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April 18, 2014

01:57

—Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429B Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Call for Symposia for 2015 Annual Meeting The 2015 annual meeting of the Society for the Study of Evolution is planned for June 26-30, 2015 in Guaruja, Brazil. The SSE Council invites proposals for the two Society-sponsored symposia to be held in conjunction with the meeting. Symposium proposals should include: (1) a synopsis of the symposium theme (about one page); (2) a tentative list of speakers, including institutional affiliations, and topics; (3) a rationale for the symposium explaining why this topic and this group of speakers are particularly appropriate for a Society-sponsored symposium; and (4) a statement that all potential speakers have been contacted and agree to participate in the symposium. In evaluating proposals, SSE Council seriously considers the diversity of participants as a major qualification. Symposium organizers are expected to take into account gender, seniority, nationality, and other aspects traditionally underrepresented in Society symposia when preparing proposals. In addition, Council will favor those proposals whose topics concern newly emerging fields, fields ripe for syntheses, and fields different from those that have been included in recent Society symposia. The Council will select two proposals for half-day symposia at the annual meeting in June 2014. All applicants will be notified of the Council’s decision in August. The Society provides travel support for organizers and participants in sponsored symposia. Details are available on request. To be assured of full consideration, proposals must be received by midnight Eastern Standard Time on June 6, 2014: Proposals should be sent by email (bbrodie@virginia.edu) as a single attachment in PDF format (under subject heading: SSE Symposia Proposal). Please expect and request confirmation of receipt of the proposal. Butch Brodie Executive Vice President, SSE —Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429B Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii

Call for Symposia for 2015 Annual Meeting

The 2015 annual meeting of the Society for the Study of Evolution is planned for June 26-30, 2015 in Guaruja, Brazil. The SSE Council invites proposals for the two Society-sponsored symposia to be held in conjunction with the meeting. Symposium proposals should include: (1) a synopsis of the symposium theme (about one page); (2) a tentative list of speakers, including institutional affiliations, and topics; (3) a rationale for the symposium explaining why this topic and this group of speakers are particularly appropriate for a Society-sponsored symposium; and (4) a statement that all potential speakers have been contacted and agree to participate in the symposium.

In evaluating proposals, SSE Council seriously considers the diversity of participants as a major qualification. Symposium organizers are expected to take into account gender, seniority, nationality, and other aspects traditionally underrepresented in Society symposia when preparing proposals. In addition, Council will favor those proposals whose topics concern newly emerging fields, fields ripe for syntheses, and fields different from those that have been included in recent Society symposia.

The Council will select two proposals for half-day symposia at the annual meeting in June 2014. All applicants will be notified of the Council’s decision in August. The Society provides travel support for organizers and participants in sponsored symposia. Details are available on request. To be assured of full consideration, proposals must be received by midnight Eastern Standard Time on June 6, 2014: 

Proposals should be sent by email (bbrodie@virginia.edu) as a single attachment in PDF format (under subject heading: SSE Symposia Proposal). Please expect and request confirmation of receipt of the proposal.

Butch Brodie

Executive Vice President, SSE

—Apple-Mail=_44AFA882-40CA-4424-AE77-B105B833429 via Gmail
Source: EVOLDIR
01:24
—_000_ea828d69bb414cd4a4c6c9b66b2038ceBLUPR07MB513namprd07pro_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Hello all, I am working on a study of the evolutionary genetics of house mice (Mus musculus), and I am looking for fresh tissue samples from populations of house mice specifically from the eastern shore of Maryland and anywhere in Delaware. Because the tissue must be relatively fresh, I am specifically looking for anyone who is currently, or will soon be, doing small mammal trapping (whether for research purposes or to remove a nuisance species), and who might be willing to collect some tissue from any house mice collected. I can provide a sampling kit and pay for shipping, so the commitment would mostly be in terms of time (which should be minimal if part of an established trap line or while trying to remove a mouse infestation from a home or farm). If you are interested in helping out with this study, please email me at achunco@gmail.com and I’d be happy to provide more details about this study. Thank you in advance, Amanda Amanda Chunco Environmental Studies Elon University achunco@gmail.com —_000_ea828d69bb414cd4a4c6c9b66b2038ceBLUPR07MB513namprd07pro_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
Source: EVOLDIR
01:08
MULTIPLE POSTDOCTORAL POSITIONS are available in Dr. Adam Siepel’s research group in its new location at the Simons Center for Quantitative Biology at Cold Spring Harbor Laboratory, starting in September, 2014. The Siepel group specializes in the development of probabilistic models, algorithms for inference, prediction methods, and application of these methods in large-scale genomic data analysis. Of particular interest is research relevant to existing, NIH-supported projects in (1) human population genomics, including demography inference using Bayesian coalescent-based methods, inference of natural selection on regulatory and other noncoding sequences, and prediction of fitness consequences for noncoding mutations; and (2) transcriptional regulation in mammals and Drosophila, including the estimation of rates and patterns of transcriptional elongation from the GRO-seq data, prediction of transcription factor binding sites from DNase-seq data, and regulatory network inference based on joint patterns of transcription and binding in inducible systems. The research on transcriptional regulation will continue to be carried out in close collaboration with Dr. John Lis at Cornell University. Relevant recent papers including the following: 1. Rasmussen MD, Hubisz MJ, Gronau I, Siepel A. Genome-wide inference of ancestral recombination graphs. PLOS Genet., in press. 2. Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, et al. (30 co-authors). Genome sequencing highlights the dynamic early history of dogs. PLOS Genet.10(1):e1004016, 2014. 3. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLOS Genet. 9(8):e1003684, 2013. 4. Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nature Genetics 45(7):723- 729, 2013. 5. Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell50(2):212- 222, 2013. 6. Gronau I, Arbiza L, Mohammed J, Siepel A. Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol. Biol. Evol. 30(5):1159-1171, 2013. 7. Guertin MJ, Martins AL, Siepel A, Lis JT. Accurate prediction of inducible transcription factor binding intensities in vivo. PLOS Genetics, 8(3):e1002610, 2012. 8. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43(10):1031-1034, 2011. The ideal candidate will be enthusiastic, highly motivated, and independent, will have a strong background in comparative genomics, population genomics, or transcriptional regulation, a serious interest in molecular biology and genetics combined with good skills in mathematics and computer science, and a strong record of accomplishment in research. Postdoctoral associates in the group are expected to participate in both methods development and data analysis, to be comfortable in a fast-moving, interactive, and collaborative research environment, and to actively publish and present results. Required Qualifications 1. Ph.D. in bioinformatics, computer science, statistics, genetics, molecular biology, applied mathematics, or a related field. 2. Research experience (with first-author publications) in computational genomics or a closely related field. 3. Fluency in probabilistic modeling and computational statistics. 4. Proficiency in programming, ideally in C or C++ as well as in scripting languages such as python, perl, matlab, or R. Should be comfortable in a linux environment, with large data sets, computer clusters, and databases. Term The term for this position is flexible but most likely will be 2-3 years. The proposed start date is September 2014. As many as 4 positions may be filled, depending on the quality of the applicants. To Apply Submit a CV, a short description of research interests and experience, and contact information for three references by e-mail to acs4 at cornell dot edu. Informal inquiries are welcome. Adam Siepel 102E Weill Hall Cornell University Ithaca, NY 14853 Adam Charles Siepel via Gmail
Source: EVOLDIR
01:08
Postdoctoral Position in modeling the genetics of adaptation of invasive populations We seek to hire a post-doctoral research associate for a Grand Federative Project funded by the French Agropolis Fondation1 called BIOFIS “Bioagressors and invasive species: from individual to population to species”. The project is dedicated to develop, coordinate and communicate research actions on bioagressors in Europe (insects, mites, trees, fungi and virus) and on their associated natural enemies. Term and location: The position should start in December 2014 at the latest. Support is for one year. This position is co-supervised by E. Klein (INRA – BIOSP, Avignon France) and V. Ravigné (CIRAD – BGPI, Montpellier, France). We encourage the postdoctoral fellow to be based in Montpellier but being hosted in Avignon is also possible. Eligibility: Agropolis Fondation typically considers applications from candidates that have not resided or carried out their main activity (work, studies, etc) in France for more than 12 months in the 3 years immediately prior to the date of submission of the proposal and that have obtained their PhD degree for no more than 3 years upon the date of application. However, we encourage excellent candidates not entirely fulfilling these conditions to contact us, as these might be funded if no other eligible candidate satisfies scientific requirements for the job. Project: Bioinvasions have long been considered as purely ecological processes until researchers recognize that evolutionary processes such as drift and selection may play a substantial role in their success. Recently particular attention has been paid to evolutionary processes occurring during spatial expansions. Selection for different life-history strategies at the source and front of invasions is expected to affect the speed of spatial spread. The strong effects of genetic drift associated to the specific demography of an expansion (in particular successive funding effects distributed in space) may as well shape the neutral and selected diversity along invasion waves. To better understand the interaction between drift, selection, and dispersal, we wish to design and analyze spatially explicit simulation models allowing studying the spatial spread of beneficial/neutral/deleterious mutations during a colonization process. We are particularly interested in studying the effect of i) environmental heterogeneity and ii) non-standard mating systems (e.g., mixing sexual and asexual reproduction) on the process. In the end, these theoretical results may be confronted to population genetics data in different species. This work is mainly theoretical in its present shape but it is expected to produce useful results for approaches aiming at detecting traces of selection during bioinvasions from the analysis of the spatial genetic structure of populations at a large number of loci (genome scan). We seek a young researcher who combines with a strong conceptual background in evolutionary biology and some modeling skills (mathematics and computer science). Experience with programming, bioinformatics and theoretical population genetics is required. Skills in data analysis are not necessary but will be considered positively. Facility in writing is important. The post-doc will benefit by working as a member of the BIOFIS project team with an extent network of collaborators interested in dispersal, invasion biology, plant pathology, evolutionary biology and population genetics. Contact: Virginie Ravigné. Virginie.ravigne@cirad.fr 1 Agropolis Fondation: http://bit.ly/18BZkTN Virginie Ravigné Chercheuse CIRAD - Département BIOS - UMR BGPI UMR PVBMT Station de Ligne-Paradis Pôle de protection des plantes 7 chemin de l’IRAT 97410 Saint-Pierre - Réunion Tel : 0262 49 92 24 /06 92 32 04 97 Mail : Virginie.Ravigne@cirad.fr http://bit.ly/1aqgmda Virginie Ravigné via Gmail
Source: EVOLDIR
00:27

Master studies in Ecology and Evolution EcoEvo is a two year Master of Science programme for students interested in the functionning and evolution of the biosphere offered by the Institute of Environmental Sciences at Jagiellonian University in Krakow,Poland. The participants will investigate the mechanisms underlying ecological and evolutionary processes and will develop practical skills related to carrying out research and conservation projects. They will undertake a range of multidisciplinary courses (consisting of lectures, seminars, laboratory work and field classes) as well as carry out group and individual research projects. Starting date: October 2014 Admission: the application for the programme is a continuous process; additional application rounds start until there are no more places available or the last application round is over. The dates of application rounds for 2014 are: 19 March V 6 May, 7 May V 24 June, 25 June V 19 August and 20 August V 17 September. Tuition fees: (1) EU citizens and non-EU citizens with documented Polish background - no tuition fee; (2) non-EU citizens V 1st year: 2200, 2nd year: 2000. For more information see: www.ecoevo.uj.edu.pl — via Gmail

Source: EVOLDIR
00:09
Attention! The deadline is approaching for the 1st Greifswald Phylogenetics Meeting, which will be held in July 2014!!!! I herewith want to announce the 1st Greifswald Phylogenetics Meeting, which will be held in Greifswald (north eastern Germany) from the 14th till the 16th of July 2014. Registration is now open and the deadline (both for registration as well as for abstract submission) is the 30th of April. There are still a few free slots, so please register asap! Our conference poster can be found here: http://bit.ly/1lbEJkk Feel free to print it and forward it to anybody who might be interested! For more details, please visit the conference website: http://bit.ly/1eAnepX This meeting will have a particular focus on mathematical (e.g. graph theoretical, combinatorial, probabilistic and algebraic) aspects of evolutionary tree or network reconstruction, but it will also bring together scientists from different disciplines in order to provide the opportunity of close collaboration. Scope: Phylogenetics is an interdisciplinary research area that aims at reconstructing the evolutionary history of biological systems such as, for example, collections of species, populations or groups of bio-molecules. To achieve this, biologists work closely together with mathematicians and computer scientists. The conference will provide researchers from all three involved disciplines an opportunity to present their recent work and exchange ideas. Location: Greifswald is a beautiful little town located directly at the Baltic Sea in close proximity to the famous islands Rgen and Usedom. Greifswald university was founded in 1496 and has therefore a long tradition and history. Being a former Hanse town, Greifswald is famous for its historic market square, its cathedral and the museum harbor. Other famous towns like Stralsund with the Oceaneum or the world cultural heritage city of Wismar are nearby, as well as the city of Rostock with its newly established Darwineum. The region is a holiday region but not too crowded by tourists. In July the weather is most likely to be great and we hope that if you can come to our meeting, you will find the time to stay longer and enjoy this unique area. There is a direct and regular train connection to and from Berlin, and the nearest international airports are Hamburg and Berlin. Please note that the meeting starts early on the 14th with one of our highlight talks and ends in the evening of the 16th with another highlight talk - so if possible, please plan your stay from the 13th till the 17th of July. The registration fee is 150 Euros (100 Euros for students). Organizers: Mareike Fischer, Andreas Spillner, Martin Haase Invited speakers: Olaf Bininda-Emonds, Mike Steel, Olivier Gascuel, Vince Moulton, Allen Rodrigo For more details, visit our website http://bit.ly/1eAnepX or contact Mareike Fischer: email@mareikefischer.de Mareike Fischer via Gmail
Source: EVOLDIR

April 17, 2014

23:53
Job description: The laboratories Mathmatique Informatique et Gnome (MIG) and Gntique Animale et Biologie Intgrative (GABI) at INRA research center in Jouy-en-Josas, (30 km south of Paris) have an open post-doctoral position funded by the Domestichick ANR grant. Project description: The objective of the project is to study the evolutionary dynamics of chicken domestication, using a comparative genomics approach. The Gallus genus comprises 4 species. G. gallus is considered as the ancestral species of the domestic chicken. Previous work demonstrated the genomic contribution of G. sonneratii and it is considered that other species may also have contributed to the genomic make-up of the domestic chicken. Our approach relies on (1) deep-sequencing of a representative sample of wild Gallus species (n) and (2) deep re-sequencing of birds from various domestic breeds, to identify the genomic structure of the domestic chicken genome and to detect introgression or other evolutionary events fixed during domestication. The study is three-pronged: 1. The first step deals with genome assembly, using the domestic chicken reference genome, and variant detection (SNPs, indels, structural variants). 2. In the second step, we will build a hidden markov model (HMM) to represent the evolutionary history of both wild and domestic birds and infer local ancestry of domestic birds along the genome. 3. The third step is devoted to the evolutionary dynamics that shaped the Gallus genome at the genus level. We will more specifically develop and implement an Approximate Bayesian Computation by Population Monte-Carlo (ABC-PMC) method to test different demographic scenarios and identify the complex events underlying the current diversity: bottleneck, gene flow, selection. The post-doctoral fellow will be involved in all steps of the studies but his/her work will focus on the modeling, implementation and use of the statistical models mentioned in steps 2 and 3. Research Environment: The work will take place in MIG laboratory, an interdisciplinary laboratory that hosts around 40 people in addition to a bioinformatics platform. The work involves close collaboration with MIG and GABI researchers. The candidate will benefit from the bioinformatics expertise of both laboratories, the expert knowledge of GABI researchers about the domestic chicken and the MIGALE computation facility hosted by MIG. On a broader scale, the candidate will also benefit from the scientific environment of the INRA research center of Jouy-en-Josas, which hosts several research teams working on animal genetics, and the collaboration network of both partners, known for their skills in statistical genetics. Qualifications: The candidate should hold a PhD in bioinformatics, biostatistics or applied mathematics with applications in molecular biology. (1) Skills and/or knowledge in computational or Bayesian statistics and (2) skills with NGS data analysis would be a plus but not required. The candidate should have a strong interest in data analysis, especially in comparative genomics, and a taste for collaborative work. Funding: 21 months post-doctoral fellowship, starting as soon as possible and financed by ANR grant Domestichick. Salary will depend on the candidate’s background and experience. Additional financial compensation through the AgreenSkills program will be sought for eligible candidate (http://bit.ly/1mbR0EZ). The job will be located at the INRA research center of Jouy-en-Josas, in the South-West of Paris. Application: Send a detailed CV, a short motivation letter and references to Frdric Hospital and Mahendra Mariadassou . Applications should be submitted before June 1st, 2014 via Gmail
Source: EVOLDIR
18:00
Background: Plasticity, i.e. non-heritable morphological variation, enables organisms to modify the shape of their skeletal tissues in response to varying environmental stimuli. Plastic variation may also allow individuals to survive in the face of new environmental conditions, enabling the evolution of heritable adaptive traits. However, it is uncertain whether such a plastic response of morphology constitutes an evolutionary adaption itself. Here we investigate whether shape differences due to plastic bone remodelling have functionally advantageous biomechanical consequences in mouse mandibles. Shape characteristics of mandibles from two groups of inbred laboratory mice fed either rodent pellets or ground pellets mixed with jelly were assessed using geometric morphometrics and mechanical advantage measurements of jaw adductor musculature. Results: Mandibles raised on diets with differing food consistency showed significant differences in shape, which in turn altered their biomechanical profile. Mice raised on a soft food diet show a reduction in mechanical advantage relative to mice of the same inbred strain raised on a typical hard food diet. Further, the soft food eaters showed lower levels of integration between jaw regions, particularly between the molar and angular region relative to hard food eaters. Conclusions: Bone remodelling in mouse mandibles allows for significant shifts in biomechanical ability. Food consistency significantly influences this process in an adaptive direction, as mice raised on hard food develop jaws better suited to handle hard foods. This remodelling also affects the organisation of the mandible, as mice raised on soft food appear to be released from developmental constraints showing less overall integration than those raised on hard foods, but with a shift of integration towards the most solicited regions of the mandible facing such a food, namely the incisors. Our results illustrate how environmentally driven plasticity can lead to adaptive functional changes that increase biomechanical efficiency of food processing in the face of an increased solicitation. In contrast, decreased demand in terms of food processing seems to release developmental interactions between jaw parts involved in mastication, and may generate new patterns of co-variation, possibly opening new directions to subsequent selection. Overall, our results emphasize that mandible shape and integration evolved as parts of a complex system including mechanical loading food resource utilization and possibly foraging behaviour.
18:00
Background: Raphidioptera (snakeflies) is a holometabolous order of the superorder Neuropterida characterized by the narrowly elongate adult prothorax and the long female ovipositor. Mesozoic snakeflies were markedly more diverse than the modern ones are. However, the evolutionary history of Raphidioptera is largely unexplored, as a result of the poorly studied phylogeny among fossil and extant lineages within the order. Results: In this paper, we report a new snakefly family, Juroraphidiidae fam. nov., based on exquisitely preserved fossils, attributed to a new species Juroraphidia longicollum gen. et sp. nov., from the Jiulongshan Formation (Middle Jurassic) in Inner Mongolia, China. The new family is characterized by an unexpected combination of plesiomorphic and apomorphic characters of Raphidioptera. Based on our phylogenetic analysis, Juroraphidiidae fam. nov. together with Raphidiomorpha form a monophyletic clade, which is the sister to Priscaenigmatomorpha. The snakefly affinity of Priscaenigmatomorpha is confirmed and another new family, Chrysoraphidiidae fam. nov., is erected in this suborder. Conclusions: Juroraphidiidae fam. nov. is determined to be a transitional lineage between Priscaenigmatomorpha and Raphidiomorpha. Diversification of higher snakefly taxa had occurred by the Early Jurassic, suggesting that these insects had already had a long but undocumented history by this time.
07:19

Erick Matsen wrote:

In the paper describing MrBayes 3.2, there is the following phrase:

MrBayes 3.2 further includes a completely new type of tree proposal that is guided using parsimony scores. The details of the parsimony-biased proposals will be presented elsewhere; however, tentative empirical results show that they can improve the speed of convergence by an order of magnitude on some problems (see also Höhna and Drummond 2012).

Can someone point me to this paper? I'd like to read about them! (@Alexis_RAxML, I'm assuming that you learned about then from just reading the MB source?)

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01:53
Anisomeriini diving beetles contain only two enigmatic species, representing a remarkable disjunction between the Pacific Juan Fernández Islands (Anisomeria bistriata) and the South Atlantic Tristan da Cunha Archipelago (Senilites tristanicola). They belong to the Colymbetinae, which contain 140 species worldwide. Here we aim to reconstruct the evolutionary history of the Anisomerinii and use > 9000 bp DNA sequence data from 13 fragments of 12 loci for a comprehensive sampling of Colymbetinae species. Analyses under different optimization criteria converge on very similar topologies, and show unambiguously that Anisomeria bistriata and Senilites tristanicola belong to the Neotropical Rhantus signatus species group, a comparatively recent clade within Colymbetinae. Anisomeriini therefore are synonomized with Colymbetini and both species are transferred to Rhantus accordingly, resulting in secondary homonymy of Rhantus bistriatus (Brullé, 1835) with Rhantus bistriatus (Bergsträsser, 1778). We propose the replacement name Rhantus selkirki Jäch, Balke & Michat nom. nov. for the Juan Fernández species. Presence of these species on remote islands is therefore not relictary, but the result of more recent range expansions out of mainland South America. Finally, we suggest that Carabdytini should be synonymized with Colymbetini. Our study underpins the Hennigian principle that a natural classification can be derived only from the search for shared apomorphies between species, not from differences.
Source: Cladistics
01:28
—_000_CF745EAE8A96mitchellmcglaughlinuncoedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Graduate positions (MS or PhD) in Plant Evolution in the lab of Dr. Mitchell McGlaughlin, School of Biological Sciences, University of Northern Colorado. I am seeking MS or PhD students interested in the population genetics, conservation, speciation, and phylogeography of plant species. Research is my lab is focused on using population genetics to understand plant speciation and to inform the conservation of rare and endangered taxa. We employ a wide range of genetic data types, including low copy nuclear sequence, chloroplast sequence, nuclear microsatellite, and next generation sequence data. Current research projects include, phylogeography of the California Channel Islands, ancestral polymorphism in Acmispon, hybridization in endangered Sclerocactus, and conservation genetic research with several native Colorado taxa. Doctoral students are encouraged to develop projects within the scope of research in my lab and masters students can develop their own projects or work on research already initiated in the lab. Funding is available to support graduate students through teaching and research assistantships. I am looking for stu dents to start in Fall 2014 or Spring 2015. For more information please visit my lab website: http://bit.ly/1l5VVri or the department website: http://bit.ly/1qNmNeI The University of Northern Colorado is a public institution with about 11,000 undergraduate and 1,500 graduate students, located in Greeley, Colorado. Greeley is situated 50 miles northeast of Denver and 20 miles east of the Rockies, with easy access to Rocky Mountain National Park and other outdoor activities. Interested applicants should send a letter of interest and CV to Dr. Mitchell McGlaughlin (Mitchell.mcglaughlin@unco.edu). To apply, students will need to submit a complete application to the UNC School of Biology (http://bit.ly/1l5VY6u) and Graduate School (http://bit.ly/1qNmNeK). There is no fixed application deadline. Applications are reviewed when they are received. via Gmail
Source: EVOLDIR
00:58
—001a1133da6616035e04f7319f3b Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable A PhD position in the field of evolutionary ecology / evolutionary genomics is available, for a high achieving student, in the research group of Dr Damian Dowling at Monash University. The topic of the project can be flexible, and discussed with Dr Dowling in advance of the application. The successful applicant will have the capacity to develop their own interests within the general field of experimental evolutionary biology for the duration of the PhD candidature. Projects that draw on the following areas of interest to the Dowling lab, will be particularly encouraged: · Evolutionary coadaptation and conflict between mitochondrial and nuclear genomes · The evolution of ageing · Sexual selection and adaptation The successful applicant will be familiar with basic evolutionary concepts, understand the core tenets of experimental design, and have strong quantitative skills. Some expertise in evolutionary genomics is desirable, but not essential. The successful applicant will nominate for a scholarship to cover salary. Students who hold a four year undergraduate degree with strong academic performance, and a first-authored publication, stand an excellent chance of obtaining a scholarship. The tax-free 2014 rate of a scholarship is A$25392. The position includes funding for international and national conference visits, and for all research costs. Monash University is a member of Australia’s “Group of Eight” ” a coalition of research-intensive universities, and is internationally recognized for its excellence in research and teaching. The School of Biological Sciences ( http://bit.ly/1n2gpy2) is home to a collegial and world-class research environment, with key strengths in evolutionary ecology and genomics. Monash is located in Melbourne, a vibrant cultural and recreational centre ( http://bit.ly/1l5Q6u2’s_most_livable_cities). The deadline for scholarship applications in the current round is 31st May 2014. Interested students should contact damian.dowling@monash.edu for further information, and attach a CV, academic transcript, contact details of two academic referees, and a brief description of their research interests. For further information on these scholarships and Monash application procedures, please visit http://bit.ly/1gCAh6E For further information on the research group of Damian Dowling, http://bit.ly/1l5Q6u5 —001a1133da6616035e04f7319f3b Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

A PhD position in the field of evolutionary ecology / evolutionary genomics is available, for a high achieving student, in the research group of Dr Damian Dowling at Monash University.

The topic of the project can be flexible, and discussed with Dr Dowling in advance of the application. The successful applicant will have the capacity to develop their own interests within the general field of experimental evolutionary biology for the duration of the PhD candidature. Projects that draw on the following areas of interest to the Dowling lab, will be particularly encouraged:

·         Evolutionary coadaptation and conflict between mitochondrial and nuclear genomes

·         The evolution of ageing

·         Sexual selection and adaptation

The successful applicant will be familiar with basic evolutionary concepts, understand the core tenets of experimental design, and have strong quantitative skills. Some expertise in evolutionary genomics is desirable, but not essential.

The successful applicant will nominate for a scholarship to cover salary. Students who hold a four year undergraduate degree with strong academic performance, and a first-authored publication, stand an excellent chance of obtaining a scholarship. The tax-free 2014 rate of a scholarship is A$25392. 

The position includes funding for international and national conference visits, and for all research costs.

Monash University is a member of Australia’s “Group of Eight” ” a coalition of research-intensive universities, and is internationally recognized for its excellence in research and teaching. The School of Biological Sciences (http://bit.ly/1n2gpy2) is home to a collegial and world-class research environment, with key strengths in evolutionary ecology and genomics. Monash is located in Melbourne, a vibrant cultural and recreational centre (http://bit.ly/1gCAh6G).

 

The deadline for scholarship applications in the current round is 31st May 2014.

Interested students should contact damian.dowling@monash.edu for further information, and attach a CV, academic transcript, contact details of two academic referees, and a brief description of their research interests.

For further information on these scholarships and Monash application procedures, please visit http://bit.ly/1gCAh6E

For further information on the research group of Damian Dowling, http://bit.ly/1l5Q6u5

—001a1133da6616035e04f7319f3 via Gmail
Source: EVOLDIR
00:26
Opportunities for Graduate Study on Speciation, Ecological Genomics, and Behavior, in Timema walking-sticks. We invite applications for several graduate positions (MSc or PhD) to join an international team that uses Timema walking sticks as research systems to address several of the primary outstanding questions in evolutionary biology, ecology and genomics, with emphases of questions related to species formation, climate adaptation, genomics of adaptation, asexuality, mating systems, and cuticular hydrocarbons. The successful candidates will be based at Simon Fraser University in Burnaby, British Columbia, Canada, and conduct fieldwork in southern California. Positions would begin in Fall 2104, or in early 2015. Candidates who have secured NSERC PGS funding, or other fellowship funding, are preferred. Please send a CV and letter of interest to Dr. Bernard Crespi, Biosciences, Simon Fraser University, crespi@sfu.ca Bernard Crespi via Gmail
Source: EVOLDIR
00:10
PostDoc position in comparative genomics and phylogenomics of non-bilaterian animals (LMU Munich, Germany) We invite applications for a *PostDoc* position in the project MODELSPONGE funded by the LMUexcellent program through the German Excellence Initiative. The project is located at the *Department of Earth- and Environmental Sciences* (Chair of Paleontology and Geobiology) and the *GeoBio-Center^LMU * of the Ludwig-Maximilians-Universitt (LMU) Mnchen. The phylogenetic relationships among non-bilaterian animals (i.e. Porifera, Ctenophora, Cnidaria, Placozoa) and their relationships to the Bilateria are still discussed controversially. This project will build on recently published as well as unpublished in-house sequenced genomes of sponges and other non-bilaterians to comparatively analyse their genomes to further our understanding of early animal evolution. The project is also aimed at contributing to resolve controversies about the branching patterns at the base of the animal tree of life. Key publications in this context from the lab include Philippe et al., 2009, Current Biology; Pick et al., 2010, Molecular Biology and Evolution; Philippe et al., 2011, PLoS Biology; Wrheide et al., 2012, Advances in Marine Biology; Dohrmann & Wrheide, 2013, Integrative and Comparative Biology; Nosenko et al., 2013, Molecular Phylogenetics and Evolution. We are seeking a highly motivated applicant, ideally trained in evolutionary bioinformatics, with excellent and demonstrated (phylo)genomic skills, bioinformatics expertise as well as a sound background in biology, who is willing to tackle the challenging task of working with the genomes of non-bilaterian animals. The successful candidate will also contribute to the lab’s ongoing genome sequencing efforts, contribute to expand the bioinformatic tools available in the lab, and has the opportunity to contribute to teaching specialty courses in the Master’s programme. High-performance computing is available in the lab (64-core LINUX cluster) as well as through the Leibnitz Rechenzentrum (). The successful candidate will join an international and dynamic lab focussing on the geobiology and evolution of marine animals. More information about the lab can be found at . *Requirements*: PhD in Biology or Bioinformatics or related field; demonstrated expertise and understanding of molecular evolution including phylogenomic methods, demonstrated expertise in processing and analysing Illumina NGS genome and transcriptome data; excellent English language skills; excellent programming skills (e.g., in commonly used bioinformatic languages such Perl, Python, etc.). Evidence of this expertise must be provided through high-ranking international publications. Prior postdoctoral experience is desirable but not essential. German language skills are not necessary, the working language of the group is English. The position is initially available for 12 months, with possible extension depending on performance. The position will be paid according to the German salary scheme TV-L E13. *Application*: Send application including letter of motivation, CV, PDFs of max. 5 of your most significant publications, and contact details of 2 referees in a single PDF (only) by email to Mrs Monika Brinkrolf . Application deadline is 15 May 2014. Informal enquiries may be directed to Professor Gert Wrheide (woerheide@lmu.de). The Department of Earth- and Environmental Sciences, Palaeontology & Geobiology of the Ludwig-Maximilians-Universitt Munich offers an excellent multidisciplinary research environment, one of its particular strength being due to the close interaction between Geosciences and the Faculty of Biology in the framework of the GeoBioCenter^LMU (http://bit.ly/1r1GXjr). The LMU Munich is the leading research university in Germany, with a more than 500-year-long tradition, and builds upon its success in the Excellence Initiative, a Germany-wide competition promoting top-level university research. Munich has been repeatedly voted Germany’s most livable city and is among the Top 5 most livable cities worldwide. The LMU Munich is an Equal Opportunity/Affirmative Action Employer and has an affirmative action policy for the disabled. Prof. Dr. Gert Wrheide Department of Earth and Environmental Sciences, Division of Paleontology & Geobiology & GeoBio-CenterLMU Ludwig-Maximilians-Universitt Mnchen, and Director, Bavarian State Collections of Palaeontology and Geology Richard-Wagner-Strae 10 80333 Mnchen Germany Phone: +49 (89) 2180-6718 Fax: +49 (89) 2180-6601 E-Mail: woerheide@lmu.de www.palmuc.de | www.mol-palaeo.de Labnews: http://on.fb.me/1r1GXjt Tweets: twitter.com/gwoerhe Lab publications: http://bit.ly/1l5GyPG http://bit.ly/1l5GyPIwww.palmuc.de | www.mol-palaeo.de Labnews: http://on.fb.me/1r1GXjt Tweets: twitter.com/gwoerhe Lab publications: http://bit.ly/1l5GyPG http://bit.ly/1l5GyPI woerheide@lmu.de via Gmail
Source: EVOLDIR
00:10

Postdoctoral Fellow in Drosophila Metabolomics A postdoctoral position in the cutting-edge field of metabolomics is available in the laboratory of Laura Reed, within the Department of Biological Sciences at the University of Alabama. The Reed Lab is a highly interactive group that conducts research on the genetic basis of genotype-by-environment interactions contributing to metabolic disease and variation in Drosophila. Major areas of research include QTL mapping of loci interacting with diet to produce obesity and type-2 diabetes phenotypes, evolutionary genetics of complex traits, functional analysis of candidate genes for metabolic phenotypes, whole genome expression analysis of genetic and environmental variation, and metabolomic analyses. This opening is for a highly motivated postdoctoral fellow with familiarity with Drosophila and some background in bioinformatic methods. The postdoc will work to facilitate the data curation and experimentation goals of the International Drosophila Metabolomics Curation Consortium (IDMCC, http://bit.ly/1l5Gyz6) including working to expand publically available tools such as MetScape 2.0 developed by researchers at the University of Michigan (metscape.ncibi.org, Karnovsky et al, 2012) and MetaCyc developed by researchers at SRI International in California (www.metacyc.org, Caspi et al, 2013) to incorporate Drosophila specific data. The postdoc will also work closely with the NIH Common Fund Metabolomics Data Center and Workbench (WDCW) at UC San Diego. While collating relevant data sources the postdoc will help identify critical gaps in the available knowledge needing further empirical work to fill, and would then have the opportunity to conduct some of thos e studies. All candidates must have received a Ph.D. in a relevant field. The position is available for 2 years with the possibility of renewal contingent on securing external funding, and will include a competitive salary and full benefits. A successful applicant will have: Extensive research experience Creativity and independence Genetic or molecular lab experience Computational or bioinformatics experience Excellent communication skills, both written and oral. Application review will begin May 1, 2014 and will continue until the position is filled. The successful applicant should be able to beginning working in the position August 15, 2014. Submit an application to the departmental postdoctoral pool http://bit.ly/1r1GYUw. Materials should include: 1. Cover letter with a description of past research accomplishments and future research goals, (maximum of two pages) and the names and contact information for 3 references. 2. Curriculum vitae Contact Dr. Laura Reed (lreed1@as.ua.edu) with questions regarding the position or application process. For further information about the Reed lab visit flygxe.ua.edu. About the University of Alabama The University of Alabama is the flagship campus of the University System of Alabama, with an enrollment of over 35,000 students. The University is committed to achieving excellence as one of the country’s primary centers of research and education. It is located in the vibrant college town of Tuscaloosa, AL, which boasts many cultural and athletic activities. The campus also benefits from the close proximity to the Birmingham metropolitan community. The University of Alabama is an Affirmative Action/Equal Opportunity Employer. Women and minorities are encouraged to apply. Laura K. Reed Assistant Professor Dept. of Biological Sciences University of Alabama, Tuscaloosa Office: 2330 SEC, Lab: 2322 SEC Mailing address: Box 870344, Tuscaloosa AL 35487 office: 205-348-1345 lab: 205-348-1368 lreed1@bama.ua.edu http://bit.ly/1l5Gyzcwww.metacyc.org, Caspi et al, 2013) to incorporate Drosophila specific data. The postdoc will also work closely with the NIH Common Fund Metabolomics Data Center and Workbench (WDCW) at UC San Diego. While collating relevant data sources the postdoc will help identify critical gaps in the available knowledge needing further empirical work to fill, and would then have the opportunity to conduct some of thos e studies. All candidates must have received a Ph.D. in a relevant field. The position is available for 2 years with the possibility of renewal contingent on securing external funding, and will include a competitive salary and full benefits. A successful applicant will have: Extensive research experience Creativity and independence Genetic or molecular lab experience Computational or bioinformatics experience Excellent communication skills, both written and oral. Application review will begin May 1, 2014 and will continue until the position is filled. The successful applicant should be able to beginning working in the position August 15, 2014. Submit an application to the departmental postdoctoral pool http://bit.ly/1r1GYUw. Materials should include: 1. Cover letter with a description of past research accomplishments and future research goals, (maximum of two pages) and the names and contact information for 3 references. 2. Curriculum vitae Contact Dr. Laura Reed (lreed1@as.ua.edu) with questions regarding the position or application process. For further information about the Reed lab visit flygxe.ua.edu. About the University of Alabama The University of Alabama is the flagship campus of the University System of Alabama, with an enrollment of over 35,000 students. The University is committed to achieving excellence as one of the country’s primary centers of research and education. It is located in the vibrant college town of Tuscaloosa, AL, which boasts many cultural and athletic activities. The campus also benefits from the close proximity to the Birmingham metropolitan community. The University of Alabama is an Affirmative Action/Equal Opportunity Employer. Women and minorities are encouraged to apply. Laura K. Reed Assistant Professor Dept. of Biological Sciences University of Alabama, Tuscaloosa Office: 2330 SEC, Lab: 2322 SEC Mailing address: Box 870344, Tuscaloosa AL 35487 office: 205-348-1345 lab: 205-348-1368 lreed1@bama.ua.edu http://bit.ly/1l5Gyzc via Gmail

Source: EVOLDIR

April 16, 2014

23:39

http://bit.ly/1eLOVgU The Generic Model Organism Database (GMOD; http://gmod.org) project is offering an online training course for those interested in learning how to use and deploy GMOD’s free, open-source bioinformatics software. The GMOD project provides interoperable tools for visualising, storing, and disseminating genetic and genomic data. The course will be held from 19th-23rd May 2014, with online tuition and interaction with tutors occurring between (approximately) 9am and 5pm US Eastern time. Components covered in the online training include: -Chado database schema -Galaxy analysis pipeline -GBrowse genome browser -JBrowse genome browser -MAKER genome annotation pipeline -Tripal website generator and database interface -WebApollo manual gene annotation software By the end of the course, participants will have hands-on experience of setting up and using core components needed for a modern genomics project. More information and application form: http://bit.ly/1eLOVgU Please feel free to email help@gmod.org if you have any questions. via Gmail

Source: EVOLDIR
22:00
In the last two decades, models from evolutionary biology have made important contributions to demographic research on human fertility change. Within this evolutionary framework, two distinct traditions have focused on different processes of adaptation and time scales of change: (1) behavioral ecological perspectives have focused on how individual fertility decisions are shaped by local ecological circumstances, while (2) cultural evolutionary approaches have emphasized the role of socially transmitted information and changing social norms in shaping fertility behavior. While each tradition has made independent progress, research that integrates these approaches is necessary to improve our understanding of real fertility behavior, which results from a feedback between individual fertility decisions and social change. This approach requires combined attention to immediate ecological determinants of fertility decisions as well as the long-term processes that shape costs and benefits in a given environment. This workshop will bring together an international team of evolutionary behavioral scientists with complementary methodological and theoretical expertise in anthropology, psychology, and demography to develop (a) a synthetic article which proposes how these approaches can be integrated methodologically and theoretically, (b) an empirical article which applies our new synthetic framework to the study of fertility change in a particular fieldsite, demonstrating how the new methodological approach will work in practice and what we can learn through employing it, and (c) a multi-site grant proposal (UK, US, Bangladesh, Ethiopia, Bolivia, Poland) aimed at integrating and empirically testing these diverse evolutionary models of human fertility change.
Source: NESCent
18:00
Background: Mangroves are key components of coastal ecosystems in tropical and subtropical regions worldwide. However, the patterns and mechanisms of modern distribution of mangroves are still not well understood. Historical vicariance and dispersal are two hypothetic biogeographic processes in shaping the patterns of present-day species distributions. Here we investigate evolutionary biogeography of mangroves in the Indo-West Pacific (IWP) and western Atlantic-East Pacific (AEP) regions using a large sample of populations of Rhizophora (the most representative mangrove genus) and a combination of chloroplast and nuclear DNA sequences and genome-wide ISSR markers. Results: Our comparative analyses of biogeographic patterns amongst Rhizophora taxa worldwide support the hypothesis that ancient dispersals along the Tethys Seaway and subsequent vicariant events that divided the IWP and AEP lineages resulted in the major disjunctions. We dated the deep split between the Old and New World lineages to early Eocene based on fossil calibration and geological and tectonic changes. Our data also provide evidence for other vicariant processes within the Indo-West Pacific region in separating conspecific lineages of SE Asia and Australia-Pacific at the Oligocene-Miocene boundary. Close genetic affinities exist between extant Fijian and American lineages; East African and Australian lineages; and Australian and Pacific lineages; indicating relatively more recent oceanic long-distance dispersal events. Conclusions: Our study demonstrates that neither vicariance nor dispersal alone could explain the observed global occurrences of Rhizophora, but a combination of vicariant events and oceanic long-distance dispersals can account for historical diversification and present-day biogeographic patterns of mangroves.
18:00
Background: Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to improve phylogenetic inference. Current methods for estimating best-fit partitioning schemes, however, are only computationally feasible with datasets of less than 100 loci. This is a problem because datasets with thousands of loci are increasingly common in phylogenetics. Methods: We develop two novel methods for estimating best-fit partitioning schemes on large phylogenomic datasets: strict and relaxed hierarchical clustering. These methods use information from the underlying data to cluster together similar subsets of sites in an alignment, and build on clustering approaches that have been proposed elsewhere. Results: We compare the performance of our methods to each other, and to existing methods for selecting partitioning schemes. We demonstrate that while strict hierarchical clustering has the best computational efficiency on very large datasets, relaxed hierarchical clustering provides scalable efficiency and returns dramatically better partitioning schemes as assessed by common criteria such as AICc and BIC scores. Conclusions: These two methods provide the best current approaches to inferring partitioning schemes for very large datasets. We provide free open-source implementations of the methods in the PartitionFinder software. We hope that the use of these methods will help to improve the inferences made from large phylogenomic datasets.