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Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species. [ABSTRACT FROM AUTHOR]

Eighty nine (42%) of Canada's 215 freshwater fish species have been assessed as at risk by the Committee on the Status of Endangered Wildlife in Canada. This study examines genomic population structure of the at-risk Grass Pickerel (Esox americanus vermiculatus), a small (≤ 33 cm) predatory fish that in Canada has a range spanning approximately 114,000 km2 of southern Ontario. Within this range it occupies approximately ten sites that are mostly shallow, weedy, and slow-flowing. Its populations and habitat are declining. This study defines population clusters and quantifies genomic diversity within and between populations based on > 5500 loci and > 950 SNPs from genomes of 66 individuals representing the subspecies' entire Canadian range. Ordination and STRUCTURE analyses revealed four major geographic/genomic clusters centered in the Georgian Bay-Severn River, southeastern shore of Lake Huron, Niagara Peninsula, and upper St. Lawrence River. Major clusters were distinguished by relatively high Hudson Fst values (0.205–0.480), with Georgian Bay-Severn River being consistently most distinct. The Niagara Peninsula major cluster contained an additional three discernable sub-clusters differentiated by Fst values as great or greater than major clusters, despite spanning only ca. 200 km2. Genomically distinct Niagara sub-clusters occurred in Abino Drain, Big Forks Creek, and Tea Creek. Samples from sites between both major and minor clusters exhibited admixture from adjacent clusters. Despite current management of Grass Pickerel under a single designatable unit throughout its Canadian range, we map considerable geographic population structure that should help guide the designation of additional conservation units. [ABSTRACT FROM AUTHOR]

The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation are largely unknown despite the cultural and economic importance of the anadromous morph. We used a newly designed 87k SNP chip to investigate the character and consistency of the genomic differences among sympatric morphs within three recently deglaciated and geographically proximate lakes in Labrador, Canada. We found genetically distinct small and large morph Arctic Charr in all three lakes consistent with resident and anadromous morphs, respectively. A degree of reproductive isolation among sympatric morphs is likely given genome‐wide distributions of outlier SNPs and high genome‐wide FSTs. Across all lakes, outlier SNPs were largely nonoverlapping suggesting a lack of genetic parallelism driving morph differentiation. Alternatively, several genes and paralogous copies of the same gene consistently differentiated morphs across multiple lakes suggesting their importance to the manifestation of morphs. Our results confirm the utility of Arctic Charr as a model for investigating the predictability of evolution and support the importance of both genetic parallelism and nonparallelism to the incipient speciation of Arctic Charr morphs. [ABSTRACT FROM AUTHOR]

The common blue mussel ( Mytilus edulis ) was introduced to British Columbia, Canada, in the 1980s as an aquaculture alternative to native mussel species. Since then, the mussel industry in Pacific Canada has expanded and includes operations utilizing traditional methods of broodstock selection based on visual qualitative and quantitative traits. The impacts of hatchery propagation on genetic diversity and implications for animal fitness have been previously studied for other aquatic species, and this study further examines the effect of hatchery production on three M. edulis aquaculture populations in relation to a wild originator population. Prior to microsatellite genetic analysis, animals were identified to species using nuclear markers and were found to contain varying proportions of pure M. edulis as well as other pure species and hybrids from the ‘ Mytilus edulis complex’. Subsequently seven microsatellite markers were used to genotype 166 pure adult M. edulis individuals, all of which exhibited high levels of polymorphism. Allele frequencies at multiple loci did not conform to Hardy–Weinberg expectations and substantially less genetic diversity and very low effective population size estimates ( N e , calculated from linkage disequilibrium) were observed in farmed populations compared to the wild reference population. All populations were found to be genetically distinct based on F ST estimates. Mean allelic richness was approximately three times higher in the wild reference population than the three farmed populations (21 compared to 7.51, 7.91 in the two populations selecting for size and 8.24 in the population selecting for a colour morph). Observed heterozygosity was not significantly decreased in the cultured colour morph population, but was significantly different in the two other culture populations in comparison to the wild group. Reduced genetic diversity of the aquaculture populations is likely at least partially due to small effective breeding groups during hatchery propagation, creating genetic drift over successive generations. Speculations about the influence of broodstock selection practices are tentative and should be addressed in further temporal studies. These results indicate the need for the effective management of hatchery operations, the importance of rigorous site inventory, genetic broodstock characterization, and that ideally pedigree programs should be developed to help maintain healthy and productive shellfish culture populations with adaptive fitness capacity. Statement of relevance Hatchery methods impact species purity and genetic diversity. [ABSTRACT FROM AUTHOR]

The northern Dolly Varden ( Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in northern Dolly Varden from the western Canadian Arctic to resolve landscape and life-history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls, with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other, while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized, and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic, and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation. [ABSTRACT FROM AUTHOR]

Disentangling the origin of putatively introduced/invasive species is of increasing priority in conservation biology. The presence of a previously undocumented species may be due to an undetected recent population or range expansion associated with environmental change, or due to an introduction by humans. We used molecular tools to address the origin of a population of threespine stickleback ( Gasterosteus aculeatus) first identified in central Alberta, Canada in 1980 from a single lake. We characterized this inland, high elevation Alberta population in comparison to samples from five representative geographic regions worldwide, using mtDNA and nine microsatellite loci to elucidate genetic structure and estimate divergence times. We found significantly lower levels of genetic variation in the Alberta population, which could reflect either a recent colonization or periodic bottlenecks associated with winterkills. While we did find that the Alberta samples were most closely related to the North American West Coast populations, we did not uncover a putative source population. Alberta samples formed a clade in phylogenetic analyses, with divergence time estimates between the Alberta and British Columbia samples ca. 250-750 kya. The hypothesis that the Alberta population represents a natural colonization during North America's last glacial recession could not be rejected. Collectively, these data suggest that the genetic signature of colonizing populations following introductions may be similar to populations at their range limit, contributing to difficulties establishing population origins. [ABSTRACT FROM AUTHOR]

Fragmentation of formerly continuous habitats can have significant consequences on subpopulations in isolated fragments. This study examined the temporal genetic consequences of historical river fragmentation by hydroelectric dams on lake sturgeon ( Acipenser fulvescens Rafinesque, 1817), using temporal samples from two Ontario river systems. Temporal genetic analyses of samples from the Ottawa (dammed) and Kenogami (unregulated) river systems were used to (1) compare changes in genetic structure and diversity within and between free-flowing and regulated systems; (2) assess how impoundments have influenced the spatial and temporal genetic structure and diversity within these contrasting systems; and (3) estimate effective population sizes ( Ne) in both rivers using temporal genetic estimators. Levels of genetic diversity did not differ between impounded and free-flowing rivers, nor did genetic diversity differ through time within a river system. Levels of genetic divergence over time were similarly minimal. We did, however, detect a 65% decline in effective population size in the impounded Ottawa River over two generations. Moreover, over the same time period the Ottawa River had substantially lower Ne estimates for Lake Sturgeon than the free-flowing Kenogami River system. This study represents one of the first to observe genetic consequences of fragmentation on Lake Sturgeon. As such, this work reinforces the importance of maintaining or restoring habitat connectivity and availability for this migratory species, and mitigating other demographic threats that could compound, or be compounded by the effect of reduced genetic variation. [ABSTRACT FROM AUTHOR]

The pygmy whitefish ( Prosopium coulterii (Eigenmann and Eigenmann, 1892)) is a glacial relict species with a disjunct North American distribution that, apart from its most easterly known location in Lake Superior, is predominantly found in northern and western regions of Canada. Here we report on a new finding of pygmy whitefish from Winnange Lake in northwestern Ontario that extends the range of this species ∼320 km from its most easterly distribution in Lake Superior and almost 1500 km east of the closest previously known western localities. Genetic analyses confirmed that the fish from Winnange Lake were most closely related to the lineage that includes fish from Lake Superior and likely also originated via postglacial dispersal from a refugium in the upper Mississippi - Missouri river system. [ABSTRACT FROM AUTHOR]

Walleye Sander vitreus is one of the most important freshwater commercial and sport fishes in western Canada. It is an intensively managed species that is under considerable harvest pressure, yet little is known about the patterns of genetic variation and diversity of walleyes between connected water bodies and among river basins in this region. We examined the genetic variation of walleyes from 12 lakes in five different river basins of northern Alberta. Each lake contained a genetically distinct walleye subpopulation nested within a larger population of the river basin in which the lake was situated. Differentiation between subpopulations varied (F ST = 0.05–0.29) and exhibited a broad-scale isolation-by-distance pattern. Patterns of genetic divergence aligned closely with the current hydrogeographical landscape, as subpopulations in the same river basin were more similar than those in different river basins. The clear and distinct pattern of genetic structure is likely to have been generated and maintained by historical vicariance and natal philopatry. Because walleye populations are so clearly genetically structured by hydrogeography in western Canada, these data can be used to monitor population status, assess stocking programs, delineate management units, and enable forensic enforcement of harvest restrictions in this region. Received July 4, 2011; accepted December 6, 2011. [ABSTRACT FROM AUTHOR]

We synthesized the results of a coordinated study examining the spatial and temporal movements, genetic structure, and physiological characteristics of sympatric populations of resident and sea-run brook charr across eastern Canada. Our goal was to critically evaluate three working hypotheses that may explain anadromous behaviour in brook charr: (1) resident and anadromous forms have different phylogenic origins; (2) anadromy emerges from freshwater residents; and (3) freshwater residency emerges from anadromous individuals. Our synthesis is consistent with the conclusion that freshwater residency emerging from anadromous individuals is most probable. Overall, anadromy in brook charr is poorly developed and the tactic of sea-running may be described as partial, facultative anadromy if the species must be described in terms of anadromy. The sea-run tactic most probably results from the species' propensity to move and disperse, the over-production of juveniles, an archetypical physiological ability to tolerate saline environments, and the persistence of critical habitats. When the spatial and temporal physical environments permit, the anadromous behaviour is expressed. The tactic creates an apparent fitness advantages related to growth, but it is not necessarily the only evolutionary stable strategy for a river. Most populations with sea-run forms are declining and successful conservation of sea-run forms will depend on managing harvests and more importantly, protection of the temporally and spatially complexity of critical habitats. [ABSTRACT FROM AUTHOR]

Yukon River chum salmon are managed under the Pacific Salmon Treaty (PST), which requires conservation and equitable sharing of this fishery resource by the USA and Canada. Fall chum salmon are of special concern because they spawn in both the United States and Canada, and the focus of the PST is on Canadian-origin salmon. Yukon River chum salmon were assayed for genetic variation at 22 microsatellite loci to establish a baseline for mixed-stock analysis (MSA) applications to assist in addressing conservation and allocation issues. The baseline has been applied yearly to estimate the stock composition of Yukon River fall chum salmon from samples collected in the Pilot Station test fishery. Accuracies in MSA simulations for 12 of 14 management regions exceeded 90%, with a range of 80-98%, for the 12 most informative loci. Stock composition estimates were within 10% of the actual proportions in a known-origin mixture analysis. Stock-specific abundance estimates, which were derived from combining the estimates of genetic stock composition of Pilot Station test fishery harvests with sonar abundance estimates, were concordant with upriver escapement data. The combination of genetic MSA using the baseline developed in this study and sonar abundance provides a viable tool for assessing stock strength and assisting managers in regulating fisheries to maintain the productivity and evolutionary potential of Yukon River chum salmon. [ABSTRACT FROM AUTHOR]

We report genetic differences for resistance to the pathogen Listonella anguillarum within and among one cultured and two wild Canadian populations of Atlantic salmon, Salmo salar, using a common-garden experimental protocol. Following exposure to the causative agent for vibriosis, parr originating from the endangered Stewiacke River population experienced significantly higher mortality than cultured parr, four generations removed from the Saint John River population, and wild parr from Tusket River. Pathogen resistance differed between sexes; males consistently experienced higher survival than females. There was no evidence that maturity influenced pathogen resistance in male parr. The population and sex differences in pathogen resistance documented here have implications for risk assessments of the demographic consequences of interbreeding between wild and farmed Atlantic salmon. [ABSTRACT FROM AUTHOR]

Chinook salmon, Oncorhynchus tshawytscha (Walbaum), from a northern stream-type (Bear River) and a southern ocean-type (Robertson Creek) population in British Columbia were mated within populations in a nested breeding design and the resulting juveniles were challenged with high water temperatures. Juveniles in the southern population died significantly later than those in the northern population, but none of the variation among families in mortality rate or time to death in the southern population was attributable to additive genetic variation. Non-additive genetic or maternal effects or both were observed for mortality rates in the Robertson Creek population, whereas additive genetic effects were observed for mortality at temperatures less than 22°C in the Bear River population. Larger fish survived better during the challenges than did smaller fish, and there was a negative genetic correlation (based on dam variance components) between body weight and mortality. [ABSTRACT FROM AUTHOR]

Three microsatellite loci were used to examine genetic variation among 16 coho salmon (Oncorhynchus kisutch) populations within the Fraser River drainage system, in British Columbia, Canada. Each locus was highly polymorphic with 30 alleles at the Ots101 locus, 15 alleles at the Ots3 locus and 38 alleles at the Ots103 locus. Average observed heterozygosities were 86.1%, 70%, and 56.1%, respectively. With the exception of the Dunn and Lemieux River populations, Chi-square tests and FST values indicated that all populations had significantly different allele frequencies. Two distinct population groups within the Fraser River drainage were observed. Lower Fraser River populations were strongly differentiated from populations spawning in the upper Fraser River, which includes the Thompson River (a tributary flowing into the upper Fraser) and the portion of the Fraser River beyond the precipitous Fraser River canyon. This regional population structure may have resulted from colonization of the upper and lower Fraser River regions by different founder populations following Pleistocene glaciation, and be maintained by adaptive differences between the two groups of coho salmon. Coho salmon populations in the upper Fraser and Thompson River drainages form an evolutionarily significant unit (ESU) of importance for conservation of biodiversity in coho salmon. Microsatellite DNA loci show promise as technically simple and highly informative genetic markers for coho salmon population management. [ABSTRACT FROM AUTHOR]

Two sections of the control region and the genes coding for NADH dehydrogenase subunits 5 and 6 (ND-516) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-516 fragment was sequenced in from each end only. Additionally, the entire ND-516 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-516 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-516 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-516 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes. [ABSTRACT FROM AUTHOR]

The Canada warbler (Cardellina canadensis) is a migratory neotropical warbler species of conservation concern. The 16,807 bp genome was sequenced and contains a 1224 bp control region, 37 genes, and has a nucleotide composition of 30.6% A, 23.7% T, 14.1% G, and 31.6% C. We constructed a phylogenetic tree of species in the order Passeriformes, which placed C. canadensis closest to species of Icteridae and Emberizidae. As the first complete mitogenome of any species in the family Parulidae, this mitogenome sequence provides a resource for future genetic and phylogenetic research involving C. canadensis and other Parulidae. [ABSTRACT FROM AUTHOR]

Conservation scientists rarely have the information required to understand changes in abundance over more than a few decades, even for important species like Pacific salmon. Such lack of historical information can underestimate the magnitude of decline for depressed populations. We applied genetic tools to a unique collection of 100‐year‐old salmon scales to reveal declines of 56%–99% in wild sockeye populations across Canada's second largest salmon watershed, the Skeena River. These analyses reveal century‐long declines that are much greater than those based on modern era abundance data, which suggested that only 7 of 13 populations declined over the last five decades. Populations of larger‐bodied fish have declined the most in abundance, likely because of size‐selective commercial fisheries. Our findings illustrate how a deep historical perspective can expand our understanding of past abundances to a time before species incurred significant losses from fishing, and help inform conservation for diminished populations. [ABSTRACT FROM AUTHOR]