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April 12, 2014

00:33

Dear Evol-dir community, I would appreciate recommendations for laboratory information management systems for academic labs focused on molecular biology. As our lab does mostly population genetics-oriented research on numerous species, we are accumulating more samples and associated information than is easy to keep track of in spreadsheets and our heads. Ideally this LIMS would accommodate the use of barcodes for samples and storage locations (i.e. boxes, freezers), provide easy recording of actions on samples like extraction and library preparation, list the outcomes of those events (degraded, failed, consumed, etc.), and connect to products of those events (e.g. links to NGS fastq files). I am most interested in relatively simple out-of-the-box solutions or MS Access templates that won’t break the bank. Any suggestions or experience would be helpful. Thanks! Stuart Willis swillis4@gmail.com via Gmail

Source: EVOLDIR
00:09

Dear all, We are organising a symposium on evolutionary phylogenetics and Lepidoptera biodiversity (see details below) at the International Conference on the Biology of Butterflies, 2014 in Turku, Finland (August 11-14th). http://bit.ly/17ARV8Y We encourage submission for talks and posters: http://bit.ly/OM9lul Deadline for abstract submission is May 1. Thanks, and hope to see many of you in Turku, Marianne Elias and Karina Lucas Silva Brandao Evolutionary phylogenetics and Lepidoptera biodiversity: diversification, adapations and community ecology Why are there so many species on Earth, and why are they so concentrated in a small number of hotspots? More specifically, what are the processes underlying diversification and what are those permitting multiple species to coexist? These questions have intrigued biologists since the acceptance of Darwin’s theory of evolution and still represent a major challenge for modern evolutionary biology. The insect order Lepidoptera is an excellent model group to answer these questions, using recent approaches based on molecular phylogenies. The purpose of this symposium is to present original research on diversification, adaptation and community ecology of Lepidoptera, using phylogenetic tools. Marianne Elias CNRS Researcher UMR 7205 - CNRS Museum National d’Histoire Naturelle 45 rue Buffon, CP50, 75005 Paris phone: +33 1 40 79 37 90 http://bit.ly/Pnhkh3 melias2008@gmail.com via Gmail

Source: EVOLDIR

April 11, 2014

23:51
—_000_CF6DB4D214599templetonbiology2wustledu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable The Department of Evolutionary and Environmental Biology, University of Haifa, Israel (http://bit.ly/OSIxaN), invites candidates for a tenure-track position to begin on October 2014 or October 2015. We shall consider any excellent scientist in the fields of Evolutionary Biology and/or Ecology. Interested candidates should send a letter of research interests/plans, CV, list of publications, and contact information of at least three referees to Ms. Limor Dvir, ldaniely@univ.haifa.ac.il by April 30, 2014. Alan R. Templeton Charles Rebstock Professor Emeritus of Biology and Genetics Professor of Evolutionary and Environmental Biology ____________________________ Department of Biology Washington University St. Louis, MO 63130-4899 USA Institute of Evolution, and Department of Evolutionary and Environmental Biology University of Haifa Haifa 31905, Israel p. 314-935-6868 f. 314-935-4432 e. temple_a@wustl.edu http://bit.ly/1ex36m0 —_000_CF6DB4D214599templetonbiology2wustledu_ Content-Type: text/html; charset=”us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable The Department of Evolutionary and Environmental Biology, University of Haifa, Israel (http://bit.ly/OSIxaN), invites candidates for a tenure-track position to begin on October 2014 or October 2015. We shall consider any excellent scientist in the fields of Evolutionary Biology and/or Ecology. Interested candidates should send a letter of research interests/plans, CV, list of publications, and contact information of at least three referees to Ms. Limor Dvir, ldaniely@univ.haifa.ac.il by April 30, 2014. Alan R. Templeton Charles Rebstock Professor Emeritus of Biology and Genetics Professor of Evolutionary and Environmental Biology ____________________________ Department of Biology Washington University St. Louis, MO 63130-4899 USA Institute of Evolution, and Department of Evolutionary and Environmental Biology University of Haifa Haifa 31905, Israel p. 314-935-6868  f.  314-935-4432 e. temple_a@wustl.edu http://bit.ly/1ex36m0 —_000_CF6DB4D214599templetonbiology2wustledu via Gmail
Source: EVOLDIR
23:34

The Altermatt lab at the Institute of Evolutionary Biology and Environmental Studies (IEE) of University of Zurich and the Department of Aquatic Ecology of Eawag, Switzerland, has a vacancy for: A Postdoc Position in Metacommunity-/Metaecosystem Ecology Project title: Bridging biodiversity and ecosystem functioning in dendritic networks: a meta-ecosystem perspective Understanding the causes and consequences of biodiversity is among the most challenging goals in ecology. Recent results indicate a generally positive effect of diversity on ecosystem processes. Up to now, almost all work on biodiversity-ecosystem functioning has been conducted in a non-spatial, one-patch perspective. Natural ecosystems, however, are spatially explicit, and there is substantial flow of material and organisms among patches and ecosystems. This project aims at applying the concept of meta-ecosystems to empirical data in spatially explicit dendritic networks. In a project linked to two complementing PhD theses, the Postdoc Fellow will use a laboratory protist microcosm system to experimentally test interacting effects of habitat network structure and ecosystem functioning. As a group, we will extend these findings to mesocosm experiments and large-scale field studies with amphipods to study ecosystem functioning in Swiss river networks. The Postdoc will synthesize the findings, and link or expand existing theoretical work. In the whole project, diversity and ecosystem functioning will be studied in spatially explicit dendritic networks in a highly consistent framework. Ultimately, we want to get a comprehensive understanding of biodiversity and ecosystem functioning in riverine systems. Competitive applicants will have previous experience in ecology, biodiversity and spatial dynamics and be interested in participating in this extensive new research project. They will be highly motivated, enthusiastic and independent scientists. Candidates should have a good conceptual understanding of ecological theory, excellent experimental skills and/or a strong background in quantitative modeling. Excellent communicational and writing skills in English, experiences with publishing scientific articles, good work ethics, and creative thinking are desired. A PhD in Ecology or related subject is necessary for admission. The working language in the Altermatt lab is English. The Altermatt lab has a shared base at University of Zurich and at Eawag. It offers a stimulating and international research environment, excellent research facilities and a lively and social working place. Zurich hosts many other research groups in ecology and biodiversity research, and is among the world’s leading cities in terms of science, culture and quality of life. The positions will be for a period of two years, and could start in the second half of 2014. The project is financed by the Swiss National Science Foundation (SNSF Research Professorship to Florian Altermatt from August 2014 onwards). For further information, consult http://bit.ly/1hsKqqw http://bit.ly/1hsKrLd www.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1qLTPtXwww.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1qLTPtX Any other way of applying will not be considered. via Gmail

Source: EVOLDIR
23:34

The Altermatt lab at the Institute of Evolutionary Biology and Environmental Studies (IEE) of University of Zurich and the Department of Aquatic Ecology of Eawag, Switzerland, has a vacancy for: Two PhD Studentships in Ecology Project title: Bridging biodiversity and ecosystem functioning in dendritic networks: a meta-ecosystem perspective Understanding the causes and consequences of biodiversity is among the most challenging goals in ecology. Recent results indicate a generally positive effect of diversity on ecosystem processes. Up to now, almost all work on biodiversity-ecosystem functioning has been conducted in a non-spatial, one-patch perspective. Natural ecosystems, however, are spatially explicit, and there is substantial flow of material and organisms among patches and ecosystems. This project aims at applying the concept of meta-ecosystems to empirical data in spatially explicit dendritic networks. In a project including two complementing PhD theses and a Postdoc fellow, we will use a laboratory protist microcosm system to experimentally test interacting effects of habitat network structure and ecosystem functioning (PhD Project 1). We will extend these findings to mesocosm experiments and large-scale field studies with amphipods to study ecosystem functioning in Swiss river networks (PhD Project 2). Finally, we will synthesize the findings. In the whole project, diversity and ecosystem functioning will be studied in spatially explicit dendritic networks in a highly consistent framework. Ultimately, we want to get a comprehensive understanding of biodiversity and ecosystem functioning in riverine systems. Competitive applicants will have previous experience in ecology, biodiversity and spatial dynamics and be interested in participating in this extensive new research project. They will be highly motivated, enthusiastic and independent persons with a passion for science. Candidates should have a good conceptual understanding of ecological theory, excellent experimental skills and/or a background in quantitative modeling. Excellent communication and writing skills in English, good work ethics, and creative thinking are desired. A Masters level degree (or equivalent) in Ecology or related subject is necessary for admission. The working language in the Altermatt lab is English. The Altermatt lab has a shared base at University of Zurich and at Eawag. It offers a stimulating and international research environment, excellent research facilities and a lively and social working place. Zurich hosts many other research groups in ecology and biodiversity research, and is among the world’s leading cities in terms of science, culture and quality of life. The positions will be for a period of three years, and could start in August 2014 or soon thereafter. The PhD students will be enrolled at University of Zurich and be part of the PhD Program in Ecology. The project is financed by the Swiss National Science Foundation (SNSF Research Professorship to Florian Altermatt from August 2014 onwards). For further information, consult http://bit.ly/1hsKqqw http://bit.ly/1hsKrLd www.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1hsKqqywww.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1hsKqqy Any other way of applying will not be considered. via Gmail

Source: EVOLDIR
18:00
Background: In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in "clonal erosion", sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Results: Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Conclusions: Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into spatio-temporal dynamics in a hybridizing Daphnia species complex in a recently established lake system, and relates genetic similarities of populations to a scenario of secondary invasion enhanced by environmental factors.
00:42
BIOLOGICAL SEQUENCE ANALYSIS AND PROBABILISTIC MODELS Workshop * 16-19 July, 2014 * Venue: Merton College, Oxford * Registration and Abstract deadline: 19 May * Registration includes lodging and meals * Website for more information: alturl.com/sz33u The fields of genetics and evolutionary biology are currently developing at a huge pace. As a result our underlying theoretical understanding, our models of genetics and evolution, as well as their associated inferential methods are all undergoing rapid development, underlining the interest for a meeting dedicated to this topic. The focus of the meeting will be methods and inference in population genetics, phylogenetics and functional genomics. This meeting brings together leaders from several areas of biological sequence analysis, with an emphasis on advancing the underlying theoretical models that many problems share. Topics will include evolution of pathogens; disease epidemiology; the population genetics of cancer; and phylogenetic and population genetic models for studying sequence evolution. The conference will be held in Merton College, Oxford, UK, one of the city’s oldest colleges. The registration fee of £385 includes on-site housing and meals. For more information and signing up, go to the following website: alturl.com/sz33u We will be able to host up to ~90 participants. All participants are expected to contribute actively by presenting a talk or a poster. Additional speakers will be selected based on submitted abstracts. To promote scientific collaboration, we will distribute an abstract book that will include contact information for all attendees. Organisers: Adam Siepel Anders Krogh Gerton Lunter Gil McVean Molly Przeworski Richard Durbin Thomas Mailund Confirmed speakers: Aleksandra Walczak Alexei Drummond Amy Williams Asger Hobolth Barbara Englehardt Carolin Kosiol Dan Gusfield Daniel Wegmann David Balding Heng Li Ida Moltke Ines Hellmann Joe Pickrell Jonathan Marchini Kay Prüfer Kelley Harris Lior Pachter Peter Ralph Sharon Browning Simon Myers Yun Song Zam Iqbal Benedict Paten Jouni Sirén Guy Sella Philipp Messer Johannes Soeding Adam Charles Siepel via Gmail
Source: EVOLDIR
00:24

Dear Colleagues, Please join us in New York for “Genomes Evolving: The 13th Annual Symposium of NYU’s Center for Genomics and Systems Biology.” The one- day meeting will be Friday, June 6th. Our keynote speakers are Deborah Charlesworth and Greg Gibson. Register (free!) at http://bit.ly/1ggbOam Talks: Adam Auton (Einstein University) Understanding patterns of variation in human meiotic recombination Chip Aquadro (Cornell University) Sex, flies and conflict: the molecular evolution of germline stem cell genes in Drosophila Leonie Moyle (Indiana University) Evolutionary genomics of plant reproductive behavior Ulises Rosas (New York University) Genetic mechanisms regulating root allometry responses and variation in Arabidopsis natural populations Greg Gibson (Georgia Institute of Technology) Keynote: Are humans getting fitter, sicker, neither or both? Elodie Ghedin (New York University) Escape the virus: swarm transmission of flu Itsik Pe’er (Columbia University) Sequencing the Ashkenazi genome Kirsten Bomblies (Harvard University) Adaptation to whole genome duplication in Arabidopsis arenosa Casey Dunn (Brown University) Phylogenetics will be the new genetics Deborah Charlesworth (University of Edinburgh) Keynote: What can plants tell us about sex chromosome evolution? via Gmail

Source: EVOLDIR

April 10, 2014

23:49
A four year position as ?University assistant without doctorate? is available at the Institute of Zoology, University of Graz (Austria), in the group of Kristina Sefc. Applicants interested in completing a doctoral thesis in the framework of this position are particularly encouraged to apply. The applicant will join our ongoing research on behavioral ecology and evolutionary biology of cichlid fishes, and is invited to participate in the design of research in line with his or her specific interests. Applicants must have a MSc degree in a relevant field, and be knowledgeable in behavior, ecology and physiology of fish. Experience or interest in fish keeping is also essential, as the applicant will be responsible for the management of laboratory fish stocks. Furthermore, experience with field work, particularly in tropical aquatic ecosystems, is a plus, as the position may require the planning and realization of field work at Lake Tanganyika. The position also involves teaching in zoology, evolutionary biology or ecology. Interested applicants are referred to the University?s website (http://bit.ly/1kyQHEm) for information on the application process. Please contact me if you have any questions (kristina.sefc@uni-graz.at). The application deadline is May 7, 2014. Kristina Sefc via Gmail
Source: EVOLDIR
23:49
A postdoc position is available to work at the interface between computer science and population genetics. The mathematical tools available to computer science, and in particular to the theory of evolutionary computation, offer many exciting opportunities of application to population genetics. We aim at deploying these tools in many outstanding problems in evolutionary theory, such as the evolution of recombination, analysis and classification of fitness landscapes, and the limits to selection. There is ample freedom in choosing research directions within this framework. The position is part of SAGE (Speed of Adaptation in Population Genetics and Evolutionary Algorithms), a new European project in the Future and Emerging Technologies scheme. The post involves close collaboration with the other SAGE partners at Nottingham, Jena, IST Austria and Sheffield. For further information about SAGE, please see http://bit.ly/1fiLiuL. The position will be based at IST Austria, in the Population Genetics group headed by Nick Barton, and will be available for three years. The salary scale starts at 47.250 p.a. Applicants should have a Ph.D. in a relevant area (including computer science, mathematics, statistical physics, and population genetics), with strong mathematical skills, and an interest in fundamental research. For further details, please contact Tiago Paixao (tiago.paixao@ist.ac.at) and see the group’s webpage at http://bit.ly/1kyQHEi. Applications should include a CV, a statement of research interests or a motivation letter, and names of two to three referees. The Institute of Science and Technology is a new multidisciplinary research institute, located just outside Vienna (http://bit.ly/IhoxMf). The Institute encourages multidisciplinary research, and has strong groups at the interface between biology and physics, and in computer science. There are close links with other evolution groups in Vienna (http://bit.ly/1aSXB0e). Tiago Paixao via Gmail
Source: EVOLDIR
23:31

This is a multi-part message in MIME format. via Gmail

Source: EVOLDIR
11:37

Erick Matsen wrote:

Very interesting work from @arambaut, @alexei_drummond, @guy_baele, and @philippe_Lemey.

www.ncbi.nlm.nih.gov The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. B Vrancken, A Rambaut, MA Suchard, A Drummond, G Baele, I Derdelinckx, E Van Wijngaerden, AM Vandamme, K Van Laethem and P Lemey, PLoS computational biology, Apr 2014

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation.

Methodologically, this paper provides long-overdue inferential methods that distinguish (the rather different) within-host and between-host evolutionary processes, as well as integrate epidemiological information. I was wondering if the authors could say if this method would improve inference with data sets for which we have no epidemiological information, just stratification of sequences by host.

Biologically, it has been known for a while that viruses from chronic infections have certain mutations that are not present in primary infection. Here the authors provide further evidence that infectious HIV derives from "stored" virions rather than mutated virion lineages which have reverted. This builds on the work of:

www.ncbi.nlm.nih.gov Within-host and between-host evolutionary rates across the HIV-1 genome. S Alizon and C Fraser, Retrovirology, 2013

HIV evolves rapidly at the epidemiological level but also at the within-host level. The virus' within-host evolutionary rates have been argued to be much higher than its between-host evolutionary rates. However, this conclusion relies on analyses of a short portion of the virus envelope gene. Here, we study in detail these evolutionary rates across the HIV genome.

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02:18

Following on from earlier posts on annotating biodiversity data (Rethinking annotating biodiversity data and More on annotating biodiversity data: beyond sticky notes and wikis) I've started playing with user interfaces for editing data.

For example, here's a simple interface to edit the location of a specimen or observation (inspired by the iNaturalist observation editor). You can play with this below or on on bl.ocks.org, and the source code is on GitHub https://gist.github.com/rdmpage/9951904.



Source: iPhylo
02:13
University of Oslo, Natural History Museum Professor/Associate Professor in Evolutionary Genomics http://bit.ly/1k7oO3A The Natural History Museum (NHM) of the University of Oslo holds extensive collections of animals, fungi, and plants. Besides being the foundation for the classification of organisms, the collections are also important repositories for studying various aspects of geographical and temporal variation in biodiversity. The recent development of sequencing techniques that are suitable for ancient or historical specimens with degraded DNA, has significantly increased the potential to take advantage of the unique documentation of life on Earth preserved through natural history museum collections. The museum´s strategy emphasizes the importance of using the collections as a gene bank and to extract the genetic information of specimens for use in science. NHM is also building up collections of fresh DNA/tissue samples and is heavily involved in the global DNA barcoding initiative. The museum has established an ancient-DNA laboratory for extraction of highly degraded DNA from museum samples and from environmental samples, and runs a regular DNA laboratory. Through a strategic collaboration with the Department of Biosciences at our university, NHM has access to central high-throughput DNA sequencing facilities and is partner in a joint effort to establish a new ancient-DNA laboratory which will be hosted by the Department of Biosciences. We now want to strengthen the museum’s focus on collection-based science by increasing our competence in high-throughput sequencing techniques applied to biodiversity research and, in particular, to degraded DNA from museum collections and environmental samples. The museum has recently reorganized its research department into smaller research groups representing the main research topics within biology at NHM. These include sexual selection and speciation in animals, animal systematics, plant evolution, taxonomy and phylogeny of plants and fungi, and modelling of geo-ecological patterns and processes. More information can be found at the NHM homepages. Job description It is expected that the successful candidate should take a lead in coordinating and developing the museum´s research in evolutionary genomics and biosystematics with emphasis on the use of highly degraded DNA. He/she should be an asset for the whole research department but is expected to associate formally with one of the existing research groups. Additional internal resources, including PhD and postdoc positions, will be made available. The successful candidate will be expected to attract extramural research funding, and a proven record of accessing such funding is essential. The candidate will participate in teaching evolutionary genomics, including courses under the bachelor and master programs of UiO, and should be a capable and enthusiastic supervisor of master and PhD students. Relevant background for taking the scientific responsibility for parts of the museum´s collections is an advantage, but not a requirement. Duty work may also include providing assistance in phylogenomics and bioinformatics to the research community at NHM. Qualifications To qualify for appointment as Professor/ Associate Professor, the applicant must have documented scientific work equivalent to a doctorate, and several years of post‐doctoral experience. We seek an active researcher in evolutionary genomics with a strong publication record. The successful candidate should be on an upward trajectory and is expected to have strong potential to execute research projects at a high international level and to perform research in areas that will have synergistic effects with current research in the museum. He/she should have the ability to create an attractive research environment and the ideal candidate´s research would address fundamental questions in evolutionary genomics and biosystematics. The candidate should have a solid background in high-throughput DNA sequencing and in bioinformatics. Candidates for the position should supply a research plan, which demonstrates how the applicant’s research will strengthen or create synergy effects on current research at the museum. Applicants, who at the time of appointment cannot document formal teaching competence, must acquire such competence in the course of two years. The teaching languages at the University of Oslo are Norwegian and English. The person appointed to the position is expected to be able to teach in Norwegian or English or both. Personal qualities • Good collaborative skills and social intellect • Strong dedication and motivation • Good command of written and oral English We offer • Pay Grade 72–90 (NOK 627 100 –997 000 per year) for appointment as Professor (SKO 1013) • Pay Grade 64 - 72 (NOK 538 700 - 627 100 per year) for appointment Associate Professor (SKO 1011) • Stimulating and attractive work environment • Membership in the Norwegian Public Service Pension Fund • Attractive welfare benefits Other information In accordance with the University of Oslo´s equal opportunities policy, we invite applications from all interested individuals regardless of sex or ethnicity. However, in line with the expressed aim of the University of Oslo to recruit more women in academic positions, women are specifically encouraged to apply. At approximately equivalent qualifications, a woman will be preferred. According to the Norwegian Freedom of Information Act, information about the applicant may be included in the public applicant list, also in cases where the applicant has requested non-disclosure. Be aware that the University of Oslo has an agreement regarding acquisition of rights to work-related research results for all employees, with the aim to secure rights to research results. Reference is otherwise made to roles regarding the procedures for appointment of persons to positions as professors and associate professors at the University of Oslo and the Natural History Museum: Guidance on the application process Evaluation In the assessment of applicants, emphasis will be placed on the research potential and then teaching and other academic qualifications, as well as those for management and administration. Personal qualities, such as international networking skills, ability to collaborate, communication skills, team-working skills and scientific leadership will be emphasized. The quality and extent of the applicants’ scientific production during the last five years will be given particular weight, as well as experience in modern research methods and techniques. Interviews will be performed in the appointment process, and trial lectures may be required. Applications Applications must contain information about education, previous positions, teaching experience, academic, professional and pedagogical activity, as well as administrative experience. Applications should be submitted electronically with the following: • Letter of application • CV • A complete list of publications • Contact information of thre references Note! Publications should not be submitted with the application; the most promising candidates will be invited to submit their publications, as well as their educational certificates and diplomas, later in the process. About the procedure The applications will first be perused by an application committee with the aim of providing the appointed assessors with a short, substantiated proposal as to which applicants have the most potential and should proceed in the selection process, however without undertaking any form of ranking. Following the application committee´s report, the evaluation committee invites between five and ten of the most interesting applicants to submit a comprehensive application together with a selection of academic publications. The evaluation committee will rank order at least the three best qualified applicants. Short-listed candidates for the job will then be invited to an interview and may be asked to give a trial lecture. References will be contacted. • Region: Oslo • Job type:Permanent • Working hours: Full-time • Working days: Day • Application deadline: 18.05.2014 • Expected Start Date: ASP • Location: Oslo • Reference number:2014/761 • Home page: • http://bit.ly/16YyGW2 • Contacts: Fridtjof Mehlum, Research Director Telephone: +47 22851723 http://bit.ly/1k7oPEo Hedda Ugletveit Senior Adviser, HR Natural history Museum University of Oslo Tlf.: +47 22 85 18 19 Fax.: +47 22 85 18 32 P.O. Box 1172 Blindern NO-0318 Oslo, Norway www.nhm.uio.no Visiting address: Sars’gate 1, Oslo Hedda Ugletveit via Gmail
Source: EVOLDIR
01:55

—047d7b4179975f37d704f6a360e6 Content-Type: text/plain; charset=ISO-8859-1 Two postdoc positions are available in the lab of Jeffrey Ross-Ibarra at UC Davis to study the evolutionary genetics of maize and teosinte. We are recruiting for two projects: An NSF funded project to use population genomics to understand local adaptation and inbreeding depression of teosinte and maize landraces. We are currently sequencing >100 maize and teosinte genomes from multiple populations, which serve as the parents of two large mapping populations for which phenotyping is underway. Potential projects are flexible and include investigation of inbreeding depression, the effects of linked selection, and local adaptation. A USDA- and industry-funded project to investigate regions of the maize genome under selection during modern breeding. Using genotype, phenotype, and pedigree data from thousands of maize inbred lines, we will use a number of approaches to understand the effects and targets of selection during the last 80 years of maize breeding. Opportunities exist for both positions to additionally collaborate on a number of projects, including adaptation to high elevation in maize landraces and the population genetics of centromere evolution. Both positions are for one year, with the potential for a second year of support conditional on performance. Start dates are open-ended, with preference for earlier dates. UC Davis has extremely strong programs in both plant and evolutionary biology. Candidates would have the opportunity to interact with members of the Center for Population Biology and the Genome Center as well as the Dept. of Plant Sciences. Preference is for candidates with a strong background in evolutionary biology, proficiency in unix and experience with computational analysis of population genetic data. For more information or to apply, please send a cover letter and a CV with a list of references to rossibarra@ucdavis.edu. ____________ Jeffrey Ross-Ibarra Dept. of Plant Sciences and Genome Center 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616 Tel: 530-752-1152 Fax: 530-752-4604 www.rilab.org —047d7b4179975f37d704f6a360e6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Two postdoc positions are available in the lab of Jeffrey Ross-Ibarra at UC Davis to study the evolutionary genetics of maize and teosinte. We are recruiting for two projects: An NSF funded project to use population genomics to understand local adaptation and inbreeding depression of teosinte and maize landraces. We are currently sequencing >100 maize and teosinte genomes from multiple populations, which serve as the parents of two large mapping populations for which phenotyping is underway. Potential projects are flexible and include investigation of inbreeding depression, the effects of linked selection, and local adaptation. A USDA- and industry-funded project to investigate regions of the maize genome under selection during modern breeding. Using genotype, phenotype, and pedigree data from thousands of maize inbred lines, we will use a number of approaches to understand the effects and targets of selection during the last 80 years of maize breeding. Opportunities exist for both positions to additionally collaborate on a number of projects, including adaptation to high elevation in maize landraces and the population genetics of centromere evolution. Both positions are for one year, with the potential for a second year of support conditional on performance. Start dates are open-ended, with preference for earlier dates. UC Davis has extremely strong programs in both plant and evolutionary biology. Candidates would have the opportunity to interact with members of the Center for Population Biology and the Genome Center as well as the Dept. of Plant Sciences.Preference is for candidates with a strong background in evolutionary biology, proficiency in unix and experience with computational analysis of population genetic data. For more information or to apply, please send a cover letter and a CV with a list of references to rossibarra@ucdavis.edu. ____________Jeffrey Ross-IbarraDept. of Plant Sciences and Genome Center 262 Robbins Hall, Mail Stop 4University of CaliforniaOne Shields AveDavis, CA 95616Tel: 530-752-1152 Fax: 530-752-4604www.rilab.org —047d7b4179975f37d704f6a360e via Gmail
Source: EVOLDIR
01:34
*Context of the project *(OPOPOP ANR-BIOADAPT January 2014-december 2017) Global change linked to temperature increase and ocean acidification but also more direct anthropogenic influences, such as aquaculture, have caused a worldwide increase in reports of /Vibrio/-associated illness affecting humans but also animals such as corals and mollusks. In particular, over the last 5 years, /Vibrio splendidus/ and /V. aestuarianus/ have been associated with recurrent mortality outbreaks in oyster beds (/Crassostrea gigas/) in France. Investigating the “emergence of /Vibrio/ pathogenesis events” requires the analysis of microbial evolution at the gene, genome and population level in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift. *The aim of the post doc project is to:* /1- Compare the population structure of Vibrio in oysters and surrounding water during oyster mortality outbreaks/ In the water column, vibrios have been shown to assemble into specific populations defined by ecological preferences to attach to different types of particles and/or zooplankton, or to occur free-living. We will determine if /Vibrio/ populations are assembled neutrally in oyster or whether specific colonization processes occur and result in association with specific populations. /_Method_/: Phylogenetic (PhyML) and population prediction (Adapt ML, BAPS) as described previously (Hunt et al., 2008; Shapiro et al., 2012). /2- Compare the genome of virulent versus non-virulent strains belonging to different ecological populations/ Preliminary data suggested that not all /Vibrio/ populations harbor potential oyster pathogens.Moreover, within pathogen-containing populations (i.e., closely related, ecologically similar genotypes) pathogenicity potential ranges from non-virulent to highly virulent.We are currently testing how efficiently different strains and genotypes affect host survival.These data will be correlated with genome analyses to build hypotheses of gene function in the context of oyster pathogenesis. /_Method:_/Genome assembly from short read data using hybrid strategy (scaffolding onto closely related genomes and /de novo/ assembly), comparative genomic, phylogeny (Shapiro et al., 2012; Goudenge et al., 2013) */Competences required:/***Bioinformatician: Genome assembly, annotation, comparative genomics, phylogeny, microbial evolution, computational biology, microbial diversity, genotyping, ecology** *//* */Beginning of the post doc:/*mid 2014; 30 months *//* */Salary:/*about 1900 euros/months *//* */Professional address:/*the post doc will be based in the team of Dr Frdrique Le Roux at the station biologique de Roscoff (http://bit.ly/1sEqSE2) and will be co-supervised by Pr Martin F. Polz at the MIT (http://bit.ly/1sEqUf1). Training in the Polz lab will be funded by the project. *A letter explaining the competences and scientific interests, a CV, a publications list and letter(s) of reference should be send to Frdrique Le Roux by email: frederique.le-roux@sb-roscoff.fr* Le Roux Frdrique Head of the GV team Equipe mergente Ifremer/UPMC: “Gnomique des Vibrio” Station Biologique de Roscoff frederique.le-roux@sb-roscoff.fr Tel ext: 33 (0)2 98 29 56 47 Tel int: 416 Frdrique Le Roux via Gmail
Source: EVOLDIR
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EVOLUTIONARY SYSTEMATICS, INSTITUTE OF BOTANY, UNIVERSITY OF INNSBRUCK PostDoc position The Evolutionary Systematics group of the Institute of Botany seeks to hire a PostDoc with experience in Next Generation Sequencing (wetlab and bioinformatic analysis of restriction site associated DNA [RAD] sequencing data). The position starts in autumn 2014 (exact starting date flexible; 40 h/week employment for 26 months). Centering on the Alpine Space, the group’s mission is interdisciplinary research, embedded in international collaboration networks. A list of research topics can be found at: http://bit.ly/17ptb6J. The successful candidate will conduct NGS-based phylogeographic studies of a range of steppe organisms, including both plants and animals. The project consortium is international and includes members of the Universities of Innsbruck and Vienna (Austria), Lausanne (Switzerland) and the Real Jardn Botnico in Madrid (Spain). The project addresses the following issues: (1) Did the steppe biota colonize each Alpine dry valley independently or is there evidence for genetic exchange among the insular steppe habitats of different valleys? (2) What are the biogeographic connections of steppe biota from the Alpine dry valleys with other areas of steppe vegetation in Eurasia? (3) Are the phylogeographic patterns seen in steppe plants and animals congruent, implying range shifts of entire communities, or rather idiosyncratic, suggesting individualistic responses to climatic oscillations? (4) Our phylogeographic approach will unravel intraspecific patterns of spatial differentiation and temporal diversification across steppe plant and animal lineages. These will then not only be compared with each other, but also with data from independent sources. Changes of distribution ranges of our study taxa through time will be hindcasted using environmental niche modeling. A description of the project can be found at http://bit.ly/1iqAudJ). ***Responsibilities*** 1. optimization of a double digest RAD sequencing protocol for the study species, barcoding of individuals for pooled analyses 2. processing raw Illumina data and filtering of SNPs 3. phylogeographic and phylogenetic (BEAST, ABC-approaches, etc.) data analyses 4. species distribution modeling with Maxent 5. leading role in manuscript writing 6. contact and collaboration with scientists and laboratory technicians at the Molecular Ecology group, Institute of Ecology, Innsbruck University, as well as at other Austrian research facilities, and internationally 7. possibly (but not necessarily!) sampling of steppe species in Europe (Alps, Eastern Europe) and central Asia in 2015 ***Selection criteria*** A. PhD degree in life sciences B. published research experience in molecular systematics / evolution / biogeography, especially using high-throughput sequencing data C. proficiency in maintenance of Linux systems for bioinformatic purposes, Biopython, mysql, scripting languages (e.g. awk, Perl, R) D. experience in the use of relevant software packages for phylogeographic / phylogenetic analyses E. ability to work as part of a multi-disciplinary team F. ability to work independently G. very good knowledge of English ***Salary*** The annual gross salary is Euro 48,768 for a 40 h/week employment (26 months). This translates into a yearly net income of 31,037 EUR. Extension to 30 months and corresponding reduction of the weekly working hours are possible and welcome. The contract includes health insurance and 5 weeks of holidays annually. ***How to apply*** To apply, please submit by E-mail to : a cover letter, systematic point-by-point replies as to your readiness for the responsibilities and how you meet the selection criteria, brief statement of research interests, curriculum vitae, a complete list of publications, and two reference letters. Applications must be submitted in English until April 30th, 2014. The University of Innsbruck is striving to increase the percentage of female employees and therefore invites qualified women to apply. In the case of equivalent qualifications, women will be given preference. An offer of employment is contingent on a satisfactory pre-employment background check. ***The research institution and its environment*** Detailed information about the Evolutionary Systematics group can be found at http://bit.ly/17ptb6L. The University of Innsbruck has a long-standing and internationally renowned tradition in life sciences and offers a vibrant research atmosphere. It has 27,500 students and 4,500 staff members. Innsbruck is situated in the Alps and very close to Switzerland, Germany and Italy; scenery and outdoor recreation are fantastic. ***More information needed?*** For more information, please contact: Peter Schoenswetter Peter Schoenswetter Professor of Systematic Botany Institute of Botany, University of Innsbruck Sternwartestrasse 15, 6020 Innsbruck, Austria Tel: +43 (512) 507-51076, Fax: +43 (512) 507-51099 http://bit.ly/1iqAudN via Gmail
Source: EVOLDIR
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Two PhD opportunities: Marine and terrestrial invertebrate diversity and evolution in the Pilbara region, Australia The Western Australian Museum has secured funding from the Net Conservation Benefits fund (NCB) to undertake a five year project on the Conservation Systematics of the western Pilbara fauna. In this project we are using molecular tools to provide a systematic framework for understanding the diversity, evolutionary relationships, and distributions of marine and terrestrial fauna in the Pilbara region. Included under this broad objective are specific questions pertaining to evolutionary history, understanding the drivers of speciation, species delimitation, phylogeography, taxonomy, and co-speciation. This project has funding to support two PhD projects that broadly align with the NCB project objectives. The PhD projects will be aimed at using molecular markers to investigate biodiversity in invertebrates from the Pilbara region, and surrounds. One project will focus on marine invertebrates (eg, sponges, soft corals, nudibranchs, crinoids, or other groups) and the other will focus on terrestrial invertebrates (eg, trap-door spiders, opiliones, millipedes, or other arachnid or insect groups). The PhD students will be enrolled in the School of Animal Biology at the University of Western Australia, and based jointly at the new Molecular Systematics Unit laboratory, Western Australian Museum, Welshpool, Perth, where the successful applicants will have the opportunity to work directly with specialists in these fields. The specific project aims, questions, design and methods will be developed collaboratively by the students and supervisors. The work will include opportunities for field work in the Pilbara region, and lab costs will be generously supported by the NCB project. Currently, this opportunity is open to domestic students (Australia and New Zealand). Although the position is fully funded, students will be expected to put in an application for an Australian Postgraduate Award (APA or University Postgraduate Award (UPA) ( http://bit.ly/1k7dSmh) through UWA. The NCB funding will provide an additional top-up scholarship of $5k per year, bringing the total stipend to approx. $34k per year (tax free). Any international student should contact personnel below. Applications open 2 June, and close 11 July for a 1 Aug 2014 start. However, we encourage any applicants to contact us and begin discussions as soon as possible. Those interested in marine invertebrates should contact Nerida Wilson (Nerida.Wilson@museum.wa.gov.au) and cc Jason Kennington ( jason.kennington@uwa.edu.au). Those interested in terrestrial invertebrates should contact Joel Huey (Joel.Huey@museum.wa.gov.au) and cc Raphael Didham (raphael.didham@uwa.edu.au). hueyjoel@gmail.com via Gmail

Source: EVOLDIR
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Dear colleagues, The earlybird registration deadline is rapidly approaching — 16 April. After that, registration rates increase by $50. Also, please submit your presentation title and abstract by 16 April to be sure of making it into the program. We look forward to seeing you in Raleigh in June! Follow or join the conversation on Twitter using #Evol2014. Questions and suggestions? Please email organizer@nescent.org Allen Rodrigo Chair, Evolution 2014 Organizing Committee a.rodrigo@nescent.org via Gmail

Source: EVOLDIR
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Be at the cutting edge: 3 year postdoc at the Centre for Ecological and Evolutionary Synthesis, University of Oslo modeling paleo data using capture-recapture, occupancy and comparative approaches. http://bit.ly/1lLSpPX Lee Hsiang Liow (Ph.D) Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo, Norway folk.uio.no/leehl Lee Hsiang Liow via Gmail
Source: EVOLDIR