Amanda J. Finger

Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts

Ten primer pairs were screened to develop single nucleotide polymorphism (SNP) TaqMan assays that will distinguish California golden trout and some rainbow trouts (Oncorhynchus mykiss sspp., O. m. aguabonita) from the Paiute and Lahontan cutthroat trouts (Oncorhynchus clarkii seleniris, O. c. henshawi). From these 10 primer pairs, one mitochondrial and five nuclear fixed SNP differences were discovered and developed into TaqMan assays. These six assays will be useful for characterizing and monitoring hybridization between these groups. Additional Oncorhynchus clarkii sspp. and Oncorhynchus mykiss sspp. were assayed to determine if these assays are useful in closely related species.

Using Next‐Generation Sequencing to Assist a Conservation Hatchery: a Single‐Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt

AbstractThe Delta Smelt Hypomesus transpacificus, listed as threatened under the California Endangered Species Act, has been cultured at a conservation hatchery since 2008 in response to significant declines in the wild. The conservation hatchery relies on accurate, efficacious, and reproducible molecular techniques to help maintain the captive populations overall genetic diversity and to minimize inbreeding. We created a panel of single-nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management. For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn by using restriction site-associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single-pair crosses at 2,317 newly discovered loci with RAD-seq. We successfully mapped 1,123 loci and identified 26 linkage groups. Fluidigm SNP Type genotyping assays were developed for 104 mapped loci that were selected for minor allele frequencies (MAFs) grea...

Genomic Analysis Reveals Genetic Distinctiveness of the Paiute Cutthroat Trout Oncorhynchus clarkii seleniris

AbstractThe Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater Cutthroat Trout O. clarkii ssp. complex and is federally listed as threatened under the Endangered Species Act. However, genetic studies to date have revealed very little genetic differentiation between the PCT and its closest relative, the Lahontan Cutthroat Trout (LCT) O. clarkii henshawi. These results casted doubt on whether the PCT is a genetically distinct subspecies or merely a phenotypic variant of the LCT. Here, we present a genomic analysis of Cutthroat Trout subspecies and populations to resolve the genetic and phylogenetic relationship between PCT and LCT. Our results demonstrate substantial genetic structure and differentiation between PCT and LCT populations. In contrast to current thinking, our phylogenetic reconstructions show the PCT to be a distinct evolutionary lineage that diverged from LCT before the LCT differentiated into its current populations (i.e., rather than...

A Conservation Hatchery Population of Delta Smelt Shows Evidence of Genetic Adaptation to Captivity After 9 Generations

Genetic adaptation to captivity is a concern for threatened and endangered species held in conservation hatcheries. Here, we present evidence of genetic adaptation to captivity in a conservation hatchery for the endangered delta smelt (Fish Conservation and Culture Laboratory, University of California Davis; FCCL). The FCCL population is genetically managed with parentage analysis and the addition of wild fish each year. Molecular monitoring indicates little loss of genetic variation and low differentiation between the wild and conservation populations. Yet, we found an increase in offspring survival to reproductive maturity during the subsequent spawning season (recovery rate) in crosses that included one or both cultured parents. Crosses with higher levels of hatchery ancestry tend to produce a greater number of offspring that are recovered the following year. The recovery rate of a cross decreases when offspring are raised in a tank with fish of high levels of hatchery ancestry. We suggest changes in fish rearing practices at the FCCL to reduce genetic adaptation to captivity, as delta smelt numbers in the wild continue to decline and the use of FCCL fish for reintroduction becomes more likely.