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April 29, 2013
Global climate changes drive ecological specialization of mammal faunas: trends in rodent assemblages from the Iberian Plio-Pleistocene
Background: Several macroevolutionary hypotheses propose a synchrony between climatic changes and variations in the structure of faunal communities. Some of them focus on the importance of the species ecological specialization because of its effects on evolutionary processes and the resultant patterns. Particularly, Vrba’s turnover pulse hypothesis and resource-use hypothesis revolve around the importance of biome inhabitation. In order to test these hypotheses, we used the Biomic Specialization Index, which is based on the number of biomes occupied by each species, and evaluated the changes in the relative importance of generalist and specialist rodents in more than forty fossil sites from the Iberian Plio-Pleistocene. Results: Our results indicate that there was a decrease in the specialization degree of rodent faunas during the Pliocene due to the global cooling that triggered the onset of the glacial events of the Cenozoic (around 2.75 Ma). The subsequent faunal transition after this critical paleoenvironmental event was characterized by an increase of specialization related to the adaptation to the new environmental conditions, which was mainly associated with the Pleistocene radiation of Arvicolinae (voles). Conclusions: The pattern of faunal turnover is correlated with the development of the modern glaciations in the Northern Hemisphere around 2.75 Ma, and represents a reorganization of the rodent communities, as suggested by the turnover pulse hypothesis. Our data also support the resource-use hypothesis, which presumes the role of the degree of specialization in resources specifically related to particular biomes as a driver of differential speciation and extinction rates. These results stress the intimate connection between ecological and evolutionary changes.
Postdoctoral Position at Smith College: Interpreting the position and impact of microorganisms on the tree of life Smith College invites applications for a full-time postdoctoral research position focusing on reconstructing the tree of life, with emphasis on the placement of microbial lineages. The initial appointment is for one year, with the possibility of extending for additional years. The position will be housed in Professor Laura Katz's laboratory in the Department of Biological Sciences (http://www.science.smith.edu/departments/Biology/lkatz/Research.htm); questions should be directed to lkatz[at]smith.edu. An ideal candidate will: 1) be a productive researcher with interests in phylogenetics and phylogenomics of microorganisms; 2) have experience in bioinformatics, including managing and manipulating large data sets; 3) have excellent communication and interpersonal skills; and 4) be interested in collaborating with graduate and undergraduate students in the laboratory. The goals of the project are to synthesize data on the nature of the tree of life, with particular attention given to microorganisms. The Post-doc will participate in a large collaborative endeavor supported by the NSF AVATOL Program that is aimed at synthesizing a comprehensive tree of life from published analyses, and developing novel tools for community-driven annotation of the tree (http://opentreeoflife.org). Specific responsibilities will include: 1) assembling phylogenetic datasets from diverse microoganisms; 2) working collaboratively with other project members by contributing to method development for analyzing and integrating these datasets; and 3) outreach to the community of systematists studying microorganisms. To apply, submit application at https://secure.interfolio.com/apply/21574 with letter of application, C.V., a statement of research interests, representative publications, and the names and contact information of three references. Review of applications will begin May 15th, 2013. Smith College is a member of the Five College Consortium with Amherst, Hampshire, and Mount Holyoke Colleges and the University of Massachusetts Amherst. Smith College is an equal opportunity employer encouraging excellence through diversity. lkatz[at]smith.edu
POSTDOCTORAL RESEARCHER Washington State University School of Biological Sciences We are seeking a postdoctoral researcher to work on population and landscape genomics of Tasmanian devils and Tasmanian devil facial tumor disease. This international collaboration builds on over 15 years of research tracking the spread of this unique infectious tumor across Tasmania and consequent endangerment of the iconic Tasmanian devil. Reference genomes are available for both tumor and devil. The successful applicant will have an unprecedented opportunity to analyze thousands of devil genotypes and hundreds of tumor samples taken both before and after epizootics to test for selection throughout both genomes, coevolution, patterns of resistance, etc, across Tasmania. We will then use these data to predict the course of disease in uninfected populations. The position is centered in the lab of Dr. Andrew Storfer at Washington State University, in close collaboration with Dr. Paul Hohenlohe at the nearby University of Idaho (8 miles away). Both universities have genomics core facilities, including the Institute of Bioinformatics and Evolutionary Studies (IBEST; http://www.uidaho.edu/research/ibest) with up-to-date equipment, computational facilities and staff support. Review of applications will begin on May 15, 2013 and continue until the position is filled. A Ph.D. in Biology or a related discipline is required, and we particularly welcome applicants with experience in population genomics, infectious disease evolution, conservation, bioinformatics, and/or cancer genomics. Anticipated start date is August 16, 2013. Salary and benefits are competitive. Position is for 1-4 years, pending satisfactory progress. To apply, please send in pdf format a CV, and names, addresses and email addresses of 3 references, a research statement and up to 3 representative reprints via email to: Andrew Storfer ( astorfer[at]wsu.edu). *WSU is an Equal Opportunity/Affirmative Action/ADA educator and employer.* -- Andrew Storfer, PhD Eastlick Distinguished Professor Associate Director for Graduate Studies School of Biological Sciences Washington State University Pullman, WA 99164 USA Phone: (509) 335-7922 Fax: (509) 335-3184 astorfer[at]wsu.edu www.wsu.edu/~storfer andrew.storfer[at]gmail.com
April 28, 2013
Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.
In April last year I noted that there are not many images of phylogenetic networks on the internet, suitable for use when an icon or symbol is required, so I provided one (Network road sign). This year I thought that I might point out a far more arty image of "The Tree of Life" that ends up looking more like a network.
The original painting is by Reneé Womack, and prints are available from Fine Art America. You can also have versions with a green or a blue background, but I prefer this one, possibly because it reminds me of the cover of the "Tree Thinking" book by David Baum and Stacey Smith.
PhD Studentship Comparative analysis of grapevine genotypes with different levels of resistance to downy mildew The Research and Innovation Centre (CRI) is part of Fondazione Edmund Mach (FEM), a public research institution established by the government of the Autonomous Province of Trento. CRI-FEM is located in Trentino (the North of Italy) and supports studies in the field of agriculture, nutrition and environment, with the aim of sharing knowledge and contributing to economic growth, social development and overall improvement of life quality. Project description: Downy mildew (DM) is a widespread disease of grape caused by the oomycete Plasmopara viticola, an invasive species native to North America. This pathogen can infect grapevine cultivars as well as wild Vitis species. However, while the cultivars are highly susceptible, most of the wild species are relatively resistant. The disease is currently controlled by the application of fungicides, yet the demand for organic products is increasing and concerns that these chemicals have harmful effect on the environment and human health require growers to reduce the use of pesticides in fruit production. Natural sources of disease resistance could be found in geographic regions where populations of pathogens and host plants co-evolve. Thus, germplasm of several Vitis species native to temperate zones of North America has been investigated for the genetic base of DM resistance. It may be possible to transfer resistance to DM from these wild grape species into susceptible domesticated grapevines, but the consequences of so-called "linkage drag" of undesired traits could not be completely eliminated, even after several cycles of backcrossing. Recently, single local grapevine varieties of Near Eastern origin have attracted attention, because of their lower susceptibility to DM. These plants, unlike most of grapevine cultivars, have leaves and fruits without symptoms of disease during the growing season. Such natural sources of resistance to non-native pathogens stimulate genetic investigations and are of great significance for developing alternative resistance-breeding strategies. In this project, the PhD student will use different integrative approaches to characterize these important accessions of V. vinifera, as well as to identify and mine genes and alleles associated with plant resistance to DM. The long term objective of this PhD research is to ultimately enable effective transfer of natural resistance to the most severe disease affecting fruit quality into future plant material, and to reduce the need for using fungicides, which will make grapevine cultivation more environment-friendly. The successful candidate must have or expect to obtain a minimum of a Master's degree in a scientific discipline or equivalent qualification. Oral and writing skills in English are required to a high standard. The studentship offers a stipend of euro 20,000 per annum and is funded to pay tuition fees. The expected start date is September 2013 and the funding is provided for 3 years with the possibility of a one-year extension. The student will be based at FEM, San Michele all'Adige (Trentino), but will spend part of the time at the JKI - Federal Research Centre for Cultivated Plants (Siebeldingen, Germany) and at the University of Milan (Italy). Electronic applications can be submitted via the CRI-FEM website http://cri.fmach.eu/education/Applications-Forms/application-form-FIRS-T-Second-Call-2013 For further information about the project and selection procedure, please visit the website at http://cri.fmach.eu/education/selection/FIRS-T-Second-Call-2013 (select project A_1) and http://cri.fmach.eu/education/selection. Closing date for receipt of completed applications is Friday, 24 May 2013 at 18.00 CET. ls.grzeskowiak[at]gmail.com
April 27, 2013
Hi folks, We have five permanent academic positions available in my department at the National University of Ireland Maynooth. These are NOT tenure-track, they are permanent right from the start. Successful candidates will have their own laboratory space and will be expected to apply for grants and carry out research in addition to their teaching responsibilities. Applications from people with a background in evolution, genomics, bioinformatics are all encouraged and welcome. More details here: http://humanresources.nuim.ie/documents/JobSpec_Lecturer_Biology_SEBLB.pdf Please pass this email on to people you think might be interested. best, James. -- Prof. James McInerney, | Center for Communicable Disease Dynamics, Molecular Evolution & Bioinformatics Unit,| Harvard School of Public Health, Department of Biology, | 677 Huntington Avenue Boston, National University of Ireland Maynooth, | Massachusetts 02115 Co. Kildare, Ireland. | USA Lab site: http://bioinf.nuim.ie/james-mcinerney James McInerney
I am conducting a study of geographical variation in song characteristics and I am looking for volunteers to take a survey. Participants will rate the similarity of the songs of several species. If you are able to volunteer to take this survey, please e-mail me at nathanbwarbler[at]gmail.com, and I will send you an e-mail with the URL to the survey and more information. Thank you in advance, Nathan Burroughs Department of Ecology & Evolutionary Biology University of California, Los Angeles nathanbwarbler[at]gmail.com Nathan Burroughs
SISG Scholarship Application Deadline Extended to May 10. Some further registration-fee and travel scholarships are available for the 18th Summer Institute in Statistical Genetics in Seattle, July 8-26. Details at http://sisg.biostat.washington.edu Applications received by April 26 will be processed before May 10, others by May 17. New modules include Introduction to R and Scripting for Biologists, Omics Data and Network Analyses, Forensic Genetics, Mixed Models in Quantitative Genetics, Metagenomics, Epidemiology of Viruses. Previously popular modules include Bayesian Statistics for Genetics, Population and Quantitative Genetic Data Analysis, QTL and Association Mapping, Gene Expression, Coalescent and MCMC Theory, Human and Animal Genetic Data Analysis, Phylogenetics, Introductory Statistics, Introductory Genomics. Bruce Weir bsweir[at]uw.edu Bruce Weir
Dear Colleagues: Registration is open for the course "Disentangling evolutionary relationships with Phylogenetic Comparative Methods - Second edition"; October 7-11, 2013. INSTRUCTORS: Dr. Alejandro Gonzᬥz-Voyer (EBD, Spain) and Dr. Achaz von Hardenberg (Alpine Wildlife Research Centre, Italy) . SITE: Els Hostalets de Pierola, Barcelona, Spain. This course will provide an introduction to phylogenetic comparative methods (PCM) focusing on Phylogenetic Generalized Least Squares (PGLS) and introducing Phylogenetic Path Analysis methods. PCMs provide a means of incorporating information about the evolutionary relationships of organisms (phylogeny) in statistical analyses. To enhance the practical approach of the course, participants are encouraged to bring their own data to conduct analyses and discuss the results. More information: http://www.transmittingscience.org/courses/evol/pcm/ This course will be held in the facilities of the Centre de Restauraci Intepretacio Paleontologica (CRIP), and are co-organized by Transmitting Science, the CRIP and the Universidad Auta de Madrid. Places are limited and will be covered by strict registration order. Please feel free to distribute this information between your colleagues if you consider it appropriate. With best regards Soledad De Esteban-Trivigno soledad.esteban[at]transmittingscience.org Transmitting Science Soledad De Esteban Trivigno
Dear EVOLDIR Readers, We are looking for biologists or friends of biologists who have had 13- or 17-year cicadas on their property. We would like protected sites where we can dig nymphs once per year. We are especially interested in people who have 13-year Brood XIX (emerged in 2011), 17-year Brood XIV (emerged in 2008), and 13-year Brood XXII (will emerge in Louisiana in 2014). But other broods are also useful. We are also looking for high schools and university campuses that have periodical cicadas. We would like to find collaborator-teachers who would like to participate in following nymphal growth annually. Please contact chris.simon[at]uconn.edu Thanks! And enjoy Brood II along the east coast of the US this spring! And if you see then, report your sightings to Magicicada.org! Chris Chris Simon Professor, Ecology & Evolutionary Biology 75 North Eagleville Road, University of Connecticut Storrs, CT 06269-3043 chris.simon[at]uconn.edu Office (860) 486-4640; Lab (860) 486-3947; Fax (860) 486-6364, Office: Biopharm 305D, Lab: Biopharm 323,325 C. Simon Home page: http://hydrodictyon.eeb.uconn.edu/projects/cicada/simon_lab/member_pages/c_simon.php Simon Lab Home: http://hydrodictyon.eeb.uconn.edu/projects/cicada/simon_lab/lab_pages/current.php Reprints: http://hydrodictyon.eeb.uconn.edu/projects/cicada/resources/reprints.html Magicicada Brood II will appear along the east coast of the US in Spring 2013, watch Magicicada.org for information. chris.simon.uconn[at]gmail.com
A PhD position in the evolutionary ecology of host-parasite interactions is available for up to 4 years in Prof. Jacob Koella's lab at the University of Neuchⴥl. The position would suit an enthusiastic, motivated, and independent graduate whose degree has a strong component in parasitology, evolution or ecology. The general area of research will be the evolutlonary ecology of parasites at several levels of organization, linking the host's ecological situation with the parasite's dynamics within its host and its epidemiology, and using one of the host-parasite systems used in the lab (malaria, microsporidians and mosquitoes). The details of the project (including the balance between theoretical and empirical work) will be adapted to suit your interests, and you will be given the time to, and be expected to, have considerable input in developing the project. The position requires some teaching of undergraduate and graduate biology labs, usually in French, and you will have the opportunity to supervise undergraduate and Masters projects. An MSc (or equivalent) in Biology is required. The position is available as of August 1, 2013, with starting date preferably by October 1, 2013. The starting salary is about 35000 Fr. Neuchⴥl is located in the French part of Switzerland and is an attractive city with a high quality of life. The city is located on the shore of Lake Neuchⴥl with the Jura Mountains to the North and a view of the Bernese Alps to the South. For outdoors enthusiasts, this is an excellent area for outdoor activities such as hiking, climbing or skiing. If you are interested in the position, please send a 1-2 page cover letter indicating research interests and background, your CV, and two letters of reference to jkoella[at]gmail.com before May 18, 2013. Jacob Koella Institut de Biologie Universit頤e Neuchⴥl rue Emile-Argand 11 2000 Neuchⴥl Switzerland jkoella[at]gmail.com
April 26, 2013
Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host
Background: To understand the ecological and evolutionary consequences of species interactions in food webs necessitates that interactions are properly identified. Genetic analyses suggest that many supposedly generalist parasitoid species should rather be defined as multiple species with a more narrow diet, reducing the probability that such species may mediate indirect interactions such as apparent competition among hosts. Recent studies showed that the parasitoid Asecodes lucens mediate apparent competition between two hosts, Galerucella tenella and G. calmariensis, affecting both interaction strengths and evolutionary feedbacks. The same parasitoid was also recorded from other species in the genus Galerucella, suggesting that similar indirect effect may also occur for other species pairs. Methods: To explore the possibility of such interactions, we used mitochondrial and nuclear genetic markers to resolve the phylogeny of both host and parasitoid and to test the number of parasitoid species involved. We thus collected 139 Galerucella larvae from 8 host plant species and sequenced 31 adult beetle and 108 parasitoid individuals. Results: The analysis of the Galerucella data, that also included sequences from previous studies, verified the five species previously documented as reciprocally monophyletic, but the Bayesian species delimitation for A. lucens suggested 3--4 cryptic taxa with a more specialised host use than previously suggested. The gene data analyzed under the multispecies coalescent model allowed us to reconstruct the species tree phylogeny for both host and parasitoid and we found a fully congruent coevolutionary pattern suggesting that parasitoid speciation followed upon host speciation. Conclusion: Using multilocus sequence data in a Bayesian species delimitation analysis we propose that hymenoptera parasitoid of the genus Asecodes that infest Galerucella larvae constitute at least three species with narrow diet breath. The evolution of parasitoid Asecodes and host Galerucella show a fully congruent coevolutionary pattern. This finding strengthens the hypothesis that the parasitoid in host search uses cues of the host rather than more general cues of both host and plant.
The Barcode of Life
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology