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October 23, 2014

01:08
ANNOUNCEMENT OF POSITION VACANCY Assistant Professor of Biology”Mammal Biologist RESPONSIBILITIES: The Biological Sciences Department at Colorado Mesa University invites applications for a tenure-track faculty position in mammalian biology. The successful applicant will join a dynamic department, including field, organismal, cellular, and molecular biologists, focused on excellence in undergraduate teaching and mentorship of undergraduate researchers. Responsibilities include teaching 12 credits/semester, advising students, offering research opportunities, and participating in service to the department and university. Teaching responsibilities will include lower-division majors and non-majors courses, developing upper-division courses in mammalogy and within the candidate’s specialty, and curating the mammal teaching collection. EDUCATION & EXPERIENCE: A Ph.D. in biology or a related field is required. Preference will be given to candidates with undergraduate teaching and postdoctoral experience. Individuals with expertise as mammal biologists employing ecological, evolutionary, and/or management approaches are preferred. Colorado Mesa University is particularly interested in candidates who have experience working with students from diverse backgrounds and who have a demonstrated commitment to improving the levels of access and success for underrepresented students within higher education. TYPE OF APPOINTMENT: Full-time, tenure-track appointment beginning August 2015. SALARY: Commensurate with education and experience. Excellent health and retirement benefits package. APPLICATION DEADLINE: Open until filled. To ensure consideration, completed application packets must be received by January 16, 2015. APPLICATION: Submit a cover letter describing your qualifications and experience as they relate to the specific responsibilities, requirements, and preferences of this position, CV, unofficial transcripts for all degrees completed (official transcripts will be required upon hire), statement of teaching philosophy, statement of teaching interests and experience (including a list of courses you are qualified to teach), statement of research interests, three letters of recommendation, and the following completed forms: Applicant Authorization and Release to Conduct Reference and Background Check Background Investigation Disclosure and Authorization Voluntary Affirmative Action Form Send to: Biology Search Committee”Mammal Biologist Human Resources, LHH 237 Colorado Mesa University 1100 North Avenue Grand Junction, Colorado 81501-3122 Phone: 970 248-1820 *Colorado Mesa University is committed to providing a safe and productive learning and living community. To achieve that goal, we conduct background investigations for all final applicants being considered for employment. Background investigations include reference checks, a criminal history record check, and when appropriate, a financial and/or motor vehicle history. Applicant must be able to verify U.S. employment eligibility. Colorado Mesa University is an Affirmative Action/Equal Opportunity Employer, committed to a culturally diverse faculty, staff and student body. Women and minorities are encouraged to apply. *Pos #1624 Susan M. Longest, PhD Assistant Professor of Biology Colorado Mesa University 1100 North Avenue Grand Junction, CO 81501 Phone: (970) 248-1554 susan.m.longest@gmail.com via Gmail
Source: EVOLDIR
00:03

PhD positions Landscape and Conservation Genomics of Fish Dalhousie University Support is available for two PhD positions in the laboratory of Daniel Ruzzante at Dalhousie University (Halifax, Nova Scotia, Canada) for research in landscape and conservation genomics of fish in Labrador and Patagonia. A Masters (MSc) degree with a background in population genetics and molecular laboratory or bioinformatics experience is required. One project will involve fieldwork in Labrador and the other in Patagonia. Both positions expected to start in the 2015/2016 academic year. Applicants please send a statement of research interests, CV and the names and e-mail addresses of two people willing to act as academic references to: Dr Daniel Ruzzante, Killam Professor, Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada, B3H4J1 email: daniel.ruzzante@dal.ca, http://bit.ly/1wdmVtC Daniel.Ruzzante@Dal.Ca via Gmail

Source: EVOLDIR

October 22, 2014

22:00
Why are some genes imprinted, where the maternally or paternally inherited copies are preferentially expressed? Ever since the paradoxical pattern of imprinted gene expression was discovered evolutionary theories have strived to answer this question. Consequently, theories built on different fundamental assumptions have proliferated. Although these theories should make distinct and testable predictions, there have been few tests aimed at formally differentiating between these competing ideas. However, despite the general lack of such tests, the ‘kinship theory’, and especially its most prominent component, the ‘conflict hypothesis’, has emerged as the favored theory. This predominance is most notably reflected in the literature outside of evolutionary biology, where the conflict hypothesis is regularly used to interpret the functions and effects of imprinted genes. The conflict hypothesis rose to dominance because it appears to explain the effects of the first imprinted genes discovered. However, data from a broader array of genes in model species and emerging insights from non-model species appear to challenge whether one hypothesis adequately explains all occurrences of imprinting. We propose a working group composed of theoretical, computational and empirical biologists that will develop a set of formal predictions and devise tests to differentiate between competing models for the evolution of genomic imprinting. In doing so, we also expect to identify unexplored problems in evolutionary theory. Understanding why genes are imprinted also has important implications for evolutionary medicine since imprinted genes play a crucial role during pregnancy, in the manifestation of several behavioral disorders, and in some cancers.
Source: NESCent
22:00
Why are some genes imprinted, where the maternally or paternally inherited copies are preferentially expressed? Ever since the paradoxical pattern of imprinted gene expression was discovered evolutionary theories have strived to answer this question. Consequently, theories built on different fundamental assumptions have proliferated. Although these theories should make distinct and testable predictions, there have been few tests aimed at formally differentiating between these competing ideas. However, despite the general lack of such tests, the ‘kinship theory’, and especially its most prominent component, the ‘conflict hypothesis’, has emerged as the favored theory. This predominance is most notably reflected in the literature outside of evolutionary biology, where the conflict hypothesis is regularly used to interpret the functions and effects of imprinted genes. The conflict hypothesis rose to dominance because it appears to explain the effects of the first imprinted genes discovered. However, data from a broader array of genes in model species and emerging insights from non-model species appear to challenge whether one hypothesis adequately explains all occurrences of imprinting. We propose a working group composed of theoretical, computational and empirical biologists that will develop a set of formal predictions and devise tests to differentiate between competing models for the evolution of genomic imprinting. In doing so, we also expect to identify unexplored problems in evolutionary theory. Understanding why genes are imprinted also has important implications for evolutionary medicine since imprinted genes play a crucial role during pregnancy, in the manifestation of several behavioral disorders, and in some cancers.
Source: NESCent
18:00
Background: The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa. Results: The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago. Conclusions: Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.
03:21
The Dpartement de biologie of Universit Laval invites applications at the level of assistant (tenure-track), associate or full professor in systematics of vascular plants, bryophytes or lichens. The selected candidate will be appointed curator of the Louis-Marie Herbarium. The candidate will teach botany and plant systematics and develop an active research program in plant phylogeny, which may include a biogeographic approach and the use of genomic tools. He or she is expected to recruit and supervise graduate students. The candidate will ensure the development and promotion of the Herbarium and oversee the work of the Herbarium staff. Applicants should have a Ph.D. in biological sciences or exceptionally, in the process of being completed. Postdoctoral experience is desirable. Established researchers are welcome to apply. The appointee is expected to teach in French after a year, to possess an excellent publication record, and to demonstrate strong teaching abilities at all levels (e.g. introductory plant diversity and graduate course in plant taxonomy/systematics). Universit Laval has an affirmative action policy committed to reducing gender imbalance; qualified women are strongly encouraged to apply. Closing date: December 15, 2014. Starting date: September 1, 2015. Eligible candidates should submit a letter describing their qualifications and motivation for the position, a CV, and relevant publications to Line Lapointe, Chair, Dpartement de biologie, Universit Laval, Qubec, QC G1V 0A6. FAX: 418-656-2043, directeur@bio.ulaval.ca. The letter of intent should describe the research interests and teaching philosophy of the candidate as well as propose a development plan for the Herbarium over the next ten years. The name and address of three potential referees should be included in the CV. Le Dpartement de biologie de l’Universit Laval sollicite des candidatures pour un poste rgulier de professeure ou de professeur (adjoint, agrg ou titulaire) en systmatique des plantes vasculaires, des bryophytes ou des lichens, auquel est assorti le poste de conservateur de l’Herbier Louis-Marie. Le candidat ou la candidate devra enseigner la botanique et la systmatique vgtale, dvelopper un programme de recherche indpendant et subventionn dans le domaine de la phylognie, pouvant inclure une approche biogographique et les outils de la gnomique. Il ou elle devra contribuer significativement au recrutement et la formation d’tudiants aux 2e et 3e cycles. Il ou elle devra de plus assumer la gestion de l’Herbier Louis-Marie et de son personnel, poursuivre son dveloppement et en faire activement la promotion. Formation et comptence requises : doctorat en sciences biologiques (ou de manire exceptionnelle, en voie d’obtention); exprience postdoctorale souhaitable. Les candidatures de chercheurs tablis sont les bienvenues. Exigences : - Enseigner en franais dans un dlai d’un an. - Possder un excellent dossier de publications et de recherche. - Dmontrer une capacit offrir un enseignement dynamique aux trois cycles (dont un cours d’introduction la diversit vgtale et un cours de taxinomie/systmatique vgtale) L’Universit a une politique d’quit en matire d’emploi. Les femmes sont donc fortement encourages poser leur candidature. Date de clture : 15 dcembre 2014. Le candidat ou la candidate doit entrer en poste au plus tard le 1er septembre 2015. Les personnes intresses doivent faire parvenir un dossier de candidature  : Line Lapointe, directrice, Dpartement de biologie, Universit Laval, Qubec, QC G1V 0A6. Tlcopieur: 418-656-2043, directeur@bio.ulaval.ca. Ce dossier doit comprendre une lettre de motivation et d’intention, un curriculum vitae dtaill et un exemplaire des publications les plus pertinentes. La lettre d’intention doit prsenter les avenues d’enseignement et de recherche, ainsi qu’un plan de dveloppement de l’Herbier Louis-Marie pour la prochaine dcennie. Les noms et coordonnes de trois personnes pouvant fournir une lettre d’appui doivent galement tre inclus dans le curriculum vitae. Louis Bernatchez, MSRC, FRSC Chaire de recherche du Canada en Gnomique et Conservation des Ressources Aquatiques Dpartement de biologie, Institut de Biologie Intgrative et des Systmes (IBIS) Pavillon Charles-Eugne-Marchand 1030, Avenue de la Mdecine Local 1145 Universit Laval Qubec (Qubec) G1V 0A6 Canada Tl.: 1 418 656-3402 Tlc.: 1 418 656-7176 Courriel:Louis.Bernatchez@bio.ulaval.ca Web: http://bit.ly/1w817Qa Louis Bernatchez via Gmail
Source: EVOLDIR
03:20
FACULTY POSITIONS IN LIFE SCIENCES Yale-NUS College, a collaboration between the National University of Singapore (NUS) and Yale University, is seeking to hire one or more open rank, tenure-track, or tenured faculty members to complement our existing biology faculty. Preference will be given to those with an ability to teach across disciplinary boundaries and whose research is suitable to the involvement of undergraduates. Examples might include computational biology, microbial physiology, and developmental genetics of model organisms, but these examples are not meant to preclude any other area of research. Successful candidates will teach both within their specialties and in the Yale-NUS Common Curriculum, an innovative set of required courses that include Scientific Inquiry, Quantitative Reasoning, and Foundations of Science (or Integrated Science for those likely to major in science). For information about the Common Curriculum, please refer to http://bit.ly/1w817PY. Salary, benefits, and leave policies will be competitive at an international level. Yale-NUS College is committed to supporting faculty research through various grants, research, and travel allowances; institutional assistance with proposal preparation; and administration of external grant funding. Full-time appointments are preferred, but joint appointments with other units of NUS may be negotiated. Applications are currently being accepted and reviewed, and review will continue until the positions are filled. Candidates are encouraged to submit their materials as soon as possible. For general inquiries, please refer to http://bit.ly/1wjPmDT, or email Jon Berrick, Search Committee Chair and Professor of Science, at: yale-nus.college@yale.edu. Yale-NUS College values diversity and is committed to equality of opportunity. For additional information about the College and the faculty hiring process, including submission guidelines, and to apply, please visit our website at: http://bit.ly/1sjhreO. To directly access the application portal, please visit: http://bit.ly/1wjPmDU. Emily Marie Smith Assistant Director, Yale-NUS College New Haven Office for Planning and Development Yale Office of the Vice President for Global Initiatives 282 York Street, 2nd Floor New Haven, CT 06511 203-432-1317 (office) emily.m.smith@yale.edu http://bit.ly/1wjPmDT “Smith, Emily” via Gmail
Source: EVOLDIR
03:05
Title: MS Research- Hellbender Ecology and Conservation Agency: Purdue University Location: West Lafayette, IN Job Description: Seeking a highly motivated student for a MS position focusing on hellbender ecology and conservation. The selected candidate will assess post-release juvenile movements and survival, characterize juvenile habitat use, and conduct habitat modifications. This project will consist of intensive field work, up to nine months, at field sites located in southern Indiana. Transportation and off-campus housing will be provided. Graduate position begins in August 2015, but opportunities for field work can begin in May 2015. Qualifications: A student with a background in herpetology or related field is preferred. Experience using radio-telemetry is desired. Applicants must have a strong work ethic and the ability to work both independently and as a member of a team of graduate students working on hellbender ecology and conservation (e.g., students evaluating larval hellbender captive rearing techniques, developing ecological niche models, and hellbender genetics). Applicants also will work closely with a diverse group of scientists, state wildlife biologists, private landowners, and zoo personnel. Excellent writing and interpersonal skills are essential. Funding for research will be provided, but the successful student will need to secure a departmental assistantship through the application process from Purdues Department of Forestry and Natural Resources. Competitive students will have stellar GRE scores, grades/GPA, and letters of recommendation. Applicants are encouraged to visit http://bit.ly/MjkaSR to ensure they meet the minimum departmental requirements for admission. Students that do not meet minimum requirements will not be considered. To apply, electronically submit a single PDF that consists of a cover letter stating research and career interests, CV (including cumulative GPA and GRE scores & percentages), and contact information for three references to Dr. Rod Williams (rodw@purdue.edu). Only those applicants deemed competitive for a departmental assistantship will be asked to formally apply to the Purdue Graduate School and Department of Forestry and Natural Resources. Purdue University is an equal access/equal opportunity/affirmative action employer fully committed to achieving a diverse workforce. Stipend: ~$18,000/yr Last Date to Apply: November 14, 2014 Contact: Rod Williams E-mail: rodw@purdue.edu Web: http://bit.ly/MxYK56 Steven J.A. Kimble, PhD Postdoctoral Research Assistant and Vertebrate Collection Curator, Department of Forestry and Natural Resources Purdue University skimble@purdue.edu sjkimble@gmail.com http://bit.ly/MjkaSV Steve Kimble via Gmail
Source: EVOLDIR
03:05
The Department of BioSciences at Rice University invites applications for admission into our *Ecology & Evolutionary Biology Ph.D. program*. BioSciences is home to a vibrant community of faculty, postdoctoral, graduate, and undergraduate scholars in Ecology and Evolution, Biochemistry, Cell Biology, Genetics and Neuroscience. Our EEB program has particular strengths in animal behavior, population and community ecology, conservation biology, evolutionary ecology, and evolutionary genetics and genomics. The following faculty members are potentially accepting graduate students for Fall 2015: *Scott Egan* (scott.p.egan@rice.edu): evolution, speciation, population genetics and genomics, species interactions, conservation and invasions. http://bit.ly/1tdupdQ *Volker Rudolf* (volker.rudolf@rice.edu): Community ecology, ecological networks, climate change, intraspecific variation, predator-prey interactions, cannibalism, host-pathogen dynamics. http://bit.ly/1tdupu4 *Julia Saltz* (julia.b.saltz@rice.edu): Development and evolution of individual differences in behavior, behavioral genetics, evolutionary feedbacks, phenotypic plasticity, learning. http://bit.ly/1yjmvzH *Evan Siemann* (siemann@rice.edu): Population and community ecology, forests, grasslands, plant ecology, insect ecology, plant/herbivore interactions, biodiversity, conservation. http://bit.ly/1tdupua We offer highly competitive financial support and light teaching requirements for graduate students. We are located in Houston, Texas, an exciting, diverse, and affordable city with world-class opportunities for dining, arts, and entertainment and access to diverse terrestrial and aquatic environments. Rice is located beside one of the countrys largest medical research centers, providing additional opportunities in bioinformatics and genomics. Completed applications should be received by January 10 to ensure full consideration. There is no application fee for US citizens and permanent residents. Prospective applicants are strongly encouraged to contact potential faculty advisors before applying. Complete information about the graduate program, including application instructions, may be found at http://bit.ly/1tdupue. Julia B. Saltz Assistant Professor of Ecology & Evolutionary Biology Department of Biosciences Rice University 6100 Main Street, MS-170 Houston, TX 77005 julia.b.saltz@rice.edu Saltzlab.wordpress.com Julia Saltz via Gmail
Source: EVOLDIR
02:48
The Biology Department at Eastern Connecticut State University invites applications for a tenure track position in Vertebrate Evolutionary Ecology starting August 2015. The position will be filled at the rank of Assistant Professor. A Ph.D. in a biological science with expertise in evolutionary ecology of vertebrates is required. Expertise in animal behavior and/or biostatistics is highly desirable; post-doctoral experience is preferred. The successful candidate must have demonstrated an interest in, and an aptitude for, teaching undergraduates. Responsibilities will include: teaching introductory and upper-level courses for biology majors, teaching a course in the University’s liberal arts core curriculum and/or first-year program, and developing a research program involving undergraduates. Additional expectations include academic advisement, service to the University, and continued professional development. The Department has outstanding resources for teaching and research housed in a modern science building. Facilities include: greenhouse, environmental chambers, vivarium, confocal microscope, campus arboretum, and the nearby Church Farm Center for the Arts and Sciences. Send CV, a copy of all graduate transcripts, statements of teaching philosophy and research interests, documentation of teaching ability, and the name and contact information for three references via email to biologysearch1@easternct.edu, Dr. Patricia Szczys, Department of Biology, Eastern Connecticut State University, Willimantic, CT 06226. Search will continue until the position is filled. ECSU is an Affirmative Action/Equal Opportunity Employer. Matthew R. Graham, Ph.D. Assistant Professor Biology Department Eastern Connecticut State University Science Building, Room 366 83 Windham Street Willimantic, CT 06226 Office: 860-465-3796 Cell: 702-427-1009 Fax: 860-465-5213 http://bit.ly/1yjjcsn “Graham, Matthew R. (Biology)” via Gmail
Source: EVOLDIR
02:33

January 9-10, 2015 **/In the Light of Evolution IX. Clonal Reproduction: Alternatives to Sex /Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala Beckman Center of the National Academies, Irvine, CA *Evolutionary studies of clonal organisms have advanced considerably in recent years, but are still fledgling. Although recent textbooks on evolution and genetics might give the impression that nonsexual reproduction is an anomaly in the living world, clonality is the rule rather than the exception in many viruses, bacteria, and parasites that undergo preponderant asexual evolution in nature. Clonality is thus of crucial importance in basic biology as well as in studies dealing with transmissible diseases. This Colloquium will bring together specialists in various disciplines, including genetics, evolution, statistics, bioinformatics, and medicine. A balance will be sought between the various disciplines, including clonal animals and plants, animal and human cloning, pathogens, and cancer studies. Registration is now open, http://bit.ly/1sO2obi Registration fee is $150. Graduate students and postdoctoral researchers are eligible for discount fee of $100. All meals, break and reception refreshments listed on the agenda are included in the registration fee. For more information, contact sackler@nas.edu. via Gmail

Source: EVOLDIR
02:18

—Boundary_(ID_0LdtvJEXH/6nPkqAHXEAAA) Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: QUOTED-PRINTABLE The organizing committee of the 2015 CSEE Annual Meeting in Saskatoon invite proposals for symposia for the meeting (May 21-25). We anticipate featuring six half-day symposia occurring on the mornings of May 22-24 (two concurrent symposia each day). The theme of the meeting is Ecology and evolution in managed landscapes’. We encourage symposia reflecting this theme, but will consider exceptional symposia from across ecology and evolution. If you are interested in organizing a symposium please submit the following information to Jeff Lane > by November 1, 2014. 1. Title 2. Description of symposium (200-250 words) 3. List of 6 suggested speakers, their affiliations, and tentative presentation titles 4. An indication of whether the speaker has confirmed their participation. Each symposium organizer will have a budget of $1200 that can be used to defray speaker conference registration fees and/or travel. For more information please contact Jeff or visit the conference website at http://bit.ly/1w7KGU0 Dr. Jeffrey Lane Assistant Professor Department of Biology University of Saskatchewan www.lanelab.ca —Boundary_(ID_0LdtvJEXH/6nPkqAHXEAAA) Content-type: text/html; charset=Windows-1252 Content-transfer-encoding: QUOTED-PRINTABLE P {margin-top:0;margin-bottom:0;}

The organizing committee of the 2015 CSEE Annual Meeting in Saskatoon invite proposals for symposia for the meeting (May 21-25). We anticipate featuring six half-day symposia occurring on the mornings of May 22-24 (two concurrent symposia each day). The theme of the meeting is Ecology and evolution in managed landscapes’. We encourage symposia reflecting this theme, but will consider exceptional symposia from across ecology and evolution. If you are interested in organizing a symposium please submit the following information to Jeff Lane by November 1, 2014.

  1. Title
  2. Description of symposium (200-250 words)
  3. List of 6 suggested speakers, their affiliations, and tentative presentation titles
  4. An indication of whether the speaker has confirmed their participation.
Each symposium organizer will have a budget of $1200 that can be used to defray speaker conference registration fees and/or travel. For more information please contact Jeff or visit the conference website at
http://bit.ly/1w7KGU0 Dr. Jeffrey Lane Assistant Professor Department of Biology University of Saskatchewan www.lanelab.ca —Boundary_(ID_0LdtvJEXH/6nPkqAHXEAAA via Gmail

Source: EVOLDIR
01:47
The Department of Biology at Swarthmore College invites applications for a two-year visiting The Department of Biology at Swarthmore College invites applications for a two-year visiting assistant professor position for the 2015-16 and 2016-17 academic years. Teaching responsibilities include participation in a team-taught introductory biology course as well as teaching intermediate-level courses with weekly laboratories in evolutionary biology (2015-16)and animal behavior (2016-17). Additionally, there may be an opportunity to teach an advanced seminar-style course (with laboratory projects) in an area that is complementary to our existing curriculum. Applicants should have a Ph.D., teaching experience, and a strong commitment to undergraduate education. The College provides laboratory space and funds to support student research and faculty travel. The Biology Department is dedicated to educating and supporting a rich, diverse body of students and encourages candidates who will further advance the goals of fostering an inclusive community with diverse ideas and experiences. All application materials (curriculum vitae, statements of teaching and research interests, and three letters of recommendation) should be submitted online at http://bit.ly/1uDtMXq by January 12th, 2015. For more information, please visit our website at http://bit.ly/1uDtMXs. Questions regarding this position should be addressed to the Biology Department chair, Amy Cheng Vollmer, at avollme1@swarthmore.edu or by calling 610-328-8044. Vince Formica via Gmail
Source: EVOLDIR
01:14
Research Symposium - The Origins and Evolution of Bacterial Genomes Sunday Dec 7th Hamilton, Ontario. This symposium focuses on the evolution and comparative analysis of bacterial and archaeal genomes. How fast does gene gain and loss occur? How frequent is horizontal gene transfer? How tree-like is evolution at the genome level? What kinds of mathematical methods are necessary for analysis of genome data? Invited Speakers Robert Beiko - Dalhousie University - When Phylogenetic Trees Can’t Agree: Building a coherent network of microbial gene sharing Yuri Wolf - National Center for Biotechnology Information - Turbulent genomes: quantification of gene acquisition, loss and displacement in prokaryotes. Tal Dagan - University of Kiel - Phylogenomic networks reveal trends and barriers to lateral gene transfer during microbial evolution Daniel Brown - University of Waterloo - Fast algorithms for phylogenetic reconstruction of aligned sequences Weilong Hao - Wayne State University - Estimating evolutionary rates of discrete characters, and its application to genome evolution Radhey Gupta - McMaster University - Applications of Group specific Conserved Signature Proteins for the Identification of Microorganisms in Metagenomic Sequences Eric Collins - University of Alaska - TBA Paul Higgs - McMaster University - Phylogenetic models of bacterial genome evolution incorporating gene insertion and deletion and horizontal gene transfer   Registration and Organizational Details The Symposium is being sponsored by the Origins Institute at McMaster University and is being held at the Winter Meeting of the Canadian Mathematical Society. Those wishing to attend should register at the conference web site http://bit.ly/1rdkwrS as soon as possible. All talks in this symposium are on Sunday Dec 7th and will take place at the conference venue (Sheraton Hotel, Hamilton). A one-day registration option is possible. To facilitate discussion and collaboration between speakers, there will be a day of informal discussions at McMaster university on Monday Dec 8th. We welcome additional participants. Those interested should contact Paul Higgs (higgsp@mcmaster.ca) in order to be included in the arrangements. There will be opportunity for short submitted talks on Mon 8th, although the schedule is now complete for the conference day. Latest information will be posted on http://bit.ly/129lcsL Paul Higgs http://bit.ly/VBVQjz Dept of Physics and Astronomy, McMaster University, Hamilton, Ontario, L8S 4M1, Canada. Tel. (905) 525 9140 ext 26870 Paul Higgs via Gmail
Source: EVOLDIR
00:41

The newly established Research Group Evolutionary Immunogenomics in the Department of Evolutionary Ecology at the Max-Planck Institute for Evolutionary Biology in Plön/Germany has an opening for a Post-Doctoral Research Fellow Our research explores the evolution of immunogenetic and genomic variability and its implications for individual immunocompetence and ultimately fitness. We are mainly focusing on data from human populations, using a wide spectrum of approaches from molecular biology and high-throughput sequencing to computational analyses and theoretical modeling, but also employ experimental model systems (stickleback, mouse) to test predictions in the lab. Our scientific motivation ranges from pure curiosity about evolutionary processes to the desire to push the practical boundaries of Evolutionary and Personalized Medicine. Specific projects within the scheme of the lab are flexible and can be tailored to skills and interest of the successful candidate. The group is part of the Max Planck Institute for Evolutionary Biology with its vibrant and collaborative research community of experimental, computational, and theoretical labs that all share a common interested in Evolutionary Biology. Cutting edge infrastructure is available at all levels, including high-performance computer clusters, a next-gen sequencing core facility, as well as molecular and experimental labs with substantial fish and mouse rearing facilities. The institute also maintains strong ties to Kiel University with large communities in evolutionary biology and medical genetics. Furthermore, our lab is currently collaborating on a number of projects with groups at Harvard Medical School in Boston and the University of Texas in Austin. Working language at the institute is English. This position requires a PhD/Dr. in Evolutionary Biology, Computational Biology, Genetics/Genomics or a related field. The ideal candidate has a strong interest in evolutionary questions and is motivated to cross interdisciplinary boundaries and think outside the box. Molecular and/or computational experience is highly desirable and a background in molecular evolution, population genomics and/or immunology a plus. The initial appointment is for one year, with the possibility of extension by up to two more years, based on performance. The starting date is flexible and can be immediate. The Max Planck Fellowship is competitive and includes additional support for health insurance and family (if applicable). Furthermore, housing and living in this area is very affordable. The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply. The Society also seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages female candidates to apply. The institute is located in Plön, northern Germany, in close proximity to the university cities of Kiel and Lübeck and not far from Hamburg, the second-largest city in Germany. Frequent train connections allow for an easy commute between Plön and Kiel/Lübeck (each 30 min) and provide general access to the well-developed European train network. Plön is surrounded by a beautiful landscape with many lakes and provides ample opportunity for water sports and other outdoor activities. To apply, please send a cover letter with your motivation/interests and research experience (2 pages max), CV, and contact info of 2-3 references in one PDF file to lenz evolbio.mpg.de, using the subject line ‘Post-Doc in Evolutionary Immunogenomics’. Review of applications will start Nov 15th and will continue until the position is filled. Informal inquiries are welcome. For more information about our research and the institute, please visit the lab’s website at http://bit.ly/1yX3bvv Dr. Tobias Lenz Group Leader in Evolutionary Immunogenomics Department of Evolutionary Ecology Max Planck Institute for Evolutionary Biology August-Thienemann-Str. 2 24306 Ploen Germany lenz@evolbio.mpg.de via Gmail

Source: EVOLDIR

October 21, 2014

23:22

The newly established Research Group Evolutionary Immunogenomics in the Department of Evolutionary Ecology at the Max-Planck Institute for Evolutionary Biology in Plön/Germany has an opening for a PhD student Our research explores the evolution of immunogenetic and genomic variability and its implications for individual immunocompetence and ultimately fitness. We are mainly focusing on data from human populations, using a wide spectrum of approaches from molecular biology and high-throughput sequencing to computational analyses and theoretical modeling, but also employ experimental model systems (stickleback, mouse) to test predictions in the lab. Our scientific motivation ranges from pure curiosity about evolutionary processes to the desire to push the practical boundaries of Evolutionary and Personalized Medicine. Specific projects within the scheme of the lab are flexible and can be tailored to skills and interest of the successful candidate. The group is part of the Max Planck Institute for Evolutionary Biology with its vibrant and collaborative research community of experimental, computational, and theoretical labs that all share a common interested in Evolutionary Biology. Cutting edge infrastructure is available at all levels, including high-performance computer clusters, a next-gen sequencing core facility, as well as molecular and experimental labs with substantial fish and mouse rearing facilities. The institute also maintains strong ties to Kiel University with large communities in evolutionary biology and medical genetics. Furthermore, our lab is currently collaborating on a number of projects with groups at Harvard Medical School in Boston and the University of Texas in Austin. Working language at the institute is English. This position requires a Master’s/Diplom degree in Biology, Bioinformatics, Genetics or a related field. The ideal candidate is fascinated by evolutionary questions and eager to learn and master new skills and tools. The duration and funding of a PhD project in the German university system is generally aimed at three years. PhD candidates at the institute have the opportunity to become member of the International Max Planck Research School for Evolutionary Biology in collaboration with the University of Kiel. The PhD fellowship is funded for three years, extension possible. The starting date is flexible and can be immediate. The fellowship includes support for health insurance and family (if applicable), and housing and living in this area is affordable. The Max Planck Society is committed to employing more handicapped individuals and especially encourages them to apply. The Society also seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages female candidates to apply. The institute is located in Plön, northern Germany, in close proximity to the university cities of Kiel and Lübeck and not far from Hamburg, the second-largest city in Germany. Frequent train connections allow for an easy commute between Plön and Kiel/Lübeck (each 30 min) and provide general access to the well-developed European train network. Ploen is surrounded by a beautiful landscape with many lakes and provides ample opportunity for water sports and other outdoor activities. To apply, please send a cover letter with your motivation/interests and research experience (1 page max), CV, and contact info of 2-3 references in one PDF file to lenz evolbio.mpg.de, using the subject line ‘PhD in Evolutionary Immunogenomics’. Review of applications will start Nov 15th and will continue until the position is filled. Informal inquiries are welcome. For more information about our research and the institute, please visit the lab’s website at http://bit.ly/1yX3bvv Dr. Tobias Lenz Group Leader in Evolutionary Immunogenomics Department of Evolutionary Ecology Max Planck Institute for Evolutionary Biology August-Thienemann-Str. 2 24306 Ploen Germany lenz@evolbio.mpg.de via Gmail

Source: EVOLDIR
22:30

Phylogenomics, the idea of applying genomic data to phylogenetic studies, has been around for quite a while now (Eisen 1998), although it was probably Rokas et al. (2003) who drew the first widespread attention among phylogeneticists. Molecular phylogenetics started off using the sequence of a single locus (often small-subunit rRNA) as the data, and slowly progressed from there to multiple loci. Currently, it is considered good practice to use half-a-dozen loci, sampling the main genomes (nucleus, mitochondrion, plastid); and genomics offers the possibility of a fast and cost-effective means of generating large amounts of multi-locus sequence data.


Review papers are beginning to appear based explicitly on next-generation sequencing (NGS), such as those of Lemmon & Lemmon (2013) and McCormack et al. (2013), replacing the earlier work of Philippe et al. (2005), and there are suggestions for how phylogenetics analyses might need to change on response to NGS data (Chan and Ragan 2013). These all treat phylogenomics as being very similar to traditional molecular phylogenetics, in the sense that many people are expecting phylogenomics to provide tree-like resolution of questions that remain unresolved with the current smaller datasets. In the words of Rokas et al. (2003), phylogenomics is intent on "resolving incongruence in molecular phylogenies". That is, incongruent gene trees are seen as the major obstacle to be overcome by phylogenetics data analysis (see also Jeffroy et al. 2006).

However, this might be a naive expectation. After all, the existing phylogenetic conflicts are there for a reason. If we cannot resolve certain parts of organismal history in terms of a phylogenetic tree when we use the current levels of multi-locus data (say
22:00
Wednesday, 12:00 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street. Room A103 (1st Floor) For more information, call 919-668-4551
Source: NESCent
06:00
Background: As attested by the fossil record, Cretaceous environmental changes have significantly impacted the diversification dynamics of several groups of organisms. A major biome turnover that occurred during this period was the rise of angiosperms starting ca. 125 million years ago. Though there is evidence that the latter promoted the diversification of phytophagous insects, the response of other insect groups to Cretaceous environmental changes is still largely unknown. To gain novel insights on this issue, we assess the diversification dynamics of a hyperdiverse family of detritivorous beetles (Tenebrionidae) using molecular dating and diversification analyses. Results: Age estimates reveal an origin after the Triassic-Jurassic mass extinction (older than previously thought), followed by the diversification of major lineages during Pangaean and Gondwanan breakups. Dating analyses indicate that arid-adapted species diversified early, while most of the lineages that are adapted to more humid conditions diversified much later. Contrary to other insect groups, we found no support for a positive shift in diversification rates during the Cretaceous; instead there is evidence for an 8.5-fold increase in extinction rates that was not compensated by a joint increase in speciation rates. Conclusions: We hypothesize that this pattern is better explained by the concomitant reduction of arid environments starting in the mid-Cretaceous, which likely negatively impacted the diversification of arid-adapted species that were predominant at that time.
05:22
I'm going to the TDWG Identifier Workshop this weekend, so I thought I'd jot down a few notes. The biodiversity informatics community has been at this for a while, and we still haven't got identifiers sorted out.

From my perspective as both a data aggregator (e.g., BioNames) and a data provider (e.g., BioStor) there are four things I think we need to tackle in order to make significant progress.

Discoverability (strings to things)
A basic challenge is to go from strings, such as bibliographic citations, specimen codes, taxonomic names, etc., to digital identifiers for those things. Most of our data is not born digital, and so we spend a lot of time mapping strings to identifiers. For example, publishers do this a lot when they take the list of literature cited at the end of a manuscript and add DOIs. Hence, one of the first things CrossRef did was provide a discovery service for publishers. This has now morphed into a very slick search tool http://search.crossref.org. Without discoverabilty, nobody is going to find the identifiers in the first place.

Resolvability
Given an identifier it has to be resolvable (for both people and machines), and I'd argue that at least in the early days of getting that identifier accepted, there needs to be a single point of resolution. Some people are arguing that we should separate identifiers from their resolution, partly based on arguments that "hey, we can always Google the identifier". This argument strikes me as wrong-headed for a several of reasons.

Firstly, Google is not a resolution service. There's no API, so it's not scalable. Secondly, if you Google an identifier (e.g., 10.7717/peerj.190) you get a bunch of hits, which one is the definitive source of information on the thing with that identifier? It's not at all obvious, and indeed this is one of the reasons publishers adopted DOIs in the first place. If you Google a paper you can get all sorts of hits and all sorts of versions (preprint, manuscripts, PDFs on multiple servers, etc.). In contrast the DOI gives you a way to access the definitive version.

Another way of thinking about this is in terms of trust. At some point down the road we might have tools that can assess the trust worthiness of a source, and we will need these if we develop decent tools to annotate data (see More on annotating biodiversity data: beyond sticky notes and wikis). But until then the simplest way to engender trust is to have a single point of resolution (like http://dx.doi.org for DOIs). Think about how people now trust DOIs. They've become a mark of respectability for journals (no DOIs, you're not a serious journal), and new ideas such as citing diagrams and data gained further credence once sites like figshare started using DOIs.

Another reason resolvability matters is that I think it's a litmus test of how serious we are. One reason LSIDs failed is that we made them too hard to resolve, and as a consequence people simply minted "fake" LSIDs, dumb strings that didn't resolve. Nobody complained (because, let's face it, nobody was using them), so LSIDs became devalued to the point of uselessness. Anybody can mint a string and call it an identifier, if it costs nothing that's a good estimate of its actual value.

Persistence
Resolvability leads to persistence. Sometimes we hear the cliche that "persistence is a social matter, not a technological one". This is a vacuous platitude. The kind of technology adopted can have a big impact on the sociology.

The easiest form of identifier is a simple HTTP URL. But let's think about what happens when we use them. If I spend a lot of time mapping my data to somebody else's URLs (e.g., links to papers or specimens) I am taking a big risk in assuming that the provider of those URLs will keep those "live". At the same time, in linking to those URLs, I constrain the provider - if they decide that their URL scheme isn't particularly good and want to change it (or their institution decides to move to new servers or a new domain), they will break resources like mine that link to them. So a decision they made about their URL structure - perhaps late one Friday afternoon in one of those meetings where everybody just wants to go to the pub - will come back to haunt them.

One way to tackle this is indirection, which is the idea behind DOIs and PURLs, for example. Instead of directly linking to a provider URL, we link to an intermediate identifier. This means that I have some confidence that all my hard work won't be undone (I have seen whole journals disappear because somebody redesigned an institutional web site), and the provider can mess with different technologies for serving their content, secure in the knowledge that external parties won't be affected (because they link to the intermediate identifier). Programmers will recognise this as encapsulation.

Some have argued that we can achieve persistence by simply insisting on it. For example, we fire off a memo to the IT folks saying "don't break these links!". Really? We have that degree of power over our institutional IT policies? This also misses the great opportunity that centralised indirection provides us with. In the case of DOIs for publications, CrossRef sits in the middle, managing the DOIs (in the sense that if a DOI breaks you have a single place to go and complain). Because they also aggregate all the bibliographic metadata, they are automatically able to support discoverability (they can easily map bibliographic metadata to DOIs). So by solving persistence we also solve discoverability.

Network effects
Lastly, if we are serious about this we need to think about how to engineer the widespread adoption of the identifier. In other words, I think we need network effects. When you join a social networking site, one of the first things they do is ask permission to see your "contacts" (who you already know). If any of those people are already on the network, you can instantly see that ("hey, Jane is here, and so is Bob"). Likewise, the network can target those you know who aren't on the network and prompt them to join.

If we are going to promote the use of identifiers, then it's no use thinking about simply adding identifiers to things, we need to think about ways to grow the network, ideally by adding networks at a time (like a person's list of contacts), not single records. CrossRef does this with articles: when publishers submit an article to CrossRef, they are encouraged to submit not just that article and it's DOI, but the list of all references in the list of literature cited, identified where possible by DOIs. This means CrossRef is building a citation graph, so it can quickly demonstrate value to its members (through cited-by linking).

So, we need to think of ways of demonstrating value, and growing the network of identifiers more rapidling than one identifier at a time. Otherwise, it is hard to see how it would gain critical mass. In the context of, say, specimens, I think an obvious way to do this is have services that tell a natural history collection how many times its specimens have been cited in the primary literature, or have been used as vouchers for DNA seqences. We can then generate metrics of use (as well as start to trace the provenance of our data).


Summary
I've no idea what will come out of the TDWG Workshop, but my own view is that unless we tackle these issues, and have a clear sense of how they interrelate, then we won't make much progress. These things are intertwined, and locally optimal solutions ("hey, it's easy, I'll just slap a URL on everything") aren't enough ("OK, how exactly do I find your URL? What happens when it breaks?"). If we want to link stuff together as part of the infrastructure of biodiversity informatics, then we need to think strategically. The goal is not to solve the identifier problem, the goal is to build the biodiversity knowledge graph.
Source: iPhylo