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Alex Fraik publishes a Tasmanian devil transcriptomics paper in Genes!

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. In this study, Fraik et al. identified environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. No transcriptome-wide patterns of differential gene expression were detected, consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation (Fraik et al. 2019, Biorxiv) to abiotic environment in devils were enriched for differentially expressed genes. Additionally, modules of co-expressed genes were significantly associated with both geographic location and sex. This study revealed that candidate-gene approaches to transcriptomic studies of naturally sampled wildlife populations may be necessary to capture gene expression changes in response to complex multivariate environments.

Fraik, A.K.Quackenbush, C., Margres, M.J., Comte, S., Hamilton, D.G., Kozakiewicz, C.P., Jones, M., Hamede, R., Hohenlohe, P.A., Storfer, A., Kelley, J.L. Transcriptomics of tasmanian devil (Sarcophilus harrisii) ear tissue reveals homogeneous gene expression patterns across a heterogeneous landscape. Genes 201910, 801. *Corresponding author

Luana is going to Antarctica!

We are all very excited that Luana Lins, a postdoctoral researcher in our lab, has been selected to be part the NSF Advanced Training Program in Antarctica for Early Career Scientists (https://www.usfca.edu/arts-sciences/antarctic-biology-training-program).

She will spend a month in Antarctica as part of the program where researchers will get involved in research projects and will be more knowledgeable of the logistics of conducting studies in this unique environment. Luana Lins is following on the footsteps of our PI Joanna Kelley who participated in the same program in 2008, and her PI Willie Swanson who participated several years before that.

Our lab is very interested in adaptations to extreme environments and Luana is working in a project focused on the adaptations of fish to polar environments, Luana’s training will be great to the development of our polar adaptations project. She will be posting about her preparations and experiences in Antarctica at her blog (https://www.drluanalins.com/blog).

Here’s a nice write-up from WSU (https://news.wsu.edu/2018/03/09/visiting-antarctica/)

Scott Hotaling joins the lab

Scott Hotaling has arrived in Pullman! We are very happy Scott has decided to join the lab as a postdoctoral researcher. He has already started wading through the vast amounts of data we have been hoarding in the lab and making great progress!

 

We’re going to Evolution 2017!

The lab (and many labs from WSU) are going to Evolution 2017! See you there? If you’re interested in finding out more about our research we have several talks and posters. You can find us at the following:

Name Day Time Session name Room
Laura Helou (poster) Saturday 6:30-8:30 PM Bioinformatics EHA-04
Shawn Trojahn (poster) Saturday 6:30-8:30 PM Phylogenomics EHA-31
Anthony Brown Sunday 8:45 AM Inbreeding / conservation biology B114-115
Enrique J-S Sunday 3:30 PM Sex / recombination 3 Ball204
Alex Fraik Sunday 3:45 PM Adaptation / genomics 4 B117-119
Omar Cornejo Sunday 4:00 PM Disease A106
Carlie Harding (poster) Sunday 6:30-8:30 PM Genomics EHA-14
Luana Lins Monday 10:30 AM Molecular ecology / genomics C124
Joel Nelson Monday 11:00 AM Molecular ecology / genomics C124
Joanna Kelley Monday 3:15 PM SSE Symposium – The impact of stress on genetic variation 2 Ball203

Note, I have added links to YouTube videos from the Evolution Meeting channel for the talks that were recorded, just click on the presenter’s name.

Poeciliid 2017

Just returned from Poeciliid 2017 in Norman, OK. It was a fantastic meeting! The organizers Ingo Schlupp and Edie Marsh-Matthews did a fantastic job planning the meeting. The meeting was small and intimate, with only one session at a time, which was the perfect opportunity to connect with other poeciliid biologists. The topics were varied and ranged from genomics to behavior to phylogenetics to nutrient transfer. The participants ranged from new graduate students to senior faculty members, which made for a great mix of experiences, ideas and knowledge. There was ample time for sharing ideas and, at least for me, it was one of the best meetings I have attended in a while! I will definitely attended the next meeting (likely 2019) and I encourage everyone who is tangentially involved in poeciliid research to attend too!

 

Exciting spring for awards

It has been an exciting spring in the lab! We wanted to acknowledge the awards that several students and postdocs received this spring.

Anthony Brown received the James R. King Graduate Fellowship from the School of Biological Sciences to fund his research and part of his stipend this summer!

Joanna Kelley received the College of Arts and Sciences Early Career Award!

Luana Lins received a scholarship to the Summer Institute in Statistical Genetics at University of Washington this summer and a travel award from the Society for the Study of Evolution to attend Evolution 2017!

Samantha Kallinen received the Undergraduate Summer Minigrant from the College of Arts and Sciences to support her research over the summer!

Allegra Sundstrom received the Youth Activity Fund award from the Explorer’s Club and a School of Biological Sciences research award to conduct research in Alaska this summer!

Congratulations to Shawn Trojahn – NSF GRFP!

Congratulations to Shawn for receiving the NSF Graduate Research Fellowship Program (GRFP)! We are thrilled for Shawn. This is a fantastic testament to his accomplishments and promise as a graduate student!

“The NSF Graduate Research Fellowship Program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based Master’s and doctoral degrees at accredited United States institutions… For the 2017 competition, NSF received over 13,000 applications, and made 2,000 award offers.” from https://www.nsfgrfp.org/.

Welcome Intern Laura Helou!

Laura has arrived from France! We are very excited to have Laura visiting the lab for 5 months to work on detecting and annotating transposable elements in extreme species!

Laura obtained her Bachelor’s Degree in Microbiology at the Montpellier University (France) and now she is in the last year of a Master’s Degree in Bioinformatics at the same university. During her master’s degree she has done two internships and developed a strong interest for comparative genomics and the impact of structural variation on the evolution of species. She worked on benchmarking of several tools for the detection of structural variation in the rice genome.

Alex Fraik and Michael Saxton give their first presentations

Congratulations to Alex Fraik and Michael Saxton on presenting their first oral presentations at the School of Biological Sciences Graduate Research Symposium! They both gave great talks! The School of Biological Sciences Graduate Research Symposium is organized by graduate students annually and coincides with our recruitment event for visiting prospective graduate students.