTION, EVOLUTION AND THE MAINTENANCE OF VARIATION SYMPOSIUM DESCRIPTION: Infectious diseases are assumed to be among the most important selective forces in nature. Yet, phenotypic traits involved in host defense against parasites and pathogens, and their underlying genes, often exhibit considerable variation. This symposium aims to integrate studies of selection on host defense at the phenotypic and molecular genetic level across diverse taxa to advance our understanding of how defense mechanisms evolve and how parasite- and pathogen-mediated selection can maintain variation in host defense, both at the level of the individual and the population. The symposium will take place during the 15th Congress of the European Society for Evolutionary Biology (ESEB 2015, August 10-14, Lausanne, Switzerland). REGISTRATION: Deadline: 10 January 2015 http://bit.ly/1twJGll INVITED SPEAKERS: ANDREA L: GRAHAM (Princeton University, USA) http://bit.ly/1yatCMw BRIAN P. LAZZARO (Cornell University, USA) http://bit.ly/1FmvfXK ABSTRACT SUBMISSION: When submitting your abstract, please state your preference for a talk or a poster. Abstracts will be selected by early March. Should you have any question, please, do not hesitate to contact the organizers: Barbara Tschirren (email@example.com) Lars Rberg (firstname.lastname@example.org) We are looking forward to seeing you in Lausanne! Barbara & Lars Barbara Tschirren Institute of Evolutionary Biology and Environmental Studies University of Zurich, Switzerland Lars Rberg Department of Biology Lund University, Sweden via Gmail
November 23, 2014
The Department of Natural History of the University Museum of Bergen (University of Bergen, Norway) is seeking a new Head of Department, with management and scientific responsibilities. Please see full announcement at: http://bit.ly/1vhh3xY Deadline: 15 December 2014 Further details about the position can be obtained from Prof. Henrik von Achen (Director), e-mail email@example.com, telephone (+47) 55583120, mob. (+47) 92445843. Manuel Malaquias, Associate Professor Department of Natural History University Museum of Bergen University of Bergen PB7800 5020 Bergen Norway http://bit.ly/1FibdzI http://bit.ly/1vhh5pH “Manuel Antonio E. Malaquias” via Gmail
Infographics have become very popular in recent decades, with the advent of computer graphics packages. Infographics combine data and pictures, trying to produce an aesthetically pleasing but still informative presentation of numeric information. Recently, the following book appeared:
The Infographic History of the World (2013)
by Valentina D’Efilippo & James Ball
HarperCollins (UK) / Firefly Books (US)
A selection of the the infographics can be perused at the senior author's web page:
http://www.valentinadefilippo.co.uk/ihw/At the visual.ly blog the author also explains her intentions:
The Infographic History of the World is a new book that continues to push the field of infographics forward. Our task required research, organization and the selection of topics. Then, we needed to decide how to display data in order to tell a coherent and compelling story. We have never considered this to be an alternative to tons of books of history, but hopefully a refreshing interpretation of what history is about. With this book, we hope to lead readers on a journey, to interpret the data and find the implications that resonate with them. We don’t pretend that every set of data presents an unquestionable truth. And, rather than looking to define the world’s history, we were looking to present readers with an unconventional interpretation of the subject.Sadly, these good intentions have not always been achieved. As noted by a review at Amazon:
the book showcases *clever* ways of displaying data, not *clear* ways of displaying it ... Far too often I had to pore over the graphic to figure out what it was trying to say.What is worse for the readers of this blog, the information is not always correct. Consider this version of the Tree of Life, which has a long-standing tradition in systematics as one of the world's first examples of an infographic:
Click to enlarge.
Quite a number of the taxonomic labels are misplaced. You can check them for yourselves, but here is a selection of some of the surprising information contained in this infographic:
Quick notes on an experimental feature I've added to BioNames. It attempts to identify possible taxonomic synonyms by extracting pairs of names with the same species name that appear together on the same page of text. The text could be full text for an open access article, OCR text from BHL, or the title and abstract for an article. For example, the following paper creates a new combination, Hadwenius tursionis, for a parasite of the bottlenose dolphin. This name is a synonym of Synthesium tursionis.
Fernández, M., Balbuena, J. A., & Raga, J. A. (1994, July). Hadwenius tursionis (Marchi, 1873) n. comb. (Digenea, Campulidae) from the bottlenose dolphin Tursiops truncatus (Montagu, 1821) in the western Mediterranean. Syst Parasitol. Springer Science + Business Media. doi:10.1007/bf00009519
The taxonomic position of Synthesium tursionis (Marchi, 1873) (Digenea, Campulidae) is revised, based on material from 147 worms from four bottlenose dolphins Tursiops truncatus stranded off the Comunidad Valenciana (Spanish western Mediterranean). The species is transferred to Hadwenius, as H. tursionis n. comb., and characterised by a high length/width ratio of the body, spinose cirrus and unarmed metraterm. Synthesium, a monotypic genus, becomes a synonym of Hadwenius. The intraspecific variation of some morphological traits is briefly discussed.
If we extract taxonomic names from the title and abstract we have the pair (Synthesium tursionis, Hadwenius tursionis). If we do this across all the text currently in BioNames then we discover other pairs of names that include Synthesium tursionis, joining these together we can create a graph of co-occurrence of names that are synonyms (see Synthesium tursionis).
Synthesium tursionisHadwenius tursionisDicrocoelium tursionisDistomum tursionisOrthosplanchnus tursionisSynthesium (Orthosplanchnus) tursionis
These graphs are computed automatically, and there is inevitably scope for error. Taxa that are not synonyms may have the same specific name (e.g., parasites and hosts may have the same specific name), and some of the names extracted from the text may be erroneous. At the same time, anecdotally it is a useful way to discover links between names. Even better, this approach means that we have the associated evidence for each pair of names. The interface in BioNames lists the references that contain the pairs of names, so you can evaluate the evidence for synonymy. It would be useful to try and evaluate the automatically detected synonyms by comparisons with existing lists of synonyms (e.g., from GBIF).
November 22, 2014
Position: Lab Technician in the Conservation Genetics Lab of the Missouri Botanical Garden. * Hourly * Full Time, Regular * Full Benefits The Center for Conservation and Sustainable Development (CCSD) at the Missouri Botanical Garden explores and implements new, science-based approaches to the conservation and sustainable use of plant diversity. CCSD’s strategies for conservation are based on a sound, scientific understanding of the occurrence and distribution of plants. CCSD applies the knowledge of plant diversity accumulated by Missouri Botanical Garden researchers over many years, making that knowledge usable for conservation planning and decision-making. Operating under the auspices of the Garden and as part of its division of Science and Conservation, CCSD builds upon the Garden’s institutional expertise, scientific programs, influence and resources. Summary: Lab Technician at the Conservation Genetics Lab Under the direction of the Assistant Scientist, works on projects that employ genetic analyses (DNA metabarcoding, genotyping-by-sequencing, and microsatellites) to help provide information that will contribute to the management of species of conservation concern. Essential Duties and Responsibilities: * Carries out DNA extractions, gel electrophoresis, PCR, sample quantification, preparation and submission of samples for genotyping, sanger sequencing, or next-generation sequencing. * Conducts post-processing/bioinformatics such as editing DNA sequences or scoring genotype data, compiling and managing data matrices, etc. * Ensures experiments are performed according to specifications in the conservation genetics lab. * Provides technical guidance, including training of students, as necessary. * Assists with dissemination of results of the conservation genetic projects by preparing tables, figures and summaries of research methods. * Contributes to the maintenance of the lab. * Demonstrates highest level of professional and ethical conduct. * Adherence to all health and safety guidelines * Adheres to guidelines and protocols for working with plant species listed on the Endangered Species Act. * Behaves and communicates in a manner that promotes and fosters a culture of teamwork and cooperation, within our division and throughout the Garden, with co-workers, supervisors/managers, volunteers, visitors and employees. Qualifications: * Strong background including 2 or more years’ experience in one or more of the following fields: biology, ecology, genetics or related discipline. * Prior experience using standard laboratory techniques to extract and sequence or genotype DNA. * Familiarity with preparation of samples for Illumina DNA sequencing. * Strong organizational skills and ability to multi-task. * Excellent communication and interpersonal skills. * Ability to work independently and as a team. * The requirements and duties listed above are representative and do not constitute an exhaustive list of the knowledge, skill, and/or abilities required. Education and/or Experience: * H.S. diploma or equivalent required with coursework in one or more of the following fields: genetics, evolution, ecology, conservation biology, botany, or a related discipline (Bachelor’s degree preferred). * A strong interest in conservation biology and/or applied conservation genetics a plus. * Demonstrated ability, including a minimum of (1) year experience using standard laboratory techniques to extract and sequence or genotype DNA. Experience generating and analyzing next-generation DNA sequence data or with experience in handling environmental (eDNA) samples preferred. * An equivalent combination of education, skills, and experience may be considered. Computer Skills: Proficient with Microsoft Office suite (i.e., Word, Excel, PowerPoint, etc.). Prior experience with bioinformatics and genetic analysis software. Certificates, Licenses, Registrations: * Must be able to maintain a valid driver’s license. Physical Demands: * Ability to lift 35 lbs. and over. * Manual dexterity to use a computer keyboard for the purpose of accurately communicating, writing, and managing research data. * Ability to walk, stand, kneel, or climb as required and move about for extended periods of time in indoor and outdoor environment. * Physical fitness necessary for field work sometimes in inclement weather. Work Environment: * Indoor office and laboratory environment. Please apply online by 02-Dec-2014 (CST) at http://bit.ly/1vBaBE4 Christine E. Edwards Assistant Scientist, Conservation Genetics Center for Conservation and Sustainable Development Missouri Botanical Garden Phone: 314-577-9473 x6244 Fax: 314-577-9596 Christine.Edwards@mobot.org via Gmail
CUNY.NewYork.ComparativePopulationGenetics The Hickerson lab at the City University of New York has an opening for a PhD student who is interested in community-level population genetics and comparative phylogeography. The group is focusing on developing and implementing population genetic methods for understanding the evolutionary and demographic histories of species assemblages. The ideal candidate will have a strong interest or aptitude in quantitative biology, modeling, and programming as well as an interest in evolutionary genetics and biogeography. The lab welcomes qualified applicants with diverse backgrounds, including biology, anthropology, mathematics, physics, computer science, and related fields. This opening offers an opportunity for independent research in joint quantitative and empirical labs that now have 2 postdoctoral researchers, 3 PhD students and access to a wide array of population genomic datasets. We are in active collaboration with the lab of Ana Carnaval (CCNY) on an NSF-funded Dimensions of Biodiversity project (www.afbiota.org) focusing on the Atlantic Forest ecosystem of Brazil. There is a tight collaboration with the Kyle McDonalds group at City College of New York as well as with the research groups of Michelangeli and Thomas at the New York Botanical Garden. Through our 5 year NSF CAREER grant (http://1.usa.gov/1uM3lCZ), our group is also in close collaboration with the research groups led by Konrad Lohse (http://bit.ly/151xXaq) and Graham Stone at the University of Edinburgh (http://bit.ly/1AedKuC), as well as with Elizabeth Derryberry (Tulane; http://bit.ly/1EWRzHp) and curator Brian Smith from the nearby American museum of Natural History (http://bit.ly/1xkZwWq). The lab benefits from a thriving academic environment in New York City and has close ties with other biogeographically focused labs at CUNY and the American Museum of Natural History, as well as being part of the CUNY subprogram in Evolution, Ecology and Behavior (http://bit.ly/1F0kpZc). We anticipate that the position would start in the Fall of 2015. If interested please contact Mike Hickerson (mhickersion at ccny.cuny.edu). Note that applications for Fall 2015 to the CUNY EEB subprogram must be received before January 1rst. For more information visit: http://bit.ly/1a2oJFKwww.afbiota.org) focusing on the Atlantic Forest ecosystem of Brazil. There is a tight collaboration with the Kyle McDonalds group at City College of New York as well as with the research groups of Michelangeli and Thomas at the New York Botanical Garden. Through our 5 year NSF CAREER grant (http://1.usa.gov/1uM3lCZ), our group is also in close collaboration with the research groups led by Konrad Lohse (http://bit.ly/151xXaq) and Graham Stone at the University of Edinburgh (http://bit.ly/1AedKuC), as well as with Elizabeth Derryberry (Tulane; http://bit.ly/1EWRzHp) and curator Brian Smith from the nearby American museum of Natural History (http://bit.ly/1xkZwWq). The lab benefits from a thriving academic environment in New York City and has close ties with other biogeographically focused labs at CUNY and the American Museum of Natural History, as well as being part of the CUNY subprogram in Evolution, Ecology and Behavior (http://bit.ly/1F0kpZc). We anticipate that the position would start in the Fall of 2015. If interested please contact Mike Hickerson (mhickersion at ccny.cuny.edu). Note that applications for Fall 2015 to the CUNY EEB subprogram must be received before January 1rst. For more information visit: http://bit.ly/1a2oJFK Mike Hickerson Associate Professor City College of New York - Biology Department; City University of New York Ecology, Evolution and Behavior Sub-Program 160 Convent Ave New York, NY 10031 phone 212-650-8530 lab 212-650-3457 Research Associate - Division of Invertebrate Zoology American Museum of Natural Historyhttp://hickerlab.wordpress.com/ firstname.lastname@example.org Mike Hickerson via Gmail
Dear Colleagues, I am seeking a highly motivated postdoctoral researcher with an exceptional background in bioinformatics, functional genomics, or evolutionary genomics. Experience analyzing Illumina sequence data, computer programming proficiency, and training in ecological or evolutionary genetics are highly desirable. We recently received generous funding for yeast evolutionary genomics research from the National Science Foundations Dimensions of Biodiversity Program (http://1.usa.gov/1vnuUlV) and the Pew Charitable Trusts (http://bit.ly/1ruTJKa). With Antonis Rokas (Vanderbilt) and Cletus P. Kurtzman (USDA), the Y1000+ Project (http://1.usa.gov/1vnuUlW) seeks to sequence and analyze the to complete genomes of all ~1,000 known species of Saccharomycotina yeasts and determine the genetic basis of their metabolic, ecological, and functional diversification. Yeasts are genetically more diverse than vertebrates and have remarkable metabolic dexterity, but most remain minimally characterized. They compete vigorously for nutrients in every continent and biome and can produce everything from beer to oil. The history of yeasts is recorded in their genome sequences. Now is the time to read it and tell their story! The Hittinger Lab has diverse funding for other basic and applied research from NSF, DOE, and USDA, but we are specifically expanding our basic research in ecological and evolutionary genomics. The complete advertisement and application instructions can be found here: http://bit.ly/1ruTKhh. The precise start date is flexible, but candidates should apply by November 30th to receive full consideration. Sincerely, Chris Todd Hittinger, Assistant Professor of Genetics Genome Center of Wisconsin J. F. Crow Institute for the Study of Evolution University of Wisconsin-Madison 425-G Henry Mall, 2434 Genetics/Biotechnology Center Madison, WI 53706-1580 email@example.com, (608) 890-2586 http://bit.ly/1vnuUm0 Chris Hittinger via Gmail
Postdoctoral Position Genomics of Migration My group combines several biological disciplines including behavioural observation, evolutionary genomics, molecular ecology, and bioinformatics, and utilises emergent technologies to identify the genetic basis of migratory traits. Here we focus on identifying the genes and signaling pathways behind the components shaping the migratory phenotype in the blackcap, a well characterised migratory songbird species. We will complement the sequencing approach with gene expression profiling and characterisation of chromatin modification to investigate the extent of phenotypic variation manifested by expression differences, either through slight genetic differences or epigenetic processes. The key focus of this project is to understand: Which genes harbour coding variation with relevant consequences for migratory traits, and which signalling cascades are involved in shaping the migratory phenotype? Within this project that is funded through a Max Planck Research Group Grant, I am offering a 2 year postdoctoral position with the possibility for extension. The postdoc will assume a central position within this project that is funded through an independent Max Planck Research Group Grant. Project start is January 2015 and the ideal starting date for the postdoc is April 2015. The ideal candidate has a biological training, background in bioinformatics with skills in programming (scripts and analysis pipelines), next generation sequence analysis, genome assembly and annotation. The successful candidate will be involved in fundamental research questions on migratory genomics, and I highly appreciate a creative postdoc who is motivated to contribute to and extends our research agenda to understand the genetic architecture of migratory traits. The core dataset that will be generated includes Illumina sequencing of the blackcap genome from populations with varying migratory phenotypes, some of which will be used for de novo genome assembly. The expected output of the postdoc is to contribute to the genome assembly and to compare the genomic makeup and underlying signaling pathways of different populations with various migratory phenotypes. We offer an English speaking and ambitious working environment at the Max Planck Institute for Evolutionary Biology in Pln, Germany. Cutting edge infrastructure is available at all levels, including high-performance computer clusters and next-generation sequencing core facility. The Institutes main fields of work include evolutionary ecology (Prof. Dr. M. Milinski), evolutionary genetics (Prof. Dr. D. Tautz) and evolutionary theory (Prof. Dr. A. Traulsen) and hosts a number of research groups providing ample opportunities for collaborations and interactions. The MPI in Pln further collaborates with the nearby Christian Albrechts University of Kiel in a joint International Max Planck Research School that attracts PhD students from abroad which contributes to a multicultural working atmosphere. The Max Planck Society is committed to also employing handicapped individuals and especially encourages them to apply. The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Applications should include 1) a cover letter outlining your motivation to work on this project as well as relevant experience, 2) a detailed curriculum vitae and copies of certificates, and 3) the contact details of three academic referees. Please send the above as a single .pdf file to firstname.lastname@example.org. Review of applications will start on January 1st 2015, but candidates will be considered until the position is filled. For more information, feel free to contact me! Miriam Liedvogel email@example.com Max Planck Research Group Behavioural Genomics Max-Planck-Institute for Evolutionary Biology August-Thienemann-Strae 2 24306 Pln, Germany http://bit.ly/1uOKA0F Miriam Liedvogel via Gmail
Marine Invertebrate Biologist The Department of Marine Biology and Ecology (MBE) formerly known as the Division of Marine Biology and Fisheries (MBF) at the University of Miami’s Rosenstiel School of Marine and Atmospheric Science, RSMAS , invites applications for a tenure-track position in Marine Invertebrate Biology as part of a broad strategic plan involving 16 faculty hires over the coming few years. This will be a 9-month guaranteed salary position and is intended to be at the rank of Assistant Professor but exceptional applicants at other ranks will be considered. The anticipated start date is August 2015. We are searching for an outstanding candidate working on any marine invertebrate group and questions. Potential research areas include, but are not restricted to: comparative or developmental physiology, organism-environment interactions, toxicology, climate change impacts, ecological and/or evolutionary genomics, or ecology. Preference will be given to applicants applying a broad range of techniques and approaches with strong potential for within and among department collaborations, as well as interactions with our Coral Gables and Medical campuses . Research interests of the faculty in MBE span, in no particular order, fisheries/population level biology; coastal and coral reef biology, ecology and conservation; organismal biology; marine health and biomedicine, and biological oceanography. The successful applicant will be housed in the recently inaugurated 85,000 sf Marine Technology and Life Sciences Seawater Complex that hosts state-of-the-science biological and chemical labs for seawater research and hands-on teaching. In addition, the hire would have access to marine invertebrate culture facilities associated with our NIH-supported National Resource for Aplysia, as well as the extensive collections of our Marine Invertebrate Museum . The hire will also have access to on-campus research vessels, including the F.G. Walton Smith (a 96-foot research catamaran), multiple smaller boats, Broad Key (a 63-acre island recently acquired as a field station for marine research and education, as well as a pool currently under construction for the training of scientific divers. The successful candidate will contribute to teaching and mentoring students at the undergraduate and graduate level, and is expected to teach Invertebrate Zoology in our top-ranked Marine Sciences undergraduate (B.S.) program, and related courses in our graduate programs (Ph. D., M. S. and Professional Masters). The RSMAS campus is located on Virginia Key, a unique community of marine research and educational institutions 15 minutes from downtown Miami, Florida. Approximately $250M per year is invested in marine science and education on Virginia Key, including RSMAS, the NOAA Atlantic Oceanographic and Meteorological Laboratory, the NOAA Southeast Fisheries Science Center, the Miami Seaquarium, and the Maritime and Science Technology Academy (MAST). Applicants must have a Ph. D. in a relevant field, appropriate postdoctoral training, and the ability to establish and maintain a vigorous, extramurally-funded research program. A complete application includes a cover letter, curriculum vitae, separate statements of research and teaching interests, and the names and contact information of at least three references. The position will remain opened until filled, but to receive full consideration, applications should be received by January 15, 2014. We anticipate conducting interviews for the positions in February 2015. Inquiries should be directed to MBEsearch@rsmas.miami.edu The University of Miami is an Equal Opportunity Employer, and we encourage qualified individuals to apply regardless of race, gender, disability, age, national origin, religion, sexual orientation, or gender expression. Andrew C. Baker, Ph.D. Associate Professor, University of Miami Pew Fellow in Marine Conservation Visit the lab on Facebook by clicking here Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Cswy. Miami, FL 33149, USA Office: +1 (305) 421-4642 Lab: +1 (305) 421-4226 Fax: +1 (305) 421-4600 Email: firstname.lastname@example.org Associate Conservation Scientist Wildlife Conservation Society www.wcs.org/marine Andrew Baker via Gmail
Hi, We have been having serious problems with the PC supplied with our ABI 3130 sequencer. It is now looking very likely that the PC will have to be replaced. I have therefore been wondering if it is possible to successfully run a 3130 sequencer using a different PC to that with which it is supplied. I would be interested to know how well the Genemapper software runs on different PCs. Thank you, Robert Donnelly email@example.com Robert Donnelly via Gmail
Conference: Lausanne.ESEB2015_ExperimentalEvolutionOfEcosystems.Aug10-14 Dear evoldir members, We would like to announce the symposium Experimental evolution and ecology of (microbial and other) ecosystems at the ESEB 2015 conference and would like to invite abstract submissions. This symposium aims at showcasing recent studies and bringing together ecological and (experimental) evolutionary approaches to study the evolution of ecosystems. In natural systems, organisms and species evolve not in isolation but embedded into ecosystems. Several models describe such relationships, for example the Red Queen and niche construction theories as well as metabolism-based models. Such models have shown that evolutionary processes on the ecosystem level can be highly complex. To investigate this phenomenon experimentally, laboratory approaches have simplified the situation by studying evolutionary dynamics using a (very) limited number of strains at a time under controlled laboratory conditions in the powerful approach of experimental evolution. Others studies have utilized a more ecological approach by observing and describing complex systems and how organisms and species can V or cannot V co-exist over time. Increasingly, research has been initiated that combines these two approaches by tracking evolutionary changes of complex ecosystems in laboratory and natural conditions. Examples include studies of the dynamics of species composition in (microbial) ecosystems over space and time and in response to various stresses, the evolution of social interaction between microbes, and long-term co-evolutionary studies between different (sets of) species or genotypes. For this symposium, we invite submissions of experimental and theoretical studies in this area. * Invited speakers: Susi Remold (University of Louisville) http://bit.ly/11NqzhB Tom Bell (Imperial College London) http://bit.ly/1uOKxSl * Organisers: Sijmen Schoustra (Wageningen University and University of Zambia) and Susanne Kraemer (University of Edinburgh). * Deadline for submission for abstracts for contributed talks and posters is 10th January 2015. More information can be found at http://bit.ly/11NqzxR submission/ . We look forward to receiving your submissions and to seeing you at the conference and our symposium. Dr Sijmen E Schoustra Laboratory of Genetics, Wageningen University, the Netherlands & Department of Food Science and Nutrition, University of Zambia Phone: +31 317 483142 and +260 974 572686 http://bit.ly/1veNTR5 “Schoustra, Sijmen” via Gmail
Opening for a PhD student Genomics of Migration My group combines several biological disciplines including behavioural observation, evolutionary genomics, molecular ecology, and bioinformatics, and utilises emergent technologies to identify the genetic basis of migratory traits. Here we focus on identifying the genes and signalling pathways behind the components shaping the migratory phenotype in the blackcap, a well characterized migratory songbird species. We will complement the sequencing approach with gene expression profiling and characterisation of chromatin modification to investigate the extent of phenotypic variation manifested by expression differences, either through slight genetic differences or epigenetic processes. Within this project that is funded through a Max Planck Research Group Grant, I am offering a PhD position. Project start is January 2015 and the ideal starting date for the PhD is April 2015. The ideal candidate for this position has a biological training, a background in using next-generation sequencing data to answer evolutionary questions, and is eager to learn and master new skills and tools to understand the genetic architecture of behavioural traits. Experience in genome assembly or annotation, and skills in programming are a bonus. The core project focuses on various levels of genomic analysis, but the focus of the PhD project is flexible and can be tailored to both skills and interest of the successful candidate, and could cover genome assembly and annotation, or comparison of the genomic makeup and underlying signaling pathways of different populations with various migratory phenotypes, and may also involve behavioural experiments and field work. PhD candidates at the institute have the opportunity to become member of the International Max Planck Research School (IMPRS) for Evolutionary Biology in collaboration with the nearby Christian Albrechts University of Kiel (for more information see: http://bit.ly/11NqzxT) We offer an English speaking and ambitious working environment at the Max Planck Institute for Evolutionary Biology in Pln, Germany. Cutting edge infrastructure is available at all levels, including high-performance computer clusters and next-generation sequencing core facility. The Institutes main fields of work include evolutionary ecology (Prof. Dr. M. Milinski), evolutionary genetics (Prof. Dr. D. Tautz) and evolutionary theory (Prof. Dr. A. Traulsen) and hosts a number of research groups providing ample opportunities for collaborations and interactions. The Max Planck Society is committed to also employing handicapped individuals and especially encourages them to apply. The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Applications should include 1) a cover letter outlining your motivation to work on this project as well as relevant experience, 2) a detailed curriculum vitae and copies of certificates, and 3) the contact details of three academic referees. Please send the above as a single .pdf file to firstname.lastname@example.org. Review of applications will start on January 1st 2015, but candidates will be considered until the position is filled. For more information, feel free to contact me! Dr. Miriam Liedvogel email@example.com Max Planck Research Group Behavioural Genomics Max-Planck-Institute for Evolutionary Biology August-Thienemann-Strae 2 24306 Pln, Germany http://bit.ly/1uOKA0F Miriam Liedvogel via Gmail
WHAT: Postdoctoral position in Ecological-Epidemiological Modelling WHERE: at IZW in Berlin, Germany, for 2 years, with regular visits to CEFE/CNRS in Montpellier, France. APPLICATION DEADLINE: 04.01.2015 For WHOM: Ecological-epidemiological modeller; computational biologist SUBJECT: evolutionary ecology, ecology of infectious diseases, epidemiology TO DO: Developing process-based dynamical models to understand complex disease dynamics in the light of heterogeneity of host behaviour and contact rates due to social processes. Research will focus on a highly social carnivore, the spotted hyena, and long-term data on demography, social processes and viral genotypes determined by the IZW’s long-term spotted hyena project in the Serengeti National Park, Tanzania. Dr. Stephanie Kramer-Schadt Senior Scientist Department Evolutionary Ecology Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V. Alfred-Kowalke-Straße 17 10315 Berlin GERMANY P.O.Box 70 04 30, 10324 Berlin Fon. + 49 - 30 - 51 68 -714 Fax + 49 - 30 - 51 26 - 104 http://bit.ly/1xBHEqw :: Evolutionary wildlife research for conservation :: “Kramer-Schadt, Stephanie” via Gmail
Post-doctoral position in viral bioinformatics : Lyon, France We are welcoming applications from enthusiastic and independent post-doctoral candidates to participate in our ECOFECT LabEx grant-funded project. We will develop a new bioinformatic approach to identify the sites of the Dengue virus genome that interact with the mosquito cell machinery. Background To control the Dengue virus epidemics, the most promising strategies target the mosquito host to stop viral transmission to humans. However, it is very hard to optimise these strategies and predict whether they could be successful because little is known about how the virus interacts with its mosquito host. Project We will implement a new approach that combines viral evolution experiments in mosquito cells with deep sequencing runs (collaboration with Marlne Dreuxs team). The postdoctoral project aims at developing bioinformatic and statistical methods to infer a map of interactions between the mosquito cell machinery and the viral genome. Doing so requires addressing two important problems in viral bioinformatics, i/ the assembly of viral haplotypes from short reads and ii/ fitness prediction for assembled haplotypes. Environment The host laboratory (LBBE) is a stimulating and pleasant place to work, where one can meet biologists, physicians, computer scientists, mathematicians and statisticians working on problems that range from ecology to medicine, through genomics and evolution. In addition, the post-doctoral researcher will enjoy close interactions with virologists in the team of Marlne Dreux (CIRI, ENSLyon). Lyon is the second largest city in France, is famous for its food, is a UNESCO World Heritage site and enjoys a very convenient central location in Europe. Candidates The applicants are expected to have a strong background in bioinformatics or phylogenetics or population genetics or computer science or statistics. The ideal candidate should be highly motivated, curious and enthusiastic to work in a collaborative team. Proven ability to identify research objectives and meet agreed deadlines, self-motivation and flexibility are essential. Excellent written and oral skills in English are required. Applicants: Please send one PDF file to Bastien Boussau, firstname.lastname@example.org, with the following: - cover letter - concise summary of previous research activities - curriculum vitae including publication list and contact details for 2-3 referees Ad: http://bit.ly/1xYq2Ed Bastien Boussau UMR CNRS 5558 Biometry and Evolutionary Biology Laboratory Lyon, France http://bit.ly/1xYq2Ef Collaboration with Marlne Dreux CIRI - Inserm U1111 - CNRS UMR5308 ENS Lyon, France http://bit.ly/1xYpZYX Bastien Boussau via Gmail
November 21, 2014
—=_alternative 0045F999C1257D97_Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable PhD. position in Plant Systematics & Evolution, Univ Zurich Project description: The selected student will work with Dr. Colin Hughes http://bit.ly/1p7NvCg on a research project entitled “Global Legume diversity patterns: macroevolutionary and ecological processes shaping biodiversity”, funded by the Swiss National Science Foundation in the Institute of Systematic Botany at the University of Zürich. http://bit.ly/1jNq6NX We are interested in how diversity evolves and understanding the processes and factors that determine the spatial distribution of life on Earth. Using comparative approaches and one of the most evolutionary successful families of flowering plants, the legumes (Leguminosae = Fabaceae), as a study system, we are addressing a set of inter-related questions about global plant diversity patterns. We are making use of recent developments in comparative phylogenomics and global-scale species distribution modelling to quantify phylogenetic turnover and the ecological factors underlying patterns of diversity across large-scale ecological gradients. The PhD project will focus on the legume subfamily Mimosoideae, a pantropical clade spanning all lowland tropical biomes and will involve fieldwork, laboratory work to generate DNA sequence data using NGS, herbarium specimen database work, and phylogenetic and macroevolutionary analysis. This will build on foundations already established in Zurich in terms of genomic data, development of suitable NGS approaches, taxonomic knowledge and research material for the mimosoid legumes. Position characteristics: The Institute of Systematic Botany in Zurich offers excellent research facilities and a stimulating working environment for graduate students in plant systematics and evolution. The project will also involve collaboration with legume researchers in Brasil, the Netherlands, U.K., U.S.A. and Canada. Salary is according to the Swiss National Science Foundation guidelines. Funding, including for laboratory and field costs, is available for 3 years. Requirements: Applicants should hold a Masters degree in systematics, biodiversity or evolutionary biology. Experience in molecular laboratory techniques, working with NGS data, phylogenetic analysis, macroevolutionary analysis, fieldwork and GIS are all potentially relevant. Excellent knowledge of English, written and oral, is essential. How to apply: Send the following documents by email AS A SINGLE PDF FILE to Dr. Colin Hughes, email@example.com: i) a two-page application letter describing your research interests, clearly stating why are you interested in a Ph.D. position in systematic botany and your career goals; ii) your CV, including a list of publications (if applicable); iii) a copy of your undergraduate and graduate academic record; iv) names and contact details of at least two referees selected from your academic advisors. Deadline: Applications will be screened from January 1st 2015 onwards until the position is filled. Starting date: early 2015. —=_alternative 0045F999C1257D97_Content-Type: text/html; charset=UTF-8 Content-ID: Content-Transfer-Encoding: quoted-printable
PhD. position in Plant Systematics & Evolution, Univ Zurich
Project description: The selected student will work with Dr. Colin Hughes http://bit.ly/1p7NvCi on a research project entitled “Global Legume diversity patterns: macroevolutionary and ecological processes shaping biodiversity”, funded by the Swiss National Science Foundation in the Institute of Systematic Botany at the University of Zürich. http://bit.ly/1p7Nw94
We are interested in how diversity evolves and under standing the processes and factors that determine the spatial distribution of life on Earth. Using comparative approaches and one of the most evolutionary successful families of flowering plants, the legumes (Leguminosae = Fabaceae), as a study system, we are addressing a set of inter-related questions about global plant diversity patterns. We are making use of recent developments in comparative phylogenomics and global-scale species distribution modelling to quantify phylogenetic turnover and the ecological factors underlying patterns of diversity across large-scale ecological gradients.
The PhD project will focus on the legume subfamily Mimosoideae, a pantropical clade spanning all lowland tropical biomes and will involve fieldwork, laboratory work to generate DNA sequence data using NGS, herbarium specimen database work, and phylogenetic and macroevolutionary analysis. T his will build on foundations already established in Zurich in terms of genomic data, development of suitable NGS approaches, taxonomic knowledge and research material for the mimosoid legumes.
Position characteristics: The Institute of Systematic Botany in Zurich offers excellent research facilities and a stimulating working environment for graduate students in plant systematics and evolution. The project will also involve collaboration with legume researchers in Brasil, the Netherlands, U.K., U.S.A. and Canada. Salary is according to the Swiss National Science Foundation guidelines. Funding, including for laboratory and field costs, is available for 3 years.
Requirements: Applicants should hold a Masters degree in systematics, biodiversity or evolutionary biology. Experience in molecular laboratory techniques, working with NGS data, phylogenetic analysis, macroevolutionary analysis, fieldwork and GIS are all potentially relevant. Excellent knowledge of English, written and oral, is essential.
How to apply: Send the following documents by email AS A SINGLE PDF FILE to Dr. Colin Hughes, firstname.lastname@example.org: i) a two-page application letter describing your research interests, clearly stating why are you interested in a Ph.D. position in systematic botany and your career goals; ii) your CV, including a list of publications (if applicable); iii) a copy of your undergraduate and graduate academic record; iv) names and contact details of at least two referees selected from your academic advisors.
Deadline: Applications will be screened from January 1st 2015 onwards until the position is filled.
Starting date: early 2015.—=_alternative 0045F999C1257D97_ via Gmail
Dear colleagues, We are very happy to invite your to attend and contribute to the symposium “Evolutionary ecology of cooperation: theory and experiment” which will be held at the 15th European Society for Evolutionary Biology (ESEB) Meeting in Lausanne, Switzerland, 10th - 14th August 2015. We are excited about the opportunity to bring together scientist who use either theoretical or experimental approaches (or ideally both!) to study the ecology and evolution of cooperation. We hope this will allow us to to mak connections between our lines of research and start a productive dialog on research questions of common interest. You can see the full symposium description below. We have two excellent invited speakers confirmed: Ashleigh Griffin, University of Oxford http://bit.ly/1Aw7heM Jeff Gore, MIT http://bit.ly/1Aw7heQ Ours is the symposium 9 in this list: http://bit.ly/1AEbj5O The call for abstract and registration are officially open, and the deadline for submission is 10th January 2015. http://bit.ly/1Aw7heR Please be sure to state your preference for a talk or a poster when submitting your abstract. Do not hesitate to contact either one of us with any further questions. Sorry i you are receiving this email multiple times and feel free to forward it to any colleagues who may be interested. Looking forward to seeing many of you in Lausanne! Your symposium organizers, Dusan Misevic & Sam Brown Symposium description: Understanding the ecology and evolution of cooperation remains one of the great challenges in biology. Why do individuals help others at a personal cost? How do patterns of social interaction emerge from behavioral, evolutionary, and ecological processes? What are the selective forces that maintain multi-species cooperative interactions within communities? Theory has been a vital driver in answering these and other questions, especially when engaged with data. Making the data-theory connections is often complex, as cooperation is studied in the lab, the field and the clinic, at all levels of biological complexity, in natural systems that range from cancerous cells and pathogenic microbes to birds, bees and humans. Robotic and other in silico computational systems have a potential to act as an intermediary between the different approaches to cooperation research. During the symposium we aim to move beyond ineffective debates over kin versus group selection, and focus instead on theory as a problem-solving tool, both fully driven by data and directly informing future experiments. Testable theoretical predictions and theoretical frameworks based on real-world data are essential for moving the field forward. More than just an overview of theory, simulations, and experiments about cooperation, at this symposium we wish to bring together researchers who aim to make connections between these approaches, refocus our joint efforts, and move the field forward. email@example.com via Gmail
The Genealogical World of Phylogenetic Networks
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