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April 10, 2014
—047d7b4179975f37d704f6a360e6 Content-Type: text/plain; charset=ISO-8859-1 Two postdoc positions are available in the lab of Jeffrey Ross-Ibarra at UC Davis to study the evolutionary genetics of maize and teosinte. We are recruiting for two projects: An NSF funded project to use population genomics to understand local adaptation and inbreeding depression of teosinte and maize landraces. We are currently sequencing >100 maize and teosinte genomes from multiple populations, which serve as the parents of two large mapping populations for which phenotyping is underway. Potential projects are flexible and include investigation of inbreeding depression, the effects of linked selection, and local adaptation. A USDA- and industry-funded project to investigate regions of the maize genome under selection during modern breeding. Using genotype, phenotype, and pedigree data from thousands of maize inbred lines, we will use a number of approaches to understand the effects and targets of selection during the last 80 years of maize breeding. Opportunities exist for both positions to additionally collaborate on a number of projects, including adaptation to high elevation in maize landraces and the population genetics of centromere evolution. Both positions are for one year, with the potential for a second year of support conditional on performance. Start dates are open-ended, with preference for earlier dates. UC Davis has extremely strong programs in both plant and evolutionary biology. Candidates would have the opportunity to interact with members of the Center for Population Biology and the Genome Center as well as the Dept. of Plant Sciences. Preference is for candidates with a strong background in evolutionary biology, proficiency in unix and experience with computational analysis of population genetic data. For more information or to apply, please send a cover letter and a CV with a list of references to email@example.com. ____________ Jeffrey Ross-Ibarra Dept. of Plant Sciences and Genome Center 262 Robbins Hall, Mail Stop 4 University of California One Shields Ave Davis, CA 95616 Tel: 530-752-1152 Fax: 530-752-4604 www.rilab.org —047d7b4179975f37d704f6a360e6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printableTwo postdoc positions are available in the lab of Jeffrey Ross-Ibarra at UC Davis to study the evolutionary genetics of maize and teosinte. We are recruiting for two projects: An NSF funded project to use population genomics to understand local adaptation and inbreeding depression of teosinte and maize landraces. We are currently sequencing >100 maize and teosinte genomes from multiple populations, which serve as the parents of two large mapping populations for which phenotyping is underway. Potential projects are flexible and include investigation of inbreeding depression, the effects of linked selection, and local adaptation. A USDA- and industry-funded project to investigate regions of the maize genome under selection during modern breeding. Using genotype, phenotype, and pedigree data from thousands of maize inbred lines, we will use a number of approaches to understand the effects and targets of selection during the last 80 years of maize breeding. Opportunities exist for both positions to additionally collaborate on a number of projects, including adaptation to high elevation in maize landraces and the population genetics of centromere evolution. Both positions are for one year, with the potential for a second year of support conditional on performance. Start dates are open-ended, with preference for earlier dates. UC Davis has extremely strong programs in both plant and evolutionary biology. Candidates would have the opportunity to interact with members of the Center for Population Biology and the Genome Center as well as the Dept. of Plant Sciences.Preference is for candidates with a strong background in evolutionary biology, proficiency in unix and experience with computational analysis of population genetic data. For more information or to apply, please send a cover letter and a CV with a list of references to firstname.lastname@example.org. ____________Jeffrey Ross-IbarraDept. of Plant Sciences and Genome Center 262 Robbins Hall, Mail Stop 4University of CaliforniaOne Shields AveDavis, CA 95616Tel: 530-752-1152 Fax: 530-752-4604www.rilab.org —047d7b4179975f37d704f6a360e via Gmail
*Context of the project *(OPOPOP ANR-BIOADAPT January 2014-december 2017) Global change linked to temperature increase and ocean acidification but also more direct anthropogenic influences, such as aquaculture, have caused a worldwide increase in reports of /Vibrio/-associated illness affecting humans but also animals such as corals and mollusks. In particular, over the last 5 years, /Vibrio splendidus/ and /V. aestuarianus/ have been associated with recurrent mortality outbreaks in oyster beds (/Crassostrea gigas/) in France. Investigating the “emergence of /Vibrio/ pathogenesis events” requires the analysis of microbial evolution at the gene, genome and population level in order to identify genomic modifications linked to increased virulence, resistance and/or prevalence, or to recent host shift. *The aim of the post doc project is to:* /1- Compare the population structure of Vibrio in oysters and surrounding water during oyster mortality outbreaks/ In the water column, vibrios have been shown to assemble into specific populations defined by ecological preferences to attach to different types of particles and/or zooplankton, or to occur free-living. We will determine if /Vibrio/ populations are assembled neutrally in oyster or whether specific colonization processes occur and result in association with specific populations. /_Method_/: Phylogenetic (PhyML) and population prediction (Adapt ML, BAPS) as described previously (Hunt et al., 2008; Shapiro et al., 2012). /2- Compare the genome of virulent versus non-virulent strains belonging to different ecological populations/ Preliminary data suggested that not all /Vibrio/ populations harbor potential oyster pathogens.Moreover, within pathogen-containing populations (i.e., closely related, ecologically similar genotypes) pathogenicity potential ranges from non-virulent to highly virulent.We are currently testing how efficiently different strains and genotypes affect host survival.These data will be correlated with genome analyses to build hypotheses of gene function in the context of oyster pathogenesis. /_Method:_/Genome assembly from short read data using hybrid strategy (scaffolding onto closely related genomes and /de novo/ assembly), comparative genomic, phylogeny (Shapiro et al., 2012; Goudenge et al., 2013) */Competences required:/***Bioinformatician: Genome assembly, annotation, comparative genomics, phylogeny, microbial evolution, computational biology, microbial diversity, genotyping, ecology** *//* */Beginning of the post doc:/*mid 2014; 30 months *//* */Salary:/*about 1900 euros/months *//* */Professional address:/*the post doc will be based in the team of Dr Frdrique Le Roux at the station biologique de Roscoff (http://bit.ly/1sEqSE2) and will be co-supervised by Pr Martin F. Polz at the MIT (http://bit.ly/1sEqUf1). Training in the Polz lab will be funded by the project. *A letter explaining the competences and scientific interests, a CV, a publications list and letter(s) of reference should be send to Frdrique Le Roux by email: email@example.com* Le Roux Frdrique Head of the GV team Equipe mergente Ifremer/UPMC: “Gnomique des Vibrio” Station Biologique de Roscoff firstname.lastname@example.org Tel ext: 33 (0)2 98 29 56 47 Tel int: 416 Frdrique Le Roux via Gmail
EVOLUTIONARY SYSTEMATICS, INSTITUTE OF BOTANY, UNIVERSITY OF INNSBRUCK PostDoc position The Evolutionary Systematics group of the Institute of Botany seeks to hire a PostDoc with experience in Next Generation Sequencing (wetlab and bioinformatic analysis of restriction site associated DNA [RAD] sequencing data). The position starts in autumn 2014 (exact starting date flexible; 40 h/week employment for 26 months). Centering on the Alpine Space, the group’s mission is interdisciplinary research, embedded in international collaboration networks. A list of research topics can be found at: http://bit.ly/17ptb6J. The successful candidate will conduct NGS-based phylogeographic studies of a range of steppe organisms, including both plants and animals. The project consortium is international and includes members of the Universities of Innsbruck and Vienna (Austria), Lausanne (Switzerland) and the Real Jardn Botnico in Madrid (Spain). The project addresses the following issues: (1) Did the steppe biota colonize each Alpine dry valley independently or is there evidence for genetic exchange among the insular steppe habitats of different valleys? (2) What are the biogeographic connections of steppe biota from the Alpine dry valleys with other areas of steppe vegetation in Eurasia? (3) Are the phylogeographic patterns seen in steppe plants and animals congruent, implying range shifts of entire communities, or rather idiosyncratic, suggesting individualistic responses to climatic oscillations? (4) Our phylogeographic approach will unravel intraspecific patterns of spatial differentiation and temporal diversification across steppe plant and animal lineages. These will then not only be compared with each other, but also with data from independent sources. Changes of distribution ranges of our study taxa through time will be hindcasted using environmental niche modeling. A description of the project can be found at http://bit.ly/1iqAudJ). ***Responsibilities*** 1. optimization of a double digest RAD sequencing protocol for the study species, barcoding of individuals for pooled analyses 2. processing raw Illumina data and filtering of SNPs 3. phylogeographic and phylogenetic (BEAST, ABC-approaches, etc.) data analyses 4. species distribution modeling with Maxent 5. leading role in manuscript writing 6. contact and collaboration with scientists and laboratory technicians at the Molecular Ecology group, Institute of Ecology, Innsbruck University, as well as at other Austrian research facilities, and internationally 7. possibly (but not necessarily!) sampling of steppe species in Europe (Alps, Eastern Europe) and central Asia in 2015 ***Selection criteria*** A. PhD degree in life sciences B. published research experience in molecular systematics / evolution / biogeography, especially using high-throughput sequencing data C. proficiency in maintenance of Linux systems for bioinformatic purposes, Biopython, mysql, scripting languages (e.g. awk, Perl, R) D. experience in the use of relevant software packages for phylogeographic / phylogenetic analyses E. ability to work as part of a multi-disciplinary team F. ability to work independently G. very good knowledge of English ***Salary*** The annual gross salary is Euro 48,768 for a 40 h/week employment (26 months). This translates into a yearly net income of 31,037 EUR. Extension to 30 months and corresponding reduction of the weekly working hours are possible and welcome. The contract includes health insurance and 5 weeks of holidays annually. ***How to apply*** To apply, please submit by E-mail to : a cover letter, systematic point-by-point replies as to your readiness for the responsibilities and how you meet the selection criteria, brief statement of research interests, curriculum vitae, a complete list of publications, and two reference letters. Applications must be submitted in English until April 30th, 2014. The University of Innsbruck is striving to increase the percentage of female employees and therefore invites qualified women to apply. In the case of equivalent qualifications, women will be given preference. An offer of employment is contingent on a satisfactory pre-employment background check. ***The research institution and its environment*** Detailed information about the Evolutionary Systematics group can be found at http://bit.ly/17ptb6L. The University of Innsbruck has a long-standing and internationally renowned tradition in life sciences and offers a vibrant research atmosphere. It has 27,500 students and 4,500 staff members. Innsbruck is situated in the Alps and very close to Switzerland, Germany and Italy; scenery and outdoor recreation are fantastic. ***More information needed?*** For more information, please contact: Peter Schoenswetter Peter Schoenswetter Professor of Systematic Botany Institute of Botany, University of Innsbruck Sternwartestrasse 15, 6020 Innsbruck, Austria Tel: +43 (512) 507-51076, Fax: +43 (512) 507-51099 http://bit.ly/1iqAudN via Gmail
Two PhD opportunities: Marine and terrestrial invertebrate diversity and evolution in the Pilbara region, Australia The Western Australian Museum has secured funding from the Net Conservation Benefits fund (NCB) to undertake a five year project on the Conservation Systematics of the western Pilbara fauna. In this project we are using molecular tools to provide a systematic framework for understanding the diversity, evolutionary relationships, and distributions of marine and terrestrial fauna in the Pilbara region. Included under this broad objective are specific questions pertaining to evolutionary history, understanding the drivers of speciation, species delimitation, phylogeography, taxonomy, and co-speciation. This project has funding to support two PhD projects that broadly align with the NCB project objectives. The PhD projects will be aimed at using molecular markers to investigate biodiversity in invertebrates from the Pilbara region, and surrounds. One project will focus on marine invertebrates (eg, sponges, soft corals, nudibranchs, crinoids, or other groups) and the other will focus on terrestrial invertebrates (eg, trap-door spiders, opiliones, millipedes, or other arachnid or insect groups). The PhD students will be enrolled in the School of Animal Biology at the University of Western Australia, and based jointly at the new Molecular Systematics Unit laboratory, Western Australian Museum, Welshpool, Perth, where the successful applicants will have the opportunity to work directly with specialists in these fields. The specific project aims, questions, design and methods will be developed collaboratively by the students and supervisors. The work will include opportunities for field work in the Pilbara region, and lab costs will be generously supported by the NCB project. Currently, this opportunity is open to domestic students (Australia and New Zealand). Although the position is fully funded, students will be expected to put in an application for an Australian Postgraduate Award (APA or University Postgraduate Award (UPA) ( http://bit.ly/1k7dSmh) through UWA. The NCB funding will provide an additional top-up scholarship of $5k per year, bringing the total stipend to approx. $34k per year (tax free). Any international student should contact personnel below. Applications open 2 June, and close 11 July for a 1 Aug 2014 start. However, we encourage any applicants to contact us and begin discussions as soon as possible. Those interested in marine invertebrates should contact Nerida Wilson (Nerida.Wilson@museum.wa.gov.au) and cc Jason Kennington ( email@example.com). Those interested in terrestrial invertebrates should contact Joel Huey (Joel.Huey@museum.wa.gov.au) and cc Raphael Didham (firstname.lastname@example.org). email@example.com via Gmail
Dear colleagues, The earlybird registration deadline is rapidly approaching — 16 April. After that, registration rates increase by $50. Also, please submit your presentation title and abstract by 16 April to be sure of making it into the program. We look forward to seeing you in Raleigh in June! Follow or join the conversation on Twitter using #Evol2014. Questions and suggestions? Please email firstname.lastname@example.org Allen Rodrigo Chair, Evolution 2014 Organizing Committee email@example.com via Gmail
Be at the cutting edge: 3 year postdoc at the Centre for Ecological and Evolutionary Synthesis, University of Oslo modeling paleo data using capture-recapture, occupancy and comparative approaches. http://bit.ly/1lLSpPX Lee Hsiang Liow (Ph.D) Centre for Ecological and Evolutionary Synthesis (CEES) Department of Biosciences University of Oslo, Norway folk.uio.no/leehl Lee Hsiang Liow via Gmail
April 9, 2014
2014 American Genetic Association Presidential Symposium - Evolution and Plasticity: Adaptive responses by species to human-mediated changes to their ecosystems 27-29 June 2014 University of Washington, Seattle STUDENT AWARD APPLICATIONS AND ALL POSTER ABSTRACTS DUE APRIL 15 Awards are available to cover registration ($150), and a limited number to cover both travel and registration ($650). See the Symposium website for details - http://bit.ly/1eZIdSq AGA meetings are small and friendly, offering students a great opportunity to interact with top international researchers. Early Registration till May 15 only $150 for students, $200 general includes 2 hosted receptions SCHEDULE: Friday 27 June 6 - 9 PM Hosted reception and poster session Saturday 28 June 8 AM - 5 PM Symposium, Day 1 Key Lecture by David Reznick, UC Riverside, “Hard and soft selection revisited:How evolution by natural selection works in the real world” Saturday 28 June 6 - 9 PM Hosted reception and poster session Sunday 29 June 8 AM - 5 PM Symposium, Day 2 Noon brown-bag discussion, “What should conservation biologists and evolutionary biologists know about epigenetics?” moderated by Katie Peichel, AGA president-elect. This will follow a special presentation by Michael Skinner, WSU, “Epigenetic transgenerational inheritance of phenotypic variation in evolution: Lessons from Darwin’s finches” Please visit the AGA website to register and book housing: http://bit.ly/1eZIdSq Robin Waples, AGA President firstname.lastname@example.org via Gmail
The following position is available in the Evolutionary Biology Program at the Cornell Lab of Ornithology. It is currently posted through April 30, 2014 on the Jobs at Cornell web page at http://bit.ly/R4DqGI Lab Manager-23382 Research Support Specialist I - Band E Lab of Ornithology, College of Agriculture and Life Sciences Cornell University The Cornell Lab of Ornithology is the world’s leading resource for conservation, research, education, and citizen science focused on birds. The Lab is a vibrant unit within Cornell’s College of Agriculture and Life Sciences (CALS), where twelve world-class, mission-driven programs are directed by full-time faculty and other professionals. Lab staff teach undergraduate courses, advise graduate students, collect and disseminate digital resources on biodiversity, and engage with partner organizations and citizens around the world to conduct scientific research and conservation actions. Our management and staff are committed to the highest standards of ethics and excellence in all areas of our work, and our Board leadership includes faculty from Cornell and other universities, successful leaders and managers from the business and non-profit sectors, and conservation-minded citizens from the United States and beyond. The Fuller Evolutionary Biology Program at the Lab of Ornithology is currently seeking a Lab Manager. Duties include: * Provide high level technical oversight for an animal molecular genomics laboratory that supports research on a broad variety of organisms and topics using a diverse array of traditional and next- generation technologies. * Oversee the work of the lab’s large research community of students, postdoctoral scholars, affiliated faculty, and visiting researchers (25-30 people in total at any given time, with high turn-over among visiting affiliates). * Train and subsequent independent oversight of students and other lab users (including novices) learning traditional and next- generation molecular lab skills, including DNA extraction, PCR amplification, microsatellite and SNP analysis, and DNA sequencing. * Provide equivalent training of lab users in project design and implementation skills. * Provide oversight of lab users in the design, troubleshooting, and implementation of projects using next generation genetic/genomic tools, potentially including GBS, ddRAD, high throughput SNP genotyping, Illumina sequencing, transcriptome analysis, and similar approaches. * Independently generate and analyze next-generation genomic datasets in support of lab-wide research projects. * Manage all day-to-day laboratory operations and infrastructure. * Oversee and ensure long-term security of data and sample archives, including an extensive collection of 30,000+ genomic and tissue samples. * Ensure that laboratory and its users meet all standard laboratory safety guidelines. * Pursue independent research and publications using avian genetics. Applicants to provide cover letter, resume, contact information for 3 references Required Qualifications: * Bachelor’s degree in a biology-related field. * 2-3 years of experience in a molecular biology laboratory. * Mastery of routine methods in molecular biology such as DNA sequencing and extraction and PCR amplification. * Ability to prepare reports and analyses for presentation to others. * Must be personable, flexible, possess excellent organizational and communication skills and take pride in their work. * Ability to develop effective working relationships and maintain positive working relationships within a diverse laboratory group. * Visual concentration, attention to detail and manual dexterity required. * Must be able to work independently as well as in a team environment. * Ability to respond effectively in an environment in which priorities change. * Must exercise sound and ethical judgment when acting on behalf of the University. * Experience using some combination of next generation genetic/genomic tools such as GBS, ddRAD, SNP genotyping, Illumina sequencing, transcriptome analysis, and similar approaches. * Prior supervision experience. * Prior experience with budgets and financial transactions. Preferred Qualifications: * Advanced degree in a relevant area and research experience relevant to genetic/genomic studies of any group of organisms. * Previous laboratory management experience strongly preferred. * Applicants to be adept at both traditional and next-generation molecular laboratory and analysis skills, including current genomic and transcriptomic tools. * Experience with genetic and field studies of wild vertebrates such as birds. email@example.com via Gmail
Mini-course on genome-scale phylogeny, talk 1 of 3. Inferring gene trees with species trees Gergely Szllsi Etvs Lornd Tudomnyegyetem Tuesday, April 15, 2014 9:00 AM PDT Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. I introduce models that describe the relationship between gene trees and species trees. I begin with models that account for gene duplication and loss, and subsequently introduce models that account for the horizontal transfer of genes. I review results from simulations as well as empirical studies on genomic data that show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. I also discuss the possibility of extracting information on the timing of speciation events from ancient horizontal transfer events. Frederick “Erick” Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://bit.ly/18kRSvK firstname.lastname@example.org via Gmail
Miao Sun wrote:
I 've run a 4-gene 12,000-taxon super tree. Given I increased the bootstrap repliactes (200 to 1000), the support for the most internal nodes improved a lot (say 80 - 90% BS). However, the support for external nodes are remain low (some of them are 0-10% BS). Regarding to the knowledge that not all the taxa are fully sampled under the 4 genes, so there are great portion of missing data. Well, beside this, any other way to compensate for this shortage?
Background: In most species, males compete to gain both matings (via pre-copulatory competition) and fertilizations (via post-copulatory competition) to maximize their reproductive success. However, the quantity of resources devoted to sexual traits is finite, and so males are predicted to balance their investment between pre- and post-copulatory expenditure depending on the expected pay-offs that should vary according to mating tactics. In Artiodactyla species, males can invest in weapons such as horns or antlers to increase their mating gains or in testes mass/sperm dimensions to increase their fertilization efficiency. Moreover, it has been suggested that in these species, males with territory defence mating tactic might preferentially increase their investment in post-copulatory traits to increase their fertilization efficiency whereas males with female defence mating tactic might increase their investment in pre-copulatory sexually selected traits to prevent other males from copulating with females. In this study, we thus test the prediction that male's weapon length (pre-copulatory trait) covaries negatively with relative testes size and/or sperm dimensions (post-copulatory traits) across Artiodactyla using a phylogenetically controlled framework. Results: Surprisingly no association between weapon length and testes mass is found but a negative association between weapon length and sperm length is evidenced. In addition, neither pre- nor post-copulatory traits were found to be affected by male mating tactics. Conclusions: We propose several hypotheses that could explain why male ungulates may not balance their reproductive investment between pre- and post-copulatory traits.
Source: BMC Evolutionary Biology
The NIHR BioResource - Rare Diseases Translational Research Collaboration has been established to identify genetic causes of rare diseases, improve rates of diagnosis and enable studies to develop and validate treatments; thus improving care for those with rare diseases and their families. However, each specific disease is rare, and affects <5 in 10,000 of the population. This presents logistical challenges for translational research, and the NIHR BioResource for Rare Disorders aims to address these challenges. The BioResource RD has the responsibility to sequence 15,000 patients with rare diseases. Analysing this number of genomes requires around 10 PB of data and 40 M core hours. The bioinformatics pipeline is responsible for delivering this service.
The Head of Pipelines is responsible for the line management of a team of four bioinformaticians. He or she is also responsible for technical leadership in managing the development of a sequence analysis pipeline. This pipeline and the group of bioinformaticians are responsible for the delivery of high quality sequence variant calls for 15,000 whole genomes over the next three years. The Head of Pipelines will lead the further development of the sequence analysis pipeline and supervise bioinformatics staff to ensure the successful execution of the pipeline to analyse thousands of samples.
The role holder will develop links with the other bioinformatics teams within the Cambridge University Hospital BRC as well as the NIHR BioResource. They will also be able to present research material at national and international meetings and be able to teach non-bioinformaticians avoiding jargon and explaining the principles of pipeline analysis in simple terms.
Applicants will be educated to degree/masters in a discipline with a strong computational component such as software engineering, bioinformatics, computer science, or physics. They will have significant experience in analysing re-sequencing data for calling sequence variation. They will also have significant experience in the use of high performance computing clusters together with an understanding of databases and software systems to handle Big Data problems.
In addition it is expected that applicants will have the ability to communicate effectively with project managers, senior analysts, to manage staff and possess good project management skills. They also need to be excellent oral and written communicators and be able to interact effectively with staff at all levels.
The post will appeal to candidates keen to develop their career in research genomics at the frontier of high throughput Next Generation Sequencing Technology, clinical genomics and translational research.
Further information can be found at http://www.platelets.haem.cam.ac.uk/joinus.
Informal enquiries can be made to Augusto Rendon at email@example.com.The closing date for this vacancy is 6 May 2014.
Interviews will be held in the week commencing 12 May 2014.
Source: Systematics jobs at ResearchGate
*POST-DOC IN EVOLUTIONARY BIOLOGY (BRAZIL)* *Post-Doctoral Research position *in Goiania, Brazil with a competitive salary (49,200 BRL a year) for one year, extendable to second based on performance, focusing on developing next-generation sequence data and comparing it to fossil pollen data for a population genomics study. *Applicants* must have experience in population genomics or phylogenomics, as well as a strong interest in evolutionary biology and ecology. Programming skills are important and should include proficiency working in the Unix environment as well as experience with R, Python/Perl and/or standard sequence analysis tools. Highly enthusiastic applicants with a strong disposition to learn the needed tools to succeed are also encouraged to apply. *Informal inquiries as well as applications (including a CV, copies of relevant publications, and two names of recommenders) should be emailed to Christine Bacon (**firstname.lastname@example.org* *) prior to May 15th, 2014.* *Starting date*: July 1st, 2014, or upon agreement *Project*: The de-evolution of diversity in Amazonia Tropical America (the Neotropics) is recognized as harboring biodiversity hotspots, such as Amazonia, but there are some areas where diversity has decreased over time, particularly in oligarchic (monodominant) forests. This project aims to understand the evolutionary origins and maintenance of oligarchic forests in the context of geologic change and historical climate, thereby improving our predictions of how organisms, habitats, and Neotropical biomes may respond to comparable changes in the face of climate change. The genus *Mauritia *(Arecaceae, the palm family) presents an ideal system for investigating the evolution of oligarchic forests, or the de-evolution of Amazonian biodiversity. The genus has a rich pollen record, the taxonomy of palms is well known, and next- generation sequencing techniques, gene capture probes, have been developed specifically for palms that are appropriate for investigating demographic structure on both ecological and evolutionary time-scales. Furthermore, *Mauritia *is the most widely used and economically important native South American palm. We hypothesize that historical extinctions in *Mauritia *correlate with increased diversification rates in eudicotyledonous plants, the expansion of South American savannas, and/or the constriction of lowland rainforests during the Neogene. The inference of biogeography and diversification is an integral window into the past that enables the investigation of how geographic regions, biomes, and communities assembled through time and how they may evolve in the future. By integrating data across fields, for example from geology, genetics, fossils, species distribution and abundance, and morphology, we can reach a more comprehensive framework for the understanding of biome evolution and extinction. *Keywords*: Amazon, biodiversity, fossil, next-generation sequencing, palms, pollen *Institution*: Laboratory of Genetics and Biodiversity, Universidad Federal de Goias, Goiania, GO, Brazil (http://bit.ly/1i0xb04) *Remuneration*: Monthly, untaxed salary is 4,100.00 Brazilian Reais per month. Moving costs and health insurance are not included. The position is for one year, extendable to two years based on a performance evaluation at the end of the first year. The position is funded by the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq; the Brazilian National Science Foundation). The post-doc position includes funding for travel abroad or within Brazil for project development, either for conferences, workshops, or training visits. One trip to the Antonelli Lab at the University of Gothenburg, Sweden is planned for early 2015. *The research project team*: The Laboratory of Genetics and Biodiversity at the Universidad Federal de Goias is actively working on various next-generation sequencing projects of key plant taxa from the Cerrado, as well as other organisms (herpetofauna, ichtyofauna, etc.). The core supervisor for this position is Rosane Collevatti ( http://bit.ly/1i0xb06), known for her breadth of research on phylogeography and population genomics. The co-PI on the CNPq grant is Christine Bacon ( http://bit.ly/1i0xbwS), who studies evolution and biogeography in palms (Arecaceae). Christine is based on Santander, Colombia and will be at UFG working on the project 1-3 months per year for the duration of the grant. Other associates of the project are Thiago Rangel ( http://bit.ly/1i0xbwU) and Alexandre Jose Diniz Filho ( http://bit.ly/1i0xbwW), both well-known for their contributions to macroecology. *Post-doctoral researcher tasks*: The post-doc will sequence the *Mauritia flexuosa* transciptome and annotate it using reference genomes in the Arecaceae ( http://1.usa.gov/1qi6rKY). Using the annotated transciptome and palm genomic resources, putatively single-copy orthogroup targets will be identified for probe design (Mycroarray; http://bit.ly/1qi6qqh). Target sequencing using a *Mauritia flexuosa*-specific bait kit will be used to amplify variable sites in *Mauritia flexuosa* from populations across its biogeographic distribution in the Amazon Basin. After hybrid capture, Illumina sequencing reads will be filtered, paralogs will be removed, nuclear reads will be assembled and extended into contigs and alignments will be made. Nuclear gene trees will be built, age estimation will be inferred, and phylgeographic models will be implemented (e.g., Bayesian Skyline Plots, Drummond et al. 2005; http://bit.ly/1qi6rL1). *Optional tasks* include leading or participating in field work aimed at collecting leaf and pollen samples in the field. Two regions of particular interest are near Belem, Brasil and near Pucallpa and the Parque Nacional Alto Purus in Peru. Involvement with the fossil team and collaboration with Carina Hoorn (http://bit.ly/1qi6rL3) on the integration of genetic and pollen data. Co-supervise a PhD student at the Universidade de Goiania on their project development and research. *Goiania*: A safe, affordable, medium-sized city in the Cerrado - http://bit.ly/1i0xbx8 http://1.usa.gov/1i0xbgs http://bit.ly/1qi6qqu http://bit.ly/1i0xbgt http://bit.ly/1qi6s1o Christine D. Bacon Post-Doctoral Researcher Antonelli Lab University of Gothenburg Gothenburg, Sweden - and - Universidad Industrial de Santander Bucaramanga, Colombia http://bit.ly/1qi6s1p Christine Bacon via Gmail
PhD Studentship, University of Glasgow A genomic approach to uncovering the mechanisms driving host restriction and virulence in louping ill virus Why particular viruses are able to infect and to cause disease in some host species but not others are fundamental questions that are critical for controlling viral pathogens. This project aims to uncocver the molecular and evolutionary mechanisms underlying host restriction and virulence of louping-ill virus (LIV), one of several closely related tick-borne flaviviruses in Europe that exhibit high phenotyopic variability: whereas LIV mainly causes disease in British sheep and grouse, other LIV strains and related viruses elsewhere in Europe tend to affect other livestock species or human hosts. Using a combination of whole genome sequencing, bioinformatics, in vitro experiments and reverse genetics the project aims to 1) examine the genome-wide diversity and evolutionary history of LIV across its current range; 2) compare the ability of different LIV strains and related virus species for in vitro growth in a range of host species; 3) to experimentally verify putative genotype -phenotype relationships through a reverse genetics system. Through the application of powerful new technologies and analytic approaches, the project will provide novel insights about the biology of a significant animal pathogen in the UK and advance our general understanding of the factors governing virus-host interactions. This exciting studentship opportunity will draw on expertise from academics within the University of Glasgow and The Moredun Research Institute. The student will spend an equal percentage of their time at both locations. BBSRC WestBio DTP studentships will follow a 4-year PhD model. The financial package will include a 4-year stipend, approved University of Glasgow fees and a consumables budget per annum. The successful student will participate in the robust MVLS College skills training programme throughout their studies. Please follow URL for further information regarding the programme structure: http://bit.ly/1iwmikb (please note that this project will not involve the Mini-Project rotations as detailed in the programme structure). Supervisors: Dr Roman Biek, Dr Colin J McInnes, and Dr Alain Kohl Stipend: 13,726 per annum (2013/14 rate) Start date: 1 October 2014 Application Deadline: 28 April 2014 For informal enquiries contact the main supervisor (Roman.Biek@glasgow.ac.uk). Eligibility This position is restricted to UK and EU nationals who meet the residence criteria below. Qualifications criteria: Applicants applying for a BBSRC WestBio DTP studentship must have obtained, or be about to obtain, a first or upper second class UK honours degree or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. Residence criteria: The BBSRC DTP grant provides funding for tuition fees and stipend for UK and *EU nationals that meet all the required eligibility criteria. *Note that EU nationals must be able to demonstrate that they have resided in the UK for three years prior to commencing the studentship. If not, EU nationals are still able to apply to the programme, but would be eligible to receive a fees only’ award. Full qualifications and residence eligibility details are available here: BBSRC Guide to Studentship Eligibility - http://bit.ly/HQzS5Y via Gmail
Research Assistant / Associate in Epidemiological/Phylodynamic Modelling - Ref: 008448 Grade 6/7: 26,527 - 29,837 / 32,590 - 36,661 per annum The Institute of Biodiversity, Animal Health and Comparative Medicine (University of Glasgow) is looking to recruit a postdoctoral research assistant with excellent computational skills and an interest in epidemiological models to support our research on the transmission dynamics of bovine Tuberculosis (bTB) in British and Irish cattle and badgers. BTB is the most prominent disease of livestock in Britain and Ireland, and an exceptional exemplar for developing general principles regarding the transmission dynamics of multi-host pathogens. Possessing excellent quantitative skills and academic qualification at Degree and/or PhD you will contribute to this BBSRC funded project by developing novel methodologies to explore the dynamics of bTB spread, exploiting dense demographic data and whole genome sequence data generated from the vast archive of bacterial samples available. The project is led by Prof. Rowland Kao and builds on a broad consortium of collaborators at Glasgow, the AHVLA and AFBI in Northern Ireland. The holder will be embedded within the Boyd Orr Centre for Population and Ecosystem Health (http://bit.ly/OBSo4P), a vibrant research grouping of scientists interested in the application and development of cutting edge quantitative methods to solve real disease problems. The work of the Boyd Orr Centre was recently acknowledged by the award of the Queen’s Anniversary Prize to the University of Glasgow, on the basis of the Centre’s research excellence and commitment to broader impact on human and an imal health (http://bit.ly/OBSo4R). This position is funded until 31 May 2017. For more details and online application see: http://bit.ly/OBSo4S (Reference: 008448) Closing date: 9 May 2014 Informal inquiries to Rowland Kao (Rowland.Kao@glasgow.ac.uk) or Roman Biek (email@example.com) via Gmail
—_000_277B082AA8C049A99D24339F267B30AAbayloredu_ Content-Type: text/plain; charset=”Windows-1252” Content-Transfer-Encoding: quoted-printable The Danley Lab at Baylor University (http://bit.ly/1g6vPAd) seeks a Ph.D. student broadly interested in evolutionary biology using East African cichlid fish as a model system. The exact nature of the research will be developed by the student in collaboration with Pat Danley though it should relate to the lab’s previous research on sexual selection (mate choice, aggression), phylogeography, and speciation. Applicants with a background in behavioral, phylogenetic, and genomic methods are encouraged to apply. Applicants experienced with R, Perl, and Python are a plus. Applicants are expected to have completed (or will soon complete) either a BS/BA or Msc. by the start of the 14-15 academic year. The successful applicant will be admitted to the Department of Biology’s Ph.D. program which provides 5 years of 12 month stipend ($21,000, plus possible enhancements for outstanding students), tuition remission, and benefits. The Baylor’s Department of Biology has an active graduate community of over 50 students and possesses strengthens in the areas of integrative organismal biology and aquatic ecology. Waco, home of Baylor University, is conveniently located 90 minutes from both Dallas and Austin and was recently ranked as one of America’s Awesomest (sic) Cheap Cities making it a perfect home for would be graduate students. http://bit.ly/1g6vPAf To apply, please send a cover letter, CV, unofficial transcripts, and GRE scores to firstname.lastname@example.org. —_000_277B082AA8C049A99D24339F267B30AAbayloredu_ Content-Type: text/html; charset=”Windows-1252” Content-ID: Content-Transfer-Encoding: quoted-printable The Danley Lab at Baylor University (http://bit.ly/1g6vPAd) seeks a Ph.D. student broadly interested in evolutionary biology using East African cichlid fish as a model system. The exact nature of the research will be developed by the student in collaboration with Pat Danley though it should relate to the lab’s previous research on sexual selection (mate choice, aggression), phylogeography, and speciation.Applicants with a background in behavioral, phylogenetic, and genomic methods are encouraged to apply. Applicants experienced with R, Perl, and Python are a plus. Applicants are expected to have completed (or will soon complete) either a BS/BA or Msc. by the start of the 14-15 academic year. The successful applicant will be admitted to the Department of Biology’s Ph.D. program which provides 5 years of 12 month stipend ($21,000, plus possible enhancements for outstanding students), tuition remission, and benefits. The Baylor’s Department of Biology has an active graduate community of over 50 students and possesses strengthens in the areas of integrative organismal biology and aquatic ecology. Waco, home of Baylor University, is conveniently located 90 minutes from both Dallas and Austin and was recently ranked as one of America’s Awesomest (sic) Cheap Cities making it a perfect home for would be graduate students. http://bit.ly/1g6vPAf To apply, please send a cover letter, CV, unofficial transcripts, and GRE scores to email@example.com. —_000_277B082AA8C049A99D24339F267B30AAbayloredu via Gmail
—Apple-Mail=_FE263D9E-1D06-40A7-BEF1-4C7A78B56908 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Postdoctoral fellow in fungal metagenomics and ecology A postdoctoral position is available in the department of Plant Biology, in the School of Integrative Biology, at the University of Illinois in Urbana-Champaign. PIs Astrid Ferrer (aquatic mycologist), Katy Heath (plant and microbe evolution), and Jim Dalling (plant and fungal community ecology) are looking for a highly motivated postdoc to work on a NSF-funded Dimensions of Biodiversity project aimed at understanding the ecological and genetic controls on fungal community assembly and decomposition function in tropical wood-decomposing aquatic fungi. Both the Heath and Dalling labs are lively, highly-collaborative environments with students and postdocs working on a range of topics in ecology and evolution of plants, bacteria, and fungi. The duties of the project postdoc will include preparing libraries for metagenomic sequencing of aquatic fungi communities from environmental DNA samples, RNAseq of cultured fungi in response to various environmental treatments, downstream bioinformatic and statistical analyses, and writing manuscripts based on these results. Expertise in some or all of the following areas is desired: Molecular biology, (meta)genomics, bioinformatics, statistical analysis, ecology, evolution. Strong candidates will also possess the following attributes: - A strong publication record from their PhD (papers published, in press, or submitted). - Creativity, independence, and the desire to learn new things. - Excellent communication skills, both written and oral. All candidates must have received a Ph.D. in a relevant field. The position is available for 2 years, with the first year as a probationary period, and will include a competitive salary and full benefits. Application review will begin May 1, 2014 and will continue until the position is filled. Start date is flexible, with a rough target date of August 2014. All materials should be submitted to the PIs below for consideration. Applications should include a brief cover letter, curriculum vitae, a brief description of past research accomplishments and future research goals (under two pages), and the names and contact information for three references. Contact Dr. Katy Heath regarding the position or application process. For further information about the Heath lab, visit the lab webpage accessible at: http://bit.ly/1eqdWby Katy Heath Assistant Professor Department of Plant Biology University of Illinois firstname.lastname@example.org —Apple-Mail=_FE263D9E-1D06-40A7-BEF1-4C7A78B56908 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii
Postdoctoral fellow in fungal metagenomics and ecology
A postdoctoral position is available in the department of Plant Biology, in the School of Integrative Biology, at the University of Illinois in Urbana-Champaign. PIs Astrid Ferrer (aquatic mycologist), Katy Heath (plant and microbe evolution), and Jim Dalling (plant and fungal community ecology) are looking for a highly motivated postdoc to work on a NSF-funded Dimensions of Biodiversity project aimed at understanding the ecological and genetic controls on fungal community assembly and decomposition function in tropical wood-decomposing aquatic fungi. Both the Heath and Dalling labs are lively, highly-collaborative environments with students and postdocs working on a range of topics in ecology and evolution of plants, bacteria, and fungi.
The duties of the project postdoc will include preparing libraries for metagenomic sequencing of aquatic fungi communities from environmental DNA samples, RNAseq of cultured fungi in response to various environmental treatments, downstream bioinformatic and statistical analyses, and writing manuscripts based on these results.
Expertise in some or all of the following areas is desired: Molecular biology, (meta)genomics, bioinformatics, statistical analysis, ecology, evolution.
Strong candidates will also possess the following attributes:
- A strong publication record from their PhD (papers published, in press, or submitted).
- Creativity, independence, and the desire to learn new things.
- Excellent communication skills, both written and oral.
All candidates must have received a Ph.D. in a relevant field. The position is available for 2 years, with the first year as a probationary period, and will include a competitive salary and full benefits.
Application review will begin May 1, 2014 and will continue until the position is filled. Start date is flexible, with a rough target date of August 2014. All materials should be submitted to the PIs below for consideration. Applications should include a brief cover letter, curriculum vitae, a brief description of past research accomplishments and future research goals (under two pages), and the names and contact information for three references.
Contact Dr. Katy Heath regarding the position or application process. For further information about the Heath lab, visit the lab webpage accessible at: http://bit.ly/1eqdWby
Department of Plant Biology
University of Illinois
—_000_28d8a123f00e4051b9dda89157503a3esvwexmb2unifrch_ Content-Type: text/plain; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable Dear colleagues, I am pleased to inform you that registration for our 2014 ‘Fribourg Ecology & Evolution days’ workshop is now open. The event will take place on 4-5 September 2014 at University of Fribourg, Switzerland. The theme of this year’s workshop is ‘GENOMICS OF THE SPECIATION CONTINUUM’. Invited Speakers: NICOLAS BIERNE, CNRS Montpellier (FR) ALEX BUERKLE, University of Wyoming (USA) MIKKEL SCHIERUP, Aarhus University (DK) OLE SEEHAUSEN, EAWAG (CH) TANJA SLOTTE, Uppsala University (SE) JOHN WIENS, University of Arizona (USA) Organizers: CHRISTIAN LEXER, University of Fribourg (CH) DANIEL WEGMANN, University of Fribourg (CH) HEINZ MUELLER-SCHAERER, University of Fribourg (CH) ALEX WIDMER, Swiss Federal Institute of Technology (ETH), Zurich (CH) Our yearly Fribourg Ecology & Evolution workshops gather lively small crowds of PhD students and researchers around our invited speakers. Previous editions of this workshop series have triggered stimulating discussions on topics of mutual interest in an informal setting, and we look forward to continuing this tradition with this year’s event. For more information about the workshop and venue, please visit: http://bit.ly/1eiFqW5 Abstract submission is now open and closes 1 July. Registration is now open and closes 1 August. Christian Lexer Professor of Evolutionary Biology University of Fribourg, Department of Biology Unit of Ecology & Evolution Chemin du Muse 10, CH-1700 Fribourg, Switzerland Tel (office) +41 (0)26 300 8868 Tel (lab): +41 (0)26 300 8895 Fax: +41 (0)26 300 9698 Mobile: +41 (0)77 472 0789 Email: email@example.com Web: http://bit.ly/HlgoXa —_000_28d8a123f00e4051b9dda89157503a3esvwexmb2unifrch_ Content-Type: text/html; charset=”iso-8859-1” Content-Transfer-Encoding: quoted-printable
PhD Fellowship in Paleobiology/Paleontology at the University of Pennsylvania A PhD fellowship in Paleobiology is available in the Department of Earth and Environmental Science at the University of Pennsylvania. Prof. Lauren Sallan seeks a graduate student to address major paleobiological questions, such as how global change has affected life over time, how life evolves at high levels (macroevolution), and the origins of living biodiversity. Specific topics include, but are not limited to: the causes and consequences of the end-Devonian mass extinction and similar events, the role of predation in setting marine biodiversity, the origins of $B!H(Bliving fossils,$B!I(B the effect of the Late Paleozoic Ice Age on the evolution of major groups, and early vertebrate evolution. The student can also develop a new project that address the same major questions using quantitative, phylogenetic and descriptive methods. While research in the lab has focused on fishes, any suitable and well-preserved group of fossil animals may be used. Interested students should contact Prof. Sallan directly (firstname.lastname@example.org; arriving at Penn in July 2014) for details. Lauren Sallan, PhD Assistant Professor, Ecology and Evolutionary Biology & Michigan Fellow, Michigan Society of Fellows University of Michigan Office: 1076 Ruthven Museums Bldg Phone: (954) 895-9192 or (734) 764-7797 Websites: http://bit.ly/1jsXZ93 www.LaurenSallan.com Lauren Sallan via Gmail
Undergraduate Diversity at Evolution 2014 - DEADLINE LESS THAN ONE WEEK AWAY! We are pleased to announce an undergraduate travel award to bring talented and diverse undergraduates to the Evolution meetings this June 20-24 in Raleigh, NC (http://bit.ly/1akNCO3). For the 12th year in a row we will fly a cohort of undergraduates from throughout the US and Puerto Rico to present a poster at the meetings, receive mentoring from graduate students, postdocs and faculty, and participate in a career-oriented ‘Undergraduate Futures in Evolutionary Biology’ panel and discussion. The program covers the costs of travel, registration, food and accommodation at the meetings. The application deadline is Monday, April 14th, and decisions will be announced by Monday, April 21st. Applications are welcomed from all undergraduates, and the admissions goal is to create a diverse pool of students. An overview of the program and student eligibility, and a link to the online application can be found at: http://bit.ly/1ajYoHo Applications consist of a short statement of interest, a letter of recommendation and the title and abstract of the poster to be presented. In addition, we will be soliciting names of graduate students, postdocs and faculty members who would like to serve as mentors during the meetings. Mentors meet with pairs of students and attend talks with them, introduce them to colleagues, network and generally make the meetings a welcoming place for them. Although costs are not covered for mentors it is an unusually rewarding experience. Contact Richard Kliman (email@example.com) if you are interested in serving as a mentor. For inquires contact one of the organizers: Jory Weintraub - firstname.lastname@example.org Richard Kliman - email@example.com Scott Edwards - firstname.lastname@example.org Jory P. Weintraub, PhD Assistant Director, Education & Outreach National Evolutionary Synthesis Center (NESCent) 2024 West Main St., Suite A200, Durham, NC 27705 Phone: 919.668.4578 Fax: 919.668.9198 Email: email@example.com Skype: jory.weintraub “Weintraub, Jory P” via Gmail
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology