Mentor & Lab: Dr. Joanna Kelley & Dr. Sam Bogan – Kelley Lab
Positions: 2 interns
Tentative dates: 6/23/25 – 8/29/25
Project Location: Lab on Coastal Campus
Project Background: Adaptation to novel habitats like polar oceans is generally predicted to reduce genetic diversity and effective population size (Ne) due to founder effects. After initial declines, populations can rebound or grow beyond historical levels due to reduced competition and rapid growth in new habitats. However, periods of extreme cold have been linked to widespread reductions in Ne. Zoarcidae (eelpout fishes) is one of two fish families that have independently adapted to both the Arctic and Southern Oceans multiple times, offering a unique system to study polar adaptation and invasion effects on population size. This project will use eleven new eelpout genome assemblies to reconstruct Ne during Arctic cooling and subsequent polar invasions using pairwise sequentially Markovian coalescent. It will provide interns with valuable experience in molecular and genomic tools for studying environmental impacts on biodiversity, including training in comparative genomics, spatiotemporal analysis, phylogenetics, and molecular lab techniques.
Intern duties: Interns will engage in diverse research activities, including collecting temperate fish species native to Monterey Bay with mentors and collaborators at Moss Landing Marine Labs using seine and dip nets. They will assist with extracting and quality-checking high molecular weight DNA for next-generation sequencing, learn and apply bioinformatics pipelines for genome construction, and conduct spatiotemporal analyses of historical and contemporary temperature data from oceanographic and paleoclimatology sources. Under mentor guidance, interns will implement data management protocols for large-scale projects and develop skills in comparative genomics and phylogenetics by constructing time-calibrated phylogenetic trees and reconstructing effective population sizes using whole-genome data via pairwise sequential Markovian coalescent (PSMC).
Intern qualifications: Interns must have passed Genetics with a C or better. Willingness to learn computational analyses. We will teach interns all of the computational skills necessary to excel in this project.
Do you recommend the intern(s) volunteer in your lab during Spring quarter?
If possible, yes.