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Since the first introduction from North America more than a century ago, rainbow trout (Oncorhynchus mykiss) have rapidly established self-sustaining populations in major river basins of Patagonia. Many generations later, only the freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas both the resident and anadromous life histories are found in the Santa Cruz River of southern Argentina. Despite previous studies that have tried to identify the sources of these introduced populations, uncertainty still exists. Here we combined data from many single-nucleotide polymorphisms and microsatellite loci in O. mykiss populations from Argentina and North America to evaluate putative source populations, gene flow between Argentinian river basins, and genetic diversity differences between Argentinian and North American populations. We found that populations from northern and southern Patagonia are highly differentiated and have limited gene flow between them. Phylogeographic analysis also confirmed that they have separate origins, with the northern populations most closely related to the domesticated rainbow trout strains that are raised worldwide and the Santa Cruz River populations most closely related to North American populations from California and Oregon that have an anadromous component. In addition, fish with different life histories in the Santa Cruz River were found to constitute a single interbreeding population. No evidence was found of reduced genetic variation in introduced rainbow trout, suggesting multiple contributing sources. In spite of these advances in understanding, significant questions remain regarding the origins and evolution of the introduced O. mykiss in Patagonia.

In temperate climates, the recurring seasonal exigencies of winter represent a fundamental physiological challenge for a wide range of organisms. In response, many temperate insects enter diapause, an alternative developmental program, including developmental arrest, that allows organisms to synchronize their life cycle with seasonal environmental variation. Geographic variation in diapause phenology contributing to local climatic adaptation is well documented. However, few studies have examined how the rapid evolution of a suite of traits expressed across the diapause program may contribute to climatic adaptation on a contemporary timescale. Here, we investigate the evolution of the diapause program over the past 35 years by leveraging a natural experiment presented by the recent invasion of the Asian tiger mosquito, Aedes albopictus, across the eastern United States. We sampled populations from two distinct climatic regions separated by 6° of latitude (∼700 km). Using common-garden experiments, we identified regional genetic divergence in diapause-associated cold tolerance, diapause duration, and postdiapause starvation tolerance. We also found regional divergence in nondiapause thermal performance. In contrast, we observed minimal regional divergence in nondiapause larval growth traits and at neutral molecular marker loci. Our results demonstrate rapid evolution of the diapause program and imply strong selection caused by differences in winter conditions.

Captive‐breeding programs are increasingly implemented to curb population declines but can have unintended negative effects on genetic diversity and phenotypes. Through an analysis of ~10 years of genetic monitoring, pedigree information, and phenotypic data, we evaluated a captive‐breeding program that uses adaptive management to reduce inbreeding and improve captive broodstock performance. A captive‐breeding program was established in 2012 to reintroduce spring‐run Chinook salmon to the southern edge of their range in California's San Joaquin River (SJR), using fish produced each year at the nearby Feather River Hatchery (FRH). We found that the SJR program adequately captured the genetic diversity of the FRH source population and that mate pairings guided by genetic relatedness reduced inbreeding. However, the SJR broodstock reared in captivity had smaller body size at maturity in comparison to the FRH source broodstock which matures at sea, but this effect disappeared when SJR juveniles were released from captivity to mature at sea. Phenotypic traits of SJR female parents also influenced reproductive performance; older mothers and those with smaller eggs had offspring with lower survival. These findings demonstrate that adaptive genetic monitoring and pedigree information can be powerful tools for reducing risks of captive breeding and evaluating program effectiveness. [ABSTRACT FROM AUTHOR]

Objective: Genetic stock identification (GSI) can be an effective tool for fisheries management, but development of reference baselines for species with broad geographic distributions can be challenging. Mixed‐stock fisheries for Chinook Salmon Oncorhynchus tshawytscha have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping. Thus, our goals were to (1) create nested baselines of genotypic data for Chinook Salmon throughout their entire natural range using existing data from multiple sources and (2) evaluate the utility of those nested baselines to conduct accurate hierarchical GSI of mixture proportions or the stock identification of individual fish. Methods: In this study, we compiled a large genetic baseline of single‐nucleotide polymorphism (SNP) markers for 389 populations that encompass the entire geographic range of Chinook Salmon. We used cross validation and realistic mixture simulations to test the accuracy of the baseline in generating GSI estimates. Result: We demonstrated that a multi‐tiered assignment approach can provide high accuracy at both tier 1 (broadscale, with three coastwide reporting groups; 97.8% mean accuracy) and tier 2 (fine‐scale regional reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture simulations showed that this multi‐tiered approach can provide highly effective GSI results for several common mixed‐stock fisheries applications in the Pacific Ocean. Conclusion: This new SNP baseline and the multi‐tiered assignment approach provide the most comprehensive rangewide GSI baseline for Chinook Salmon over any previous application and enable highly accurate estimates for GSI purposes. Impact statementA Chinook Salmon genetic stock identification baseline encompassing the species' entire range has broad applications in fishery management and harvest allocation as well as in basic research. [ABSTRACT FROM AUTHOR]

Abstract: The accelerating rate at which DNA sequence data are now generated by high‐throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short‐read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine “microhaplotypes” and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi‐allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false‐positive rates by several orders of magnitude, relative to calling bi‐allelic SNPs, for two challenging analytical procedures, full‐sibling and single parent–offspring pair identification. We also show how the identification of half‐sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short‐read DNA sequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species. [ABSTRACT FROM AUTHOR]

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population- and pedigree-based analyses across the southern part of the species native range. [ABSTRACT FROM AUTHOR]