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Kelley Lab News

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

Kerry McGowan publishes cavefish transcriptomics paper in Biology Letters!

Various animals have colonized caves, and in the course of evolution, many have lost their eyes. We still do not fully understand how the loss of an entire organ unfolds as organisms adapt to dark caves. In this study, Ph.D. student Kerry McGowan and colleagues examined a small fish, the cave molly, that colonized caves relatively recently and exhibits functional eyes that are reduced in size. Using gene expression analyses, McGowan et al. showed that several eye-related genes are expressed less in cave mollies compared to their surface ancestors. Evolution has modified many of these genes in other completely blind cavefishes, suggesting that cave adaptation may occur in similar fashions.

McGowan KL*, Passow CN, Arias-Rodriguez L, Tobler M, Kelley JL. 2019. Expression analyses of cave mollies (Poecilia mexicana) reveal key genes involved in the early evolution of eye regression. Biol Lett. 15(10):1-7.

*Corresponding author

A cavefish from the Cueva del Azufre system in southern Mexico.

Note the small eye. PC: Michael Tobler.



Scott Hotaling publishes ecological stoichiometry paper in Frontiers in Ecology and Evolution!

Permanent ice cover by glaciers and snowfields is a dominant physical force in mountain ecosystems. From an ecological perspective, constant ice cover places harsh controls on life including cold temperature, limited nutrient availability, and often prolonged darkness due to snow cover for much of the year. Despite these limitations, glaciers, and perennial snowfields support diverse, primarily microbial communities. In a new review, postdoc in the lab Scott Hotaling and colleagues we synthesize existing knowledge of ecological stoichiometry, nutrient availability, and food webs in the mountain cryosphere (specifically glaciers and perennial snowfields).

Ren, Z.*, Martyniuk, N.*, Oleksy, I.A.*, Swain, A.*, & Hotaling, S.† (2019) Ecological stoichiometry of the mountain cryosphere. Frontiers in Ecology and Evolution 7:360. *co-first author; †corresponding author



Brown bear hibernation paper

Thrilled that our paper on gene expression changes in brown bears during hibernation is out today in @CommsBio with co-authors Shawn Trojahn, Heiko Jansen, Omar Cornejo, Charlie Robbins, and others.  #WSUbears A link to the article is here:


Alex Fraik at NOAA

Graduate student Alex Fraik started her 6 month NSF funded internship with Krista Nichols at NOAA. While most of her project will be analyzing existing datasets on fish before and after dam removal, she had a chance to participate in some fieldwork.

NHGRI Comparative Genomics Workshop

Joanna Kelley presented at the NHGRI Comparative Genomics Workshop in Bethesda, MD. It was a fantastic event bringing together ~115 genome biologists from around the country to discuss comparative genomics and the NHGRI strategic plan as it relates to comparative genomics. The schedule of speakers is here:

You can view Joanna’s talk here:

You can view the moderated discussion here: