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February 24, 2015

01:22
Field Assistants Required-Columbian ground squirrels Kananaskis, Alberta, Canada We are looking for 2 volunteers to assist with fieldwork for the period of April 10 to Aug 31, 2015. The project investigates the ecology of Columbian ground squirrels. As a member of the study, assistants will be involved with monitoring the phenology (when animals emerge from hibernation), reproduction and survival of individuals. Fieldwork will involve live-trapping and handling of animals, radio-telemetry, behavioural observation and assistance with the measurement of physiological (metabolism) traits on free-ranging animals. This is an excellent opportunity to gain experience working with a collaborative research team on a long-term study of a wild mammal. All fieldwork is carried out in the spectacular Rocky Mountains of southwestern Alberta, Canada, home to some of the most majestic wildlife in North America. We will be staying at the University of Calgarys R.B. Miller and Barrier Lake research stations in Kananaskis, Alberta (http://bit.ly/1gxdHxd). You will interact with other researchers working with ground squirrels on a diversity of projects in behavioural and population ecology. Additionally, the field stations are home to a number of other researchers working on a variety of projects, ranging from insects to large mammals. Food and accommodation are provided. Volunteers are required to provide for their own travel to either Calgary, Alberta or Saskatoon, Saskatchewan. Travel between the field station and Calgary or Saskatoon is provided. Training will be provided and specific experience is not necessary, but candidates should have an interest in a number of the following (the more the better!): ecology, evolutionary biology, wildlife, field biology, and animal behaviour. Periods of time will be spent camping and, as such, successful applicants need to enjoy the outdoors, be up-beat, positive, responsible and work well as a member of a team. If you wish to apply for one of these posts then please send a CV with a cover letter and contact details for three references (with e-mail addresses), by email to Jeff Lane (contact info below). Applications will be accepted until by Mar 9, 2015, but will be evaluated as they are received. To ensure full consideration for one of these positions, therefore, it is best to apply ASAP. Contact: Dr. Jeff Lane Department of Biology University of Saskatchewan u.columbianus@hotmail.com “Lane, Jeffrey” via Gmail
Source: EVOLDIR
00:32
Subject: PhD position in Experimental Biodemography at University of Zurich (March 23rd deadline) We are looking for an enthusiastic PhD student with quantitative skills to work in experimental biodemography at University of Zurich. Details of the position can be found at http://bit.ly/1D6iO0X Potential candidates can get in touch with me for more information. The application deadline is March 23rd. Arpat Ozgul Assistant Professor of Population Ecology Institute of Evolutionary Biology and Environmental Studies | University of Zurich Office: 34-J-24 | +41 (0)44 63 *54746* | arpat.ozgul@ieu.uzh.ch | www.popecol.org Arpat Ozgul via Gmail
Source: EVOLDIR
00:14
Reminder! Deadline closing soon! Job announcement In the Faculty 10 Biology, Zoological Institute, Department of Evolutionary Biology at the University of Mainz is looking for an Assistant Professor / Junior group leader (Akademischer Rat at a University / Bes.Gr. A 13 BBesG) Field: Evolutionary Genomics / Behavioral Genomics from April 15st 2015 on. The contract is initially for 3 years with the possibility of extension to up to a total of nine years depending on previous employment at German universities (12-year rule). In case the prerequisites of civil service law are not fulfilled, an engagement as a Scientific Assistant (EG 13 TV-L) is possible. More information on potential contract length and position can be given on an individual basis. We invite applications for an Assistant Professor (Akademischer Rat / A 13) position in the Department of Evolutionary (Prof. Dr. Susanne Foitzik) at the Institute of Zoology at Johannes Gutenberg University of Mainz, Germany. This young international research team focusses on the evolution, behavior, genetics, chemical ecology of social insects (http://bit.ly/1zbZVaE). Collaboration with other groups of in the department of Evolutionary Biology are desirable. Excellent research conditions are available at the newly renovated and well-equipped genetic and chemical laboratories in Mainz. Furthermore, new climate chambers are available for animal maintenance. A NextGen sequencing facility is available on campus. For further information, please contact foitzik@uni-mainz.de. We are seeking a highly motivated young researcher with a strong background in evolutionary genomics or behavioral genomics to establish a junior research group within Department of Evolutionary Biology. Candidates must hold a Ph.D. and postdoctoral experience is necessary. The successful candidate should address evolutionary or behavioral questions in social insects or other arthropods and should preferentially apply the newest genomic methods including the necessary bioinformatics (e.g. next-gen sequencing and transcriptomics). The successful candidate should have an excellent publication record. Experience with grant acquisition and teaching is advantageous. The candidate should set-up an independent, competitive research group and is encouraged to apply for grants in Germany or the EU (e.g., DFG, ERC). The position comes with a teaching requirement of 4 h per week during the semester in the Master and Bachelor programme. Some basic zoology classes are preferably taught in German. Consequently, a willingness to learn German is required. The candidate has the option to acquire a “Habilitation”. The working language of the lab is English. Requirements of appointment: - University degree and a PhD in biology (or related field) - a full-time employment of at least two years and six month after Master or PhD The Johannes Gutenberg-University Mainz is interested in increasing the number of women in science. Applications from female scientists are strongly encouraged. Similarly, qualified candidates with disabilities will be preferred. The University of Mainz hosts many excellent scientific institutions (http://bit.ly/1B7xxvZ) and Mainz is a historic city located on the Rhine River with many students and a rich social and cultural life (http://bit.ly/1B7xz7c). Interested candidates should send an application (as a single e-mail pdf attachment) containing a CV, a list of publications (including reprints of the three most important publications), research and teaching statements, and contact information for two potential referees to: Prof. Dr. Susanne Foitzik Evolutionary Biology Institute of Zoology Johannes-v.- Mller-Weg 6 55099 Mainz Germany foitzik@uni-mainz.de Closing date for the application is February 28th, 2015 Starting date for the position is negotiable, earliest possible date is April 15st 2015 Prof. Dr. Susanne Foitzik Evolutionsbiologie Institut fr Zoologie Johannes Gutenberg Universitt Mainz Johannes von Mller Weg 6 55099 Mainz Tel: +49 (0) 6131 39 27 840 Fax: +49 (0)6131 39 27 850 Email: foitzik@uni-mainz.de “Foitzik, Susanne” via Gmail
Source: EVOLDIR

February 23, 2015

00:35

Registration for the inaugural meeting of the Pan American Society for Evolutionary Developmental Biology is open! Mark your calendars for the meeting dates, 5-9 August, 2015, and be sure to register before all 350 slots are filled! The registration deadline is April 1, 2015. To register, go to http://bit.ly/1D23EcV. Join us in Berkeley, California for the first EvoDevo meeting in the Americas sponsored by a new professional society dedicated to supporting the EvoDevo field! A few meeting highlights: - Confirmed speakers: Chris Amemiya, Alexa Bely, Sean Carroll, Rachel Collin, Kim Cooper, Tamara Franz-Odendaal, Matt Gibson, Angela Hay, Vivian Irish, Catherine Linnen, Mark Martindale, Jose Xavier Neto, Natalia Pabn-Mora (Early Career Award Recipient), Richard Palmer, Rudy Raff (Pioneers Award recipient), Bob Reed, Matt Rockman, Neelima Sinha, Stacey D. Smith, Ralf Sommer, Mansi Srivastava, James Umen - Additional speakers will be selected from submitted abstracts - Posters will be on display throughout the entire meeting - Poster prizes for PhD students and postdocs All details about registration, accommodation options, child care services, and the conference program are available at the following website: http://bit.ly/1D23EcV Support the Society and Become a Member!! To learn more about PASEDB, visit the following website: http://bit.ly/1ElPbx4 The Organizing Committee and the PanAm SEDB Executive Council look forward to welcoming you to Berkeley in August! Chelsea D. Specht, PhD Associate Professor; Departments of Plant and Microbial Biology & Integrative Biology Curator of Monocots; University and Jepson Herbaria University of California, Berkeley 111 Koshland Hall, MC 3102 Berkeley, CA 94720 510.642.5601 cdspecht@berkeley.edu http://bit.ly/16diOlZ cdspecht@berkeley.edu via Gmail

Source: EVOLDIR
00:18

—f46d043be12a5c3e64050faea8b4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable FIELD ASSISTANTS for monitoring SAPROXYLIC PROTECTED BEETLES in the LIFE-MIPP Project. Website: www.lifemipp.eu. Reference Institutions: CFS, National Forest Service (project coordinator); CRA ” ABP, Council for Agricultural Research and Economics ” Research Center for Agrobiology and Pedology . The field assistants will help in fieldwork for the monitoring of 5 species of saproxylic beetles (*Cerambyx cerdo*, *Rosalia alpina*, *Morimus asper/funereus*, *Osmoderma eremita* and *Lucanus cervus*) in five protected areas in Central and Northern Italy (Appennines and Alps). The sampling seasons will be from May to August 2015 (field assistants are expected to join the project for at least 2 weeks). The aim of the research is to develop standard monitoring protocols for the saproxylic beetles listed in the Habitats Directive, as required by the European Community. The field assistants will work with a team consisting of master students, PhD, post-docs and researchers. The work will consist in not-invasive methods as the count of animals in transects, capture/mark/recapture, photographic identification, interception traps, collection of remains. Moreover, the project also benefits from an innovative technique by the use of a sniffer dog. Duties will include insects handling (marking, measuring), data entry and data management. The fieldwork will be demanding and will be organized in 4-5 day sessions. Qualifications/Experience Candidates must have experience with fieldwork in general and interest in insect. Field work hours will be long and tiring and applicants should be prepared to work at any time including weekends and holidays. No financial compensation will be provided but accommodation and meals will be covered by the project. Candidates should have at least a BSc in Biology or in Natural Science or a related field. Ideal candidates are highly motivated, well organized and able to work independently, while at the same time able to work in a group. Applications Review of the applications will begin Mid-February and continue until the positions are available. To apply, please send (1) a statement of relevant experience and motivation, (2) a very short resume or CV to both Dr. Alessandro Campanaro (ale.naro@gmail.com) and Dr. Fabio Mosconi (fabio.mosconi@gmail.com). Best regards, Alessandro Campanaro and Fabio Mosconi —f46d043be12a5c3e64050faea8b4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

FIELD ASSISTANTS for monitoring SAPROXYLIC PROTECTED BEETLES in the LIFE-MIPP Project. Website: www.lifemipp.eu. Reference Institutions: CFS, National Forest Service (project coordinator); CRA ” ABP, Council for Agricultural Research and Economics ” Research Center for Agrobiology and Pedology . The field assistants will help in fieldwork for the monitoring of 5 species of saproxylic beetles (Cerambyx cerdo, Rosalia alpina, Morimus asper/funereus, Osmoderma eremita and Lucanus cervus) in five protected areas in Central and Northern Italy (Appennines  and Alps). The sampling seasons will be from May to August 2015 (field assistants are expected to join the project for at least 2 weeks). The aim of the research is to develop standard monitoring protocols for the saproxylic beetles listed in the Habitats Directive, as required by the European Community. The field assistants will work with a team consisting of master students, PhD, post-docs and researchers. The work will consist in not-invasive methods as the count of animals in transects, capture/mark/recapture, photographic identification, interception traps, collection of remains. Moreover, the project also benefits from an innovative technique by the use of a sniffer dog. Duties will include insects handling  (marking, measuring), data entry and data management. The fieldwork will be demanding and will be organized in 4-5 day sessions. Qualifications/Experience Candidates must have experience with fieldwork in general and interest in insect. Field work hours will be long and tiring and applicants should be prepared to work at any time including weekends and holidays.No financial compensation will be provided but accommodation and meals will be covered by the project.C andidates should have at least a BSc in Biology or in Natural Science or a related field. Ideal candidates are highly motivated, well organized and able to work independently, while at the same time able to work in a group. Applications Review of the applications will begin Mid-February and continue until the positions are available. To apply, please send (1) a statement of relevant experience and motivation, (2) a very short resume or CV to both Dr. Alessandro Campanaro (ale.naro@gmail.com) and Dr. Fabio Mosconi (fabio.mosconi@gmail.com). Best regards, Alessandro Campanaro and Fabio Mosconi —f46d043be12a5c3e64050faea8b via Gmail
Source: EVOLDIR

February 22, 2015

23:46

POSTDOCTORAL RESEARCH FELLOW STREPTOCOCCUS PNEUMONIAE ANTIGENIC VARIATION LIPSITCH LABORATORY DEPARTMENTS OF EPIDEMIOLOGY AND IMMUNOLOGY & INFECTIOUS DISEASES HARVARD T.H. CHAN SCHOOL OF PUBLIC HEALTH POSTED 22 FEBRUARY 2015 A postdoctoral research fellowship is available for work in the Lipsitch Laboratory at Harvard T.H. Chan School of Public Health to study phenotypic and antigenic effects of sequence variation in surface proteins of Streptococcus pneumoniae. Genomic analysis has indicated extensive sequence variation and hotspots of recombination in surface proteins of S. pneumoniae (1, 2). Two lines of evidence suggest that these phenomena result from selection for escape from host immune responses: concentration of nonsynonymous changes within identified antibody targets and, among these, within epitope regions (3); age-specific variation in gene content, such that nonessential surface proteins (or common alleles of conserved surface proteins) are more common among isolages from younger (presumably immunologically nave) carriers of S. pneumoniae (2, 4). Such results would be expected if these genes or their common alleles are net-beneficial in younger/more nave hosts but are subject to immune responses that select against their presence in more immunologically experienced persons. However, there is little direct, mechanistic evidence for hypothesis that losing or diversifying these antigens produces an immune escape benefit for the bacteria. As part of an interdisciplinary R01-funded project involving (a) mathematical transmission modeling, (b) population genomics, (c) analysis of human sera from a pneumococcal carriage study for comparison with the sequences of subsequently carried pneumococci, and (d) mechanistic studies in the laboratory of the specificity of anti-protein immunity in pneumococci, we are seeking a postdoctoral fellow to design and carry out assays to measure the impact of allele-specific immunity against particular surface proteins on bacterial fitness, as well as assays of allele-specific variation in the function of these proteins. The aim is to test the hypothesis that varying or losing these proteins is beneficial in the presence of specific antibodies. Studies will include characterization of allele-specific antibody binding specificity and function (eg opsonization, adhesion-blocking). They will also include functional assays of the allelic variants of the surface proteins in the presence and absence of antibody. The postdoctoral fellow will be part of a larger multidisciplinary research team within the Center for Communicable Disease Dynamics (which Dr. Lipsitch directs), including researchers in population genomics and transmission dynamics of multiple infectious diseases. For more information about the group see http://bit.ly/1BaZt3F . Opportunities for projects in some of these areas may be available depending on interests. Applicants should have a doctorate and publication record in experimental microbiology, immunology, molecular biology and/or biochemistry and an interest in evolutionary problems. Interested candidates should send a letter of inquiry and CV with 2+ references to Marc Lipsitch, mlipsitc@hsph.harvard.edu. REFERENCES 1. Croucher NJ, Harris SR, Fraser C, Quail MA, Burton J, van der Linden M, McGee L, von Gottberg A, Song JH, Ko KS, Pichon B, Baker S, Parry CM, Lambertsen LM, Shahinas D, Pillai DR, Mitchell TJ, Dougan G, Tomasz A, Klugman KP, Parkhill J, Hanage WP, Bentley SD. 2011. Rapid pneumococcal evolution in response to clinical interventions. Science 331:430-434. http://1.usa.gov/1w0SgM3 2. Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM, Parkhill J, Bentley SD, Hanage WP, Lipsitch M. 2013. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet 45:656-663. http://1.usa.gov/1BaZt3I 3. Li Y, Gierahn T, Thompson CM, Trzcinski K, Ford CB, Croucher N, Gouveia P, Flechtner JB, Malley R, Lipsitch M. 2012. Distinct effects on diversifying selection by two mechanisms of immunity against Streptococcus pneumoniae. PLoS Pathog 8:e1002989. http://bit.ly/1w0Sh2l 4. Regev-Yochay G, Hanage WP, Trzcinski K, Rifas-Shiman SL, Lee G, Bessolo A, Huang SS, Pelton SI, McAdam AJ, Finkelstein JA, Lipsitch M, Malley R. 2010. Re-emergence of the type 1 pilus among Streptococcus pneumoniae isolates in Massachusetts, USA. Vaccine 28:4842-4846. http://1.usa.gov/1BaZuVg via Gmail

Source: EVOLDIR
22:00
It is easily demonstrable that organisms with rapid, appropriate plastic responses to environmental change will prevail over genotypes with fixed phenotypes. It is also accepted that the general dearth of organisms successful across a wide environmental range indicates fundamental limits to or costs of plasticity. The nature of constraining factors has been broadly discussed (DeWitt et al. 1998), and numerous studies have been done to quantify them. However, a curious pattern has emerged: although hypothesized to be widespread, costs are absent more often than they are detected. The issue of costs of plasticity (CoP) lies at the intersection of a range of evolutionary and ecological questions: What are the limits to plasticity? Are CoP associated with life history tradeoffs? Are CoP expected in all environments? Does plasticity enhance invasiveness? etc. This working group will address two fundamental questions. 1) Are the expectations that costs of plasticity should be universal well-founded (i.e., the “no free lunch” principle)? Several authors have proposed that, in situations where the intensity of selection for adaptive plasticity is strong, there should be corresponding pressure to ameliorate costs. 2) Independently of the answer to the first question, Are analytical and experimental methods for detecting CoP appropriate or sufficiently sensitive? CoP have most often been studied using common garden style plasticity experiments and analyzed via van Tienderen’s (1991) multiple regression approach.
Source: NESCent
16:30

As a means of motivating his interest in speciation, in The Origin of Species Charles Darwin highlighted the diversity of morphological forms among the finches of the Galápagos Islands, in the south-eastern Pacific Ocean, which he visited while circumnavigating the world in The Beagle. He considered this to be a prime example of biodiversity related to adaptation and natural selection, what we would now call an adaptive radiation.

Recently, the following paper, which provides a genomic-scale study of these birds, has attracted considerable attention:
Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L (205) Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature 58: 371-375.The authors note:
Darwin's finches are a classic example of a young adaptive radiation. They have diversified in beak sizes and shapes, feeding habits and diets in adapting to different food resources. The radiation is entirely intact, unlike most other radiations, none of the species having become extinct as a result of human activities.Here we report results from whole genome re-sequencing of 120 individuals representing all Darwin's finch species and two closely related tanagers. For some species we collected samples from multiple islands. We comprehensively analyse patterns of intra- and inter-specific genome diversity and phylogenetic relationships among species. We find widespread evidence of inter-specific gene flow that may have enhanced evolutionary diversification throughout phylogeny, and report the discovery of a locus with a major effect on beak shape.Sadly, the authors try to study the intra- and inter-specific variation principally using phylogenetic trees. They do this in spite of noting that:
Extensive sharing of genetic variation among populations was evident, particularly among ground and tree finches, with almost no fixed differences between species in each group.Clearly, this situation requires a phylogenetic network for adequate study, as a network can always display at least as much phylogenetic information as a tree, and usually considerably more. The authors do recognize this:
A network constructed from autosomal genome sequences indicates conflicting signals in the internal branches of ground and tree finches that may reflect incomplete lineage sorting and/or gene flow ... We used PLINK to calculate genetic distance (on the basis of proportion of alleles identical by state) for all pairs of individuals separately for autosomes and the Z chromosome. We used the neighbour-net method of SplitsTree4 to compute the phylogenetic network from genetic distances.However, this network is tucked away as Fig. 3 in the appendices. It is shown here in the first figure. The authors attribute the gene flow to introgression, but occasionally refer to hybridization and convergent evolution. Indeed, they suggest both relatively recent hybridization as well as the possibility of more ancient hybridization between warbler finches and other finches.


Clearly, this network is not particularly tree-like in places, especially with respect to the delimitation of species based on their morphology, as reflected in their current taxonomy. Nevertheless, the authors prefer to present as their main result as a:
maximum-likelihood phylogenetic tree based on autosomal genome sequences ... We used FastTree to infer approximately maximum-likelihood phylogenies with standard parameters for nucleotide alignments of variable positions in the data set. FastTree computes local support values with the Shimodaira–Hasegawa test.This tree is shown in the second figure.


This apparently well-supported tree is not a particularly accurate representation of the pattern shown by the network. Indeed, it makes clear just why it is inadequate to use a tree to study the interplay of intra- and inter-specific variation. Gene flow requires a network for accurate representation, not a tree.

The authors do acknowledge this situation. While they try to date the nodes on their tree, they do note that:
Although these estimates are based on whole-genome data, they should be considered minimum times, as they do not take into account gene flow.Actually, in the face of gene flow the concept that a node has a specific date is illogical, because the nodes do not represent discrete events (see Representing macro- and micro-evolution in a network). Given the authors' final conclusion, it seems quite inappropriate to rely on trees rather than networks:
Evidence of introgressive hybridization, which has been documented as a contemporary process, is found throughout the radiation. Hybridization has given rise to species of mixed ancestry, in the past and the present. It has influenced the evolution of a key phenotypic trait: beak shape ... The degree of continuity between historical and contemporary evolution is unexpected because introgressive hybridization plays no part in traditional accounts of adaptive radiations of animals.
00:53

Hello evoldir community, don’t miss the early bird deadline - register by the end of the month to save up to 30% on the registration fee for SMBE 2015, held in one of the most beautiful cities at the spectacular Imperial Palace (Hofburg) in the heart of Vienna! A few meeting highlights: - All posters will be on display throughout the entire meeting. - At least four poster sessions - 27 symposia on cutting edge topics suggested by SMBE members and one Open Symposium for which 5 featured speakers will be selected though the Local Organising Committee (LOC). - Plenary speakers: Doris Bachtrog (UC Berkeley), Joe Felsenstein (Univ. of Washington), Johanna Schmitt (UC Davis) and Diethard Tautz (MPI for Evolutionary Biology). - Heavily subsidized child care - many awards (http://bit.ly/1yG2HVK): via Gmail

Source: EVOLDIR
00:21
Dear Colleague, This email is to remind you that the upcoming deadline for UNDERGRADUATE SUMMER INTERNSHIP funding from the Evo-Devo-Eco Network (EDEN) is March 11, 2015. EDEN is a program funded by the National Science Foundation of the USA. The goal of this program is to train undergraduates in the field of Evo-Devo-Eco, with an emphasis on emerging model systems. Eligible students should be undergraduates of any nationality at any college or university, including liberal arts colleges, community colleges, and universities, both within and outside of the U.S.. Eligible host labs should be conducting research using new and emerging model organism and must be at a U.S.-based institution. If the proposed host lab is working on a well-established model organism, your application must explain how the techniques or skills that you learn in the host lab will be applied to work on new or emerging model organisms at your home institution. Students may apply to work in a lab that is at their home institution, as long as the proposed research involves new and emerging model organisms. However, in cases where all other aspects of applications are considered to be equally competitive, preference will be given to applicants who propose to travel to a lab that is not at their home institution. Please visit http://bit.ly/1mvebe6 for complete program details. For examples of previous undergraduate projects supported by EDEN, please visit http://bit.ly/1eVAeAz. Please note that the updated eligibility for EDEN funding is as follows: Students based anywhere in the world can apply for funding to visit labs in the US. Students based in the US are eligible for funding to visit labs anywhere in the world. Please feel free to email edenrcn@fas.harvard.edu with questions about the program, and forward this email to colleagues who you think would be interested in EDEN. Best wishes, Cassandra Extavour “Perlo, Barbara” via Gmail
Source: EVOLDIR
00:06

*** Postdoc in Phylogenetics & Biodiversity, Cambridge *** The Ecosystems and Global Change Group in the Department of Plant Sciences at the University of Cambridge (http://bit.ly/1CXHwk2) is seeking a full-time Research Associate with interests in plant and animal diversification, biogeography, and computational phylogenetics. Based in central Cambridge, the postholder will join an existing project focused on mapping the evolutionary potential of the world’s biodiversity. They will be responsible for generating time-calibrated phylogenetic trees and using them to estimate evolutionary rates. Applicants should have a PhD in evolutionary biology, ecology, or a closely related field, and strong skills in phylogenetic and macro-evolutionary modelling. A track record of publication in leading peer-reviewed journals is essential. Laboratory experience with DNA sequencing is desirable, as is experience with tools such as DPPDiv, BEAST, and MrBayes. Interest in conservation science is helpful. Fixed-term: The funds for this post are available for 22 months in the first instance. To apply online for this vacancy, please click on the ‘Apply’ button at http://bit.ly/19VnGyN. This will route you to the University’s Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form. Applicants should provide a CV, the filename of which should be “CV-followed by your name”, including contact details of two academic referees, and a covering letter addressing the selection criteria. For further information see http://bit.ly/19VnGyN Please quote reference PD05272 on your application and in any correspondence about this vacancy. The University values diversity and is committed to equality of opportunity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK. via Gmail

Source: EVOLDIR

February 21, 2015

23:50

Graduate position: Developmental plasticity and evolution of the germline in Caenorhabditis nematodes (CNRS, Nice, France) A PhD fellowship is available in the Braendle lab at the Institute of Biology Valrose in Nice. The candidate will be involved in one of our on-going research projects aiming to integrate mechanistic and evolutionary understanding of how gene-environment interactions shape development and evolutionary processes. We address this problem using the nematode Caenorhabditis elegans, focusing on molecularly well-characterized systems, such as the development of the hermaphrodite germline. These analyses combine developmental and quantitative genetic approaches and are further complemented by experimental evolution assays and ecological studies. A current key research focus is the mapping of natural genetic variation in C. elegans developmental plasticity. Applicants are expected to be highly motivated and participate in the planning of the project. Candidates with a background in quantitative genetics, bioinformatics, or C. elegans biology are particularly encouraged to apply. This 3-year position is open to all nationalities and will start in October 2015. Our team belongs to the Institute of Biology Valrose (IBV), an international research institute hosting over 20 research groups working on diverse topics in development, genetics and cell biology. The institute, located in the city centre, has excellent research facilities and provides an interactive, stimulating scientific environment. To apply, send a summary of your research motivation and interests, CV, names and contact information for three references to Christian Braendle (braendle@unice.fr) in a single PDF file. Application deadline: March 20, 2015. For more information, please visit: http://bit.ly/1EE8uQ7 http://ibv.unice.fr Christian Braendle Institute of Biology Valrose CNRS UMR7277 - INSERM U1091 Universite Nice Sophia Antipolis Parc Valrose 06108 NICE cedex 2 France Tel +33 (0) 4 92 07 68 97 Fax +33 (0) 4 92 07 68 34 braendle@unice.fr http://bit.ly/1EE8uQ7 http://ibv.unice.fr via Gmail

Source: EVOLDIR
17:00
Background: Thelytoky, the parthenogenetic development of females, has independently evolved in several insect orders yet the study of its mechanisms has so far mostly focussed on haplodiploid Hymenoptera, while alternative mechanisms of thelytoky such as polyploidy are far less understood. In haplodiploid insects, thelytoky can be encoded in their genomes, or induced by maternally inherited bacteria such as Wolbachia or Cardinium. Microbially facilitated thelytoky usually results in complete homozygosity due to gamete duplication and can be reverted into arrhenotoky, the parthenogenetic development of males, through treatment with antibiotics. In contrast, genetically encoded thelytoky cannot be removed and may result in conservation of heterozygosity due to gamete fusion. We have probed the obligate thelytoky of the greenhouse thrips, Heliothrips haemorrhoidalis (Bouché), a significant cosmopolitan pest and a model species of thelytoky in the haplodiploid insect order Thysanoptera. Earlier studies suggested terminal fusion as a mechanism for thelytoky in this species, while another study reported presence of Wolbachia; later it was speculated that Wolbachia plays a role in this thrips’ thelytokous reproduction. Results: By using PCR and sequence analysis, we demonstrated that global population samples of H. haemorrhoidalis were not infected with Wolbachia, Cardinium or any other known bacterial reproductive manipulators. Antibiotic treatment of this thrips did also not result in male production. Some individuals carried two different alleles in two nuclear loci, histone 3 and elongation factor 1 alpha, suggesting heterozygosity. However, the majority of individuals had three different alleles suggesting that they were polyploid. Genetic diversity across both nuclear loci was low in all populations, and absent from mitochondrial cytochrome oxidase I, indicating that this species had experienced genetic bottlenecks, perhaps due to its invasion biology or a switch to thelytoky. Conclusions: Geographically broad sampling and experimental manipulation revealed low genetic diversity, absence of Wolbachia but presence of three different alleles of nuclear loci in most analysed individuals of obligately thelytokous H. haemorrhoidalis. This suggests that polyploidy may be involved in the thelytokous reproduction of this thrips species, and polyploidy may be a contributing factor in the reproduction of Thysanoptera and other haplodiploid insect orders.
01:01

Applicants Now Being Accepted – See Link Below! Ecological and Evolutionary Genomics Gordon Research Conference July 12-17 2015 at University of New England, Biddeford, ME  >From Genomes to Biomes:  Using Biodiversity to Explore Biocomplexity. >From genomes to biomes, from microbes to plants and animals, the 2015 Gordon Research Conference on Ecological and Evolutionary Genomics will highlight how genome-enabled approaches are helping to rapidly advance our understanding of the complicated relationship between genotype, phenotype and the environment. Topic areas such as population genomics, adaptation & speciation, symbiosis and interacting organisms, biodiversity & phylogenomics, community & ecosystem genomics, genetic and ecological networks, methods & non-model organisms, genomics & animal behavior, and applications of ecological and evolutionary genomics, will highlight how biodiversity can be used to illuminate complex biological relationships and inform ecological and evolutionary processes and molecular mechanisms of adaptation to changing environments. The conference will also feature emerging approaches and technologies to aid further exploration of the genomes from organisms that span the tree of life. Gordon Conferences are famous for fostering in depth interactions that yield new insights in a collegial atmosphere. Co-chairs, Jack Werren (University of Rochester) and Michael Herman (Kansas State University) along with Vice-chairs Felicity Jones (Max Plank Institute, Tubingen) and Michael Pfrender (University of Notre Dame) invite you to join us on the ocean-side campus of the University of New England in Biddeford, Maine for a stimulating conference. We are assembling a diverse group of established and early career investigators to discuss their latest work. Discussion leaders and symposium speakers for “Young Investigators: Advances in Eco and Evo Genomics” session will be chosen from among the registrants. The organizers are actively seeking funds to assist students and others attend the meeting. Applications for attendance will be accepted until the meeting is full, so don’t delay! Applications to attend are now open and information can be found at http://bit.ly/1zvxau2 Symposim Topic Areas & Speakers - Advances in Computational and Genomic Approaches to Non-Model Organisms (Steven Salzberg, Wes Warren, Beth Shapiro) - Applications of Ecological and Evolutionary Genomics (John Colbourne, Sherry Flint-Garcia, Joseph Shaw) - Behavioral Ecology Meets Genomics (Laurent Keller, Amy Toth, Todd Schlenke) - Biodiversity and Phylogenomics (Holly Bik, Casey Dunn, Davide Pisani) - Community and Ecosystem Genomics (Jack Gilbert, Blake Matthews, Jenn Schweitzer) - Networks: From Genes to Ecosystems (Karoline Faust, Cedric Feschotte, Alvaro Sanchez, Patricia Wittkopp) -  Population Genomics, Adaptation and Speciation (Andrew Clark, Asher Cutter, Elodie Ghedin, Josephine Pemberton) -  Symbiosis and Interacting Organisms (Siv G. Andersson, Angela Douglas, Takema Fukatsu, Wayne Potts) - Young Investigator Presentations: Advances in Ecological and Evolutionary Genomics (TBA, from submitted abstracts) Please plan on joining us in Biddeford in 2015! Michael Herman Professor Division of Biology Kansas State University 266 Chalmers Hall Manhattan, KS  66506 Office: (785) 532-6741 Lab: (785) 532-6773 FAX (785) 532-6653 Email : mherman@ksu.edu http://bit.ly/16yKKRM mherman@ksu.edu via Gmail

Source: EVOLDIR
01:01
Dear Colleagues, I am happy to announce an opportunity for training in sponge biodiversity. Please distribute this announcement to individuals that you think will benefit from this course. Thanks, Bob thacker@uab.edu Sponge Biodiversity in a Changing Ocean: Species, Ecosystems, Processes August 9-16, 2015 Mote Marine Laboratory, Summerland Key, Florida A 7-day intensive course consisting of lectures, fieldwork, and laboratory experiments will be offered at Mote Marine Laboratory, Tropical Research Lab, Summerland Key, Florida, from August 9 to 16, 2015. The course is organized by Cristina Diaz, Shirley Pomponi, and Bob Thacker; other instructors include Janie Wulff, Thierry Perez, John Stevely, and Charles Bigger. The course is open to graduate students, researchers, and resource managers who have a primary interest in the role of sponges as key components of tropical ecosystems in a changing ocean. Sponges constitute an essential component of coral reefs, mangroves, and seagrass beds. Their high diversity and biomass in most benthic marine ecosystems and their unique physiology makes them important targets to understand, manage, and protect those ecosystems. Through this course, students will learn how to identify and describe common sponge species from Florida Keys seagrass, mangrove, and coral reef ecosystems. They will also gain experience using sponges as models to address questions related to biodiversity, biotechnology, and climate change. Apply by mailing a letter of intent, your CV, and a letter of recommendation (sent separately) to taxochica@gmail.com. Your letter should state why it is important for you to participate in this course, and how your work, education, and/or research will benefit from it. The deadline for applications is March 31, 2015. Applicants will be notified of acceptance by April 30, 2015. Space is limited to 12-14 students. Tuition is $1000 and includes accommodation, breakfast/lunch, field trips (scuba and snorkeling), and laboratory fees. Tuition assistance may be available. Participants planning to scuba dive must meet the certification and training requirements of Mote Marine Laboratory: http://bit.ly/1zuyKZC Application instructions are available at: http://bit.ly/1zuyKZE Information that must be included in the application: Name Address Phone number Email CV (should include education, research and field experience) One letter of recommendation Brief description of why you want to take the course and how you intend to use what youve learned Dive experience: - Are you a scuba diver? - Do you intend to scuba dive? Participants planning to scuba dive must meet the certification and training requirements of Mote Marine Laboratory: http://bit.ly/1zuyKZC - Current diving certification - Indicate if you are currently certified to dive under the auspices of an AAUS-affiliated institution. Bob Thacker via Gmail
Source: EVOLDIR
01:01
*Postdoctoral research fellowship* Stouffer Lab, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand We invite applications for a postdoctoral research fellowship to study the structure, dynamics, and evolution of ecological networks in the Stouffer Lab (School of Biological Sciences, University of Canterbury, New Zealand). Requirements: The ideal candidate has a strong quantitative background, demonstrated research excellence, and a PhD in ecology, engineering, applied mathematics, physics, computer science, or related fields. Programming experience in both a compiled language (C or C++ preferred) and one or more scripting languages (such as Python or R) is highly desirable. Position details: The position is part of a Fast-Start grant from the Marsden Fund Council, administered by the Royal Society of New Zealand. The salary will be in the range of NZ$55,000-65,000 per year (depending on experience), and the starting date is negotiable. The initial appointment will be made for 1.5 years, with renewal dependent on progress, mutual agreement, and funding availability. How to apply: Applicants should submit (1) a cover letter describing their research interests and background, (2) a detailed CV (including publications), and (3) the contact details of three references to daniel.stouffer@canterbury.ac.nz. The cover letter should also include possible starting dates. Review of applications will start immediately and will continue until the position has been filled. Dr. Daniel B. Stouffer Senior Lecturer School of Biological Sciences University of Canterbury Christchurch, New Zealand http://bit.ly/1qe6N6E @StoufferLab daniel.stouffer@canterbury.ac.nz via Gmail
Source: EVOLDIR
00:44
Registration is now open and abstracts are currently being accepted for: Next Generation Pteridology: An International Conference on Lycophyte & Fern Research 1-5 June 2015 in Washington D.C. National Museum of Natural History & United States Botanic Garden http://bit.ly/1u2HO9P The past decade has seen remarkable advances in our understanding of fern and lycophyte biology. New sources of data have emerged and novel methods for analyzing these data are being developed. At the same time, many traditional approaches have been revitalized as their unique and specific contributions are more fully realized. With a recent influx of students and early career researchers, the international pteridological community continues to grow. Through more widespread and far-reaching collaborations, the pace of scientific discovery is accelerating, new parts of the globe are being included, and the conservation of these important species in a rapidly changing world is being investigated. This conference aims to bring together the world’s pteridologists to celebrate the progress to date and to forecast developments still on the horizon. The early registration and abstract submission deadline is 1 April 2015. If you have questions, or would like to be added to the distribution list for conference-related announcements, please email sbs@si.edu Eric Schuettpelz Research Botanist National Museum of Natural History Smithsonian Institution Department of Botany MRC 166 PO Box 37012 Washington DC 20013-7012 Telephone 202.633.0914 Fax 202.786.2563 E-mail schuettpelze@si.edu “Schuettpelz, Eric” via Gmail
Source: EVOLDIR
00:13
We have 2 years of funding for an MS or PhD student, beginning this summer or later, to help determine levels of genetic differentiation between two sedge species. The project would involve setting up and caring for common gardens in remote parts of Alaska, carrying out lab work (microsatellites or next-gen sequencing), data analysis and paper writing. The goal of the research is to determine whether the common circumpolar sedge, Carex subspathacea, and the less common C. ramenskii are genetically distinct. Natural populations of the two taxa are morphologically distinct, with one being tall and the other short. It has been suggested that C. subspathacea and C. ramenskii are actually a single species, and that the short stature of C. subspathacea is maintained by heavy goose grazing. In an experiment excluding geese on the YK Delta where the two species co-occur, C. subspathacea reverted to the tall form resembling C. ramenskii, while C. ramenskii reverted to the short-statured C. subspathacea when grazed, suggesting that the two species are actually grazing morphs of the same species However on the north slope of Alaska, C. ramenskii does not occur, and C. subspathacea maintains its short growth form even when excluded from grazing. This poses the questions as to whether there is genetic differentiation among populations of C. subspathacea at the regional scale, and whether C. subspathacea and C. ramenskii are indeed grazing morphs of the same species. If interested, please contact Diana Wolf and/or Roger Ruess Diana Wolf phone:(907)474-5538 Associate Professor fax:(907)474-7666 Institute of Arctic Biology Dept. of Biology and Wildlife 311 Irving I 902 N Koyukuk Drive University of Alaska Fairbanks Fairbanks, AK 99775-7000 http://bit.ly/1EAmFFZ dewolf@alaska.edu via Gmail
Source: EVOLDIR

February 20, 2015

05:42

Quick notes on another example of data duplication in GBIF. I'm in the process of building a tool to map specimen codes to GBIF records, and came across the following example. Consider the specimen code "AM M.22320", which is the voucher for the sequence KJ532444 (GenBank gives the voucher as M22320, but the associated paper doi:10.1016/j.ympev.2014.03.009 clarifies that this specimen comes from the Australian Museum). Locating this specimen in GBIF I found a series of records that were identical except for the catalogNumbers, which looked like this: M.22320.001, M.22320.002, etc. What gives?

Initially I thought this may be a simple case of data duplication (maybe the suffixes represent different versions of the same record?). Then I managed to locate the records on the Australian Museum web site:.

  • M.22320.009 - Wet Preparation - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.008 - Skull Preparation - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.001 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.005 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.006 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.007 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.003 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.004 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.002 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990 , Holotype
  • M.22320.010 - Tissue sample - Pteralopex taki Parnaby, 2002 - Solomon Islands, 5 km north of Patutiva Village, Marovo Lagoon, New Georgia Island , (8° 31' S , 157° 52' E), 25 Jun 1990

Turns out we have 10 records for "M.22320", which include various preparations and tissue samples. The holotype specimen for Pteralopex taki (originally described in doi:10.1071/AM01145, see BioNames) has generated 10 different records., all of which have ended up in GBIF. Anyone using GBIF occurrence data and interpreting the number of occurrence records as a measure of how abundant an organism is at a given locality is clearly going to be misled by data like this.

One way to tackle this problem would be if GBIF (or the data provider) could cluster the records that represent the "same" specimen, so GBIF doesn't end up duplicating the same information (in this case, 10-fold). The Australian Museum records don't seem to specify a direct link between the 10 records. I then located the same records in OZCAM, the data provider that feeds GBIF. Here is the OZCAM record for "M.22320.001": http://ozcam.ala.org.au/occurrence/223d1549-1322-419e-8af4-649a4b145064. OZCAM doesn't have the information on whether the record is a skull, a wet preparation, or a tissue sample, that information has been lost, and hence doesn't make it as far as GBIF.

Note that OZCAM has resolvable identifiers for each specimen in the form of UUIDs that are appended to "http://ozcam.ala.org.au/occurrence/". The corresponding UUIDs are included in the Darwin Core dump that OZCAM makes available to GBIF. Here they are for the parts of M.22320:


"223d1549-1322-419e-8af4-649a4b145064","M.22320.001",...
"c40a7eea-6e04-4be6-8dcb-4473402e48c4","M.22320.002",...
"21fcaea1-c645-49d9-9753-dbd9dd2bc64a","M.22320.003",...
"34ffd935-9fb4-44a5-acb8-2cd4df5ade62","M.22320.004",...
"03635fb8-f9ac-4c4c-898b-859cd42f1e26","M.22320.005",...
"a1c4dd5a-dc03-45cc-8971-931c739df8b2","M.22320.006",...
"71c91030-405c-4390-8ec3-42a5478a2fd8","M.22320.007",...
"0f1a9326-34d0-4fb2-b89a-9856bd9082f0","M.22320.008",...
"86270ef7-07f6-4395-84c7-66d5d497cc01","M.22320.009",...

But when GBIF parses the dump it ignores these UUIDs, which means the GBIF user can't easily go to the OZCAM site (which has a bunch of other useful information, compare http://ozcam.ala.org.au/occurrence/223d1549-1322-419e-8af4-649a4b145064 with http://www.gbif.org/occurrence/774916561/verbatim ). It also means that GBIF has stripped out an identifier that we might make use of to unambiguously refer to each record (and, presumably, this UUID doesn't change between harvests of OZCAM data).

In summary, this is a bit of a mess: we have multiple records that are really just bits of the same specimen but which are not linked together by any data provider, and as the data is transmitted up the chain to GBIF clues as to what is going on are stripped out. For a user like me who is trying to link the GenBank sequence to its voucher this is frustrating, and ultimately all rather avoidable if we took just a little more care in how we represent data about specimens, and how we treat that data as it gets transmitted between data bases.

Source: iPhylo
04:32
Quantitative Genomics 2015 Friday 29 May 2015 Wellcome Trust Headquarters, London We are excited to announce Quantitative Genomics 2015 (QG15), a conference for students in quantitative genomics that will take place on Friday 29th of May at the Wellcome Trust Headquarters at Euston square in the very heart of London. The conference will focus on giving early-career researchers (Masters and PhD students) working at the forefront of mathematical and quantitative genomics a chance to present their work and learn from their peers. The conference will feature talks by Professor Brian Charlesworth from the University of Edinburgh and Nicole Soranzo from the Wellcome Trust Sanger Institute. Our renowned speakers represent the two sides of the spectrum of topics QG15 aims for: from evolutionary theory and mathematical models to new omics tools applied in biomedical research. It will provide an ideal opportunity to build international networks with current and future leaders in the field in an informal and relaxed environment. Registration costs have been kept to a minimum to ensure that QG15 is accessible to all interested students. Please refer to the QG15 website for more information and do not hesitate to contact us for further information ( quantgen@damtp.cam.ac.uk). We encourage you to pre-register (open now ) so we can keep you updated regarding deadlines and steps for abstract submission and registration. We hope to see you in London, QG15 Organising Committee Kaur Alasoo - PhD in Computational Biology, Wellcome Trust Sanger Institute/University of Cambridge, Cambridge, UK- Rajbir Batra - Wellcome Trust PhD in Mathematical Genomics and Medicine, Cancer Research UK Cambridge Institute/University of Cambridge, Cambridge, UK- Moises Exposito-Alonso -PhD in Evolutionary Genomics; Max Planck Institute,Tbingen Germany- Tiphaine Martin - DPhil in Genetics and Molecular Medicine; Kings College London, London, UK- Hannah Meyer - PhD in Bioinformatics, EBI/University of Cambridge, Cambridge, UK- Sarah Morgan - PhD in Genetics of Neurodegeneration using Next-Generation Sequencing, University College London, London, UK- Matthias Thurner - DPhil in Genomic Medicine and Statistics, University of Oxford, Oxford, UK- via Gmail
Source: EVOLDIR