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July 17, 2014
A recent article published in Cladistics is critical of a number of heuristic methods for phylogenetic inference based on parsimony scores. One of my papers is among those criticized, and I would appreciate the opportunity to make a public response. The specific criticism is that I have re-invented an algorithm for economizing parsimony calculations on trees that differ by a subtree pruning and regrafting (SPR) rearrangement. This criticism is justified, and I apologize for incorrectly claiming originality for my presentation of this algorithm. However, I would like to clarify the intent of my paper, if I can do so without detracting from the sincerity of my apology. My paper is not about that algorithm, nor even primarily about parsimony. Rather, it is about a novel strategy for Markov chain Monte Carlo (MCMC) sampling in a state space consisting of trees. The sampler involves drawing from conditional distributions over sets of trees: a Gibbs-like strategy that had not previously been used to sample tree-space. I would like to see this technique incorporated into MCMC samplers for phylogenetics, as it may have advantages over commonly used Metropolis-like strategies. I have recently used it to sample phylogenies of a biological invasion, and I am finding many applications for it in agent-based Bayesian ecological modelling. It is thus my contention that my 2005 paper retains substantial value.
Hi, I’d like to request a job announcement be posted for a molecular bio tech with pop gen experience. It can be found here: http://bit.ly/1yv46jR Let me know if I need to edit or clarify anything Thanks, Chris Whipps Posting is as follows: Title: Senior Research Support Specialist (Molecular Biologist) Department: Environmental Forest and Biology Salary: $38,750 per year (Full time) Duration: Two years, possible renewable The Fish and Wildlife Disease lab at The Research Foundation of the State University of New York for the College of Environmental Science and Forestry (ESF) is seeking to fill a full-time appointment for a Senior Research Support Specialist (molecular biologist) to work on 2 projects: 1) Population genetics and genetic identification of wildlife species from non-invasive samples (80%), and 2) molecular biology and strain typing of Mycobacterium species from laboratory zebrafish (20%). The Senior Research Support specialist will work on molecular biology projects led by Dr. Christopher Whipps working with a team of faculty and graduate students (Whipps lab http://bit.ly/1riV3C3; Cohen lab http://bit.ly/1yv46jT; Ryan lab http://bit.ly/1riV4FR). This position will require strong organization, communication, and math skills; also must be able to handle high volume testing accurately and effectively and work with biological tissues and infectious agents safely. Brief Description of Duties: DNA extraction from tissues, cultures, and scats; running and modifying PCR assays for genotyping microsatellites from cottontail rabbits and other wildlife species; PCR-RFLP assays for species identification of rabbits and bacteria; preparation for DNA sequencing and sequence analysis; troubleshooting microsatellite genotyping data; ordering supplies; assisting graduate and undergraduate students with research; general laboratory management. Required Qualifications: A Bachelor’s degree in Genetics, Microbiology or related fields; experience in DNA extraction techniques and PCR. Preferred Qualifications: A strong background in population genetics, laboratory management, and microbiology. Genetics techniques including optimizing and troubleshooting PCR, and genetic analysis. Experience with isolation of bacteria from animal tissues, bacterial culture media preparation, growth and preservation of cultures, bacteriological staining and biochemical techniques. Application Deadline: Although applications will be accepted until the position is filled, candidates should submit their application by August 1, 2014 to assure optimal consideration. Application Procedure: Employment application is required to be submitted on-line at http://bit.ly/1yv46jU Attach cover letter, curriculum vitae, resume and contact information for three employment references. SUNY-ESF provides an intimate small-college atmosphere with faculty and staff dedicated to solving environmental problems through research, teaching and service. The Department of Environmental and Forest Biology (www.esf.edu/efb) has over 30 faculty focused on a variety of biological disciplines. The ESF campus is contiguous with that of Syracuse University and in close proximity to SUNY Upstate Medical University, giving students and faculty the added resources of a larger institution of higher education. Located in central New York State, Syracuse is a lively city (http://bit.ly/1riV6xr) within a day drive of major urban centers (New York, Boston, Washington DC, Philadelphia, Toronto, Ottawa, Montreal), as well as abundant natural beauty (Adirondacks, Thousand Islands, Niagara Falls). In accordance with the “Jeanne Clery Disclosure of Campus Security Policy and Campus Crime Statistics Act” institutions of higher education are required to prepare an annual report containing information on campus security policies and campus statistics. This report includes statistics for the previous three years concerning reported crimes that occurred on-campus; in certain off-campus buildings or property owned or controlled by SUNY-ESF; and on property within, or immediately adjacent to and accessible from the campus. The report also includes institutional policies concerning campus security, such as policies concerning sexual assault, and other matters. You can obtain a printed copy of this report by contacting SUNY-ESF University Police at 315-470-6667 or by accessing the following web site: http://bit.ly/1yv48bJ As an Equal Opportunity / Affirmative Action employer, the Research Foundation will not discriminate in its employment practices due to an applicant’s race, color, religion, sex, national origin and veteran or disability status Visit SUNY-ESF at www.esf.edu Christopher M. Whipps, Ph.D. Associate Professor SUNY-ESF 1 Forestry Dr. Syracuse, NY, 13210 ph# 315-470-4762 http://bit.ly/1riV3C3www.esf.edu/efb) has over 30 faculty focused on a variety of biological disciplines. The ESF campus is contiguous with that of Syracuse University and in close proximity to SUNY Upstate Medical University, giving students and faculty the added resources of a larger institution of higher education. Located in central New York State, Syracuse is a lively city (http://bit.ly/1riV6xr) within a day drive of major urban centers (New York, Boston, Washington DC, Philadelphia, Toronto, Ottawa, Montreal), as well as abundant natural beauty (Adirondacks, Thousand Islands, Niagara Falls). In accordance with the “Jeanne Clery Disclosure of Campus Security Policy and Campus Crime Statistics Act” institutions of higher education are required to prepare an annual report containing information on campus security policies and campus statistics. This report includes statistics for the previous three years concerning reported crimes that occurred on-campus; in certain off-campus buildings or property owned or controlled by SUNY-ESF; and on property within, or immediately adjacent to and accessible from the campus. The report also includes institutional policies concerning campus security, such as policies concerning sexual assault, and other matters. You can obtain a printed copy of this report by contacting SUNY-ESF University Police at 315-470-6667 or by accessing the following web site: http://bit.ly/1yv48bJ As an Equal Opportunity / Affirmative Action employer, the Research Foundation will not discriminate in its employment practices due to an applicant’s race, color, religion, sex, national origin and veteran or disability status Visit SUNY-ESF at www.esf.edu Christopher M. Whipps, Ph.D. Associate Professor SUNY-ESF 1 Forestry Dr. Syracuse, NY, 13210 ph# 315-470-4762 http://bit.ly/1riV3C3 Chris Whipps via Gmail
Evolutionary Genetics and Genomics October 8-12, 2014 - Suzhou China at Cold Spring Harbor Asia Invited Speakers include: Loren Reiseberg, Doris Bachtrog, Kirsten Bomblies, Rasmus Neilsen, Steve Eichten, Hong-Ya Gu, Xionglei He, Molly Prezeworski, Leonie Moyle, Libby King, Manyuan Long, Soojin Yi, John Wang For more info: http://bit.ly/1yv48bu Brandon Gaut via Gmail
—_000_140552266997718003tulaneedu_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Research Assistant Professor Position in Coastal Sciences OR Urban Ecology The Tulane / Xavier Center for Bioenvironmental Research (cbr.tulane.edu) at Tulane University invites applications for a Research Assistant Professor faculty position in Coastal Sciences or Urban Ecology. The CBR aims to recruit an outstanding researcher with a PhD and prior postdoctoral research experience who will merge excellence in research (65%), teaching (20%), and service (15%), as follows: Coastal Sciences Research: The incumbent will work closely with the Director of the CBR, Dr. Michael Blum, to engage in independent and collaborative research exploring aspects of coastal restoration in the Mississippi River Delta and elsewhere in the northern Gulf Coast. The incumbent will be expected to contribute to research on one or more of the following topics (1) riverine and delta hydrology; (2) sediment transport and deposition; (3) coastal wetland ecosystem formation, including eco-evolutionary dynamics; (4) coastal finfish and/or shellfish responses to river diversions. The incumbent will be encouraged to pursue other research areas that complement these topics. OR Urban Ecology Research: The incumbent will work closely with the Director of the CBR to engage in independent and collaborative research exploring aspects of urbanization and counter-urbanization in New Orleans and elsewhere. The incumbent will be expected to contribute to research on one or more of the following topics (1) the ecology and evolution of infectious disease in urban and surrounding environments; (2) green infrastructure and the ecology of urban streams and wetlands; (3) coupled human natural ecosystem dynamics; (4) valuation of ecosystem services of urban forests and greenways. The incumbent will be encouraged to pursue other research areas that complement these topics. AND Teaching: The incumbent will teach or team-teach one undergraduate course per year. The course, entitled “Global Change Biology”, is intended for non-major and major undergraduates with an interest in climate change, biological responses to climate change, and conservation in a changing climate. Service: The work carried out by the incumbent will contribute to larger programmatic efforts to develop expertise in, as appropriate, coupled human natural ecosystem dynamics or coastal restoration across the university. The incumbent will assist the CBR Director with programmatic development by contributing to the development of grant proposals and other materials to support topical research, education, and public engagement including programs that will be hosted at the new Tulane River and Coastal Center. Preference will be given to candidates possessing in-depth topical knowledge in coastal sciences (e.g., coastal geosciences, coastal ecology, or coastal fisheries) or urban ecology (e.g. stormwater hydrology, epidemiology of zoonotic diseases, or environmental economics). Preference will also be given to candidates who have the desire to develop new skills and training. The potential to obtain competitive extramural funding is also an important consideration. An initial appointment will be for two years, with continuation dependent upon performance and funding. A start date in in early fall 2014 or a mutually agreeable date in late Fall 2014 is strongly preferred. Salary will be commensurate with experience and qualifications. A PDF-format application package including of a curriculum vitae, statement of research interests, statement of teaching philosophy and interests, and contact information for three professional references should be submitted via e-mail to Ms. Shelley Meaux (email@example.com). Please write “Research Assistant Professor” in the subject line. For earliest consideration, apply by 15 August 2014. Applications will be accepted until the position is filled. Tulane University is an Affirmative Action/Equal Employment Opportunity/ADA Employer. Women and minorities are encouraged to apply. via Gmail
The Paris Saclay BASC LABEX offers a doctorate fellowship in environmental demogenetics Place CNRS LEGS Gif-sur-Yvette, France Laboratory DEEIT, activities in collaboration with other labs of BASC labex. Director Stéphane DUPAS Profile Master in evolutionary ecology, bioinformatics or biostatistics and training in statistical inference, preferably in a Bayesian framework and in random walks or Markov chains. Deadline for application August 15th 2014 Description The development of new sequencing technologies brings markers for the analysis of spatial dynamics of species. This large data can allow to improve significantly models of species response to environmental changes. Current model used, based on niche theory are inferred from correlation between environmental variables and species occurrences. They do not account for migration and adaptive abilities of species, which can affect the responses. Genes are markers of migration and adaptations. Inferring models of biodiversity dynamics from genomic data constitutes therefore a new challenge for population biology and ecology. There is however no tool or statistical theory that integrate in a single model of inference the stochastic (neutral model) and deterministic (niche model) processes determining these distributions to link spatial genetic data to environmental and connectivity variables related to geography, climate or socioecosystem. In the flagship project aiming to understand and improve adaptive abilities of socioecosystems, the labex Biodiversity, Agriculture, Society, Climate (BASC) of Paris- Saclay, wishes to train a doctorate in the area of integrative modeling from gene to socioecosystem. The stochastic model is an extension from on circuit theory model. Inferred parameters concern both mechanisms of connectivity and response to environment. The task will consist in taking charge in collaboration of the development of an inference tool of environmental demogenetic models and to exploit several data sets. The project has three stages. I – Finalization of the development of an inference tool assuming a non changing environment. And valorization of the tool on several genetic – environmental data sets on BASC insect, plant and plant pathogens datasets. II – The development of an inference tool that takes into account spatial heterogeneity. III – The construction of scenario for species response to environmental changes and the evaluation of ecosystem services or disservices provided by some practices or country planning, bsed on the software SIMADAPT. Contact Three years fellowship will start in September 2014. Send CV and cover letters before august 15th to firstname.lastname@example.org et email@example.com. For more information on the specific researches to be held, please contact Stéphane Dupas, Phone : +33 1 69 82 37 25, firstname.lastname@example.org References  Dupas S, Le Ru B, Branca a et al. (2014) Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae). Molecular ecology, 33, 1–13.  Rebaudo F, Le Rouzic A, Dupas S et al. (2013) SimAdapt: an individual- based genetic model for simulating landscape management impacts on populations (M Spencer, Ed,). Methods in Ecology and Evolution, 4, 595–600. Stephane DUPAS via Gmail
PhD student position in Whole-genome sequencing and genotyping of non-model Eukaryotes for evolutionary biology * Project description New generation sequencing technologies offer exciting new prospects for studying evolution, but also create great challenges related to the large amount of sequence data to be analysed in a single project. We seek a PhD candidate that will work on developing software pipelines for whole genome sequencing and analyse genomic variation for non model organisms, for several evolutionary biology projects. The projects involved concern (1) investigating adaptation of an herbivorous insect to its host plant at the genomic level, (2) inferring demographic history of various plant species from genomic variation, and (3) identification of candidate sex pheromones from transcriptome sequencing. * Promotor information The student will work at the Interuniversity Institute of Bioinformatics in Brussels (IB)2 (http://ibsquare.be), located on the campus of the Universit Libre de Bruxelles (ULB), and will enrol at both ULB, with promotor Patrick Mardulyn (http://bit.ly/1zLgrlG) and Vrije Universiteit Brussel (VUB), with promotor Tom Lenaerts (http://bit.ly/1l6vmgv). Other co-promotors will supervise specific aspects of the research: Olivier Hardy (ULB, http://bit.ly/1zLgrlG), Ludwig Triest (VUB, http://bit.ly/1zLgrlI), Guillaume Smits (ULB, http://ibsquare.be), and Franky Bossuyt (VUB, http://bit.ly/1l6vnRv). * Student skills The ideal candidate has a Masters Degree with a strong background in bioinformatics, with good programming and statistical skills, and a good understanding of the processes that govern biological evolution. Because the PhD candidate is expected to contribute to several projects, his ability to communicate and collaborate with others is essential. In general, the (IB)2 is a highly collaborative environment, and good interpersonal skills and an open attitude are expected. The candidate should also be fluent in English, the main language of the institute. Note that some language requirements (related to knowledge of english or dutch) have to be fulfilled for enrolment at the VUB (http://bit.ly/1zLgrC3). * Important note We can only guarantee one year of funding; prospects exist for full 4 years funding, but this will depend on the success of project grant applications and/or on personal grant applications by the candidate. Full support will be provided by the promotors to succeed with these personal grant applications. * Interested? Please send a CV, letter of motivation, and contact information of two references to Patrick Mardulyn (email@example.com). Further enquiries about the position can be directed to the same address. The candidate is expected to start 1st October 2014 and the position will be filled as soon as a suitable candidate is found. Patrick Mardulyn Evolutionary Biology and ecology, CP 160/12 Free University of Brussels (ULB) av. FD Roosevelt 50 1050 Brussels Belgium Phone: (32)(2)6502649 Fax: (32)(2)6502445 e-mail: firstname.lastname@example.org homepage: http://bit.ly/1l6vmgx lab website: http://bit.ly/1zLguhe Patrick via Gmail
Call for 2015 SSB Symposia The Society for Systematic Biologists invites proposals for symposia to be held at the 2015 SSB meeting in Guaruja, Brazil from June 26-30, 2015. The meeting will be held jointly with the American Society of Naturalists (ASN) and the Society for the Study of Evolution (SSE). Proposals should include (1) a descriptive title, (2) one or two paragraphs explaining the purpose of the symposium and its relevance to systematics, (3) a list of presentations including proposed speakers, their institutions or affiliations, and their presentation titles, and (4) an indication of whether the speakers have been invited and whether they have agreed to participate. Symposia are restricted to half-day sessions (typically 6 half hour talks). The society is particularly interested in symposia whose topics do not overlap with those from previous meetings, that introduce new ideas or synthesize important concepts, or those that are particularly good examples of the analysis of empirical data. Proposals that unite systematics with other fields are also desirable. We encourage participation from young investigators and others typically under-represented in symposia. Limited funding is available. The deadline for full consideration is September 1, 2014. Proposals should be emailed (Word or PDF format) to the Program Chairperson, Stacey D. Smith, Stacey.D.Smith@Colorado.edu (Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309-0334). Please use the subject heading: SSB Symposium Proposal. The program chair will confirm receipt of submitted proposals; please inquire if you do not receive email confirmation. The proposals will be considered by the SSB Council, and the two selected symposia will receive funds to partially defer participant costs. email@example.com via Gmail
Field Assistants Required IMMEDIATELY- Black-tailed prairie dogs Grasslands National Park, Saskatchewan, Canada We are looking for 1-2 volunteers to assist with fieldwork beginning ASAP and continuing until Aug 31 or Oct 10 (preference will be given to those who can stay for the full duration). The project investigates the ecology of Black-tailed prairie dogs and will involve live-trapping, handling and monitoring of individuals. Prairie dog towns are home to (among others): burrowing owls, swift fox and, the recently reintroduced, black-footed ferret. Assistants will have the opportunity of seeing all of these iconic grassland species, plus the many more resident in the Park. This is an excellent opportunity to gain experience working with a population of wild mammals in a spectacular setting. All fieldwork is carried out in Grasslands National Park, southern Saskatchewan, one of the largest remaining tracts of native prairie in Canada. We will be staying in Parks Canada housing in the heart of the Park. Food and accommodation are provided. Volunteers are required to provide for their own travel to Saskatoon, Saskatchewan. Travel between the field station and Saskatoon is provided. Training will be provided and no experience is necessary, but candidates should have an interest in the following (the more the better!): ecology, evolutionary biology, wildlife, field biology, and animal behaviour. The field house and study population is isolated and, as such, successful applicants need to be able to cope under these conditions, enjoy the outdoors, be up-beat, positive, responsible and work well as a member of a team. If you wish to apply for one of these posts then please send a CV with a cover letter and contact details for three references (with e-mail addresses), by email to Jeff Lane (contact info below) ASAP. Contact: Dr. Jeff Lane Department of Biology University of Saskatchewan firstname.lastname@example.org www.lanelab.ca email@example.com via Gmail
July 16, 2014
Dear EvolDir Members: I would like entering in contact with someone who is working on ancient DNA from museum otters (any of the 13 living species). I am working with Lutrogale perspicillata (smooth-coated otter) museum samples, mostly toe pads (foot pads). But in some cases I also used “skin” fragments from skull (i.e. turbinal bones). I am facing with much more difficulties with respect to the work on toe pads from museum galliforms, and I am starting to think that toe pads in otters are not source of aDNA as good as skin fragments from skull (or toe pads in galliforms). Although I am aware that generalisations are quite hard in this field, might this depend on the fact that when these animals die this may occur in water (or on the fact they spend a lot of time in the water)? Any opinion in this respect? Any suggestions? Thank you, Filippo Barbanera University of Pisa, Italy firstname.lastname@example.org via Gmail
—_000_016E5005C6D68045B5294CF56C223027927FDDcnmb01wvpcoreresr_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Opportunities available for motivated students to participate in an ongoing project investigating social behavior and cognition in wild and captive blue and great tits. Starting times, duration of the internship and tasks can be flexible. We seek a committed research assistant available as soon as possible to help with analysis of behaviour from videos recorded at feeders during winter and ideally able to continue into Autumn (October/November). Another position will be available from September/October until end of November for a field and aviary assistant. The assistant is expected to help with caring of captive birds, perform experiments in captivity (e.g cognitive trials, tests of dominance at feeders, mate choice experiments), and to assist with capturing of birds in the field. For the latter task, experience with mistnetting and ringing of birds would be highly desirable. Candidates will hold, or be pursuing, a relevant degree in behavioral ecology, and should have experience with bird handling and running of experiments. Good organizational skills, commitment, attention to details (video analysis) as well as ability of working both in a team and independently, area highly desired. We can cover accommodation; however assistants will have to provide their own food and cover their travel expenses. Applicants should send a cover letter and CV, including names and e-mail addresses of three potential referees, as soon as possible. For further information and applications, please contact Enrico Sorato: email@example.com —_000_016E5005C6D68045B5294CF56C223027927FDDcnmb01wvpcoreresr_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
Opportunities available for motivated students to participate in an ongoing project investigating social behavior and cognition in wild and captive blue and great tits.
Starting times, duration of the internship and tasks can be flexible.
We seek a committed research assistant available as soon as possible to help with analysis of behaviour from videos recorded at feeders during winter and ideally able to continue into Autumn (October/November).
Another position will be available from September/October until end of November for a field and aviary assistant. The assistant is expected to help with caring of captive birds, perform experiments in captivity (e.g cognitive trials, tests of dominance at feeders, mate choice experiments), and to assist with capturing of birds in the field. For the latter task, experience with mistnetting and ringing of birds would be highly desirable.
Candidates will hold, or be pursuing, a relevant degree in behavioral ecology, and should have experience with bird handling and running of experiments. Good organizational skills, commitment, attention to details (video analysis) as well as ability of working both in a team and independently, area highly desired. We can cover accommodation; however assistants will have to provide their own food and cover their travel expenses. Applicants should send a cover letter and CV, including names and e-mail addresses of three potential referees, as soon as possible. For further information and applications, please contact Enrico Sorato: firstname.lastname@example.org—_000_016E5005C6D68045B5294CF56C223027927FDDcnmb01wvpcoreresr via Gmail
The National Center for Ecological Analysis and Synthesis (NCEAS) is co-sponsoring Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest. This conference may be of interest to the EvolDir network. Cheers, Morgan Visalli Are you a researcher with a coding project that needs some help? Are you developing software for the earth sciences and would like some feedback and collaboration from a diverse group of scientists? Open Science Codefest September 2-4, 2014 Santa Barbara, CA Open Science Codefest will gather researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest. Design. Code. Discuss. Learn more on the Codefest website: http://bit.ly/W9D3gl Inspired by hack-a-thons and organized in the participant-driven, unconference style, the Open Science Codefest is for anyone with an interesting problem, solution, or idea that intersects environmental science and computer programming. This is the conference where you will actually get stuff done — whether that’s coding up a new R module, developing an ontology, working on a data repository, creating data visualizations, dreaming up an interactive eco-game, discussing an idea, or any other concrete collaborative goal that interests a group of people. Open Science Codefest 2014 will be held in *Santa Barbara on September 2-4, 2014* at the Fess Parker Santa Barbara Hotel. Registration is *free*. Register at http://bit.ly/W9D3wC. Suggest a session topic or review proposed sessions in the Open Science Codefest Github project . To suggest a session, create a “New Issue” and apply the “proposed session” label. Alternatively, email the Codefest team at email@example.com. Forward this invite and spread the word about Open Science Codefest 2014. People from a wide variety of disciplines, geographic regions, and skill levels are encouraged to attend! Follow us on Twitter #OSCodefest Contact Open Science Codefest at firstname.lastname@example.org Morgan Visalli via Gmail
—_000_BD21BECB2AF1994DA91AA9D93CD88DF49E1D49ACShempintraecued_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable East Carolina University ASSISTANT PROFESSOR OF CONSERVATION BIOLOGY Position Number: 934002 The Department of Biology at East Carolina University, Greenville, NC, the third largest campus in the University of North Carolina system, invites applications for a nine-month tenure-track position at the Assistant Professor level with expertise in Conservation Biology, to begin August 17, 2015. We seek a broadly trained individual with a successful, innovative research program involving the development and application of ecological and evolutionary principles to address fundamental questions in conservation biology. In support of ECU’s strategic emphasis in coastal research, we seek applicants whose research programs can be applied to aquatic or terrestrial ecosystems of coastal areas, including offshore, nearshore or adjacent onshore physiographic provinces. The successful candidate will be expected to establish a vigorous, externally funded research program that involves work in a coastal area, teach undergraduate and graduate-level courses in conservation biology and related disciplines, mentor students in the M.S. and Ph.D. programs, be an active member of ECU’s Center for Biodiversity and engage in university, community and professional service. Collaborative opportunities exist in Biology as well as other University departments and centers, including the Institute for Coastal Science and Policy and the Center for Sustainability. Departmental resources include computational facilities, a central environmental lab, next generation sequencing, university-owned natural areas and field vehicles and vessels. East Carolina University is in close proximity to the Croatan National Forest, the coast, and North Carolina’s Research Triangle. Please visit our website at http://bit.ly/1t2kZzB for more information on the depar tment. Appointment at the Associate Professor or Professor level may be considered for a candidate with a well-established record of teaching and research. Qualifications: A Ph.D. in Biology or Biology-related fields with training in conservation biology and at least one year of postdoctoral research experience are required. Qualifying degrees must be received from appropriately accredited institutions. Applicants must complete a candidate profile and submit a cover letter, curriculum vitae, a list of three references (including contact information), and statements of research interests and teaching experience/philosophy online at www.jobs.ecu.edu using the position number 934002 -Assistant Professor of Conservation Biology. We will ask short-listed candidates to have three reference letters sent to the Search Committee Chair via email within 7 days of short-list notification. Official transcript and original hard-copy reference letters are required upon employment. Inquiries may be directed to Dr. David Chalcraft (email@example.com), Search Committee Chair. Review of applications will begin on September 2, 2014 and continue until the position is filled. East Carolina University is an Equal Opportunity/Affirmative Action Employer. Visit this job posting at http://bit.ly/1t2kYvh. —_000_BD21BECB2AF1994DA91AA9D93CD88DF49E1D49ACShempintraecued_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
*Description of Work:* The Division of Public Health Informatics and Analytics (DPHIA) within the Center for Food Safety and Applied Nutrition (CFSAN) at the US Food and Drug Administration seeks a creative and enthusiastic research fellow to assist in the analysis of next-generation DNA sequencing data. The primary focus of the research fellow will be the analysis of whole genome sequence data from food-borne pathogens. The fellow is expected to be proficient with 1) algorithms and programs to perform whole genome assembly, 2) software for detection of variant nucleotide positions with respect to a reference genome, and 3) the construction and interpretation of phylogenies based on next-generation sequence data. The fellow would also serve as a genome database specialist to help curate genomic sequence data generated both at CFSAN and externally. As part of the curation work, the fellow will contribute to improving the entire process of formatting, loading, and vetting both genomic data and associated meta-data from food borne pathogens. The production of reference data sets for the evaluation of analysis methodologies will be an important aspect of this work, as will be the use of statistical and bioinformatics analysis tools to explore analysis methodologies. The curation work and associated analysis methodology work is expected to play an important role in providing faster and better traceback information for bacterial isolates during outbreak investigations. The fellow is also encouraged to develop an independent research project that furthers the mission of the FDA and the analytics group within CFSAN. Examples of such a project include the development of novel genomic analyses, evaluating alternative strategies for identifying variant sites, and the visualization and extraction of information contained in large whole genome sequence datasets and associated phylogenies. CFSAN and the Biostatics Branch is a vibrant community of specialists from a number of different disciplines (e.g., epidemiologists, chemists, microbiologists, biostatisticians, and bioinformaticians). Applicants should email Dr. James Pettengill at james.pettengill(at)fda.hhs.gov with questions about the position. *Desired Skills:* Educational background (PhD or MS) in microbiology, genetics/genomics, phylogenetics, bioinformatics, statistics and/or computer science. Familiarity with next-generation sequence data (e.g., fastq format). Proficient at running de novo assembly algorithms (e.g., Velvet, SPADES, SOAPdenovo) and reference based mapping programs (e.g., Bowtie2, BWA). Proficient in a computer language such as R, Python, or Perl. Skilled in the management, organization, and querying of large files/databases. *Application Materials:* Cover letter describing previous and future research interests CV/Resume Contact information for three references To be mailed as a single pdf to james.pettengill(at)fda.hhs.gov *Duration:* 2 years *Location:* FDA, Center for Food Safety and Applied Nutrition 5100 Paint Branch Parkway College Park, MD 20740-3835 USA *Salary/Benefits:* The position is offered through the Oak Ridge Institute for Science and Education. The position does not include funds to offset moving. The position does not include benefits. ORISE offers a plan or the fellow can have her/his own but proof of insurance is required before beginning the position. However, funds are available for travel to conferences/workshops. Stipend: $6,091.67/month x 12 months $73,100.00 per year firstname.lastname@example.org via Gmail
University of North Carolina at Charlottes Plant Population Genomics and Biotic Stress A postdoctoral position is available in the laboratory of Bao-Hua Songs lab at University of North Carolina at Charlotte to study wild soybean biotic stress. The primary research involves identifying genes that are responsible for wild soybean biotic stress. Specific tasks include stress resistance/tolerance assays, genomic analysis of diverse ecotypes, transcriptome analysis and candidate gene selection. The candidate must be passionate and hard working, able to create an environment that fosters diversity, and ability to work in a multi-cultural setting. The position is full-time for two years subject to satisfactory performance in the first year. The position is available immediately and will remain open until filled. To apply, please send a cover letter that describes your background, motivation, and interests as well as a full CV to email@example.com. Please also arrange to have two letters of recommendation sent directly by the letter writer to the above email address as well. The University of North Carolina at Charlotte is an EOE/AA employer and an ADVANCE Institution that strives to create an academic climate in which the dignity of all individuals is respected and maintained. Therefore, we celebrate diversity that includes, but is not limited to ability/disability, age, culture, ethnicity, gender, language, race, religion, sexual orientation, and socio-economic status. “Song, Bao-Hua” via Gmail
Faculty Position in Microbiology Texas A&M University The Department of Biology at Texas A&M University (TAMU) invites applications for a tenure-track Assistant Professor position in microbiology. We will consider candidates pursuing innovative research in all disciplines of microbiology, including, but not limited to, bacteriology, mycology, virology, immunology, host-pathogen/parasite interactions, developmental-, environmental-, evolutionary- or behavioral microbiology, genetic mechanisms and genomics, synthetic biology and biotechnology. The criteria for selection will be uniqueness, creativity and excellence in research and scholarship. We strongly encourage applications from candidates who will increase the exposure of our students to a diverse culture. The successful candidate will be expected to develop an externally funded research program and to teach undergraduate and graduate courses. We offer an interactive and collegial research environment, a modern infrastructure, and a competitive startup package. More information about our department can be found at www.bio.tamu.edu. For full consideration, applicants should email a letter of intent, curriculum vitae, statement of research and teaching interests, and three letters of recommendation by October 1, 2014 to firstname.lastname@example.org If you have questions about this search, please direct e-mails to Dr. L. Rene Garcia, Chair of the Search Committee, at email@example.com Texas A & M University is an Equal Opportunity/Affirmative Action employer that is dedicated to the goal of building a culturally diverse and pluralistic faculty and staff who are committed to teaching and working in a multicultural environment. We strongly encourage applications from women, minorities, veterans, and individuals with disabilities. In addition, the University is responsive to the needs of dual career couples. Gil Rosenthal via Gmail
Terrestrial Invasive Plant Species II: Pre-Conference Registration Deadline July 20 ============================================================= The Terrestrial Invasive Plant Species II meeting will be held at the University of Toronto Mississauga on 6-8 August 2014, with major support from the Invasive Species Centre (Ontario) and the University of Toronto. A draft schedule is now available on-line; please visit our website (http://bit.ly/1kz0M1Y) for details. The pre-conference registration deadline is July 20. Please see http://bit.ly/1kz0M1Y for on-line registration information. Program and Invited Speakers: A draft schedule is now available on the website (http://bit.ly/1m5bQSs), including many exciting presentations. Our keynote speakers are Spencer Barrett from the University of Toronto, and Kirsten Prior from the University of Florida. We also are organizing a special session devoted to biocontrol of invasive plants; confirmed speakers to date include Bernd Blossey (Cornell University), Rob Bourchier (Agriculture and AgriFood Canada), Richard Casagrande (University of Rhode Island), John Gaskin (USDA-ARS), Hariet Hinz (CABI Switzerland), Lindsey Milbrath (USDA-ARS) and Richard Shaw (CABI UK). We still have space for late-breaking posters and 2-minute talks. Field Trips: We are offering a pre-conference field trip on August 6, at a modest additional cost: the Carden Plain Alvar (http://bit.ly/1kz0Mic). If you would like to participate, please submit your payment with your conference registration; see our registration page for details. If you already have registered, or wish to add a field trip at a later date, please contact Antonia Maughn (firstname.lastname@example.org) for instructions. There also will be a lunchtime walk from the conference venue into the Credit River valley on August 8. See you in August! TIPS II Organizing Committee: Peter Kotanen, University of Toronto Mississauga (lead organizer) Sandy Smith, University of Toronto (St. George) Roberta Fulthorpe, University of Toronto Scarborough Ben Gilbert, University of Toronto (St. George) Marc Cadotte, University of Toronto Scarborough Pedro Antunes, Algoma University Colin Cassin, University of Toronto Mississauga (student member) via Gmail
Graduate Students (MSc and PhD) and postdoctoral position in Fisheries Genomics and Evolutionary Ecology - Halifax, NS, Canada Positions: Graduate student positions and a postdoctoral fellow position are available at Dalhousie University and Fisheries and Oceans Canada (Halifax, NS) working on the ecology, evolution, and conservation genomics of fishes and invertebrates. Species of primary interest are Atlantic salmon and Atlantic cod, but current projects include other anadromous fish and species of marine invertebrates as well. The labs research is broadly concerned with resolving adaptation and how it may influence both the geographic and genomic scale of divergence among allopatric and sympatric populations. (seefor more details). The specific projects willinvolve using next generation sequencing approaches to resolve signatures of adaptation across genomes and populations and the use of molecular tools in mixture analysis and individual assignment. Themes include adaptation to climate, invasive species, and the impact of escaped farmed salmon on natural populations. These multidisciplinary projects represent training in state of the art genomic tools and techniques while experiencing both university and government laboratory environments. Graduate students will have access to technical support both in the field and laboratory through DFO staff and expertise and be part of the Marine Gene Probe Laboratory (Dal). Qualifications: Honours degree or equivalent in biology (for a MSc position) and a MSc or equivalent (for a PhD position), and strong interests in evolutionary ecology, molecular ecology, and conservation biology. Application: Please email (email@example.com) (1) a letter describing your interests in this position and your previous research experience, (2) a recent CV. Ian Bradbury Ian Bradbury via Gmail
Please note the following DEADLINES: Registration and abstract submission:4 August, 2014 Accommodation:availability cannot be guaranteed after 28 July, 2014 The United Kingdom is home to exceptional evolutionarybiologists. However, compared to the number of evolutionaryzoologists, the number of their botanical counterparts is few. In many cases, U.K. plant evolutionary biologists are in small numbers at any one institution, and such isolation hinders progress. The Royal Botanic Gardens, Edinburgh will host a conference on 8, 9 September, 2014 to help address this situation. The conference will showcase evolutionary research on plants by UK researchers to foster new collaborations. The conference will also hold a workshop, where discussion will identify challenges faced and suggest strategies to overcome them. We see this as a first step towards developing a longer-terms strategy for strengthening the UK community of plant evolutionary biologists. The conference will include a poster and networking session, open speaking slots (both standard and “lightning” talks), as well as an exciting lineup of invited speakers. For more information and to register, please visit the website at: http://bit.ly/1h7xbNN Invited speakers: Mating system: Dr. Mario Vallejo-Marin Speciation: Dr. Richard Buggs Ecological Speciation: Dr. Patrik Nosil Evo-Devo: Dr. Beverley Glover Phylogeny: Dr. Toby Pennington Polyploidy: Dr. Barbara Mable Biogeography: Dr. Bill Baker Population Genetics (Molecular ecology): Dr. Simon Hiscock Population Genetics (Genomics): Dr. Rob Ness International Speaker: Dr. Spencer Barrett (University of Toronto) via Gmail
We all worked hard during the workshop. Here is our fearless leader, in deep thought:
While some of the younger participants enjoyed drawing on the walls:
Professor Whitfield has come up with a great new model of evolution: phylogenetic windmills:
There was not only work, but also time to relax and enjoy the beautiful Dutch summer weather:
And not to forget the delicious Dutch food:
But really, most of the time we were busy touching the data, which you can find on this website:
For more photos, see the Touching the Data website.
Description of Work: The Division of Public Health Informatics and Analytics (DPHIA) within the Center for Food Safety and Applied Nutrition (CFSAN) at the US Food and Drug Administration seeks a creative and enthusiastic research fellow to assist in the analysis of next-generation DNA sequencing data. The primary research focus of the fellow will be on the analysis of metagenomic datasets as a means to (1) better quantify the microbial diversity associated with foodborne pathogens and (2) evaluate the utility of metagenomics as a culture-independent method for pathogen detection (e.g., of Salmonella Montevideo, Salmonella Enterititidis, Salmonella Heidelberg, and Listeria monocytogenes). The fellow will also support microbiologists in the analysis of data from sequencing projects of bacterial pathogens (e.g., whole genome sequencing, RNA-Seq). The projects using whole genome sequence data from bacterial pathogens include samples collected from foodborne outbreaks, and the research will include the construction of phylogenies from whole genome sequence data, gene specific analyses, and identification of mobile elements. The fellow is also encouraged to develop an independent research project that furthers the mission of the FDA and the analytics group within CFSAN. Examples of such a project include the development of novel metagenomic analyses, evaluating alternative strategies for assigning taxonomy to reads, and the visualization and extraction of information contained in large metagenomic datasets. CFSAN and the Biostatics Branch is a vibrant community of specialists from a number of different disciplines (e.g., epidemiologists, chemists, microbiologists, biostatisticians, and bioinformaticians). Applicants should email Dr. James Pettengill at james.pettengill(at)fda.hhs.gov with questions about the position. Desired Skills: • Educational background (PhD or MS) in microbiology, genetics/genomics, phylogenetics, bioinformatics, statistics and/or computer science • Familiarity with next-generation sequence data (e.g., fastq format) • Proficient at running programs for the analysis of metagenomic data (e.g., mother, QIIME) • Proficient at running de novo assembly algorithms (e.g., Velvet, SPADES, SOAPdenovo) and reference based mapping programs (e.g., Bowtie2, BWA) • Proficient in a computer language such as R, Python, or Perl. • Skilled in the management, organization, and querying of large files/databases Application Materials: • Cover letter describing previous and future research interests • CV/Resume • Contact information for three references • To be mailed as a single pdf to james.pettengill(at)fda.hhs.gov Duration: 2 years Location: FDA, Center for Food Safety and Applied Nutrition 5100 Paint Branch Parkway College Park, MD 20740-3835 USA Salary/Benefits: The position is offered through the Oak Ridge Institute for Science and Education. The position does not include funds to offset moving. The position does not include benefits. ORISE offers a plan or the fellow can have her/his own but proof of insurance is required before beginning the position. However, funds are available for travel to conferences/workshops. Stipend: $6,091.67/month x 12 months $73,100.00 per year firstname.lastname@example.org via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology