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October 12, 2014
Some years ago Larisa Lehmer, Bruce Ragsdale, John Daniel, Edwin Hayashi and Robert Kvalstad published a medical report about an ingested plastic bag closure caught in someone's colon (Plastic bag clip discovered in partial colectomy accompanying proposal for phylogenic plastic bag clip classification. BMJ Case Reports 2011). This sounds quite painful.
What is more interesting, though, is that the report was accompanied by a phylogenetic and taxonomic evaluation of plastic ties in general, which the authors named Occlupanids.
Note that the proposed morphological changes in the phylogeny match Cope's Rule of phyletic size increase, as discussed in a previous blog post (Steven Jay Gould was wrong).
Shortly afterwards, one of the authors, John Daniel, set up a web page with a more detailed analysis, under the guise of the Holotypic Occlupanid Research Group (HORG).
Among a lot of other interesting information, there is a revised phylogenetic analysis.
Given the data, it seems fairly clear that the genealogical relationship among these objects is reticulate, and that the trees should thus actually be networks. This follows from the simple fact that these phylogenies are rather uninformative (they are bushes showing a few character transformation series). Also, note that contemporary taxa are ancestors, so that the diagrams are more like population networks than species networks.
These ties are used for packets of sliced bread (a relatively recent invention), and so there has been an explosion of Occlupanid forms as they occupy a new adaptive zone. This is a classic instance of recent speciation that is not yet complete. Occlupanids have now reached pest proportions, except where governments have instituted erradication programmes (such as Europe, where they are no longer found).
Part of the difficulty of analysis is that the objects shown constitute only a small part of the known diversity of Occlupanids (e.g. see this photo and this one). There are a number of manufacturers, and their products constitute separate historical lineages. Morphological features have been transferred from one lineage to another, which is a classic case of reticulate history that has not been taken into account in the above phylogenies.
Indeed, the HORG page is not the only detailed web resource about bread ties — see also the now-defunct but fascinating Transactoid page.
—Apple-Mail=_23A91202-765D-4789-AC04-30A00FC8A823 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi…can you please post this under graduate positions? Thanks, Spence +++++++++++++++++++ Interested in pursuing a PhD? Come take a look at Texas A&M! The Department of Entomology at Texas A&M University, a growing and vibrant Department with stimulating and diverse research opportunities, is pleased to announce the availability of travel grants for prospective PhD students. These grants, which provide airfare (within the continental United States), hotel accommodations and a modest per diem for food, give prospective PhD students the opportunity to meet our faculty, students and staff, tour the department and campus, and explore College Station. For more information on how to apply for a PhD travel grant, please visit us at http://bit.ly/1suja1s. Spencer T. Behmer Professor Department of Entomology | Faculty of Ecology and Evolutionary Biology | Faculty of Neuroscience Texas A&M University Heep Building, room 509 College Station, TX 77843-2475 | Phone: (979) 845-7304 | FAX: (979) 845-6305 Email: email@example.com | Website: http://bit.ly/1qJhU47 —Apple-Mail=_23A91202-765D-4789-AC04-30A00FC8A823 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-asciiHi…can you please post this under graduate positions?Thanks,Spence+++++++++++++++++++Interested in pursuing a PhD? Come take a look at Texas A&M! The Department of Entomology at Texas A&M University, a growing and vibrant Department with stimulating and diverse research opportunities, is pleased to announce the availability of travel grants for prospective PhD students. These grants, which provide airfare (within the continental United States), hotel accommodations and a modest per diem for food, give prospective PhD students the opportunity to meet our faculty, students and staff, tour the department and campus, and explore College Stati on. For more information on how to apply for a PhD travel grant, please visit us at http://bit.ly/1suja1s.
Spencer T. BehmerProfessorDepartment of Entomology | Faculty of Ecology and Evolutionary Biology | Faculty of NeuroscienceTexas A&M UniversityHeep Building, room 509College Station, TX 77843-2475 | Phone: (979) 845-7304 | FAX: (979) 845-6305 Email: firstname.lastname@example.org | Website: http://bit.ly/1qJhU47
—Apple-Mail=_23A91202-765D-4789-AC04-30A00FC8A82 via Gmail
The Evolution lab (School of Sciences, University of Buenos Aires) has an opening for a postdoctoral researcher beginning in february 2015 (a later start is possible). The postdoc will contribute to ongoing projects that use genomic tools to address questions about the processes that generate morphological diversity. The core projects in which the successful applicant will be involved are related to the genomics of rapid adaptive evolution of genital organs. . The work involves the analysis of whole genomes and RNA-seq data in cactophilic flies of the genus Drosophila (buzzatii complex repleta group).As well as research duties, applicants are expected to write papers and train graduate students in the field of genomics. The successful applicant should have a PhD in the areas of population, evolutionary genetics and some. Prior experience with NGS data and script programming is a plus. Applications will be accepted until November 30th 2014. Applicants should a submit a CV, two references and a one page research statement to: Esteban Hasson email@example.com firstname.lastname@example.org Esteban Hasson Dr Cs Biolgicas Dept. Ecologa Gentica y Evolucin Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Ciudad Universitaria Pab. 2 C1428 EHA Buenos Aires Argentina Esteban Hasson via Gmail
October 11, 2014
I note that Charles Dawson was the name of the man who “found” the Piltdown man in 1912 Since this matches the supposed identity of this “historian” I strongly suspect a creationist troll looking to misquote scientists. I strongly urge the community NOT to help his cause Mark Farmer Univ. Georgia via Gmail
Colorado State University is seeking outstanding graduate students in the field of evolutionary biology. CSU is home to a strong and diverse group of evolution-focused labs, many of which are accepting grad students this year. Interested students are highly encouraged to explore the research pages of CSU faculty and contact professors before applying to a CSU graduate program. The university is home to a number of departmental and interdisciplinary graduate programs, and prospective faculty mentors can assist in selecting the program that would be the best match for a student’s interests. CSU faculty members currently accepting graduate students include: Chris Funk Department of Biology http://bit.ly/1kKPRUq Kim Hoke Department of Biology http://bit.ly/1wkJ5q7 Ruth Hufbauer Bioagricultural Sciences and Pest Management http://bit.ly/1wkJ3yG John McKay Bioagricultural Sciences and Pest Management http://bit.ly/16jyOAz Rachel Mueller Department of Biology http://bit.ly/1wkJ5qg Dhruba Naug Department of Biology http://bit.ly/1sALf6c Paul Ode Bioagricultural Sciences and Pest Management http://bit.ly/1wkJ5GA Mark Simmons Department of Biology http://bit.ly/1wkJ5GC Dan Sloan Department of Biology http://bit.ly/1asiBKM Colleen Webb Department of Biology http://bit.ly/1wkJ3OU CSU is a world-class research university located in Fort Collins, CO, about an hour north of Denver and right at the foothills of the Rocky Mountains. Fort Collins is widely regarded as having a great quality of life at a reasonable cost of living. It has excellent opportunities for outdoor recreation, an active music scene, a strong biking culture, and numerous great restaurants and breweries. email@example.com via Gmail
PhD fellowships at the University of Lausanne (Switzerland) Each year the University of Lausanne offers competitive PhD fellowships in broadly defined biological sciences, including evolution and ecology. The winners can choose a supervisor among those participating in the program, including many group leaders at the Department of Ecology of Evolution (www.unil.ch/dee). The Department of Ecology and Evolution is one of the strongest centers in evolutionary biology in Europe and the organizer of the next congress of the European Society for Evolutionary Biology. It consists of over 20 research groups including about 50 postocs and 70 PhD students; several of those PhD students are winners of the fellowship in previous years. The fellowships are for three years plus a fourth year funded by grants of the supervisor. A Master or an equivalent degree is a prerequisite of being admitted into a PhD program in Switzerland (but the candidates do not yet have to hold a master at the time of application). Information about the fellowships, requirements and the application procedure can be found under http://bit.ly/1wkJ3yuwww.unil.ch/dee). The Department of Ecology and Evolution is one of the strongest centers in evolutionary biology in Europe and the organizer of the next congress of the European Society for Evolutionary Biology. It consists of over 20 research groups including about 50 postocs and 70 PhD students; several of those PhD students are winners of the fellowship in previous years. The fellowships are for three years plus a fourth year funded by grants of the supervisor. A Master or an equivalent degree is a prerequisite of being admitted into a PhD program in Switzerland (but the candidates do not yet have to hold a master at the time of application). Information about the fellowships, requirements and the application procedure can be found under http://bit.ly/1wkJ3yu Note that to assure consideration, the application must be sent in paper form by mail and have arrived by November 1. Lausanne is a medium-sized city on the shores of Lake Geneva, surrounded by a wine growing region (recognized as one of UNESCO Heritage sites) and within one hour of the Alps. It offers a great variety of cultural, recreational and outdoor opportunities. Tadeusz J. Kawecki via Gmail
Background: Five basic taste modalities, sour, sweet, bitter, salt and umami, can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. Results: Here, all five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. The sequence characteristics and evolutionary analyses of taste receptor genes suggested that nearly all cetaceans may have lost all taste modalities except for that of salt. Conclusions: This is the first study to comprehensively examine the five basic taste modalities in cetaceans with extensive taxa sampling. Our results suggest that cetaceans have lost four of the basic taste modalities including sour, sweet, umami, and most of the ability to sense bitter tastes. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na+ reabsorption, which is key to osmoregulation and aquatic adaptation.
WageningenZambia.ExpEvolutionMicrobialEcosystems Three (3) PhD projects on the experimental evolution of microbial ecosystems in traditional fermented products from Zambia. Location: Wageningen University (the Netherlands) and the University of Zambia (Lusaka, Zambia). Like commonly known products such as yoghurt, wine, and beer, Zambia has numerous local fermented foods. Many are consumed on a daily basis by large parts of the population and are part of Zambian and African culture. Fermented food products rely on microbial activity and have significant added value compared to unfermented food products due to higher nutritional value, longer shelf life and better taste and are produced locally according to ancient traditions. Producers are mainly women, who produce at home by continuously re-using their bacterial cultures from batch to batch by serial transfer. They sell the products at local markets generating a livelihood for themselves and their families. To stimulate development of the products through both fundamental and applied research, this NWO-WOTRO funded project will study to the microbial ecology and evolution that underlies product properties and key elements of the food value chains of two exemplary products, Mabisi (based on milk) and Munkoyo/Chibwantu (based on cereal). This project is a collaboration of consortium led by Wageningen University in the Netherlands and the University of Zambia, further consisting of other partners in the Netherlands (CSK Food Enrichment and Yoba-for-Life) and in Zambia (Tropical Diseases Research Centre, Heifer International). We are looking to fill three PhD positions. PhD position 1. In this PhD project, we will use traditional fermented foods from Zambia as experimental model systems to study microbial community dynamics and evolution. We aim to address fundamental questions relating to eco-system evolution both experiments and modelling on the microbial ecology and evolution of fermenting microbes. We will also relate this to compositional and functional stability of the community of fermenting microbes. This PhD position will be part of a larger research programme on traditional fermented foods in Zambia. Candidate profile: Masters in (evolutionary) biology, genetics, microbiology, food (bio)technology or related field. Proven experimental skills in microbiology and molecular tools. Experience with of microbial community analysis is a bonus. Affinity with modelling (such as metabolic flux models, niche competitive exclusion models). Willingness and ability to travel to Zambia on occasion to visit field sites and to discuss with the other PhD candidates in the programme. The candidate will stationed at Wageningen University at the Laboratory of Genetics on the basis of the CAO Nederlandse Universiteiten for 4 years. http://bit.ly/1qCpSMf PhD positions 2 and 3. PhD candidates 1 and 2 will establish consumer preference and requirements and how taste, nutritional value, food stability and food safety of the products are affected by production procedures, fermentation processes and the ecology the micro-organisms responsible for fermentation. Phd candidate 2 will focus on Mabisi, PhD candidate 3 will focus on Munkoyo/Chibwantu. Candidate profiles: Masters degree in food science and technology, microbiology or related field. Willingness and ability to perform field as well as laboratory based research and affinity with conditions in rural Zambia. Willingness and ability to spend 50% of time in Zambia (mostly Lusaka) and 50% in Wageningen. Candidates will be offered a contract for 4 years out of Wageningen University on the basis of Nuffic guidelines (see www.nuffic.nl) and will be stationed at Wageningen University (Food Quality and Design and Food Microbiology), as well as the University of Zambia (Department of Food Science and Nutrition). Preference will be given to candidates from Zambia and the Southern African region. The 3 PhD candidates will be working with a multidisciplary team of supervisors at Wageningen University: Dr Sijmen Schoustra and prof Bas Zwaan (Evolutionary Biology and Genetics), Dr Anita Linnemann (Food Quality and Design) and Prof. dr. Eddy Smid (Food Microbiology). In Zambia, supervision will be by Dr Sijmen Schoustra and Dr John Shindano (Department of Food Science and Nutrition, School of Agriculture, University of Zambia). Representatives of other members of the programme consortium will also be involved in the project. To apply for PhD position 1, please send your application through the electronic system of Wageningen University, see http://bit.ly/1qCpSMf. To apply for PhD positions 2 or 3, send one file containing a motivation letter, your CV and names and contact details of three references to Sijmen Schoustra via email. Sijmen.Schoustra@wur.nl. Closing date for applications: 7 November 2014. Start of the PhD projects is planned for 1 February 2015. For more information and informal enquiries you may contawww.nuffic.nl) and will be stationed at Wageningen University (Food Quality and Design and Food Microbiology), as well as the University of Zambia (Department of Food Science and Nutrition). Preference will be given to candidates from Zambia and the Southern African region. The 3 PhD candidates will be working with a multidisciplary team of supervisors at Wageningen University: Dr Sijmen Schoustra and prof Bas Zwaan (Evolutionary Biology and Genetics), Dr Anita Linnemann (Food Quality and Design) and Prof. dr. Eddy Smid (Food Microbiology). In Zambia, supervision will be by Dr Sijmen Schoustra and Dr John Shindano (Department of Food Science and Nutrition, School of Agriculture, University of Zambia). Representatives of other members of the programme consortium will also be involved in the project. To apply for PhD position 1, please send your application through the electronic system of Wageningen University, see http://bit.ly/1qCpSMf. To apply for PhD positions 2 or 3, send one file containing a motivation letter, your CV and names and contact details of three references to Sijmen Schoustra via email. Sijmen.Schoustra@wur.nl. Closing date for applications: 7 November 2014. Start of the PhD projects is planned for 1 February 2015. For more information and informal enquiries you may contact Sijmen Schoustra - project coordinator. Full project description is available upon request. (firstname.lastname@example.org; phone +260 974 572686; +31 317 483142). Wageningen University and Research Centre (Wageningen UR) is a leading international organization. Within the field of healthy nutrition and living environment we are working on the quality of life. We are always looking for talented colleagues. Professionals with passion who want to work with us for the world of tomorrow. The University of Zambia is the main academic institution in Zambia. Within the School of Agriculture, the Department of Food Science and Nutrition studies Zambia related foods, their properties, processing and nutritional impact. Dr Sijmen Schoustra Laboratory of Genetics, Wageningen University, The Netherlands & Department of Food Science and Nutrition, University of Zambia Email: email@example.com Phone: +31 317 483142 and +260 974 572686 Website “Schoustra, Sijmen” via Gmail
The position (Research Curator, Ichthyology at the NC Museum of Natural Sciences) will is re-opened for only a brief time (10 days), and previous applicants must re-apply. Thank you! Jason Job Class Title: Natural Science Research Curator II Working Title: Research Curator, Ichthyology Position Number: 60034991 Department: Dept of Environment & Natural Resource Division/Section: NC Museum of Natural Sciences/Research and Collections Salary Range: $42,667.00 - $69,177.00 Annually Recruitment Range: $42,667 - $53,437 Salary Grade / Salary Grade Equivalent: 72 Appointment Type: Permanent Full-Time Pos. Location: Wake County, North Carolina Opening Date: Thu. 10/09/14 Closing Date/Time: Sat. 10/18/14 5:00 PM Eastern Time THIS IS A REPOST. PREVIOUS APPLICANTS MUST RE-APPLY TO BE CONSIDERED. This position is located in Raleigh, North Carolina at the NC Museum of Natural Sciences, an award-winning major institution with a prominent State-wide, national and international profile. This key position is in the Museum’s Research & Collections section and is located at the Museum’s Research Laboratory, approximately 15 minutes away from the downtown Raleigh Museum buildings. This position of Research Curator, Ichthyology, has several areas of responsibility, including: 1. Development of original scientific research programs in ichthyological systematics (taxonomy, phylogenetics), genomics, ecology, and/or related fields; research programs may have local, regional, and/or international focus and will include pursuit of external research funding, data generation and analyses, and publication/dissemination of results; some aspects of this research should, ideally, include collaborations with other agencies, universities, and/or citizen scientists. 2. Curatorial responsibilities for the Ichthyology Research Collection, including maintenance and growth of collection, migrating collections data to database format, specimen loan activities, and setting curatorial best-practice guidelines for collection. 3. Operational management and administration of the Ichthyology unit, a subdivision of the Research & Collections section; duties include supervision of laboratory with oversight of equipment, budgets, and personnel. 4. Participation in science communication initiatives, including participation in Museum educational programming, delivering public science-based presentations, interacting with Museum visitors, serving as a role model for students and citizen scientists, and creating programmatic themes that raise the science literacy of visitors. Knowledge, Skills and Abilities / Competencies: **To receive credit for your work history and credentials, you must list the information on the application form. Any information omitted from the application form, listed under the text resume section, or on an attachment will not be considered for qualifying credit** A successful candidate will have the following knowledge, skills and abilities: (1) Taxonomic/systematic expertise in Ichthyology (2) Experience applying principles and practices of research, with special expertise in at least one aspect of fish systematics (taxonomy, phylogenetics), genomics, ecology, and/or related fields. (3) Experience with specimen collections and/or curatorial activities. (4) Experience in science communications to diverse audiences (i.e., academic and/or public presentations, academic journal publications and/or experience with popular media). (5) Experience in preparing grant proposals to fund biological research and/or administering budgets supporting research or collections- related activities. Minimum Education and Experience Requirements: Possession of a master’s degree in biology, zoology, or a science curriculum related to area of expertise and three years of experience in specialty area; or an equivalent combination of education and experience. Preferred: A Ph.D. in biology, zoology, or related science field. Supplemental and Contact Information: To apply for this position, please click APPLY link above. All relevant experience must be included on application to receive proper credit. Resumes are not accepted in lieu of state application. Persons eligible for veteran preference must submit a copy of Form DD-214. DENR uses the Merit-Based Recruitment and Selection Plan to fill positions subject to the State Personnel Act with the most qualified applicants. When a salary range is posted, the actual salary will be based on relevant competencies, knowledge, skills and abilities, internal equity and budgetary considerations pertinent to the advertised position. The State of North Carolina is an Equal Opportunity Employer. For additional information, please contact: Eileen Head(919) 707-9819 or Eileen.firstname.lastname@example.org Jason R. Cryan, Ph.D. Deputy Museum Director, Research & Collections North Carolina Museum of Natural Sciences 11 W. Jones Street Raleigh, NC 27601 Phone: (919) 707-9933 Fax: (919) 715-2614 email: email@example.com Museum Website: http://bit.ly/1krSgkd Research Website: www.planthopper.com “Cryan, Jason R” via Gmail
The Department of Anthropology at Texas A&M University invites applications for a tenure-track assistant professor position in ancient genetics/genomics beginning August 2015. We seek an energetic scholar with an active research program in molecular anthropology/archaeology and strong records of publishing in top-tier venues and participating in sponsored research. While geographic specialization is open, preference will be given to candidates who use ancient genetics to investigate evolution, dispersal, and migration in an archaeological context, and who can cooperate with existing faculty investigating these problems in the department and the department’s Center for the Study of the First Americans. The successful candidate will be expected to teach two courses in anthropology each semester ranging from introductory and upper-level undergraduate classes to graduate seminars; conduct research in the area of ancient genetics/genomics; advise and mentor students; and participate in service to the department, college, and university. Minimum qualifications: Applicants are required to have a PhD in hand by 2014 or earlier, demonstrated experience in ancient DNA analysis either at the doctoral or post-doctoral level, and ability to teach undergraduate and graduate courses in anthropology. Post-doctoral research in an ancient DNA laboratory, prior teaching experience, an active field research program, research publications, and success in obtaining grants for research will be considered as strengths in the search process. Applicants are encouraged to articulate how they may contribute to the diversity and excellence of the academic community through their research, teaching and/or service. Review of applications will begin November 1, 2014 and continue until the position is filled. Applicants should submit a cover letter, CV and contact information for three references preferably as a single pdf file by email or mail to Dr. Ted Goebel, Chair, Anthropological Genetics Search Committee, Department of Anthropology, Mailstop 4352, Texas A&M University, College Station, Texas 77843-4352 (firstname.lastname@example.org). Texas A&M University is a leading public research university with over 55,000 students. Texas A&M is located in the city of College Station which is within 90 minutes of both Houston and Austin metropolitan areas. Texas A&M University is an equal opportunity/affirmative action institution and prohibits discrimination based on race, color, religion, sex, national origin, disability, age, veteran status, genetic information, sexual orientation, gender identity or gender expression. “Goebel, Ted” via Gmail
PhD fellow in Ancient DNA and Evolutionary Genomics Applications are invited for a three-year PhD fellowship in the field of Ancient DNA and Evolutionary Biology in the Paleomix group led by Dr. Ludovic Orlando at the Centre for GeoGenetics, University of Copenhagen, Denmark. Research in the Paleomix group is focused on developing integrative approaches for studying ancient DNA molecules, promoting the field of palaeomics by the merger of biochemistry, molecular biology, genomics and computational biology. These approaches are presently mainly used to reconstruct the evolutionary history of horses and other equids and have strong implications for conservation. Recent work from the group includes the characterization of the oldest genome hitherto sequenced and the first ancient human epigenome. *Project* The project will concern retrieval, sequencing and analyses of ancient horse genomes, metagenomes and epigenomes for tracking the prehistorical and historical modifications that have accompanied the transformation of wild horses into modern domesticated breeds. The principal supervisor is Associate Professor Dr Ludovic Orlando, one of the six PIS of the Centre for GeoGenetics, University of Copenhagen. We are seeking a highly motivated, hard worker and productive student who is interested and capable of contributing to a research team consisting of molecular biologists, bioinformaticians, statisticians, and evolutionary biologists. The ideal candidate will show great abilities to work in a team environment and strong expertise in experimental genetics, and the molecular tools used in next-generation sequencing and population genomics. She/he should have strong background in molecular biology, particularly in molecular methods for generating large-scale sequence/SNP datasets, and be familiar with basic concepts in computational science and optionally, with Bash or other programming languages such as R, Perl and/or Python. Experience in the analysis of ancient DNA and/or Next-Generation Sequencing will be considered positively but is not mandatory. Principal supervisor is professor, Ludovic Orlando, Centre for GeoGenetics, mail: email@example.com. *Job description* PhD students at Science are expected to: - Manage and carry through their research project - Take PhD courses (equivalent to 30 ECTS) - Write scientific articles as well as the PhD thesis - Participate in scientific meetings - Stay at an external research institution, preferably abroad, for a up to 3 months - Teach and disseminate research - Possibly partake curation work in the Collections of the Natural History Museum of Denmark *Key criteria for the assessment of candidates* - A masters degree related to the subject area of the project. - The grade point average achieved - Professional qualifications relevant to the PhD programme - Previous publications - Relevant work experience - Other professional activities - Language skills (English is the language at the Centre for GeoGenetics) *Terms of employment* The position is covered by the Memorandum on Job Structure for Academic Staff. Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State . The starting salary is currently up to DKK 305,291 including annual supplement (+ pension up to DKK 42,171). Negotiation for salary supplement is possible. The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. The language of the Centre is English. *Application Procedure* The application, in English, must be submitted electronically by visiting http://bit.ly/1yYiFA7 Please include: - Curriculum vitae (with publication record, if any) - Diplomas and transcripts of records (BSc and MSc) - Motivation letter - Contact details from two references - Documentation of English language qualifications, cf. general rules and guidelines, p. 5 Review of applications will begin October 7st 2014 and will continue until the position is filled, with a deadline on November 15th 2014. The appointment is expected to start in February 1st 2015. *Questions* For specific information about the PhD scholarship, please contact the principal supervisor. General information about PhD programmes at SCIENCE is available at PhD Regulations. Further information: On the Department and the Centre for GeoGenetics. Alan Wervick via Gmail
A PhD position in poultry genetics and genomics is available (Fall 2015) in the Department of Animal and Food Sciences at the University of Delaware. The primary goal for this position is to work on a next-generation sequencing project on poultry genetics and genomics. The project will primarily be focused on using the whole-genome sequence data (i) to discover and characterize polymorphisms within and among purebred populations and (ii) to characterize genomic landscape and relatedness of purebred populations. We are looking for a self-motivated and enthusiastic person who possesses good interpersonal skills and willing to work in close collaboration with others. The individual is expected to interact with our industry partner and have determination to gain insight and publish papers in leading, international scientific journals. The Research Assistantship includes a competitive stipend, as well as covering 100% of tuition, and funds for presenting the research results at regional, national and international scientific meetings. The student will also have opportunities to perform internships or on-site research with our industry partner in the U.S. Candidates from different fields of biology are encouraged to apply; however, those with background in animal breeding and genetics with experience in analyzing large datasets are preferred. In your application, please include a letter of interest; a curriculum vita as well as the names and contact details of 3 references; GRE and TOEFL or ILTS (if foreign students whose primary language is not English) scores. The application materials should be sent to Dr. Behnam Abasht (abasht@UDel.edu) no later than November 15, 2014. The University of Delaware is an equal opportunity employer, which encourages applications from minority group members and women. “Abasht, Behnam” via Gmail
Dear EvolDir Members, if you have seen our announcement of three weeks ago and you have a study that satisfies the criteria specified then (see below), we would be very grateful, if you could contact us in the next week. Thank you Margarita Lpez-Uribe firstname.lastname@example.org> Shalene Jha email@example.com Antonella Soro firstname.lastname@example.org As part of a meta-analysis on bee population genetics, I request information regarding population differentiation indices in bees. This request is part of a collaborative study between myself, Shalene Jha (Assistant Professor in the Department of Integrative Biology at the University of Texas at Austin), and Margarita Lpez-Uribe (Postdoctoral Researcher at North Carolina State University). So far, we have examined studies acquired through the Web of Science, but we would like to increase our sample size with the incorporation of additional studies (published or unpublished). Specifically, we are looking for data sets where bee population genetics analyses have been conducted with: at least 5 microsatellite markers at least 20 unrelated individual per population at least 5 populations If you have one or more data sets that satisfy these criteria and are willing to contribute, please provide us with the reference to your work (if published) and the Fst estimator with 95% CI. We would also be interested in Gst (Hedrick 1995) and Josts D (Jost 2008) if you have those available, too. Your contribution would obviously be acknowledged and your publication(s) cited. Wed like to publicly thank the individuals whom weve already contacted directly and who generously offered their data. Thank you very much in advance Antonella Soro email@example.com Antonella Soro via Gmail
October 10, 2014
Doctoral Research Fellowship in Speciation Genetics A PhD position is available at the Department of Biosciences (IBV), Faculty of Mathematics and Natural Sciences, University of Oslo (UiO). The PhD project is part of a larger research program on the ‘Evolvability of genomic architecture during hybrid speciation’. Far from being an evolutionary dead end, hybridization may even generate lineages that can speciate even under the most constraining of conditions. The Italian sparrow (Passer italiae) is the first documented case of hybrid speciation in birds (Hermansen et al. 2011). This hybrid species originated from past events of hybridization between two divergent parental species, the house sparrow (P. domesticus) and the Spanish sparrow (P. hispaniolensis) some thousands of years ago. The Italian sparrow is both phenotypically and genetically variable across the Italian peninsula and its genome is a composite mosaic of DNA from both parentspecies’ genomes. But little is known about the consequences of such major genomic rearrangements on the evolutionary potential of hybrid species and how hybridization in general may favor novel evolutionary trajectories. This project integrates ecological and molecular approaches to develop an understanding of the evolution of genomic architecture during hybridization events and its evolutionary implications, using the Italian sparrow as the model system. The successful candidate will be allowed to choose aspects of the evolutionary genetics and genomics of the larger study as best fits her/his skills and research interests. She/he will also be encouraged to develop additional, complementary avenues of research. Interested candidates should have a Master degree or equivalent in a relevant field of biology, such as in genetics, genomics and/or bioinformatics. Documented knowledge in evolutionary biology is required. A good command of English and laboratory experience is likewise required. In addition, a special interest in the field of speciation and previous fieldwork or bird handling experience would be advantageous. The position is affiliated with the Centre for Ecological and Evolutionary Synthesis (CEES), and research will be conducted in close collaboration with Prof. Saetre and his group at CEES. The research team will also include other scientists from Norway, the US and Switzerland. The working language will be English. Fieldwork may be conducted at a variety of locations, including Norway, Italy and other Mediterranean countries. The appointment is for 3 years, but may be extended to 4 years conditional on 25% teaching obligations and approval from the Department of Biosciences. Candidates interested in a 4-year position should state so, in which case previous teaching experience would be considered a merit. Application deadline: Octiber 31st Expected starting date: January-February 2015 Informal enquiries can be made to Fabrice Eroukhmanoff and Glenn-Peter Saetre: firstname.lastname@example.org email@example.com For more information and how to apply: http://bit.ly/1qaNo3A Fabrice Eroukhmanoff Research Fellow Department of Biosciences, CEES University of Oslo Norway Fabrice.firstname.lastname@example.org Fabrice Eroukhmanoff via Gmail
Dear all, I am a historian of scientific thought. My research focuses on Neo-Lamarckian evolutionary principles. There has been a lot of recent work in this regard, what with epigenetic mechanisms and the like. I am currently revising a manuscript and seeking input from the broader evolutionary biology community. Basically, the central thesis is that Darwin and Wallace were wrong and that their work should be re-evaluated. The main issue is that the ideas of both Darwin and Wallace were due to work conducted on islands, and it is a well-known fact that evolution on islands is dominated by the forces of drift. Moreover, since most work predating the work of Darwin and Wallace was conducted in mainland European populations, it would have behooved them to stick to what others have been studying. I think this would clearly have been more relevant to the scientific community at the time. I am looking forward to hearing your thoughts and opinions on these ideas. Sincerest regards, Charlie Dawson email@example.com via Gmail
Recovering species demographic history from multi-model inference: the case of a Neotropical savanna tree species
Background: Glaciations were recurrent throughout the Quaternary and potentially shaped species genetic structure worldwide by affecting population dynamics. Here, we implemented a multi-model inference approach to recover the distribution dynamics and demographic history of a Neotropical savanna tree, Tabebuia aurea (Bignoniaceae). Exploring different algorithms and paleoclimatic simulations, we used ecological niche modelling to generate alternative hypotheses of potential demographic changes through the last glacial cycle and estimated genetic parameters using coalescent modelling. Results: Comparing predictions from demographic hypotheses with genetic parameters of modern populations, our findings revealed a likely scenario of population decline, with spatial displacement towards Northeast Brazil from the last glacial maximum to the mid-Holocene. Subsequently, populations expanded in response to the return of the climatically suitable conditions in Central-West Brazil. Nevertheless, a wide historical refugium across Central Brazil likely maintained large populations connected throughout time. The expected genetic signatures from such predicted distribution dynamics are also corroborated by spatial genetic structure observed in modern populations. Conclusion: By exploring uncertainties inherent in multiple working hypotheses, we have shown that multi-model inference is a fruitful and efficient approach to recover the nature, timing and geographical context of the Tabebuia aurea population dynamic in response to the Quaternary climate changes.
Erick Matsen wrote:
From Gascuel & co--www.ncbi.nlm.nih.gov Searching for virus phylotypes. F Chevenet, M Jung, M Peeters, T de Oliveira and O Gascuel, Bioinformatics (Oxford, England), Mar 2013 1
Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance.
News to me!
Background: Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results: We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate). Conclusions: The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions.
MULTIMEDIA SPECIALIST (PHILADELPHIA) The Center for Biodiversity at Temple University (Philadelphia) is interested in hiring a Multimedia Specialist. Duties include, but are not limited to, graphics illustration for publication, image and video editing, web site design and editing, and assisting the center in other activities. The successful applicant should be proficient in multimedia design and production, and familiarity with web programming (HTML and/or PHP coding) is preferred. A bachelor’s degree is preferred. The Center for Biodiversity is located in the new Science, Education, and Research Center (SERC building) on Temple’s main campus (http://bit.ly/10Z0cVa). Interested persons should send an e-mail to firstname.lastname@example.org, stating their interest in this position, and attach a curriculum vitae that also contains contact information for three references. The e-mail may be addressed to the director, S. Blair Hedges (http://bit.ly/1vT6hvF). Review of applications will begin on November 1 and continue until the position is filled. Temple University is located in the heart of historic Philadelphia and is the sixth largest provider of graduate school education in the USA. Situated in close proximity to New York City and Washington DC, Philadelphia is the birthplace of America and home to many academic and research institutions as well as numerous cultural attractions. via Gmail
Dear Colleagues (with apologies for duplicate postings): *PLEASE DISTRIBUTE TO OTHER LISTS AS YOU THINK APPROPRIATE*: I am asking for help in locating active tissue/cell line cryopreservation programs for endangered species. The extant population of the Catarina Pupfish, *Megupsilon apodus*, now consists solely of two males at the Dallas aquarium; the single known natural population was wiped out in the 1990$B!G(Bs. The species is essentially already extinct. I have been trying to find a program that would be interested in establishing and preserving cell lines or even simply storing tissue samples from one or both of the last surviving individuals. I thought I had located one such program associated with the San Diego zoo. What follows is the text of an e-mail I sent that program on 6 October: $B!H(BSan Diego Zoo Institute for Conservation Research 15600 San Pasqual Valley Road Escondido, California 92027 The unique $B!H(BCatarina Pupfish,$B!I(B *Megupsilon aporus*, is now effectively extinct, because the captive refugium population previously maintained by the Dallas Aquarium now consists of two males and 0 females. The single known natural population, confined to a single spring in central Mexico, was wiped out in the early 1990$B!G(Bs when the habitat was completely destroyed, and the two Dallas individuals are the last representatives of the species on the planet. I am therefore asking if your $B!H(Bfrozen zoo$B!I(B program would be interested in adding biological material from *M. apodus* to your collection. Assuming that is the case, I would appreciate it if you would let me know the steps that need to be taken so that this may be accomplished. I am not well versed in tissue culture and related techniques, but I suspect that the technology does exist to derive cell lines from the extant animals and cryopreserve them. Put more simply, we need to know just what to do next. It is my understanding that the surviving two *M. apodus* males will shortly be in the possession of Dr. Chris Martin at Berkeley. He is planning to attempt to hybridize them with females of a related species, *Cyprinodon alverezi *(which has been accomplished by others in the past*) *and hopes to eventually to use new genome editing tools to selectively remove the *C. alverezi* genes from the hybrid lineage. I believe that it will very likely be possible for him to take tissue samples (perhaps from fin clips) from one or both males that could be used to initiate cell lines. Among the many ways in which *M. apodus* is unusual or unique is its multiple sex chromosome system, which was the first example to be described in vertebrates. While similar systems have subsequently been described in other fish species, the enormous Y chromosome of *M. apodus* has no known equivalent, and it should be of great interest to students of sex chromosome evolution. Even if the species itself cannot be restored by contemporary conservation efforts, it would be extremely worthwhile to preserve its cells so that its Y chromosome will be available to cytogeneticists in the future. $B!H(B This e-mail has thus far elicited no response. While I do realize that only a few days have passed since I sent it, I would have thought that the obvious urgency of the situation would have merited at least a formal acknowledgement of receipt. I am concerned that my information may not be correct, or that I addressed it to the wrong person, and that precious time may be wasted. Consequently, I$B!G(Bm asking for help in locating other programs and/or finding the proper routes to approach them, or in networking that might lead to these goals. Any help would be greatly appreciated. Bruce Turner Bruce Turner via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution