Population genetic analysis of invasive populations can provide valuable insights into the source of introductions, pathways for expansion, and their demographic histories. Flathead catfish (Pylodictis olivaris) are a prolific invasive species with high fecundity, long-distance dispersal, and piscivorous feeding habits that can lead to declines in native fish populations. In this study, we analyse the genetics of invasive P. olivaris in the Mid-Atlantic region to assess their connectivity and attempt to reconstruct the history of introduced populations. Based on an assessment across 13 microsatellite loci, P. olivaris from the Susquehanna River system (N = 537), Schuylkill River (N = 33), and Delaware River (N = 1) have low genetic diversity (global Hobs = 0.504), although we detected no evidence of substantial inbreeding (FIS = -0.083 to 0.022). P. olivaris from these different river systems were genetically distinct, suggesting separate introductions. However, population structure was much weaker within each river system and exhibited a pattern of high connectivity, with some evidence of isolation by distance. P. olivaris from the Susquehanna and Schuylkill rivers showed evidence for recent genetic bottlenecks, and demographic models were consistent with historical records, which suggest that populations were established by recent founder events consisting of a small number of individuals. Our results show the risk posed by small introductions of P. olivaris, which can spread widely once a population is established, and highlight the importance of prevention and sensitive early detection methods to prevent the spread of P. olivaris in the future.

First posted August 24, 2023 For additional information, contact: Director, Eastern Ecological Science CenterU.S. Geological Survey11649 Leetown RoadKearneysville, WV 25430Contact Pubs Warehouse Acipenser oxyrinchus oxyrinchus (Atlantic sturgeon) were once abundant and supported large-scale fisheries throughout much of the east coast of the United States. However, historic overharvest and habitat loss resulted in dramatic declines in abundance and eventual listing under the Endangered Species Act of the United States. As part of this listing, Atlantic sturgeon populations were divided into five distinct population segments (DPSs), with many management activities occurring at the level of the DPS. However, because subadult and adult Atlantic sturgeon can make large, coast-wide migrations and often mix extensively with individuals from other populations, individuals may be exposed to conservation threats away from their natal river or DPS, ultimately making it difficult to determine the appropriate spatial scale for management activities. To help address this uncertainty, the U.S. Geological Survey performed genetic assignment tests to determine the natal origin of 329 Atlantic sturgeon that were encountered as mortalities or taken during permitted activities in 2021. Overall, most individuals assigned to the Hudson River population, with additional major contributions from the James River Fall and Delaware River populations. However, a sizeable proportion of individuals were assigned to more distantly located populations in the southeastern United States. These results highlight the prevalence of long-distance movements in Atlantic sturgeon and underscore that populations may be vulnerable to threats far from their natal rivers.

Many tiger beetles (Family Cicindelidae ) are critically imperiled due to their dependence on small patches of suitable habitat that are frequently threatened by natural and anthropogenic disturbances. In the eastern United States, conservation of three tiger beetles - Habroscelimorpha dorsalis dorsalis , H. dorsalis media , and Ellipsoptera puritana - has been inhibited by the absence of population genetic information that is needed for effective recovery planning and potential reintroductions. Using microsatellite panels, we performed population genetic analyses and compared patterns in diversity and differentiation within and between taxa. Nearly all collections of the three taxa had less observed heterozygosity than expected under Hardy-Weinberg Equilibrium, and there was a strong latitudinal gradient in genetic diversity in H. d. dorsalis distributed along the eastern and western shores of the Chesapeake Bay. We also found clear spatial patterns of genetic differentiation which reflected strong isolation-by-distance within all three taxa and between collections of H. d. dorsalis and H. d. media. However, there was evidence of admixture in current (mouth of the Chesapeake Bay) and former (coastal New Jersey) contact zones of H. d. dorsalis and H. d. media . Taken together, our study suggests that relatively few adult tiger beetles may maintain many populations, and that gene flow among nearby habitat patches is common in all three taxa – a characteristic that may help tiger beetles persist in dynamic coastal environments. Results of our analyses can be used to support conservation and management by identifying the spatial scale of metapopulation connectivity and locating populations at the greatest risk of extirpation.

The Smoky Madtom Noturus baileyi is a federally endangered species, whose native distribution includes lower Abrams Creek in Great Smoky Mountains National Park (GRSM) and Citico Creek in nearby Cherokee National Forest. Due to challenges for bio-monitoring posed by its nocturnality and cryptic life history, an environmental DNA (eDNA)-based approach for detection would be useful to complement existing electrofishing and seining efforts to better understand the distribution of this species. We developed a probe-based droplet digital PCR (ddPCR) assay to detect Smoky Madtoms from non-invasively collected water samples. The assay was specific to N. baileyi and did not amplify concentrated genomic DNA of 16 co-occurring or regional fish species, including the yellowfin madtom N. flavipinnis and stonecat N. flavus . The assay limit of detection (LOD) was determined to be 4.18 copies (95% CI: 3.95, 4.41). Several 2 L water samples collected from throughout various streams in GRSM in 2016 and 2017 were tested for the presence of N. baileyi using the ddPCR assay. N. baileyi was detected at two different sites in 2016 and 2017 within Abrams Creek previously known to contain N. baileyi , but no novel detections in other sampled streams were observed. This assay should prove useful for continued surveys of N. baileyi in GRSM.

Management of the American horseshoe crab Limulus polyphemus in the Delaware Bay region is aimed at promoting the sustainability of fished populations and providing abundant eggs to support the foraging of migrating shorebirds. To advance understanding of regional horseshoe crab population structure and frame recommendations for management, we conducted population genetics and mark-recapture studies to characterize metapopulation dynamics of horseshoe crabs in the mid-Atlantic region, USA. We used new microsatellite DNA data on seven regional-fished populations and an existing dataset on 25 spawning assemblages to estimate contributions to fisheries. We found that about 90% of the crabs landed originated from the mid-Atlantic management unit, but could not estimate contributions from its subpopulations with precision. A mark-recapture study supported the inference of high rates of migration and metapopulation structure among regional spawning assemblages. Horseshoe crabs spawning in Tom’s Cove on Assateague Island, Virginia, during new and full moons in May–June 2008 included 39 individuals that had already been tagged in Delaware Bay and off of Ocean City, Maryland. Of the 8574 crabs that we marked in this study, 1019 were recaptured in the local commercial fishery the same summer. After spawning in Tom’s Cove, horseshoe crabs dispersed and within 6 months, 58 were collected in offshore biomedical and research trawls. After 10 years, resightings of marked crabs were made as far away as South Carolina and Massachusetts, but with a strong directional bias towards the northeast. The population genetics and movement studies illustrated how mid-Atlantic coastal populations are linked genetically and demographically to the Delaware Bay population, a finding with implications for management of fisheries and recovery of the threatened red knot Calidris canutus rufa.

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 (NS ) are particularly amenable to genetic-based approaches as the parameter can be estimated using pedigrees reconstructed from genetic data gathered from discrete juvenile cohorts, therefore eliminating the need to sample adults in the population. However, a critical evaluation of how genotyping and sampling effort influence bias in pedigree reconstruction, and how these biases subsequently influence estimates of NS , is needed to evaluate the efficacy of the approach under a range of scenarios. We simulated a model system to understand the interactive effects of genotyping and sampling effort on error in genetic pedigrees reconstructed from the program COLONY. We then evaluated how errors in pedigree reconstruction influenced bias and precision in estimates of NS using three different rarefaction estimators. Results indicated that pedigree error can be minimal when adequate genetic data are available, such as when juvenile sample sizes are large and/or individuals are genotyped at many informative loci. However, even in cases for which data are limited, using results of the simulation analysis to understand the magnitude and sources of bias in reconstructed pedigrees can still be informative when estimating NS . We applied results of the simulation analysis to evaluate N̂$$ \hat{N} $$S for a population of federally endangered Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Delaware River, USA. Our results indicated that NS is likely to be three orders of magnitude lower compared with historic breeding population sizes, which is a considerable advancement in our understanding of the population status of Atlantic sturgeon in the Delaware River. Our analyses are broadly applicable in the design and interpretation of studies seeking to estimate NS and can help to guide conservation decisions when ecological uncertainty is high. The utility of these results is expected to grow as rapid advances in genetic technologies increase the popularity of genetic population monitoring and estimation.

Atlantic sturgeon ( Acipenser oxyrinchus oxyrinchus ) is a large, anadromous fish native to the Atlantic Coast of North America. Although this species once supported important fisheries, centuries of exploitation and habitat degradation have resulted in dramatic declines, presumed extirpation in some rivers, and ultimately listing under the U.S. Endangered Species Act (ESA). Under the ESA, Atlantic sturgeon are listed as five separate Distinct Population Segments (DPSs), which form the basis for federal management. Despite state and federal protections Atlantic sturgeon still face significant threats to their recovery, including fisheries bycatch mortality, marine construction, dredging, dams, and vessel strikes. However, because subadult and adult Atlantic sturgeon migrate extensively across estuarine and marine environments and frequently form mixed-stock aggregations in non-natal habitats, it can be difficult to determine how these threats impact specific populations and DPSs. To better understand ontogenetic shifts in habitat use and stock-specific exposure to anthropogenic threats, we performed a mixed-stock analysis of 1704 Atlantic sturgeon encountered across the U.S. Atlantic Coast. Collections made north of Cape Cod, MA and south of Cape Hatteras, NC were dominated by individuals from regional stocks; however, we found extensive stock mixing in the mid-Atlantic region, particularly in coastal environments where individuals from all five DPSs were commonly observed. Subadults and adults that were encountered in offshore environments had moved, on average, 277 km from their natal source; however, 23% were sampled over 500 km from their natal river suggesting long-distance movements are relatively common in these age classes. Overall, our work highlights that Atlantic sturgeon populations are vulnerable to threats over vast areas and emphasizes the need for continued genetic monitoring to track recovery progress.

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) is a long-lived, anadromous species that is broadly distributed along the Atlantic coast of North America. Historic overharvest and habitat degradation resulted in significant declines to Atlantic sturgeon populations and, following decades of limited recovery, the species was listed under the Endangered Species Act of the United States in 2012. Given continued threats to recovery and limited information about population demography, there is a need for new tools to assist in Atlantic sturgeon conservation. Here, we present a range-wide microsatellite genetic baseline for North American Atlantic sturgeon that is comprised of 2510 individuals from 18 genetically distinct groups collected in 13 rivers and one estuary. Analysis of this baseline suggested that populations from the northern range of Atlantic sturgeon were more highly differentiated than those from the southern extent, where patterns of differentiation were complicated by rivers with genetically distinct spring and fall spawning runs and less geographic distance separating populations. Despite significant demographic bottleneck events, all populations showed at least moderate levels of genetic diversity across a suite of metrics. Additionally, individual-based assignment tests had over 80% accuracy for assigning individuals to their river of origin, highlighting the utility of this baseline for characterizing the composition of mixed-stock aggregations and understanding stock-specific vulnerability and recovery. The expanded spatial coverage of this baseline dataset enabled novel inferences about patterns of genetic differentiation and spawning phenology in Atlantic sturgeon which can be used to support conservation and management efforts.

AbstractThe shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.

OBJECTIVE:Flathead catfish are rapidly expanding into nonnative waterways throughout the United States. Once established, flathead catfish may cause disruptions to the local ecosystem through consumption and competition with native fishes, including species of conservation concern. Flathead catfish often become a popular sport fish in their introduced range, and so management strategies must frequently balance the need to protect native and naturalized fauna while meeting the desire to maintain or enhance fisheries. However, there are currently few tools available to inform management of invasive flathead catfish (Pylodictis olivaris). We describe a suite of microsatellite loci that can be used to characterize population structure, predict invasion history, and assess potential mitigation strategies for flathead catfish.RESULTS:Our panel of 13 microsatellite loci were polymorphic and appear to be informative for population genetic studies of flathead catfish. We found moderate levels of diversity in four nonnative collections of flathead catfish in the Pennsylvania and Maryland sections of the Susquehanna River and the Schuylkill River, Pennsylvania. Analyses suggested patterns of genetic differentiation within- and among-rivers, highlighting the utility of this marker panel for understanding the structure and assessing the degree of connectivity among flathead catfish populations.

A targeted commercial fishery for Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus once operated in the New York Bight, where it was assumed that most harvested Atlantic Sturgeon were natal to the Hudson River population. However, more recent evidence suggests that the fishery may have been targeting a mixed-stock aggregation, in which case harvested Atlantic Sturgeon could have been comprised of individuals from multiple populations throughout the species' range. Although there is now a moratorium on Atlantic Sturgeon harvest in the New York Bight, modern molecular approaches provide an opportunity to use archived tissues to perform a retrospective mixed-stock analysis on the fishery. Genomic DNA extracted from archived fin spines from 80 Atlantic Sturgeon collected nearly 30 years ago suggests that the fishery primarily harvested individuals from the Hudson River population. However, based on individual-based assignment tests, our results indicate that the fishery also harvested individuals from at least eight other populations located throughout the species' range. This study highlights how archival hard parts that were previously used for age and growth analyses can be employed for retrospective genetic analyses. Further, because the New York Bight harbors relatively high concentrations of Atlantic Sturgeon, the study shows how localized management decisions can influence Atlantic Sturgeon conservation at rangewide scales. When integrated with more recent knowledge of species ecology, these analyses can be used to evaluate the efficacy of previous management strategies and understand the effects of historical processes on contemporary demography.

We developed single nucleotide polymorphism (SNP) markers to support a genetics-based capture-mark-recapture (CMR) project implemented for the management of Pacific walrus (Odobenus rosmarus divergens). Using a combination of Restriction-site Associated DNA sequencing (RADSeq) and genome resequencing, 57,504 single nucleotide variants were identified from Pacific walrus DNA. RADSeq was performed on genomic DNA from 192 walruses (63 males; 94 females; 35 unknown sex) whereas genome resequencing was performed on 41 individual walruses (21 males, 20 females). All read mappings were subjected to quality-based variant detection and screened for SNPs. These efforts generated a pool of 909 putative SNPs from which 217 unique TaqMan® assays were developed for validation. Ultimately, 116 validated, biallelic SNPs were combined to create a genetic tag for identifying individual walrus during the multi-year CMR project. Conversion to a 116-SNP TaqMan® OpenArray® enabled use of a high-throughput genotyping qPCR platform, which expedited accurate discrimination of individual walrus and reduced the probability of genotyping errors, thereby providing improved resolution for assessing the size and demographic rates of this population.

Abstract Objective Tiger beetles inhabiting sandy beaches and cliffs along the east coast of the United States are facing increasing habitat loss due to erosion, urbanization, and sea level rise. The northeastern beach tiger beetle Cicindela dorsalis dorsalis and Puritan tiger beetle Cicindela puritana are both listed as threatened under the Endangered Species Act of 1973, while the white beach tiger beetle Cicindela dorsalis media is not listed but has been declining. Extirpation of these beetles, in some cases from entire states, has isolated many populations reducing gene flow and elevating the risk for the loss of genetic variation. To facilitate investigations of population genetic structure, we developed suites of microsatellite loci for conservation genetic studies. Results Shotgun genomic sequencing of all species identified thousands of candidate microsatellite loci, among which 17 loci were optimized and verified to cross-amplify within C. d. media and C. d. dorsalis, and eight separate loci were optimized for C. puritana. Most loci conformed to Hardy–Weinberg equilibrium, showed no evidence of linkage disequilibrium or null alleles, and revealed population genetic characteristics informative for natural resource managers among the populations tested.

The freshwater mussels Alasmidonta heterodon and A. varicosa historically inhabited rivers along the North American Atlantic coast from the Carolinas, U.S.A., to New Brunswick, CA. However, many populations have been extirpated, and A. heterodon is now federally listed in the U.S.A. as endangered, and both A. heterodon and A. varicosa are listed as vulnerable on the IUCN Red List. To facilitate genetic study of these species, we sequenced the complete female mitochondrial genomes of A. heterodon (15,909 bp; GenBank accession no. MG905826), and A. varicosa (15,693 bp; GenBank accession no. MG938673). Both mitogenomes contained 14 protein coding genes, 2 rRNA genes, and 22 tRNAs with the same gene order as reported for other members of the subfamily Anodontinae. When these two genomes were put into a phylogenetic context with other members of the Unionidae, they clustered together with other species in the subfamily Anodontinae, Tribe Anodontini.

The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

The New England cottontail (Sylvilagus transitionalis) is a species of high conservation priority in the Northeastern United States, and was a candidate for federal listing under the Endangered Species Act until a recent decision determined that conservation actions were sufficient to preclude listing. The aim of this study was to develop a suite of microsatellite loci to guide future research efforts such as the analysis of population genetic structure, genetic variation, dispersal, and genetic mark-recapture population estimation.

We have sequenced the female and male mtDNA of Unio delphinus and inferred the Unionidae phylogeny using 41 complete mtDNA sequences. Additionally, we compared the concatenated mtDNA trees with those using single or combination of two mtDNA genes to identify the best genes to use in the absence of complete mitogenomes. The gender-specific mtDNAs of U. delphinus contain all Unionida mtDNA specific features. The mtDNA phylogeny supports the reciprocal monophyly of the gender-specific clades but it was inconclusive regarding Unionidae subfamilies relationships. The gene trees topologies using ND5 or 16S-rRNA with ND1 were the closest trees to the mtDNA trees.

Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan ( Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated from two three-hour runs on the Ion Torrent PGM can generate a sufficient number of nuclear and mitochondrial markers to improve understanding of the evolutionary and ecological dynamics of non-model and in particular, invasive species.

The hermaphroditic flat-spired three-tooth land snail (Triodopsis platysayoides) is endemic to a 21-km stretch of the Cheat River Gorge of northeastern West Virginia, USA. We document isolation and characterization of ten microsatellite DNA markers in this at-risk species. The markers displayed a moderate level of allelic diversity (averaging 7.1 alleles/locus) and heterozygosity (averaging 58.6 %). Allelic diversity at seven loci was sufficient to produce unique multilocus genotypes; no indication of selfing was detected in this cosexual species. Minimal deviations from Hardy–Weinberg equilibrium and no linkage disequilibrium were observed within subpopulations. All loci deviated from Hardy–Weinberg expectations when individuals from subpopulations were pooled. Microsatellite markers developed for T. platysayoides yielded sufficient genetic diversity to (1) distinguish all individuals sampled and the level of selfing; (2) be appropriate for addressing fine-scale population structuring; (3) provide novel demographic insights for the species; and (4) cross-amplify and detect allelic diversity in the congeneric T. juxtidens.