September 20, 2015

A Graduate Research Assistantship for a M.Sc. or Ph.D. student in the Oregon State University Herbarium is available beginning Fall, 2016, under the supervision of Dr. Aaron Liston. Research in the Liston lab focuses on the application of genomic approaches to questions of plant systematics and evolution. No prior herbarium experience is required, but candidates should have a strong interest in broadening their knowledge of plant diversity. Applications for the graduate program in the Department of Botany and Plant Pathology are due on December 1, 2015. For additional details, please contact  Aaron Liston .

 

April 10, 2015

Two Postdocs in Plant Evolution & Ecology at the University of Pittsburgh

Seeking two Postdoctoral fellows to join a collaborative project examining functional, population genetic and ecological mechanisms underlying success of polyploid plants.

The work aims to predict the effect of whole genome duplication on ecological and evolutionary responses to environmental change.  The postdocs will identify the ecological, population genetic and genomic factors that underlie functional trait (e.g., phenotypic plasticity in repose to climate, tolerance of drought and freeze) variation, ecological amplitude and gene expression diversity using the wild strawberry (Fragaria) as a model system (see Liston et al 2014. AJB101:1686-1699 ; Johnson et al 2014 Bot J Linn Soc 176:99-114 ). The specific goals are to 1) characterize functional responses to climate and how they vary with natural variation in ploidy, with experimental hybridization and whole genome duplication, 2) analyze gene expression (transcriptomes) and physiological traits of natural and synthetic polyploids and their diploid progenitors in the greenhouse and common gardens at climatically diverse sites, 3) use NGS of target-captured sequence from natural populations of plants to identify patterns of genetic diversity and signatures of selection, reconstruct phylogenetic relationships and generate high density linkage maps ( Tennesson et al 2014 GBE 6:3295–3313) .

Postdoc candidates are sought with expertise in one of two areas (with ample opportunities for cross training between them):

  1. Population genetic, comparative genomics, transcriptome analysis to address ecological or evolutionary questions
  2. Population, physiological or functional plant ecology 

Candidates interested in a combination of field work and genomic work especially encouraged to apply.

Responsibilities will include the establishment and monitoring of experiments in the field and under controlled conditions in the lab, collection and analysis of population genetic/genomic, phenotypic and physiological data, and the preparation of manuscripts for publication. Ability to travel between field sites in Oregon and laboratory in Pennsylvania is required.  

In addition to cross training, the project affords opportunities for international travel and training as part of an US-China international research collaboration, and to design and implement additional allied projects tailored to the skills and interests of the postdoc.

The postdoc position is for two years, renewable for additional years. Start date is negotiable, but June 2015 is preferred. 

The project is collaboration among the labs of Dr. Tia-Lynn Ashman, Department of Biological Sciences at the University of Pittsburgh and Dr. Aaron Liston, Department of Botany and Plant Pathology, and Dr. Richard Cronn US Forest Service at Oregon State University.

TO APPLY: Please send a CV and a description of your experience and interests as relevant to the position to tia1 at pitt dot edu, along with the names and contact information for three referees. In a covering letter clearly highlight skills and experience related to key responsibilities. Informal enquiries are also welcome!

Application materials will be reviewed as they are received, until positions are filled.

 

December 4, 2014

New paper on octoploid subgenomes published in Genome Biology and Evolution

Our recent publication (Tennessen et al. 2014) will be relevant both to strawberry geneticists and to anyone interested in the evolution and genomics of polyploids. There are six important advances that we would like to highlight:

  1. We have substantially improved the genome assembly for wild strawberry (Fragaria vesca), using dense targeted capture linkage maps. The new assembly can be downloaded from Figshare and can be browsed at SGR: Strawberry Genomic Resources
  2. We have generated dense linkage maps (1000s of markers) for two octoploid strawberry species, paving the way for functional genetics in previously intractable polyploid taxa.
  3. Our novel bioinformatic approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), allows researchers to identify segregating SNPs in next-generation sequence data from polyploids and build phylogenies of the resultant linkage groups and their diploid relatives. 
  4. Our robust phylogeny of the octoploid progenitors of cultivated strawberry revises the established genomic model and reveals that one of the four subgenomes originates with the diploid F. vesca, while the other three are closest to the diploid F. iinumae.
  5. We observe extensive introgression of F. vesca-like sequence to the F. iinumae-like subgenomes, but never the reverse. This pattern may have adaptive significance in the origin and success of octoploid strawberries.
  6. Numerous interchromosomal rearrangements produce many of the differences among homeologous chromosomes.