The NOAA Southwest Fisheries Science Center (SWFSC) announces an opportunity to fund a postdoctoral associate for up to 3 years to work on a project aimed at developing groups of genetic loci (referred to as panels) that can be used to efficiently and affordably genotype large numbers of individuals from multiple marine mammal species. The Genotyping-in-Thousands by Sequencing (GTseq; Campbell et al., 2015) technique enables the simultaneous genotyping of hundreds-to-thousands of samples in an efficient and affordable way. GTseq is also highly reproducible, allowing for data generated in different laboratories and across many years to be combined. However, GTseq assays have historically been developed as single-species panels, with each panel containing between ~90 and 500+ loci. Consequently, applying GTseq to a new species requires the time-consuming development of a new panel and the purchase of costly species-specific locus primers. Recently, researchers have had success developing panels that work for multiple closely-related species (Baetscher et al., 2019; 2023). The development of these multi-species panels can greatly reduce the per-project cost, both in terms of time and money, of generating genetic data for addressing management questions for marine mammals.
We are seeking a postdoctoral associate to collaborate on a project designed to generate the data sets and code needed to develop multi-species GTseq panels for groups of marine mammal species that are of high management concern: the Balaenopteridae/Eschrichtiidae super-family (which includes blue, fin, Rice’s, humpback, and gray whales), Balaenids (right and bowhead whales), Globicephalids (including false killer whales and short-finned pilot whales), and Phocids (e.g., harbor, spotted, and ice seals). The scope of the project includes: (1) compiling currently available genomic data from the taxonomic groups of interest, (2) generating additional genomic data, such as from double digest restriction-site associated DNA sequencing (ddRAD) or low-coverage whole genome sequencing (lcWGS), for the species of interest, (3) identifying single nucleotide polymorphism (SNP) loci that are variable within and across species, and (4) designing and optimizing multi-species GTseq panels for the four taxonomic groups enumerated above. All data processing is to be conducted using bash scripts and the statistical programming language R, with scripts written so that they are generally applicable to future GTseq panel design projects and made publicly available on GitHub. The associate will be stationed at SWFSC in La Jolla, CA, and expected to travel occasionally to present at meetings and conferences.
References:
Baetscher, D. S., et al. (2019). "Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast." Molecular Ecology 28(7): 1611-1623.
Baetscher, D. S., et al. (2023)
Campbell, N. R., et al. (2015). "Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing." Molecular Ecology Resources 15(4): 855-867.
Bioinformatics; cetacean; pinniped; single nucleotide polymorphism; genomics; population structure; conservation; next generation sequencing