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December 6, 2014
—Apple-Mail=_01AEE7C8-AFE1-4F1D-AA4B-596E59D51CE4 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Carl R. Woese Postdoctoral Fellowship Program As a faculty member of the University of Illinois for nearly 50 years and a founding member of the Institute for Genomic Biology, we honor the legacy of Carl R. Woese with the establishment of the Woese Fellowship. Woese Fellows will be truly exceptional young scholars who have completed their Ph.D. within the last several years, and are at the forefront of their field in evolution and the emergence of life, or other rapidly developing areas of quantitative biology and genomics. The closing date for all positions is February 1, 2015. Visit http://bit.ly/12LFCsx to apply. —Apple-Mail=_01AEE7C8-AFE1-4F1D-AA4B-596E59D51CE4 Content-Disposition: attachment; filename=UI.CarlRWoese.Postdoc.txt Content-Type: text/plain; name=”UI.CarlRWoese.Postdoc.txt” Content-Transfer-Encoding: quoted-printable Carl R. Woese Postdoctoral Fellowship Program As a faculty member of the University of Illinois for nearly 50 years and a founding member of the Institute for Genomic Biology, we honor the legacy of Carl R. Woese with the establishment of the Woese Fellowship. Woese Fellows will be truly exceptional young scholars who have completed their Ph.D. within the last several years, and are at the forefront of their field in evolution and the emergence of life, or other rapidly developing areas of quantitative biology and genomics. The closing date for all positions is February 1, 2015. Visit http://bit.ly/12LFCsx to apply. —Apple-Mail=_01AEE7C8-AFE1-4F1D-AA4B-596E59D51CE4 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii —Apple-Mail=_01AEE7C8-AFE1-4F1D-AA4B-596E59D51CE via Gmail
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Postdoc position in Behavioural Ecology and Experimental Population Dynamics of Common Lizards (Zootoca vivipara) at the University of Lausanne, Switzerland. A 20-month postdoc position in behavioural ecology and experimental population dynamics is available in the research group of Prof. Patrick S. Fitze (University of Lausanne, Department of Ecology and Evolution www.unil.ch/dee). The position is part of an SNF-funded project aimed at studying the link between experimental population dynamics, sexual selection and coloration in the common lizard (Zootoca vivipara). It will investigate trans-generational survival selection in Rock-Paper-Scissors games. The project will involve both field and laboratory work. Applied methodologies will include the analyses of behaviour, colouration, and population dynamics. Fieldwork will be conducted over several months (5-8 month: March to October) per year in Jaca, in the Spanish Pyrenees. Our international laboratory has a wide range of research interests, ranging from behavioural analyses, to the study of experimental population dynamics, population genetics and phylogenetics. Please browse our group website for further details: http://bit.ly/1FWYhxy. We are seeking an enthusiastic, highly motivated and creative candidate with keen interest in evolutionary biology, and the capacity to work independently and as a team member. Applicants must have a PhD in biological sciences with expertise in statistics (knowledge of the R statistical package is an advantage). Good English writing and organisational skills are essential. The ideal candidate will have prior experience in experimental design, behavioural and colorimetric analyses, experimental population dynamics, and reptile handling, as well as good communication skills. Moreover, he is interested in coloration and colour polymorphisms and has previous experience with lizards. The working language of the laboratory is English. Knowledge of French and/or Spanish is useful, but not essential. Applications should be sent by email to Prof. Patrick S. Fitze (Patrick.Fitze@unil.ch). The application should consist of a single pdf-file, including a CV, a letter outlining motivation and research interests (max. 1 A4 page), the names of three referees (including e-mail address and phone number), and a summary of the candidates PhD or postdoc project (max. 2 A4 pages). Relevant, publications should be included at the end of the file. The deadline for application is January 15th 2015. Preferred starting date is March 1st 2015. Short listed candidates will be invited to Lausanne for interview at the end of January/ start of February 2015. The salary of the successful candidate will be determined in accordance with the guidelines of the Swiss National Science Foundation (www.snf.ch). The successful candidate will join a bustling research department consisting of 22 research groups with diverse study interests, ranging from evolutionary biology and ecology to applied ecology and conservation biology http://bit.ly/1FWYhxC For additional information, please do not hesitate to contact: Patrick S. Fitze Assistant Professor SNF Department of Ecology and Evolution (DEE) Biophore, University of Lausanne room: 4309 1015 Lausanne phone: + 41 (0) 216924270 Switzerland Fax: + 41 (0) 216924165 http://bit.ly/1w8BTlwwww.unil.ch/dee). The position is part of an SNF-funded project aimed at studying the link between experimental population dynamics, sexual selection and coloration in the common lizard (Zootoca vivipara). It will investigate trans-generational survival selection in Rock-Paper-Scissors games. The project will involve both field and laboratory work. Applied methodologies will include the analyses of behaviour, colouration, and population dynamics. Fieldwork will be conducted over several months (5-8 month: March to October) per year in Jaca, in the Spanish Pyrenees. Our international laboratory has a wide range of research interests, ranging from behavioural analyses, to the study of experimental population dynamics, population genetics and phylogenetics. Please browse our group website for further details: http://bit.ly/1FWYhxy. We are seeking an enthusiastic, highly motivated and creative candidate with keen interest in evolutionary biology, and the capacity to work independently and as a team member. Applicants must have a PhD in biological sciences with expertise in statistics (knowledge of the R statistical package is an advantage). Good English writing and organisational skills are essential. The ideal candidate will have prior experience in experimental design, behavioural and colorimetric analyses, experimental population dynamics, and reptile handling, as well as good communication skills. Moreover, he is interested in coloration and colour polymorphisms and has previous experience with lizards. The working language of the laboratory is English. Knowledge of French and/or Spanish is useful, but not essential. Applications should be sent by email to Prof. Patrick S. Fitze (Patrick.Fitze@unil.ch). The application should consist of a single pdf-file, including a CV, a letter outlining motivation and research interests (max. 1 A4 page), the names of three referees (including e-mail address and phone number), and a summary of the candidates PhD or postdoc project (max. 2 A4 pages). Relevant, publications should be included at the end of the file. The deadline for application is January 15th 2015. Preferred starting date is March 1st 2015. Short listed candidates will be invited to Lausanne for interview at the end of January/ start of February 2015. The salary of the successful candidate will be determined in accordance with the guidelines of the Swiss National Science Foundation (www.snf.ch). The successful candidate will join a bustling research department consisting of 22 research groups with diverse study interests, ranging from evolutionary biology and ecology to applied ecology and conservation biology http://bit.ly/1FWYhxC For additional information, please do not hesitate to contact: Patrick S. Fitze Assistant Professor SNF Department of Ecology and Evolution (DEE) Biophore, University of Lausanne room: 4309 1015 Lausanne phone: + 41 (0) 216924270 Switzerland Fax: + 41 (0) 216924165 http://bit.ly/1w8BTlw Patrick Fitze via Gmail
Graduate Fellowship Insect Systematics and Evolution Pennsylvania State University The Deans Lab at the Frost Entomological Museum has an opening for a PhD student interested in the evolution of parasitoid Hymenoptera. The project includes the collection and analysis of molecular and morphological data, development and testing of semantic approaches to phenotype representation, and next generation monography. The student will be part of a highly integrative and energetic lab group, led by Drs. Andrew R. Deans, Heather M. Hines, and Istvn Mik. The student will also have myriad opportunities to participate in collecting expeditions and museum visits, both domestic and abroad. PIs: http://deanslab.org/ (Deans; email@example.com) via Gmail
December 5, 2014
The Science Education And Society (SEAS) research program (http://bit.ly/1FWJJOw) is recruiting graduate students as RAs and TAs (Masters and PhD) to be a part of many exciting projects related to science education. We are a new lab housed in the College of the Environment and Life Sciences (CELS) at the University of Rhode Island (http://bit.ly/1z6dEnb). We pursue broad questions relating to educational psychology, identity constructs and social belonging among K-PhD students (especially URMs), with an interest in how our findings can inform curriculum development and general campus climate. We seek students who have a strong disciplinary background in biology and are primarily interested in pursuing a career relating to science education research. Our program collaborates closely with the College of Education, the Department of Sociology and Anthropology and the Department of Cell and Molecular Biology. Students have the option of pursuing courses and collaborations with these departments and others in line with their research interests. Students interested in PhD or Masters course of study are strongly encouraged to contact me (Dr. Bryan M. Dewsbury) directly by email (firstname.lastname@example.org) with a CV and an introductory letter indicating why you might be a good fit for this program. The university deadline for application is January 15th, 2015, so interested students should contact me well in advance of that deadline. Thanks in advance. Bryan Dewsbury, PhD Assistant Professor Department of Biology University of Rhode Island 120 Flagg Road, Kingston, RI, 02881 Phone - (401) 874 2248 Fax - (401) 874 4256 Office: CBLS 483 Lab: Woodward Hall 112 http://bit.ly/1FWJJOy @BMDewsbury Bryan Dewsbury via Gmail
Conservation genomics: predicting the adaptive potential of the endangered New Zealand hihi (stitchbird; *Notiomystis cincta*) A PhD scholarship, funded by a New Zealand Marsden Fund Grant, is available with Dr Anna Santure in the School of Biological Sciences, University of Auckland, New Zealand. This project is an exciting opportunity to use genomics and statistical genetics approaches to understand and predict the adaptive potential of the endangered New Zealand hihi (stitchbird; *Notiomystis cincta*). Determining the adaptive potential of wild populations requires that we understand the genetic basis of traits that are important for survival and reproduction in these populations. In this project, we will characterise the genetic basis of morphological and life history traits in the reintroduced Tiritiri Matangi Island population of hihi, in order to understand the potential of the species to respond to changing environmental pressures, including anthropogenic climate change. Hihi are an ideal study system because, in addition to being a wonderful example of eccentric New Zealand wildlife, a reintroduced population of birds on Tiritiri Matangi Island has been intensively monitored since introduction and we have a wealth of data on morphological and life history traits, social and genetic relationships, DNA samples and environmental variables. The project student will be responsible for helping to develop a genomic toolkit for hihi, using this toolkit to determine the genetic basis of traits in the population using genetic linkage mapping and association, and investigating genetic trade-offs between traits that may constrain the adaptive potential of the species. We are looking for a candidate with a strong background in statistics, bioinformatics, mathematics, computer programming or similar, as well as a passion for genetics, ecology and conservation biology. The PhD position requires the applicant to be eligible for admission to the PhD programme at the University of Auckland (see http://bit.ly/1vv5DHt; please note the English language proficiency requirements). Candidates should ideally have a GPA of 7 or above; international students are welcome to apply. This project is a collaboration with Drs Patricia Brekke and John Ewen at the Institute of Zoology, Zoological Society of London, see http://bit.ly/1vv5DHv. To apply for this position, please email Dr Anna Santure (email@example.com) with your cv, names and details of two referees, your academic transcript, and a short statement of interest. I welcome informal enquiries. The PhD scholarship is available from 1 March 2015 and covers tuition fees and provides an annual tax free allowance of NZD$25,000 for three years. The closing date is 16 January 2015. firstname.lastname@example.org via Gmail
EMPLOYMENT OPPORTUNITY December 3, 2014 14-113 POSTDOCTORAL SCIENTIST – GENETICS Searching for an enthusiastic postdoctoral researcher to work on single cell genomics of the malaria parasites, Plasmodium falciparum and Plasmodium vivax. Plasmodium parasites are of huge medical importance, causing ~700,000 deaths per year and millions of infections. However, we know little about how genetic diversity of parasites within an infection partitions between individual parasite genomes, or how this impacts disease pathogenesis and treatment. This work will explore this “black box” in malaria research. It will be a cross-disciplinary project which combines fluorescence activated cell sorting, single genome sequencing and statistical genetics approaches to ask key questions about within-host variation of malaria infections in Malawi and Thailand. The postdoctoral scientist will report to Dr. Ian Cheeseman. RELEVANT PUBLICATIONS Nair S, Nkhoma SC, Serre D, Zimmerman PA, Gorena K, Daniel BJ, Nosten F, Anderson TJ, Cheeseman IH. Single-cell genomics for dissection of complex malaria infections. Genome Res 2014; Jun; 24(6):1028-38. PMCID: PMC4032849 Nkhoma SC, Nair S, Cheeseman IH, Rohr-Allegrini C, Singlam S, Nosten F, Anderson TJ: Close kinship within multiple-genotype malaria parasite infections. Proc Biol Sci 2012; 279(1738):2589-2598. PMCID: PMC3350702. EDUCATION/EXPERIENCE/SKILLS: REQUIRED: Ph.D. in genetics, parasitology, molecular biology or a related discipline. The applicant is expected to work closely with the PI on this project, though there will be opportunities to pursue independent research projects. Preferred: Applicants with strong laboratory skills and experience in flow cytometry, cell culture or molecular biology, though training will be available in the approaches used in this project. POTENTIAL HAZARDS: This position may involve exposure to cryogenics, bulk cleaning products, and infectious materials (BSL-2). Participation in a medical monitoring and surveillance program is required. Safety training and protective clothing, equipment and supplies will be provided. OTHER: This is a full-time salaried (exempt) position. Texas Biomedical Research Institute business hours are Monday through Friday - 8:00 a.m. to 5:00 p.m. Apply online at http://bit.ly/1CLQkyZ. Application packets are accepted electronically or in hard copy. A completed application packet is a requirement for all positions. Incomplete applications will not be accepted. EOE Ian Cheeseman via Gmail
Subject: Annual call for proposals CEBA 2015, French Guiana The CEnter for the study of Biodiversity in Amazonia (CEBA) is a Laboratory of Excellence based in French Guiana aimed at fostering knowledge on terrestrial biodiversity. The Labex CEBA aims to coordinate research capacity in France on the topic of Amazonian terrestrial biodiversity, and to reinforce collaborations with South American and other international partners. Details are available at http://bit.ly/1aQNBAs The Labex CEBA opens an annual competitive call for proposals to encourage innovative research on biodiversity in French Guiana. Projects will be evaluated by the Scientific Board and by external referees. The submission deadline is January 23th, 2015. To access the call for proposals form: http://bit.ly/ICgz0L Amaia IRIBAR-PELOZUELO Charge de coordination scientifique CEBA Laboratoire Evolution et Diversit Biologique UMR 5174 Universit Paul Sabatier, bt 4R1, bureau 124 118 route de Narbonne, 31062 Toulouse Cedex 9 - France tl : + 33 (0)5 61 55 64 95 fax : + 33 (0)5 61 55 73 27 link: www.labex-ceba.fr Amaia Iribar-Pelozuelo via Gmail
# Population Genetics in R Hackathon - Open Call for Participation # Do you develop population genetics methods or algorithms in R? Are you a researcher wrestling with analyzing population genetics data in R? Have you run into difficulties with passing data or metadata from one R package to another? Have you run into problems with large datasets? Have you found documentation on building workflows from packages for population genetics analysis difficult to come by? Do you have expertise and ideas to share and energy to spend on overcoming these challenges? Do you enjoy collaborating with like-minded others to do so? If you answered some (or all) of these questions with yes, then the following event may be for you. ## Synopsis NESCent is sponsoring a hackathon to be held at NESCent in Durham, North Carolina, on March 16-20, 2015, with the objective to help foster an interoperating ecosystem of scalable tools and resources for population genetics data analysis in the popular R platform. The event is designed to target interoperability, scalability, and workflow building challenges among the many population genetics R packages that already exist. The gathering provides an opportunity for a diverse group of population genetics researchers, method developers, and people with other relevant areas of expertise to collaborate on code, documentation, use-cases, and other resources that will aid their communities. Full details and additional background are available at the following website: http://bit.ly/1CLN5Yh ## How to participate Applications to participate in the hackathon are now being accepted. To apply, please fill out the following form: http://goo.gl/forms/siwNo1P3ti Deadline for receiving your application is December 11, 2014. Support for travel, food and lodging costs are available to successful applicants who indicate need. We particularly welcome applications from women and members of other groups underrepresented in science and in software engineering. Our plan is to begin sending out acceptance letters December 15, 2014, and if your application is successful, we will need you to confirm attendance within 2 days of receiving notice, so please ensure you can receive and send email during the week of December 15. Sincerely, The organizing team: Thibaut Jombart, Hilmar Lapp, St?phanie Manel, Emmanuel Paradis, Bastian Pfeifer, and Greg Warnes via Gmail
The Evolution, Medicine, & Public Health Foundation invites nominations for the Omenn Prize of $5000 to be awarded in March 2015 for the best article published in 2014 in any scientific journal on a topic related to evolution in the context of medicine and public health. Full information at http://bit.ly/1ymlt9q The prize, provided by the generosity of Gilbert S Omenn, will be awarded to the first author of the winning article. Authors are encouraged to nominate their own articles, but nominations of articles by others are also welcome. Nominations, including a brief statement in the body of the email (max. 250 words), a copy of the article (if distribution is permitted) or abstract and article link, must be submitted by 21 January, 2015 at 5 PM US Eastern Standard Time. All applications should be sent to OmennPrize@evolutionarymedicine.org Any relevant peer-reviewed article published online or in print in 2014 is eligible, but the prize is intended for work that uses evolutionary principles to advance understanding of a disease or disease process. The prize committee will give priority to articles with implications for human health, but many basic science or theoretical articles have such implications. The Prize Committee for this year is chaired by Sarah Tishkoff, and its members are Joe Alcock, Noah Rosenberg, and Alison Galvani. Papers by committee members, their students and lab group members are not eligible, and articles by their co-authors or close associates are subject to special conditions. The winner will be invited to present a talk at the March 19-21 meeting of the International Society for Evolution and Medicine in Tempe Arizona. http://bit.ly/1ymlr1g Randolph Nesse President, The Foundation for Evolution, Medicine, & Public Health http://bit.ly/1fzv2mt email@example.com via Gmail
The Department of Ecology, Evolution and Organismal Biology at Iowa State University has a strong and growing group of evolutionary biologists. We are actively recruiting highly motivated students as MS and PhD candidates in our program. The following faculty are seeking graduate students for the fall 2015: Dean Adams: Evolution of the multivariate phenotype. We strive to understand microevolutionary and macroevolutionary patterns of phenotypic diversification, and the historical and ecological processes responsible for them using a comparative evolutionary framework to examine patterns and processes across related species over evolutionary time. http://bit.ly/17WymFM Anne Bronikowski: Integrative genomics of senescence in reptiles. We study senescence across multiple biological scales and use transcriptome sequencing, physiological assays, and mathematical modeling to understand molecular pathway evolution in reptiles and correlated evolution in cellular/organismal phenotypes and population demography. http://bit.ly/18ePs7B Tracy Heath: Statistical phylogenetics, computational biology, macroevolution, molecular evolution. Research involves integrative Bayesian modeling to understand evolutionary processes driving patterns of diversification in the tree of life. http://bit.ly/1BjIriH Matthew Hufford: Evolutionary Genomics of Wild and Domesticated Maize. Opportunities are available to study gene flow, adaptive introgression, and parallel adaptation to high altitude (e.g., in central Mexico and the Andes) in maize and its wild relatives. http://bit.ly/17Di5bm. John Nason: Evolution and ecology of plant-insect interactions. Research employs observational, experimental, and genetic approaches to understand how plant population size and reproductive traits are influenced by environmental gradients and how this variation, in turn, influences local- and geographical-scale dynamics in a pollination mutualism subject to parasitism. http://bit.ly/17Wyl4E Kevin Roe: Systematics and conservation genetics of aquatic organisms. Current projects include 1) conservation genetics of endangered species including the endemic Iowa Pleistocene Snail, 2) molecular ecology of freshwater mussels (Unionoida, especially the role of hosts in maintaining gene flow or driving diversification, and 3) phylogenetic systematics and biogeography of molluscs, crustaceans and fishes. http://bit.ly/18ePpZv Jeanne Serb: Evolution of sensory systems in invertebrates. We take a comparative approach to examine the origin of, and links between, sensory signaling pathways. Research approach integrates transcriptomics, molecular biology, protein expression, and phylogenetics. http://bit.ly/17WymFO Amy Toth: Evolution, behavior, and genetics of social insects, with a focus on honey bees and paper wasps, including research on the impacts of nutrition, disease, and landscape on pollinator health. http://bit.ly/18ePs7F Nicole Valenzuela: Evolution of sex determination and chromosomes in turtles: Our research spans classic ecology and evolutionary biology to evo-devo, ecological & evolutionary genomics to understand 1) Why do organisms vary so remarkably in the ways they produce males and females? and 2) What are the causes and consequences of chromosome evolution? http://bit.ly/17Wyl4I Jonathan Wendel: Molecular and genomic evolution of plants. We use genomic and systems biology approaches to study the mysterious and common phenomenon of polyploidy, with a special focus on the cotton genus. http://bit.ly/18ePpZx Interested students are encouraged to contact faculty directly with a letter of interest and CV. Research and teaching assistantships and a variety of fellowship opportunities are available. Students may apply to one of the interdepartmental graduate programs, such as Ecology and Evolutionary Biology (http://bit.ly/17WymFS), Interdepartmental Genetics (http://bit.ly/17WymFU) or Bioinformatics and Computational Biology (http://bit.ly/18ePpZy). The deadline for receipt of all application materials for graduate programs is 10 January 2015, although earlier submission is encouraged to ensure full consideration for available fellowships. Jeanne M. Serb Associate Professor Ecology, Evolution and Organismal Biology 245 Bessey Hall Iowa State University Ames, IA 50011 USA Tel: 515-294-7479 Fax: 515-294-1337 http://bit.ly/17WymFO “Serb, Jeanne M [EEOBA]” via Gmail
Vince Richards lab in the Department of Biological Sciences at Clemson University is accepting applications for a post-doctoral position available January 2015. The post-doc’s primary responsibility will be a USDA project investigating genetic population structure and transmission dynamics of the zoonotic pathogen Streptococcus agalactiae. This bacteria is an important pathogen that infects multiple species including humans, livestock, and aquaculture. Towards a better understanding of the evolution and transmission dynamics of S. agalactiae both within and across host species, this project leverages comparative genomic approaches to a global collection of hundreds of S. agalactiae strains isolated from a diverse range of host species. Other responsibilities include contributing to the ongoing research within the laboratory. The candidate should have a strong publication record, a background in population and evolutionary genetics, experience analyzing next-generation sequence data, and be well versed in Linux/bash. Strong communication and writing skills are essential. The position is available for 1.5 years, with the possibility of extension. Applicants should contact Vince Richards directly at firstname.lastname@example.org. Please provide a cover letter, CV, PDFs of representative publications, and contact information for three references. Clemson University is ranked 20th among national public universities by U.S. News & World Report and is located on Lake Hartwell near the Blue Ridge mountains in beautiful Upstate South Carolina. Vincent P Richards, Ph.D. Assistant Professor of Microbial Genomics Department of Biological Sciences Clemson University Clemson, SC 29634 email: email@example.com Lab website: http://bit.ly/1lgQmH6 Vincent Paul Richards via Gmail
We are pleased to announce details for the 2015 Evolutionary Genetics & Genomics Symposium (EGGS), a Genetics Society (http://bit.ly/1ci5jiG) sponsored sectional interest group. The meeting will be taking place in Cambridge (UK) on Tuesday 17th March 2015. The meeting is free to attend and no registration is required. The meeting aims to bring together people working on various aspects of evolutionary genetics, and has previously attracted an international line up of speakers and attendees. We have three invited speakers: -Josephine Pemberton, University of Edinburgh http://bit.ly/1yuxIPU -Nathan Bailey, University of St Andrews http://bit.ly/1vSLoSz -Aoife McLysaght, University of Dublin http://bit.ly/1yuxIQ0 Abstract registration is now open- please email your name, institution, position (student/postdoc/PI) and abstract by the 19th Feb 2015 to firstname.lastname@example.org Full details can be found on the meeting website: http://bit.ly/1ajPZUg via Gmail
December 4, 2014
—_000_998E9DE436A8FE48B11AFCE1F62451270C59A562expdag1n1uollea_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable Where : Univeristy of Leicester, UK What: Next Generation Sequencing Data analysis. When: 7th-9th January 2015 A few places are still remaining and are available for external applicants. Places will be allocated on a first-come-first-served basis. Next Generation Sequencing methods are becoming ubiquitous in all areas of biology. This three day workshop aims to enable wet-lab biologists to understand and implement basic pipelines for analysis of NGS data. Topics covered will include: * An overview of NGS technology * A brief introduction to library preparation * Common file formats * Quality Control * Genome Assembly * Mapping * Variant Calling The workshop will consist of a mixture of short talks and practical work. Participants are required to have some basic knowledge of Unix to enable them to follow the practical work. Further details and the registration form are available on the University of Leicester Bioinformatics and Biostatistics Analysis Support Hub (http://goo.gl/SKq27X). Please email me directly if you have any queries. Best wishes, Kate Kate Lee Research assistant Bioinformatics and Biostatistics Analysis Support Hub (BBASH) University of Leicester Tel: 0116 252 3350 Web: www.le.ac.uk/bbash —_000_998E9DE436A8FE48B11AFCE1F62451270C59A562expdag1n1uollea_ Content-Type: text/html; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable
Background: The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have recently been developed for parameter estimation and calculation of model likelihoods based on the joint AFS from two or more populations. We conducted a simulation study of one of these approaches, implemented in the Python module ?a?i, to compare parameter estimation and model selection accuracy given different sample sizes under one- and two-population models. Results: Our simulations included a variety of demographic models and two parameterizations that differed in the timing of events (divergence or size change). Using a number of SNPs reasonably obtained through next-generation sequencing approaches (10,000 - 50,000), accurate parameter estimates and model selection were possible for models with more ancient demographic events, even given relatively small numbers of sampled individuals. However, for recent events, larger numbers of individuals were required to achieve accuracy and precision in parameter estimates similar to that seen for models with older divergence or population size changes. We quantify i) the uncertainty in model selection, using tools from information theory, and ii) the accuracy and precision of parameter estimates, using the root mean squared error, as a function of the timing of demographic events, sample sizes used in the analysis, and complexity of the simulated models. Conclusions: Here, we illustrate the utility of the genome-wide AFS for estimating demographic history and provide recommendations to guide sampling in population genomics studies that seek to draw inference from the AFS. Our results indicate that larger samples of individuals (and thus larger AFS) provide greater power for model selection and parameter estimation for more recent demographic events.
Body size and allometric shape variation in the molly Poecilia vivipara along a gradient of salinity and predation
Background: Phenotypic diversity among populations may result from divergent natural selection acting directly on traits or via correlated responses to changes in other traits. One of the most frequent patterns of correlated response is the proportional change in the dimensions of anatomical traits associated with changes in growth or absolute size, known as allometry. Livebearing fishes subject to predation gradients have been shown to repeatedly evolve larger caudal peduncles and smaller cranial regions under high predation regimes. Poecilia vivipara is a livebearing fish commonly found in coastal lagoons in the north of the state of Rio de Janeiro, Brazil. Similar to what is observed in other predation gradients, lagoons inhabited by P. vivipara vary in the presence of piscivorous fishes; contrary to other poeciliid systems, populations of P. vivipara vary greatly in body size, which opens the possibility of strong allometric effects on shape variation. Here we investigated body shape diversification among six populations of P. vivipara along a predation gradient and its relationship with allometric trajectories within and among populations. Results: We found substantial body size variation and correlated shape changes among populations. Multivariate regression analysis showed that size variation among populations accounted for 66% of shape variation in females and 38% in males, suggesting that size is the most important dimension underlying shape variation among populations of P. vivipara in this system. Changes in the relative sizes of the caudal peduncle and cranial regions were only partly in line with predictions from divergent natural selection associated with predation regime. Conclusions: Our results suggest the possibility that adaptive shape variation among populations has been partly constrained by allometry in P. vivipara. Processes governing body size changes are therefore important in the diversification of this species. We conclude that in species characterized by substantial among-population differences in body size, ignoring allometric effects when investigating divergent natural selection?s role in phenotypic diversification might not be warranted.
Empirical demonstration of environmental sensing in catalytic RNA: evolution of interpretive behavior at the origins of life
Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically. Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca2+ ion as a sign for the more catalytically useful Mg2+ ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. In particular we demonstrate that in vitro, the wild-type version of the Tetrahymena ribozyme is not interpretive, in that it cannot use Ca2+ as a sign for Mg2+. Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca2+ ion engenders a strong interpretive characteristic in this RNA. Conclusions: We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life’s history.
Background: Detailed knowledge of spatial and temporal variation in the genetic population structure of hosts and parasites is required for understanding of host − parasite coevolution. As hot-spots of contemporary coevolution in natural systems are difficult to detect and long-term studies are restricted to few systems, additional population genetic data from various host − parasite systems may provide important insights into the topic. This is particularly true for parasites, as these players have been under-investigated so far due to the lower availability of suitable molecular markers. Here, we traced genetic variation (based on sequence variants in the internal transcribed spacer region, ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili, a common microparasite of the cladoceran Daphnia (here, the D. longispina hybrid complex). At three sites, we also studied parasite genetic variation over time (three to four sampling points) and tested for associations between parasite genotypes and host species. Results: Parasite (and host) populations were significantly structured across space, indicating limited dispersal. Moreover, the frequency of parasite genotypes varied significantly over time, suggesting rapid evolutionary change in Caullerya. However, the distribution of parasite genotypes was similar across different host species, which might in turn have important consequences for parasite epidemiology. Conclusions: The approach proposed here can be applied to track spatial and temporal changes in the population structure of other microparasite species for which sequence variation in the ITS or other highly variable genome regions has been documented but other types of polymorphic markers are lacking. Screening of parasite sequence variants allows for reliable detection of cross-species infections and, using advanced sequencing techniques in the near future, for detailed studies of parasite evolution in natural host − parasite systems.
Variable interaction specificity and symbiont performance in Panamanian Trachymyrmex and Sericomyrmex fungus-growing ants
Background: Cooperative benefits of mutualistic interactions are affected by genetic variation among the interacting partners, which may have consequences for interaction-specificities across guilds of sympatric species with similar mutualistic life histories. The gardens of fungus-growing (attine) ants produce carbohydrate active enzymes that degrade plant material collected by the ants and offer them food in exchange. The spectrum of these enzyme activities is an important symbiont service to the host but may vary among cultivar genotypes. The sympatric occurrence of several Trachymyrmex and Sericomyrmex higher attine ants in Gamboa, Panama provided the opportunity to do a quantitative study of species-level interaction-specificity. Results: We genotyped the ants for Cytochrome Oxidase and their Leucoagaricus fungal cultivars for ITS rDNA. Combined with activity measurements for 12 carbohydrate active enzymes, these data allowed us to test whether garden enzyme activity was affected by fungal strain, farming ants or combinations of the two. We detected two cryptic ant species, raising ant species number from four to six, and we show that the 38 sampled colonies reared a total of seven fungal haplotypes that were different enough to represent separate Leucoagaricus species. The Sericomyrmex species and one of the Trachymyrmex species reared the same fungal cultivar in all sampled colonies, but the remaining four Trachymyrmex species largely shared the other cultivars. Fungal enzyme activity spectra were significantly affected by both cultivar species and farming ant species, and more so for certain ant-cultivar combinations than others. However, relative changes in activity of single enzymes only depended on cultivar genotype and not on the ant species farming a cultivar. Conclusions: Ant cultivar symbiont-specificity varied from almost full symbiont sharing to one-to-one specialization, suggesting that trade-offs between enzyme activity spectra and life-history traits such as desiccation tolerance, disease susceptibility and temperature sensitivity may apply in some combinations but not in others. We hypothesize that this may be related to ecological specialization in general, but this awaits further testing. Our finding of both cryptic ant species and extensive cultivar diversity underlines the importance of identifying all species-level variation before embarking on estimates of interaction specificity.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology