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April 14, 2014

April 13, 2014

23:58

POST-DOCTORAL RESEARCH GENETICIST/ECOLOGIST A postdoctoral research position is available at the USDA Forest Service Pacific Northwest Research Station in Corvallis, Oregon. The candidate will conduct ecological genetics research to explore population variation in adaptive traits of native grasses and forbs of the western United States. The primary goal of the research is to model responses in adaptation and adaptive traits as a function of the environments of planting sites and seed sources. The employee will use the knowledge gained to evaluate alternatives for guiding population movement for restoration of native plant communities including considerations of climate change. The position is a two-year, full-time term position, with the possibility for extension of an additional two years dependent upon funding and performance. Shorter appointments may be possible (e.g., sabbaticals for university faculty). Salary is approximately $61,867 per year (GS-11) depending on qualifications. The employee will be eligible for health and life insurance, annual (vacation) and sick leave, and will be covered by the Federal Employees Retirement System. Qualifications: US citizen with PhD in ecology, botany, forestry, genetics or related field prior to beginning employment; demonstrated knowledge of statistical analysis and associated software (including SAS and R) for nonlinear mixed-effects models and multivariate analysis; demonstrated skills in communicating science through publications and public speaking; knowledge of GIS is desirable. The position is full-time for 13 to 48 months and will be filled at the GS-11 level. To apply: Send curriculum vitae and cover letter indicating interests and qualifications along with a copy of your college transcripts (unofficial copies are fine). Include a list of your publications (including a pdf or link to one or more featured publications) and at least three professional references with information on how to contact them (email and phone number). Indicate when you would be available in your cover letter and please state that you are a US citizen. Applications will be accepted until close of business by April 30, 2014, but it is in the applicant’s best interest to turn in their application as soon as possible. Send the information to Dr. Brad St.Clair at bstclair@fs.fed.us. Please pass this advertisement on to interested parties. Brad St.Clair Research Geneticist US Forest Service, Pacific Northwest Research Station 3200 SW Jefferson Way, Corvallis, Oregon 97331-4401 ph: (541) 750-7294, fax: (541) 750-7329 email: bstclair@fs.fed.us bstclair@fs.fed.us via Gmail

Source: EVOLDIR
23:43

Are you organizing a workshop for 2015 or the near future? The American Society of Naturalists provides workshop support to help defray the cost to students for attending. In particular, ASN is interested in sponsoring workshops for graduate students that provide training in modeling, data analysis, or other professional skills. The ASN workshop committee anticipates supporting 1-4 workshops per year at a rate of $1000-2000 each, which can be used towards workshop expenses or deferment of student fees. The application for workshop support should include descriptions of: the workshop (including tangible benefits to participants), venue, procedures for selecting participants, anticipated number of participants, and a budget that includes plans for use of ASN funds. Applications should be submitted as a pdf on or before 15 May 2014 to mbutler@hawaii.edu and should carry the label ASN Workshop Sponsorship’ in the subject line to assure full consideration. Inquiries should be directed to Marguerite A. Butler at the same address. Recent workshops (co-)sponsored by the American Society of Naturalists: 2013 - present “Workshop on Molecular Evolution”, organized by D. Hillis and M. Sogin at MBL (student applications due 4/15 http://bit.ly/1iLSsbG ) 2012 “Mathematical modeling in evolutionary ecology” by H. Kokko - at the Joint Congress on Evolutionary Biology in Ottawa 2012 “Graduate Workshop: The tree of sex - a comprehensive synthesis of sex determination systems in eucaryotes” by D. Bachtrog, J. Mank, and K. Peichel - at the Joint Congress on Evolutionary Biology at Ottawa 2011 - present “Workshop on Evolutionary Quantitative Genetics”, organized by S. Arnold and J. Felsenstein at NESCENT mbutler808@gmail.com via Gmail

Source: EVOLDIR
23:28

This postdoctoral position is an opportunity to contribute to the design of the upcoming 701 and 702 HIV vaccine trials to maximize power in subsequent statistical analyses. Specifically, it will be to develop new statistical and molecular evolution methods to design the trials so that infection time and founder sequences can be inferred with maximum fidelity. The scope of the study design includes sampling times and sequencing protocol, and also may afford some opportunities to design novel ways of combining sequencing methodologies. The project will last two years, with some possibility of extension. It may also offer an option to travel to South Africa to help teach a short course at the University of Cape Town, and possibly interact with the Fred Hutchinson Research Institute there. This position will require significant statistics expertise, programming ability, and of course interest in collaboration. A background in molecular evolution would be very helpful, but isn’t strictly required. For more details, see http://bit.ly/1knaKTr Frederick “Erick” Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://bit.ly/18kRSvK ematsen@gmail.com via Gmail

Source: EVOLDIR
16:30

In Australia at the time I was born, the most popular first name for boys was "David" and the second most popular was "Andrew". Not unexpectedly, the most popular middle name was "Andrew" and number two was "David". It then comes as no surprise to you that I ended up with this pair of given names.

Names come and go in popularity (these are called fads), and if your parents have no imagination then you will grow up knowing that you are not unique, because half the people in your classroom will have the same name as yourself. You may even end up being numbered (David #1, David #2, etc). What's worse, if you are not careful then you may end up doing the same thing to your own children.

Indeed, having a common name has only one known advantage — no matter where you go in the world everyone can recognize it, although they may not always spell it and pronounce it the way you expect (David, Davide, Dawit ...). Therefore, you will have no problems making restaurant bookings where ever you happen to be (see Leonard S. Bernstein. 1981. Never Make a Reservation in Your Own Name. Rand McNally).

These days in Australia, "David" struggles to be in the top 100 in popularity for boys. However, currently it appears to be in the top 10 in places like Armenia, Austria, Hungary, Italy, Spain and Israel (in 2012 or 2013), as well as the top 20 in Poland and Portugal. This information comes from The Baby Name Wizard. This site has current lists for many countries (Popular Names From Around the World), but has historical data only for the USA.

So, let's look at the U.S. data in more detail. As for Australia, the peak popularity in the USA was from 1955-1965, as shown in the first graph.

Note that the peak is truncated from 1950-1960.
The site's Name Mapper web page has annual data for each state from 1960-2009, which is precisely 50 years. These data show the ranking of names by popularity within each state. The average rank for the name "David" across the 50 states is shown in the next graph. "David" was one of the top 10 names for boys born from 1936-1992, the #1 name in 1960, and it remains inside the top 20 to this day.


We can also look at the data for each state individually, as shown in the next graph, where darker shading represents greater popularity of the name. From the peak in the 1960s there was a steady decrease in almost every state until 1995, after which the popularity has been more erratic. For example, in 1960 "David" was the #1 boys name in 28 of the 50 states (and in the top 5 in every state), but by 1968 it was not #1 anywhere. The last time it was ranked #1 was in Utah in 1970, which was also the last year in which it was in the top 6 in every state.

Note that the states are grouped and colored geographically / culturallu.
Only in California and Texas has the name stayed in the top 10 over the past 50 years. In the other states it has stayed in the top 50 or so, except for North Dakota, where it is currently struggling to stay in the top 100. In Nevada and Alaska it has even made a bit of a comeback in the past 10 years.

We can look at the relationship between the states using a phylogenetic network. The next graph is a NeighborNet (based on the manhattan distance) of the 1960-2009 data for the popularity ranking of "David" as a boy's name. States near each other in the network have a similar naming popularity, while states further apart are progressively more different from each other. The network shows a simple trend of increasing average popularity of "David" from the top-left to the bottom-right.


I have also colored the states using the same color scheme as for the previous graph (ie. geographically / culturally). Note that the orange, red, yellow and blue states are fairly neatly grouped, indicating that their alleged geographical / cultural similarity extends to the popularity of given names ("David" has continued to be popular in all of these states). The purple, brown and green states are not grouped very much, indicating much more diversity in the popularity of "David". For example, "David" has continued to be popular in New York and New Jersey but not in Maine, New Hampshire or Vermont. The extreme disinterest of North Dakotans in the name is very clear.

The fall of "David" is not as bad as that of "James" and "John", which were in the top 3 most popular names in the USA all the way from the 1880s to the 1950s, but which are now in 17th and 27th place, respectively (see the timeline graph in the Name Voyager).

I am not sure what has led to the eclipse of these names, other than the whims of faddishness. For example, in Britain and Ireland the name "Harry" has shot to the top in recent years (guess why!), while it still languishes near #700 in the USA. Otherwise, "Noah" and "Liam" seem to have the most widespread popularity for boys in the western world at the moment.

Footnote: I actually got the name Andrew because it is my father's middle name, and his father's before him, and his father's first name.

April 12, 2014

23:44

Symposio: Biodiversidad del gnero Solanum: Caracterizacin, conservacin y aprovechamiento; 7 y 8 de Mayo del 2014, Loja, Ecuador (Symposium: Biodiversity in Solanum: Characterization, Conservation and Utilization; 7-8 May 2014, Loja, Ecuador) Los invitamos al 2014 simposio intrenacional: “Biodiversidad del gnero Solanum: Caracterizacin, conservacin y aprovechamiento”. A realizarse los das 7 y 8 de Mayo del 2014 en la Universidad Tcnica Particular de Loja, Ecuador El sur del Ecuador es una de las regiones de mayor diversidad en el mundo, debido a la presencia de la depresin de Huancabamba (Andes), donde la ruptura de la cordillera de los Andes ha dado lugar a la fragmentacin del hbitat. La radiacin adaptativa de especies de plantas y animales en esta regin la convierten en un laboratorio natural para el estudio de la especiacin. Este simposio ser un escaparate de la biodiversidad de Solanum, un gnero complejo, con muchas especies silvestres y de cultivos comerciales importantes, como la papa, el tomate, el pimiento y la berenjena, as como otros cultivos regionales como naranjilla, tomate de rbol, y pepino dulce, que tienen el potencial para una mayor distribucin. Adems, la reunin de dos das incluir paneles y discusiones informales de la proteccin del germoplasma silvestre, y el desarrollo de la investigacin en colaboracin internacional para identificar, conservar y utilizar la biodiversidad en este rico y diverso grupo de organismos. La lista de ponentes incluye: - Pablo Acosta, Universidad Tcnica Particular de Loja, Ecuador - Patricia Bedinger, Colorado State University, USA - Merideth Bonierbale, Centro Internacional de la Papa, Lima, Peru - Joaquın Canizares, Instituto de Conservacin y Mejora de la Agrodiversidad Valenciana. Valencia, Espaa -Patricio Castro, Universidad Nacional de Loja, Ecuador - Roger Chetelat, Director, Tomato Genetics Resource Center, University of California, Davis, USA - Robert Last, Michigan State University, USA - Bruce McClure, University of Missouri, USA - Leonie Moyle, Indiana University, Bloomington - Jaime Prohens, Instituto de Conservacin y Mejora de la Agrodiversidad Valenciana. Valencia, Espaa - Flor Rodriguez, Centro Internacional de la Papa, Lima, Peru La inscripcin para el Simposio de 2 das es de $ US30. Detalles (en Espaol y Ingls), incluyendo la informacin de registro y los viajes, se pueden encontrar en la pgina web del Simposio: http://bit.ly/1kK82ua ****************** Symposium: Biodiversity in Solanum: Characterization, Conservation and Utilization Universidad Tcnica Particular de Loja, Loja, Ecuador, 7-8 May 2014 We are pleased to announce the Symposium Biodiversity in Solanum: Characterization, Conservation and Utilization’ to be held at Universidad Tcnica Particular de Loja, Loja, Ecuador, May 7-8. Southern Ecuador is one of the megadiverse regions of the world due to the presence of the Huancabamba (Andes) depression, where the breakup of the Andes cordillera has led to habitat fragmentation. Adaptive radiation of both plant and animal species in this region make it a natural laboratory for the study of speciation. This symposium will showcase the biodiversity of Solanum, a complex genus with many wild species and important crop species including potato, tomato, pepper and eggplant, as well as other regional crops such as naranjilla, tamarillo, and pepino, which have the potential for wider distribution. In addition, the two day meeting will involve panel and informal discussions of the protection of wild germplasm, and the development of international collaborative research to identify, conserve, and utilize biodiversity in this richly diverse group of organisms. Confirmed symposium speakers include: - Pablo Acosta, Universidad Tcnica Particular de Loja, Ecuador - Patricia Bedinger, Colorado State University, USA - Merideth Bonierbale, International Potato Institute, Lima, Peru - Joaquın Canizares, Institute for the Conservation and Improvement of Agricultural Biodiversity, Valencia, Spain -Patricio Castro, Universidad Nacional de Loja, Ecuador - Roger Chetelat, Director, Tomato Genetics Resource Center, University of California, Davis, USA - Robert Last, Michigan State University, USA - Bruce McClure, University of Missouri, USA - Leonie Moyle, Indiana University, Bloomington - Jaime Prohens, Institute for the Conservation and Improvement of Agricultural Biodiversity, Valencia, Spain - Flor Rodriguez, International Potato Institute, Lima, Peru Registration for the 2-day symposium is $US30. Details (in English and Spanish), including information for registration and travel, can be found at the Symposium website: http://bit.ly/1kK82ua via Gmail

Source: EVOLDIR
23:17

Funded Ph.D. position to investigate the genetics of early life history variation in Pacific salmon (immediate start) We are offering an exciting opportunity for an outstanding doctoral student (preference for Canadian citizen and landed immigrants) to address a question central to our understanding of the evolution of life history variation and local adaptation in salmon: does life history variation reflect traditional adaptation to local conditions, or have salmon evolved novel forms of life history plasticity? The successful candidate will use molecular, population, and quantitative genetic methods combined with captive breeding experiments and field-based measurements to partition the relative contribution of genetic, epigenetic, GxE interactions and environmental effects to early life history trait variation in Pacific salmon. Your fieldwork would take place on coastal British Columbia, and your lab work would take place primarily in GLIER’s innovative Environmental Genomics Facility, where you would have hands-on experience using diverse and cutting edge genetics technologies such as nano-fluidic qRT-PCR and NextGen RNAseq. You will collaborate with salmon farms, scientists at the Department of Fisheries and Oceans as well as researchers at government agencies in BC and Ontario. Join us at the Great Lakes Institute of Environmental Research (GLIER) for a unique interdisciplinary doctoral experience where you will be mentored by our team of internationally renowned researchers and have unmatched hands-on access to cutting edge genetics facilities. All inquiries should be directed to Dr. Daniel Heath, Director of GLIER, at 519-253-3000 x3762 (dheath@uwindsor.ca). via Gmail

Source: EVOLDIR
15:54

Erick Matsen wrote:

This postdoctoral position is an opportunity to contribute to the design of the upcoming 701 and 702 HIV vaccine trials to maximize power in subsequent statistical analyses. Specifically, it will be to help design the trials so that infection time and founder sequences can be inferred with maximum fidelity. The scope of the study design includes sampling times and sequencing protocol, and also may afford some opportunities to design novel ways of combining sequencing methodologies. The project will last two years, with some possibility of extension. It may also offer an option to travel to South Africa to help teach a short course at the University of Cape Town, and possibly interact with the Fred Hutchinson Research Institute there.

This position will require significant statistics expertise, programming ability, and of course interest in collaboration. For a bit more detail, see the post on my website.

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15:39

Erick Matsen wrote:

www.ncbi.nlm.nih.gov Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads. F Bertels, OK Silander, M Pachkov, PB Rainey and E van Nimwegen, Molecular biology and evolution, Mar 23 2014

Studies of microbial evolutionary dynamics are being transformed by the availability of affordable high-throughput sequencing technologies, which allow whole-genome sequencing of hundreds of related taxa in a single study. Reconstructing a phylogenetic tree of these taxa is generally a crucial step in any evolutionary analysis. Instead of constructing genome assemblies for all taxa, annotating these assemblies, and aligning orthologous genes, many recent studies 1) directly map raw sequencing reads to a single reference sequence, 2) extract single nucleotide polymorphisms (SNPs), and 3) infer the phylogenetic tree using maximum likelihood methods from the aligned SNP positions. However, here we show that, when using such methods to reconstruct phylogenies from sets of simulated sequences, both the exclusion of nonpolymorphic positions and the alignment to a single reference genome, introduce systematic biases and errors in phylogeny reconstruction. To address these problems, we developed a new method that combines alignments from mappings to multiple reference sequences and show that this successfully removes biases from the reconstructed phylogenies. We implemented this method as a web server named REALPHY (Reference sequence Alignment-based Phylogeny builder), which fully automates phylogenetic reconstruction from raw sequencing reads.

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Hello there Felsenstein and Farris zones!

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01:44

Graduate position: UAdelaide.PlantDomestication.AncientDNA PhD scholarships at the Australian Centre for Ancient DNA, Adelaide, Australia A PhD position is currently available at the Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, at the University of Adelaide (http://bit.ly/1iMxMoF). The position is open to both international and domestic students with a strong academic achievement in either molecular biology, evolutionary and plant biology or Bioinformatics. Project: The Fertile Crescent region of the Near East (encompassing Iran, Iraq, Kuwait, Turkey, Syria, Jordan, Palestine, Lebanon) was an important region for the development of human civilisation and agriculture. Many of the founding crops (such as wheat, barley and rye) and livestock (cattle, sheep, pigs, etc) were first cultivated there. But as crops were selectively bred for characteristics such as height and yield, many unique phenotypes and their underlying genomic counterparts were lost over time. Now, as genetic diversity is extremely reduced in crops like wheat and barley, breeders are turning to wild cultivars to introduce new traits to continue to improve agricultural populations. With the improvement of next-generation genome sequencing (NGS) technology and ancient DNA extraction methodology it is now possible to directly access ancient alleles from 5,000-year-old wheat and barley seeds, preserved in ancient storage jars buried in a cave in Armenia. This project a ims to investigate ancient wheat and barley genomes and identify lost genes and alleles through comparison with modern breeds. Experience: This project will ideally suit an enthusiastic student who is interested in learning more about ancient DNA experimental work and Next-Generation Sequencing (NGS), and investigating the mechanisms of plant domestication and evolution by using these unique ancient samples. A good level of molecular biology is essential, and computational knowledge (especially in UNIX systems) is desireable. Competitive scholarships are available via the University of Adelaide Graduate Centre for domestic (http://bit.ly/1ktxIHU) and international students (http://bit.ly/1iMxKwV). To be eligible for these, applicants should have a 1st Class Honours or MSc degree and high undergraduate academic record. Both the Australian Department of Immigration and University of Adelaide expect international applicants to meet the English Language Proficiency (ELP) requirements. The ELP is based on high scores in IELTS (International English Language Testing System) or TOEFL (Test of English as a Foreign Language). For further information please refer to http://bit.ly/1ktxIY8. There is the potential for fieldwork, and training in ancient DNA, bioinformatics and next-generation sequencing. Interested applicants are encouraged to send a resume and a cover letter to Dr Jimmy Breen (jimmy.breen@adelaide.edu.au) via Gmail

Source: EVOLDIR
01:27

—14dae94732b9ab2dce04f6ca9c93 Content-Type: text/plain; charset=ISO-8859-1 *Research technician position: lizard behavioral evolution* A full-time, NSF-funded, technician position is available in the laboratory of Dr. Michele Johnson at Trinity University in San Antonio, Texas. Projects in the Johnson lab focus on behavioral evolution in lizards, using approaches from the fields of ecology and neuroscience to study the physiological traits underlying social behaviors. We are searching for a motivated, team-oriented technician to join our dynamic research group. The ideal candidate will have a B.S. or B.A. in biology, biochemistry, or a related field, and a minimum of one year of experience working in a researchlaboratory. The primary duties of the position include data collection in the lab and field (with likely summer fieldwork in the Caribbean), general maintenance of the laboratory, general care of laboratory animals, and training and supervision of undergraduate researchers. Previous research experience with vertebrates and facility with basic molecular and histological techniques are desirable. Facility with basic laboratory equipment, enthusiasm for working in the field, ability to adhere to safety requirements, excellent organizational and interpersonal skills, and the ability to handle multiple priorities are required. This job is ideal for persons who have an interest in gaining additional research skills and experience prior to graduate school. The Johnson lab is housed in Trinity University’s brand new Center for the Sciences and Innovation (http://goo.gl/cLZ8KP). San Antonio is among the fastest-growing cities in the United States, and the low cost of living, many cultural opportunities, and warm climate make the city a wonderful place to live. To apply for the position, please send the following materials to Dr. Michele Johnson at michele.johnson@trinity.edu: CV or resume, including contact information for 2-3 references, and a cover letter explaining why you are interested in the position. Review of applications will begin immediately, and the ideal start date is May 12, 2014. We strongly encourage women and minority candidates to apply, as we value working with a diverse team. Trinity University is an Equal Opportunity Employer. via Gmail

Source: EVOLDIR
01:07

—Apple-Mail-131-166903207 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 A Postdoctoral Research Assistant position is available for three years in the School of Biological and Chemical Sciences at Queen Mary University of London (QMUL) with Dr Richard Buggs, using genome sequencing and phylogenomics methods to identify candidate genes for low pest and pathogen susceptibility in ash trees. QMUL is one of the UK’s leading research-focused higher education institutions, with a budget of 285 million per annum. Richard Buggs’ research group works on the evolutionary genomics of trees, and this project collaborates with Stephen Rossiter whose group studies the phylogenomics of mammals. This project is funded jointly by a grant from BBSRC, Defra, ESRC, the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative. The PDRA will be responsible for sequencing and assembling the genomes of 35 ash species. Using pipelines developed by the group of co-PI Rossiter to study convergence (Nature 502, no. 7470 (2013): 228-231), the PRDA will use phylogenomic methods to identify genes and alleles associated with low susceptibility to ash dieback and the emerald ash borer. The PDRA will liaise with collaborators at Forest Research (UK) and the United States Forest Service (Ohio) who will experimentally determine the susceptibility phenotypes for each species. The PDRA will also interact with social scientists seeking to understand the attitude of the UK public to the potential use of genus-wide genome diversity in trees to combat tree health threats. The successful candidate will have a PhD in a relevant area of bioinformatics, molecular systematics, molecular evolution or a related field. Candidates must have experience in genomics, phylogenetics and programming, with a solid grounding in plant systematics, evolutionary biology and/or handling next generation sequence data. Previous post-doctoral experience is essential criteria for this post. During the project, the PDRA will also have opportunities to develop their supervision, writing, communication, media, and organisational skills, excellent preparation for a career in academia or industry. Duties will also include assisting in the training and supervision of PhD and final year project students. The position is full time and available for 36 months. The starting salary will be 38,579 per annum, inclusive of London Allowance. Benefits include 30 days annual leave, defined benefit pension scheme and interest-free season ticket loan. Candidates must be able to demonstrate their eligibility to work in the UK in accordance with the Immigration, Asylum and Nationality Act 2006. Where required this may include entry clearance or continued leave to remain under the Points Based Immigration Scheme. http://bit.ly/1kfVUOO For informal enquiries via email: r.buggs@qmul.ac.uk The closing date for applications is 25th April 2014. Interviews will be held soon thereafter. _______ Dr Richard Buggs | Senior Lecturer | School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, United Kingdom | email: r.buggs@qmul.ac.uk | website: http://bit.ly/1lSzRgM | office: +44(0)207 882 8441 | mobile: +44(0)772 992 0401 | twitter: @RJABuggs —Apple-Mail-131-166903207 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252

A Postdoctoral Research Assistant position is available for three years in the School of Biological and Chemical Sciences at Queen Mary University of London (QMUL) with Dr Richard Buggs, using genome sequencing and phylogenomics methods to identify candidate genes for low pest and pathogen susceptibility in ash trees. QMUL is one of the UK’s leading research-focused higher education institutions, with a budget of 285 million per annum. Richard Buggs’ research group works on the evolutionary genomics of trees, and this project collaborates with Stephen Rossiter whose group studies the phylogenomics of mammals. This project is funded jointly by a grant from BBSRC, Defra, ESRC, the Forestry Commission, NERC and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative.  The PDRA will be responsible for sequencing and assembling the genomes of 35 ash species. Using pipelines developed by the group of co-PI Rossiter to study convergence (Nature 502, no. 7470 (2013): 228-231), the PRDA will use phylogenomic methods to identify genes and alleles associated with low susceptibility to ash dieback and the emerald ash borer. The PDRA will liaise with collaborators at Forest Research (UK) and the United States Forest Service (Ohio) who will experimentally determine the susceptibility phenotypes for each species. The PDRA will also interact with social scientists seeking to understand the attitude of the UK public to the potential use of genus-wide genome diversity in trees to combat tree health threats.The successful candidate will have a PhD in a relevant area of bioinformatics, molecular systematics, molecular evolution or a related field. Candidates must have experience in genomics, phylogenetics and progr amming, with a solid grounding in plant systematics, evolutionary biology and/or handling next generation sequence data. Previous post-doctoral experience is essential criteria for this post. During the project, the PDRA will also have opportunities to develop their supervision, writing, communication, media, and organisational skills, excellent preparation for a career in academia or industry. Duties will also include assisting in the training and supervision of PhD and final year project students.The position is full time and available for 36 months. The starting salary will be 38,579 per annum, inclusive of London Allowance. Benefits include 30 days annual leave, defined benefit pension scheme and interest-free season ticket loan.Candidates must be able to demonstrate their eligibility to work in the UK in accordance with the Immigration, Asylum and Nationality Act 2006. Where required this may include entry clearance or continued leave to remain under the Points Based Immigration Scheme.http://bit.ly/1kfVUOOFor informal enquiries via email: r.buggs@qmul.ac.ukThe closing date for applications is 25th April 2014. Interviews will be held soon thereafter. _______Dr Richard Buggs | Senior Lecturer | School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, United Kingdom | email: r.buggs@qmul.ac.uk | website: http://bit.ly/1lSzRgM | office: +44(0) 207 882 8441 | mobile: +44(0)772 992 0401 | twitter: @RJABuggs —Apple-Mail-131-16690320 via Gmail
Source: EVOLDIR
00:51

Bioinformatician in transcriptomics Full time permanent position. The position is available as soon as possible. 6 months trial period. Uppsala University is an international research university focused on the development of science and education. Our most important assets are all the individuals who with their curiosity and their dedication makes Uppsala University one of Sweden’s most exciting work places. Uppsala University has 40,000 students, 6,500 employees and a turnover of SEK 5,500 million. Next-generation sequencing (NGS) is a rapidly growing field that provides fascinating new insights into the genetic underpinnings of cellular functions and diseases. However, these new methods place increasing demands on computational expertise and data management. The Swedish Bioinformatics Infrastructure for Life Sciences (BILS; http://bils.se) is therefore seeking a motivated bioinformatician to join their ranks and provide support to projects in the field of transcriptomics and next-generation sequencing. Job description: The position will be placed at Uppsala University and will be linked to Science for Life Laboratory. Among the main objectives for this newly created post will be the reconstruction of transcripts from read data, using both mapping-based but also de-novo assembly algorithms. In addition, the candidate is expected to provide support to projects working with RNA sequencing to study the expression of genes and transcripts. Finally, a major aspect of the study of transcriptomes is the ability to assign functions to individual sequences. Together with the team at the BILS annotation platform, the successful applicant will spend part of the time on the development and implementation of workflows for the functional annotation of genes and transcripts. Qualifications: We seek a candidate with a PhD in bioinformatics, molecular biology, computer science or any related field who has a strong competence in working with large sequencing data sets and analysis methods in the field of NGS, including but not limited to, RNA-seq. The ability to drive projects and work in a collaborative, yet service-minded environment is a must. Special consideration will furthermore be given to applicants with proficiency in one or more scripting languages (e.g. Perl, Python, Ruby) as well as experience in pipeline design. Excellent communication skills in both written and spoken English are required, since the candidate will collaborate with scientists of very different backgrounds. Emphasis will be placed on personal suitability for the position. Information: For questions regarding BILS, please check out our website at http://www.bils.se or contact the director of BILS, Bengt Persson (bengt.persson@bils.se). For questions regarding the position, please send an Email to Henrik Lantz (henrik.lantz@imbim.uu.se). You are welcome to submit your application no later than 12 May 2014. Please see the link below for full details and to access the application form: http://bit.ly/1kEYjoV via Gmail

Source: EVOLDIR
00:33

Dear Evol-dir community, I would appreciate recommendations for laboratory information management systems for academic labs focused on molecular biology. As our lab does mostly population genetics-oriented research on numerous species, we are accumulating more samples and associated information than is easy to keep track of in spreadsheets and our heads. Ideally this LIMS would accommodate the use of barcodes for samples and storage locations (i.e. boxes, freezers), provide easy recording of actions on samples like extraction and library preparation, list the outcomes of those events (degraded, failed, consumed, etc.), and connect to products of those events (e.g. links to NGS fastq files). I am most interested in relatively simple out-of-the-box solutions or MS Access templates that won’t break the bank. Any suggestions or experience would be helpful. Thanks! Stuart Willis swillis4@gmail.com via Gmail

Source: EVOLDIR
00:09

Dear all, We are organising a symposium on evolutionary phylogenetics and Lepidoptera biodiversity (see details below) at the International Conference on the Biology of Butterflies, 2014 in Turku, Finland (August 11-14th). http://bit.ly/17ARV8Y We encourage submission for talks and posters: http://bit.ly/OM9lul Deadline for abstract submission is May 1. Thanks, and hope to see many of you in Turku, Marianne Elias and Karina Lucas Silva Brandao Evolutionary phylogenetics and Lepidoptera biodiversity: diversification, adapations and community ecology Why are there so many species on Earth, and why are they so concentrated in a small number of hotspots? More specifically, what are the processes underlying diversification and what are those permitting multiple species to coexist? These questions have intrigued biologists since the acceptance of Darwin’s theory of evolution and still represent a major challenge for modern evolutionary biology. The insect order Lepidoptera is an excellent model group to answer these questions, using recent approaches based on molecular phylogenies. The purpose of this symposium is to present original research on diversification, adaptation and community ecology of Lepidoptera, using phylogenetic tools. Marianne Elias CNRS Researcher UMR 7205 - CNRS Museum National d’Histoire Naturelle 45 rue Buffon, CP50, 75005 Paris phone: +33 1 40 79 37 90 http://bit.ly/Pnhkh3 melias2008@gmail.com via Gmail

Source: EVOLDIR

April 11, 2014

23:51
—_000_CF6DB4D214599templetonbiology2wustledu_ Content-Type: text/plain; charset=”us-ascii” Content-Transfer-Encoding: quoted-printable The Department of Evolutionary and Environmental Biology, University of Haifa, Israel (http://bit.ly/OSIxaN), invites candidates for a tenure-track position to begin on October 2014 or October 2015. We shall consider any excellent scientist in the fields of Evolutionary Biology and/or Ecology. Interested candidates should send a letter of research interests/plans, CV, list of publications, and contact information of at least three referees to Ms. Limor Dvir, ldaniely@univ.haifa.ac.il by April 30, 2014. Alan R. Templeton Charles Rebstock Professor Emeritus of Biology and Genetics Professor of Evolutionary and Environmental Biology ____________________________ Department of Biology Washington University St. Louis, MO 63130-4899 USA Institute of Evolution, and Department of Evolutionary and Environmental Biology University of Haifa Haifa 31905, Israel p. 314-935-6868 f. 314-935-4432 e. temple_a@wustl.edu http://bit.ly/1ex36m0 —_000_CF6DB4D214599templetonbiology2wustledu_ Content-Type: text/html; charset=”us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable The Department of Evolutionary and Environmental Biology, University of Haifa, Israel (http://bit.ly/OSIxaN), invites candidates for a tenure-track position to begin on October 2014 or October 2015. We shall consider any excellent scientist in the fields of Evolutionary Biology and/or Ecology. Interested candidates should send a letter of research interests/plans, CV, list of publications, and contact information of at least three referees to Ms. Limor Dvir, ldaniely@univ.haifa.ac.il by April 30, 2014. Alan R. Templeton Charles Rebstock Professor Emeritus of Biology and Genetics Professor of Evolutionary and Environmental Biology ____________________________ Department of Biology Washington University St. Louis, MO 63130-4899 USA Institute of Evolution, and Department of Evolutionary and Environmental Biology University of Haifa Haifa 31905, Israel p. 314-935-6868  f.  314-935-4432 e. temple_a@wustl.edu http://bit.ly/1ex36m0 —_000_CF6DB4D214599templetonbiology2wustledu via Gmail
Source: EVOLDIR
23:34

The Altermatt lab at the Institute of Evolutionary Biology and Environmental Studies (IEE) of University of Zurich and the Department of Aquatic Ecology of Eawag, Switzerland, has a vacancy for: A Postdoc Position in Metacommunity-/Metaecosystem Ecology Project title: Bridging biodiversity and ecosystem functioning in dendritic networks: a meta-ecosystem perspective Understanding the causes and consequences of biodiversity is among the most challenging goals in ecology. Recent results indicate a generally positive effect of diversity on ecosystem processes. Up to now, almost all work on biodiversity-ecosystem functioning has been conducted in a non-spatial, one-patch perspective. Natural ecosystems, however, are spatially explicit, and there is substantial flow of material and organisms among patches and ecosystems. This project aims at applying the concept of meta-ecosystems to empirical data in spatially explicit dendritic networks. In a project linked to two complementing PhD theses, the Postdoc Fellow will use a laboratory protist microcosm system to experimentally test interacting effects of habitat network structure and ecosystem functioning. As a group, we will extend these findings to mesocosm experiments and large-scale field studies with amphipods to study ecosystem functioning in Swiss river networks. The Postdoc will synthesize the findings, and link or expand existing theoretical work. In the whole project, diversity and ecosystem functioning will be studied in spatially explicit dendritic networks in a highly consistent framework. Ultimately, we want to get a comprehensive understanding of biodiversity and ecosystem functioning in riverine systems. Competitive applicants will have previous experience in ecology, biodiversity and spatial dynamics and be interested in participating in this extensive new research project. They will be highly motivated, enthusiastic and independent scientists. Candidates should have a good conceptual understanding of ecological theory, excellent experimental skills and/or a strong background in quantitative modeling. Excellent communicational and writing skills in English, experiences with publishing scientific articles, good work ethics, and creative thinking are desired. A PhD in Ecology or related subject is necessary for admission. The working language in the Altermatt lab is English. The Altermatt lab has a shared base at University of Zurich and at Eawag. It offers a stimulating and international research environment, excellent research facilities and a lively and social working place. Zurich hosts many other research groups in ecology and biodiversity research, and is among the world’s leading cities in terms of science, culture and quality of life. The positions will be for a period of two years, and could start in the second half of 2014. The project is financed by the Swiss National Science Foundation (SNSF Research Professorship to Florian Altermatt from August 2014 onwards). For further information, consult http://bit.ly/1hsKqqw http://bit.ly/1hsKrLd www.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1qLTPtXwww.eawag.ch or directly contact Dr. Florian Altermatt: Tel: +41 58 765 55 92, E-mail: florian.altermatt@eawag.ch Applications must be submitted by 10th May 2014 and should include a motivation letter with a description of pertinent experience, a complete CV (incl. publication list), the names (with e-mail addresses) of three academic references, and copies of certificates of academic qualifications. The application should be submitted as one single pdf-file. We look forward to receiving your application through the online application form at: http://bit.ly/1qLTPtX Any other way of applying will not be considered. via Gmail

Source: EVOLDIR