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Atlantic salmon populations face a number of significant, human-driven threats such as overfishing and thermal stress from anthropogenically-accelerated climate change. A considerable body of research has been devoted to such large-scale threats as well as catch-and-release fishing, while the potential impacts of other recreational activities on Atlantic salmon while in rivers have been largely overlooked. Here, we undertook a systematic literature review of the effects that recreational activities (excluding direct impacts of catch-and-release angling) might have on the welfare and survival of Atlantic salmon in riverine systems at all relevant life history stages. Examples of relevant activities examined here include swimming, all-terrain vehicle (ATV) use, and underwater photography. We also performed a relative risk assessment of such activities based on the likelihoods of their occurrence and the severities of their potential impacts. For the most part, the impacts of non-angling recreational activities on Atlantic salmon are likely widespread but largely temporary. Redds, eggs, and juveniles were generally found to be more susceptible to most threats than smolts and adults. However, some activities have significant destructive potential such as ATV use in or around spawning habitats. Significant risks also remain concerning pathogen and invasive species transfer via angling gear, waders, canoes, and other equipment that may be moved across systems without proper cleaning. Although we focused primarily on risks to native Atlantic salmon populations in eastern Canada, the risk assessment framework developed here is broadly applicable and easily adaptable for management in other contexts and jurisdictions with populations of riverine Atlantic salmon and potentially other migratory salmonids too. [ABSTRACT FROM AUTHOR]

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large‐effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large‐effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans‐Atlantic genomic basis to sea age. Here, we used a large single‐nucleotide polymorphism (SNP) array and low‐coverage whole‐genome resequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with a large‐effect locus (vgll3) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified nonrepeated sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of genomic parallelism. Despite low genome‐wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons, including calcium signaling, MapK signaling, focal adhesion, and phosphatidylinositol signaling. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large‐effect genes and molecular pathways despite population‐specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation. [ABSTRACT FROM AUTHOR]

Allopatric speciation may be the principal mechanism generating new species. Yet, it remains difficult to judge the generality of this process because few studies have provided evidence that geographic isolation has triggered the development of reproductive isolation over multiple species of a regional fauna. Here, we first combine results from new empirical data sets (7 taxa) and published literature (9 taxa) to show that the eastern Great Lakes drainage represents a multispecies suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. Second, we performed amplified fragment length polymorphism analyses among four pairs of lineages. Results indicate that lineages with relatively deep levels of mt DNA 5′ COI (barcode) sequence divergence (>2%) developed strong reproductive barriers, while lineages with lower levels of divergence show weaker reproductive isolation when found in sympatry. This suggests that a threshold of 2% sequence divergence at mt DNA could be used as a first step to flag cryptic species in North American freshwater fishes. By describing different levels of divergence and reproductive isolation in different co-occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of north-eastern American freshwater fishes and confirm that Pleistocene glacial cycles can be viewed as a 'speciation pump' that played a predominant role in generating biodiversity. [ABSTRACT FROM AUTHOR]