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October 6, 2014
Fast log likelihood given a fixed alignment, fixed tree, and fixed huge arbitrary sparse transition rate matrix
I know some ways to compute this, but I wonder who has the best current implementation? This would just be a tool for methods development testing rather than for doing anything practical, for example it wouldn't estimate anything and it wouldn't need to know anything about biology.
> This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. —B_3495396793_14882824 Content-type: text/plain; charset=”US-ASCII” Content-transfer-encoding: 7bit The Veeramah Lab at Stony Brook (http://bit.ly/1vGcJX0) has an opening for a postdoctoral researcher to begin in January 2015 (earlier or later start dates may be negotiable). The position will primarily involve the analysis of 2nd generation sequencing data from primates using model-based quantitative frameworks within two specific research themes. The first will be using whole genome data from small pedigrees to examine mutation and recombination rate variation amongst different primate lineages. The second will be using ancient DNA from early Medieval European skeletons to infer the population demographic dynamics of the European migration period, with a particular emphasis on the Lombards. As well as primary research duties applicants will be expected to write papers, help in grant writing and train/mentor graduate students. The successful applicant should have or will shortly obtain a PhD in the areas of population, evolutionary or anthropological genetics, while at least some computer programming experience (particularly in python, equivalent or lower level languages) is required. Prior experience analyzing 2nd generation sequencing data, analyzing ancient DNA and/or modeling demographic scenarios with genetic data is desirable. Applications will be accepted until November 3rd 2014. Applicants should a submit a State employment application, cover letter, resume, two references and a one page research statement to: Dr. Krishna R. Veeramah Department of Ecology & Evolution Life Sciences Building, Room 650 Stony Brook University Stony Brook, NY 11754-5245 The official posting and online application can be found at http://bit.ly/1vGcKKy 236e/32986ef9d10c3a9a85257d65004eaa31?OpenDocument. The official REF# is: WC-S-9227-14-10-S Queries regarding this position can be made by email to: firstname.lastname@example.org —B_3495396793_14882824 Content-type: text/html; charset=”US-ASCII” Content-transfer-encoding: quoted-printableThe Veeramah Lab at Stony Brook (http://bit.ly/1vGcJX0) has an opening for a postdoctoral researcher to begin in January 2015 (earlier or later start dates may be negotiable). The position will primarily involve the analysis of 2nd generation sequencing data from primates using model-based quantitative frameworks within two specific research themes. The first will be using whole genome data from small pedigrees to examine mutation and recombination rate variation amongst different primate lineages. The second will be using ancient DNA from early Medieval European skeletons to infer the population demographic dynamics of the European migration period, with a particular emphasis on the Lombards. As well as primary research duties applicants will be expected to write papers, help in grant writing and train/mentor graduate students.The successful applicant should have or will shortly obtain a PhD in the areas of population, evolutionary or anthropological genetics, while at least some computer programming experience (particularly in python, equivalent or lower level languages) is required. Prior experience analyzing 2nd generation sequencing data, analyzing ancient DNA and/or modeling demographic scenarios with genetic data is desirable. Applications will be accepted until November 3rd 2014. Applicants should a submit a State employment application, cover letter, resume, two references and a one page research statement to:Dr. Krishna R. VeeramahDepartment of Ecology & EvolutionLife Sciences Building, Room 650Stony Brook UniversityStony Brook, NY 11754-5245The official posting and online application can be found at http://bit.ly/1xUHgEy. The official REF# is: WC-S-9227-14-10-SQueries regarding this position can be made by email to: email@example.com —B_3495396793_1488282 via Gmail
PhD position: Disentangling the drivers of invasive alien trees in East Africa An exciting PhD position is available at Stellenbosch University’s Centre of Excellence for Invasion Biology (C*I*B, http://bit.ly/1vGcJWR). The C*I*B is a world-leading research centre in the field of biological invasions. The proposed project forms part of a multi-national research initiative between European and African partners. The overarching goal of the research project is to help to mitigate the effects of invasive alien trees on biodiversity, ecosystem services and human well-being in East Africa. We are seeking a creative and motivated student who wishes to carry out original research in the field of invasion biology, with a strong evolutionary focus. The PhD project is specifically aimed at understanding the drivers of alien tree invaders (Prosopis species) in East Africa and to relate species traits and habitat characteristics to invasions in East African biodiversity hotspots. The PhD candidate will determine the incidence and extent of hybridization between Prosopis species in various East African countries, assess genotype X environment interactions in these areas, assess how genotypic identity and/or incidence of hybridization links with habitat suitability, map Prosopis invasions in East African forest reserves to determine the effects of reserve isolation, proximity to propagule sources, and edge effects on invasion extent. The student will be based at Stellenbosch University (http://bit.ly/1vGcKKs) but will spent substantial periods of time in East Africa (Ethiopia, Kenya, Tanzania) to conduct field research and interact with other consortium members at various host institutions. The project is suitable for students interested in environmental management, GIS, and population ecology, population genetics and/or evolutionary biology. Applicants should hold an MSc degree in one or more of the following fields: Ecology, Botany, Evolutionary biology or Population genetics. Preference will be given to individuals with demonstrated skills in one or more of these fields and an excellent academic track record (grades, publications in international journals, etc.). Successful candidates will be fully funded for 3.5 years, for full time research, with no teaching requirements. An attractive annual stipend will be offered, along with additional expenses for research, international travel and subsistence and conference attendance. Individuals of all nationalities are eligible. To apply, please send a CV, academic transcript, contact details for at least two academic references, and a brief outline of research interests to Dr. Jaco Le Roux (firstname.lastname@example.org) and Prof. Brian van Wilgen (email@example.com) by 30 November 2014. Informal inquiries are welcome. Review of applications will begin immediately, and short-listed candidates will be contacted to set up phone/Skype interviews. The envisaged start date for the project would be March/April 2015. The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://bit.ly/1xUHgoc “Le Roux, JJ, Dr " via Gmail
The Kawahara Lab at the University of Florida, Florida Museum of Natural History is accepting one graduate student (M.S. or Ph.D.) for the fall of 2015. Research in the Kawahara Lab focuses on integrating many approaches, including phylogenomics, behavior, functional genomics, and biodiversity informatics to test hypotheses pertaining to the evolution of insects, especially Lepidoptera (butterflies and moths). Recent projects have focused on utilizing genome scale data to resolve phylogenetic relationships of Lepidoptera, study evolution of hawkmoth bat ultrasound interactions, and the diversification and evolution of Hawaiian leaf miners. The team regularly travels to conduct fieldwork in remote areas of Hawaii, Borneo, Central Africa, and the Amazon. The lab is seeking a highly motivated candidate with interests in bioinformatics, evolution, genomics, and systematics. Applicants should be proficient at writing and speaking English and enjoy working with a team of researchers. A master’s degree is desired but not required. We are located in the McGuire Center for Lepidoptera and Biodiversity on the University of Florida (UF) campus. University of Florida is one of the nation’s leading research institutions with 35,000 undergraduates, 15,000 graduate students, and over 4,500 faculty and academic staff. UF offers all resources of a top research university to study insect evolution, behavior, and genomics. In addition to the Florida Museum of Natural History (FLMNH), Florida State Collection of Arthropods (FSCA), and collections and molecular sequencing lab of the McGuire Center for Lepidoptera and Biodiversity, UF is equipped with the High-Performance Computing Center (HPC) and a state-of-the-art next-generation genome sequencing facility at the Interdisciplinary Center for Biotechnology Research (ICBR). Students can be co-advised through many departments at UF, such as the Department of Biology, Department of Entomology and Nematology, School of Natural Resources and Environment, Department of W ildlife Ecology and Conservation, School of Forest Resources and Conservation, Department of Microbiology and Cell Science, among others. The selected candidate will join a team of 3 postdocs, 5 graduate students (1 M.S., 4 Ph.D.), a lab manager, technician, undergraduate and high school students. The candidate will also have the opportunity to work and interact closely with students in other lab groups at the McGuire Center. Further information can be found on the lab website: http://bit.ly/1vGcKKi Interested candidates should contact Akito Kawahara at kawahara at flmnh.ufl.edu with a C.V. and a short paragraph explaining his or her research interests and why they would like to join the group. via Gmail
October 5, 2014
Studies characterizing the composition of host-associated (mostly human) microbiota under different conditions, such as healthy or diseased state, age progression, contrasting diets, etc. have skyrocketed in the past 5 years. There is a growing recognition that host-associated, especially the gut-associated microbiota influences host metabolism, immune responses and overall wellbeing. Understanding how the community of gut microbes evolved and functions requires applying ecological and evolutionary principles. We propose to bring together evolutionary biologists, community ecologists, microbial ecologists and medical microbiologists to develop a synthesis of the existing studies and a roadmap to move the field forward. In particular, we aim to determine what evolutionary and ecological principles can be applied to the existing data and what new data need to be gathered to increase our understanding of the biotic interactions among the gut microbes and the host. To move from describing patterns to understanding the processes, we need to develop novel mechanistic frameworks. Eco-evolutionary trait-based approaches can be a useful framework to understand the role of competitive, mutualistic and other interactions in structuring microbiota and regulating functioning. So far, there has been little interaction across relevant disciplines and this may hinder our progress in understanding the microbiota-host interactions. This meeting will help break the disciplinary barriers, establish new collaborations and achieve synergy in the analysis and synthesis of the ecology and evolution of the host-associated microbiota.
There is a tolerably well-known exercise for illustrating the graphical superiority of a Non-Metric Multidimensional Scaling (NMDS) ordination over a Principal Components Analysis (PCS) ordination. The latter is often subject to distortions, so that the relative positions in the scatter-plot of points do not represent the original measured distances between those points (see the post Distortions and artifacts in Principal Components Analysis analysis of genome data). The exercise consists of using the geographical distances between locations on a map as the input distances to the analyses. The NMDS ordination will re-create the map quite accurately while the PCA ordination will usually not do so.
Some time ago I had the idea of doing this same exercise using a data-display network. Unfortunately, I was beaten to it by Barbara Holland (2013. The rise of statistical phylogenetics. Australian and New Zealand Journal of Statistics 55: 205-220). I will go ahead, anyway, disappointed though I am.
I have chosen the Ukraine as my map. The road distances between 25 of the cities were taken from Ukraine Connections (the same data occur on several other sites, as well).
The geographical data were processed in SplitsTree to produce both a Neighbor-Joining tree and a NeighborNet network.
If these techniques are to be effective as data displays, then the positions of the cities in the line graphs should be approximately the same as those in the map. This is, indeed, roughly so, although I had to spend some time manually adjusting the branch angles in the tree (for the best match). The two graphs are more rectangular in overall shape than is the Ukraine, which is somewhat closer to a square, but the relative locations of the points in the graphs do tell you where to look for the cities on the map.
However, the network is the better of the two representations on two grounds. First, the points are constrained to certain locations, and do not need manual adjustment. Second, the network more accurately gives a sense that these are road distances, and there are multiple roads from one city to another — the tree incorrectly implies that there is only one way to get between the cities.
—_000_FF1D4D841D5E47DDBDADDF65403757ADcornelledu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Curatorial/Research Associate Ornithology and Mammalogy Collections Department of Ecology and Evolutionary Biology Cornell University The Cornell University Museum of Vertebrates (CUMV) is seeking an ornithologist or mammalogist to curate and grow the collections through an organized program of accession involving Cornell students in all aspects of museum-based activities. We are interested in a leader for all aspects of the program, from field collections through specimen preparation and curation, to use of the collections in modern specimen-based research. The successful candidate will curate the Ornithology and Mammalogy Collections (including co-supervision of a full-time collections manager) and maintain an active research program in collections-based research. The CUMV is a unit of the Department of Ecology and Evolutionary Biology and is housed in the modern Imogene Powers Johnson Center for Birds and Biodiversity, along with the Lab of Ornithology and its 200 plus faculty and staff. The CUMV holdings include over 1.25 million specimens, including over 60,000 bird and 38,000 mammal specimens and a substantial tissue collection. The CUMV includes space for teaching, specimen preparation and molecular work; a walk-in freezer, X-ray lab, dermestarium, etc. Cornell supports a diverse community of faculty, staff and students pursuing an uncommonly large number of programs and projects in vertebrate biology, ecology and evolution. Qualifications: Applicants should have a Ph.D. in ornithology, mammalogy, or related area, have broad knowledge of birds and/or mammals, have experience working with natural history collections, and display an interest in interacting with students and the broader scientific communities at the Lab, Cornell and beyond. Inquiries are encouraged to either of the co-chairs of the search committee: Prof. David W. Winkler (firstname.lastname@example.org) or Prof. Jeremy B. Searle (email@example.com). Please send a CV, three letters of reference and a letter describing your vision for future collections-based research and education to: Curator Search, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853. Review of applications will begin 20 October 2014 and continue until the position is filled. Cornell University is an equal opportunity/affirmative action employer. Applications from women and minorities are encouraged. —_000_FF1D4D841D5E47DDBDADDF65403757ADcornelledu_ Content-Type: text/html; charset=”us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable Curatorial/Research Associate
Ornithology and Mammalogy Collections
Department of Ecology and Evolutionary Biology
The Cornell University Museum of Vertebrates (CUMV) is seeking an ornithologist or mammalogist to curate and grow the collections through an organized program of accession involving Cornell students in all aspects of museum-based activities. We are interested in a leader for all aspects of the program, from field collections through specimen preparation and curation, to use of the collections in modern specimen-based research. The successful candidate will curate the Ornithology and Mammalogy Collections (including co-supervision of a full-time collections manager) and maintain an active research program in collections-based research.
The CUMV is a unit of the Department of Ecology and Evolutionary Biology and is housed in the modern Imogene Powers Johnson Center for Birds and Biodiversity, along with the Lab of Ornithology and its 200 plus faculty and staff. The CUMV holdings include over 1.25 million specimens, including over 60,000 bird and 38,000 mammal specimens and a substantial tissue collection. The CUMV includes space for teaching, specimen preparation and molecular work; a walk-in freezer, X-ray lab, dermestarium, etc. Cornell supports a diverse community of faculty, staff and students pursuing an uncommonly large number of programs and projects in vertebrate biology, ecology and evolution.
Qualifications: Applicants should have a Ph.D. in ornithology, mammalogy, or related area, have broad knowledge of birds and/or mammals, have experience working with natural history collections, and display an interest in interacting with students and the broader scientific communities at the Lab, Cornell and beyond.
Inquiries are encouraged to either of the co-chairs of the search committee: Prof. David W. Winkler (firstname.lastname@example.org) or Prof. Jeremy B. Searle (email@example.com). Please send a CV, three letters of reference and a letter describing your vision for future collections-based research and education to: Curator Search, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853. Review of applications will begin 20 October 2014 and continue until the position is filled.
Cornell University is an equal opportunity/affirmative action employer.
Applications from women and minorities are encouraged.
—_000_FF1D4D841D5E47DDBDADDF65403757ADcornelledu via Gmail
PhD opportunity - *Microbial diversity and its role in the resilience of large brown seaweeds* A PhD position focusing on interactions between brown seaweeds (Cystoseira, Fucus) in the Mediterranean Sea and associated microbial communities is currently being advertised. The grant concerns a joint PhD position between the University of Bologna (Laura Airoldi) and Ghent University (Olivier De Clerck) in the framework of the Mares programme. More information on the subject and application procedure can be found at: http://bit.ly/1nV5Thp Feel free to contact Laura Airoldi (firstname.lastname@example.org) or myself (email@example.com) for additional information. Kind regards, Olivier De Clerck Laura Airoldi Olivier De Clerck Onderzoeksgroep Algologie, UGent. Krijgslaan 281, S8, 9000 Gent; Belgium [lokaal 130.046] Tel -32-9-2648500 http://bit.ly/19FFqfP http://on.fb.me/19FFqfQ firstname.lastname@example.org via Gmail
October 4, 2014
Reminder - two weeks left before the deadline! A link to the add and the online application forms can be found here: http://bit.ly/1rKc0Dr Postdoctoral research fellow in ancient DNA and evolutionary genomics of Viking Age plants and animals Applications are invited for a two-year position as a postdoctoral research fellow in the field of ancient DNA and evolutionary genomics of Viking Age plants and animals at the Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo. The Postdoctoral fellow will be part of the team working on the project $B!H(BTracking Viking-assisted dispersal of biodiversity using ancient DNA$B!I(B funded by the Norwegian Research Council. Project description The primary objective of this project is to investigate how Viking trade and agriculture have shaped the genomic composition of plants and animals, and increase our understanding of the evolutionary heritage left in contemporary varieties. We focus on species of profound agricultural, cultural and industrial importance (horse, flax and barley) for which excellent genomic tools have recently been developed. In this project we have access to unique samples from different countries that will be analyzed using whole genome, high-throughput sequencing approaches. The successful applicant will join a multi-disciplinary, international team that brings together experts from the fields of biology, archaeology and palaeontology. Furthermore, this project forms a close collaboration between the CEES, the Natural History Museum (NHM) and the Museum of Cultural History (KHM) at the University of Oslo. Requirements Applicants must hold a PhD-degree (or other corresponding education equivalent to a Norwegian doctoral degree) with a background within population genomics, evolutionary genomics and/or ancient DNA research. The candidate should be able to document strong analytical skills and experience in the laboratory. Experience with ancient DNA, analytical or experimental, will be an advantage. The candidate will work in close collaboration with the rest of the team at CEES, NHM and KHM, as well as our national and international partners (Denmark and Great Britain) within this project. Some time will be spent visiting the collaborating partners overseas. We seek a highly motivated, enthusiastic person with the ambition to gain insight and publish papers in leading, international journals, and in possession of good interpersonal skills and willing to work in close collaboration with others. The Faculty of Mathematics and Natural Sciences has a strategic ambition of being a leading research faculty. Candidates for these fellowships will be selected in accordance with this, and expected to be in the upper segment of their class with respect to academic credentials. Please also refer to the regulations pertaining to the conditions of employment for post-doctoral fellowship positions. Language A good command of English is required. Salary (applicable for the University of Oslo) Pay Grade: 57-65 (NOK 482 800 -559 600 per year, depending on qualifications) The application must include: Application letter including a statement of interest, briefly summarizing your scientific work and interests, and a personal assessment focusing on how you fit the description of the person we seek A brief (1 A4) project plan for the research to be undertaken CV (summarizing education, positions, pedagogical experience, administrative experience and other qualifying activities) Copies of educational certificates and transcript of records A complete list of publications and unpublished works, and up to 5 academic work that applicant wishes to be considered by the evaluation committee Names and contact details of 2-3 references (name, relation to candidate, e-mail and telephone number) Foreign applicants are advised to attach an explanation of their University$B!G(Bs grading system. Please remember that all documents should be in English or a Scandinavian language. The University of Oslo has an agreement for all employees aiming to secure rights to research results a.o.: In accordance with the University of Oslo$B!G(Bs equal opportunities policy, we invite applications from all interested individuals regardless of gender or ethnicity. Application deadline: 17 October 2014 Expected Start Date: 1 April 2015 Reference number: 2014/10577 Contacts: Dr Sanne Boessenkool (email@example.com), Dr Anneleen Kool (firstname.lastname@example.org) Sanne Boessenkool via Gmail
Dear friends of NESCent, I wanted to bring your attention to additional calls for proposals. Please help us spread the word among your societies, lists, and newsletters. Cheers Craig CATALYSIS MEETINGS Proposals for Catalysis Meetings in Evolutionary Medicine are now being accepted at The National Evolutionary Synthesis Center (NESCent). We are looking to support innovative approaches to outstanding problems, specifically in areas realted to evolutionary medicine. Appropriate areas of inquiry include any field of evolutionary science that is relevant to medicine, or to human or animal health. Examples include, but are not limited to, evolution of infectious or zoonotic disease, evolutionary issues in global health, evolution of aging, evolution of fertility, autoimmune disease and allergy, evolutionary perspectives on cancer, and evolution of disease-relevant micro-organisms. Proposals that have a clear interdisciplinary focus, and involve evolutionary concepts in any health- or disease-related area, are strongly encouraged, as are proposals that demonstrate international participation and a mix of senior and emerging researchers, including graduate students. Deadline for proposals is Nov 1, 2014. All meetings must be completed by Sep 30, 2015. For more information, please see our website at http://bit.ly/1rKc0Dd GRADUATE FELLOWSHIPS for NC GRADUATE STUDENTS Proposals for 1-semester Graduate Fellowships in fields related to Evolutionary Medicine are now being accepted at The National Evolutionary Synthesis Center (NESCent). We are looking to support innovative approaches to outstanding problems in any field of evolutionary science that is relevant to medicine, or to human or animal health. Examples include, but are not limited to, evolution of infectious or zoonotic disease, evolutionary issues in global health, evolution of aging, evolution of fertility, autoimmune disease and allergy, evolutionary perspectives on cancer, and evolution of disease-relevant micro-organisms. Eligible students are those at any North Carolina academic institution with an accredited graduate program in a relevant field; students may remain resident at their home institution during the fellowship, or travel to another institution. Evidence of engagement, during the fellowship, with other activities relevant to evolutionary or comparative medicine in NC will be viewed positively. The deadlines is Nov 1 (for the spring semester 2015 fellowship), Feb 1 (for the summer semester 2015 fellowship) and Apr 1 (for the fall semester 2015fellowship). For more information, please see our website http://bit.ly/1rKc0De Craig R. McClain, Ph.D. Assistant Director of Science National Evolutionary Synthesis Center 2024 W. Main St. Suite A200, Box 104403 Durham, NC 27705 919-668-4590, email@example.com Assoc. Editor for Proceedings of the Royal Society, B http://bit.ly/1rKc0Df Chief Editor for Deep-Sea News: http://bit.ly/1ovcnTI National Evolutionary Synthesis Center: http://bit.ly/1epDrIk Research Homepage: http://bit.ly/1qTxNHt McClain Craig via Gmail
The Edinburgh Alliance for Complex Trait Genetics, E-ACTG will run its seventh meeting, sponsored by the Genetics Society, on Friday 31st October 2014 at the Royal Society of Edinburgh, 22-26 George Street, EH2 2PQ. Programme below. The event is free. Anyone wanting to attend should sign up at http://bit.ly/1vw3A2G by 24th October (or earlier if the meeting room reaches capacity). Josephine Pemberton & Chris Haley, University of Edinburgh *** 13.00 Arrival, registration, coffee and biscuits 13.30 Gail Davies (Centre for Cognitive Ageing and Cognitive Epidemiology, Edinburgh) General cognitive function: a meta-analysis of genome-wide association studies in the CHARGE Consortium (N = 53 949) 14.00 Doug Speed (UCL Genetics Institute, London) Gene-based association testing and other fun things to do with heritability analysis. 14.30 Eileen Wall (SRUC, Edinburgh) Genetic improvement options for reducing of greenhouse gas emissions from ruminant production systems. 15.00 Santosh Atanur (Institute of Genetics and Molecular Medicine, Edinburgh) Genome sequencing reveals loci under artificial selection in laboratory rats. 15.30 Tea 16.00 Jacob Moorad (Institute of Evolutionary Biology, Edinburgh) Indirect genetic effects on post-reproductive lifespan in humans. 16.30 Heather Cordell (Institute of Genetic Medicine, Newcastle University) Comparison of family-based association tests in complex genetic diseases: Application to a Brazilian family study of visceral leishmaniasis. 17.00 Peter Joshi (Centre for Population Health Sciences, Edinburgh) Inbreeding depression for complex traits in humans. 17.30 Discussion and refreshments *** Prof. J.M. Pemberton Institute of Evolutionary Biology University of Edinburgh West Mains Road EH9 3JT Tel: 0131 650 5505 Fax: 0131 650 6564 Web: http://bit.ly/1goFwKR via Gmail
Research Scientist/Engineer III Position in STEM Education Research at University of Washington The Department of Biology has an exciting opportunity for a Research Scientist/Engineer 3, working on issues in STEM education research. This is a full-time, 11-month per year position, to begin as early as November 2014 and continuing for up to five years, working on a Howard Hughes Medical Institute-funded initiative to design and implement authentic research experiences in UW Biologys introductory course sequence, based on experimental evolution in E. coli. The research scientist will develop, test, and assess the experimental evolution systems use in the introductory biology series (Biology 180, 200, 220), including setting up training protocols to build student expertise in reading the primary literature, lab safety, proper use of equipment, maintenance of lab notebooks, data acquisition and analysis, and scientific communication. The research scientist will work closely with course staff and with upper-division undergraduates who will serve as mentors for the introductory students. Requirements Candidates should have1) completed a PhD in evolutionary biology in the last three years, 2) proficiency with bioinformatics and an array of molecular biology techniques, 3) excellent organizational, interpersonal, and communication skills, and 4) a demonstrated interest in innovative teaching and discipline-based education research. English fluency is required. Post-doctoral research experience and expertise in project management and course design will be considered an asset. To apply Applicants must apply through the University of Washingtons Hiring System (http://bit.ly/1vw3x6Z) in response to Requisition #111509. In addition to your resume or curriculum vita (entered directly into the system), please also submit an application letter, statement of research interests, statement of teaching philosophy, and contact information for three references when prompted to complete the assessments. Review of applications will continue until the position is filled. Dr. Scott Freeman, Principal Lecturer Department of Biology, Box 355320 University of Washington Seattle WA 98115 USA Scott Freeman via Gmail
Postdoc in Evolutionary Genomics UC Berkeley An evolutionary genomics postdoc position is available in the laboratory of Dr. Erica Bree Rosenblum at UC Berkeley. The postdoc will join a dynamic research group and will be affiliated with the Department of Environmental Science, Policy and Management, the UC Berkeley Museum of Vertebrate Zoology, and the Berkeley Initiative for Global Change Biology. The postdoc will contribute to several funded projects in the lab that use genomic tools to address fundamental questions about the processes that generate and threaten biological diversity. The specific research focus will be finalized in collaboration with the successful applicant, but the core projects will relate to the genomics of rapid adaptive evolution and the genomics of wildlife disease. From a methodological standpoint, the postdoc will be involved in the analysis and synthesis of genome-scale datasets, with a particular emphasis on analysis of RAD, RNAseq, and exon capture datasets. The postdoc will also share res ponsibility for day-to-day lab operations including laboratory administration, regulatory compliance, and mentoring undergraduate researchers. Ideal start-date would be January 2015, but there may be enough flexibility to accommodate an earlier or later start-date. Salary will be commensurate with current NIH guidelines. More information about research activities in the Rosenblum Lab is available at http://bit.ly/YZSubD. Minimum qualifications include a Ph.D. in Biology, Computer Science, Molecular Biology or a related field. Demonstrated experience in computational or ecological genomics is essential including a track record of successful project coordination, data analysis, and manuscript preparation. A strong background in bioinformatics, proficiency coding, and basic molecular wet-lab skills are desired. Ability to communicate clearly, work independently, and interact collaboratively is essential. If interested, please send a CV, a letter of interest, and the contact information for three references to firstname.lastname@example.org by October 24, 2014. The letter of interest should be no more than 2 pages and address prior experience, current interests, career goals, and fit for the position. Please also indicate your ideal start-date. via Gmail
POSTDOCTORAL POSITIONS IN EXPERIMENTAL MICROBIAL EVOLUTION Two postdoctoral research positions are available in the Department of Biology at Indiana University. Positions will be supported with a five-year Multidisciplinary University Research Initiative (MURI) grant from the US Department of Defense (DoD) program on $B!H(BInnovation in Prokaryotic Evolution$B!I(B. The goals of the project are to reveal the molecular causes and consequences of evolution in highly replicated lines of a phylogenetically diverse range of microbial taxa in response to changes in the internal population-genetic environment (e.g., population size) and the external natural environment (i.e., starvation). We seek individuals with expertise in microbiology, bioinformatics, population genetics, and/or evolutionary theory and an ability to design long-term evolution experiments and analyze whole-genome sequencing data derived from them. This project involves collaborative work between Michael Lynch, Pat Foster, Jay Lennon, and Jake McKinlay in the Department of Biology, Indiana University, Bloomington (http://bit.ly/1cfCtA9), which has an excellent infrastructure for conducting microbiological, evolutionary, and ecological research, and Allan Drummond (University of Chicago). The positions are based at Indiana University in Bloomington, IN. Postdocs will be in residence in the Lynch Lab (http://bit.ly/YZSubv) and/or the Lennon Lab (http://bit.ly/1rUKdCB), but will have the opportunity to interact and collaborate with partnering labs. These positions are available immediately, although the start dates are somewhat flexible. Interested parties should email a cover letter containing a brief statement of research interests, a CV, and names of three potential letter writers to email@example.com. Applications will be evaluated as they are received and will continue until the position has been filled. Jay T. Lennon Associate Professor Department of Biology Indiana University 1001 E. 3rd Street Bloomington, IN 47405 812-856-0962 (office) 812-856-7235 (lab) 812-855-6082 (fax) firstname.lastname@example.org web: http://bit.ly/YZSubz wiki: indiana.edu/~lennon Lennon Jay via Gmail
—_000_D2C74099CC0943129CB5184F21A3E060exchangePrincetonEDU_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable RESEARCH TECHNICIAN POSITION AVAILABLE McBride Lab Dept. Ecology & Evolutionary Biology and Princeton Neuroscience Institute Princeton University The laboratory of Carolyn (Lindy) McBride at Princeton University is seeking a technician to support research on the molecular, neural, and evolutionary basis of host-seeking behavior in a recently evolved form of the dengue fever mosquito that specializes in biting humans. This is a unique opportunity to assist in exciting research on mosquitoes and help start a research laboratory from the ground up. Individuals looking for a research opportunity before applying to graduate school are encouraged to apply. Responsibilities — Mosquito breeding, transgenics, and behavioral experiments — Molecular genetic and neuroscientific studies using techniques such as DNA and RNA extraction, cloning, PCR based genotyping, library preparation for next-gen sequencing, microscopy, and/or electrophysiogy — General maintenance and development of the research lab, including purchasing, organization, and the training of undergraduate and graduate students — Participation in laboratory meetings and planning sessions Essential Qualifications The interested candidate should have a bachelor’s degree in biology or related field and previous experience in a research laboratory (beyond lab classes). Previous experience rearing insects and carrying out molecular biology protocols in a research setting is strongly preferred. A demonstrated interest in evolution, neuroscience, and/or genetics is also preferred. It is absolutely essential that candidates be highly organized, detail-oriented, and demonstrate enthusiasm for working and communicating with others in a collaborative lab setting. Applications Please apply online at http://bit.ly/1EccNn5 (requisition #1400714) and/or send the following in a single pdf file to email@example.com: — Cover letter explaining your qualifications and interest in the position — CV — Names and contact information for 3 references —_000_D2C74099CC0943129CB5184F21A3E060exchangePrincetonEDU_ Content-Type: text/html; charset=”Windows-1252” Content-ID: Content-Transfer-Encoding: quoted-printable RESEARCH TECHNICIAN POSITION AVAILABLE McBride Lab Dept. Ecology & Evolutionary Biology and Princeton Neuroscience Institute Princeton University The laboratory of Carolyn (Lindy) McBride at Princeton University is seeking a technician to support research on the molecular, neural, and evolutionary basis of host-seeking behavior in a recently evolved form of the dengue fever mosquito that specializes in biting humans. This is a unique opportunity to assist in exciting research on mosquitoes and help start a research laboratory from the ground up. Individuals looking for a research opportunity before applying to graduate school are encouraged to apply. Responsibilities — Mosquito breeding, transgenics, and behavioral experiments — Molecular genetic and neuroscientific studies using techniques such as DNA and RNA extraction, cloning, PCR based genotyping, library preparation for next-gen sequencing, microscopy, and/or electrophysiogy — General maintenance and development of the research lab, including purchasing, organization, and the training of undergraduate and graduate students — Participation in laboratory meetings and planning sessions Essential Qualifications The interested candidate should have a bachelor’s degree in biology or related field and previous experience in a research laboratory (beyond lab classes). Previous experience rearing insects and carrying out molecular biology protocols in a research setting is strongly preferred. A demonstrated interest in evolution, neuroscience, and/or genetics is also preferred. It is absolutely essential that candidates be highly organized, detail-oriented, and demonstrate enthusiasm for working and communicating with others in a collaborative lab setting. Applications Please apply online at http://bit.ly/1EccNn5 (requisition #1400714) and/or send the following in a single pdf file to firstname.lastname@example.org: — Cover letter explaining your qualifications and interest in the position — CV — Names and contact information for 3 references —_000_D2C74099CC0943129CB5184F21A3E060exchangePrincetonEDU via Gmail
Postdoctoral Position in Microbial Ecology and Evolution Jessica Green at the University of Oregon Green (http://bit.ly/1hBUxFf) is currently seeking a postdoctoral researcher to explore fundamental questions in microbial ecology and evolution. Applicants should have a PhD in a biological, computational, mathematical, or statistical field with extensive training using theory and/or modeling to understand the ecology and evolution of complex biological communities, and strong writing skills. Experience developing and applying quantitative phylogenetic ecological methods is highly desirable, but not explicitly required for candidates who have otherwise demonstrated strong quantitative skills. The successful candidate will play a key role in the Seagrass Microbiome Project (http://bit.ly/1pzwQlr) in collaboration among Jonathan Eisen http://bit.ly/1pzwTxI), Jay Stachowicz http://bit.ly/1pzwTxJ, and Jenna Lang (http://bit.ly/1rVnWDR) at the University of California, Davis. The Seagrass Microbiome Project aims to integrate the long interest in seagrass ecology and ecosystem science with more recent work on microbiomes to produce a deeper, more mechanistic understanding of the ecology and evolution of seagrasses and the ecosystems on which they depend. Our studies of the community of microorganisms that live in and on seagrasses V the seagrass microbiome V will contribute to a broader understanding of host-microbe systems biology, and will benefit from ongoing University of Oregon research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://bit.ly/1pzwQlx) and the Biology and Built Environment Center (http://bit.ly/1jC1tsQ). The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (email@example.com). To apply A complete application will consist of the following materials: (1) a brief cover letter explaining your background and career interests (2) CV (including publications) (3) names and contact information for three references Submit materials to firstname.lastname@example.org. Subject: Posting 14431 To ensure consideration, please submit applications by November 1, 2014, but the position will remain open until filled. Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status. via Gmail
Applicants can apply at www.iapws.com or contact me directly at email@example.com Thank You *Fisheries Biologist II (Mammal Genetics Technician)* FLSA Exempt *Location:* Lafayette, LA *Reports to: * Project Manager, NOAA unit leaders *Period of Performance:* Two years from the official start date or until the funds for the position are depleted. *Summary:* The SEFSC Marine Mammal Program (MMP) is responsible for science-based assessment and conservation of marine mammal populations in the Southeast Region. Accurate assessments of population status require an accounting of the human-induced mortalities, accurate estimates of abundance, and a complete understanding of the population structure and mixing rates among populations. The MMP conducts small-boat field research and tissue samples collected from strandings and obtained through remote dart-biopsy techniques from both small and large vessels provide DNA for genetic studies of population structure and health at the Lafayette facility which houses a state-of-the-art molecular genetics laboratory. In addition to genetic analyses of population structure and gene flow, the genetics lab conducts research into the evolutionary relationships among cetacean species, social structure, and genetic species identifications. Tissue samples are also used to examine the levels of pollutants in the bodies of marine mammals. The contractor (Mammal Genetics Technician) shall work within the SEFSC Protected Resources and Biodiversity Divisions Marine Mammal Unit and will be located in Lafayette, Louisiana. The contractor shall support research projects focused on molecular genetic analyses of marine mammal populations and species. The contractor shall assist with processing marine mammal tissue samples for collection of a variety of types of molecular genetic data and shall play a role in the day-to-day maintenance of a molecular genetics lab. The Contractor shall: perform DNA extractions from cetacean and pinniped species tissue samples collected from strandings, live captures, bycatch and biopsies; perform PCR (polymerase chain) reactions, gel electrophoresis; collect DNA sequence and microsatellite data on ABI 310 or ABI 3130 automated Genetic Analyzers; and maintain an accurate and complete laboratory notebook. The Contractor shall log and archive tissue samples, DNAs and associated data into a database. The Contractor shall conduct data QA/QC, assist with basic data analysis, provide summaries of progress and results, provide data reports and presentations. The Contractor shall perform basic laboratory upkeep and maintenance as assigned, prepare reagents, prepare, ship and log tissue sample tubes, participate in bi-weekly laboratory meetings. The contractor may be required to perform marine mammal fieldwork as necessary. *Essential Job Functions:* - Knowledge of applying basic concepts, principles and methodologies of marine mammal science or related biological field sufficient to independently perform scientific tasks using standard molecular methods and techniques. - Proficiency with DNA extractions, the polymerase chain reaction (PCR), DNA sequencing and microsatellite data collection and ability to independently perform scientific tasks using standard molecular biological methods and techniques. - Experience with analysis of sequence or microsatellite data; computer literate and experience with common word processing, spreadsheet, statistical and graphics programs. - Capable of writing reports at the college level and making oral presentations. - Excellent problem solving and critical thinking skills. Good organizational skills and ability to plan daily duties. Ability to work independently as well as with other employees. Clear oral and written communication with Federal Managers and other employees. *Level of Supervision:* None *Education and Experience:* MS Degree in Marine Science or a related field of study (including Genetics, Molecular Biology, or Biology) or BS Degree in Marine Science or a related field of study (including Genetics, Molecular Biology, Biology) plus three (3) years of relevant experience. *License and Certifications:* None *Physical Demands/Working Environment:* The contractor may be required to perform marine mammal fieldwork as necessary. Overtime (up to 20 hours per week, on occasion) may be required. *Travel:* Periodic travel will be required for field work in estuaries and coastal regions of the Gulf of Mexico. *Security Clearance:* NACI - National Agency Check plus written Inquiries via Gmail
Doctoral student positions in evolutionary immunology of human and nonhuman primates Doctoral positions in evolutionary immunology and functional genomics are available in the Brinkworth Evolutionary Immunology and Genomics lab, Department of Anthropology, University of Illinois Urbana-Champaign. The lab investigates how primate genome expression has diverged and diversified, with particular attention paid to the evolution of the human innate immune response. Applicants should have strong interests in human/non-human primate evolution, immunology, genomics, bioinformatics or infectious disease. Positions are contingent on acceptance into the Department of Anthropology PhD program. Projects: Students will be involved in the conceptual development, execution and publication of research concerned with evolutionary genomics, including but not limited to, primate comparative immunity, and the diversification of the human immune response. Students will use a broad range of immunological and cell biology techniques, in combination with bioinformatic methods to investigate questions of how immune function has evolved in humans and other primates. Funding: Students are guaranteed full funding for 5.5 years. Support is provided via a combination of RAships, TAships and writing fellowships. Who should apply: Candidates with an interest in the evolution of immune function/evolutionary genomics. Diverse educational backgrounds are welcome including anthropology, biology, bioinformatics, economics, computer science, epidemiology etc. Experience with genetics/genomics, immunological bench and analytical methods and clean technique are preferred, but not necessary. UIUC: The positions offer an exceptional opportunity for highly collaborative research in a new facility, using state of the art immunological, genomic and computational techniques to answer questions relevant to both human evolutionary biology and disease. The UIUC is a competitive very high research/R1 institution, with a selective and very well respected Department of Anthropology and a worldwide reputation for excellence in genomics, supercomputing and engineering. The Institute for Genomic Biology, The Beckman Institute for Advanced Science and Technology, National Center for Supercomputing Applications foster a thriving research environment and provide many unique resources that can be woven into a students projects. Located a few hours outside of Chicago, Urbana-Champaign is home to the Krannert Center for the Performing Arts, Roger Ebert film Festival, Krannert Art and Spurlock Museums, a host of local cooperative theatres and farmers and art markets. Chicago is readily accessible via Amtrak, bus or car. Application and Deadline: Queries should be sent to jfbrinkworth AT gmail DOT com. Please include a statement of interest (1 page), and a CV describing your previous education/internships/projects/employment/scholarships and publications, along with contact information for three references. Positions in this lab require acceptance into the UIUC Department of Anthropology PhD program. Applications for acceptance into the graduate program should be made online http://bit.ly/1uJeIMY by the *program deadline December 1, 2014. *Please visit the labs website at www.jfbrinkworth.com for lab information. Jessica Brinkworth via Gmail
We are looking for a researcher that has a strong background in phylogenetics to be part of a grant application for NIH, together with NIH colleagues, named: “Using phylogenetic evolutionary tools to study cancer biology: from big omic data to personalized medicine”. If you have such a background and are interested in doing a 2-year postdoc in the beautiful and green Washington DC, both at NIH and the historical Howard University, at multi-awarded lab, followed by strong chances of getting a potential tenure-track position, please contact Rui Diogo and send him your CV by email: firstname.lastname@example.org If you know someone that has such a background, please forward him/her this message. To see other subjects studied in the lab, please see www.ruidiogolab.com. Thanks, Rui Rui Diogo, PhD in Evolutionary and Functional Morphology & PhD in Hominid Paleobiology | Assistant Prof. at Howard Univ. & Resource Faculty at GWU Dep. of Anatomy, Howard Univ. College of Medicine, 520 W St. NW, Numa Adams Building, room 1111, Washington DC 20059, USA. Homepage: www.ruidiogolab.com email@example.com via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution