Inbreeding depression and genetic rescue reflected in variance in parentage in cutthroat trout

Authors: Sierra Love Stowell, Kevin B. Rogers, Andrew P. Martin

Year: 2014 (xlvi)

Abstract

The cold, swift waters of Colorado were once home to a diverse clade of cutthroat trout, but at least three of those lineages have gone extinct. A fourth lineage is on the brink: the greenback cutthroat trout, Oncorhynchus clarkii stomias, persists as single population of fewer than 800 individuals in a small stream in the Arkansas drainage, outside of its native range in the South Platte drainage. This population, Bear Creek (WBC), is morphologically and genetically distinct from other cutthroat trout lineages. WBC trout are being propagated in a state fish hatchery with the intent of reestablishing wild populations within the South Platte drainage. The hatchery population has passed through at least two recent population bottlenecks: first during the founding of the wild population and subsequently during the establishment of the hatchery population. Genetic analysis of shows depleted genetic diversity, and reduced fitness is common in the hatchery population, both suggestive of inbreeding depression (ID). To determine the extent of inbreeding and ID in WBC and to assess the potential for genetic rescue, we used a combination of reciprocal crosses and a genotyping-by-sequencing approach to generate lineage-specific SNPs. We performed three crosses: between two WBC parents, between two parents from another cutthroat trout subspecies native to west of the Continental Divide (CAR), and between WBC and CAR parents. We measured survival and growth of all offspring in a common environment and collected all individuals that died during development. We extracted and barcoded DNA from all parents and a subset of the offspring, including individuals that died as eggs and fry and those that survived to fingerlings. Using a reduced representation library from the pooled samples sequenced with a 2x300 Illumina MiSeq run, we found several hundred SNPs between the two lineages, and multiple SNPs that allowed assignment of parentage to the offspring. We found that outbred offspring show significantly higher fitness than inbred offspring, suggesting recovery from inbreeding depression by genetic rescue. Intriguingly, not all parents in the cross contributed equally to the pool of surviving offspring. Future work on subsequent generations will demonstrate whether heterosis and the effects of genetic rescue persist after sexual reproduction disrupts interacting gene complexes. In general, the quantification of inbreeding depression and, potentially the identification of genomic regions and individual genes involved in inbreeding, can be used to plan genetic rescue and breeding efforts in a diversity of taxa threatened by small population size.

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