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September 18, 2014

07:19

Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic data sets grow larger, spanning thousands of samples and millions of markers, there is a need for a fast and efficient implementation of these scans for general use. Here, we present selscan, an efficient multithreaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population EHH (XPEHH). selscan accepts phased genotypes in multiple formats, including TPED, and performs extremely well on both simulated and real data and over an order of magnitude faster than existing available implementations. It calculates iHS on chromosome 22 (22,147 loci) across 204 CEU haplotypes in 353 s on one thread (33 s on 16 threads) and calculates XPEHH for the same data relative to 210 YRI haplotypes in 578 s on one thread (52 s on 16 threads). Source code and binaries (Windows, OSX, and Linux) are available at https://github.com/szpiech/selscan.

01:34
Note we have not yet begun reviewing applications, so you have a few weeks to get your materials in! The Department of Biology at the University of North Carolina at Chapel Hill seeks applicants for a permanent 9 month Lecturer position, effective January 1, 2015. The position involves teaching 2-3 classes per semester, including courses in Ecology/Evolution and Introductory Biology. The successful candidate will also contribute to the implementation and evaluation of newly funded programs to bring evidence-based teaching methods to introductory courses, collaborate with faculty conducting biology education research, and work closely with tenure-track faculty in their discipline. Applicants should have a Ph.D. in the biological sciences or science education with at least one semester of full-time college teaching as instructor of record. Candidates should have clearly demonstrated a commitment to using evidence-based teaching methods in the classroom and have strong interdisciplinary content knowledge. To apply: Click on http://bit.ly/1v9Fvmq from any internet browser to apply for this position. Candidates must submit a letter of interest, a CV, and a concise statement of teaching philosophy and experience. In addition, candidates must also submit a link to a 10-minute teaching video as part of the application. We require 2 letters of reference to be emailed with the subject line of $B!H(BLECTURER$B!I(B to fncrawf@email.unc.edu The University of North Carolina is an Equal Opportunity Employer. http://bit.ly/19fawEi JB John Bruno Professor, Dept of Biology UNC Chapel Hill www.johnfbruno.com “Bruno, John” via Gmail
Source: EVOLDIR
01:20
The University of California, Los Angeles (UCLA) Department of Ecology and Evolutionary Biology seeks to fill an open-rank (tenure track or tenured) faculty position in Plant Sciences. Qualified candidates will have a Ph.D. in a related field of biological sciences. We are interested in all subfields within organismal plant biology but especially in candidates with experimental or comparative approaches in plant evolution, systematics, ecology, conservation biology, and/or biogeography. The successful candidate is expected to establish an internationally recognized and externally funded research program. Although not required, we encourage applicants with interest in the Mildred E. Mathias Botanical Garden, a seven-acre garden on the UCLA campus, through teaching, research, and/or public outreach/education to indicate so in their cover letter. As a campus with a diverse student body, individuals with a history of mentoring under-represented minorities in the sciences are encouraged to apply and include details in cover letter. Applicants should submit materials online to http://bit.ly/Xm6P1c including detailed cover letter; curriculum vitae; statements of research and teaching; and names and contact information of four references. Review of candidates will begin on October 3, 2014 and continue until the position is filled. Please use job number JPF00342 in all correspondence. Additional information about the Department and the Botanical Garden and may be found at http://bit.ly/1wGtwN2 and http://bit.ly/Xm6Rq0 respectively. Inquiries regarding the position should be directed to Grace Angus (gracea@lifesci.ucla.edu) or Search Chair, Professor Lawren Sack (lawrensack@ucla.edu). Women and minority applicants are encouraged to apply. The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see: UC Nondiscrimination & Affirmative Action Policy “Sork, Victoria” via Gmail
Source: EVOLDIR
01:01
FACULTY POSITION IN MICROBIOME RESEARCH THE UNIVERSITY OF CONNECTICUT The Department of Molecular and Cell Biology (mcb.uconn.edu) in the College of Liberal Arts and Sciences (clas.uconn.edu) and the recently established Institute for Systems Genomics (http://bit.ly/1wGpDYt) invite applications for a tenure-track faculty position at the assistant professor level, with an expected start date of August 23, 2015. We are particularly interested in candidates working on microbiomes, host associated microbial communities, or microbiome ecology and evolution. The Department has strengths in microbial ecology, evolutionary biology, and symbiosis research, as well as other research clusters in cell biology, genetics, genomics, structural biology, biochemistry and biophysics. Information on microbiological research at the University of Connecticut can be found at http://bit.ly/Xm2IlG. Successful candidates will be expected to actively engage in collaborative research projects and to teach in the departmental and new institute-based graduate programs. About the Institute for Systems Genomics The University of Connecticut recently established the Institute for Systems Genomics (http://bit.ly/1wGpDYv) to coalesce the interdisciplinary research strengths of 10 schools and colleges at the university ( http://bit.ly/Xm2HOP) and the Jackson Laboratory (http://www.jax.org/). The Institute leverages the significant investment from the state, including the $865M Bioscience CT initiative, $172M Tech Park program, the $200M Bioscience Innovation Fund, and $1.7B Next Generation CT. Appointment Terms This is a 9-month tenure-track position with an expected start date of August 23, 2015. The successful candidate will have a primary academic appointment in the Department of Molecular and Cell Biology within the College of Liberal Arts and Sciences and a joint appointment in the Institute for Systems Genomics. Salary and rank will be commensurate with qualifications. Primary Duties The successful candidates will: * Develop, sustain, and grow an externally funded research program of excellence * Teach undergraduate and graduate courses that meet the curricular needs of the Department of Molecular and Cell Biology and the Institute for Systems Genomics * Advise and mentor undergraduate and graduate students. * Provide service and leadership to all units of the University of Connecticut, to external academic and scientific communities, and to the general public. Minimum Qualifications 1. Completion of all requirements for a Ph.D. in an appropriate field by the time of the appointment. Equivalent foreign degrees are acceptable. 2. Postdoctoral experience 3. A background that provides preparation for teaching excellence in undergraduate and graduate courses 4. Excellent oral and written communication skills 5. Demonstrated success in original research, and publication of that work in archival journals. Preferred Qualifications 1. Possess the ability to contribute to the diversity and excellence of the learning experience through research, teaching and/or public genomic literacy engagement 2. Relevant teaching experience 3. Expertise that complements current research strengths in the MCB Department and the ISG 4. Experience with oral presentations at national or international scientific meetings 5. Record of developing research grant applications to federal funding agencies. To Apply Please apply online using Husky Hire to submit a cover letter, curriculum vita, list of references, research plan, teaching statement, and other applicable materials. The required submission format is a single PDF file in the order listed. In addition, applicants should arrange to have at least three letters of reference sent to microbiome@uconn.edu as a PDF document on letterhead with signature. To ensure full consideration, applications should be received by December 1, 2014. Employment of the successful candidate will be contingent upon the successful completion of a pre-employment criminal background check. (Search # 2015104) Link to advertisement on Husky hire: http://bit.ly/Xm2HOQ This job posting is scheduled to be removed at 11:59 PM eastern on December 1, 2014. All employees are subject to adherence to the State Code of Ethics which may be found at http://1.usa.gov/1wGpDYy. The University of Connecticut is committed to building and supporting a multicultural and diverse community of students, faculty and staff. The diversity of students, faculty and staff continues to increase, as does the number of honors students, valedictorians and salutatorians who consistently make UConn their top choice. More than 100 research centers and institutes serve the Universitys teaching, research, diversity, and outreach missions, leading to UConns ranking as one of the nations top research universities. UConns faculty and staff are the critical link to fostering and expanding our vibrant, multicultural and diverse University community. As an Affirmative Action/Equal Employment Opportunity employer, UConn encourages applications from women, veterans, people with disabilities and members of traditionally underrepresented populations. J. Peter Gogarten Board of Trustees Distinguished Professor and Microbiology Program Chair Department of Molecular and Cell Biology, Co-Chair of the Bioinformatics Facility at the UConn Biotechnology/Bioservices Center 91 North Eagleville Road, Unit 3125, BPB 404 Storrs CT 06269-3125 USA Phone: 860 486 4061 (office) 860 486 1887 (lab) 860 465 6267 (cell) FAX: 860 486 4331 Email: gogarten@uconn.edu www: http://bit.ly/Xm2HOS JohannPeter Gogarten via Gmail
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01:01
Bioinformatics Scientist - 2-3 years limited term Job Description Bayer Biologics, a division of Bayer CropScience in Davis, CA, is currently seeking to fill a Bioinformatics Scientist position within the Biologics Informatics group. The candidate will be responsible for: . Participating in a multi-disciplinary team of scientists to offer bioinformatics, genomics, transcriptomics and other omics solutions for controlling pests and diseases in plant and promoting plant health using microbes; . Proactively identifying and incorporating new algorithms and technology to automate the analysis of microbial genomes and to extend the features of existing analysis pipeline; . Understanding the dynamics of plant, microbe and pest/pathogen interaction using various omics technologies; . Managing next-generation sequencing (NGS) data and analyses; . Training research staff on the use of relevant bioinformatics software and tools; . Working with other non-bioinformatics team member in the Informatics group to understand their roles and to serve as backups as needed; . Communicating effectively through listening, documentations and presentations, especially using compelling visualization tools to share analysis and interpretation of data. The candidate is required to possess the following: . M.S or Ph.D. or equivalent in Computational Biology, Bioinformatics, Genomics, Microbiology, Plant Biology or related field and any level of post-graduate industry and/or academic experience; . Ability to handle a large data set efficiently using scripts, particularly in the analysis of NGS data; . Familiar with commercial and open-source bioinformatics tools; . In depth familiarity with various public genomic databases; . Genome assembly of microbial genomes; . Experiences in three or more of the following areas: comparative genomics, transcriptome sequencing analysis, phylogenetic analysis, pathway modeling and analysis, metagenomics analysis, and/or genome wide association studies. Preferred Skills/Experience: . Experiences working in the biotech sector focusing on plant health and crop protection; . Knowledge of statistical software tools and packages; . Familiar with SQL and relational database, particularly PostgreSQL; . Fluent in Python, Perl, or other scripting languages; . Previous laboratory experience; . Knowledge of bacterial and plant genetics; . Working with high performance computing clusters. Thank you, Matt Armstrong Senior Recruiter Bayer Corporation HR//Services 100 Bayer Road Pittsburgh, PA 15205-9741 USA Office: (412) 778-6688 Email: matthew.armstrong@bayer.com Web: http://www.bayer.com Career Site: http://bit.ly/Xm2HOK Matthew Armstrong via Gmail
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00:29
Subject Header: Graduate Position: DrexelUniversity.SymbiosisAndAntEvolution The Russell lab at Drexel University seeks driven and enthusiastic Ph.D candidates to join them in the Department of Biology for the Fall of 2015. The best applicants will have background experience in molecular ecology, microbiology, microscopy, or entomology. Students would work on a collaborative, NSF-funded project focused on symbiosis in Cephalotes ants (NSF Award ID 1442144; url: http://1.usa.gov/1sspJMF) The central theme in the Russell lab is the ecology and evolution of symbiosis, and we are addressing the following questions in the ant system: What are the functions of symbiotic gut bacteria in herbivorous ants? How do the genomes of gut symbionts evolve and how do genome evolution and functional genomic signatures relate to symbiont roles in ant biology? What features correlate with the composition of symbiotic communities across the ants? What do such correlations tell us about the likely causes and consequences of symbiosis in this group? We are specifically interested in the question of whether microbes have facilitated the origins of herbivory across the ants, and are using experimental and metagenomic approaches to address this possibility. Collaborators on this project come from other departments at Drexel and several renowned institutions beyond, providing access to a wide network with diverse expertise. Students will be trained in the realms of molecular ecology, metagenomics, experimental biology, and field research. Through Jake Russells joint appointment with Drexels new Biodiversity, Earth, and Environmental Sciences, students will interact with a broad range of faculty and other grad students with interests in organismal biology, systematics, ecology, and evolution. FOR MORE INFORMATION Russell lab website: http://bit.ly/1d5fUik Researchgate website: http://bit.ly/1aboa1M Application website: http://bit.ly/1mdYgla Biology department website: http://bit.ly/1sspMId BEES department website: http://bit.ly/1mdYdG9 Interested students SHOULD contact Jake Russell to discuss their background and aspiraitons for Ph.D research. Dr. Jacob A. Russell Associate Professor Department of Biology Drexel University Philadelphia, PA 19104 phone: 215-895-1643 e-mail: jar337@drexel.edu “Dr. Jacob Russell” via Gmail
Source: EVOLDIR
00:13
—_000_1728EEFA12FC4C17B018386BA72FF2F1siedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable NEXT GENERATION PTERIDOLOGY An International Conference on Lycophyte & Fern Research 13th Smithsonian Botanical Symposium 12th Symposium of the International Organization of Plant Biosystematists 1-5 June 2015 in Washington D.C. National Museum of Natural History & United States Botanic Garden http://bit.ly/1u2HO9P If you have questions, or would like to be added to the distribution list for conference-related announcements, please email: sbs@si.edu CALL FOR COLLOQUIA Each colloquium will consist of either six 30-minute or twelve 15-minute time slots and will likely include a combination of invited and contributed presentations. Topics centered on newly emerging fields, synthesizing existing areas of research, or otherwise being of broad interest will be most competitive. Colloquium organizers are expected to assemble a diverse (in terms of gender, seniority, nationality, etc.) lineup of speakers. Colloquium proposals should include: (1) the colloquium title; (2) the names and institutional affiliations of the organizers; (3) a short abstract outlining the rationale and goals of the colloquium; (4) a preference for 30-minute or 15-minute time slots; and (5) a list of proposed speakers, with institutional affiliations and focal areas (please also indicate whether or not each speaker has been contacted and is planning to attend). Proposals (PDF) should be emailed to Eric Schuettpelz (schuettpelze@si.edu), who will confirm receipt. The deadline for full consideration of colloquium proposals by the selection committee is 1 October 2014. CALL FOR WORKSHOPS Each workshop will focus on a specific topic and directly engage the participants in a particular activity. Possible formats or elements may include hands-on activities, demonstrations, tutorials, discussions. Workshops relevant to newly emerging fields, targeting understudied/neglected topics, or otherwise being of broad interest will be most competitive. Workshop proposals should include: (1) the workshop title; (2) the names and institutional affiliations of the organizers; (3) a short abstract outlining the rationale and goals of the workshop; (4) the preferred duration of the workshop; and (5) the anticipated number of participants. Proposals (PDF) should be emailed to Eric Schuettpelz (schuettpelze@si.edu), who will confirm receipt. The deadline for full consideration of workshops proposals by the selection committee is 15 October 2014. —_000_1728EEFA12FC4C17B018386BA72FF2F1siedu_ Content-Type: text/html; charset=”us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable NEXT GENERATION PTERIDOLOGY An International Conference on Lycophyte & Fern Research 13th Smithsonian Botanical Symposium 12th Symposium of the International Organization of Plant Biosystematists 1-5 June 2015 in Washington D.C. National Museum of Natural History & United States Botanic Gardenhttp://bit.ly/1u2HO9P If you have questions, or would like to be added to the distribution list for conference-related announcements, please email: sbs@si.eduCALL FOR COLLOQUIA Each colloquium will consist of either six 30-minute or twelve 15-minute time slots and will likely include a combination of invited and contributed presentations. Topics centered on newly emerging fields, synthesizing existing areas of research, or otherwise being of broad interest will be most competitive. Colloquium organizers are expected to assemble a diverse (in terms of gender, seniority, nationality, etc.) lineup of speakers. Colloquium proposals should include: (1) the colloquium title; (2) the names and institutional affiliations of the organizers; (3) a short abstract outlining the rationale and goals of the colloquium; (4) a preference for 30-minute or 15-minute time slots; and (5) a list of proposed speakers, with institutional affiliations and focal areas (please also indicate whether or not each speaker has been contacted and is planning to attend). Proposals (PDF) should be emailed to Eric Schuettpelz (schuettpelze@si.edu), who will confirm receipt. The deadline for full consideration of colloquium proposals by the selection committee is 1 October 2014. CALL FOR WORKSHOPS Each workshop will focus on a specific topic and directly engage the participants in a particular activity. Possible formats or elements may include hands-on activities, demonstrations, tutorials, discussions. Workshops relevant to newly emerging fields, targeting understudied/neglected topics, or otherwise being of broad interest will be most competitive. Workshop proposals should include: (1) the workshop title; (2) the names and institutional affiliations of the organizers; (3) a short abstract outlining the rationale and goals of the workshop; (4) the preferred duration of the workshop; and (5) the anticipated number of participants. Proposals (PDF) should be emailed to Eric Schuettpelz (schuettpelze@si.edu), who will confirm receipt. The deadline for full consideration of workshops proposals by the selection committee is 15 October 2014. —_000_1728EEFA12FC4C17B018386BA72FF2F1siedu via Gmail
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00:13
—Apple-Mail-20-1008958027 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=”us-ascii” TENURE TRACK, ASSISTANT PROFESSOR PLANT BIOLOGY (ANY SPECIALTY OR STUDY SYSTEM) DEPARTMENT OF BOTANY OKLAHOMA STATE UNIVERSITY APPLICATION REVIEW BEGINS NOVEMBER 1, 2014 The Department of Botany at Oklahoma State University in Stillwater (http://bit.ly/XlS3aM) seeks to hire a tenure-track Assistant Professor in Plant Biology to begin August 2015. The ideal candidate will address fundamental questions in biology with a focus on plants, and will complement or build upon departmental strengths in cell and molecular biology, evolutionary biology, and ecology. The successful applicant will contribute to undergraduate and graduate teaching and mentoring, and is expected to build an innovative externally-funded research program. Ph.D. in plant biology or related field is required; postdoctoral experience is desired. Submit application to mary.kendall@okstate.edu. In a single pdf, include cover letter, CV, statements of research accomplishments and future objectives, teaching philosophy and goals, and contact information for at least four references. Review of applications will begin November 1 and continue until position is filled, contingent u pon available funding. Contact information: Linda Watson, linda.watson10@okstate.edu, 405-744-5559. http://bit.ly/XlS3aM Oklahoma State University is an AA/EEO/E-Verify employer committed to diversity. All qualified applicants will receive consideration for employment and will not be discriminated against based on race, color, religion, sex, national origin, disability or protected veteran status. OSU-Stillwater is a tobacco-free campus. -Mark Fishbein —Apple-Mail-20-1008958027 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=”us-ascii” TENURE TRACK, ASSISTANT PROFESSORPLANT BIOLOGY (ANY SPECIALTY OR STUDY SYSTEM)DEPARTMENT OF BOTANYOKLAHOMA STATE UNIVERSITYAPPLICATION REVIEW BEGINS NOVEMBER 1, 2014The Department of Botany at Oklahoma State University in Stillwater (http://bit.ly/XlS3aM) seeks to hire a tenure-track Assistant Professor in Plant Biology to begin August 2015. The ideal candidate will address fundamental questions in biology with a focus on plants, and will complement or build upon departmental strengths in cell and molecular biology, evolutionary biology, and ecology. The successful applicant will contribute to undergraduate and graduate teaching and mentoring, and is expected to build an innovative externally-funded research program. Ph.D. in plant biology or related field is required; postdoctoral experience is desired. Submit application to mary.kendall@okstate.edu. In a single pdf, include cover letter, CV, statements of research accomplishments and future objectives, teaching philosophy and goals, and contact information for at least four references. Review of applications will begin November 1 and continue until position is filled, contingent upon available funding. Contact information: Linda Watson, linda.watson10@okstate.edu, 405-744-5559.  http://bit.ly/XlS3aM Oklahoma State University is an AA/EEO/E-Verify employer committed to diversity.  All qualified applicants will receive consideration for employment and will not be discriminated against based on race, color, religion, sex, national origin, disability or protected veteran status.  OSU-Stillwater is a tobacco-free campus. -Mark Fishbein —Apple-Mail-20-100895802 via Gmail
00:13
*MS position*: A graduate research assistantship position (NSF funded) is available in the lab of Dr. Kyle Piller in the Department of Biological Sciences at Southeastern Louisiana University. The student will develop a MS project focusing on molecular systematics and evolution of the freshwater fish family Goodeidae (Teleostomi). The applicant should have previous lab experience, including DNA extraction and PCR amplification, though training in these areas can be provided. There will likely be opportunities for international travel. The student will be part of a dynamic and active lab that addresses general questions in fish biodiversity. Ideally, the applicant should be able to begin the position in January 2015, but a later start date could be considered. Please send inquiries to Kyle Piller (kyle.piller@selu.edu). Kyle R. Piller, PhD Professor, Curator of Vertebrates, and Graduate Coordinator Southeastern Louisiana University, Dept. of Biological Sciences Hammond, LA 70402 Kyle.Piller@selu.edu 985-549-2191 www.kylepiller.com Kyle Piller via Gmail
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September 17, 2014

23:41
Dear EvolDir Members, As part of a meta-analysis on bee population genetics, I request information regarding population differentiation indices in bees. This request is part of a collaborative study between myself, Shalene Jha (Assistant Professor in the Department of Integrative Biology at the University of Texas at Austin), and Margarita López-Uribe (Postdoctoral Researcher at North Carolina State University). So far, we have examined studies acquired through the Web of Science, but we would like to increase our sample size with the incorporation of additional studies (published or unpublished). Specifically, we are looking for data sets where bee population genetics analyses have been conducted with: at least 5 microsatellite markers at least 20 unrelated individual per population at least 5 populations If you have one or more data sets that satisfy these criteria and are willing to contribute, please provide us with the reference to your work (if published) and the Fst estimator with 95% CI. We would also be interested in G’st (Hedrick 1995) and Jost’s D (Jost 2008) if you have those available, too. Your contribution would obviously be acknowledged and your publication(s) cited. We’d like to publicly thank the individuals whom we’ve already contacted directly and who generously offered their data. Thank you very much in advance Antonella Soro antonella.soro@zoologie.uni-halle.de Dr. Antonella Soro Institut für Biologie / Allgemeine Zoologie Martin-Luther-Universität Halle-Wittenberg Hoher Weg 8 D-06120 Halle (Saale) Germany t: 0049 345 55 26 504 f: 0049 345 55 27 428 Antonella Soro via Gmail
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00:27
ASSISTANT PROFESSOR POSITION UNIVERSITY OF NEBRASKA-LINCOLN (UNL) SCHOOL OF BIOLOGICAL SCIENCES The School of Biological Sciences continues to expand its faculty and invites nominations and applications for a tenure-track, assistant professor position in Infectious Disease Biology. For this academic-year position we seek a scientist who studies the ecology and evolution of infectious disease. The successful candidate will study population processes of infectious agents and work at the interface between theoretical models and empirical data. An interdisciplinary research approach is encouraged, as the successful candidate will have excellent opportunities to work with other faculty in fields of virology, parasitology, microbiology, epidemiology, population biology, evolutionary ecology, mathematical biology, and stress biology. It is expected that the successful candidate will establish a nationally recognized and extramurally funded research program and contribute to the undergraduate and graduate teaching missions of the School of Biological Sciences. A PhD (or equivalent) and experience in infectious disease biology or a related field is required. A minimum of one year of postdoctoral research experience is preferred. This position is part of the strategic plans of UNL, the College of Arts and Sciences and the School of Biological Sciences directed to strengthen the life sciences. The successful candidate will receive a highly competitive start-up package. Lincoln, Nebraska boasts an outstanding quality of life that includes a vibrant downtown with lively music and art scene and a collection of over 120 parks and 130 miles of bike trails, plus a low cost of living. To learn more about the University of Nebraska and the School of Biological Sciences, visit http://bit.ly/IhoxM6. Applicants should go to http://bit.ly/1cwLj13, search for requisition number F_140108 complete the Faculty Academic/Administrative Information form, attach a letter of application, Curriculum Vitae, a statement of research plans, a statement of teaching interests, and include the names and contact information for three references. Questions regarding the application process may be sent to biologysearch@unl.edu. Review of applications will begin on November 15, 2014 and continue until the position is filled or the search is closed. The University of Nebraska is committed to a pluralistic campus community through affirmative action, equal opportunity, work-life balance, and dual careers. Kristi Montooth Associate Professor of Biology University of Nebraska kmontooth2@unl.edu Kristi Montooth via Gmail
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September 16, 2014

23:55

Research Scientist Position in Genomics A research scientist position in bioinformatics and computational biology is available in the Malone Laboratory of Gene Dosage and Evolution. The laboratory addresses questions of gene dosage, aneuploidy, sex chromosome evolution, and sex determination to ultimately understand the relationship between gene dose, genome balance, and phenotype. The research scientist will take part in de novo assembly analyses of several frog species and analyze a variety of high-throughput sequencing datasets to address questions of dose, dosage compensation, and genome evolution. Proficiency with multiple scripting languages, high-throughput sequencing analysis, and tools for computational, comparative, and evolutionary genomic analysis are required. The environment for genomic research at the University of Connecticut is vibrant, including the Institute of Systems Genomics, University of Connecticut Health Center, Jackson Laboratory for Genomic Medicine, and Center for Genome Innovation. These research institutions are bolstered by a 1.5+ billion dollar investment in STEM by the state of Connecticut that will produce major advances in genomics and personalized medicine. The Malone laboratory interacts closely with these centers and resources, creating exciting new avenues for answering questions in genome biology. Candidates should expect to engage with the local genome analysis community, develop and pursue their own research ideas, and receive mentoring and guidance from the PI. Applicants should send a single PDF file that contains a cover letter describing your research interests and experience (maximum 2 pages), C.V., and contact information for three references to john.malone@uconn.edu. Review of applications will begin 30 September and continue until the position is filled. Start period: January 2015. Candidates interested in a postdoctoral position are also encouraged to apply and informal inquires from candidates with other backgrounds in genomics and evolutionary biology are welcome. The University of Connecticut is an EEO/AA employer John H. Malone, PhD Assistant Professor of Genetics and Genomics Institute of Systems Genomics Department of Molecular and Cell Biology University of Connecticut http://bit.ly/1u5Io2T john.malone@uconn.edu via Gmail

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23:22
Hello, I wonder if anyone out there has a pdf of this paper please. Boesiger, E., 1968: Estimation globale de l’age des femelles de Drosophila melanogaster capturees dans des populations oaturelles. Compte Rendu des Seances de la Societe de Biologie, 162: 358-361 Thanks in advance David Prof DJ Hosken University of Exeter, Cornwall Tremough, Penryn TR10 9FE UK 01326 371843 D.J.Hosken@exeter.ac.uk http://bit.ly/1bMLIqH DJ Hosken via Gmail
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22:00

Phylogenetic networks are of two types: those that produce direct evolutionary inferences about gene flow (eg. hybridization networks, HGT networks), and those that display multiple patterns in multivariate datasets without any necessary evolutionary implications. The latter (called data-display networks) can be used both a priori as tools for exploratory data analysis (EDA), and a posteriori as a means of evaluating (or cross-checking) the support for inferences derived from other analyses (such as evolutionary networks).

Here, I present an example of the a posteriori usage.


The data and initial analysis come from:
Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S. (2013) DNA analysis of an early modern human from Tianyuan Cave, China. Proceedings of the National Academy of Sciences of the USA 110: 2223-2227.They describe their genome data and evolutionary analysis like this:
We have extracted DNA from a 40,000-year-old anatomically modern human from Tianyuan Cave outside Beijing, China.To investigate the relationship of the Tianyuan individual to present-day populations, we compared it to chromosome 21 sequences from 11 present-day humans from different parts of the world (a San, a Mbuti, a Yoruba, a Mandenka, and a Dinka from Africa; a French and a Sardinian from Europe; a Papuan, a Dai, and a Han from Asia; and a Karitiana from South America) and a Denisovan individual, each sequenced to 24- to 33-fold genomic coverage. Denisovans are an extinct group of Asian hominins related to Neandertals [and used as an outgroup]. In the combined dataset, 86,525 positions variable in at least one individual are of high quality in all 13 individuals.To more accurately gauge how the population from which the Tianyuan individual is derived was related to Eurasian populations, while taking gene flow between populations into account, we used a recent approach that estimates a maximum-likelihood tree of populations and then identifies relationships between populations that are a poor fit to the tree model and that may be due to gene flow [using the TreeMix program] ... The maximum-likelihood tree [reproduced above] shows that the branch leading to the Tianyuan individual is long, due to its lower sequence quality. However, among Eurasian populations, Tianyuan clearly falls with Asian rather than European populations (bootstrap support 100%). The strongest signal not compatible with a bifurcating tree is an inferred gene-flow event that suggests that 6.7% of chromosome 21 in the Papuan individual is derived from Denisovans ... When this is taken into account, the Tianyuan individual appears ancestral to all Asian individuals studied. We note, however, that the relationship of the Tianyuan and Papuan individuals is not resolved (bootstrap support 31%).Setting aside the faux pas about the Tianyuan individual being "ancestral" to the others (it is shown in the tree-based figure as the sister group not the ancestor), most of the other interpretations can be assessed by looking at the multivariate data independently of any evolutionary inference. This can be done using the pairwise nucleotide differences among the samples (provided in Table 1 of the paper) and a NeighborNet data-display network, as shown in the splits graph below.


We can note the following points, some of which support the authors' conclusions and some of which don't. [Note: the authors refer to their figure as a "tree", although it is an introgression network.]:
  • All terminal edges in the network are long, and so there is actually not much genomic information on chromosome 21 about relationships.
  • The network splits do roughly match the tree splits, and so the network apparently does reflect some evolutionary information.
  • The identified gene flow from the Denisovan to the Papuan is represented by a clear split in the network. The weight (0.7335) makes it the fifth largest non-trivial split. That is, it is larger than some of the splits that purportedly represent tree-like evolution.
  • The largest split (weight = 2.8942) separates the non-African samples from the African samples + Denisovan outgroup, which does accord with the postulated dispersal of humans out of Africa.
  • The second (1.1459) and third (0.8073) largest splits are near the root of the tree.
  • The European split is the fourth largest (0.7670). The South American sample is included with the Asian group, reflecting the idea that the native people of the Americas migrated there from Asia across the Bering Strait.
  • The relationships among the Asian samples in the network do not all match those in the tree. Notably, the Han+Dai split (0.5124) is smaller than the Han+Karitiana split (0.6292), and yet the former appears in the tree with 100% bootstrap support.
  • The Han+Dai+Karitiana split is well supported (0.4450), but the Han+Dai+Karitiana +Papuan split is not (0.0152), as reflected in the 31% bootstrap value for the latter in the tree.
  • The Han+Dai+Karitiana+Papuan+Tianyuan split is not displayed in the network, although it has a long edge in the tree. The closest network split, as displayed, includes the Denisovan sample. Thus, the network emphasizes the reticulate Denisovan-Papuan relationship at the expense of the showing all of the tree-like relationship among the Asian samples.
  • The Tianyuan edge is not long in the network whereas it is long in the tree. This is likely to be because of uncertainty in its placement in the tree, rather than poor sequence quality, as claimed by the authors.

Thus, the data-display network questions some of the details of the authors' evolutionary network. However, it does support placing the Tianyuan sample with the Asian ones, as well as possible gene flow from the Denisovan sample to the Papuan one.

It thus seems to be a valuable procedure to cross-check any evolutionary analysis with a data-display network. As I have noted before (Networks and bootstraps as tree-support criteria; How networks differ from bootstrapped trees), bootstap values on a tree are insufficient as a means of assessing the robustness of evolutionary diagrams.

22:00
Wednesday, 12:00 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street, Suite A200. For more information, call 919-668-4551
Source: NESCent
03:38

New Call For Proposals The Canadian Institute of Ecology and Evolution (CIEE) seeks proposals for Thematic Programs (Working Groups). These new thematic programs will be staged over the 12 month period from January to December 2015. The proposals should outline a plan to address significant questions in ecology and evolution through synthesis and integration of existing data (e.g., quantitative research synthesis, compilation and meta-analysis of existing data sets). Applicants must define the project scope, meeting agenda, inclusive budget, and plan for publication. CIEE/ICEE provides logistic support and travel expenses. In the past, working groups were awarded grants valued from $ 6,000 to $17,000. Programs can be also co-sponsored with other organizations. Working group involve 10 to 20 participants, including graduate students. Meetings can be held at any location in Canada; however preference will be given to meetings hosted at member organizations. The deadline for submission of proposals is 1 November 2014. Please visit our website (http://bit.ly/1u0G3Gm) for details in the application. Dr. Peter R. Leavitt, Director Dr. Diego F. Steinaker, Assistant Director CIEE /ICEE, Canadian Institute of Ecology and Evolution / Institut canadien d’écologie et d’évolution Email: ciee-icee@uregina.ca Twitter: @CIEEICEE www.ciee-icee.ca — via Gmail

Source: EVOLDIR
03:38
The Jasper Loftus-Hills Young Investigator Award: Jasper Loftus-Hills (1946-1974) was an Australian biologist of exceptional promise when he was killed by a hit-and-run driver while recording frog calls along a Texas highway, three years after receiving his degree. The award was established in 1984 to recognize promising outstanding work by investigators who received their doctorates in the three years preceding the application deadline, or who are in their final year of graduate school. It involves presentation of a research paper in the Young Investigator’s Symposium at the ASN annual meeting and includes a $500 prize, a travel allowance of $700, cost of registration for the meetings, and a supplement of $800 for travel and other expenses for this year’s case of intercontinental travel. Four awards are made annually. Recipients need not be members of the Society. The prize committee encourages direct applications and welcomes suggestions of people who should be encouraged to apply. Applications should consist of no more than three pages that summarize the applicant’s work (excluding tables, figures, and references), no more than four appropriate reprints, and a CV combined as a single pdf. Two letters from individuals familiar with the applicant’s work should be sent separately. All application materials should be sent via e-mail by January 1, 2015, to Jonathan Shurin (jshurin@ucsd.edu). Please indicate “Young Investigators’ Award” in the subject line, and for reference letters, the name of the applicant. The Edward O. Wilson Naturalist Award: This award is given to an active investigator in mid-career who has made significant contributions to the knowledge of a particular ecosystem or group of organisms. Individuals whose research and writing illuminate principles of evolutionary biology and an enhanced aesthetic appreciation of natural history will merit special consideration. The recipient need not be a member of the Society. The award will consist of an especially appropriate work of art and a prize of $2,000. The ASN strongly encourages its members to submit nominations of deserving people. The names of former recipients can be found here http://bit.ly/1qIghJy. Nominations will be held over for two years. The application packet should be in the form of a single pdf consisting of a letter of nomination, curriculum vitae of candidate including a publication list, and three key publications to be sent electronically by January 1, 2015, to Bernard Crespi (crespi@sfu.ca). Please indicate “E. O. Wilson Award” in the subject line. The Sewall Wright Award: This award was established in 1991 for a senior (but still highly active) investigator who has made major contributions that relate to the goals of the ASN (namely, to further the conceptual unification of the biological sciences). The award includes an honorarium of $1,000. The winner need not be a member of the Society or an American. The ASN strongly encourages its member to submit nominations of deserving people. The names of former recipients can be found here http://bit.ly/1qIghJy. Nominations will be held over for two years. The application packet should be in the form of a single pdf consisting of a letter of nomination, curriculum vitae of candidate including a publication list, and three key publications to be sent electronically by January 1, 2015, to Ilkka Hanski (ilkka.hanski@helskini.fi). Please indicate “Sewall Wright Award” in the subject line. The ASN Student Research Awards: Student Research Awards support research by student members that advances the goals of the society: the conceptual unification of ecology, evolution, or behavior. Each award consists of a $2,000 check to the candidate. An applicant must be a member of the ASN (membership is international), must hold a bachelor ‘s degree or equivalent, must have passed to candidacy in a PhD program or equivalent, and must be at least one year from completing the PhD. Applicants should send a two-page proposal (not including references). In addition, applicants should include a budget with justification (one page), a short curriculum vitae (two pages), a statement from the PhD supervisor that verifies that the applicant meets the eligibility requirements, and the supervisor ‘s recommendation supporting the research proposed by the student (one page). Projects in all types of research (i.e., laboratory, field, theory) are encouraged. A total of ten proposals will receive awards. Proposals will be judged on originality, strength and significance of the questions being addressed, prospects for significant results, and the match between the proposed research and the ASN mission. All materials should be compiled into one PDF file and sent via e-mail to Jennifer Lau (jenlau@msu.edu). Please indicate `ASN Student Research Award’ in the subject line. Deadline for submission of all materials is January 31, 2015. More information is available at www.asnamnat.org. Dr. Rebecca Jo Safran Associate Professor Department of Ecology & Evolutionary Biology N317 Ramaley Hall University of Colorado Boulder Colorado 80309 email: rebecca.safran@colorado.edu phone: 303.735.1495 Research Lab: http://bit.ly/VojorU Climate Change Outreach: http://bit.ly/1qIgg8hwww.asnamnat.org. Dr. Rebecca Jo Safran Associate Professor Department of Ecology & Evolutionary Biology N317 Ramaley Hall University of Colorado Boulder Colorado 80309 email: rebecca.safran@colorado.edu phone: 303.735.1495 Research Lab: http://bit.ly/VojorU Climate Change Outreach: http://bit.ly/1qIgg8h Rebecca J Safran via Gmail
Source: EVOLDIR
03:04
Postdoctoral Research Associate Position in Evolutionary Plant Genomics The Lowry lab in the Department of Plant Biology at Michigan State University (MSU) is seeking a Postdoctoral Research Associate who will conduct genomic research in multiple plant species. The successful candidate will lead population genomic studies as well as analyses of gene expression, metabolite, and methylome differences between plant ecotypes. The research of the Lowry lab is centered on identifying the genetic and genomic mechanisms of ecological adaptations and how those adaptations contribute to the formation of new species. A key goal of our research is to link adaptive genetic variation with features of the natural landscape. To understand the physiological, developmental, and genetic mechanisms of adaptive divergence between plant populations, the Lowry lab is focused on research in two major emerging model systems for evolutionary genomics: Monkeyflowers (Mimulus) and Panicum grasses, including the bioenergy crop switchgrass. Two large communities of collaborative scientists have established extensive genomic and molecular biology resources for these systems. To see a more detailed description of ongoing projects in the Lowry Lab, please see: http://bit.ly/1lgcs68 Qualifications: PhD in a field related to Evolution, Genetics, Genomics, Bioinformatics, and/or Plant Biology. Experience with programming for biology, especially population genomic, methylome, and RNA-sequencing analyses. To Apply: Potential candidates should send a brief statement of research accomplishments and future goals, CV, and list of three references to David Lowry at dlowry@msu.edu by October 10, 2014. David B. Lowry Assistant Professor Plant Biology Department Michigan State University http://bit.ly/1lgcs68 David Lowry via Gmail
Source: EVOLDIR