Hi, I'm Kara! I am currently a PhD student in Joanna Kelley's Lab at UCSC. I use biological big data to understand how animals adapt to extreme environments, such as dark caves and sulfide-rich springs. I analyze genomes and transcriptomes to uncover the evolutionary history of populations and species. Ultimately, I am fascinated by the repeatability of evolution and I am motivated by our limited understanding of the genomic basis of convergence.
Projects
Conway's Game of Life (for the command line)
Click here to download and play Conway's Game of Life that I wrote in python3!
Targeted Capture Seq of Sulfide Adapted Populations of Poecilia mexicana
For the first chapter of my Ph.D., I used targeted capture sequencing of regions associated with hydrogen sulfide response and toxicity to understand if populations that have independently adapted to sulfide springs did so via the same or different genes.
This systems-level project analyzed expression from seven fish species to determine if there were differences in expression between ancestors of extremophiles and ancestors of non-extremophiles after exposure to hydrogen sulfide.
Genomic Basis of Eye Loss in Subterranean Amphipods
This analysis was for my Master's thesis project. Using pooled RNA-seq, we compared gene expression between two closely related species of amphipods, one of which is eye- and pigment-less. A majority of this project used shell (bash) scripting and R.
Publications
Selection on standing genetic variation mediates convergent evolution in extremophile fish
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Molecular Ecology, vol. 32, 2023, pp. 5042-5054
Regional sequence expansion or collapse in heterozygous genome assemblies
Kathryn C. Asalone, Kara M. Ryan, Maryam Yamadi, Annastelle L. Cohen, William G. Farmer, Deborah J. George, Claudia Joppert, Kaitlyn Kim, Madeeha Froze Mughal, Rana Said, Metin Toksoz-Exley, Evgeny Bisk, John R. Bracht
PLOS Computational Biology, vol. 16, Public Library of Science, 2020 Jul, pp. 1-22
