Publication Date

Summer 2025

Degree Type

Thesis

Degree Name

Master of Science (MS)

Department

Moss Landing Marine Laboratories

Advisor

Amanda Kahn; Jonathan Geller; Kevin Johnson; Luke Gardner; Sarah Smith

Abstract

Olympia oysters (Ostrea lurida), critical members of estuarine ecosystems along the California Current Ecosystem (CCE), have faced significant population declines due to historical overfishing and habitat deterioration. Today, managers from multiple estuaries across the CCE are focusing on conservation aquaculture breeding efforts to aid in restoration; however, the genetic implications of these efforts remain unexplored. As with other Ostrea spp, Olympia oysters have a viviparous reproductive strategy that creates unique challenges for aquaculture-mediated restoration. This study evaluates the genetic impact of current captive breeding practices on Olympia oyster cohorts produced in three California estuaries: Elkhorn Slough (EHS), Morro Bay (MB), and Tomales Bay (TB). We used low-coverage whole genome sequencing to analyze genetic diversity and inbreeding metrics across wild and hatchery-produced oysters. DNA samples from 280 oysters were collected, sequenced to an average depth of 2.19x, and mapped to a newly sequenced, high-quality reference genome developed from a single individual from ES. Analysis of data for each estuary used ANGSD software to estimate allele frequencies, SNPs, and F-statistics, revealing no significant genetic differentiation between populations (FST: ES & MB 0.027; ES & TB 0.025; TB & MB 0.048). Finally, we estimate inbreeding levels across generations and populations using runs of homozygosity. By analyzing 4,104,815 genomic sites, we provide evidence that inbreeding is occurring but is minimal, and not recent (mean ROH lengths<1MB) in captive-bred Olympia oysters. Because inbreeding can have deleterious effects on population growth and resilience, these insights can inform future breeding efforts. This research supports conservation efforts to sustain and restore these ecologically important organisms along the California coast.

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