Conservation genomics of two California endangered native species: Delta smelt and Upper McCloud River Redband trout
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Conservation genomics of two California endangered native species: Delta smelt and Upper McCloud River Redband trout

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Abstract

In this dissertation, genomic tools were applied to investigate populations of two endangered native species of California for conservation purposes. The first species is the McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei), a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions. To help address this concern, I collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. I found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, I saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, I discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. The results provide a valuable resource for the conservation and management of MRRT.The second species is the endangered delta smelt (Hypomesus transpacificus). A refuge population of delta smelt has been maintained in a conservation hatchery system at the Fish Conservation and Culture Lab at UC Davis (FCCL). The FCCL uses a pedigree-based breeding system to keep the hatchery fish genetically close to the wild population. Despite intense genetic management at the FCCL, evidence of fitness differences between wild and cultured fish was reported. To investigate domestication selection, I used RAD-sequencing and Whole Genome Bisulfite Sequencing to collect genomic and epigenomic data on archived FCCL fin clip samples. For the genomic experiment, I grouped 240 individuals based on their level of hatchery ancestry (Domestication Index = DI) to low, medium, and high DI groups plus wild group. Selection signatures were examined using two FST comparisons: early (wild/low ID) vs. late (medium/high DI) groups, and wild vs. hatchery (low/medium/high DI) groups. I identified one candidate region on chromosome 22 as being putatively under domestication selection and discovered four genes located in this region through its annotation. Other candidate regions identified in this study need to be investigated further. My results also suggest domestication selection happens quickly (i.e., in early generations). For the epigenomic experiment, I investigated the methylation change between the wild and hatchery environments, and the inheritance patterns of the methylation changes after three generations in captivity. To do this, I collected 104 males and females from wild and hatchery delta smelt. I chose families with individuals grouped based on their generation number: G0, G1, G2, and G3. The most informative differentially methylated regions (DMRs) between the two environments were discovered by comparing methylation differences of individuals between G0 (n=12) and G3 (n=10) groups. A total of 201 significant DMRs (p-value < 0.05) were discovered across 26 chromosomes. The ratio of hypermethylated DMRs was 2.4 times more than hypomethylated DMRs in the hatchery group versus the wild group (71% to 29%). Genes associated with the DMRs in our study were predominantly involved in swimming and transmembrane activity. Methylation status of those DMRs in all the individuals at the group level, revealed possible evidence of methylation inheritance across generations but further examination at the level of individual family did not illustrate a clear inheritance pattern. Collectively, our findings may ultimately help the FCCL to adjust their protocol to minimize the rate of hatchery adaptation, and thus improve the likelihood of success for future supplementation.

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This item is under embargo until December 2, 2028.