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Coregonine fishes are important to Laurentian Great Lakes food webs and fisheries and are central to basin-wide conservation initiatives. In Lake Ontario, binational management objectives include conserving and restoring spawning stocks of cisco (Coregonus artedi) and lake whitefish (C. clupeaformis), but the spatial extent of contemporary coregonine spawning habitat and the environmental factors regulating early life success are not well characterized. In Spring 2018, we conducted a binational ichthyoplankton assessment to describe the spatial extent of coregonine spawning habitat across Lake Ontario. We then quantified the relative importance of a suite of biophysical variables hypothesized to influence coregonine early life success using generalized additive mixed models and multimodel inference. Between April 10 and May 14, we conducted 1,092 ichthyoplankton tows and captured 2,350+ coregonine larvae across 17 sampling areas, predominantly within embayments. Although 95% of catches were in the eastern basin, coregonine larvae were also found in historical south shore spawning areas. Most coregonine larvae were cisco

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high‐throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (1.4 km2) in Michigan, USA, from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish‐specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Applications of genetic-based estimates of population size are expanding, especially for species for which traditional demographic estimation methods are intractable due to the rarity of adult encounters. Estimates of breeding population size (N

Declines in abundance and genetic diversity in plant and animal populations are increasingly of conservation concern. Genetic rescue, or the supplementation of declining populations with individuals from genetically different sources, may aid in demographic and genetic recovery efforts, assuming introduced individuals successfully reproduce following translocation. However, the relative reproductive contributions of resident and translocated individuals are not frequently evaluated. In the northern lower peninsula of Michigan, USA, fourteen brown trout (Salmo trutta) from each of three different tributaries were introduced into a research stream (Hunt Creek) to supplement a small, isolated resident brown trout population. Mean expected heterozygosity and mean allelic richness differed between the three translocated populations compared to residents. Additionally, inter-population variance in allele frequency (FST) between resident and translocated populations ranged from 0.024 to 0.098. Using genetic parentage assignments, we documented that translocated and resident brown trout did interbreed; however, intra-population mating events were more common. Simulations indicated that increases in genetic diversity among age-1 offspring were the result of reproduction by translocated adults, as genetic variation was significantly above levels expected by reproduction among residents alone (p

Reintroductions are widely implemented as a means of reestablishing wild populations and genetic parentage methods can be used in concert with these efforts to monitor and evaluate efficacy. In addition to understanding demographic outcomes, reconstructed pedigrees, when combined with phenotypic data, can provide insight into the adaptive potential of reintroduced individuals. Here, we examined the heritability and evolvability of life-history traits and lifetime reproductive success in two threatened Chinook salmon populations undergoing reintroduction to historical habitats above dams in Oregon, USA, using previously-developed multigenerational genetic pedigrees. All of the examined life-history traits: length-at-maturity, age-at-maturity, and arrival timing to the spawning grounds, and lifetime reproductive success exhibited significant narrow-sense heritabilities and evolvabilities. There was also a detectable influence of parental effects (i.e., paternal or maternal effects) on life-history trait variation, suggesting that in addition to genetic effects, nongenetic inheritance mechanisms are influencing life-history diversity in the populations. Additionally, our analyses revealed evidence of natural selection on the date of reintroduction, although the form and intensity of selection differed between the two populations; the forms of selection also point to the potential for phenotype-environment mismatch under some conditions. Overall, our results suggest that these threatened Chinook salmon populations exhibit significant adaptive potential, a factor that should be important to the longer-term success of recovery efforts.

Understanding biodiversity in aquatic systems is critical to ecological research and conservation efforts, but accurately measuring species richness using traditional methods can be challenging. Environmental DNA (eDNA) metabarcoding, which uses high-throughput sequencing and universal primers to amplify DNA from multiple species present in an environmental sample, has shown great promise for augmenting results from traditional sampling to characterize fish communities in aquatic systems. Few studies, however, have compared exhaustive traditional sampling with eDNA metabarcoding of corresponding water samples at a small spatial scale. We intensively sampled Boardman Lake (137 ha) in Michigan, USA from May to June in 2019 using gill and fyke nets and paired each net set with lake water samples collected in triplicate. We analyzed water samples using eDNA metabarcoding with 12S and 16S fish-specific primers and compared estimates of fish diversity among methods. In total, we set 60 nets and analyzed 180 1 L lake water samples. We captured a total of 12 fish species in our traditional gear and detected 40 taxa in the eDNA water samples, which included all the species observed in nets. The 12S and 16S assays detected a comparable number of taxa, but taxonomic resolution varied between the two genes. In our traditional gear, there was a clear difference in the species selectivity between the two net types, and there were several species commonly detected in the eDNA samples that were not captured in nets. Finally, we detected spatial heterogeneity in fish community composition across relatively small scales in Boardman Lake with eDNA metabarcoding, but not with traditional sampling. Our results demonstrated that eDNA metabarcoding was substantially more efficient than traditional gear for estimating community composition, highlighting the utility of eDNA metabarcoding for assessing species diversity and informing management and conservation.

Dams contribute to declines in fish abundance, in part, by blocking access to historical habitat. When fish ladders are infeasible, fish can be trapped below a dam and transported above to provide access to habitat. However, this conservation strategy has received little attention in the literature, and many questions regarding efficacy remain unanswered. Here, we used a genetic parentage approach to evaluate cohort replacement rate (CRR), defined as the number of future spawners produced by a spawner, for a spring Chinook salmon Oncorhynchus tshawytscha trap and transport reintroduction program. We used CRRs to determine if the population can sustain itself in the absence of immigration, which is important when assessing demographic viability. We also evaluated the effects of release locations and dates on the fitness of reintroduced fish. Counts of adult offspring per spawner were used to estimate fitness of salmon reintroduced in 2007 and 2008. We found that fitness decreased slightly as adults were released later in the spawning season in 2007, but not in 2008. Release location did not affect fitness in either year. We also found a seasonal decline in the likelihood that a Chinook salmon collected at the trap and transport facility was produced above the dam. Finally, 2007 and 2008 CRRs were both well below one, indicating that improvements are needed to achieve demographic stability. We demonstrate that genetic monitoring of a reintroduction program helped to inform demographic viability assessments, and suggest that our approach may be broadly applicable to other philopatric species.

The establishment and spread of aquatic invasive species are ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic‐based approaches can provide valuable sources of inference. Restriction site‐associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N = 440) from 18 sampling locations in the Great Lakes and in three Michigan, USA, drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man‐made dispersal barriers. Population levels of genetic diversity and interpopulation variance in SNP allele frequency were used in coalescence‐based approximate Bayesian computation (ABC) to statistically compare models representing competing hypotheses regarding source population, postcolonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (

Dams have contributed to the decline of migratory fishes by blocking access to historical habitat. The active transport (trap and haul) of migratory fish species above existing dams can sometimes support population recovery when the use of fish ladders or dam removal is infeasible. However, little is known about the efficacy of trap and haul conservation strategies. Here we used genetic parentage assignments to evaluate the efficacy of reintroducing adult Chinook salmon (Oncorhynchus tshawytscha) above Cougar Dam on the South Fork McKenzie River, Oregon, USA, from 2008 to 2011. We found that mean reproductive success (RS) declined as adults were released later in the spawning season in 2009 and 2010; however, release location did not affect RS. In 2010 and 2011, we tested for RS differences between hatchery and natural origin (HOR and NOR, respectively) adults. HOR males were consistently less fit than NOR males, but little evidence for fitness differences was apparent between HOR and NOR females. Interestingly, the effect of origin on RS was not significant after accounting for variation explained by body length. Our results indicate that release date and location have inconsistent or no effect on the reproductive success of reintroduced adults when active transport strategies are employed for migratory fishes.

Reintroductions are used to reestablish populations to historical habitats from which they were extirpated. The long-term success of these efforts will depend on genetic diversity and the ability of reintroduced individuals to adapt to ecological change. We examined variation at circadian clock (OtsClock1b and OmyFbxw11) and reproductive timing (Ots515NWFSC)—associated genes in two threatened spring-run Chinook salmon (Oncorhynchus tshawytscha) populations that are undergoing restoration to historical habitats above dams. We also tested for an association between the genes and individual variation in arrival time to the spawning grounds. Our findings indicate that levels of genetic diversity in reintroduced individuals are similar to those found in previously studied spring, summer, fall and winter-run Chinook salmon populations. Captive-rearing programs established following dam construction and the more recent reintroduction efforts thus appear to have maintained diversity at these genes. We observed temporal (between run-years) and spatial (between populations) patterns of genetic differentiation, but little evidence that selection underlies these differences. However, there was a relationship between the circadian-associated gene, OmyFbxw11, and arrival time to the spawning grounds, and in one year of the study, “early” and “late” arrivers to the spawning grounds were more differentiated at the gene than at neutral markers. Taken together, these findings suggest that reintroduced salmon may be capable of an evolutionary response to ecological shifts that alter the adaptive landscape between fitness and arrival timing to the spawning grounds.

Pelagic dispersal of most benthic marine organisms is a fundamental driver of population distribution and persistence and is thought to lead to highly mixed populations. However, the mechanisms driving dispersal pathways of larvae along open coastlines are largely unknown. To examine the degree to which early stages can remain spatially coherent during dispersal, we measured genetic relatedness within a large pulse of newly recruited splitnose rockfish (Sebastes diploproa), a live-bearing fish whose offspring settle along the US Pacific Northwest coast after spending up to a year in the pelagic environment. A total of 11.6% of the recruits in a single recruitment pulse were siblings, providing the first evidence for persistent aggregation throughout a long dispersal period. Such protracted aggregation has profound implications for our understanding of larval dispersal, population connectivity, and gene flow within demersal marine populations.