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October 15, 2014

03:05
FACULTY POSITION ANNOUNCEMENT Schlinger Endowed Chair in Insect Systematics University of California, Davis Title: Associate Professor or Professor in the College of Agricultural and Environmental Sciences, and Associate Entomologist or Entomologist in the Agricultural Experiment Station. This is an academic year (9 mo.) tenured position. Responsibilities: The appointee will be required to organize and present undergraduate and graduate courses in the areas of systematics and phylogenetics, as well as contribute to other courses in the departmental teaching program. Supervision of graduate students, involvement in curricular development, participation in outreach programs, and performance of University service are expected. The appointee to the Endowed Chair is expected to maintain an innovative research program on the systematics of insects or other terrestrial arthropods, and to interact collaboratively with the diverse community of systematists and evolutionary biologists on campus. The appointee will also be designated as a curator in the Bohart Museum of Entomology, and will be expected to contribute towards the development of this internationally recognized systematics resource. Qualifications: Ph.D. in the biological sciences, demonstrated leadership in insect or terrestrial arthropod systematics, with training and experience commensurate with a comprehensive and cutting-edge research program. Examples of fields considered appropriate include species delimitation and description, phylogenetics, revisionary taxonomy, biogeography, character evolution, and comparative biology. Demonstrated competence in molecular systematics and field-based research are required. Familiarity with natural history collections and their development is also highly desirable. Salary: Commensurate with experience within the Associate Professor or Professorial ranks at the University of California. Appointment Date: July 1, 2015 Applications: Applications should be submitted on-line at http://bit.ly/1vc8KmQ and inquiries should be directed to Dr. Philip Ward, Search Committee Chair, Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, telephone (530) 752-0486, e-mail: psward@ucdavis.edu. UC Davis is an affirmative action/equal employment opportunity employer and is dedicated to recruiting a diverse faculty community. We welcome all qualified applicants to apply, including women, minorities, veterans, and individuals with disabilities. Thank you, Amanda Amanda Isaac Executive Academic Assistant The Phoenix Cluster (Plant Pathology, Entomology and Nematology) 367 Briggs Hall 530-752-0492 alisaac@ucdavis.edu Amanda Lee Isaac via Gmail
Source: EVOLDIR
02:50
PhD Fellowship in Paleobiology/Paleontology at the University of Pennsylvania A PhD fellowship in Paleobiology is available in the Department of Earth and Environmental Science at the University of Pennsylvania, starting in Fall 2015. Prof. Lauren Sallan seeks a graduate student to address major paleobiological questions, such as how global change has affected life over time, how life evolves at high levels (macroevolution), and the origins of living biodiversity. Specific topics include, but are not limited to: the drivers and ecological consequences of mass extinction (e.g. the end-Devonian Hangenberg event), the role of predation and competition in setting marine biodiversity, the characteristics of adaptive radiations and $B!H(Bliving fossils,$B!I(B the effects of long-term environmental events (e.g. the Late Paleozoic Ice Age) on biodiversity trends, and transitions in early vertebrate evolution (e.g. origin of jaws, invasion of land). The student can also develop a novel project that address similar questions using quantitative, phylogenetic and descriptive methods. While research in the lab has focused on fishes, any suitable group of fossil animals may be used. Applicants are encouraged to contact Prof. Sallan (lsallan@sas.upenn.edu) for more details. Additional information on the fellowship is available on the departmental website: http://bit.ly/11muDER. Applications for entry in Fall 2015 are due December 15, 2014. Applications to graduate school at Penn must be submitted online at http://bit.ly/1w6z9AK Lauren Sallan Assistant Professor Earth and Environmental Science & Evolution Cluster University of Pennsylvania Office: 154B Hayden Hall Phone: (215) 898-5650 Website: www.LaurenSallan.com E-mail: lsallan@sas.upenn.edu Lauren Sallan via Gmail
Source: EVOLDIR
02:34
*MS position*: A graduate research assistantship position (TA funded) is available in the lab of Dr. Matt Hale in the Biology Department at Texas Christian University starting in August 2015. The student will develop a MS project on the genetic basis of complex phenotypic traits. Some possible research projects include questions relating to the genetic basis of migration in salmonid fishes, and the presence and identity of genes showing patterns of sex-bias in expression, also in the salmonid fishes. The applicant should have some previous lab experience, including DNA extraction, PCR amplification, and DNA sequencing. Ideally, the candidate will also have experience with RNA extraction, cDNA synthesis and bioinformatics, although training in these areas will be provided. Interested applicants should send a CV, a cover letter describing their research interests and reasons for applying, and the names and contact details of two potential referees. Review of applications will begin on December 1st 2014. Please send inquires and applications to Matt Hale (m.c.hale@tcu.edu) Interested students are encouraged to view the Biology Department website (http://bit.ly/1qrsWeV) for more information on the graduate program. Matt C. Hale, PhD Assistant Professor, Biology Department Texas Christian University 2800 S University Drive Fort Worth, Texas 817-257-8707 “Hale, Matthew” via Gmail
Source: EVOLDIR
02:34

PhD student position in Ethology at the Department of Zoology. Reference number SU FV-2909-14. Deadline for applications: November 20, 2014. Project description We are seeking a highly motivated PhD student with an interest in evolutionary biology and behavioral ecology to take part in the research project “Life-history variation, behavior and methylation patterns”, funded by the Swedish Research Council. The aim of the project is to investigate the association between methylation patterns and variation in life-history traits and behavior across species. Methylation is one of several epigenetic inheritance mechanisms, which may play an important role in phenotypic plasticity and genetic accommodation. Understanding epigenetic effects has implications for core evolutionary processes such as heritability, maintenance of genetic variation and speciation. Still, we have only a rudimentary understanding of how evolutionary processes are affected by these epigenetic effects. The project involves a combination of modern phylogenetic comparative methods and experimental approaches to analyze the association between methylation and inter-specific variation in life-history and behavior using killifish (Cyprinodontiformes) as a model system. The selected candidate will gain experience in modern phylogenetic comparative methods, experimental design, molecular analyses and statistics. This is an ambitious project which will be demanding and require excellent organization and analytical skills. However, we think it will also be very rewarding and exciting. The candidate will be based in Stockholm, the capital of Sweden and a beautiful and vibrant Scandinavian city. Since one of the PIs of the project has a joint affiliation between Stockholm University and the Universidad Nacional Autónoma de México, research visits to the later, in Mexico City, another vibrant and diverse city with plenty of cultural offer, are also highly likely. The proposed project combines the different areas of expertise of the two principal investigators, who will jointly supervise the candidate. Alejandro Gonzalez Voyer is interested in phenotypic evolution and speciation, topics that are mainly addressed using modern phylogenetic comparative methods. Björn Rogell has a broad interested in environmental stress, local adaptation and phenotypic plasticity. Qualifications To be qualified for research studies in ethology the applicant must have completed a research degree (e.g. Master’s), or have passed at least 120 hp (2 years) of biological studies, including an approved independent project of at least 30 hp at advanced level (“examensarbete”) within ethology, evolutionary biology or related subjects. Applicants who have in principle acquired the corresponding competence in Sweden or abroad are also qualified. Criteria for selection Among qualified applicants, selection is made according to the ability to benefit from the studies. The criteria to be used are properly documented competence within the described research area, capabilities with regards to speaking and writing in English (note that English is the working language in the groups), analytical thinking, organizational skills, creativity, initiative, independence, and team work performance. Experience with statistical analysis and molecular data is an advantage. The applicant’s earlier experience within the field of research can be of relevance especially when further documented by university courses, independent research works, personal references, interview and an application indicating the applicant’s motivations in written form. Terms of employment The PhD studies include 48 months of full-time studies with employment as PhD student. The salary currently starts at 23.700 SEK/month. Stockholm University aims to be a workplace free from discrimination and with equal opportunities for everyone. Information For further details, please contact Dr. Alejandro Gonzalez Voyer, a.gonzalezvoyer@zoologi.su.se, or Dr. Bjorn Rogell, bjorn.rogell@zoologi.su.se, at the Department of Zoology. Union representatives Anqi Lindblom-Ahlm (Saco-S) and Lisbeth Häggberg (Fackförbundet ST), telephone: +46 8 16 20 00 (switchboard), and Gunnar Stenberg (SEKO), telephone: +46 70 316 43 41. Application The application should contain: personal presentation and letter of intent/motivation: maximum one A4-page CV (including methodological skills) copy of independent project thesis copies of degree certificates and transcripts of academic records (attested) two reference letters and contact details for these academic referees. Please send your application, marked with the reference number SU FV-2909-14, no later than November 20, 2014, by e-mail to: registrator@su.se. Documents sent by e-mail should be in Word or PDF format. NOTE! State the reference number SU FV-2909-14 also in the subject line of your e-mail. via Gmail

Source: EVOLDIR
01:48
The Department of Biology at the University of Kentucky in Lexington, KY seeks outstanding candidates for a tenure-track ASSISTANT PROFESSOR in the area of MICROBIAL ECOLOGY. This includes but is not limited to the study of human and non-human animal microbiomes and the ecology and evolution of disease, symbiont-host interactions, and extremophile communities. The successful candidate will be expected to develop an independent, extramurally funded research program that complements growing research strengths within the Department and across a highly interactive life science community at the university, as well as participate in undergraduate and graduate education in microbiology. The startup package will include a competitive salary in an affordable community, a generous startup budget, modern laboratory facilities and an outstanding collegial environment. A Ph.D. (or equivalent) and postdoctoral research experience are required. Send cover letter, *curriculum vitae*, statements of research and teaching philosophy and three letters of recommendation to http://bit.ly/1ru3dlq Questions regarding this position may be directed to Dr. Vincent Cassone: 859-257-6766 / vincent.cassone@uky.edu The University of Kentucky is an Affirmative Action/Equal Opportunity University that values diversity and is located in an increasingly diverse geographic region. It is committed to becoming one of the top public institutions in the country. Women, persons with disabilities, and members of other underrepresented groups are encouraged to apply. Catherine Linnen via Gmail
Source: EVOLDIR
01:48

The conference *Mathematical Models in Ecology and Evolution Paris 2015 ** **http://bit.ly/1ru3dlk will host 6 selected mini-symposia, with 6 speakers each: 2 invited speakers (approx. 25’ talk) and 4 contributed speakers (approx. 15’ talk). If you consider participating in the conference, we invite you to propose a mini-symposium devoted to your favourite subject. We ask you to provide a title of your symposium, along with a short introduction to the subject and a list of (2+2 spare) invited speakers. You can propose 1 or 2 (related) mini-symposia by email to info-mmee2015@list01.biologie.ens.fr Deadline Dec 12, 2014. Decision mid-January 2015. Mini-symposia close to the following themes are especially appreciated: epigenetics and information transfer, evolution of cooperation, modelling of speciation, adaptive dynamics, individual-based models of phylogenies, microbial ecology, and adaptation in a changing environment. Once the list of 6 mini-symposia is established, a call for contributions of 3 kinds will be sent: oral contributions within a mini-symposium (6*4 = 24 slots), free oral contributions, posters (deadline April 2015). Please feel free to share this call with interested colleagues and relevant emailing lists. The organisers, Amaury Lambert (UPMC, Collge de France) Guillaume Achaz (UPMC, Collge de France) Minus van Baalen (CNRS, ENS) Silvia De Monte (CNRS, ENS) Todd Parsons (UPMC, CNRS, Collge de France) Emmanuel Schertzer (UPMC, Collge de France) PS. If you are not yet part of the MMEE list, you can check http://bit.ly/1sKt92I to find out how to receive regular information about the conference (no more than approx. 5 emails per year). You can also follow us on twitter using @MMEE2015Paris. Amaury Lambert, professeur UPMC http://bit.ly/1sKt92L SMILE group http://bit.ly/1ru3dlo Stochastics & Biology group http://bit.ly/1sKt7Ih amaury.lambert@ens.fr via Gmail

Source: EVOLDIR
01:33

A meeting dealing specifically with research on topics related to human mutation rates will be held at the Max Planck Institute for Evolutionary Anthropology from 25th - 27th February 2015. URL: http://bit.ly/1v6L5Ee This meeting aims at bringing together researchers from different fields that are interested in estimating the rate of mutations in humans and apes, the application of these rates to date events in the past, the differences in male and female mutation rates, the evolution of the mutation rate, the molecular and chemical mechanisms leading to germline and somatic mutations, and other topics related to the human mutation rate. The meeting is limited to a total of 90 participants and we would like all attendees to actively participate in the meeting by presenting results and joining discussions. Interested scientists are invited to submit an application including an abstract through our application website by 15th December 2014. Suitable abstracts will be selected on a first come, first serve basis and applicants will be informed as soon as possible whether they are accepted to attend the meeting. Registration for the meeting is free of charge and includes coffee breaks and small meals during the conference. Unfortunately, we are not able to support participants by funding travel or accommodation. The meeting will start on the evening of 25th February 2015 to allow guests to fly in on the first day of the meeting. Invited Speakers: * Kelley Harris * Agnar Helgason * Jean-Jacques Hublin * Michael Lynch * Kateryna Makova * Gilean McVean (tbc) * Molly Przeworski * David Reich * Aylwyn Scally * Mikkel Schierup * Michael Stratton * Shamil Sunyaev For further information, please visit our website or contact us by email: THMR2015@eva.mpg.de capone@cap1.eu via Gmail

Source: EVOLDIR
01:15

The University of Tennessee, Knoxville EEB department would like to invite students, postdocs, faculty, and others to attend SEPEEG 2014! This year, the 39th annual SouthEast Population, Ecology, and Evolutionary Genetics (SEPEEG) meeting will take place at the facilities of Outdoor Adventure Rafting (www.raft.com) on October 24-26 in Ocoee, TN. This years keynote speaker will be Prof. Dr. Margret Ptacek from Clemson University. Dr. Ptacek studies processes that control genetic divergence among populations and the contributions of these processes to local adaptation and speciation. For more information and to register, please see the website below and/or locate SEPEEG on Facebook. http://bit.ly/1sQcJ88 Registration is now open: full registration is $145 for a bed in a bunkhouse or $135 for camping and covers all meals and participant costwww.raft.com) on October 24-26 in Ocoee, TN. This years keynote speaker will be Prof. Dr. Margret Ptacek from Clemson University. Dr. Ptacek studies processes that control genetic divergence among populations and the contributions of these processes to local adaptation and speciation. For more information and to register, please see the website below and/or locate SEPEEG on Facebook. http://bit.ly/1sQcJ88 Registration is now open: full registration is $145 for a bed in a bunkhouse or $135 for camping and covers all meals and participant costs. If you have questions, please email Zach Marion atzmarion@utk.edu. If you come, you will have a blast! There will be bonfires both nights, plenty of beverages, great company, and the opportunity for rafting and other opportunities on Sunday for those who are interested. It is an excellent opportunity to network, support education and research, and learn about great new science! omeara.brian@gmail.com via Gmail

Source: EVOLDIR
00:27

The International Society for Evolution, Medicine, & Public Health Society will be hold its inaugural meeting March 19-21 in Tempe, Arizona. Registration and abstract submission are open now. Early registrants receive a substantial discount, and all fees are refundable until February 15th. This meeting will bring together scientists, scholars, teachers, clinicians, and students in the evolution and medicine community to share ideas and create new connections that will advance the field. Students and clinicians with an interest in the field are especially welcome. This meeting is co-sponsored by The Society and the Arizona State University Center for Evolution & Medicine. Full information on the conference site http://bit.ly/1vaNFak Registration at http://bit.ly/1vaNHis Plenary Speakers include Harvey Fineberg, Institute of Medicine, Stephen Stearns, Yale University, Barbara Natterson-Horowitz, UCLA, Sir Peter Gluckman, University of Auckland, Ann Demogines, (Omenn Award Winner) BioFire Diagnostics, Ruslan Medzhitov, Yale Other confirmed speakers include Carl Bergstrom, University of Washington, Sudhir Kumar, Temple University, Daniel Lieberman, Harvard University , Gilbert Omenn, University of Michigan, Allen Rodrigo, NESCent, Frank Rhli, University of Zurich, Elizabeth Uhl, University of Georgia, Robert Perlman, University of Chicago, Ajit Varki, UC San Diego, Gillian Bentley, Durham University, Bernard Crespi, Simon Fraser University, David Haig, Harvard University, Andrew Read, Penn State University, Mark Schwartz, New York University, Marlene Zuk, University of Minnesota, Cynthia Beall, Case Western University, Charles Nunn, Duke University, Randolph Nesse, Arizona State University, Carlo Maley, UCSF, Athena Aktipis, UCSF, Wenda Trevathan, New Mexico State University, Matthew Keller, University of Colorado, Boulder, Lewis Wolpert, University College London, Joshua Schiffman, University of Utah, Joseph Alcock, University of New Mexico, Kathleen Barnes, Johns Hopkins University, Fabio Zampieri, University of Padua, Italy, Michael Ruse, Florida State University, Detlev Ganten, World Health Summit, Berlin, Grazyna Jasienska, Jagellonian University, Poland, Beverly Strassmann, University of Michigan, Daniel Blumstein, UCLS, Mark Flinn, University of Missouri, and Koos Boomsma, University of Copenhagen. Wednesday on March 18 Noon-5 PM is a pre-meeting for Directors of Evolutionary Medicine Programs, Centers, and Institutes, and those who are considering organizing such units. The event, organized by Randolph Nesse, Gillian Bentley, Daniel Blumstein, Barbara Natterson-Horowitz, and Frank Rhle, will provide an informal opportunity to share strategies and resources and coordinate efforts. Randolph Nesse ASU Center for Evolution & Medicine http://bit.ly/1mP32pF rmnesse@gmail.com via Gmail

Source: EVOLDIR
00:11

The course “Integrative taxonomy and taxonomic expertise in the framework of the DNA-barcoding initiative” will be from the 9th to the 13th of March, 2015 at the MNHN of Paris, France. This course is also part of the DEST- Taxonomy training program (http://bit.ly/1w1N7F5). The course is in English. To register, please fill the form on the website of the course (http://bit.ly/1z9pjnb) before the the 4th of January, 2015. If you have any question, please contact: Line Le Gall (legall@mnhn.fr) Nicolas Puillandre (puillandre@mnhn.fr) Sarah Samadi (sarah@mnhn.fr) Nicolas PUILLANDRE, McF MNHN, ISyEB +33 (0)1 40 79 31 73 nicolaspuillandre@gmail.com via Gmail

Source: EVOLDIR

October 14, 2014

23:40

Postdoctoral position: Genetics of adaptation to fluctuating environments Centre of Excellence in Biological Interactions, University of Jyvskyl, Finland. Finnish Academy funded post doc position for two years is available (from 1.1.2015) in a project led by Tarmo Ketola (Academy research fellow, PhD). The project concentrates mapping genetic changes associated with adaptation to fluctuating thermal environments vs. adaptation to constant environments (see: Ketola et al. 2013 in Evolution67: 2936-2944). This part of the project is conducted in close collaboration with Dr. Juan Galarza. Applicant must possess excellent programming skills and demonstrated experience in the use of next-generation data and a PhD from the relevant field. Backgroundin evolutionary biology isvery much appreciated, as applicant is also expected to develop independent research questions utilizing the genetic data, for example on genetic and environmental canalization and on phenotypic plasticity. Since sequenced bacterial strains (Serratia marcescens) are stored in suspended animation they can be easily used for additional experiments. The salary ranges from ca. 3000-3500 euro / month, based on the personal qualifications. Note that starting date is negotiable and PhD must be obtained before the starting date. Deadline for applications is 30. 10. 2014. (Please send CV, expression of interest, and contact details of 3 persons who can provide references, as a single pdf-file) For enquiries and submitting the applications contact: Tarmo Ketola tketola(at)jyu.fi http://bit.ly/1z9lQFe Informative/relevant webpages: http://bit.ly/1w1KG5f http://bit.ly/1awsze5 http://on.fb.me/1z9lRZV http://bit.ly/1w1KG5h tarmo.t.ketola@jyu.fi via Gmail

Source: EVOLDIR
23:40
Course title; ‘SPATIAL ANALYSIS OF ECOLOGICAL DATA USING R’ The course will be delivered by Jason Matthiopoulos who is a Professor of Spatial and Population Ecology at the University of Glasgow (Institute of Biodiversity Animal Health and Comparative Medicine) and the author of ‘How to be a Quantitative Ecologist’ the A to R of Green Mathematics and Statistics. The course content will cover the concepts and R tools that can be used to analyse spatial data in ecology covering elementary and advanced spatial analysis techniques applicable to both plants and animals. It will investigate analyses appropriate to transect (e.g. line surveys, trapping arrays), grid (e.g. occupancy surveys) and point data (e.g. telemetry). The focal questions will be on deriving species distributions, determining their environmental drivers and quantifying different types of associated uncertainty. Novel methodology for generating predictions will be introduced. We will also address the challenges of applying the results of these methods to wildlife conservation and resource management and communicate the findings to non-experts. Module 1 Introductory lectures; key questions in spatial ecology, the main types of data on species distributions, concepts, challenges and different types of environmental data; useful concepts from statistics; GLM’s Module 2 Density estimation, spatial autocorrelation, Smoothing, Kernel Smoothers, Kriging, Trend-fitting (linear, generalised linear, generalised additive models) Module 3 Habitat preference, Resource selection functions, MaxEnt: What’s it all about? Overview and caveats related to Niche models Module 4 Analysing grid data, Poisson processes, Occupancy models, Use-availability designs Module 5 Analysing telemetry data, Presence-only data, Spatial and serial autocorrelation, partitioning variation by mixed effects models Module 6 Analysing transect data, Detection functions for point and line transects, Using covariates in transect models Module 7 Advanced methods, Generalised Estimation Equations for difficult survey designs, GAM’s for habitat preference, Dealing with boundary effects using soap smoothers, Spatial point processes with INLA Module 8 Prediction, Validation by resampling, Generalised Functional Responses for species distribution, quantifying uncertainty, dealing with the effects of population density Module 9 Applications, Designing protected areas, thinking about critical habitat, representing uncertainty Module 10 Round table discussions, About 4 groups, each of 5-10 people working on a particular problem, to be worked out in advance of the course starting. The course is aimed at PhD students and post docs (although people at any stage of their career are welcome) with basic to moderate knowledge in R. The course will be held at SCENE (Scottish Center for Ecology and the Natural Environment), Glasgow, United Kingdom from 16th – 20th March 2015. The cost is £450 for the 5 days including lunches and refreshments or £650 for an all inclusive option which includes the addition of accommodation, all meals and refreshments, (accommodation is multiple occupancy (max 3 people) single sex en-suite rooms). For further details or questions please email oliverhooker@prstatistics.co.uk or visit http://bit.ly/1v1Pet4 Oliver Hooker PhD research student University of Glasgow +44 (0) 1360 870 510 +44 (0) 7966 500 340 o.hooker.1@research.gla.ac.uk Oliver Hooker via Gmail
Source: EVOLDIR
22:30

Periodically, mathematicians and other computationalists produce lists of what they refer to as "Open Problems" in their particular field. Phylogenetics is no exception. We have had a few on this blog before today (e.g.  An open question about computational complexity; Phylogenetic network Millennium problems).

I thought that I should draw your attention to the fact that last year, Barbara Holland produced a few of her own (2013. The rise of statistical phylogenetics. Australian and New Zealand Journal of Statistics 55: 205-220). These are:

Open problem 1: What is the natural analogue of a confidence interval for a phylogenetic tree?

Open problem 2: What are useful residual diagnostics for phylogenetic models?

Open problem 3: What makes a good phylogenetic model?

Open problem 4: Should DAGs be acceptable objects for inference or should network methods be restricted to exploratory data analysis?

It is obviously the latter problem that is of most interest to us here:
DAGs [directed acyclic graphs] can be constructed by beginning with a good tree and then progressively adding edges until the fit between the model and the data is deemed good enough or there is no sufficient improvement in fit by continuing to add edges. The trouble with using DAGs to define mixture models is that this approach doesn’t actually capture the biological processes of interest within the model. The sorts of things we’d like the data to tell us are what is the relative rate of recombination events or hybridisation events to mutation events or speciation events. The danger with using phylogenetic networks in an "add an extra edge until the fit is good enough" approach is that by giving ourselves the capacity to explain everything we risk explaining nothing. At some point have we stopped doing inference and got back to just summarising our data? In phylogenetics we rely on our models for their explanatory power — in the context of network evolution we need to make careful decisions about what biological processes should be included within the model such that inferences about reticulate (non-treelike) processes of evolution can be brought within the realm of stochastic uncertainty rather than being left as a source of inductive uncertainty. This is not a straightforward task, and will require the collaboration of evolutionary biologists and statisticians.One of the principal issues here is that it is almost impossible to consistently distinguish one reticulation process from another based on the structure of the resulting network. These processes all produce gene flow in the biological world, and they all appear as reticulations in the graphical representation of a network. In practice, phylogenetic analysis may boil down to only two biological processes in the model (vertical gene inheritance and horizontal gene flow), followed by biologists trying to sort out the details with post hoc analyses. Deep coalescence and gene duplication are part of the vertical inheritance, while hybridization, introgression, horizontal gene flow and recombination are part of gene flow. It would be nice to think that this model would simplify network analyses.

22:00
Wednesday, 12:00 PM at NESCent, Ninth Street and Main Street, Erwin Mill Building, 2024 W. Main Street. Room A103 (1st Floor) For more information, call 919-668-4551
Source: NESCent
06:00
Background: Annual Nothobranchius fishes are distributed in East and Southern Africa and inhabit ephemeral pools filled during the monsoon season. Nothobranchius show extreme life-history adaptations: embryos survive by entering diapause and they are the vertebrates with the fastest maturation and the shortest lifespan. The distribution of Nothobranchius overlaps with the East Africa Rift System. The geological and paleoclimatic history of this region is known in detail: in particular, aridification of East Africa and expansion of grassland habitats started 8 Mya and three humid periods between 3 and 1 Mya are superimposed on the longer-term aridification. These climatic oscillations are thought to have shaped evolution of savannah African mammals. We reconstructed the phylogeny of Nothobranchius and dated the different stages of diversification in relation to these paleoclimatic events. Results: We sequenced one mitochondrial locus and five nuclear loci in 63 specimens and obtained a robust phylogeny. Nothobranchius can be divided in four geographically separated clades whose boundaries largely correspond to the East Africa Rift system. Statistical analysis of dispersal and vicariance identifies a Nilo-Sudan origin with southwards dispersion and confirmed that these four clades are the result of vicariance events In the absence of fossil Nothobranchius, molecular clock was calibrated using more distant outgroups (secondary calibration). This method estimates the age of the Nothobranchius genus to be 8.3 (6.0 – 10.7) My and the separation of the four clades 4.8 (2.7-7.0) Mya. Diversification within the clades was estimated to have started ~3 Mya and most species pairs were estimated to have an age of 0.5-1 My. Conclusions: The mechanism of Nothobranchius diversification was allopatric and driven by geographic isolation. We propose a scenario where diversification of Nothobranchius started in rough coincidence with aridification of East Africa, establishment of grassland habitats and the appearance of the typical African bovid fauna of the savannah. Although confidence intervals for the estimated ages of the four Nothobranchius clades are quite large, this scenario is compatible with the biology of extant Nothobranchius that are critically dependent on savannah habitats. Therefore, Nothobranchius diversification might have been shaped by the same paleoclimatic events that shaped African ungulate evolution.
00:58

A meeting dealing specifically with research on topics related to human mutation rates will be held at the Max Planck Institute for Evolutionary Anthropology from 25th - 27th February 2015. URL: http://bit.ly/1v6L5Ee This meeting aims at bringing together researchers from different fields that are interested in estimating the rate of mutations in humans and apes, the application of these rates to date events in the past, the differences in male and female mutation rates, the evolution of the mutation rate, the molecular and chemical mechanisms leading to germline and somatic mutations, and other topics related to the human mutation rate. The meeting is limited to a total of 90 participants and we would like all attendees to actively participate in the meeting by presenting results and joining discussions. Interested scientists are invited to submit an application including an abstract through our application website by 15th December 2014. Suitable abstracts will be selected on a first come, first serve basis and applicants will be informed as soon as possible whether they are accepted to attend the meeting. Registration for the meeting is free of charge and includes coffee breaks and small meals during the conference. Unfortunately, we are not able to support participants by funding travel or accommodation. The meeting will start on the evening of 25th February 2015 to allow guests to fly in on the first day of the meeting. Invited Speakers: * Kelley Harris * Agnar Helgason * Jean-Jacques Hublin * Michael Lynch * Kateryna Makova * Gilean McVean (tbc) * Molly Przeworski * David Reich * Aylwyn Scally * Mikkel Schierup * Michael Stratton * Shamil Sunyaev For further information, please visit our website or contact us by email: THMR2015@eva.mpg.de via Gmail

Source: EVOLDIR
00:42

The Rosenthal lab in the Department of Environmental and Plant Biology at Ohio University, in Athens, OH is looking for independent, motivated graduate students interested in pursuing PhD in Plant Evolutionary Ecophysiology. I am particularly interested in applicants with a strong foundation in evolutionary genetics or breeding and a demonstrated interest in plant physiological ecology. The student will be expected to develop a thesis or dissertation that seeks to elucidate physiological, genetic (genomic) mechanisms constraining plant ecophysiological performance and productivity. Please contact me via email rosentha@ohio.edu prior to submitting an application. Highly qualified applicants who have completed their degrees by December 2014 could begin as early as January of 2015. To be considered for January admission a complete application must be received before November 7th, 2014. Application instructions can be found here: http://bit.ly/1vpGtuj David M Rosenthal Assistant ProfessorDepartment of Environmental and Plant Biology 309 Porter Hall Ohio University Athens, OH, 45701 740 593 0792 http://bit.ly/17d8uVu davidrosenthal2@gmail.com via Gmail

Source: EVOLDIR
00:12

GRADUATE OPPORTUNITIES IN ECOLOGY AND EVOLUTIONARY BIOLOGY The Graduate Program in Ecology and Evolution in the Department of Ecology and Evolution at Stony Brook University is recruiting doctoral and master’s level graduate students for Fall 2012. The program trains students in Ecology, Evolution and Biometry. The following faculty are seeking graduate students this year: Stephen B. Baines - Aquatic Ecosystem Ecology http://bit.ly/1qZ3zk2 Michael A. Bell - Contemporary Evolution and Evolutionary Genetics http://bit.ly/15pztQp Liliana M. Dvalos - Vertebrate Phylogenetics, Biogeography and Conservation http://bit.ly/1qZ3zk7 Lev Ginzburg - Theoretical Ecology http://bit.ly/15pzwvr Catherine Graham - Tropical Vertebrate Biogeography and Ecology http://bit.ly/GPOPnC Jessica Gurevitch - Plant Population and Invasion Ecology http://bit.ly/15pzwLP Brenna Henn - Human Evolutionary Genomics http://bit.ly/1sErBY3 Jesse D. Hollister - Plant Evolutionary Genomics and Epigenetics http://bit.ly/1qZ3zAu Dianna K. Padilla - Invertebrate Aquatic Ecology and Conservation Biology http://bit.ly/GPORMk Joshua Rest - Evolutionary genomics http://bit.ly/15pzwvt Alistair Rogers - Plant Physiology and Climate Change www.bn.gov/TEST John True - Evolutionary Developmental Biology http://bit.ly/1sErCeq Kishna M. Veeramah - Primate Comparative Genomics http://bit.ly/1vGcJX0 For more information regarding the Graduate Program in Ecology and Evolution see http://bit.ly/GPOPnG and http://bit.ly/15pzwvv The deadline for receipt of all application materials for the PhD program is January 15, 2015 although earlier submission is encouraged to ensure full consideration for available fellowships. The deadline for receipt of all application materials for the master’s program is April 15, 2015. The Graduate School’s Center for Inclusive Education is offering application fee waivers if a studentwww.bn.gov/TEST John True - Evolutionary Developmental Biology http://bit.ly/1sErCeq Kishna M. Veeramah - Primate Comparative Genomics http://bit.ly/1vGcJX0 For more information regarding the Graduate Program in Ecology and Evolution see http://bit.ly/GPOPnG and http://bit.ly/15pzwvv The deadline for receipt of all application materials for the PhD program is January 15, 2015 although earlier submission is encouraged to ensure full consideration for available fellowships. The deadline for receipt of all application materials for the master’s program is April 15, 2015. The Graduate School’s Center for Inclusive Education is offering application fee waivers if a student has met with SBU representatives at a recruitment event and provided SBU with their contact information. For assistance, with this or other aspects of the application process, e-mail our Graduate Program Coordinator, Melissa Cohen melissa.j.cohen@stonybrook.edu. lmdavalos@gmail.com via Gmail

Source: EVOLDIR
00:12

next talk: David Rasmussen: Statistical inference for phylodynamics, 2014-10-16 09:00 PDT Phylodynamic methods are widely used to estimate demographic parameters and historical population dynamics from genealogies of individuals sampled from a population. In this phyloseminar, I will describe how we can understand genealogies in terms of basic demographic or ecological processes, and how these concepts can be used to develop statistical models for inference. In particular, I will discuss some similarities and differences between the two main modeling frameworks in phylodynamics: the coalescent and birth-death models. I will also briefly introduce some of the latest statistical methods currently used to fit these models to genealogies. I will end by discussing one of the main challenges facing the fiel via Gmail

Source: EVOLDIR

October 13, 2014

23:40

A PhD position is available in the lab of Adam Eyre-Walker at the University of Sussex to work on bacterial population genetics. The vast majority of organisms on this earth are prokaryotes and they are responsible for many of the biggest problems facing mankind, from diseases such as tuberculosis and typhoid, to hospital infections, such as those caused by methicilin resistant Staphylococcus aureus (MRSA). However, despite their prevalence and importance we still have a poor understanding of bacterial population genetics. We know the genome of many bacteria is highly labile so that any two strains of a bacterial “species” share only some genes; this has led to the concept of a core genome and an accessory genome. However, the evolutionary forces that act upon both genomes have not been extensively investigated. The aim of this project is to rectify this and to look at several aspects of bacterial population genetics in over 100 bacterial species for which multiple strains have been completely sequenced. The project will involve the bioinformatic analysis of publicly available data. Students with a str ong background in evolutionary biology, genetics and/or bioinformatics are particularly encouraged to apply. The position is available to UK and EU residents only. It is fully funded for 3.5 years; funding includes fees and a stipend equivalent to the standard UK research council rate (currently 13,863 per annum). The position involves 50 hours of teaching a year. Informal enquiries should be directed to Adam Eyre-Walker - a.c.eyre-walker@sussex.ac.uk. Further details about the group can be found at http://bit.ly/11hpRZ7. Applications must be made through the University of Sussex’s clunky graduate school application system http://bit.ly/1D8yd2Q. Apply for September 2015 entry. Mention the name of supervisor in “suggested supervisor” section. In funding mention sponsored or seeking funding. In Award details mention School of Life Sciences funded studentship. Include brief statement of interest (upto 2 pages), CV, two academic references, UG/PG transcripts, IELTS/TOEFL results if residing in EU. Only full time students will be accepted. Deadline for applications is 30/11/14 via Gmail

Source: EVOLDIR