Estimates Of Effective Population Size Research Articles

Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa.

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500–700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

Hybridization and Population Genetics of Alligator Gar in Lake Texoma

AbstractThe Alligator Gar Atractosteus spatula (AG) is a long‐lived fish of growing management and conservation interest. Situated on the border of Texas and Oklahoma, Lake Texoma supports one of the last robust AG populations in Oklahoma; however, a genetic evaluation of this population is lacking. We genotyped AG individuals with 17 microsatellite loci, 7 of which also cross‐amplified in three sympatric Lepisosteus species: the Longnose Gar L. osseus (LN), Shortnose Gar L. platostomus (SN), and Spotted Gar L. oculatus (SP). Bayesian assignment analyses conducted in STRUCTURE and NewHybrids confirmed that a field‐identified hybrid was an F1 AG × LN and identified five other individuals that were suspected backcrosses (three LN × SN; two SN × SP). Alligator Gar had the lowest observed heterozygosity (0.179) and the lowest allelic richness (1.682) among the nonhybrid individuals of the four gar species examined. We also examined the potential for population structure and differences in pairwise relatedness (r) between two areas where AG are commonly encountered within Lake Texoma: the Red River and Washita River arms. No population structure was detected using noninformative or location priors in STRUCTURE, and estimates of r produced by the TrioML estimator in COANCESTRY were not significantly different between arms (overall mean r = 0.199). Point estimates of effective population size ranging from 16.3 to 29.2 suggested that the AG population may be vulnerable to the effects of inbreeding depression and random genetic drift. Results provide a genetic status assessment of AG in Lake Texoma and a baseline for future management and conservation decisions within Lake Texoma and surrounding regions.

Phylogeography and Historical Demography of Two Sympatric Atlantic Snappers: Lutjanus analis and L. jocu

Lutjanus analis (mutton snapper) and L. jocu (dog snapper) are mesopredator species with extensive geographic distribution in the Atlantic Ocean. Although historically overfished, their genetic diversity, population structuring, and historical demography along the Brazilian coast are unknown. Here we present genetic data for the hypervariable region 1 (HVR1) of the mtDNA control region of both L. jocu and L. analis, and for cytB of L. analis from distinct geographic regions. Phylogeographic analyses based on HVR1 sequences revealed no geographic structuring of mtDNA lineages for either species. The bimodal mismatch distribution plots of mutton and dog snapper populations implied that they might have experienced secondary contact. Historical demographic parameters estimated that population expansions ranged from 13,631 to 61,171 years before present (ybp) for L. analis and 36,783-55,577 ybp for L. jocu, associated with events that occurred at the end of the last glaciation period. Estimates of the average effective population size for L. jocu were higher than those for L. analis, with the largest population occupying the Brazilian northeastern region coast. High migration rates are maintained among the three northernmost locations, with a substantial decrease to the further southern region. Our study suggests that a tripartite interaction of larval dispersion and interregional adult movement (aggregate spawning), allied to historical contingencies, contributed to contemporary population genetic patterns of these species, and adds relevant information for conservation management of such vulnerable - and valuable - marine resources.

High Frequency of Multiple Paternity in Eastern Red Bats, Lasiurus borealis, Based on Microsatellite Analysis.

Most species of bats give birth to only 1 pup each year, although Eastern red bats (Lasiurus borealis) can produce up to 5 pups per litter. Offspring in a single litter have been documented to be at different stages of development, suggesting that multiple paternity occurs. We tested the null hypothesis of genetic monogamy in red bats using 6 autosomal microsatellites and 1 X-linked microsatellite from 31 parent/offspring groups for a total of 128 bats. We sampled both pregnant females and mothers with pups that were obtained from bats submitted to departments of health in Oklahoma and Texas for rabies testing. Multiple paternity was assessed using a maximum-likelihood approach, hypothesis testing, and X-linked locus exclusion. The mean polymorphic information content of our markers was high (0.8819) and combined non-exclusion probability was low (0.00027). Results from the maximum-likelihood approach showed that 22 out of 31 (71%) parent/offspring groups consisted of half siblings, hypothesis testing rejected full sibship in 61% of parent/offspring groups, and X-linked locus exclusion suggested multiple paternity in at least 12 parent/offspring groups, rejecting our hypothesis of genetic monogamy. This frequency of multiple paternity is the highest reported thus far for any bat species. High levels of multiple paternity have the potential to impact interpretations of genetic estimates of effective population size in this species. Further, multiple paternity might be an adaptive strategy to allow for increased genetic variation and large litter size, which would be beneficial to a species threatened by population declines from wind turbines.

Use of genetic data in a species status assessment of the Sicklefin Redhorse (Moxostoma sp.)

Under the United States Endangered Species Act, a species is granted protection if it is in danger of extinction throughout all or a significant portion of its range. Since 2016, the United States Fish and Wildlife Service has adopted a more analytical approach to determining significant portion of its range. Termed Species Status Assessment (SSA), this approach addresses whether loss of individuals from a portion of its range will influence at least one of the conservation biology principles of redundancy (ability to withstand catastrophic events), resiliency (ability to withstand stochastic events), and representation (ability to adapt over time to long-term changes in the environment). Using Sicklefin Redhorse (Moxostoma sp.), we illustrate the use of genetic data to evaluate each SSA metric. We sampled (n = 382) Sicklefin Redhorse from three major river basins throughout its contemporary distribution and estimated genetic parameters using ten microsatellite markers. Using STRUCTURE analyses, we showed that redundancy was three, but our approximate Bayesian computation analysis revealed that this value could be reduced to two if admixture, due to anthropogenic stressors of the 1900s, continues. We used estimates of effective population size (Ne) to measure resiliency and representation and found that all populations showed resiliency and representation with Ne ≥ 479. Genetic monitoring of the Little Tennessee and Tuckasegee populations will be necessary to assess the future status of redundancy for this species. Any reduction in redundancy would warrant further ESA evaluation.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

AbstractThe Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

Coancestry rate\u2019s estimate of effective population size for genetic variability monitoring

Different methods and formulae have been suggested to estimate effective population size based on pedigree data. These methods vary in their sensitivity to various sources of bias related to heterogenous pedigree knowledge or pedigree structure. We propose here to adapt a pre-existing method estimating coancestry rate for the specific purpose of monitoring genetic variability within livestock and captive populations. Coancestry rate is computed by averaging coancestries between pairs of individuals corrected by their equivalent numbers of generations, while restricting pedigree information to a maximum number of generations. Simulation demonstrated that restricting the number of generations allows a much clearer observation of the impact of recent events on genetic variability. Restricting the number of generations for the calculation of coancestry also has less bias related to incomplete pedigree, although it may overestimate effective population size due to non-independence in family sizes across generations. This strategy was tested on the Norwegian Nordland Lyngen horse, the Colblood Trotter horse, the French Avranchin sheep, and Bresse chicken, illustrating the applications of the approach for the monitoring of genetic variability.

Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo.

Pedigrees provide the genealogical relationships among individuals at a fine resolution and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of the short-term effective population size [Formula: see text], which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and [Formula: see text] from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals within a single generation with the use of a composite likelihood, which significantly increases computational efficiency. We show, on simulated data, that our method is able to jointly estimate relationships up to first cousins and [Formula: see text] with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.

Population genetic assessment of two critically endangered freshwater mussel species, Tennessee bean Venustaconcha trabalis and Cumberland bean Venustaconcha troostensis

The Cumberland bean Venustaconcha troostensis (Conrad in Academy of Natural Sciences of Philadelphia. http://biodiversitylibrary.org/page/16346317/ , 1834) and Tennessee bean V. trabalis (Lea in Proc Acad Nat Sci Phila 13:38–41, 1861) are both endangered freshwater mussel species endemic to the Cumberland and Tennessee river basins, respectively. These species are closely related and morphologically similar in appearance, and now exist only in small, fragmented populations relative to their historical abundances and distributions throughout the southeastern United States. A critical management need is to understand genetic differences among populations, so that informed decisions can be made to promote demographic and genetic viability of remaining populations. Against this background, we conducted a population genetic analysis by assessing variation at eight microsatellite DNA loci across 127 individuals. Our results showed five population clusters across five rivers, V. trabalis in the Clinch, Obed-Emory, Holston, and Hiwassee rivers; and V. troostensis in the Cumberland river. There was moderate to high differentiation among populations based on FST (range 0.09 − 0.18) and high differentiation among populations based on Jost’s D (range 0.33 − 0.67). The highest differentiation was observed between populations in the Cumberland and Tennessee River basins (mean FST = 0.155, mean D = 0.559). Analysis of allele frequencies suggest that all populations likely have lost genetic diversity and are bottlenecked to various degrees. Linkage disequilibrium-based estimates of recent-current effective population sizes (Ne) ranged from 42 in the Cumberland River population to 130 individuals in the Hiwassee River population, suggesting that populations have become small and fragmented by natural historical processes and by man-made impediments to gene flow. Using approximate Bayesian computation to estimate Ne over longer-term coalescent time, median posterior distributions of Ne ranged from 7130 for the Clinch River population to 901 for the Holston River population. The inferences gained in this study may warrant action by conservation managers to artificially cross extant stocks within basins for purposes of genetic and demographic augmentation. However, based on our initial results, we do not recommend interspecific mixing of individuals between the Cumberland and Tennessee River basins.

Microgeographic variation in recruitment under adult trees: arrival of new genotypes or perpetuation of the existing ones?

Investigating spatial variation in the relative importance of sexual reproduction and clonal propagation is critical to obtain more accurate estimates of future effective population sizes and genetic diversity, as well as to identify ecological correlates of clonality. We combined a stratified sampling scheme with microsatellite genetic analyses to estimate variation in the proportion of sexual versus clonal recruits among saplings in five populations of the tree Pyrus bourgaeana. Using a likelihood framework, we identified clones among the genotypes analysed and examined variation among populations regarding the proportion of saplings coming from clonal propagation. We also examined the relationship between the relative abundance of clonal shoots across the studied populations and their herbivory levels. Our results revealed that one third of the saplings examined (N=225 saplings) had a probability above 0.9 of being clones of nearby (<10m) trees, with the ratio between clonal propagation and sexual recruitment varying up to eight-fold among populations. A small portion of these putative clonal shoots reached sexual maturity. Relative abundance of clonal shoots did not significantly relate to the herbivory by ungulates. Our results call into question optimistic expectations of previous studies reporting sufficient levels of recruitment under parental trees without animal seed dispersal services. Nevertheless, given that some of these clonal shoots reach sexual maturity, clonal propagation can ultimately facilitate the long-term persistence of populations during adverse periods (e.g. environmental stress, impoverished pollinator communities, seed dispersal limitation).

Do estimates of contemporary effective population size tell us what we want to know?

Estimation of effective population size (N e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N e such as inbreeding (N eI), variance (N eV), additive genetic variance (N eAV), linkage disequilibrium equilibrium (N eLD), eigenvalue (N eE) and coalescence (N eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N e‐estimators target N eV or N eLD of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N eI) and additive genetic variance (N eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation. The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.

Genetic Assessment Reveals Population Fragmentation and Inbreeding in Populations of Brook Trout in the Laurel Hill of Pennsylvania

AbstractWhether natural or man‐made, landscape features often influence the patterns of genetic variation within a species and can have important conservation implications. This is especially true for Brook Trout Salvelinus fontinalis, which are typically restricted to high‐quality headwater streams. In this study, we characterized the patterns of genetic partitioning and diversity among Brook Trout populations in the Laurel Hill of southwestern Pennsylvania with respect to landscape features and potential barriers to migration. In total, 354 wild Brook Trout samples collected across 10 streams were analyzed using 12 microsatellite loci. Our results showed a wide range of genetic diversity (allelic richness AR = 3.404–7.124; expected heterozygosity He = 0.432–0.727) and effective population size estimates (Ne = 13.5–1,106.6) and indicated that some sites contained small, low‐diversity populations of Brook Trout. Three populations were located upstream of reservoirs; however, our results did not show significant differences in the genetic diversity metrics between upstream and downstream populations. Although isolation by distance could be a factor, the patterns of genetic differentiation revealed minimal contemporary gene flow between watersheds and among most streams. Overall, our results highlight the need for continued population monitoring and habitat restoration for Brook Trout populations in southwestern Pennsylvania.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish.

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development-the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

Inbreeding and effective population size in French dairy sheep: Comparison between genomic and pedigree estimates

Before availability of dense SNP data, genetic diversity was characterized and managed with pedigree-based information. Besides this classical approach, 2 methodologies have been proposed in recent years to characterize and manage diversity from dense SNP data: the SNP-by-SNP approach and the alternative based on runs of homozygosity (ROH). The establishment of criteria to identify ROH is a current constraint in the literature dealing with ROH. The objective of this study was, using a medium-density SNP chip, to quantify by 3 methods (pedigree, SNP-by-SNP, and ROH) the genetic diversity on 5 selected French dairy sheep subpopulations and breeds and to assess the effect of the definition of ROH on these estimates. The data set available included individuals from the breeds Basco-Béarnaise, Manech Tête Noire, Manech Tête Rousse, and 2 subpopulations of Lacaune: Lacaune Confederation and Lacaune Ovitest. Animals were genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA). After filtering, the genomic data included 38,287 autosomal SNP and 8,700 individuals, which comprised 72,803 animals in the pedigree. The results indicated that no significant differences were observed in effective population size estimates obtained from pedigree or genomic (SNP-by-SNP or ROH) information. In general, estimates of effective population size were above 200 in Lacaune Confederation and Lacaune Ovitest subpopulations and below 200 in Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse breeds. The minimum length that constituted a ROH, the minimum number of SNP that constituted a ROH, as well as the minimum density and the maximum distance allowed between 2 homozygous SNP are ROH-defining factors with important implications in the estimation of the rate of inbreeding. The ROH-based rates of inbreeding in concordance with those obtained from pedigree information require a specific set of values. This particular set of values is different from that identified to obtain ROH-based rates of inbreeding similar to those obtained on a SNP-by-SNP basis. Factors to define ROH do not change the results much unless extreme values are considered, although further research on ROH-based inbreeding is still required.

Demographic and genetic description of Greenland's only indigenous Atlantic salmon Salmo salar population.

A survey of the Kapisillit River system was conducted in 2005 and 2012 to study the only indigenous Atlantic salmon Salmo salar population in Greenland. Little is known about its characteristics or its relationship with other S. salar populations across the species range. Juvenile S. salar were captured in all stations surveyed within the lower river with the highest densities lower in the river and decreasing densities with increasing distance from the river mouth. Captured juveniles ranged from 0+ to 7+ years old and the predominant smolt age was between 4 and 6 years. Median length of 0+ and 1+ juveniles in August-September was 38.8 and 70.4 mm, respectively. The proportion of mature male parr increased from 4% for 1+ year old fish to 95% for fish greater than 2 years old. Genetic analysis using 96 single nucleotide polymorphisms (SNP) revealed a high degree of genetic similarity between collections, extremely low genetic diversity and low estimates of effective population size (Ne = 28.7; 95% CI = 19.7-42.4). Genetic comparison to range-wide S. salar populations demonstrated that the Kapisillit River S. salar is an outgroup of the eastern Atlantic stock complex, which is consistent with the hypothesised colonisation from the east. River morphology and the absence of glacier runoff are hypothesised to be the main reasons for the relatively high river temperatures supporting this self-sustaining population of S. salar. Given its uniqueness and persistence, this population represents an important part of range-wide biodiversity of S. salar.

Spatio-temporal population genetic structure, relative to demographic and ecological characteristics, in the freshwater snail Biomphalaria pfeifferiin Man, western Côte d'Ivoire.

Combining the analysis of spatial and temporal variation when investigating population structure enhances our capacity for unravelling the biotic and abiotic factors responsible for microevolutionary change. This work aimed at measuring the spatial and temporal genetic structure of populations of the freshwater snail Biomphalaria pfeifferi (the intermediate host of the trematode Schistosoma mansoni) in relation to the mating system (self-fertilization), demography, parasite prevalence and some ecological parameters. Snail populations were sampled four times in seven human-water contact sites in the Man region, western Côte d'Ivoire, and their variability was measured at five microsatellite loci. Limited genetic diversity and high selfing rates were observed in the populations studied. We failed to reveal an effect of demographic and ecological parameters on within-population diversity, perhaps as a result of a too small number of populations. A strong spatial genetic differentiation was detected among populations. The temporal differentiation within populations was high in most populations, though lower than the spatial differentiation. All estimates of effective population size were lower than seven suggesting a strong effect of genetic drift. However, the genetic drift was compensated by high gene flow. The genetic structure within and among populations reflected that observed in other selfing snail species, relying on high selfing rates, low effective population sizes, environmental stochasticity and high gene flow.

Genetic and phenotypic differentiation of lumpfish (Cyclopterus lumpus) across the North Atlantic: implications for conservation and aquaculture.

Demand for lumpfish (Cyclopterus lumpus) has increased exponentially over the last decade, both for their roe, which is used as a caviar substitute, and increasingly also as cleaner fish to control sea lice in salmon farming. The species is classified as Near Threatened by the IUCN and there are growing concerns that over-exploitation of wild stocks and translocation of hatchery-reared lumpfish may compromise the genetic diversity of native populations. We carried out a comparative analysis of genetic and phenotypic variation across the species’ range to estimate the level of genetic and phenotypic differentiation, and determined patterns of gene flow at spatial scales relevant to management. We found five genetically distinct groups located in the West Atlantic (USA and Canada), Mid Atlantic (Iceland), East Atlantic (Faroe Islands, Ireland, Scotland, Norway and Denmark), English Channel (England) and Baltic Sea (Sweden). Significant phenotypic differences were also found, with Baltic lumpfish growing more slowly, attaining a higher condition factor and maturing at a smaller size than North Atlantic lumpfish. Estimates of effective population size were consistently low across the North East Atlantic (Iceland, Faroe Islands and Norway), the area where most wild lumpfish are fished for their roe, and also for the aquaculture industry. Our study suggests that some lumpfish populations are very small and have low genetic diversity, which makes them particularly vulnerable to over-exploitation and genetic introgression. To protect them we advocate curtailing fishing effort, closing the breeding cycle of the species in captivity to reduce dependence on wild stocks, restricting the translocation of genetically distinct populations, and limiting the risk of farm escapes.

Development of a Standardized Molecular Tool and Estimation of Genetic Measures for Responsible Aquaculture‐Based Fisheries Enhancement of American Shad in North and South Carolina

AbstractAs pressure from anthropomorphic stressors continues to negatively affect the abundance of wild fish populations, aquaculture‐based fisheries enhancement (i.e., sea ranching, stock enhancement, restocking) is being used increasingly as a management option to augment and restore wild stocks. However, as supplementation with cultured individuals may have unintended impacts on the genetic fitness of a target species, emphasis is placed on scientifically based protocols for fisheries enhancement, which involves continuous observation of genetic measures within and among populations. American Shad Alosa sapidissima, which had once‐abundant spawning runs that experienced major declines throughout the early 20th century, are currently stocked in several rivers in North Carolina and South Carolina. A set of eight microsatellite markers was compiled and standardized to allow for the long‐term monitoring of genetic measures between rivers as hatchery‐based initiatives with multistate collaborators continue. Data sets from multiple spawning runs of American Shad within North and South Carolina compared using this standardized marker suite exhibited relatively high levels of genetic diversity, low inbreeding, and large effective population sizes. Furthermore, although migration is likely occurring between rivers, significant differences exist between some spawning runs. These estimates of genetic diversity and differentiation are comparable with analogous studies of American Shad, which demonstrate that these markers will be valuable for fisheries research, and the novel estimates of effective population size and bottleneck indices acquired in this study supply new information useful for management. Our results, along with future work, can be used for responsible aquaculture‐based fisheries enhancement of American Shad in North and South Carolina and can aid in the recovery efforts for this important species.

Neutral Genetic and Phenotypic Variation within and among Isolated Headwater Populations of Brook Trout

AbstractIsolated populations are challenging to manage and conserve, as they are particularly vulnerable to genetic drift, allelic fixation, and inbreeding and may express markedly reduced phenotypic variability. We sought to improve our understanding of how spatial isolation, occupancy range, and restricted gene flow influence contemporary phenotypic variation within and among native populations of Brook Trout Salvelinus fontinalis by examining the neutral genetic and phenotypic characteristics of 35 isolated headwater populations from Great Smoky Mountains National Park. Across a suite of 13 neutral microsatellite loci, we observed high levels of allelic fixation and considerable genetic differentiation among populations, subwatersheds, and watersheds that were consistent with patterns of isolation. We found significant positive correlations between allelic diversity and estimates of effective population size. In contrast, we observed considerably less phenotypic structure among streams, subwatersheds, and watersheds. Much of the observed phenotypic variation occurred among individuals within populations. Pairwise Mann–Whitney tests revealed no significant phenotypic differences among the populations of Brook Trout we examined. Similarly, there was no significant relationship between the amount of phenotypic variation within populations and any of the examined measures of genetic diversity or the amount of occupied habitat sampled, which suggests that unmeasured variables may be influencing morphometric and meristic variation within isolated populations. The observed patterns of isolation, genetic drift, and allelic fixation highlight the importance of enhancing population connectivity but also suggest that considerable phenotypic variability may persist within small, fragmented populations. Our results elucidate some challenges associated with managing and conserving isolated populations of Brook Trout and reinforce the importance of conducting genetic studies on fragmented populations to inform management decisions.

Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FSTrankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.