The Kelley and Cornejo Labs enjoyed a festive evening of pumpkin carving this past Tuesday. We were joined by Evan, Tina, Sam, MC, Joanna, Omar as well as partners and family for dinner before transforming pumpkins into cats, unicorns, nucleotides, and more!

This week, MC, Isabel, and Kara performed the first DNA extraction in the new Kelley Lab space at UC Santa Cruz!

Thanks to everyone for working to get our new space up and running!

Kara’s first lead-author paper is out now in Molecular Ecology! Huge congrats to Kara and coauthors!

Link to the open-access study in Molecular Ecology.

Abstract

Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.

Kara was awarded the Vern Parish Fund award from the American Livebearer Association to continue her work on Poeciliid fish genomes!

Congrats Kara!

On June 6th, the UC Santa Cruz Postdocs Association (USPA) held their annual symposium at the Seymour Marine Discovery Center. The event showcased the breadth of work being carried out by postdocs and graduate students across the university spanning physics, chemistry, and biology. In addition to a number of talks from UCSC postdocs, three invited speakers presented at this year’s symposium, covering a number of different fields including entrepreneurship, cosmology, and evolution.

Rishi gave a short presentation titled “Evolutionary dynamics of a complex supergene in the African monarch butterfly”. This talk started by outlining the key differences between using variation in nucleotides (e.g. A or T) to study evolutionary patterns compared to structural variation (including inversions, deletions, and duplications). He then outlined his work in the African monarch (Danaus chrysippus) system showing how long-read sequencing allows us to study complex structural variants to better understand how structural variation arises and is maintained through time.

The lab recently published a one-of-a-kind dataset of gene expression from multiple tissues of two hibernating brown bears at BMC Genomic Data.

Congrats to all coauthors!

Abstract

Objectives. Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of interest can provide a foundation for understanding the genomic basis of these phenotypes, and the degree to which these resemble, or contrast, those of traditional model organisms. Here, we present a one-of-a-kind gene expression dataset generated from multiple tissues of two hibernating brown bears (Ursus arctos).

Data description. This dataset is comprised of 26 samples collected from 13 tissues of two hibernating brown bears. These samples were collected opportunistically and are typically not possible to attain, resulting in a highly unique and valuable gene expression dataset. In combination with previously published datasets, this new transcriptomic resource will facilitate detailed investigation of hibernation physiology in bears, and the potential to translate aspects of this biology to treat human disease.

Link to the article at BMC Genomic Data.