Many salmonid species exist in highly structured and isolated populations, and are susceptible to habitat fragmentation and disturbances. Gila Trout (Oncorhynchus gilae) is a threatened species found in the Southwestern United States. Gila trout is managed to preserve remnant populations (i.e. lineages) distributed across a fragmented landscape. We evaluated genomic variation within and among remaining lineages of Gila Trout using RADseq to assess how drift and selection have structured populations using neutral and outlier loci. We also examined whether a signature of hybridization was evident in relict populations. Despite Gila Trout lineages being significantly differentiated and highly structured with low effective population sizes, we found that most lineages maintained genomic diversity and were potentially locally adapted. Hybridization with non-native Rainbow Trout (O. mykiss) was not detected in any lineage. Some lineages may have experienced recent population bottlenecks perhaps associated with mortality from drought and severe wildfires. Current management strategies should be reevaluated and adapted to better account for long-term effects of climate change. Specifically, we suggest reconnecting some populations via dendritic stream networks to facilitate natural dispersal in a metapopulation context. This would allow natural genetic mixing on the landscape and potentially increase adaptive potential. Furthermore, genetic rescue should be implemented to preserve integrity of the unique Spruce Creek lineage that is currently compromised by extremely low diversity.

Man-made structures, and habitat changes they impose, affect how fish are able to move up and downstream, between the channel and floodplain, and from habitats with unfavorable abiotic conditions to those that promote survival and reproductive output. Here we show that unidirectional stream-flow and dams affect patterns of effective population size (Ne) and genetic diversity in Rio Grande silvery minnow; a species with buoyant eggs that drift with river flow. We used archived DNA from 25 annual collections and targeted amplicon sequencing to test several predictions including that Ne and genetic diversity would be reduced upstream and increase in downstream reaches, and that augmentation and upstream stocking would disrupt these patterns. We found that Ne is reduced in the upstream-most reach and that there is a strong correlation between Ne in this reach and range-wide Ne suggesting that processes that act to reduce Ne and genetic diversity upstream, have a disproportionate impact on the population as a whole. In the absence of population augmentation, allelic diversity was reduced upstream and stocking with captive reared fishes in this reach restored diversity while other reach-specific patterns persisted despite augmentation. Up- to downstream trends in diversity and Ne imply that there is no longer sufficient spawning and retention in the natal reach to maintain large Ne and diversity is eroded through genetic drift. Movement of juveniles and adults and ongoing stocking may be insufficient to replenish depleted populations, maintain large Ne and genetic diversity. These results underscore a need for fish passage and habitat restoration promoting egg/larval retention.

not-yet-known not-yet-known not-yet-known unknown Genotyping-in-Thousands by sequencing emerged as a promising tool for genetic monitoring. For the past 25 years, genetic monitoring of Rio Grande silvery minnow (Hybognathus amarus) has been conducted annually by surveying variation at microsatellite loci. Here we developed a GT-seq panel to maintain the analytical and inferential continuity of the long-term genetic monitoring program for this species. We identified 2,983 microhaplotypes in 373 individuals using nextRAD-seq from archived samples spanning 20 years using a conspecific reference genome. This dataset provided estimates of genetic diversity and temporal genetic structure across the time-series. These results were used as a baseline to test subsets of loci that effectively tracked those changes. A panel including 250 loci with higher FST and 250 loci selected randomly offered the highest power and was used for GT-seq optimization. A sex-linked marker from another study was also included for sex assignment. The optimized GT-seq panel included 284 loci. Comparisons of genotypes from those loci obtained for the same samples with nextRAD-seq and GT-seq revealed high genotype accuracy (98.3%). Estimates of genetic diversity and patterns of temporal genetic structure were similar between datasets and accuracy of sex assignment was 100%. We discuss the utility of using a conspecific genome for both loci identification and primer design in the face of reduced genetic diversity, and the importance of temporal metrics representative of ongoing genetic monitoring. The strategy used here, effectively preserved the long-term genetic monitoring while transitioning to a more efficient and cost-effective marker system.

Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.