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Conservation programs that release captivebred individuals into the wild to mix with naturally produced individuals are an increasingly common method of supporting or enhancing weak or reduced populations that otherwise may not be self-sustaining. Captive and supportive breeding can be important conservation tools for species with small or declining populations; however, in the case of hatcheries producing salmonid fishes, detailed evaluation of spawning programs is rare. We examined variation in reproductive success, measured by adult offspring production, from three parental generations of hatchery-bred steelhead trout (Oncorhynchus mykiss) using an exclusion-based method of genetic parentage assignment. Reproductive success varied greatly among individuals (especially males) and was correlated with fecundity and maternal spawning date. Estimates of egg to smolt survival for the population as a whole among years ranged from 64% to 95%, marine survival ranged from 0.32% to 2.30%, and the number of adults produced per female ranged from 0 to 18 and the number of adults produced per male ranged from 0 to 32. The effective number of breeders ranged from 11% to 31% of the census population size for that brood year. These ratios fell within estimates from estimates of Ne/N in chinook (O. tshawytscha) and rainbow trout (O. mykiss) hatchery populations. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Two general processes may influence gene flow among populations. One involves divergent selection, wherein the maladaptation of immigrants and hybrids impedes gene flow between ecological environments (i.e. ecological speciation). The other involves geographic features that limit dispersal. We determined the relative influence of these two processes in natural populations of Trinidadian guppies ( Poecilia reticulata). If selection is important, gene flow should be reduced between different selective environments. If geography is important, gene flow should be impeded by geographic distance and physical barriers. We examined how genetic divergence, long-term gene flow, and contemporary dispersal within a watershed were influenced by waterfalls, geographic distance, predation, and habitat features. We found that waterfalls and geographic distance increased genetic divergence and reduced dispersal and long-term gene flow. Differences in predation or habitat features did not influence genetic divergence or gene flow. In contrast, differences in predation did appear to reduce contemporary dispersal. We suggest that the standard predictions of ecological speciation may be heavily nuanced by the mating behaviour and life history strategies of guppies. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Fisheries & Aquatic Sciences is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Atlantic spiny lobsters support major fisheries in northeastern Brazilian waters and in the Caribbean Sea. To avoid reduction in diversity and elimination of distinct stocks, understanding their population dynamics, including structuring of populations and genetic diversity, is critical. We here explore the potential of using the hypervariable domain in the control region of the mitochondrial DNA as a genetic marker to characterize population subdivision in spiny lobsters, using Panulirus argus as the species model. The primers designed on the neighboring conserved genes have amplified the entire control region (approx. 780 bases) of P. argus and other closely related species. Average nucleotide and haplotype diversity within P. argus were found to be high, and population structuring was hypothesized. The data suggest a division of P. argus into genetically different phylogeographic groups. The hypervariable domain seems to be useful for determining genetic differentiation of geographically distinct stocks of P. argus and other Atlantic spiny lobsters. [ABSTRACT FROM AUTHOR]

Hatcheries have been built and operated to buffer salmon and trout populations from overfishing and to compensate for habitat lost or degraded by human activities. These facilities are now so prevalent that in some cases hatchery-produced salmon outnumber salmon produced in the wild. By default, this makes them an important component in the current ecology and evolution of salmonids. Hatcheries differ from natural environments in many ways, and among the most fundamental is the necessity that humans select fish for breeding instead of allowing natural processes of mate choice and competition. We examined the mating system for steelhead trout () at Forks Creek Hatchery in southwest Washington and investigated factors affecting selection of individual steelhead for spawning by the hatchery staff. Despite efforts by the staff to not spawn selectively, data on steelhead spawned over 7 years revealed selection for large adult body size and early reproductive timing and a tendency for size-assortative mating (i.e., large with large). Selection on size was related to selection on reproductive timing because early returning fish tended to be larger than those returning later. To improve the fitness of both hatchery fish destined to spawn in the wild and hatchery fish designated to be spawned in the hatchery, a better understanding of factors associated with the range of reproductive success and mate-choice mechanisms in the wild is vital. This knowledge may then be applied to artificial propagation programs designed for conservation or enhancement. [ABSTRACT FROM AUTHOR]

Estimates of reproductive Success and the factors that affect it can be inferred from observations of behavior or data on life history traits (e.g., dominance hierarchies, clutch size). Genetic parentage analysis, however, can precisely determine the number of offspring attributable to individual parents. We coupled multilocus microsatellite genotype- based parentage assignment exclusion testing with morphological and behavioral data to test hypotheses concerning the effects of specific traits on fitness of naturally spawning steelhead trout (Oncorhynchus mykiss). With eight microsatellite loci (mean heterozygosity 89%), we examined two parental generations (n1 = 198, n2 = 226) and their offspring as smolts (age 2: n1 = 365, n2 285) and as adults (n1 = 81, n1 = 77) to determine the effects of size, reproductive timing, and origin (hatchery or wild) on reproductive success. The mating system was complex; monogamy, polygamy, polyandry, polygyny, and polygynandry were all observed. Males had a greater variance in reproductive success than females, wild steelhead produced more offspring than hatchery steelhead, and the timing of reproduction had a significant role in production of smolt and adult offspring, especially for females. There was no indication that body size contributed to offspring production, in stark contrast to the literature and theory on the subject. A more complete knowledge of traits associated with fitness in salmonids is important for understanding salmonid ecology and evolution and crucial for the design of appropriate conservation programs. [ABSTRACT FROM AUTHOR]

Early life history stages in most marine animals are subject to high mortality through predation, starvation, and dispersal. Accordingly, the potential exists for the selection of behavioral mechanisms that reduce mortality. We examined the ecological significance of synchronization in hatch and the initiation of larval drift in rainbow smelt, Osmerus mordax, populations in St. Mary's Bay, Newfoundland. Larval abundances from six 24-h ring net surveys (2-h intervals) in Colinet and Salmonier Rivers during 2002/2003 suggest synchronized hatch following dusk (∼2200 h). Monitoring of egg hatching in situ confirmed synchrony was at hatch and not emergence. Larval abundance showed no relationship with temperature or flow rates, and the consistency in hatch pattern suggested a light/dark cue. In experimental manipulations in which eggs were exposed to light and dark conditions for 2-h periods, hatch percentages were up to five times higher (p < 0.005) in dark treatments. We hypothesized that the linkage of hatch to low light levels represents a mechanism to avoid elevated larval predation in daylight conditions. Egg predation determined from predator gut content analysis suggested that extreme predation risk from small (<20 cm) salmonids peaked during the day, prior to dusk, and was lowest during night (2200-0400 h). Microcosm experiments demonstrated that newly hatched larvae exposed to predators in dark conditions did not change in number, but mortality averaged 60% in light conditions. Our results suggest that predation pressure during the early life history of aquatic organisms might play a strong role in the optimization of aquatic life histories. [ABSTRACT FROM AUTHOR]

The isolation, PCR amplification, and descriptive statistics of six microsatellite loci are described for the Dungeness crab, Cancer magister. Also reported is the inheritance of these loci in two families obtained from artificial crosses in the laboratory. All six loci conform to expectations under Mendelian inheritance and there is no evidence for linkage between any of the loci. Allelic size ranges for three of the loci are relatively large, ranging from 135–357 bp between the smallest and largest allele detected at that locus. At two of these loci upper allelic drop out (non-amplification of the larger allele in a heterozygous individual) can be problematic for scoring. Results from cross-species amplification in nine congeners are summarized. These loci will be valuable in studies requiring high-resolution genetic markers in Dungeness crabs and related species. [ABSTRACT FROM AUTHOR]

Hatchery propagation of salmonids has been practiced in western North America for over a century. However, recent declines in wild salmon abundance and efforts to mitigate these declines through hatcheries have greatly increased the relative abundance of fish produced in hatcheries. The over-harvest of wild salmon by fishing mixed hatchery and wild stocks has been of concern for many years but genetic interactions between populations, such as hybridization, introgression and outbreeding depression, may also compromise the sustainability of wild populations. Our goal was to examine whether a newly established hatchery population of steelhead trout successfully reproduced in the wild and to compare their rate of reproductive success to that of sympatrically spawning native steelhead. We used eight microsatellite loci to create allele frequency profiles for baseline hatchery and wild populations and assigned the smolt (age 2) offspring of this parental generation to a population of origin. Adults originating from a generalized hatchery stock artificially selected for early return and spawning date were successful at reproducing in Forks Creek, Washington. Although hatchery females (N = 90 and 73 in the two consecutive years of the study) produced offspring that survived to emigrate as smolts, they produced only 4.4–7.0% the number produced per wild female (N = 11 and 10). This deficit in reproductive success implies that the proportion of hatchery genes in the mixed population may diminish since deliberate releases into the river have ceased. This hypothesis is being tested in a long-term study at Forks Creek. [ABSTRACT FROM AUTHOR]

To determine the relative importance of adult size and arrival date for reproductive success in a natural setting, we first genetically determined relationships between all spawning adult steelhead (Oncorhynchus mykiss) and juvenile offspring in four brood years and then tested hypothesized relationships between parents' phenotypes and the number and size of their juvenile offspring. Patterns of reproductive success varied among years, but in all cases, a few adults of each sex produced most of the offspring. The number of offspring showed a weak, positive relationship to the mother's size but not to her arrival date. Paternal reproductive success varied considerably but was only weakly associated with size in 1998 and weakly related to arrival date in 2000. In 1997, 1998, and 1999, the offspring of early-spawning females were larger at the end of their first and second summers in the stream; however, in 2000, both arrival date and length were positively related to offspring size. There was no general trend in offspring size in relation to paternal size or arrival date; however, paternal length affected offspring size in 1998 and male arrival date affected offspring size in 2000. [ABSTRACT FROM AUTHOR]

Salmonid fishes aggregate for breeding at spatially defined, suitable habitats. These aggregations may evolve into discrete populations when precise natal homing leads to reproductive isolation, and local regimes of selection lead to adaptation. Population structure is often defined by persistent differences in selectively neutral genetic markers and in mean values of morphological and life-history traits between locations. This approach is limited by the spatial scale at which traits diverge; low levels of reproductively successful straying, combined with similar selective pressures on life-history traits resulting from similar habitat features and environmental conditions, can significantly reduce the power of these discriminatory methods. We compared data on three life-history traits and polymorphism of DNA microsatellites for evidence of population subdivision among sockeye salmon spawning on spatially discrete but physically similar beaches on islands in Iliamna Lake, Alaska. We found small but significant differences in average body length, body depth and age composition between sites as well as significant interactions between site and year. These interactions, reflecting random variation in growth or recruitment among sites, are a powerful tool for discriminating populations with similar mean trait values. These results suggest fine-scale homing to natal sites, but the microsatellite data revealed no evidence of restricted gene flow among sites. There seems to be enough straying among the populations to prevent differentiation at neutral traits but enough homing for them to be functionally distinct. [ABSTRACT FROM AUTHOR]

Compares the reproductive success of spawning wild steelhead trout with an established sympatric hatchery population in Forks Creek, Washington. Characteristics of reproductive success; Background on Forks Creek; Genetic variation of the microsatellite loci examined in the steelhead trout.

The producer-scrounger model suggests that the number of producers (animals that search for food) and scroungers (animals that consume food found by producers) may be an evolutionarily stable strategy. We investigated the role of kinship and social affiliation on these strategies by combining microsatellite DNA-based measures of relatedness with focal animal behavioral sampling of northwestern crows in the field. Scrounges were either passive (quiet ground approach without pursuit) or aggressive (noisy approach with pursuit). The combination of individually marked animals and information on relatedness allowed investigation of the roles of dominance and kinship in scrounging, including the target and form of the scrounge. Crows in foraging groups were more likely to be associated (i.e., socially affiliated) than were birds in the background population, but were not more likely to be genetically related than were birds in the background population. There was no difference between the average association of the foraging group and the average association between the scrounge interactors. There was also no difference in the average association between passive and aggressive scrounge interactions. Adults were more likely than juveniles to demonstrate a preference for social companions, and males were more likely than females to demonstrate a preference for social companions. Within foraging groups, passive scrounges tended to occur between more closely related individuals, and aggressive scrounges among less closely related individuals. Thus, scroungers modulate their mode of scrounging according to relatedness, or producers modulate their response, or both. They discriminate close from more distant relatives or unrelated individuals by adjusting the level of aggressiveness associated with theft. [ABSTRACT FROM AUTHOR]

Presents information on a study that determined the classes of genetic markers that are useful for the study of American lobster biology. Review of related literature; Materials and methods used; Results and discussion.

Presents a study which examined microsatellite DNA and mitochondrial DNA variation in remnant and translocated otter or Enhydra lutris populations in Amchitka Island. central coastal California and Alaska. Information wildlife conservation; Details of genetic variation within and among populations; materials and methods; Results and discussion.

Five tetranucleotide microsatellite loci developed from Atlantic haddock (Melanogrammus aeglefinus) are presented. Loci were isolated using a modified magnetic bead-hybridization selection procedure that enriched for tetranucleotide microsatellites. Loci were polymorphic (3–99 alleles per locus; mean, 33.2) and exhibited high levels of observed heterozygosity (0.07–0.99; mean, 0.73) in a sample of 70 haddock collected from the Scotian Shelf in the Northwest Atlantic Ocean. Primer sets for 5 tetranucleotide microsatellites, originally developed from cod (Gmo34), were also tested in Atlantic haddock; one pair yielded readily detectable product and was variable in the population assayed (29 alleles; heterozygosity, 0.96). These loci are suitable for kinship analyses in aquaculture-related applications, and are potentially useful for resolving population structure in the wild. [ABSTRACT FROM AUTHOR]

Efforts to restore depressed populations of Pacific salmon Oncorhynchus spp. are often hampered by the inability to assign population identity to individuals in an admixture. This knowledge is of particular concern in supportive breeding programs, in which misidentification of individuals to population may result in progeny of mixed heritage, which, in turn, results in the erosion of the genetic population structure and of the existing genetic diversity and local adaptations of the target population. We evaluated two classes of genetic markers, allozymes and microsatellites, for estimating population identity of pink salmon Oncorhynchus gorbuscha in a supportive breeding program on the Dungeness River in Washington State. Fall-run pink salmon of the Dungeness River are the target of restoration, but they presumably overlap, in terms of timing, with an earlier summer run. Both marker types revealed similarly low estimates of relative genetic differentiation ( = 0.02), which suggests that there is little variation in allele frequency among populations. However, microsatellites provided a more accurate estimate of population identity. When applying a log-likelihood ratio criterion of greater than 1.3, 74.8% of individuals were correctly assigned to population using microsatellites (versus 3.1% of individuals using allozymes). The difference in assignment accuracy was best predicted by the statistic , which estimates cumulative allele frequency differences among populations. Our results suggest that genetic markers with many alleles are preferred when populations exhibit little genetic differentiation (as is the case in pink salmon), because is more likely to be large, presumably as a result of genetic drift at each allele. The use of microsatellites to select fall-run pink salmon for supportive breeding confirmed the run-timing overlap and prevented unintentional crosses between the two populations. [ABSTRACT FROM AUTHOR]

We described the isolation and characterization of 23 microsatellite loci from the stingless bee ( Melipona subnitida). Out of 52 microsatellite primer pairs screened, 17 loci displayed polymorphism and 6 were monomorphic. The analysis of variability was performed in 56 individuals. The number of alleles per locus ranged from 2 to 22 among populations; values for expected and observed heterozygosities ranged from 0.125 to 1.000 and from 0.121 to 0.923, respectively. These are the first microsatellite markers characterized for M. subnitida and they will be useful in obtaining estimates of population-level genetic diversity studies in a near future. [ABSTRACT FROM AUTHOR]

Aim: In northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high‐resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to date to infer glacial refugia and the geographic scales of post‐glacial secondary contact. Location: North America. Taxon: Atlantic salmon, Salmo salar. Methods: Samples were collected for 5455 individuals from 148 populations, encompassing the majority of the Atlantic salmon's native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K single nucleotide polymorphism array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (principal component analysis, k‐means clustering, admixture) was evaluated in conjunction with genomic comparisons of these identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization. Results: Spatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was observed within the northern Gulf of St. Lawrence, and evidence of trans‐Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence. Main Conclusions: These findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans‐Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations. [ABSTRACT FROM AUTHOR]

Studies on the rainbow smelt (Osmerus mordax), a fish that exhibits extensive diversity throughout watersheds of northeastern North America. Sample collections; Morphological analysis; Data analysis; mtDNA extraction and analysis; Morphological variation.

Bonytail, Gila elegans, is an endangered species of fish native to the Colorado River. Primers are presented for 17 microsatellites cloned from bonytail as well as the results of test amplifications in bonytail and humpback chub, G. cypha. Bonytail exhibited three to 18 alleles per locus across the 17 microsatellites and a mean expected heterozygosity of 0.58 among 10 loci used to screen 160 broodstock. Humpback chub exhibited one to six alleles and a mean expected heterozygosity of 0.69 among 10 loci that were successfully amplified in that species. [ABSTRACT FROM AUTHOR]

In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus , is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70 K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy analysis identified climate associations both in the Northeast (N  = 1269 loci) and Northwest (N  = 1637 loci), with 103 shared loci between them. Clinal patterns in allele frequencies were observed in some loci (15%—Northwest and 5%—Northeast) of which 708 loci were shared and involved with growth, developmental processes, and locomotion. The combined evidence of trans-Atlantic differentiation, environmental associations, and clinal loci, suggests that both regional and large-scale potentially-adaptive population structuring is present across the North Atlantic. [ABSTRACT FROM AUTHOR]

Chromosomal rearrangements (e.g., inversions, fusions, and translocations) have long been associated with environmental variation in wild populations. New genomic tools provide the opportunity to examine the role of these structural variants in shaping adaptive differences within and among wild populations of non‐model organisms. In Atlantic Salmon (Salmo salar), variations in chromosomal rearrangements exist across the species natural range, yet the role and importance of these structural variants in maintaining adaptive differences among wild populations remains poorly understood. We genotyped Atlantic Salmon (n = 1429) from 26 populations within a highly genetically structured region of southern Newfoundland, Canada with a 220K SNP array. Multivariate analysis, across two independent years, consistently identified variation in a structural variant (translocation between chromosomes Ssa01 and Ssa23), previously associated with evidence of trans‐Atlantic secondary contact, as the dominant factor influencing population structure in the region. Redundancy analysis suggested that variation in the Ssa01/Ssa23 chromosomal translocation is strongly correlated with temperature. Our analyses suggest environmentally mediated selection acting on standing genetic variation in genomic architecture introduced through secondary contact may underpin fine‐scale local adaptation in Placentia Bay, Newfoundland, Canada, a large and deep embayment, highlighting the importance of chromosomal structural variation as a driver of contemporary adaptive divergence. [ABSTRACT FROM AUTHOR]

Reports on the development of primers for seven polymorphic microsatellite loci in pink salmon. Extraction of DNA from heart tissue from a single individual; Uses of a Molecular Dynamics FluoroImager 575 to visualize positive colonies on probed membranes; Test of primer pairs for amplification effectiveness.

Examines the characterization of coastal cutthroat trout, Oncorhynchus clarki clarki microsatellites and their conservation in other salmonids. Indications on the need for genetic markers for coastal cutthroat to facilitate population and kinship analyses; Sequencing of positive clones using Applied Biosystems Inc. Taq DyeDeoxy terminator chemistry and an ABI 373A automated sequencer; Primer pairs that yielded specific amplification of single microsatellite loci.

Complete mitochondrial genomes of two northwest Atlantic sand lances (Ammodytes americanusandAmmodytes dubius) were sequenced, assembled, and annotated. Both genomes were 16 519 bp in length and were differentiated by a genetic distance of only 0.01. Furthermore, mitochondrial gene annotations were identical for both species. Phylogenetic analysis revealed that divergence between the two species was shallow, relative to other members of the genus. [ABSTRACT FROM AUTHOR]

Three Arctic marine fishesIcelus spatula, Aspidophoroides olrikiiandLeptoclinus maculatushave been identified as target species for investigating the effects of ocean warming on population patterns in high-latitude marine habitats around Canada. In preparation for this research, we have resolved whole mitochondrial genome sequences of 16 384, 17 200 and 16 384 bp for each species, respectively. GC content for each species was 47.5%, 44.2% and 45.3%, respectively. Mitogenome gene composition included 13 protein-encoding genes, 2 rRNA and 22 tRNA genes, forI. spatulaandL. maculatus, consistent with other teleosts. Only 20 tRNA genes were annotated forA. olrikii, because tRNA-Pro and tRNA-Thr are poorly characterized and aberrantly located in this species. [ABSTRACT FROM AUTHOR]

Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so‐called "50‐year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events – perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods – one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short‐lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances. [ABSTRACT FROM AUTHOR]

Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common-garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common-garden experiments. The models failed because (1) size at maturity and fitness both decreased with increases in population density, (2) offspring experienced higher population densities than their parents, and (3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common-garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models. [ABSTRACT FROM AUTHOR]

As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 single nucleotide polymorphisms (SNPs) and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and the processes shaping them. We found evidence of high (mean FST = 0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans‐Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1–3 Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16 and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium, despite no significant reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near‐fixed and potentially adaptive trans‐Atlantic differences concurrent with a background of high genome‐wide differentiation supports subspecies designation in Atlantic salmon. [ABSTRACT FROM AUTHOR]

The development of molecular markers has allowed behavioral ecologists to link parents to specific offspring, providing insights into breeding systems that were not apparent from direct observations of the social system. Studies of this type in fishes have focused on species with male parental care such as centrarchids, and on salmonids, a family with little parental care. In order to gain further insight into the mating system of steelhead trout, Oncorhynchus mykiss, a winter-spawning species whose reproductive system is poorly known, adults returning to spawn were captured in four consecutive years in a small, unfished, wild population. Juvenile offspring were sampled by electrofishing and parentage was determined by exclusion based on a 12 locus microsatellite genotype. Both males and females mated with multiple individuals, though single pair matings were also inferred. Females and males tended to have the same number of mates (median = 1), but males were more likely to have no apparent partner (43% vs. 23% for females) and the maximum number of mates were obtained by males (range 0–10 vs. 0–5 for females). There was no difference in median arrival date by sex, but 80% of the females mated with males that had already arrived rather than males arriving with or after the females (median = 7.5, range = 1–63 days difference). Contrary to expectations, there was no evidence of size-assortative mating; larger males and larger females did not tend to mate with each other more often than would have occurred by chance. Of the juveniles with only one identified parent, most had a known mother and an unknown father rather than the reverse (88% vs. 11%). We interpret this as indirect evidence that non-anadromous males achieved a significant number of fertilizations. Thus the steelhead mating system was complex, being more strongly structured by arrival date than fish size, and including a significant genetic contribution by mature male parr. [ABSTRACT FROM AUTHOR]

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at‐risk wild populations. Here, we characterize the spatial population structure and genomic‐environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole‐genome re‐sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome‐wide variation in FST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at‐risk species throughout Atlantic Canada. [ABSTRACT FROM AUTHOR]

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at‐risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed "designatable units"; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to "big data" is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non‐model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in‐depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit. [ABSTRACT FROM AUTHOR]

Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (Tautogolabrus adspersus) is a temperate reef fish with both pelagic early life‐history stages and strong site‐associated homing as adults; the species is also of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. We aimed to characterize genomic and geographic differentiation of cunner in the Northwest Atlantic. To achieve this, a chromosome‐level genome assembly for cunner was produced and used to characterize spatial population structure throughout Atlantic Canada using whole‐genome sequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes; whole‐genome sequencing of 803 individuals from 20 locations from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four regional Atlantic Canadian groups. Pairwise FST and selection scans revealed signals of differentiation and selection at discrete genomic regions, including adjacent peaks on chromosome 10 across multiple pairwise comparisons (i.e. FST 0.5–0.75). Redundancy analysis suggested association of environmental variables related to benthic temperature and oxygen range with genomic structure. Results suggest regional scale diversity in this temperate reef fish and can directly inform the collection and translocation of cunner for aquaculture applications and the conservation of wild populations throughout the Northwest Atlantic. [ABSTRACT FROM AUTHOR]

Evolutionary analyses of population translocations (experimental or accidental) have been important in demonstrating speed of evolution because they subject organisms to abrupt environmental changes that create an episode of selection. However, the strength of selection in such studies is rarely measured, limiting our understanding of the evolutionary process. This contrasts with long-term, mark–recapture studies of unmanipulated populations that measure selection directly, yet rarely reveal evolutionary change. Here, we present a study of experimental evolution of male colour in Trinidadian guppies where we tracked both evolutionary change and individual-based measures of selection. Guppies were translocated from a predator-rich to a low-predation environment within the same stream system. We used a combination of common garden experiments and monthly sampling of individuals to measure the phenotypic and genetic divergence of male coloration between ancestral and derived fish. Results show rapid evolutionary increases in orange coloration in both populations (1 year or three generations), replicating the results of previous studies. Unlike previous studies, we linked this evolution to an individual-based analysis of selection. By quantifying individual reproductive success and survival, we show, for the first time, that males with more orange and black pigment have higher reproductive success, but males with more black pigment also have higher risk of mortality. The net effect of selection is thus an advantage of orange but not black coloration, as reflected in the evolutionary response. This highlights the importance of considering all components of fitness when understanding the evolution of sexually selected traits in the wild. [ABSTRACT FROM AUTHOR]

In semelparous populations, dormant germ banks (e.g. seeds) have been proposed as important in maintaining genotypes that are adaptive at different times in fluctuating environments. Such hidden storage of genetic diversity need not be exclusive to dormant banks. Genotype diversity may be preserved in many iteroparous animals through sperm-storage mechanisms in females. This allows males to reproduce posthumously and increase the effective sizes of seemingly female-biased populations. Although long-term sperm storage has been demonstrated in many organisms, the understanding of its importance in the wild is very poor. We here show the prevalence of male posthumous reproduction in wild Trinidadian guppies, through the combination of mark-recapture and pedigree analyses of a multigenerational individual-based dataset. A significant proportion of the reproductive population consisted of dead males, who could conceive up to 10 months after death (the maximum allowed by the length of the dataset), which is more than twice the estimated generation time. Demographic analysis shows that the fecundity of dead males can play an important role in population growth and selection. [ABSTRACT FROM AUTHOR]

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre‐existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at‐risk wild North American salmon populations. Here, we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7‐SSR, 100‐SSR and 220K‐SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three datasets showed that the 100‐SSR panel and 7‐SSR panels replicated the full 220K‐SNP‐based admixture estimates with low accuracy (r2 of .64 and .49, respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K‐SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301‐SNP) for European admixture detection in future monitoring work and then developed and tested a python package, salmoneuadmix (https://github.com/CNuge/SalmonEuAdmix), which uses a deep neural network to make de novo estimates of individuals' European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at‐risk species conservation and management. [ABSTRACT FROM AUTHOR]

When females prefer mates with rare phenotypes, sexual selection can maintain rather than deplete genetic variation. However, there is no consensus on why this widespread and frequently observed preference might evolve and persist. We examine the fitness consequences of female preference for rare male color patterns in a natural population of Trinidadian guppies, using a pedigree that spans 10 generations. We demonstrate (i) a rare male reproductive advantage, (ii) that females that mate with rare males gain an indirect fitness advantage through the mating success of their sons, and (iii) the fitness benefit that females accrue through their “sexy sons” evaporates for their grandsons as their phenotype becomes common. Counter to prevailing theory, we show that female preference can be maintained through indirect selection. [ABSTRACT FROM AUTHOR]

Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole‐genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range‐wide pattern of isolation‐by‐distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long‐term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes. [ABSTRACT FROM AUTHOR]

Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar, used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon (n = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon (n = 403) and escapees (n = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals (p < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild. [ABSTRACT FROM AUTHOR]

Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of SD and sex chromosomes. Here we sequenced the genome of the common lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70 K single nucleotide polymorphism array and tissue‐specific expression data. The chromosome‐level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb and genome annotation‐predicted 21,480 protein‐coding genes. Genome‐wide association analysis located a highly sex‐associated region on chromosome 13, suggesting that anti‐Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto‐XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits lumpfish conservation management and aquaculture. [ABSTRACT FROM AUTHOR]

Driven by competition and mate choice, size-assortative mating has been seen in many organisms. The breeding system of salmonid fish, Oncorhynchus spp., has been extensively investigated and many examples of size-assortative mating have been found. However, assortative mating is not always observed and many reported examples involved cases with a large dichotomy in size classes or were conducted in artificial arenas where other factors influencing mate choice and competition were controlled. This study investigated size-assortative mating in a population of naturally reproducing pink salmon, O. gorbuscha. We made direct observations of courtship behaviour over 3 years on fish of known sizes. To determine the extent to which these observations corresponded to reproductive success, we assessed the parentage of the offspring produced by the fish in the first 2 years of the study using DNA fingerprinting. Size-assortative mating was not seen in the behavioural observations. Parentage results showed that our measure of dominance (proximity of males to ripe females) corresponded with successful matings, suggesting that the fish that we observed as dominant were in fact involved in more matings or more successful matings. We also saw no size-assortative mating in male and female pairs that produced adult offspring. We are not suggesting that the processes that can lead to size-assortative mating are not occurring, but that many other factors, such as female ripeness, male availability, predation threat and changing environmental conditions, may minimize the importance or mask the occurrence of size-assortative mating under natural conditions. [Copyright &y& Elsevier]

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in N e. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species. [ABSTRACT FROM AUTHOR]