news aggregator

March 18, 2015

02:14

—_000_86127EEB693F4898B4F702CD437B5D2Cmssmedu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Stahl Lab | Post-doctoral scientist in statistical/human genomics Two positions are available, one with a primary focus on data analysis, and one with a primary focus on genetic modeling and inference methods. Both using GWAS and/or sequence data; range of applications in discovery, integration, prediction; any disease area. Focus on medical genetics, evolutionary impacts and implications are of course relevant. Secondary evolutionary/population genetic focused projects are welcome/available. Please see the Stahl Lab Positions web page http://bit.ly/1Ev5mqx for more information and how to apply. The Stahl Lab is part of the Center for Statistical Genetics (Dir. Shaun Purcell), in the Division of Psychiatric Genomics (Chief Pamela Sklar). Thank you via Gmail

Source: EVOLDIR
02:14

—089e0149397a91a24f05117ddf69 Content-Type: text/plain; charset=UTF-8 The University of Michigan Biological Station (UMBS) is pleased to offer the Project CLEAR Fund Fellowship for summer 2015. We are North America’s largest inland field station and are situated in the heart of the Great Lakes. http://bit.ly/1Ev5mqz ELIGIBILITY: Graduate or undergraduate students who will conduct independent research on freshwater ecosystems (e.g. water quality improvement, ecosystem protection or stewardship, or freshwater sustainability); involve/engage local communities in their research/research findings; and enroll concurrently in 1 summer session field class at UMBS. (http://bit.ly/1FA9oPT) SUPPORT: This fellowship provides room, board, research fees and supplies at UMBS. The Tip of the Mitt Watershed Council is participating with UMBS to help fellows find and engage appropriate communities. A note about course enrollment: This fellowship does not cover tuition for the field class. However, we have separate financial aid for students taking classes for which you should apply. TO APPLY: Send resume and letter of interest to UMBS Associate Director Karie Slavik, slavik@umich.edu. DEADLINE: Friday, April 3, 2015. —089e0149397a91a24f05117ddf69 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

The University of Michigan Biological Station (UMBS) is pleased to offer the Project CLEAR Fund Fellowship for summer 2015. We are North America’s largest inland field station and are situated in the heart of the Great Lakes.http://bit.ly/1Ev5mqzELIGIBILITY: Graduate or undergraduate students who will conduct  independent research on freshwater ecosystems (e.g. water quality improvement, ecosystem protection or stewardship, or freshwater sustainability); involve/engage local communities in their research/research findings; and enroll concurrently in 1 summer session field class at UMBS. (http://bit.ly/1FA9oPT)SUPPORT: This fell owship provides room, board, research fees and supplies at UMBS. The Tip of the Mitt Watershed Council is participating with UMBS to help fellows find and engage appropriate communities.A note about course enrollment: This fellowship does not cover tuition for the field class. However, we have separate financial aid for students taking classes for which you should apply.TO APPLY: Send resume and letter of interest to UMBS Associate Director Karie Slavik, slavik@umich.edu.DEADLINE: Friday, April 3, 2015. —089e0149397a91a24f05117ddf6 via Gmail
Source: EVOLDIR
01:58
01:42
Graduate research opportunity to study the comparative transcriptomics of extreme phenotypes. Department of Biological Sciences - University of Tulsa A graduate student at the M.S. or Ph.D level is sought to work with Drs. Warren Booth and Charles Brown in the Department of Biological Sciences at The University of Tulsa, Oklahoma. The successful applicant will develop a research project focused on understanding the evolution of extreme phenotypes examined through a comparative transcriptomic approach. In the Booth-Lab we use cimicid insects as models to study rapid evolutionary processes and the genetics of spatiotemporal metapopulations. Here, we will investigate extreme phenotype evolutionary in the swallow bug (Oeciacus vicarius: Cimicidae), a disease vectoring ectoparasite of cliff swallows (Petrochelidon pyrrhonota). The PIs have amassed a large collection of swallow bugs exhibiting phenotypes of interest, specifically relating to metabolic quiescence, thermal tolerance, and dispersal, and are in the process of sequencing the transcriptomes of an exploratory set on our inhouse Illumina MiSeq. The work will draw on a long-term (32-year) study on social behavior and reproductive ecology of cliff swallows in western Nebraska and the student will have opportunities to visit the field site, and collect and sequence the transcriptomes of additional samples should interesting questions arise. Applicants for this position should have a strong background in population genetics, molecular ecology, or evolutionary biology, and meet the admission requirements for the Department of Biological Sciences graduate program. (http://bit.ly/1aOtTdZ). If a non-U.S citizen, the applicant must already have a valid VISA permitting them to enter and study in the United States. Funds are not available to cover this as part of this project. The students stipend, tuition, and medical insurance, is covered as part of the teaching assistantship. Applications should include the following: 1) A letter of interest (not exceeding two pages). 2) A curriculum vitae. 3) Names and email addresses for at least two academics/researchers willing to provide a letter of recommendation 4) Copies of undergraduate/post-graduate transcripts 5) Electronic copies of published manuscripts, if any. For more information about this opportunity, contact Drs. Booth (warren-booth@utulsa.edu). Anticipated start date is mid-August 2015. Additional information regarding our research can be found at our current departmental webpages: Dr. Warren Booth - www.booth-lab.org Dr. Warren Booth Assistant Professor of Molecular Ecology Department of Biological Sciences University of Tulsa 315 Oliphant Hall Tulsa, OK 74104 Tel. (918) 631-3421 - Office (918) 631-3136 - Lab Web site - TU academic Lab website “Booth, Warren” via Gmail
Source: EVOLDIR
01:42

20th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology (VEME) Dates: 9th - 14th August 2015 Venue: University of the West Indies, Trinidad and Tobago DEADLINE FOR APPLICATIONS IS EXTENDED TO 31 MARCH 2015 The International Bioinformatics Workshop on VEME workshop is recognized as one of the best international virus bioinformatics courses in the world and has so far been organized in Belgium, Brazil, Finland, Greece, Portugal, the USA, South Africa, The Netherlands, Serbia and Italy. The 20th edition will be held from 9 - 14 August 2015 at the University of the West Indies in the Caribbean island of Trinidad and Tobago. The workshop will provide 90 participants with intensive training in the mathematical principles and computer applications used in the study virus evolution and for conducting detailed molecular epidemiological investigations. The workshop will include lectures and computer practical session where students will have the opportunity to analyse their own research data. Each student will also present a poster about their research. The target group are trainee scientists starting their scientific career, i.e. graduate research student, postdoctoral researchers and specialised research technicians (bio informaticians). The workshop teachers will be 24 world-renowned researchers from top international universities and research institutions. Interaction among participants and teaching staff is a key element, so the ratio of teachers to students will be maintained at no less than 1:4. A limited number of scholarships will be provided. There is no country restriction to attend, but scholarships are restricted to resource limited countries. Participants will have the opportunity to attend one of the three 4-day modules and their choice of two of the 6 half-day modules: Three 4-day modules • ‘Phylogenetic Inference’ offers the theoretical background and hands-on experience in phylogenetic analysis for those who have little or no prior expertise in sequence analysis • ‘Evolutionary Hypothesis Testing’ is targeted to participants who are well familiar with alignments and phylogenetic trees and would like to extend their expertise to likelihood and Bayesian inference in phylogenetics, coalescent and phylogeographic analyses (‘phylodynamics’) • ‘Large Dataset Analysis’ will cover the more complex analysis of full genomes, huge datasets of pathogens including Next Generation Sequencing data, and combined analyses of pathogen and host. Six 1/2-day modules: • Morning - ‘Large Phylogenies’, ‘Transmission Chain Investigation’ and ‘Molecular Adaptation’ • Afternoon - ‘Visualization of Large Phylogenies with Metadata’, ‘Recombination and Networks’ and ‘Virus Analysis Tools’ Practical sessions in these modules will involve various software packages, including PHYLIP, PAUP*, PHYML, MEGA, PAML or HYPHY, TREE-PUZZLE, SplitsTree, BEAST, MrBayes, Simplot, RDP3, QuRE. Detailed information and online applications may be accessed at: http://bit.ly/1HZ3xmV OR http://bit.ly/1wYWvNR via Gmail

Source: EVOLDIR
00:55
ScotFly 2015 Any Drosophilists in Scotland or nearby are warmly invited to attend the 4th 1-day “Scottish Fly Meeting”, which will take place at St Andrews on Friday 8th May. This is a very informal meeting of researchers with any interest in Drosophila and is relatively unusual in bringing together people from a broad range of backgrounds including evolution, development, neurobiology and physiology. New synergisms have emerged from previous meetings. Invited speakers are Barry Denholm (development), Alistair McGregor (morphology), Megan Neville (behaviour), Darren Obbard (immunology) & Stefan Pulver (neurogenetics). Contributed talks and posters, from researchers at all career stages, are welcomed. To register and submit an abstract please send an e-mail to scotfly@st-andrews.ac.uk. Please send abstracts as one page using font Arial 12 pt. The closing date is 24 April 2015. Please visit our website for further information: http://bit.ly/1Fz5MOt The organisers, Mike Ritchie and Marcus Bischoff Mike Ritchie Centre for Biological Diversity, School of Biology, University of St Andrews, Fife. Scotland KY16 9TH UK Phone: 0 (44 outside UK) 1334 463495 Some websites: Lab: http://bit.ly/1b9rz1H Uni: http://bit.ly/19JB5SP Google: http://bit.ly/1b9rBq5 CBD: http://bit.ly/19JB4yd Michael Ritchie via Gmail
Source: EVOLDIR
00:41
Faculty position (non-Korean) in ecology at Ewha Womans University, Seoul, Korea Department of Life Science and Division of EcoScience at Ewha Womans University invites application for a faculty position in ecology (broadly defined). This position is open to candidates without Korean citizenship, with primary language for teaching and research being English. It is a tenure-track full-time (12-month) position at the ranks of either Assistant or Associate Professor starting in September 2016. Applicants must have PhD degree in ecology and at least two years of post-doctoral research experience. The candidate will teach about two courses per semester, including graduate classes, and establish a strong research program leading to publications in major journals in the fields of ecology. We are especially interested in candidates studying central problems in ecology that have broad impacts and potential to generate productive collaboration with ecologists and evolutionary biologists in Korea. Collaborative research opportunity exits with the National Institute of Ecology in Seochon, Korea. The successful applicant will be a member of the Division of EcoScience at Ewha, faculty research areas of which include acoustic animal behavior and ecology, population genetics of freshwater and marine fish, theoretical population genetics, marine invertebrate animal diversity, plant diversity and systematics, primate (gibbon) behavior and ecology, and microbial metabolism. For initial consideration and inquiry, send CV, research plan and, if possible, link to candidates’ Google Scholar Citation profile by email to Yuseob Kim (yuseob@ewha.ac.kr) by the 2nd of April. Applicants can also directly submit the application material to the faculty recruitment system of Ewha (http://bit.ly/1GV8EU9) which will be open for application from March 30 to April 8. Yuseob Kim via Gmail
Source: EVOLDIR

March 17, 2015

23:52
*The final program for the inaugural meeting of the International Society for Evolution, Medicine, & Public Health is now available online. * http://bit.ly/1EpERQX All talks on Thursday March 19 will be live streamed at http://bit.ly/1LsjWFS The time zone is the same as California, so 3 hours earlier that EDT, and 7 hours earlier than London UK. *Thursday* *At ASU Memorial Union* *Ventena Room*6:30 7:00Continental Breakfast7:30 8:00Barbara Natterson- Horowitz, UCLA Zoobiquity and Evolutionary Medicine Introduction by Charlie Nunn8:15 8:30 8:45Short break Chair: Gillian Bentley9:00Joe Alcock, University of New Mexico, “Identifying normal function in abnormal results: Reaction norms lead to a new normal for medical practice”9:15Gillian Pepper, Newcastle University, ” Extrinsic mortality risk and socioeconomic differences in health behaviour: observational and experimental evidence “9:30Harvey Kliman, Yale University, “The pelvis skull conflict: why trophoblast inclusions are a marker of autism and may be the evolutionary basis of human intelligence.” 9:45Anne Stone, Arizona State University, “Mycobacterium tuberculosis: origins and evolutionary history of a major pathogen. “10:00Martin Häusler, University of Zurich, “Are musculoskelatal disorders evolutionary trade-offs of bipedalism”10:15Break10:30 Chair: Daniel Lieberman10:45Welcome remarks by Dean Garcia-Pichel and Manfred Laubichler (on behalf of Provost Page)11:00Marlene Zuk, University of Minnesota, “Evolution in sickness and in health”11:15Frank Ruhli, University of Zurich, “Evolutionary medicine as part of the medical curriculum in Switzerland and Australia: a qualitative and quantitative feedback “11:30Mark Schwartz, NYU School of Medicine, “Integrating evolutionary science into medical education “11:45Michael Muehlenbein, Indiana University, “Survey on evolution in health education” 12:00Lunch at Memorial Union at ASU12:15 12:30 12:45 13:00Harvey Fineberg President, Gordon and Betty Moore Foundation Keynote: “Evolution in Medicine: Past, Present, and Future”13:15Introduction by: Randolph Nesse13:30 13:45Short break Chair: Robert Perlman14:00Michael Gurven, UC Santa Barbara, “Costs of reproduction in a high fertility and mortality population”14:15Grazyna Jasienska, Jagiellonian University, “Trade-offs between reproduction and aging: biomarkers, confounders and genetic factors”14:30Katie Hinde, Harvard University, “Insights into co-evolution of milk and microbes: subsistence strategy predicts glycan profile in breast milk among diverse human populations”14:45Daniel Lieberman, Harvard University, “An evolutionary medical perspective on shoes”15:00Allen Rodrigo, NEScent, “Neutral models of microbiome evolution”15:15Break15:30 Chair: Ajit Varki15:45Sudhir Kumar, iGEM Temple, “Phylomedicine: Evolutionary Lessons and Solutions for Genomic Medicine”16:00David Haig, Harvard University, “Microchimerism and inclusive fitness”16:15Elizabeth Uhl, University of Georgia “Origin of canine distemper as a reverse zoonosis from human measles: insights from history, evolution and studies of codon usage bias”16:30Bernard Crespi, Simon Frazer University, “Imagination as a core diametric phenotype of autism spectrum and psychotic-affective spectrum conditions: evidence from schizophrenia genetic risk scores “16:45Jacobus (Koos) Boomsma, University of Copenhagen, “Parent-of-origin gene-dosage effects in the womb may affect physical and mental health later in life “17:00Baba Brinkman-Rap Preview & RapUp17:15Flash talks Chair: Marlene Zuk17:30 17:45Poster session/ Appetizers18:00La Paz & Cochise rooms18:15 18:30 18:45 19:00 19:15Education and Outreach Committee Meeting19:30at Engrained Patio at the Memorial Union 19:45 20:00 20:15 Randolph M. Nesse, MD The ASU Center for Evolution & Medicine Full ISEMPH Conference Program available here rmnesse@gmail.com via Gmail
Source: EVOLDIR
23:36
JOB 1: Early Stage Researcher ESR B3 Biogeography Institute/ Supervisor Giessen – Christian Albrecht Title Drivers of Pontocaspian biodiversity Rise and Demise: satellite regions as source/sinks of Pontocaspian biota Summary The Justus Liebig University Giessen is looking for prospective candidates with a background in phylogenetics and biogeography and an interest in interdisciplinary palaeoenvironmental and biodiversity research in the Pontocaspian region (Black Sea, Caspian Sea and Anatolia and surroundings). Description The successful candidate will be employed as researcher without a PhD and enrolled as PhD student to complete a PhD thesis within the contract period of 3 years to assess the role of satellite regions (Anatolian and possibly Balkan lake systems) in the evolution of Pontocaspian biota over the past 3 Ma. Lakes and Quaternary lake deposits in Anatolia and the Balkans contain various groups of Pontocaspian taxa. However, it remains largely unknown whether these satellite areas served as sink or source (cf. refuges) for Pontocaspian biota. Combined molecular phylogenetic analyses of extant Pontocaspian species from Anatolian and Balkan lakes with a rigorous updated study of fossil occurrences and their depositional/geochemical context in these lake basins will allow testing their role as sinks and/or sources. The environmental context of biotic change in selected lake successions will be determined through sedimentological and geochemical analyses and compared with ostracod data through parallel projects. The successful applicant will test the role of selected satellite regions as sources/sinks of Pontocaspian biota using fossil‐calibrates molecular clock approaches and phylogeographical analyses (gene‐flow analyses and ancestral area reconstructions). This project will include a combined secondment at Naturalis Biodiversity Center and GiMaRIS in Leiden (NL) to study fossil molluscs and to train for conservation biodiversity assessment techniques. The candidate will enroll in an extensive Network Training Program. Research Fields Comparative biogeography, phylogeography, biodiversity, paleontology, Biostratigraphy Career Stage Early stage researcher or 04 yrs (Post graduate) Research Profiles First Stage Researcher (R1) Type of contract Temporary employment with the Federal State of Hesse. Full time 40 hrs/wk Salary a month/year A salary that matches the MSCAITN and local rules, a monthly mobility allowance of 600,gross and a possible monthly family allowance of 500,gross. Benefits In accordance with Marie Sklodowska Curie Regulations Information about the Marie Sklodowska Curie actions is available at http://bit.ly/1ADssYq http://bit.ly/1H0nV9C Financial and other technical information is available at http://bit.ly/1ADssYr www.pontocaspian.eu Address details of workplace Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Specific demands from your country/ institute Ability to work in an internationally oriented environment, including fluency in English; M.Sc. in relevant field Applicants are invited to submit the following documents: Letter of application (max 2 pages); Resume (Curriculum vitae); The names, position and e-mail addresses of at least two persons that can be contacted for reference; List of publications, including submitted manuscripts or papers in press, if any; Transcript of BSc and MSc diploma. The required documents should be submitted by email to sollicitaties@naturalis.nl before 16 April 2015. Job 2: Early Stage Researcher ESR B4 Evolution Institute/ Supervisor Giessen – Tom Wilke Title Drivers of Pontocaspian biodiversity Rise and Demise: Molecular evolution of Pontocaspian biota Summary The Justus Liebig University Giessen is looking for prospective candidates with a background in evolutionary biology and an interest in interdisciplinary palaeontological and phylogenetic research in the Pontocaspian region (Black Sea, Caspian Sea and Anatolia and surroundings). Description The successful candidate will be employed as researcher without a PhD and enrolled as PhD student to complete a PhD thesis within the contract period of 3 years to reconstruct past evolutionary events and diversity changes over ~2 Ma in several Pontocaspian species flocks (e.g., lymnocardiine and dreissenid bivalves, pyrguline gastropods) using genetic information from extant taxa combined with fossil occurrences as a baseline for understanding the current species richness and distribution patterns (biodiversity). Of interest are coalescent analyses based on mt‐DNA data for reconstructing past demographic and spatial expansion events, molecular clock analyses for timing past diversification events and lineage‐through‐time (LTT) plots to test for deviations from a constant speciation rate over time. The latter two approaches are based on multi‐locus genetic datasets. The inferred evolutionary events will be compared to major hydrological and climatic events of the Pontocaspian derived from parallel projects to obtain an understanding of the biotic and abiotic factors driving evolution in space and time. This project will include a secondment at the Natural History Museum Grigore Antipa in Bucharest (RU) for analyses of extant Black Sea taxa and a secondment at Naturalis Biodiversity Center in Leiden (NL) to study fossil mollusk occurrences. The candidate will enroll in an extensive Network Training Program. Research Fields Evolution, phylogeny, phylogeography, paleontology, Career Stage Early stage researcher or 04 yrs (Post graduate) Research Profiles First Stage Researcher (R1) Type of contract Temporary employment with the Federal State of Hesse. Full time 40 hrs/wk Salary a month/year A salary that matches the MSCAITN and local rules, a monthly mobility allowance of 600, gross and a possible monthly family allowance of 500, gross. Benefits In accordance with Marie Sklodowska Curie Regulations Information about the Marie Sklodowska Curie actions is available at http://bit.ly/1ADssYq http://bit.ly/1H0nV9C Financial and other technical information is available at http://bit.ly/1ADssYr www.pontocaspian.eu Address details of workplace Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Specific demands from your country/ institute Ability to work in an internationally oriented environment, including fluency in English;M.Sc. in relevant field Applicants are invited to submit the following documents: Letter of application (max 2 pages); Resume (Curriculum vitae); The names, position and e-mail addresses of at least two persons that can be contacted for reference; List of publications, including submitted manuscripts or papers in press, if any; Transcript of BSc and MSc diploma. The required documents should be submitted by email to sollicitaties@naturalis.nl before 16 April 2015. Job 3: Early Stage Researcher ESR C4 Biodiversity Modeling Institute/ Supervisor Giessen – Tom Wilke Title Drivers of Pontocaspian biodiversity Rise and Demise: modelling and predicting Pontocaspian biodiversity change and crisis Summary The Justus Liebig University Giessen is looking for prospective candidates with a background in biodiversity modelling and an interest in interdisciplinary palaeoenvironmental and biodiversity research in the Pontocaspian region (Black Sea, Caspian Sea and Anatolia and surroundings). Description The successful candidate will be employed as researcher without a PhD and enrolled as PhD student to complete a PhD thesis within the contract period of 3 years to model and predict Pontocaspian biodiversity change and crisis. This project integrates the various information sources on natural (biotic and abiotic) and anthropogenic drivers of biotic changes inferred in parallel projects in empirical modeling approaches to generate informed spatially‐explicit risk estimates for species and communities and to predict future changes (forward modeling) under different Global Change scenarios. It thus serves as baseline for identifying areas of highest conservation management priority in the region. Candidate natural drivers and anthropogenical drivers for the models include climate, lake basin geochemistry, nutrient regimes and invasive species and will be obtained from parallel projects. Models will be validated using backward modelling of data derived from the short cores and the high resolution age model generated in parallel projects. Forward modelling will be applied to the modern Kura biota (local scale) and to the Pontocaspian area as a whole (regional scale). This project specifically aims to (1) assess the relative contribution of natural vs. anthropogenic drivers to the current Pontocaspian biodiversity crisis using MaxEnt and Generalized Dissimilarity Modelling, (2) develop a spatially explicit risk model for the Holocene biodiversity crises by projecting the model outputs from aim 1 in space and time, (3) use backward modelling by hindcasting the Holocene environmental parameters and validating the accuracy of the model results with available faunal successions, and (4) perform forward modelling to predict future biodiversity changes under different Global Change scenarios. Secondment (host, timing, length & purpose) ‐Leiden, NR (month 12, 2 months): modelling; Leiden, FPW (month 20, 2 months): palaeontology and habitat reconstruction. This project will include a secondment at Naturalis, Leiden (NL) for coordinating modelling exercises and inclusion of results and scenarios of the PCIS (Pontocaspian Information System) developed at Leiden. The candidate will enroll in an extensive Network Training Program. Research Fields biodiversity, biodiversity modeling Career Stage Early stage researcher or 04 yrs (Post graduate) Research Profiles First Stage Researcher (R1) Type of contract Temporary employment with the Federal State of Hesse. Full time 40 hrs/wk Salary a month/year A salary that matches the MSCAITN and local rules, a monthly mobility allowance of 600, gross and a possible monthly family allowance of 500, gross. Benefits In accordance with Marie Sklodowska Curie Regulations Information about the Marie Sklodowska Curie actions is available at http://bit.ly/1ADssYq http://bit.ly/1H0nV9C Financial and other technical information is available at http://bit.ly/1ADssYrwww.pontocaspian.eu Address details of workplace Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Specific demands from your country/ institute Ability to work in an internationally oriented environment, including fluency in English; M.Sc. in relevant field Applicants are invited to submit the following documents: Letter of application (max 2 pages); Resume (Curriculum vitae); The names, position and e-mail addresses of at least two persons that can be contacted for reference; List of publications, including submitted manuscripts or papers in press, if any; Transcript of BSc and MSc diploma. The required documents should be submitted by email to sollicitaties@naturalis.nl before 16 April 2015. Job 2: Early Stage Researcher ESR B4 Evolution Institute/ Supervisor Giessen – Tom Wilke Title Drivers of Pontocaspian biodiversity Rise and Demise: Molecular evolution of Pontocaspian biota Summary The Justus Liebig University Giessen is looking for prospective candidates with a background in evolutionary biology and an interest in interdisciplinary palaeontological and phylogenetic research in the Pontocaspian region (Black Sea, Caspian Sea and Anatolia and surroundings). Description The successful candidate will be employed as researcher without a PhD and enrolled as PhD student to complete a PhD thesis within the contract period of 3 years to reconstruct past evolutionary events and diversity changes over ~2 Ma in several Pontocaspian species flocks (e.g., lymnocardiine and dreissenid bivalves, pyrguline gastropods) using genetic information from extant taxa combined with fossil occurrences as a baseline for understanding the current species richness and distribution patterns (biodiversity). Of interest are coalescent analyses based on mt‐DNA data for reconstructing past demographic and spatial expansion events, molecular clock analyses for timing past diversification events and lineage‐through‐time (LTT) plots to test for deviations from a constant speciation rate over time. The latter two approaches are based on multi‐locus genetic datasets. The inferred evolutionary events will be compared to major hydrological and climatic events of the Pontocaspian derived from parallel projects to obtain an understanding of the biotic and abiotic factors driving evolution in space and time. This project will include a secondment at the Natural History Museum Grigore Antipa in Bucharest (RU) for analyses of extant Black Sea taxa and a secondment at Naturalis Biodiversity Center in Leiden (NL) to study fossil mollusk occurrences. The candidate will enroll in an extensive Network Training Program. Research Fields Evolution, phylogeny, phylogeography, paleontology, Career Stage Early stage researcher or 04 yrs (Post graduate) Research Profiles First Stage Researcher (R1) Type of contract Temporary employment with the Federal State of Hesse. Full time 40 hrs/wk Salary a month/year A salary that matches the MSCAITN and local rules, a monthly mobility allowance of 600, gross and a possible monthly family allowance of 500, gross. Benefits In accordance with Marie Sklodowska Curie Regulations Information about the Marie Sklodowska Curie actions is available at http://bit.ly/1ADssYq http://bit.ly/1H0nV9C Financial and other technical information is available at http://bit.ly/1ADssYr www.pontocaspian.eu Address details of workplace Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Specific demands from your country/ institute Ability to work in an internationally oriented environment, including fluency in English;M.Sc. in relevant field Applicants are invited to submit the following documents: Letter of application (max 2 pages); Resume (Curriculum vitae); The names, position and e-mail addresses of at least two persons that can be contacted for reference; List of publications, including submitted manuscripts or papers in press, if any; Transcript of BSc and MSc diploma. The required documents should be submitted by email to sollicitaties@naturalis.nl before 16 April 2015. Job 3: Early Stage Researcher ESR C4 Biodiversity Modeling Institute/ Supervisor Giessen – Tom Wilke Title Drivers of Pontocaspian biodiversity Rise and Demise: modelling and predicting Pontocaspian biodiversity change and crisis Summary The Justus Liebig University Giessen is looking for prospective candidates with a background in biodiversity modelling and an interest in interdisciplinary palaeoenvironmental and biodiversity research in the Pontocaspian region (Black Sea, Caspian Sea and Anatolia and surroundings). Description The successful candidate will be employed as researcher without a PhD and enrolled as PhD student to complete a PhD thesis within the contract period of 3 years to model and predict Pontocaspian biodiversity change and crisis. This project integrates the various information sources on natural (biotic and abiotic) and anthropogenic drivers of biotic changes inferred in parallel projects in empirical modeling approaches to generate informed spatially‐explicit risk estimates for species and communities and to predict future changes (forward modeling) under different Global Change scenarios. It thus serves as baseline for identifying areas of highest conservation management priority in the region. Candidate natural drivers and anthropogenical drivers for the models include climate, lake basin geochemistry, nutrient regimes and invasive species and will be obtained from parallel projects. Models will be validated using backward modelling of data derived from the short cores and the high resolution age model generated in parallel projects. Forward modelling will be applied to the modern Kura biota (local scale) and to the Pontocaspian area as a whole (regional scale). This project specifically aims to (1) assess the relative contribution of natural vs. anthropogenic drivers to the current Pontocaspian biodiversity crisis using MaxEnt and Generalized Dissimilarity Modelling, (2) develop a spatially explicit risk model for the Holocene biodiversity crises by projecting the model outputs from aim 1 in space and time, (3) use backward modelling by hindcasting the Holocene environmental parameters and validating the accuracy of the model results with available faunal successions, and (4) perform forward modelling to predict future biodiversity changes under different Global Change scenarios. Secondment (host, timing, length & purpose) ‐Leiden, NR (month 12, 2 months): modelling; Leiden, FPW (month 20, 2 months): palaeontology and habitat reconstruction. This project will include a secondment at Naturalis, Leiden (NL) for coordinating modelling exercises and inclusion of results and scenarios of the PCIS (Pontocaspian Information System) developed at Leiden. The candidate will enroll in an extensive Network Training Program. Research Fields biodiversity, biodiversity modeling Career Stage Early stage researcher or 04 yrs (Post graduate) Research Profiles First Stage Researcher (R1) Type of contract Temporary employment with the Federal State of Hesse. Full time 40 hrs/wk Salary a month/year A salary that matches the MSCAITN and local rules, a monthly mobility allowance of 600, gross and a possible monthly family allowance of 500, gross. Benefits In accordance with Marie Sklodowska Curie Regulations Information about the Marie Sklodowska Curie actions is available at http://bit.ly/1ADssYq http://bit.ly/1H0nV9C Financial and other technical information is available at http://bit.ly/1ADssYr www.pontocaspian.eu Address details of workplace Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Specific demands from your country/ institute Ability to work in an internationally oriented environment, including fluency in English; M.Sc. Applicants are invited to submit the following documents: Letter of application (max 2 pages); Resume (Curriculum vitae); The names, position and e-mail addresses of at least two persons that can be contacted for reference; List of publications, including submitted manuscripts or papers in press, if any; Transcript of BSc and MSc diploma. The required documents should be submitted by email to sollicitaties@naturalis.nl before 16 April 2015. Dr. Christian Albrecht Assistant Professor Department of Animal Ecology and Systematics Systematics and Biodiversity Group Justus Liebig University Giessen H.-Buff-Ring 26-32 (IFZ) D-35392 Giessen, Germany Tel.: ++49 641 9935722 Fax: ++49 641 9935709 Christian Albrecht via Gmail
Source: EVOLDIR
23:30

Multiple sequence alignment software have not yet met their primary aim for evolutionary biologists: maximizing homology of characters. If our goal is to develop an automated procedure for homology assessment, then we need someone to produce a program that explicitly implements this aim.

Alignment is just as much a part of phylogenetics as is tree or network building. It is the procedure that expresses the homology relationships among the characters, rather than the historical relationships among the taxa. Therefore, we need a computer program that accurately expresses homology relationships, as well as one that accurately expresses the historical relationships. We have some programs for the latter but currently nothing for the former.

Unfortunately, homology is a rather nebulous concept. It has to do with inheriting characters from a shared ancestor, which is not something that we can directly observe. Therefore we have to infer it. Somehow.

Homology criteria

Systematists have developed criteria for making decisions about potential homologies in an objective and (hopefully) repeatable manner, and these are directly applicable to nucleotide sequences, which these days are the most common form of data used in phylogenetics. These criteria are:

• Similarity
  1. Compositional = apparent likeness or resemblance between sequences (% similarity)
  2. Topographical = apparent likeness or resemblance between sequences (second- and third-order structure of proteins or RNA)
  3. Functional = functional relationship to other characters in the same sequence (annotated function of the sequence in protein or RNA)
• Conjunction = possible within-genome copies of the same sequence (i.e. paralogy)

• Congruence = agreement with other postulated homologies elsewhere in the same sequences (synapomorphy).

Traditionally, characters have been first proposed as homologous using the criteria of similarity and conjunction (together called primary homology), and then tested with the criterion of congruence (secondary homology).

It is important to note that these criteria do not necessarily always agree with each other in their inferences of homology. Changes that occur during evolutionary history can weaken the connection between these criteria so that, for example, nucleotide homology inferred from structural similarity is no longer the same as nucleotide similarity inferred from compositional similarity. It is for this reason that compositional similarity of the sequences is insufficient to establish gene orthology, for example. The same limitation applies to nucleotides.

Current computer programs

It is clear that these criteria have been incorporated singly into current computerized procedures for producing multiple sequence alignments, but rarely in combination. For example, compositional similarity is the criterion used by the most popular computer programs, such as CLUSTAL, MAFFT and Muscle. Topographical similarity is being invoked whenever structure-based alignments are produced. such as for RNA-coding sequences (eg. PicXAA-R; PMFastR), or when nucleotide sequences are translated to amino acids before alignment (eg. PROMALS). Functional similarity is used for specialist studies of conserved motifs and binding sites, for instance. Ontogenetic similarity of nucleotide sequences is based on inferring the possible molecular processes that cause the observed sequence variation — the program Prank uses this criterion by distinguishing between insertions and deletions.

Congruence as a criterion involves the observation of repeated patterns of synapomorphy in a phylogeny. Among alignment algorithms, both Direct Optimization (e.g. POY; MSAM; BeeTLe) and Statistical Alignment (e.g. BAli-Phy; StatAlign) try to simultaneously produce a multiple alignment and a phylogenetic tree, thus optimizing the criterion of congruence.

The fact that none of the current crop of programs basically apply more than one criterion is, I contend, the principal reason why so many phylogeneticists adjust their alignments manually. Personal judgment may not be perfect, but at least it can be consciously based on homology as a general character concept. Since the different criteria may conflict with each other, at the moment only human judgment is available to compare them and thus make a final decision.

Required program

To make the homology criteria fully operational, we need to compare their inferences by evaluating the comparative evidence. That is, since the different criteria may conflict with each other, we need an automated way to compare them and evaluate their relative probabilities for any alignment column. What we need is a computerized procedure that will includes all of the known criteria for homology assessment. Sadly, there are currently no mathematical models for doing this.

I suspect that there are two reasons for the failure of such a program to appear by now. First, biologists have not been clear about homology as a concept, and have not been able to express it in a form that computationalists could use to develop an algorithm. That is, we have criteria but they are not really operational criteria in a computational sense. Second, it will not be easy, because there is no obvious algorithm for inferring inheritance of characters. That is, we cannot easily separate homology from analogy.

Interactive editor

Another proposal is to have an interactive alignment editor. This editor would have the ability to show the conflicting hypotheses of homology (eg. where the homology suggested by structural pairing in a stem conflicts with homology suggested by tandem repeats), and then to annotate each column in the final alignment with the reason for the researcher having chosen to align those particular nucleotides. For example, one could press a button and see the RNA stem pairs in different colors (irrespective of whether the stem nucleotides are aligned), or press again and see the tandem repeats and inversions in different colours (once again, irrespective of how the nucleotides are aligned). One could also choose to see the annotations for the columns (summarized, using some coded schema), or simply look at the unadorned alignment itself.

This seems to me to be an achievable goal in the short-term; and the PhyDE editor already does some of it. Such an editor would also serve as a necessary step on the way to working out how to automate as much of the process as possible. The ultimate goal for some people may be total automation (ie. a black box), but I see no way to achieve that in the immediate term. Besides, I suspect that phylogeneticists will always want some judgemental control over the process, which would be best achieved with a semi-automated interactive editor. That is, we might ask the program to work out what the alternative alignments are for any specified subsequence (in an automated manner), and then we evaluate their relative merits for ourselves.

Note that I am treating the alignment as a set of hypotheses independent of their phylogenetic analysis. Subsequences can still be tentatively aligned even if the researcher intends masking those subsequences out of any subsequent tree-building analysis. Also, subsets of the taxa might be aligned confidently while other subsets are left unaligned. With current editors, this involves having a separate alignment file for each subset, which is very cumbersome, as well as error-prone.

18:00
Background: The diversity of the symbiotic dinoflagellate Symbiodinium sp., as assessed by genetic markers, is well established. To what extent this diversity is reflected on the amino acid level of functional genes such as enzymatic antioxidants that play an important role in thermal stress tolerance of the coral-Symbiodinium symbiosis is, however, unknown. Here we present a predicted structural analysis and phylogenetic characterization of the enzymatic antioxidant repertoire of the genus Symbiodinium. We also report gene expression and enzymatic activity under short-term thermal stress in Symbiodinium of the B1 genotype. Results: Based on eight different ITS2 types, covering six clades, multiple protein isoforms for three of the four investigated antioxidants (ascorbate peroxidase [APX], catalase peroxidase [KatG], manganese superoxide dismutase [MnSOD]) are present in the genus Symbiodinium. Amino acid sequences of both SOD metalloforms (Fe/Mn), as well as KatG, exhibited a number of prokaryotic characteristics that were also supported by the protein phylogeny. In contrast to the bacterial form, KatG in Symbiodinium is characterized by extended functionally important loops and a shortened C-terminal domain. Intercladal sequence variations were found to be much higher in both peroxidases, compared to SODs. For APX, these variable residues involve binding sites for substrates and cofactors, and might therefore differentially affect the catalytic properties of this enzyme between clades. While expression of antioxidant genes was successfully measured in Symbiodinium B1, it was not possible to assess the link between gene expression and protein activity due to high variability in expression between replicates, and little response in their enzymatic activity over the three-day experimental period. Conclusions: The genus Symbiodinium has a diverse enzymatic antioxidant repertoire that has similarities to prokaryotes, potentially as a result of horizontal gene transfer or events of secondary endosymbiosis. Different degrees of sequence evolution between SODs and peroxidases might be the result of potential selective pressure on the conserved molecular function of SODs as the first line of defence. In contrast, genetic redundancy of hydrogen peroxide scavenging enzymes might permit the observed variations in peroxidase sequences. Our data and successful measurement of antioxidant gene expression in Symbiodinium will serve as basis for further studies of coral health.
18:00
Background: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae. Results: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots. Conclusions: Phylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.
02:54
Background: A March of Dimes/Burroughs Wellcome Trust funded post-doctoral position is available in the Lynch Lab, in the Department of Human Genetics at The University of Chicago, for a highly motivated scientist to study the mechanisms that underlie the evolutionary origin of progesterone responsiveness and decidualization in endometrial stromal cells. The project will use comparative transcriptomics to identify genes that evolved endometrial expression during the origins of pregnancy, and siRNA-screens to characterize the functions of recruited genes. The project is expected to contribute to a basic understanding of the mechanisms that underlie decidualization and the evolution of pregnancy. Skills: Candidate must have a Ph.D. in molecular or cell biology, genetics, or a related discipline, be self-motivated, have excellent communication and organizational skills. A strong background with basic methods in molecular biology (for example: PCR, cloning, sequencing, Western blotting, protein-protein interaction assays such as co-IP) and demonstrated expertise in cell culture and gene expression manipulation (for example: siRNA mediated gene knockdown and overexpression) are required. Previous experience or strong interests in gene expression analyses, bioinformatics, and genome editing are desirable. Application information: To apply, please email a cover letter describing previous research experience, current research interests, and career goals, a current CV, and the names and contact information for three professional references to Dr. Vincent Lynch at lynchlabpositions@gmail.com. Consideration of applications will begin immediately and continue until the position is filled. Lab website: http://bit.ly/18VLP7s Location: Chicago, IL USA “Vincent J. Lynch, Ph.D.” via Gmail
Source: EVOLDIR
02:54

—Boundary_(ID_DDmTsNii19FRDai8jJczNg) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: quoted-printable A postdoctoral research associate position is available in the laboratory of John Doebley at the University of Wisconsin-Madison to study the quantitative genetics and genomics of teosinte, the progenitor of maize. The postdoctoral associate will work as a member of the NSF-funded Panzea project (www.panzea.org) and use population genomics to understand the genetic architecture of domestication traits and inbreeding depression in natural populations of teosinte. We bred 120 teosinte individuals (parent plants) from multiple natural populations to create a set of 10,000 progeny of known pedigree. These progeny are being phenotype for traits related to domestication and local adaptation. A combination of whole genome sequences for the 120 parents along with GBS data for the 10,000 progeny provides a knowledge of the whole genome sequences of the all 10,000 progeny. These data will be used to address questions about quantitative genetic parameters in teosinte, map genes for trait variation, investigate inbreeding depression, and compare the contributions of different functional classes of genomic variants to trait variation. Potential projects are flexible within the scope of the project. The postdoctoral associate will work with other team members on the creation and analysis of this large dataset combining phenotypes, pedigrees, and GBS marker data for the 10,000 of teosinte plants. Approximately of these data are currently available and ready for analysis, thus the postdoctoral associate can expect to begin working on analyses for publication during the first year of their appointment. There is also an opportunity to collaborate with other Panzea labs to compare teosinte population genomic data to that for maize landraces. The initial appointment is one year, with the potential for additional years of support conditional on performance. Start dates are open-ended, with preference for earlier dates. A Ph.D. in statistical genetics, quantitative genetics, or closely related field is required. We seek applicants with proficiency in R and/or SAS programing and a strong background in quantitative genetics. To apply, please send (1) a cover letter explaining your interest in the position, (2) a CV, and (3) contact information (phone number and email) for three references to jdoebley@wisc.edu. SALARY: $42,840 PROPOSED HIRE DATE: June 1, 2015 or later —Boundary_(ID_DDmTsNii19FRDai8jJczNg) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: quoted-printable

A postdoctoral research associate position is available in the laboratory of John Doebley at the University of Wisconsin-Madison to study the quantitative genetics and genomics of teosinte, the progenitor of maize. 

The postdoctoral associate will work as a member of the NSF-funded Panzea project (www.panzea.org) and use population genomics to understand the genetic architecture of domestication traits and inbreeding depression in natural populations of teosinte.

We bred 120 teosinte individuals (parent plants) from multiple natural populations to create a set of 10,000 progeny of known pedigree. These progeny are being phenotype for traits related to domestication and local adaptation.  A combination of whole genome sequences for the 120 parents along with GBS data for the 10,000 progeny provides a knowledge of the whole genome sequences of the all 10,000 progeny. These data will be used to address questions about quantitative genetic parameters in teosinte, map genes for trait variation, investigate inbreeding depression, and compare the contributions of different functional classes of genomic variants to trait variation.  Potential projects are flexible within the scope of the project.   

The postdoctoral associate will work with other team members on the creation and analysis of this large dataset combining phenotypes, pedigrees, and GBS marker data for the 10,000 of teosinte plants.  Approximately of these data are currently available and ready for analysis, thus the postdoctoral associate can expect to begin working on analyses for publication during the first year of their appointment. There is also an opportunity to collaborate with other Panzea labs to compare teosinte population genomic data to that for maize landraces.  

The initial appointment is one year, with the potential for additional years of support conditional on performance. Start dates are open-ended, with preference for earlier dates.

A Ph.D. in statistical genetics, quantitative genetics, or closely related field is required. We seek applicants with proficiency in R and/or SAS programing and a strong background in quantitative genetics.  To apply, please send (1) a cover letter explaining your interest in the position, (2) a CV, and (3) contact information (phone number and email) for three references to jdoebley@wisc.edu.

SALARY:  $42,840

PROPOSED HIRE DATE:  June 1, 2015 or later

—Boundary_(ID_DDmTsNii19FRDai8jJczNg via Gmail
Source: EVOLDIR
02:40

—_000_37A911CEA0DC4FA68E9E535B22CDEDEFexeteracuk_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable We are seeking PhD candidates for a funded PhD at the University of Exeter working on eukaryotic cell and genome evolution. This award is funded through the generous donation from the Lawrence Charitable Trust and Mrs Carlotta Palmer and from the College of Life and Environmental Sciences. As a result of philanthropic gifts and with the aim of supporting research into understanding complex systems through interdisciplinary study and analysis of large datasets, the University of Exeter is looking to recruit a student to study for PhD starting in 2015. The appointed graduate researcher will be based in the research team of Tom Richards who use omics’ technologies to understand the evolutionary history of complex cellular life (i.e. the rise and diversification of the eukaryotes). Due to the nature of this studentship and the unique manner in which it is funded, applicants are encouraged to identify and develop their own line of research within the wider research aims of host laboratory. Currently, the work of the host laboratory covers four areas: 1) Using environmental DNA analysis and single cell genomics to understand the diversity of microbial life and how this fits into the tree of life. 2) The role of horizontal gene transfer in the evolution of pathogenic traits. 3) Understanding the nature and characteristic of the last eukaryotic common ancestor. 4) Developing experimental model systems to study cell-cell mutualistic interactions. Candidates are encouraged to contact the supervisor and discuss project topics of interest prior to making an application at t.a.richards@exeter.ac.uk Further information about the studentship application can be found here: http://bit.ly/1Fuhl9m —_000_37A911CEA0DC4FA68E9E535B22CDEDEFexeteracuk_ Content-Type: text/html; charset=”Windows-1252” Content-ID: Content-Transfer-Encoding: quoted-printable We are seeking PhD candidates for a funded PhD at the University of Exeter working on eukaryotic cell and genome evolution. This award is funded through the generous donation from the Lawrence Charitable Trust and Mrs Carlotta Palmer and from the College of Life and Environmental Sciences.

As a result of philanthropic gifts and with the aim of supporting research into understanding complex systems through interdisciplinary study and analysis of large datasets, the University of Exeter is looking to recruit a student to study for PhD starting in 2015. The appointed graduate researcher will be based in the research team of Tom Richards who use omics’ technologies to understand the evolutionary history of complex cellular life (i.e. the rise and diversification of the eukaryotes). Due to the nature of this studentship and the unique manner in which it is funded, applicants are encouraged to identify and develop their own line of research within the wider research aims of host laboratory. Currently, the work of the host laboratory covers four areas:

1)      Using environmental DNA analysis and single cell genomics to understand the diversity of microbial life and how this fits into the tree of life.

2)      The role of horizontal gene transfer in the evolution of pathogenic traits.

3)      Understanding the nature and characteristic of the last eukaryotic common ancestor.

4)      Developing experimental model systems to study cell-cell mutualistic interactions.

Candidates are encouraged to contact the supervisor and discuss project topics of interest prior to making an application  at t.a.richards@exeter.ac.uk

Further information about the studentship application can be found here: http://bit.ly/1Fuhl9m —_000_37A911CEA0DC4FA68E9E535B22CDEDEFexeteracuk via Gmail

Source: EVOLDIR
02:22

—089e0115eca6a2d2fd051173266e Content-Type: text/plain; charset=UTF-8 Postdoctoral Fellow position, Mathematical Modeling of Infectious Disease, Harvard University, Boston, MA, USA The Program for Evolutionary Dynamics at Harvard University welcomes applications for a postdoctoral fellow to work in the field of infectious disease modeling with Dr. Alison Hill and Professor Martin Nowak. We are seeking a motivated and creative PhD-level scientist with experience applying mathematics to biological systems. The successful candidate would be invited to work on established projects, as well as be encouraged to pursue independent research of mutual interest. A major focus of the group is on an NIH-funded effort to develop mathematical models to predict the outcomes of new, potentially-curative treatment strategies for HIV infection. We also use viral dynamic models to understand outcomes of antiretroviral therapy, the risks of drug resistance, the influence of patient adherence, and the potential impact of new drug delivery mechanisms. We regularly work with data from experimental collaborators testing new therapies in vitro, in animal models, and in patients. More generally, we are interested in factors influencing the evolution of infectious diseases and the emergence of drug resistance, both at the individual and population levels. Our work is conducted in close collaboration with experimental and clinical researchers. More information about the position can be found at : http://bit.ly/1CqCDFX Inquiries can be directed to Alison Hill (alhill@fas.harvard.edu) —089e0115eca6a2d2fd051173266e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Postdoctoral Fellow position, Mathematical Modeling of Infectious Disease, Harvard University, Boston, MA, USAThe Program for Evolutionary Dynamics at Harvard University welcomes applications for a postdoctoral fellow to work in the field of infectious disease modeling with Dr. Alison Hill and Professor Martin Nowak. We are seeking a motivated and creative PhD-level scientist with experience applying mathematics to biological systems. The successful candidate would be invited to work on established projects, as well as be encouraged to pursue independent research of mutual interest. A major focus of the group is on an NIH-funded effort to develop mathematical models to predict the outcomes of new, potentially-curative treatment strategies for HIV infection. We also use viral dynamic models to understand outcomes of antiretroviral therapy, the risks of drug resistance, the influence of patient adherence, and the potential impact of new drug delivery mechanisms. We regularly work with data from experimental collaborators testing new therapies in vitro, in animal models, and in patients. More generally, we are interested in factors influencing the evolution of infectious diseases and the emergence of drug resistance, both at the individual and population levels. Our work is conducted in close collaboration with experimental and clinical researchers. More information about the position can be found at : http://bit.ly/1CqCDFXInquiries can be directed to Alison Hill (alhill@fas.harvard.edu) —089e0115eca6a2d2fd051173266 via Gmail
Source: EVOLDIR
02:06
Graduate position: Berlin.ConservationFisheries A three–year Early Stage Researcher (ESR), preferably a doctoral (PhD) student, in the field of “Economic and Social Value of Conservation of Endangered Migratory Fishes” is sought within a newly funded EU Marie Skłodowska-Curie Initial Training Network (ITN) entitled IMPRESS. IMPRESS (Improved production strategies for endangered freshwater species, www.impress-itn.eu) is coordinated by the Norwegian University of Life Sciences (NBUM) in Oslo, Norway, and involves 15 ESRs hosted by 9 different organizations in Europe. The candidate sought here will join the Fisheries Research group of Prof. Dr. Robert Arlinghaus in the Department of Biology and Ecology of Fishes at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries in Berlin, Germany and shall be recruited by June, 1, 2015. More details on the position and how to apply can be found here: http://bit.ly/1MHZpsh Robert Arlinghaus Prof. Dr. Robert Arlinghaus Leibniz-Institute of Freshwater Ecology and Inland Fisheries Department of Biology and Ecology of Fishes Müggelseedamm 310 12587 Berlin and Laboratory for Integrative Fisheries Management Faculty of Life Sciences Albrecht-Daniel-Thaer-Institute of Agriculture and Horticulture Humboldt-Universität zu Berlin For running projects: www.besatz-fisch.de http://bit.ly/1MHZpsj http://bit.ly/1LmiyEF For further information and publication download: http://bit.ly/1LmiyEH www.besatz-fisch.de http://bit.ly/1MHZrR3 http://bit.ly/1LmiyEM News on twitter: http://bit.ly/1Lmiwwxwww.impress-itn.eu) is coordinated by the Norwegian University of Life Sciences (NBUM) in Oslo, Norway, and involves 15 ESRs hosted by 9 different organizations in Europe. The candidate sought here will join the Fisheries Research group of Prof. Dr. Robert Arlinghaus in the Department of Biology and Ecology of Fishes at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries in Berlin, Germany and shall be recruited by June, 1, 2015. More details on the position and how to apply can be found here: http://bit.ly/1MHZpsh Robert Arlinghaus Prof. Dr. Robert Arlinghaus Leibniz-Institute of Freshwater Ecology and Inland Fisheries Department of Biology and Ecology of Fishes Müggelseedamm 310 12587 Berlin and Laboratory for Integrative Fisheries Management Faculty of Life Sciences Albrecht-Daniel-Thaer-Institute of Agriculture and Horticulture Humboldt-Universität zu Berlin For running projects: www.besatz-fisch.de http://bit.ly/1MHZpsj http://bit.ly/1LmiyEF For further information and publication download: http://bit.ly/1LmiyEH www.besatz-fisch.de http://bit.ly/1MHZrR3 http://bit.ly/1LmiyEM News on twitter: http://bit.ly/1Lmiwwx Kate Laskowski via Gmail
Source: EVOLDIR
01:35
Position or Title: Postdoctoral Researcher in Fish Genomics and Genetics Agency/State: University of Toledo, Ohio Responsibilities: The research entails helping to develop, test, and publish a Next-generation sequence assay for detecting and identifying all Great Lakes native and invasive fish species, including those anticipated to invade, from environmental DNA and plankton samples. The postdoc will organize large DNA sequence databases, train and co-supervise students and technicians, and publish results in high-impact journals. Qualifications: Ph.D. degree required in hand. Publication of Ph.D. results in peer-reviewed journals required. Excellent recommendation from former advisors required. Teaching and supervisory experience preferred. Data management experience, bioinformatics, and data analysis experience in molecular phylogenetics and population genetics required. DNA extraction, PCR, DNA Sequencing (Sanger and Illumina MiSeq), alignment, and GenBank experience required. Familiarity with QIMME, Unix/Linux operating systems and writing Perl is a plus. Strong communication (written, oral) skills required. Salary: Competitive salary, full benefits. Ad Closing Date: April 15, 2015 or until filled Contact/Email: carol.stepien@utoledo.edu How to Apply Send (1) cover letter, (2) CV, (3) 2 letters of reference, (4) unofficial copies of graduate and undergraduate transcripts via .pdf to Dr. Stepien at carol.stepien@utoledo.edu. The University of Toledo is an Equal Access, Equal Opportunity, Affirmative Action Employer and Educator and is committed to increasing the diversity of our campus. Weblink: http://bit.ly/1seQy6U Carol A. Stepien, Ph.D. Distinguished University Professor of Ecology & Director of the Lake Erie Center University of Toledo 6200 Bayshore Rd. Oregon OH 43616 carol.stepien@utoledo.edu 419-530-8362 http://bit.ly/YNTWi5 “Stepien, Carol” via Gmail
Source: EVOLDIR
01:20
PhD position at Bournemouth University: Project Title Human Biogeography: Comparative Phylogeography of Modern Humans and Other Organisms Project Summary Aims and Rationale - We will compare the published phylogeographies (genetic biogeographies) of modern humans with those of other vertebrates to elucidate the patterns of population movement in the past. The science of phylogeography provides an understanding of the population dynamics of species in relation to landscape, climate and human related processes over the last 50 thousand years. Species respond to these processes individually, for example using different refugia at different times. The location of these refugia is also determined by the geography and topography of the landscape. Phylogeography can be used to identify the location of these species refugia and/or the place of origin of domestic / commensal species. Methods - Phylogeographic studies have been performed on organisms as varied as red deer, trout, snails, oak trees, ferns and bacterial and viral pathogens like Black Death and Rabies. Studies have also been done on domestic (sheep, cattle, wheat) and commensal (house mouse, black rat) plants and animals. The data from most of these studies are deposited on GenBank (a freely accessible online database). The project will analyse such data to look at the various patterns seen in each species which can then be grouped by similarity according to geographical and genetic diversity indices. These will include the likely divergence dates of the diversity as well as the topology of the species’ phylogenetic tree or network diagrams. The data will also be analysed using GIS and associated geospacial statistics to help identify the place of origin and source of spread of populations. Hypotheses: Human phylogeographic patterns in Europe that relate to Upper Palaeolithic distribution change will generally have a North/South distribution similar to wild species coming out of ice age climate refugia. Those patterns with an East/West distribution will be similar to taxa whose climate refugia was in the East (or South East) or to that of domestic/commensal plants and animals whose origins lay in the South East, representing Neolithic or later distribution change. Clearly defined outputs - The outputs would include a paper submitted to a high impact journal (Nature, Science, PNAS) summarising the general results of the project. A further three papers are envisaged in subject specific journals like Molecular Ecology, Journal of Human Evolution and the Journal of Biogeography. The results of the work will also be presented at international meetings such as that of the Society of Molecular Biology and Evolution, the European Society of Human Evolution etc. Academic Impact Stewart’s paper in Science which looks at Late Pleistocene Humans outside of Africa in relation to the biogeographical patterns of other organisms suggests that there would be an appetite amongst the people in the human evolution community for such an analysis. The research will have an impact on biological anthropology (human evolution), biogeography and molecular ecology thanks to the production of a minimum of 4 publications as well as the participation at international conferences (see above). The evolution and population genetics (phylogeography) of humans receives a disproportionate amount of attention. Other organisms, although they do not receive the same depth of attention as humans represent the breadth of possible patterns and corresponding processes that can exist in organisms over these time scales. Comparing the genetic patterns in humans with those in other organisms will help identify similarities and differences between them. The ecological and general biological characteristics of similar and differing species’ patterns will help reduce the possible explanations for those patterns. For example humans are widespread geographically similar to wolves, ravens and pike but their phylogeographic patterns are different which may be driven by different limitations on their dispersals or the length of time since dispersal. Societal Impact The evolution of humans receives a lot of media coverage and Stewart is regularly interviewed by the media on this topic, both relating to his own research and that of other scientists (e.g. New Scientist, BBC World Service). The response of organisms to climate change is also of great interest to the public and receives a corresponding amount of media attention in light of current climatic changes and species’ range shifts. The proposed project will undoubtedly have a significant impact due to the public interest it generates. The understanding of population dynamics in species is important to future conservation of biotas, so the proposed project will have an important contribution to make to conservation planning. Stewart was involved in a Natural England consultancy project looking at the identification of future climate refugia and guide strategy. The proposed project will enhance the likelihood of the supervisory team, as well as the PhD student, being involved in such initiatives in the future which seem to be increasingly on the agenda of NDPDs (Natural England) and NGOs (RSPB) and which will likely influence UK government policy-makers. Such project will have the potential to be used as case impact for the REF2020. Training Opportunities The student will come away from this project with a unique skill set that bridges a number of important fields in modern day science such as biogeography, molecular ecology as well as human evolution. 1) The student will get training in performing analysis of molecular data (tree and network construction, BEAST etc.) as well as innovative meta-analytical methods developed by Stewart and Hardouin to analyse data from GenBank. The student will be trained in laboratory techniques used in analyses such as PCR, sequencing, electrophoresis and will likely take part in house mouse phylogeographic analyses (Hardouin). There will also be an opportunity for aDNA training with Richards in Huddersfiled University in his Leverhulm Trust funded Doctoral Scholarship Centre in Evolutionary Genomics. 2) The student will be trained in the essential tools of modern biogeography and conservation: statistical techniques and GIS methods for exploring species’ responses to climatic and anthropogenic changes (Stafford). 3) The student will also receive training in relevant human evolutionary science SUPERVISORY TEAM First Supervisor Dr John Stewart Additional Supervisors Emilie Hardouin Rick Stafford External Supervisor: Prof. Martin Richards, Huddersfiled University Recent publications by supervisors relevant to this project Stewart, J.R. and Stringer, C. B., 2012. Human Evolution Out of Africa: The Role of Refugia and Climate Change. Science, 335 (6074), 1317-1321. (IF- 31.48). Brace, S.; Palkopoulou, E.; Daln, L.; Lister, .M.; Miller, R. ; Otte, M. ; Germonpr, M.; Blockley, S.P.E. ; Stewart, J.R. & Barnes, I. 2012. Serial population extinctions in a small mammal indicate Late Pleistocene ecosystem instability. Proceedings of the National Academy of Sciences 109(50): 20532-6. (IF: 9.809). Lagerholm, V.K., Sandoval-Castellanos, E., Ehrich, D., Abramson, N.I., Nadachowski, A., Kalthoff, D.K., Germonpr, M., Angerbjrn, A., Stewart, J.R., Daln, L. 2014. On the origin of the Norwegian lemming. Molecular Ecology. doi:10.1111/mec.12698 (IF: 5.52). Stewart, J.R., Barnes, I., Lister, A.M. and Daln, L. 2010. Refugia Revisited: Individualistic responses in space and time. Proc. Roy. Soc. B. 277: 661 - 671. (IF: 5.683). Hardouin EA, Orth A, Teschke M, Tautz D, Bonhomme F: Worldwide mouse differentiation at microsatellite loci identifies the Iranian plateau as a phylogeographic hotspot. Accepted in BMC Evolutionary Biology (IF: 3.41). Hardouin EA, Tautz D: High mitochondrial mutation rates after an island colonization event - selection or near-neutrality? Biology Letters 2013, doi: 10.1098/rsbl.2012.1123. (IF: 3.35) Linnenbrink M, Wang J, Hardouin EA, Knzel K, Metzler D, Baines JF: The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Molecular Ecology 2013, doi: 10.1111/mec.12206. (IF: 5.52). Myles S, Lea AR, Ohashi J, Chambers KG, Weiss GJ, Hardouin E, Engelken J, Macartney-Coxson PD, Eccles AD, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M: Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics 2011, 12:10doi:10.1186/1471-2350-12-10. (IF: 2.33). Stafford R., Smith V.A., Husmeier D. Grima T. and Guinn B. 2013. Predicting ecological regime shift under climate change: new modelling and molecular-based approaches. Current Zoology. 59: 403-417. (F: 1.81) Stafford R., Goodenough A.E. and Hart A.G. 2013. A visual method to identify significant latitudinal changes in species’ distributions. Ecological Informatics.15: 74-84. (IF: 1.980) Pala, M., Olivieri, A., Achilli, A., Accetturo, M., Metspalu, E., Reidla, M., Tamm, E., Karmin, M., Reisberg, T., Hooshiar Kashani, B., Perego, U.A., Carossa, V., Gandini, F., Pereira, J.B., Soares, P., Angerhofer, N., Rychkov, S., Al-Zahery, N., Carelli, V., Sanati, M.H., Houshmand, M., Hatina, J., Macaulay, V., Pereira, L., Woodward, S.R., Davies, W., Gamble, C., Baird, D., Semino, O., Villems, R., Torroni, A., Richards, M.B. (2012). Mitochondrial DNA signals of Late Glacial re-colonisation of Europe from Near Eastern refugia. The American Journal of Human Genetics 90: 915-924. (IF: 10.987 ) Mellars, P., Gori, K., Carr, M., Soares, P., Richards M.B. (2013) Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc. Natl. Acad. Sci. USA 110:10699-10704. (IF: 9.809) Costa, M.D., Pereira, J.B., Pala, M., Fernandes, V., Olivieri, A., Achilli, A., Perego, U., Rychkov, Y., Naumova, O., Hatina, J., Woodward, S.R., Eng, S., Macaulay, V., Carr, M., Soares, P., Pereira L., Richards, M.B. (2013) A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications, 4: 2543. (IF: 10.742) INFORMAL ENQUIRIES Please feel free to contact John Stewart via email - jstewart@bournemouth.ac.uk for queries related to the research project. ELIGBILITY CRITERIA All candidates must satisfy the University’s minimum doctoral entry criteria for studentships of an honours degree at Upper Second Class (2:1) and/or an appropriate Masters degree. An IELTS (Academic) score of 6.5 minimum (or PhD Studentship Project Description March 2015 equivalent) is essential for candidates for whom English is not their first language The ideal candidate should have GIS skills, quantitative ecological modelling skills and field research skills and an MSc/ MRes degree in a related field. This project requires somebody who is confident in working in an African Savannah habitat and has the maturity to deal with field work under sometimes difficult conditions, to manage a research project if required, and who can work independently in the field. Field work experience will therefore be expected. HOW TO APPLY Please complete the BU Research Degree Application 2015 and submit it via email to the Postgraduate Research Administrator for Admissions Suzy Kempinski - pgradmissions@bournemouth.ac.uk by 1 May 2015. Further information on the application process can be found at http://bit.ly/1GX0cHc Dr. Emilie Hardouin Associate lecturer in Conservation Genetics Bournemouth University Faculty of Science and Technology Christchurch House Talbot Campus Poole, Dorset BH12 5BB United Kingdom Tel: +0044 (0)1202 962402 BU is a Disability Two Ticks Employer and has signed up to the Mindful Employer charter. Information about the accessibility of University buildings can be found on the BU DisabledGo webpages This email is intended only for the person to whom it is addressed and may contain confidential information. If you have received this email in error, please notify the sender and delete this email, which must not be copied, distributed or disclosed to any other person. Any views or opinions presented are solely those of the author and do not necessarily represent those of Bournemouth University or its subsidiary companies. Nor can any contract be formed on behalf of the University or its subsidiary companies via email. Emilie Hardouin via Gmail
Source: EVOLDIR
00:16
"Dear Colleagues, Just as a gentle reminder: The abstract deadline for the "Evolutionary Medicine Conference: Interdisciplinary Perspectives on Human Health and Disease" (Juli 30-August 1 2015 in Zurich, Switzerland) is approaching now: - Abstract Deadline: March 30, 2015 - Early registration Deadline: May 31, 2015 Find all relevant information (abstract submission, registration, accommodation, etc.) on our official conference webpage: http://bit.ly/1u6ggSh Please get in contact with us if you have questions: evolmedconf@gmail.com Thanks for sharing the event and the call for abstracts among your colleagues! We would be happy to welcome you in Zurich soon… Best wishes Frank Rhli, Nicole Bender and Kaspar Staub (Conference Organisers)” Dr. Kaspar Staub Institute Manager, Senior Research Assistant Morphology/Imaging Group Institute of Evolutionary Medicine (IEM) University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Office Y42 G88a Phone +41 44 635 05 13, Mobile +41 79 473 83 55, Fax: +41446355702 kaspar.staub@iem.uzh.ch http://bit.ly/1u6getA Kaspar Staub via Gmail
Source: EVOLDIR