Postdoc - Univ. of Wisconsin-Madison - Evolutionary Genomics

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Postdoc - Univ. of Wisconsin-Madison - Evolutionary Genomics

Postby jpool » Wed Feb 01, 2012 11:18 pm

Postdoctoral Researcher in Population Genomics

A postdoctoral position is available in the recently-formed research group of John Pool at the University of Wisconsin-Madison. The focus of our research group is on (1) analyzing population genomic data, including the development of new statistical methods, and (2) integrating population genomic data with other information sources - such as mapping, expression, and phenotypic data - to investigate the genetic basis of adaptive evolution. This position is targeted for the latter focus.

We use Drosophila melanogaster as a model system to pursue the genes and mutations that underlie adaptive phenotypic differences between populations from contrasting environments. An example from previous work is melanism, which occurs in African highland populations. Previous population genetic work identified ebony as a candidate gene in one melanic population (Pool and Aquadro 2007 Mol. Ecol.), and a subsequent collaboration with Mark Rebeiz and Sean Carroll resulted in the identification of five causative mutations around the abdominal enhancer of ebony (Rebeiz et al. 2009 Science). However, at least one additional pigmentation locus awaits discovery in this population (Uganda), and for two other populations (Cameroon and Ethiopia), the genetic basis of melanism is completely unknown. I'd also like to broaden our focus to other traits involved in Drosophila altitude adaptation.

Strategies for finding genes underlying adaptive population differences may include:
* Analysis of existing population genomic data. More than 100 genomes from African populations have already been sequenced (http://www.dpgp.org/dpgp2/DPGP2.html). Population genetic scans for loci with elevated genetic differentiation between high and low altitude populations would be relevant. For larger sample sizes, genotype-phenotype associations may also be informative.
* Generation (and analysis) of new population genomic data. In terms of lab work, this would involve identifying haploid embryos, genome amplification, and DNA library preparation for the Illumina HiSeq platform. After receiving sequence data, reference alignment and quality filters are needed to produce a data object for population genomic analysis.
* Phenotypic measurements - quantification of Drosophila pigmentation (using digital photography and analysis) and other adaptive traits. The use of inbred lines allows replicated phenotyping to reduce measurement error in tests of genetic and geographic associations.
* Transcriptome analysis - to the extent that adaptive changes are regulatory, gene expression differences within and between populations could offer a valuable bridge between genomes and phenotypes. This would involve RNA isolation and bioinformatic analyses.

Our research group was started in fall 2011 and currently consists of the PI, one postdoc focusing on the analysis of population genomic data, and undergraduate researchers. I can offer a new postdoc plenty of individual attention, broadly applicable training in population genomics, and a first-hand understanding of the current faculty job market. I encourage postdocs to develop as independent scientists, and I will support you in putting together a research program that you can carry beyond this appointment.

UW-Madison offers a superb scientific environment, with colleagues in population genetics and evolutionary genomics including David Baum, Sean Carroll, Cameron Currie, Colin Dewey, John Doebley, Audrey Gasch, John Hawks, Chris Hittinger, Carol Lee, Lawrence Loewe, Bret Payseur, and Nicole Perna. There are roughly a dozen Drosophila groups on campus, including the labs of Bill Engels and Barry Ganetzky in our building.

Madison offers an exceptional quality of life in a beautiful natural setting. Downtown and campus are bordered by lakes, and the area includes a number of long distance bike trails. Madison features diverse art, music, and cultural offerings. A great farmers market and a focus on local food are complemented by a wide range of international restaurants.

Applicants should send a CV and contact information for three references to jpool@wisc.edu. In addition, applicants should send a statement of interest addressing their background and interests related to the following points (note that the successful candidate may not have every skill that I inquire about):
* Intellectual background and interests; career goals.
* Computer programming (language, experience level) and other bioinformatic skills.
* Statistical experience (such as population genetic or quantitative genetic analyses).
* Molecular lab skills relevant to the work described above.
* Experience working with Drosophila; knowledge of Drosophila biology.

Potential start dates are between April 1 and July 1, 2012. Please indicate the earliest start date you would consider.

Feel free to contact me with any questions (jpool@wisc.edu).

John Pool
Assistant Professor
Laboratory of Genetics
University of Wisconsin-Madison
jpool
 
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Joined: Wed Feb 01, 2012 6:29 pm

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