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July 16, 2014
Faculty Position in Microbiology Texas A&M University The Department of Biology at Texas A&M University (TAMU) invites applications for a tenure-track Assistant Professor position in microbiology. We will consider candidates pursuing innovative research in all disciplines of microbiology, including, but not limited to, bacteriology, mycology, virology, immunology, host-pathogen/parasite interactions, developmental-, environmental-, evolutionary- or behavioral microbiology, genetic mechanisms and genomics, synthetic biology and biotechnology. The criteria for selection will be uniqueness, creativity and excellence in research and scholarship. We strongly encourage applications from candidates who will increase the exposure of our students to a diverse culture. The successful candidate will be expected to develop an externally funded research program and to teach undergraduate and graduate courses. We offer an interactive and collegial research environment, a modern infrastructure, and a competitive startup package. More information about our department can be found at www.bio.tamu.edu. For full consideration, applicants should email a letter of intent, curriculum vitae, statement of research and teaching interests, and three letters of recommendation by October 1, 2014 to firstname.lastname@example.org If you have questions about this search, please direct e-mails to Dr. L. Rene Garcia, Chair of the Search Committee, at email@example.com Texas A & M University is an Equal Opportunity/Affirmative Action employer that is dedicated to the goal of building a culturally diverse and pluralistic faculty and staff who are committed to teaching and working in a multicultural environment. We strongly encourage applications from women, minorities, veterans, and individuals with disabilities. In addition, the University is responsive to the needs of dual career couples. Gil Rosenthal via Gmail
Terrestrial Invasive Plant Species II: Pre-Conference Registration Deadline July 20 ============================================================= The Terrestrial Invasive Plant Species II meeting will be held at the University of Toronto Mississauga on 6-8 August 2014, with major support from the Invasive Species Centre (Ontario) and the University of Toronto. A draft schedule is now available on-line; please visit our website (http://bit.ly/1kz0M1Y) for details. The pre-conference registration deadline is July 20. Please see http://bit.ly/1kz0M1Y for on-line registration information. Program and Invited Speakers: A draft schedule is now available on the website (http://bit.ly/1m5bQSs), including many exciting presentations. Our keynote speakers are Spencer Barrett from the University of Toronto, and Kirsten Prior from the University of Florida. We also are organizing a special session devoted to biocontrol of invasive plants; confirmed speakers to date include Bernd Blossey (Cornell University), Rob Bourchier (Agriculture and AgriFood Canada), Richard Casagrande (University of Rhode Island), John Gaskin (USDA-ARS), Hariet Hinz (CABI Switzerland), Lindsey Milbrath (USDA-ARS) and Richard Shaw (CABI UK). We still have space for late-breaking posters and 2-minute talks. Field Trips: We are offering a pre-conference field trip on August 6, at a modest additional cost: the Carden Plain Alvar (http://bit.ly/1kz0Mic). If you would like to participate, please submit your payment with your conference registration; see our registration page for details. If you already have registered, or wish to add a field trip at a later date, please contact Antonia Maughn (firstname.lastname@example.org) for instructions. There also will be a lunchtime walk from the conference venue into the Credit River valley on August 8. See you in August! TIPS II Organizing Committee: Peter Kotanen, University of Toronto Mississauga (lead organizer) Sandy Smith, University of Toronto (St. George) Roberta Fulthorpe, University of Toronto Scarborough Ben Gilbert, University of Toronto (St. George) Marc Cadotte, University of Toronto Scarborough Pedro Antunes, Algoma University Colin Cassin, University of Toronto Mississauga (student member) via Gmail
Graduate Students (MSc and PhD) and postdoctoral position in Fisheries Genomics and Evolutionary Ecology - Halifax, NS, Canada Positions: Graduate student positions and a postdoctoral fellow position are available at Dalhousie University and Fisheries and Oceans Canada (Halifax, NS) working on the ecology, evolution, and conservation genomics of fishes and invertebrates. Species of primary interest are Atlantic salmon and Atlantic cod, but current projects include other anadromous fish and species of marine invertebrates as well. The labs research is broadly concerned with resolving adaptation and how it may influence both the geographic and genomic scale of divergence among allopatric and sympatric populations. (seefor more details). The specific projects willinvolve using next generation sequencing approaches to resolve signatures of adaptation across genomes and populations and the use of molecular tools in mixture analysis and individual assignment. Themes include adaptation to climate, invasive species, and the impact of escaped farmed salmon on natural populations. These multidisciplinary projects represent training in state of the art genomic tools and techniques while experiencing both university and government laboratory environments. Graduate students will have access to technical support both in the field and laboratory through DFO staff and expertise and be part of the Marine Gene Probe Laboratory (Dal). Qualifications: Honours degree or equivalent in biology (for a MSc position) and a MSc or equivalent (for a PhD position), and strong interests in evolutionary ecology, molecular ecology, and conservation biology. Application: Please email (email@example.com) (1) a letter describing your interests in this position and your previous research experience, (2) a recent CV. Ian Bradbury Ian Bradbury via Gmail
Please note the following DEADLINES: Registration and abstract submission:4 August, 2014 Accommodation:availability cannot be guaranteed after 28 July, 2014 The United Kingdom is home to exceptional evolutionarybiologists. However, compared to the number of evolutionaryzoologists, the number of their botanical counterparts is few. In many cases, U.K. plant evolutionary biologists are in small numbers at any one institution, and such isolation hinders progress. The Royal Botanic Gardens, Edinburgh will host a conference on 8, 9 September, 2014 to help address this situation. The conference will showcase evolutionary research on plants by UK researchers to foster new collaborations. The conference will also hold a workshop, where discussion will identify challenges faced and suggest strategies to overcome them. We see this as a first step towards developing a longer-terms strategy for strengthening the UK community of plant evolutionary biologists. The conference will include a poster and networking session, open speaking slots (both standard and “lightning” talks), as well as an exciting lineup of invited speakers. For more information and to register, please visit the website at: http://bit.ly/1h7xbNN Invited speakers: Mating system: Dr. Mario Vallejo-Marin Speciation: Dr. Richard Buggs Ecological Speciation: Dr. Patrik Nosil Evo-Devo: Dr. Beverley Glover Phylogeny: Dr. Toby Pennington Polyploidy: Dr. Barbara Mable Biogeography: Dr. Bill Baker Population Genetics (Molecular ecology): Dr. Simon Hiscock Population Genetics (Genomics): Dr. Rob Ness International Speaker: Dr. Spencer Barrett (University of Toronto) via Gmail
We all worked hard during the workshop. Here is our fearless leader, in deep thought:
While some of the younger participants enjoyed drawing on the walls:
Professor Whitfield has come up with a great new model of evolution: phylogenetic windmills:
There was not only work, but also time to relax and enjoy the beautiful Dutch summer weather:
And not to forget the delicious Dutch food:
But really, most of the time we were busy touching the data, which you can find on this website:
For more photos, see the Touching the Data website.
Description of Work: The Division of Public Health Informatics and Analytics (DPHIA) within the Center for Food Safety and Applied Nutrition (CFSAN) at the US Food and Drug Administration seeks a creative and enthusiastic research fellow to assist in the analysis of next-generation DNA sequencing data. The primary research focus of the fellow will be on the analysis of metagenomic datasets as a means to (1) better quantify the microbial diversity associated with foodborne pathogens and (2) evaluate the utility of metagenomics as a culture-independent method for pathogen detection (e.g., of Salmonella Montevideo, Salmonella Enterititidis, Salmonella Heidelberg, and Listeria monocytogenes). The fellow will also support microbiologists in the analysis of data from sequencing projects of bacterial pathogens (e.g., whole genome sequencing, RNA-Seq). The projects using whole genome sequence data from bacterial pathogens include samples collected from foodborne outbreaks, and the research will include the construction of phylogenies from whole genome sequence data, gene specific analyses, and identification of mobile elements. The fellow is also encouraged to develop an independent research project that furthers the mission of the FDA and the analytics group within CFSAN. Examples of such a project include the development of novel metagenomic analyses, evaluating alternative strategies for assigning taxonomy to reads, and the visualization and extraction of information contained in large metagenomic datasets. CFSAN and the Biostatics Branch is a vibrant community of specialists from a number of different disciplines (e.g., epidemiologists, chemists, microbiologists, biostatisticians, and bioinformaticians). Applicants should email Dr. James Pettengill at james.pettengill(at)fda.hhs.gov with questions about the position. Desired Skills: • Educational background (PhD or MS) in microbiology, genetics/genomics, phylogenetics, bioinformatics, statistics and/or computer science • Familiarity with next-generation sequence data (e.g., fastq format) • Proficient at running programs for the analysis of metagenomic data (e.g., mother, QIIME) • Proficient at running de novo assembly algorithms (e.g., Velvet, SPADES, SOAPdenovo) and reference based mapping programs (e.g., Bowtie2, BWA) • Proficient in a computer language such as R, Python, or Perl. • Skilled in the management, organization, and querying of large files/databases Application Materials: • Cover letter describing previous and future research interests • CV/Resume • Contact information for three references • To be mailed as a single pdf to james.pettengill(at)fda.hhs.gov Duration: 2 years Location: FDA, Center for Food Safety and Applied Nutrition 5100 Paint Branch Parkway College Park, MD 20740-3835 USA Salary/Benefits: The position is offered through the Oak Ridge Institute for Science and Education. The position does not include funds to offset moving. The position does not include benefits. ORISE offers a plan or the fellow can have her/his own but proof of insurance is required before beginning the position. However, funds are available for travel to conferences/workshops. Stipend: $6,091.67/month x 12 months $73,100.00 per year firstname.lastname@example.org via Gmail
Postdoctoral position in NGS population genomics University of Vigo, Spain DESCRIPTION: A postdoctoral position is available to work on an ongoing research project on the evolution of marine snails in the Cape Verde archipelago, in David Posada’s lab at the University of Vigo, Spain (http://bit.ly/1rfGm2C). The appointment will start as soon as October 2014 and will end no sooner than December 2015. Gross annual salary including benefits will be 25,000-30,000 Euros, commensurate with experience. Starting date is negotiable. MINIMUM REQUIREMENTS: Candidates should have a doctoral degree in Science, advanced programming skills and demonstrable experience with NGS data analysis. DESIRABLE REQUIREMENTS: Background in population and/or evolutionary genomics, and statistical skills. APPLICATION: Please send a single pdf including a letter of interest, C.V., and the names and contact details of two referees to email@example.com, indicating postdoc conus application in the subject of the email. Questions and requests for additional information should be directed to the same email address. Review of applications will begin immediately, and continue until the position is filled. David Posada Facultad de Biologa Campus Universitario Universidad de Vigo 36310 Vigo Spain Phone: +34 986 812038 Cell: +34 647 343300 Fax: +34 986 812556 Email: firstname.lastname@example.org Web: http://bit.ly/1rfGm2C email@example.com via Gmail
July 15, 2014
Protodrilidae is a group of small, superficially simple-looking annelids, lacking chaetae and appendages, except for two prostomial palps. Originally considered to be one of the primitive “archiannelid” families, its affinity within Annelida is still highly debated. Protodrilids are found worldwide in the interstices of intertidal and subtidal marine sediments. Despite their simple appearance they constitute one of the most species-rich interstitial families, with 36 described species in two genera, Protodrilus and the gutless Astomus. Here we present the first phylogenetic study of Protodrilidae employing five gene fragments, 55 morphological characters and 73 terminals (including seven outgroups) analysed under direct optimization and parsimony as well as model-based methods. The large data set includes all 36 described species of Protodrilidae (17 of which are represented only by the morphological partition) as well as 30 undescribed or uncertain species (represented by both morphology and molecules). This comprehensive, inclusive and combined analysis revealed a new perspective on the phylogeny of Protodrilidae: the family is shown to contain six cosmopolitan subclades, each supported by several morphological apomorphies, and with the genus Astomus consistently nested among the other five clades rather than next to these. Consequently, the diagnosis of Protodrilus is emended, Astomus remains unchanged and the four remaining lineages are diagnosed and named Megadrilus n. gen, Meiodrilus gen. nov., Claudrilus n. gen and Lindrilus gen. nov. Character transformations showed that large size and presence of pigmentation, oviducts and eyes are plesiomorphies of the family, retained in Protodrilus, Megadrilus gen. nov. and Lindrilus gen. nov. These features are secondarily lost in the gutless Astomus with epidermal uptake of nutrients, as well as in Meiodrilus gen. nov. and some species of Claudrilus n. gen, with smaller size correlated to life in interstices of finer sediments.
Background: The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors’ remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred. Results: We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire. Conclusions: The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.
Source: BMC Evolutionary Biology
Annual Cornell Lab of Ornithology Postdoctoral Competition The Cornell Lab of Ornithology encourages applications to our competitive postdoctoral program (http://bit.ly/U6qXCS) that supports innovative, independent research by early career scholars of exceptional promise. Two or more named positions are available annually, with applications due on September 8. These postdoctoral opportunities support individuals pursuing cutting-edge scholarship, while fostering intellectual interaction with two or more of the Lab’s programs. Any area of inquiry related to the Lab’s mission “to interpret and conserve the earth’s biological diversity through research, education, and citizen science focused on birds” may be appropriate. Potential applicants are encouraged to learn more about our activities and opportunities, including our formal programs in Bioacoustics, Bird Population Studies (avian ecology), Citizen Science, Conservation Science, Communication, Education, Evolutionary Biology, Information Science, Macaulay Library (animal behavior), Multimedia Productions, and Public Engagement in Science. Research or activities involving several of these areas are particularly appropriate, and therefore each postdoctoral scholar may be co-mentored by two senior Cornell scholars. Potential applicants are encouraged to contact relevant faculty and staff at the Lab to brainstorm about areas of mutual interest and synergistic projects. We are especially interested in supporting the independent research of individuals who can bring new ideas and approaches to the Lab, while simultaneously leveraging our existing tools, data, and expertise in science, education, and communication. Each Postdoctoral Scholar will hold a two-year appointment at the Lab. Located at the Imogene Powers Johnson Center for Birds and Biodiversity in the 220-acre Sapsucker Woods sanctuary, the Cornell Lab of Ornithology is a vibrant unit within Cornell’s University’s College of Agriculture & Life Sciences. More than 200 faculty and staff work at the Lab within our 10 mission-driven programs. Our management and staff are committed to the highest standards of ethics and excellence in all areas of our work, and our Board leadership includes faculty from Cornell and other universities, successful entrepreneurs and managers from the business and non-profit sectors, and conservation-minded citizens from the United States and beyond. These appointments provide a competitive salary, standard Cornell health and other benefits, and funds to help support the Scholar’s research and professional travel needs. Start dates are flexible between February and September of the year following the application. The application package consists of a cover letter, CV, two page research proposal, pdfs of up to three representative publications, and names and contact information for three references. Postdoctoral Scholars must have received their PhD before beginning their postdoctoral appointment at Cornell. Application materials should be sent as a single pdf file to the attention of Sue Taggart (SET2@cornell.edu). Applications for the two positions available in 2014 will be accepted until September 8. The selection committee is chaired by Dr. Irby Lovette (IJL2@cornell.edu), Professor and Associate Director for Academic Affairs at the Lab. Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students and staff impart an uncommon sense of larger purpose and contribute creative ideas to further the university’s mission of teaching, discovery and engagement. Located in Ithaca, NY, Cornell’s far-flung global presence includes the medical college’s campuses on the Upper East Side of Manhattan and in Doha, Qatar, as well as the new Cornell Tech campus to be built on Roosevelt Island in the heart of New York City. Diversity and inclusion have been and continue to be a part of our heritage. Cornell University is a recognized EEO/AA employer and educator. via Gmail
—_000_3FDD755888F55C40A52B84684E43FA3F338D1DE8ORANGECOUGARSIN_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable The unPAK project (undergraduates Phenotyping Arabidopsis Knockouts - http://bit.ly/W63Xp6) seeks a project manager to coordinate activities across 10 participating institutions. The unPAK project is collecting phenotypic information associated with Arabidopsis thaliana T-DNA insertion mutants and includes extensive involvement of undergraduate researchers. This project addresses broad questions in ecological genomics and is developing a phenotypic resource for the Arabidopsis and evolutionary genomic communities. The project manager will be responsible for communication between institutions, seed stock production, seed distribution, data curation, and management of participating undergraduates. The position will be located at the College of Charleston, and will involve travel to other participating institutions. We seek a candidate who is organized, energetic, and has strong communication skills. A successful candidate will have professional, diplomatic and leadership qualities. Ideally the candidate will bring experience working in a field or laboratory setting with plants. The position has ample opportunities for developing management skills and for publishing research. Interested individuals with undergraduate, master’s or doctoral degrees are welcome to apply. Specific responsibilities - distribution of protocols to new partner schools - travel to institutions to train participants in phenotyping and data management - grow plants with student help to bulk seeds for distribution - maintain seed-stock records - coordinate seed stocks to be shipped. - maintain of tissue and genotype records - assist PI and CoPIs with maintaining CURE (course-based undergraduate research experience) plants - format datasheets for downstream bioinformatics analyses - upkeep experiment log - maintain an already existing cyber-presence including the project website and the - project google wiki site - maintain contact information for all participants - initial training of students in lab procedures - contribute to newsletters, organize joint meetings (both virtual and in person) - podcast and vodcast development For more information about the position, please contact us at: Matt Rutter (firstname.lastname@example.org) Courtney Murren (email@example.com) Allan Strand (firstname.lastname@example.org) Department of Biology College of Charleston Charleston SC USA —_000_3FDD755888F55C40A52B84684E43FA3F338D1DE8ORANGECOUGARSIN_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
*Postdoctoral Position in Mathematical Modeling of Microbial Evolution* A postdoctoral researcher position is available in the lab of Olga Zhaxybayeva at the Biological Sciences Department of Dartmouth College in Hanover, NH to study evolution of gene transfer agents via mathematical modeling. This is a 5-year project funded through the Simons Foundation program in Mathematical Modeling of Living Systems. Qualified applicant must have a Ph.D. in bioinformatics, applied mathematics, computer science, statistics, biology, microbiology, or a related field with strong interest in molecular evolution, prior research experience in computational sciences and some programming skills. The successful candidate will join a vibrant research and educational environment of Dartmouth College. Zhaxybayevas lab uses computational approaches to study how microbes evolve and adapt to their environments. Ongoing projects fall into the following broad areas: 1) Studying impact of horizontal gene transfer on microbial populations; 2) Characterization of microbial communities; and 3) Deciphering genomic signatures of microbial adaptations. More information about Zhaxybayevas lab is available at http://bit.ly/17izh1S. Review of applications will begin immediately and continue until the position is filled. Start date is negotiable. Interested applicants should send a single PDF file containing CV, one-page statement of research interests and contact information of three referees to Olga Zhaxybayeva at ECGLabJobs@gmail.com. Dartmouth offers competitive salary and benefits along with the opportunity to live in a picturesque rural region that offers year-round recreational activities and is located near cities of Boston, Montreal, and New York. Dartmouth College is an equal opportunity/affirmative action employer that has a strong commitment to diversity. via Gmail
Please consider the following job opening for EvolDir: Utrecht University$B!G(Bs Ecology & Biodiversity Group investigates the mechanisms that regulate biodiversity and allow for the maintenance of ecosystem functioning in our changing world. We pay special attention to above- and belowground species interactions, spatial processes from local to landscape scales and community assembly following dispersal and colonization. We seek to obtain process-based, mechanistic understanding of species interactions and functional responses in order to predict the future impacts of climate and land-use changes on biodiversity and ecosystem functions such as carbon sequestration and biogeochemical cycling. The integrated research mission of the Ecology and Biodiversity group is $B!H(BUnderstanding and predicting biodiversity and ecosystem functioning in a changing world.$B!I(B The Ecology & Biodiversity research group looks to advance its integrated research program (http://bit.ly/1mF8Wax) with the appointment of an enthusiastic and dedicated: Assistant/Associate Professor Plant Ecology For a more detailed job description and online application forms, please visit www.uu.nl/vacancies Application deadline: July 27th, 2014 Kind regards, and thank you, Merel Soons Dr. M.B. Soons Associate Professor in Ecology and Biodiversity Institute of Environmental Biology Utrecht University Padualaan 8 3584 CH Utrecht email@example.com +31-(0)30-253 6837 www.uu.nl/science/eb http://bit.ly/1kYeW9Pwww.uu.nl/vacancies Application deadline: July 27th, 2014 Kind regards, and thank you, Merel Soons Dr. M.B. Soons Associate Professor in Ecology and Biodiversity Institute of Environmental Biology Utrecht University Padualaan 8 3584 CH Utrecht firstname.lastname@example.org +31-(0)30-253 6837 www.uu.nl/science/eb http://bit.ly/1kYeW9P “Soons, M.B. (Merel)” via Gmail
ECCB’14 - Tutorial T05 “Protein Evolution Analysis: on the Use of Phylogenetic Trees” Tutorial of ECCB 2014, Strasbourg, France. September 7th, 2014 Website: http://bit.ly/1mF8VTX Important dates: - ECCB/Tutorial Early registration: May 12 - August 1st, 2014 - ECCB/Tutorial Late registration: August 2 - August 29, 2014 - Tutorial date: Sunday, September 7th, 2014. Motivation Homologous proteins, that share a common ancestor, can be classified into families. These homologs can be orthologs, that were separated by a speciation event, or paralogs, that were separated by a duplication event. Within a protein family, all members are related by a phylogenetic tree, which consists of a root (the last common ancestor of the protein family), nodes (which are speciation/duplication events), branches (whose lengths correspond to the number of substitutions) and tips (which correspond to modern sequences). The tree is helpful for inferring the evolutionary history of the protein family. For example, we can reconstruct the ancestral sequences at each node of the tree. These ancestral sequences can be used for homology modelling, to reveal the ancestral 3D structures, or synthesised in vitro. Or we can compare trees to reveal similar evolutionary history between protein families (co-evolution). Manipulating tree topologies are complex operations that require tools to perform operations such as reading, pruning, collapsing, rerooting. These operations can be done with programs with graphical user interfaces (GUI). However, in the area of large-scale data, in which hundreds or thousands of trees may be manipulated, it is impractical to use such programs. To this end, new software/libraries have been developed to deal with such large data sets in an automated manner. Goal This tutorial will present recent concepts regarding the evolution and adaptation of protein sequences. It will be divided into three sections, in which we will present methods relating to the use of phylogenetic trees to infer protein function. These sections will be 1) using scripts to manipulate trees, 2) using ancestral sequence reconstruction to infer history of a protein family and 3) the detection of coevolution between protein families. Each section will have an introduction explaining the concepts underlying any analysis methods, and a discussion of the power and limitations of different methods and tools used to explore these concepts and which participants will learn how to use during the practical for that section. Outline The first part will focus on tools to detect adaptation in protein sequences. It will start with a brief introduction on multiple alignment and phylogenetic trees followed by a more detailed presentation of tools available to estimate selective pressures and detect adaptation in protein sequences with CodeML / PAML. The second part will focus on the reconstruction of ancestral sequences and ancestral structures by homology modelling. The third part will focus on the identification of co-evolution between protein families. The organiser will provide protein datasets, or participants can bring their own sequences. Then, they will be able to use the different programs/libraries in a practical way. This tutorial will be in three parts (more info on the website): 1) Performing phylogenetic analyses with Biopython 2) Ancestral sequence reconstruction and homology modelling 3) Studying molecular co-evolution Level: Introductory Schedule (Sunday, September 7th): Morning session: Performing phylogenetic analyses with Biopython. 9:00 Talk (45min): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 9:45 Practical (30min): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 10:15 Coffee break 10:45 Practical (1h30): Performing phylogenetic analyses with Biopython (B. Invergo, EBI) 12:15 Lunch Afternoon session: ancestral sequence reconstuction and molecular co-evolution. 13:15 Talk (30min): Ancestral sequence reconstruction (R. Studer, EBI) 13:45 Practical (1h30): Ancestral sequence reconstruction (R. Studer, EBI) 15h:15: Coffee break 15h45: Talk (30 min): Studying molecular co-evolution (D. Ochoa, EBI) 16h15: Practical (45min): Studying molecular co-evolution (D. Ochoa, EBI) 17:00 End Intended audience: - Evolutionary biologists, biochemists, computational biologists, structural biologists. Possible prerequisites: - Unix command line. - We strongly encourage participants to learn the basics of the Python programming language. Organisers: Brandon Invergo - EMBL-EBI, Cambridge, UK (invergo [at] ebi.ac.uk) David Ochao - EMBL-EBI, Cambridge, UK (ochoa [at] ebi.ac.uk) Romain Studer - EMBL-EBI, Cambridge, UK (rstuder [at] ebi.ac.uk) via Gmail
—_000_1D503F5375C52140A2C24AB93B2DD09BA1C50B77zivexdag2wwude_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Dear all, please find below an announcement for 2 PhD positions. 2 PhD positions for international (non-German) students within the interdisciplinary “Muenster Graduate School of Evolution”: PhD projects in Biology, Medicine, or Philosophy The “Muenster Graduate School of Evolution” (MGSE) offers 2 PhD positions funded by DAAD- stipends for international (non-German) students within the stimulating environment of the University of Muenster, Germany. As an interdisciplinary graduate school, the MGSE uses the unifying concept of evolution to bridge the faculties of biology, medicine, geosciences, mathematics, and philosophy. PhD students work on their diverse disciplinary projects in one of the involved institutes and benefit from interdisciplinary curricular activities as well as a structured supervision and support throughout their PhD. The MGSE is based in the stimulating city of Muenster in a historical building opposite the Muenster castle and offers a family friendly and international atmosphere. Location: Muenster, Germany Working Language: English Start of the PhD: 2015 Duration: 3 years (4 years for students from developing and emerging countries) You can apply for one or several of the following six projects. Each project involves high-quality research and state-of-the-art techniques and is supervised by excellent researchers. 1) The genetic origin of novel protein coding genes in populations and their evolutionary constraints Prof. Erich Bornberg-Bauer (Research Group Evolutionary Bioinformatics), Prof. Matthias Loewe (Institute of Mathematical Statistics), Prof. Juergen Gadau (School of Life Sciences, Arizona State University) 2) Immunogenic males: where sex and immunity meet Dr. Claudia Fricke (Research Group Evolution and Sexual Conflict), Dr. Sophie Armitage (Research Group Animal Evolutionary Ecology) 3) The Concept of Disease in Individualized Medicine Prof. Ulrich Krohs (Research Group Philosophy of Science and of Nature) 4) Interactions of animal personality, social environment and immunity Prof. Joachim Kurtz (Research Group Animal Evolutionary Ecology), Dr. Joern Scharsack (Research Group Animal Evolutionary Ecology), Prof. Norbert Sachser (Department of Behavioural Biology) 5) Functional consequences of evolutionary conservation vs. variability in the influenza virus genome Prof. Stephan Ludwig (Institute of Molecular Virology) 6) Reconstruction of the ancient transcriptome of species Dr. Juergen Schmitz (Institute of Experimental Pathology), Dr. Francesco Catania (Research Group Evolutionary Cell Biology) More information on the projects can be found here: http://bit.ly/1zowANF Highly qualified and motivated candidates all over the world are invited to submit their application. Requirements: - MSc (or an equivalent degree) relevant for the respective project (biology, medicine, mathematics, or philosophy). At the time of application, generally no more than six years should have passed since you gained the last degree. - Excellent academic record, interest to work interdisciplinary, and motivation to actively participate in the structured PhD program of the MGSE. - Fluency in spoken and written English (or willingness to take part in a respective course). - Only international (non-German) applicants can be accepted. At the time of application you should not be living in Germany for more than 15 months. - Applications from women are particularly encouraged. Handicapped candidates with equivalent qualifications will be given preference. Application procedure: You can apply for one or several of the listed projects via the DAAD platform by 1.8.2014: http://bit.ly/1woIOS6 indicate which project(s) you are interested in! >From among the applicants, we will shortlist candidates for (Skype) interviews and subsequently nominate 4-8 applicants. From among the nominees, a DAAD committee will select the two scholarship recipients. In case of questions please contact: (Please don’t send your applications here, instead use the DAAD online application (see above)!) Dr. Rebecca Schreiber (MGSE Coordinator) Email: email@example.com Telephone: +49-(0)251 / 83-21252 Best regards, Rebecca Schreiber via Gmail
The Molecular Ecology Group at the Institute of Ecology at Innsbruck University is seeking a full-time laboratory technician as permanent employee. Main tasks: - Conduction of experiments in the molecular lab (nucleic acid extraction, PCR, qRT-PCR, electrophoresis, cloning, preparation of libraries, etc.) - Basic data analyses - Ordering of supplies and maintainance of equipment (PCR machines, near-infrared-spectrometer, centrifuges, microscopes, incubators, etc.). Further duties may include help with rearing of lab organisms (e.g. Drosophila), evolution experiments, collection of samples in the field and general support of the working group. The ideal candidate will have an education as biological/chemical/medical laboratory technician or equivalent. Solid knowledge of basic molecular and microbiological techniques, experience in the use of MS Office, web-based data collections (e.g. NCBI) and basic imaging software, and good knowledge of English are essential. Openness for independent learning and the ability to work as part of a multi-disciplinary team are also important features. Knowledge of the German language may be helpful for everyday life in Innsbruck, but is not required. Please note that for legal reasons applications of candidates holding an MSc or higher degree in biology or related fields cannot be considered. The position can be filled from August 2014. The minimum annual gross salary is EUR 26,096 including health insurance and 5 weeks of annual holidays. The salary will be higher if you have worked in a similar position before. Please apply until July 31 at: http://bit.ly/1mF1WKQ The Molecular Ecology Group uses the exciting opportunities offered by molecular biology to study ecology as a snap-shot of evolving biodiversity. Since the group’s founding in 2009, research has been conducted in integrative biodiversity assessment, rapid evolution, symbiotic interactions, and social evolution, in all instances integrating genetic data with those from other sources (e.g., niche ecology, morphology, behaviour, chemistry). Most of our study organisms are terrestrial animals, often from the Alpine region. Detailed information about the Molecular Ecology Group can be found at http://bit.ly/19cQMBY. Innsbruck is situated in the Alps and very close to Switzerland, Germany and Italy; scenery and outdoor recreation are fantastic. More information needed? Please contact Wolfgang Arthofer via Gmail
July 13, 2014
Although the Indian and Pacific Oceans (hereafter Indo-Pacific) have long been recognized as containing the majority of marine biodiversity, their vastness poses substantial challenges for empirical research. Syntheses of published data, however, can expand the geographic scope of inference. We plan to examine the recent evolution of Indo-Pacific taxa by drawing upon all available population genetic data. We have two immediate research goals: 1) compile and analyze existing datasets for multiple species using consistent and uniform methods of analysis that represent the best current practice in population genetics to better determine oceanographic and geographic features as well as biological traits correlated with population structure. These results will inform our understanding of evolutionary processes in the region and provide information directly relevant to managers and conservation organizations. We will also: 2) conduct the first large scale multispecies investigation to infer the geography of speciation among Indo-Pacific taxa that incorporates population genetic inferences, thus testing predictions of competing biogeographic hypotheses using a novel approach. These research goals are underpinned by the creation of a database that would become publicly accessible to facilitate future studies. In addition, we plan to develop a virtual collaboration space that will support international collaborations in genetic-based research, training, and education throughout the region.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology