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September 9, 2014
Background: Extant sloths present an evolutionary conundrum in that the two living genera are superficially similar (small-bodied, folivorous, arboreal) but diverged from one another approximately 30 million years ago and are phylogenetically separated by a radiation of medium to massive, mainly ground-dwelling, taxa. Indeed, the species in the two living genera are among the smallest, and perhaps most unusual, of the 50+ known sloth species, and must have independently and convergently evolved small size and arboreality. In order to accurately reconstruct sloth evolution, it is critical to incorporate their extinct diversity in analyses. Here, we used a dataset of 57 species of living and fossil sloths to examine changes in body mass mean and variance through their evolution, employing a general time-variable model that allows for analysis of evolutionary trends in continuous characters within clades lacking fully-resolved phylogenies, such as sloths. Results: Our analyses supported eight models, all of which partition sloths into multiple subgroups, suggesting distinct modes of body size evolution among the major sloth lineages. Model-averaged parameter values supported trended walks in most clades, with estimated rates of body mass change ranging as high as 126 kg/million years for the giant ground sloth clades Megatheriidae and Nothrotheriidae. Inclusion of living sloth species in the analyses weakened reconstructed rates for their respective groups, with estimated rates for Megalonychidae (large to giant ground sloths and the extant two-toed sloth) were four times higher when the extant genus Choloepus was excluded. Conclusions: Analyses based on extant taxa alone have the potential to oversimplify or misidentify macroevolutionary patterns. This study demonstrates the impact that integration of data from the fossil record can have on reconstructions of character evolution and establishes that body size evolution in sloths was complex, but dominated by trended walks towards the enormous sizes exhibited in some recently extinct forms.
Source: BMC Evolutionary Biology
Dear colleagues, Registration is open for the workshop “QUANTITATIVE CLADISTICS AND USE OF TNT”, June 29 - July 3, 2015. Instructors: Dr. Goloboff and Dr. Szumik (Conicet, Argentine). PLACE: Facilities of the Centre de Restauraci i Interpretaci Paleontologica, Els Hostalets de Pierola, Barcelona (Spain). WEBPAGE: http://bit.ly/1xBTBOL The workshop will cover the basics of parsimony analysis and character optimization, tree-searches, diagnosing and summarizing results efficiently, and measuring group supports. It will have extensive hands-on exercises which will help participants get familiar with the main aspects of phylogenetic analysis using TNT. The workshop will make extensive use of TNT. There will also be a demonstration and some practice with GB->TNT, a program to create TNT matrices from GenBank data. This course is co-organized by Transmitting Science, the Institut Catal de Paleontologia M. Crusafont and the Centre de Restauraci i Interpretaci Paleontologica. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno, Ph.D. email@example.com Transmitting Science Soledad De Esteban Trivigno via Gmail
Postdocs/Software developers to work on PhyML and tools for phylogenomics The ATGC bioinformatics platform (http://bit.ly/1xBTByf) hosted by LIRMM (http://www.lirmm.fr/, Montpellier, France) is hiring postdocs/software developers for 18 months, renewable. He will work in a stimulating environment within the MAB team (http://bit.ly/1qIwMCR) and the IBC (http://bit.ly/1xBTByk). The MAB team is internationally recognized for its contributions to research in phylogeny. Its work has led to the development of globally utilized services in evolutionary bioinformatics (e.g. phylogeny.fr: Dereeper et al. 2008). The PhyML software (Guindon and Gascuel 2003; Guindon et al. 2010) is a reference in this field with over 10,000 citations and thousands of users worldwide. In collaboration with researchers and engineers, the recruits will develop the PhyML software and tools for phylogenomics, including: - Partition and mixture models, in the line of (Le et Gascuel 2008, 2010, 2012) - Statistical methods of model selection, in the line of ModelTest and ProtTest (Posada and Crandall 1998, Abascal et al. 2005). - Ancestral sequence reconstruction based on PhyML calculations. - Develop a user-friendly web site (in the same spirit as phylogeny.fr) to provide a complete set of species and genes tree inference methods (supertree and reconciliation problems). - Develop tools to visualize phylogenetic trees, date internal nodes , and integrate extrinsic characters (ecological, geographical, etc.) particularly in the context of epidemiology (Chevenet et al. 2013). The recruits must have a solid experience in C programming, advanced knowledge in evolutionary biology and bioinformatics, and good skills in (some of): statistics, collaborative development tools, workflows (Taverna, Galaxy) and web services (WSDL, SOAP) Montpellier is a sunny city located on the south coast of France on the Mediterranean Sea. It is a university city with an important cultural and scientific heritage (for example the oldest faculty of medicine in Europe). The natural attractions around Montpellier are very diverse, which is suitable for many activities including sailing, relaxing on the beach, hiking, climbing, canoeing, … Use the web form: http://bit.ly/1qIwOL3 to apply. Your application will include detailled CV, motivation letter, references and publications. Contacts: - Olivier Gascuel (firstname.lastname@example.org) - Vincent Lefort (email@example.com) Olivier Gascuel via Gmail
—001a113491e43312a60502929e00 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Postdoc”population genetics/genomics of invasive populations of zebra mussels. A postdoctoral position is available in the Minnesota Aquatic Invasive Species Research Center (MAISRC) at the University of Minnesota. The postdoctoral scholar would work in collaboration with Dr. Michael McCartney on projects related to population genetics, genomics and ecology of invasive populations of zebra mussels in Minnesota. The first project uses microsatellite DNA and SNP genotyping, and genetic clustering methods and tests of invasion models, to examine source populations and pathways of invasion of inland lakes and rivers. A second project examines the larval ecology of spread through small streams interconnecting inland lakes, and a tributary of the Upper Mississippi. A third project will develop qPCR approaches for early detection and quantification of veliger larvae. Start date can be as early as October 2014, with two + years of funding that may be extended. PhDs with experience in one or more of the following fields: molecular population genetics/population genomics, molecular ecology, invasion genetics, qPCR and other molecular approaches to detection/quantification of organisms in environmental samples, and larval/reproductive ecology of zebra mussels should apply by first sending a letter of interest and CV to Michael McCartney at firstname.lastname@example.org . The position is posted under requisition number 192583 on the employment website at the University of Minnesota: http://bit.ly/1xBTBhQ via Gmail
PhD student position in Animal Ecology PhD student position in Animal Ecology at the Department of Zoology. Reference number SU FV-2470-14. Deadline for applications: October 1, 2014. Project: Evolutionary relevance of non-genetic inheritance We are seeking a highly motivated PhD student with an interest in evolutionary ecology to take part of the research project “Epigenetic inheritance and its evolutionary consequences on the genetic architecture of complex traits”, with financial support from the Swedish Research Council. The project aims to investigate central biological questions on how non-genetic (e.g. “epigenetic”) parental effects influence the expression of complex traits. Such epigenetic effects may be induced by, for example, environmental conditions or the interactions between the nuclear DNA and the cytoplasmic DNA. Understanding epigenetic effects has implications for core evolutionary processes such as heritability, maintenance of genetic variation and speciation. Still, we have only a rudimentary understanding of how evolutionary processes are affected by these epigenetic effects. Using two study systems (Drosophila and Poeciliid fishes) and combining experimental manipulations with molecular methods the project will explore how non-genetic parental effects can be caused by either the cytoplasmic DNA or environmental conditions. The project also aims at investigating the inheritance of these epigenetic effects, and how they affect evolutionary processes – an important and exciting field in biology. The PhD project involves experiments, molecular lab-work and statistical analysis. Qualifications To be qualified for research studies in animal ecology the applicant must have completed a research degree (e.g. Master’s), or have passed at least 120 hp (2 years) of biological studies, including an approved independent project of at least 30 hp at advanced level (“examensarbete”) within ecology, evolutionary biology or related subjects. Applicants, who have in principle acquired the corresponding competence in Sweden, or abroad, are also qualified. Criteria for selection Among qualified applicants, selection is made according to the ability to profit from the studies. The criteria to be used are properly documented competence within the described research area, capabilities with regards to speaking and writing in English, analytical thinking, creativity, initiative, independence, and team work performance. Experience with statistical analysis is an advantage. The applicant’s earlier experience within the field of research can be of relevance especially when further documented by university courses, independent research works, personal references, interview and an application indicating the applicant’s motivations in written form. Terms of employment The PhD studies include 48 months of full-time studies with employment as PhD student. The salary starts at 23.700SEK/month. Information Contact for further details Dr. Bjorn Rogell, email@example.com, at the Department of Zoology. Union representatives Anqi Lindblom-Ahlm (Saco-S) and Lisbeth Häggberg (Fackförbundet ST), telephone: +46-(0)8-16 20 00 (switchboard), and Gunnar Stenberg (SEKO), telephone: +46-(0)70-316 43 41. Application The application should contain: maximum one A4-page of personal presentation and letter of intent/motivation CV (including methodological skills) copy of independent project thesis copies of degree certificates and transcripts of academic records (attested) contact details for two academic referees. In order to apply for this position, please use the Stockholm University web-based application form (where it is possible to select language). Link: http://bit.ly/WKlcMO Welcome with your application no later than October 1, 2014. Björn Rogell via Gmail
Dear Colleagues, Please see below our ad for a tenure-track Computational Biologist. The Biology Department at Occidental College is vibrant and growing, with emphasis on both research and teaching excellence. The research angles mentioned in the ad are just a few examples. We encourage all those with an interest who meet the basic requirements to apply. Best, John McCormack *** The Department of Biology at Occidental College invites applications for a tenure-track faculty position in Computational Biology at the Assistant Professor level to expand its teaching and research offerings in the understanding of living systems through analytical and quantitative techniques. The ideal candidate will apply computational approaches to analyze large, complex data sets in biology, possibly including functional and evolutionary genomics, proteomics and protein folding, systems biology, eco-informatics (such as geospatial analysis), neurobiology, bioengineering, modeling, or bio-imaging informatics. Applicants should have a Ph.D. in Biology or related field (with postdoc experience preferred) and a strong commitment to educating undergraduates through teaching and research. The successful candidate will participate in teaching an introductory or intermediate level biology course as well as an intermediate or upper level course in the area of specialty, and to develop a rigorous, externally fundable research program involving undergraduates. Occidental is a nationally ranked small liberal arts college, located in the culturally-rich Los Angeles neighborhoods of Eagle Rock and Highland Park, near Caltech, the Jet Propulsion Lab, the Natural History Museum, and other major research institutions. The College’s location allows convenient access to marine and terrestrial research facilities. Occidental is recognized for its diverse student body and its outstanding undergraduate research program. The neighborhood surrounding the College is home to a wealth of urban amenities and major cultural attractions nearby. Applicants should submit the following: (1) a letter of interest demonstrating a commitment to academic excellence in a liberal arts environment (2 pages suggested), (2) a statement concerning instruction in a socioeconomically, ethnically, culturally and intellectually diverse environment, (3) a statement of research interests (2-3 pages), (4) a statement of teaching philosophy (2-3 pages), (5) evidence of teaching effectiveness, if available, and (6) a curriculum vitae. At the end of the cover letter, please include contact information for three references. Letters are not needed at this time and will be requested after an initial screening. Application materials should be addressed to Dr. Dan Pondella, Chair, Computational Biology Search, and sent by e-mail to firstname.lastname@example.org. Review of applications will begin on October 13, 2014. Occidental College is an equal opportunity employer. Women and minority candidates are encouraged to apply. The College is committed to academic excellence in a diverse community and supporting interdisciplinary and multicultural academic programs that provide a gifted and diverse group of students with an educational experience that prepares them for leadership in a pluralistic world. via Gmail
Group Leader Positions V 6 Year Contracts Sars International Centre for Marine Molecular Biology University of Bergen, Norway The Sars International Centre for Marine Molecular Biology performs basic research in molecular biology, developmental biology and evolution, through genetic and comparative studies of marine organisms. The Centre is a partner of EMBL (European Molecular Biology Laboratory) and is located in the Bergen High Technology Centre together with several departments of the University of Bergen. It currently employs 50 scientists and other staff originating from twenty different countries. We are seeking outstanding candidates addressing fundamental questions in organismal biology using marine animals, with priority on invertebrates. A contract of six years will be offered to successful candidates, with competitive resources for the research (scientific and technical personnel, and infrastructures related to the project). The contract may be prolonged after six years, depending on performance and institute priorities at the time of review. Group leaders at the Sars Centre are expected to obtain additional funding through grant applications to national and international funding agencies. For further information about the position please contact the Sars Centre Director (Daniel.Chourrout@sars.uib.no tel +47 5558 4360) and/or visit our website (www.sars.no). Applications for group leader positions should include a description of past and current research (3 pages), a proposal for the research at the Sars Centre (3 pages), a detailed CV and names of three references. Shortlisted candidates must be available for a seminar and interview by the Scientific Advisory Committee to be held in Bergen on 24-25 November 2014. Written applications should be marked 14Sars_02 and mailed to: Sars Centre, Human Resources, Bergen High Technology Centre, Thormoehlensgate 55, NO-5008 Bergen, Norway. Application deadline is 17 October 2014. Applications sent by e-mail only will not be considered. Carol Bruce via Gmail
September 8, 2014
PhD fellow in the field of ancient and modern human genomics Centre of Excellence in GeoGenetics, Faculty of Science at University of Copenhagen is offering a PhD scholarship in retrieval, sequencing and /or analyses of ancient and modern human genomes commencing December 1st 2014 or as soon as possible thereafter. *Project description *The project will concern retrieval, sequencing and/or analyses of ancient human genomes for addressing questions related to dispersal and admixture of human populations through time. *Principal supervisor *is* Professor DSc Eske Willerslev, Director of Centre for GeoGenetics, University of Copenhagen, **email@example.com* +45 28751308 *Job description* Your key tasks as a PhD student at Science are: - Manage and carry through your research project - Take PhD courses - Write scientific articles and your PhD thesis - Participate in scientific meetings - Stay at an external research institution for a few months, preferably abroad - Teach and disseminate your research *Key criteria for the assessment of candidates* - A masters degree related to the subject area of the project. Applicants with a strong record in experimental genetics and/or bioinformatics are preferred. - The grade point average achieved - Professional qualifications relevant to the PhD programme - Previous publications - Relevant work experience - Other professional activities - Language skills *Terms of employment* The position is covered by the Memorandum on Job Structure for Academic Staff. Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. The starting salary is currently at a minimum DKK 305,291 including annual supplement (+ pension up to DKK 42,171). Negotiation for salary supplement is possible. The position is available for a 3-year period. *Application Procedure* The application, in English, must be submitted electronically via http://bit.ly/1tporUp *Please include * - Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project. - CV - Diploma and transcripts of records (BSc and MSc) - Other information for consideration, e.g. list of publications (if any), - References - Documentation of English language qualifications, cf. general rules and guidelines, p. 5 The applicant will be assessed according to the Ministry of Science Technology and Innovation Executive Order no. 1039 of 27 August 2013PhD Order *. * The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. The deadline for applications is September 22nd 2014. Applications received later than this date will not be considered. *Questions* For specific information about the PhD scholarship, please contact the principal supervisor. General information about PhD programmes at SCIENCE is available at PhD Regulations . Med venlig hilsen/ Kind regards Alan Wervick +3318 7204 SIGNATUR | Kbmagergade 60 | 1150 Kbh K | 33 18 72 00 | www.signatur.dk ANNONCEPORTAL | ANNONCEBYGGER | REKRUTTERINGSMODUL Alan Wervick via Gmail
—Apple-Mail-401-192096518 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=”windows-1252” Florida Genetics 2014 - Call for Abstracts October 29 & 30 UF Cancer & Genetics Research Complex Including sessions on Genetics and Food Security; Genomes to Phenotypes; and Microbiomes Full details & info: http://bit.ly/WDrT3p Faculty, students, post-docs and other researchers are invited to submit abstracts of their latest genetics research for poster sessions at the Florida Genetics 2014 Symposium. Submit an Abstract: http://bit.ly/1rZCtxQ Complimentary on-line abstract submission and registration are now available at the UFGI website. Abstract Deadline: October 3rd, 2014 The submitting author is automatically registered for the conference when they submit their abstract; however, all other authors on the poster must register individually if they wish to attend. Accepted posters will be assigned to one of two sessions: Poster Session I: 2:45-4:45 p.m. on October 29th Poster Session II: 11:30 a.m.-1:30 p.m. on October 30th Best Poster Awards: Awarded to post-docs and students, 4 p.m. on October 30th In order to be eligible for an award, the applicant must be both first author and presenter, and must check the appropriate box (post-doc or student) on the abstract submission form. General Registration Deadline: October 24th, 2014 Keynote Speaker: Roger N. Beachy, PhD, The World Food Center, Davis, CA Speakers William (Brad) Barbazuk, PhD Associate Professor, Department of Biology University of Florida Samantha Brooks, PhD Assistant Professor, Department of Animal Sciences University of Florida Cameron Currie, PhD Professor, Bacteriology University of Wisconsin - Madison Joerg Graf, PhD Associate Professor and Assoc. Dept. Head for Graduate Research and Education, Molecular and Cell Biology University of Connecticut Graciela Lorca, PhD Associate Professor, Department of Microbiology & Cell Science University of Florida Thomas Mitchell-Olds, PhD Professor, Biology Department Duke University Elaine Ostrander, PhD Chief, Cancer Genetics Branch National Genome Research Institute (NIH) 2013 Genetics Society of America Medal recipient Bill Petri, Jr., MD, PhD Wade Hampton Frost Professor of Medicine Chief, Division of Infectious Diseases and International Health University of Virginia Gary P. Wang, M.D., Ph.D Assistant Professor, Medicine Division of Infectious Diseases and Global Medicine, College of Medicine University of Florida Eve Wurtele, PhD Professor, Genetics, Development, and Cell Biology University of Iowa Sponsors: Animal Molecular & Cellular Biology Graduate Program College of Liberal Arts & Sciences (CLAS) Department of Biology College of Veterinary Medicine Emerging Pathogens Institute UF/IFAS Dean for Research Office UF/IFAS Horticultural Sciences Department ICBR - Interdisciplinary Center for Biotechnology Research Plant Molecular & Cellular Biology Graduate Program Stuart McDaniel Assistant Professor Department of Biology PO Box 118525 University of Florida Gainesville FL 32611 ph: 352 273 0123 fax: 352 392 3704 http://bit.ly/WDrTjL —Apple-Mail-401-192096518 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=”windows-1252”Florida Genetics 2014 - Call for AbstractsOctober 29 & 30 UF Cancer & Genetics Research Complex
Including sessions on Genetics and Food Security; Genomes to Phenotypes; and MicrobiomesFull details & info: http://bit.ly/1rZCtOiloridaGenetics2014Faculty, students, post-docs and other researchers are invited to submit abstracts of their latest genetics research for poster sessions at the Florida Genetics 2014 Symposium.
Submit an Abstract: http://bit.ly/1rZCtxQ Complimentary on-line abstract submission and registration are now available at the UFGI website.
Abstract Deadline: October 3rd, 2014The submitting author is automatically registered for the conference when they submit their abstract; however, all other au thors on the poster must register individually if they wish to attend.
Accepted posters will be assigned to one of two sessions:Poster Session I: 2:45-4:45 p.m. on October 29thPoster Session II: 11:30 a.m.-1:30 p.m. on October 30th
Best Poster Awards:Awarded to post-docs and students, 4 p.m. on October 30thIn order to be eligible for an award, the applicant must be both first author and presenter, and must check the a ppropriate box (post-doc or student) on the abstract submission form.
General Registration Deadline: October 24th, 2014
Keynote Speaker: Roger N. Beachy, PhD, The World Food Center, Davis, CA
SpeakersWilliam (Brad) Barbazuk, PhDAssociate Professor, Department of BiologyUniversity of FloridaSamantha Brooks, PhDAssistant Professor, Department of Animal SciencesUniversity of FloridaCameron Currie, PhDProfessor, BacteriologyUniversity of Wisconsin - MadisonJoerg Graf, PhDAssociate Professor and Assoc. Dept. Head for Graduate Research and Education, Molecular and Cell BiologyUniversity of ConnecticutGraciela Lorca, PhDAssociate Professor, Department of Microbiology & Cell ScienceUniversity of FloridaThomas Mitchell-Olds, PhDProfessor, Biology DepartmentDuke UniversityElaine Ostrander, PhDChief, Cancer Genetics BranchNational G enome Research Institute (NIH)2013 Genetics Society of America Medal recipientBill Petri, Jr., MD, PhDWade Hampton Frost Professor of MedicineChief, Division of Infectious Diseases and International HealthUniversity of VirginiaGary P. Wang, M.D., Ph.DAssistant Professor, MedicineDivision of Infectious Diseases and Global Medicine, College of MedicineUniversity of Florida Eve Wurtele, PhDProfessor, Genetics, Development, and Cell BiologyUniversity of IowaSponsors: Animal Molecular & Cellular Biology Graduate Program
College of Liberal Arts & Sciences (CLAS)
Department of Biology
College of Veterinary Medicine
Emerging Pathogens Institute
UF/IFAS Dean for Research Office
UF/IFAS Horticultural Sciences Department
ICBR - Interdisciplinary Center for Biotechnology Research
Plant Molecular & Cellular Biology Graduate Program Stuart McDanielAssistant ProfessorDepartment of BiologyPO Box 118525University of FloridaGainesville FL 32611 ph: 352 273 0123 fax: 352 392 3704http://bit.ly/WDrTjL —Apple-Mail-401-19209651 via Gmail
Postdoctoral Position in Experimental Evolutionary Genomics at the University of Montana A postdoctoral position is available in the laboratory of Frank Rosenzweig at the University of Montana, Missoula, MT (http:// http://bit.ly/1w6o1XE). Our group uses comparative and experimental approaches to understand adaptation and genome evolution in microbes, specifically the commensal Escherichia coli, the opportunistic pathogen Pseudomonas aeruginosa, and the free-living yeast Saccharomyces cerevisiae. The postdoc will engage in NASA-funded research aimed at defining the genomic and environmental boundary conditions that favor emergence of metabolic interactions in simple environments. This project follows on from published work describing the genome sequences and gene expression patterns of a cross-feeding E. coli consortium that evolved under resource limitation (PLoS Genetics 5(11):e1000713 and PLoS Genetics 10(6):e1004430). Overall, this project encompasses three Specific Aims: to discover the degree to which different ancestral genotypes are likely to give rise to mutualism; to test how different limiting nutrients influence the likelihood that cross-feeding consortia evolve; to test the ecological stability of newly evolved mutualism in the face of biotic and abiotic disturbance. This research will be carried out in collaboration with investigators at Stanford (Gavin Sherlock) and Exeter University (Ivana Gudelj). The successful applicant will be expected to have practical knowledge of basic molecular genetic techniques such as PCR, gene knock-out and replacement, and transformation, as well as demonstrated expertise in at least two of the following, all of which are essential to the success of this project: theory and practice of continuous culture, mathematical modeling of population genetic processes, analysis of NextGen sequence data, microarray analysis, bacterial physiology. The successful will take primary responsibility for executing evolution experiments described for this project, and for coordinating modeling and sequencing efforts with investigators from Exeter and Stanford. Evidence of excellent oral and written communication skills and organizational abilities is therefore required, in addition to a strong interest in evolution, and a willingness to learn new techniques. The postdoc will be expected to attend weekly lab meeting, supervise undergrads working on this project, present research at national and regional conferences, and to take a lead role in the data analysis and background research required for for timely publication of research results in top-tier journals. Screening of applicants will begin October 1, 2014; the position will remain open until filled. The preferred start date is?November 15, 2014, but flexible. Interested applicants should direct a cover letter, CV, two PDFs of re-prints/pre-prints and three letters of reference to Frank Rosenzweig, Professor of Biology, Division of Biological Sciences, 32 Campus Dr., Missoula, MT 59812. Ph: (406)531-2163. Email: firstname.lastname@example.org. Frank Rosenzweig, PhD Professor of Biology University of Montana Missoula, MT 59812 Ph: (406) 243-4834 E-mail: email@example.com “Rosenzweig, Frank” via Gmail
September 7, 2014
Postdoctoral Position in Experimental Evolutionary Genomics at the University of Montana A postdoctoral position is available in the laboratory of Frank Rosenzweig at the University of Montana, Missoula, MT (http:// http://bit.ly/1w6o1XE). Our group uses comparative and experimental approaches to understand adaptation and genome evolution in microbes, specifically the commensal Escherichia coli, the opportunistic pathogen Pseudomonas aeruginosa, and the free-living yeast Saccharomyces cerevisiae. The postdoc will focus on a new NASA-Exobiology funded project directed by Research Prof Eugene Kroll. The goal of this project is to elucidate mechanisms of rapid genome evolution in yeast populations placed under severe stress; the research builds on recently published work describing such changes and their potential macroevolutionary consequences (e.g., MolBiolEvol 25(2) 310 and PLoS One 0066414). The project encompasses three Objectives: to identify, isolate and assay the fitness effects of specific large-scale genomic rearrangements in yeast that arise during starvation; to estimate the frequency with which starvation-associated genomic rearrangements arise in starvation culture; to delineate pathways that lead to starvation-induced genomic rearrangement by evaluating genes involved in homologous recombination, non-homologous end-joining, mismatch repair, environmental signal transduction and retrotransposition. The project will be carried out in collaboration with our longstanding Stanford collaborator, Gavin Sherlock, who will be responsible for identifying chromosomal breakpoints via deep sequencing. The successful applicant will be expected to have practical knowledge of basic molecular genetic techniques such as PCR, gene knock-out and replacement, as well as demonstrated expertise in at least two of the following: (i) perform pulsed-field gel analyses, (ii) prepare yeast DNA for sequencing and interact with sequencing facilities, decode and interpret sequencing results as required for finding genome breakpoints, (iii) introduce large-scale constructs in yeast using recombinase-based systems, (iv) construct plasmids with rearrangement markers in yeast, (v) introduce a range of specific mutations in yeast cells marked by specific antibiotic markers, (vi) perform competition experiments using yeast strains that harbor these mutations. The successful applicant will be expected to take primary responsibility for executing the evolution experiments described for this project, and for coordinating sequencing efforts. Evidence of excellent oral and written communication skills and organizational abilities is required, in addition to a strong interest in evolution, and a willingness to learn new techniques. The postdoctoral associate will be expected to attend weekly lab meetings, supervise undergraduate students working on this project, present research at national and regional conferences, and to take a lead role in the data analysis and background research required for timely publication of research results. Salary plus benefits are available for two years, contingent on funding and satisfactory performance in the first year. Salary is fixed at NIH scale for entry-level postdoctoral fellows. Screening of applicants will begin October 1, 2014; the position will remain open until filled. The preferred start date is?November 15, 2014, but flexible. Interested applicants should direct a cover letter, CV, two PDFs of re-prints/pre-prints and three letters of reference to Frank Rosenzweig, Professor of Biology, Division of Biological Sciences, 32 Campus Dr., Missoula, MT 59812. Ph: (406)531-2163. Email: firstname.lastname@example.org. Frank Rosenzweig, PhD Professor of Biology Division of Biological Sciences 32 Campus Dr. University of Montana Missoula, MT 59812 Ph: (406) 243-4834 E-mail: email@example.com “Rosenzweig, Frank” via Gmail
In an earlier blog post (The ultimate phylogenetic network?) I reproduced the lattice network from the anthropologist Franz Weidenreich. This comes close to being as complex as a network can get when applied to groups of organisms. However, when we study the genealogy of individuals, the network can get much more complex. This will be most true when there are marriages between close relatives (consanguinity), which creates inbreeding.
The family pedigree (or family tree!) shown here is for a group of people in a recently isolated population from the southwestern area of The Netherlands. There are 4,645 people involved, covering 18 generations (one row each). The average number of consanguineous loops for the 103 study individuals is 71.7, which is what is creating all of the cross-connections that make the network look so horrendous. (Consanguineous or inbreeding loops are illustrated here.)
The genealogy is from:
Liu F, Arias-Vásquez A, Sleegers K, Aulchenko YS, Kayser M, Sanchez-Juan P, Feng BJ, Bertoli-Avella AM, van Swieten J, Axenovich TI, Heutink P, van Broeckhoven C, Oostra BA, van Duijn CM (2007) A genomewide screen for late-onset Alzheimer disease in a genetically isolated Dutch population. American Journal of Human Genetics 81: 17-31.
Krzysztof M. Kozak wrote:
I am building a pipeline to automatically generate gene trees for about 10,000 CDS alignments (all genes from an exome). The genes were sequenced for 150 individuals in multiple species. Some individuals are worse than others and occasionally have little data in some alignments, and end up on obviously artificially inflated branches. Is anyone aware of a tool to prune those automatically? (I will also use tools to get rid of poor sequence first, but that's a different topic.)
Many thanks, Krzysztof Kozak
Dear colleagues, I would like to order larger amount of ethanol for preserving invertebrate samples for subsequent DNA work, and have it denatured for tax reasons (denatured EtOH costs a fraction of the price of pure one). The supplier can add denaturing agent of my choice. Do you have any experience which of the additives are OK for downstream applications in molecular ecology? Please, send the replies to my address, I will the collect answers, and provide a summary to Evoldir. Thank you! Adam Petrusek Adam Petrusek Department of Ecology Charles University in Prague Vinicna 7 CZ-12844 Prague 2 Czech Republic e-mail: firstname.lastname@example.org Pokud je tento e-mail soust obchodnho jednn, Prodovdeck fakulta Univerzity Karlovy v Praze: a) si vyhrazuje prvo jednn kdykoliv ukonit a to i bez uveden dvodu, b) stanovuje, e smlouva mus mt psemnou formu, c) vyluuje pijet nabdky s dodatkem i odchylkou, d) stanovuje, e smlouva je uzavena teprve vslovnm dosaenm shody na vech nleitostech smlouvy. email@example.com via Gmail
_Postdoc position in eco-evolutionary theory _ A postdoc position is available to work with PI Joanna Masel (http://bit.ly/1hmktJq) at the University of Arizona in Tucson. A popular tourist destination surrounded on all four sides by mountainous national and state parks, Tucson is a vibrant city of nearly a million people with an attractive climate. The EEB department in Tucson was ranked in the top 10 by US News & World Report. The postdoc will study evolutionary rescue in the presence of clonal interference, via a model of asexual population genetics (based on Desai & Fisher 2007). This model will be modified so that genotypes specify absolute fitness in a deteriorating environment, rather than relative fitness as is the norm in population genetics. The project is part of a broader effort to integrate the ecological density-dependence terms r and K with the classical population genetics fitness term of w, as part of an eco-evo theoretical synthesis: see http://bit.ly/1rx2C7Y for the conceptual basis. We are just beginning an experimental evolution collaboration, and side projects applying the model to experimental evolution (and to other ecological and evolutionary theory) are encouraged. A strong quantitative background together with computational and/or modeling experience is required. A background in evolutionary and/or ecological theory is strongly preferred. The Masel group’s main research interests http://bit.ly/1jQ1pAa are in robustness and evolvability, using a mixture of analytical theory, bioinformatic and simulation approaches. Contact Joanna Masel at firstname.lastname@example.org for more information and to apply. The position is available immediately and renewable over multiple years. email@example.com via Gmail
New College of Florida invites applicants for a tenure-track position in Plant Biology at the assistant professor level starting in August 2015. We seek a broadly trained candidate with a Ph.D. in the biological sciences. Research interests incorporating aquatic botany, toxicology, and/or microbiology are desirable. The successful candidate must be committed to excellence in teaching and research. New College, on Florida’s Gulf Coast, is a nationally recognized, highly-selective public honors college with a 11:1 student:faculty ratio. Students receive narrative evaluations in lieu of grades. The teaching load is two classes per semester, plus supervision of tutorials, independent study projects, and senior thesis projects. Undergraduate research has a central role in the curriculum, and a senior thesis is required of all students. The successful candidate is expected to establish and maintain a program of research appropriate to a quality liberal arts and sciences college. New College is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research, teaching and service. For details: http://bit.ly/WsypcH. An online application: http://bit.ly/1tC1xwU should be completed. A complete application will include a cover letter, curriculum vitae, names of 3 references, a statement of teaching philosophy and interests, undergraduate and graduate transcripts, and a description of proposed research including how undergraduates will be involved. Review of completed applications will start Oct. 10, 2014 and continue until the position is filled. NCF is an EOE/AA employer. Colleen Swessel via Gmail
September 6, 2014
_Postdoc position in the theory of molecular errors and evolvability_ A postdoc position is available to work with Joanna Masel (http://bit.ly/1hmktJq) at the University of Arizona in Tucson. A popular tourist destination surrounded on all four sides by mountainous national and state parks, Tucson is a vibrant city of nearly a million people with an attractive climate. The EEB department in Tucson was ranked in the top 10 by US News & World Report. All molecular processes, from transcription to protein interactions, are subject to errors. We are interested in exploring the evolutionary consequences of this simple fact. In previous work (Rajon & Masel 2011 PNAS), we found that the evolution of error rates tends towards two extremes. One attractor represents a global proofreading solution that avoids making errors at many loci at once, the other a local robustness solution, where errors happen at high rates but the consequences of each error have evolved, one locus at a time, to be benign. Populations that evolved benign, co-optable cryptic sequences via the local solution are much more evolvable. This is because through the erroneous expression of cryptic sequences, selection has already explored and prescreened possible future mutations. In other words, because errors in gene expression and in replication (i.e. mutation) are so similar at the molecular level, selection can actually occur prior to mutation. We are looking for a postdoc to study evolvability phenomena in versions of this model, and also investigate controversial hypotheses surrounding the adaptive evolution of evolvability. A strong quantitative background, good programming skills, and previous modeling experience are all required. A background in evolutionary theory is strongly preferred. Some interest in the molecular biology of transcription, translation, protein folding and binding, and the errors in each of these processes is an advantage. The position is available immediately, and is renewable, with funding secured for at least two years. Contact Joanna Masel at firstname.lastname@example.org for more information and/or to apply. email@example.com via Gmail
The Early Registration deadline for the upcoming 7th Biennial Conference of the International Biogeography Society (Bayreuth, Germany - January 2015) has been extended to September 30th, 2014 so you can take advantage of lower registration rates. Fieldtrips and workshops are on a first-come, first-served basis, so it is best to sign up soon before they fill up! Fieldtrips: http://bit.ly/1lOLkC8 Workshops: http://bit.ly/WsrujL In addition to the regular IBS facebook and twitter venues, there is now a dedicated twitter and facebook page for the conference. Sign up/follow to keep current on the latest conference notifications like impending deadlines! Web: http://bit.ly/1lOLkCa Twitter: @ibs2015 (#ibs2015) Facebook: IBS Conference in Bayreuth 2015 Hope to see you in Bayreuth this coming January! Michael N Dawson VP Public Affairs and Communications International Biogeography Society http://bit.ly/1bTNXeY http://on.fb.me/WsrujP @biogeography Frontiers of Biogeography http://bit.ly/1c86MZv @newbiogeo firstname.lastname@example.org via Gmail
Vacancy: PhD position Arctic meltdown affects tropical seagrass meadows via migrant shorebird Global warming is most pronounced in the Arctic. Hence, Arctic-breeding migrants might carry over the ecological effects of climate change to their tropical wintering grounds. Although recently discovered, reductions in body size are already considered a universal response to climate change. Red knots (Calidris canutus), medium-sized shorebirds breeding as High Arctic as possible, are no exception to this rule. Over the past 30 years, their bodies have been shrinking, notably with respect to body mass and bill length. Preliminary analyses revealed that at their main wintering site (Banc d’Arguin, Mauritania, West-Africa), small individuals with a short bill are now shifting niche by consuming readily accessible seagrass rhizomes instead of deeper buried shellfish. Here we will (A) experimentally unravel the coupling between body size and diet; (B) link survival rate to body size and diet; and (C) quantify the top-down effects of rhizome-grazing on seagrass. Whilst the field work will be carried in Mauritania, the laboratory and desk work will mainly be carried out at the Department of Marine Ecology, NIOZ Royal Netherlands Institute for Sea Research (Texel, the Netherlands; http://www.nioz.nl). However, in this MARES-EU funded project, regular visits will be made to the two partner universities, University of Aveiro (Portugal) and the University of Gdańsk (Poland). Profile The subject is open to highly motivated students that have a background in (marine) ecology, preferably with affinities to birds. The proposed fieldwork in Banc d’Arguin will be embedded in large expeditions in which a consortium of international researchers is involved. Henceforth, the candidate should be a team player, but, at the same time, should be able to work independently under seemingly pleasant, but sometimes tough, field circumstances. Because this project involves Dutch, Portuguese and Polish partners, the regulations set by MARES-EU demand that candidates should have obtained their master degree outside the Netherlands, Portugal and Poland. Employment details The candidate will be employed by NIOZ for a period of three years, under the collective agreement of Dutch universities and research institutions. This includes a gross monthly salary of € 2,800 including an 8%-vacation bonus and end-of-year payment. To apply: http://bit.ly/WsAB4r For more information: http://bit.ly/1vZDg4Q E-mail Jan.van.Gils@nioz.nl for remaining questions Jan van Gils via Gmail
16th YOUNG SYSTEMATISTS’ FORUM Friday, 28 November 2014, 9:30 am Venue: Flett Lecture Theatre, Natural History Museum, London, UK The annual Young Systematists’ Forum represents an exciting setting for Masters, PhD and young postdoctoral researchers to present their data, often for the first time, to a scientific audience interested in taxonomy, systematics and phylogenetics. This well-established event provides an important opportunity for budding systematists to discuss their research in front of their peers within a supportive environment. Supervisors and other established systematists are also encouraged to attend. Prizes will be awarded for the most promising oral and poster presentation as judged by a small panel on the day. Registration is FREE. Send applications by e-mail to (YSF.SystematicsAssociation@gmail.com), supplying your name, contact address and stating whether or not you wish to give an oral or poster presentation. Space will be allocated subject to availability and for a balanced programme of animal, plant, algal, microbial, molecular and other research. Non-participating attendees are also very welcome - please register as above. Abstracts must be submitted by e-mail in English no later than Friday 31 October 2014. The body text should not exceed 150 words in length. If the presentation is co-authored, the actual speaker (oral) or presenter (poster) must be clearly indicated in BOLD text. All registered attendants will receive further information about the meeting, including abstracts, by e-mail one week in advance. This information will also be displayed on the Systematics Association website (www.systass.org). *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Dr Ellinor MICHEL Department of Life Sciences The Natural History Museum Cromwell Road SW7 5BD London UK tel: +44-207-942-5516 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* http://bit.ly/YjDjuAwww.systass.org). *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Dr Ellinor MICHEL Department of Life Sciences The Natural History Museum Cromwell Road SW7 5BD London UK tel: +44-207-942-5516 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* http://bit.ly/YjDjuA -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution