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September 8, 2014
—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: email@example.com. Frank Rosenzweig, PhD Professor of Biology University of Montana Missoula, MT 59812 Ph: (406) 243-4834 E-mail: firstname.lastname@example.org “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: email@example.com. 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: firstname.lastname@example.org “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: email@example.com 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. firstname.lastname@example.org 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 email@example.com for more information and to apply. The position is available immediately and renewable over multiple years. firstname.lastname@example.org 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 email@example.com for more information and/or to apply. firstname.lastname@example.org 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 email@example.com 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
Postdoctoral Fellow in Metagenomics at George Washington University We are seeking a highly motivated postdoctoral researcher to design and carry out analysis of high-throughput sequencing microbiome data as part of a series of studies on the role of infectious agents on mental disorders with a focus on schizophrenia. Additionally, the researcher will also be involved in the development of the PathoScope pipeline for taxonomic profiling of metagenomic samples. The project is part of an ongoing collaboration between the Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine and the Computational Biology Institute, George Washington University. The overall goal of this research is to contribute to our program devoted to the elucidation of the role of infection and immunity in the etiology of schizophrenia and bipolar disorders. Interests also include elucidating the role of perinatal infections in subsequent brain development. Applicants must possess a PhD in a relevant discipline (Computational Biology, Bioinformatics, Microbiology, Microbial Ecology), with experience in metagenome data analysis and an understanding of the key issues and relevant tools in the field. An understanding of statistics is essential. Experience with DNA and RNA extraction and sequencing is useful but not essential. A strong quantitative background and good programming skills (R, Python/Perl) are all required. The initial contract will be for one year, renewable based on performance. Salary is competitive with benefits. The selected candidate will be based on GWs Computational Biology Institute. For further information about the Computational Biology Institute at George Washington University, please see http://cbi.gwu.edu. For questions relating to this opportunity, please contact Keith Crandall, Director, Computational Biology Institute, The George Washington University, firstname.lastname@example.org. Interested candidates can apply for this position at www.gwu.jobs where they can search on the following Posting Number: Staff - 003768. The anticipated start date is flexible, but the position can start as early as October 1, 2014. Review of candidates is ongoing and will continue until the position is filled. The George Washington University is an Equal Opportunity/Affirmative Action Employer and seeks to attract an active, culturally and academically diverse faculty of the highest caliber. Keith Crandall via Gmail
September 5, 2014
Post-Doctoral Associate in Bioinformatics For a joint position, The Biology Departments at Juniata College, a highly ranked, national liberal arts college of 1,500 students located in the scenic Allegheny Mountains of central Pennsylvania, and nearby (34 miles) Pennsylvania State University seek individuals interested in a career involving both research and teaching to fill a post-doctoral position in the area of Bioinformatics. Teaching experience and experience in performing relevant wet lab and computational analyses associated with next-generation sequencing are required. Experience with Linux, R, Perl or Python are preferred, as well as experience using compute clusters and cloud computing. The Biology Department at Juniata has developed an innovative curriculum with support from NSF and HHMI, a strong tradition of undergraduate research and a rich history of sending students on to graduate studies and productive careers. Further information about the department can be found at http://bit.ly/1cLzZO0. Successful candidates will teach one introductory or upper level undergraduate course per semester, and instruct in an HHMI/NSF funded faculty development workshop that includes RNAseq, metagenomics, eukaryotic and prokaryotic genomics approaches. Candidates will support a new national initiative, headquartered on the Juniata campus, to incorporate massively-parallel sequencing technologies into the undergraduate curriculum and research (www.gcat-seek.org). Concurrently, 25% of time will be spent on functional genomics research in collaboration with Prof. Jim Marden at Penn State, a leading institution for bioinformatics research. The position is funded from January 2015 to August 2016. Applicants with an earned Ph.D. (required) and post-doctoral and teaching experience (preferred) should submit 1) a brief statement of teaching experience, philosophy, and interests; 2) a succinct two-page summary of research interests; 3) a curriculum vitae; 4) undergraduate and graduate academic transcripts; and 5) three letters of recommendation. All materials should be addressed to Gail Leiby Ulrich, Director of Human Resources, Juniata College, 1700 Moore Street, Box B, Huntingdon PA 16652. It is the policy of both Juniata College and Penn State to conduct background checks. Review of applications will begin October 15 and continue until the position is filled. Juniata College and Penn State will take positive steps to enhance the ethnic and gender diversity on their campuses. We commit ourselves to this policy not only because of legal obligations, but because it believes that such practices are basic to human dignity. AA/EOE Dr. Vincent Buonaccorsi 601 17th St. Juniata College Huntingdon, PA 16652 Phone: 814-641- 3579 http://bit.ly/1f0d8ha email: BUONACCORSI@juniata.edu Dr. Jim Marden Dept. of Biology 208 Mueller Lab Penn State University University Park, PA 16802 814-863-1384 http://bit.ly/Wslacnwww.gcat-seek.org). Concurrently, 25% of time will be spent on functional genomics research in collaboration with Prof. Jim Marden at Penn State, a leading institution for bioinformatics research. The position is funded from January 2015 to August 2016. Applicants with an earned Ph.D. (required) and post-doctoral and teaching experience (preferred) should submit 1) a brief statement of teaching experience, philosophy, and interests; 2) a succinct two-page summary of research interests; 3) a curriculum vitae; 4) undergraduate and graduate academic transcripts; and 5) three letters of recommendation. All materials should be addressed to Gail Leiby Ulrich, Director of Human Resources, Juniata College, 1700 Moore Street, Box B, Huntingdon PA 16652. It is the policy of both Juniata College and Penn State to conduct background checks. Review of applications will begin October 15 and continue until the position is filled. Juniata College and Penn State will take positive steps to enhance the ethnic and gender diversity on their campuses. We commit ourselves to this policy not only because of legal obligations, but because it believes that such practices are basic to human dignity. AA/EOE Dr. Vincent Buonaccorsi 601 17th St. Juniata College Huntingdon, PA 16652 Phone: 814-641- 3579 http://bit.ly/1f0d8ha email: BUONACCORSI@juniata.edu Dr. Jim Marden Dept. of Biology 208 Mueller Lab Penn State University University Park, PA 16802 814-863-1384 http://bit.ly/Wslacn email: email@example.com. Jim Marden via Gmail
Going further on an intricate and challenging group of nudibranchs: description of five novel species and a more complete molecular phylogeny of the subfamily Nembrothinae (Polyceridae)
Nembrothinae is a colourful subfamily of nudibranch polycerids, which despite its large size and striking appearance, needs to be more thoroughly studied. The available scientific information about this subfamily is very recent, and pictures of living undescribed species become available every day. Nevertheless, the lack of associated material for morphological, anatomical, and molecular analysis results in scarce additional studies. In this paper, five novel species are described: Roboastra ernsti sp. nov., Roboastra nikolae sp. nov., Tambja brasiliensis sp. nov., Tambja crioula sp. nov., and Tambja kava sp. nov. In addition, Tambja divae (Marcus, ), a species previously known only from the original description, is redescribed and additional data and comments on Tambja cf. amakusana Baba, 1987 and Tambja marbellensis Schick and Cervera, 1998 are provided. Molecular data (H3, COI and 16S genes) for all these novel species and some additional ones were obtained and included in a previous molecular database. Maximum-likelihood, maximum-parsimony and Bayesian analyses were carried out. The phylogeny presented here has revealed Nembrothinae to be an intricate and challenging group of nudibranchs to study. Intermediate missing species seem to be critical to understanding the evolutionary relationships within this group.
Background: New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. Results: The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. Conclusions: The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.
Source: BMC Evolutionary Biology
Genomics postdoc to study butterfly speciation, with flexibility for the candidate to pursue their own interests within the broad goals of the project. A post-doctoral research associate position in Department of Zoology, located in Central Cambridge on Downing Street, is available from October 2014 for twenty four months, in the first instance, to work with Professor Chris Jiggins on the evolutionary genomics of adaptation and speciation in Heliconius butterflies, in collaboration with Dr Owen McMillan at the Smithsonian Tropical Research Institute in Panama. There are three important aspects of the position. First, we are looking for someone to work with the larger Heliconius community to finalize the construction of the H. erato genome. This genome will be the second full genome sequence available in Heliconius, alongside H. erato’s co-mimic, H. melpomene, and will provide a foundation for broader comparative genomic studies across the radiation. This work will primarily involve validating and improving an existing assembly using genetic linkage data. Second, we are looking for someone to produce a draft assembly of the H. cydno genome for comparison to the H. melpomene and H. erato genomes. The Postdoctoral Research Associate will then use these reference genomes to study adaptation and speciation in the genus. This could include demographic analysis of mimicry and speciation using coalescence-based methods to infer population history from whole-genome sequences and/or analysis of genomic rearrangements and their role in speciation, inferred from population resequence data for H. erato and H. melpomene species groups. There is considerable scope for the focus of the biological analyses to reflect the interests of the candidate. The research will primarily involve bioinformatic analysis of existing genomic sequence datasets. The successful applicant should have a Ph.D., completed or completion imminent, in evolutionary biology, bioinformatics or a related field, with a strong interest in population genomics. In addition, candidates should have experience with the manipulation and analysis of Illumina data and working knowledge of a programming language such as Python or Perl. Candidates should have a good collaborative spirit, as the work will involve close collaboration with researchers in Cambridge and Panama as well as coordination with many different labs working on Heliconius biology, genome assembly and genome databases. Enthusiasm, determination and the capacity to work independently are also essential. Fixed-term: The funds for this post are available for 24 months in the first instance. To apply online for this vacancy, please follow this link http://bit.ly/1pw3y64. or contact me Chris Jiggins for more information: Chris Jiggins Please quote reference PF04195 on your application and in any correspondence about this vacancy. The University values diversity and is committed to equality of opportunity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK. cj107 [at] hermes.cam.ac.uk via Gmail
Dear LAMARC users, We announce the release of Lamarc 2.1.10. This version corrects an error in the file conversion program lam_conv when customized migration matrices were used. The resulting matrices were reversed: that is, if the user specified the migration rate from A to B, this actually set the rate from B to A. If you used an asymmetrical custom migration matrix in lam_conv you will need to re-convert your files and re-run your analysis. All other results are unaffected. Source code and precompiled executables for Linux, Windows, and OSX are available on the Lamarc web site: http://bit.ly/1pRoSJn Any questions or concerns about Lamarc can be directed to firstname.lastname@example.org. We also very much enjoy hearing about successful use of Lamarc, including any resulting publications. Sincerely, Mary Kuhner Lamarc Development Team email@example.com via Gmail
Imperial College London Faculty of Natural Sciences Department of Life Sciences Two Academic Positions: One post in Ecology & Evolution One post in Biodiversity, jointly appointed between Imperial College London and the Natural History Museum Lecturer salary in the range 45,950 - 51,200 per annum Senior Lecturer/Reader minimum starting salary: 56,450 per annum Chair minimum starting salary: 71,760 per annum Imperial College’s Department of Life Sciences is looking to make two academic appointments in the broad area of Ecology, Evolution and Biodiversity. The posts will be based at the Silwood Park Campus (http://bit.ly/15Hz4X0). The Lecturer/Senior Lecturer/Reader/Chair in Ecology & Evolution, will contribute to the mission of the Department of Life Sciences at Imperial College London, and further develop and promote the College’s work in ecology and evolution. The purpose of the role is to improve fundamental scientific understanding of biological and ecological processes and systems. In addition, the post holder will be required to contribute to undergraduate and postgraduate teaching within the Department. The Lecturer/Senior Lecturer/Reader/Chair in Biodiversity will be jointly appointed with the Natural History Museum. In this case, the post holder will contribute to the missions of the Departments of Life Sciences at both Imperial College London and the Natural History Museum, and further develop and promote the College’s and Museum’s work in biodiversity omics. The purpose of this role is to improve fundamental scientific understanding of biological diversity and systems. In addition, the post holder will be required to contribute to joint postgraduate teaching within both Departments as well as undergraduate teaching at Imperial College London’s Department of Life Sciences. The successful candidates will be expected to have a good honours degree and a doctorate (or equivalent) in a relevant subject area. You will also have an international reputation for research and innovation in ecology and evolution commensurate with the current stage of your career, underpinned by a record of first-class journal publication. You must also be able to demonstrate the potential to raise significant research funding from UK and EU sources to maintain and enhance the College’s leading research activities. Experience of teaching at undergraduate and Masters’ level, and postgraduate student supervision, are not essential, but would be an advantage. You must have excellent interpersonal, verbal and written communication skill with an ability to convey ideas and concepts clearly and effectively to a range of audiences through a variety of methods and media. You must have the ability to lead a research team, managing the finances and your staff. You must also have the ability to communicate and inspire students as you will be expected to contribute to our undergraduate and postgraduate teaching programmes. For appointment to Senior Lecturer/Reader, in addition to the above, candidates must also have an exceptionally strong research record in ecology, evolution or conservation science or a closely related subject, and a proven track record of securing research funding. You will also be expected to have extensive experience in postgraduate teaching and undergraduate teaching across a range of subjects within (or close to) the fields of Ecology, Evolution or Conservation Science, together with a track record of successful postgraduate student supervision and postdoctoral mentoring. For appointment to the position of Chair, in addition to the above, you will also be expected to have an international reputation for your research, and strong leadership qualities in areas which enhance and extend those of the Group. The potential for productive research collaboration with existing staff within Imperial’s Department of Life Sciences, and the College more broadly will also be carefully assessed. Fellows and previous applicants are welcome to apply. Please contact Professor Vincent Savolainen (Deputy Head of Life Sciences at Imperial College London, firstname.lastname@example.org) for informal queries about both posts. You can also contact Professor Ian Owens (Head of Science at the Natural History Museum, email@example.com) and/or Dr Tim Littlewood (Head of Life Sciences at the Natural History Museum, firstname.lastname@example.org) for informal queries regarding the joint appointment with Natural History Museum. Our preferred method of application is online via our website http://bit.ly/1c1zTPb (please select “Job Search” then enter the job title or vacancy reference number including spaces - NS 2014 168 JT into “Keywords”). Please complete and upload an application form as directed. Alternatively, if you are unable to apply online, please contact Miss Victoria Ireton (Executive Assistant) by email: email@example.com to request an application form. Closing date: 6 October 2014 Committed to equality and valuing diversity. We are also an Athena SWAN Silver Award winner, a Stonewall Diversity Champion, a Two Ticks Employer and are working in partnership with GIRES to promote respect for trans people. “Thomas, Jenny” via Gmail
Registration for the 19th Annual NZ Phylogenomics Meeting is now open. This will be held at Portobello on the Otago Peninsula from Monday 2 February 2015 until midday Friday 6 February 2015, with a welcome gathering late afternoon on Sunday 1 February. Information and links are provided on the webpage: http://bit.ly/WjHk07. As for previous meetings, registration will be managed on a first-come first-served basis. Otago peninsula is a popular area for tourists so you are encouraged to book your accommodation early. Some suggestions are provided on the webpage. We look forward to seeing many of you in Portobello in February. Please feel free to forward this information to others you think might be interested in attending. Regards David Bryant and Mike Hendy (apologies for cross-postings) Assoc. Prof. David Bryant Department of Mathematics and Statistics University of Otago Dunedin 9056 New Zealand http://bit.ly/1CwURmb ph: +64 3 4797889 David Bryant via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution