Geology topics

Stuart A. Welsh

Publications and source records attributed to Stuart A. Welsh.

At least 19 recordsLinked to original sources

USGS2025

Quantitative PCR detection of endangered diamond darter Crystallaria Cincotta in environmental DNA: Employing locked nucleic acids and blocking probe for specificity

This study presents a quantitative PCR (qPCR) assay for the detection of the endangered diamond darter Crystallaria cincotta from environmental DNA (eDNA) in water samples. The assay design is based on an alignment of mitochondrial cytochrome b DNA sequences from 58 individuals representing 25 percid species. Leveraging genetic differences, a species-specific qPCR assay was designed, incorporating alocked nucleic acid (LNA)-enriched probe and a secondary blocking probe to enhance specificity. The assay targets a 93-base pair fragment that includes a diagnostic single nucleotide polymorphism in the probe region; combined with multiple primer mismatches, this provides specificity for distinguishing C. cincotta from other sympatric percid species. Specificity was validated by testing genomic DNA from 16 percid species and synthetic templates, confirming no cross-reactivity. Performance metrics, including the standard curve, qPCR efficiency, limit of detection, and limit of quantification, are reported. The qPCR assay exhibited sufficient sensitivity to detect C. cincotta eDNA in environmental water samples collected from occupied riverine habitats. This study illustrates the effectiveness of LNA-enriched and blocking probes in developing species-specific qPCR assays for eDNA applications, demonstrating their utility in accurately distinguishing closely related species within diverse fish communities.

Conservation Genetics Resources↗

USGS2025

Blueprints for riverine cod nest boxes draw from multiple design considerations

Designing aquatic nest boxes is rarely afforded detailed scientific account. Here we provide some historical context for nest boxes used in production of large-bodied fishes of the Australian freshwater cod genus Maccullochella . Our experience with eastern freshwater cod is used as a case study to: (a) convey aspects of the complexity of the nest box design process and to (b) demonstrate the importance of visual literacy in project communication across the variety of contributors to the eco-design process. Specifically, we describe a new, two-variant, triangular nest box design for application in rivers and modifications to a standard stainless steel nest box for hatchery-pond-based spawning of eastern freshwater cod M. ikei . We designed the boxes to test adult preference for single versus double entrance/exits to cavities in hatchery and field environments. An important consideration specific to hatchery production is harvesting demersal, adhesive eggs prior to hatching to minimise fungal infection of eggs and physical loss of larvae, in addition to providing critical first feeding of larvae. In contrast, field nest box design incorporated multiple factors and associated trade-offs related to both internal and external design, ranging from manufacturer capability, material types, cost, transportability, hydrological performance, biodegradability, retrievability, as well as biological and ecological function. Only preliminary findings from field nest box deployments are provided here, and we focus primarily on elements of visual language in the form of conceptual drawings, sketches and final schematics which have been central to our process. We emphasise the benefit of harnessing input from multiple fields of expertise and documenting and testing designs of nest boxes for cavity nesting fishes, under both controlled hatchery and more complex field conditions.

Aquaculture, Fish and Fisheries↗

USGS2025

Endemic and invasive species: A history of distributional trends in the fish fauna of the lower New River drainage

Invasive species are often central to conservation efforts, particularly when concerns involve potential impacts on rare, endemic native species. The lower New River drainage of the eastern United States is a watershed that warrants conservation assessment, as the system is naturally depauperate of native fish species and it is nearly saturated with non-native fish species: there are 31 natives, including at least nine endemic taxa, and 63 non-natives. For endemic taxa, we examined temporal distribution shifts (range expansions or contractions) based on percent change in the occupied watershed area. We contrasted these findings with time series analyses on distribution trends of non-native minnows (Leuciscidae) and darters (Percidae) based on growth curve models of the cumulative sum of the total area of occupied 12-digit hydrologic unit codes. We documented range reductions for six of nine endemic taxa. We determined that 11 of 18 non-native minnows and 6 of 8 non-native darters were invasive based on range expansions and associated invasion curve models. The endemic taxa are of conservation concern given the limited distribution ranges and documented population declines. Although among-species comparisons of range shifts do not support causal inference, documentation of changes in distribution ranges of endemic and invasive species is critical to inform conservation efforts.

North Carolina, Tennessee, Virginia, West Virginia↗

USGS2024

Paddlefish movement and dam passage in the Ohio and Kanawha Rivers, West Virginia

The Paddlefish ( Polyodon spathula ), a large-bodied and highly migratory species of large river systems, has experienced population declines or extirpation in parts of its native range. As an effort to reestablish a Paddlefish population in the Ohio River of West Virginia, the West Virginia Division of Natural Resources has stocked fingerling Paddlefish in the previous two decades. Post-stocking studies could assess the status of the reintroduced population, which includes collecting information on their seasonal movements and dam passage frequency through navigation dams of the Ohio and Kanawha Rivers. Using acoustic telemetry techniques, we monitored seasonal movements and assessed dam passage of five Paddlefish in the Robert C. Byrd Pool of the Ohio and Kanawha rivers. Paddlefish were highly mobile with two individuals using the entire R.C. Byrd Pool during the 11-month study period. Most movements occurred during the expected spawning period of April and May, where all individuals frequented the upper section of the pool in the Kanawha River. Downstream passage was documented for one individual at the R.C. Byrd lock during July 2023, but no evidence of upstream passage was documented for the locks at Racine (Ohio River) or Winfield (Kanawha River). Tagging of additional Paddlefish would be beneficial to increase sample size for future assessments and continue efforts toward the long-term conservation and management of Ohio River Paddlefish.

West Virginia↗

USGS2023

Environmental correlates of walleye spawning movements in an Appalachian hydropower reservoir

Understanding walleye ( Sander vitreus ) spawning behavior is important for managing walleye fisheries, but such information is limited for Appalachian reservoirs. We assessed spawning movements and spawning locations for a reestablished walleye population in Cheat Lake, West Virginia. We tagged fifty-two walleye with acoustic telemetry transmitters to evaluate environmental correlates associated with pre-spawn movements and to deter- mine spawning locations. Using an information-theoretic approach, we compared candidate logistic regression models to determine which environmental variables best explained upstream movements to spawning areas. The two models with the most support both included additive effects of year and water temperature, with sex also included in the second of these models. Water temperature had a significant positive relationship with pre-spawn movements in each model. Other environmental covariates such as river discharge and water elevation were not significant predictors of upstream pre-spawn move- ments. Walleye made pre-spawn upstream movements in late winter/early spring to spawning areas in the headwaters of Cheat Lake during periods of el- evated water temperatures (75 % of movement events occurred at water temperatures >4.1 C) where spawning occurred in shallow (<1.5 m), rocky habitat. Male walleye generally made upstream pre-spawn movements earlier than females. Our results also suggested the timing of walleye spawning with respect to water-level fluctuations could influence reproductive success due to stranding of eggs or reducing suitable spawning habitat. Knowledge of pre-spawn movement patterns and spawning locations could aid management of this recovering population. Benefits to management may include the prediction of spawning timing and locations for broodstock surveys and influences of water-level fluctuations and other environmental stressors on spawning success.

Pennsylvania, West Virginia↗

USGS2023

Size structure, age, growth, and mortality of flathead catfish in the Robert C. Byrd Pool of the Ohio and Kanawha Rivers

Flathead catfish ( Pylodictis olivaris ) were sampled in the Robert C. Byrd Pool of the Ohio and Kanawha rivers, West Virginia, to inform management decisions based on population characteristics of size structure, age, growth, and mortality. Sampling was conducted with low-frequency boat electrofishing during late May to early June over a four-year period (2017–2020). We examined size structure using proportional size distribution indi- ces. Growth was evaluated using otolith-derived ages, a von Bertalanffy growth curve, and mean length at age data, including comparisons to published mean length at age data of other populations. Annual mortality was estimated with a weighted catch curve. We documented a high-density population (mean CPUE = 49 fish h–1) with low mortality (A = 11.8%), characterized by slow growing individuals with a maximum recorded age of 36. Our results further demonstrate that this population is characterized by a broad size structure that likely is maintained only through low harvest and high rates of catch and release by anglers.

West Virginia↗

USGS2022

Differences in population characteristics and modeled response to harvest regulations in reestablished Appalachian Walleye populations

Historically, the Monongahela, Tygart, and Cheat River watersheds in West Virginia were impaired by acidification from acid mine drainage and Walleye Sander vitreus were extirpated from these watersheds by the 1940s. Walleye were reestablished after water quality improvements following passage of environmental legislation and subsequent reintroduction efforts. We compared population characteristics, with emphasis on growth, of Walleye and used modeling to predict the potential effects of harvest regulations in the Monongahela River and two main-stem reservoirs in the Cheat River and Tygart River watersheds. Statistical comparisons of von Bertalanffy growth curves and relative growth indices indicated that Walleye growth significantly differed across all water bodies. Relative growth index results suggested that Walleye growth was above average in Cheat Lake, average in the Monongahela River, and below average in Tygart Lake relative to other North American populations. Growth was negatively correlated with Walleye relative abundance and positively correlated with estimates of productivity (total phosphorus, chlorophyll a ). Walleye diets significantly differed across all water bodies, with diets dominated by Yellow Perch Perca flavescens and Gizzard Shad Dorosoma cepedianum in Cheat Lake, where growth was fastest. Population modeling suggested that effects of exploitation on yield, spawning potential, and size structure were similar under regulations of no length limit and a minimum length limit (381 mm). Models suggested that removing length limits in Tygart Lake could increase angler harvest opportunities and pose minimal threat to the fishery. Models suggested that a protected slot limit could provide increased protection to the spawning potential of Cheat Lake and the Monongahela River populations. Additionally, models predicted that a protected slot limit could increase the number of large (>630-mm) Walleye in these waters. Our findings demonstrate the different characteristics that Walleye populations can develop after reestablishment based on abiotic and biotic conditions and the need for watershed-specific management.

West Virginia↗

USGS2021

Epigean crayfish of the Potomac River Basin in West Virginia: Zoogeography, natural history and conservation

Crayfish are an aquatic fauna of conservation concern, yet regional studies are lacking on zoogeography and life history. We compared recent and historical species distribution data and assessed conservation standings of native and nonindigenous crayfish of the Potomac River Basin in West Virginia. From 2007–2011, a total of 1764 crayfish were collected from 159 sites. Data collection included species abundance, morphometrics, and life history parameters. Percentages of the number of individuals of each species of the total catch were 36.3% ( Cambarus bartonii ), 34.6% ( Faxonius obscurus ), 23.4% ( Faxonius virilis ), 3.6% ( Procambarus cf. zonangulus ) and 2.0% ( Cambarus carinirostris ). Cambarus bartonii was present throughout the drainage, F. obscurus was collected primarily from the North Branch, South Branch, and Cacapon river watersheds, and C. carinirostris was only collected in the South Branch watershed. Two nonnative species, F. virilis and P. cf. zonangulus , were only present in tributaries downstream of the Cacapon River watershed. Spinycheek crayfish ( Faxonius limosus ) were not collected during our survey, which suggests its possible extirpation from the West Virginia portion of its range. Our zoogeographic and life history data could serve as a baseline for future conservation-oriented monitoring efforts of the Potomac River watershed.

West Virginia↗

USGS2019

Cambarus fetzneri sp. nov., a new species of burrowing crayfish (Decapoda: Cambaridae) from the Allegheny Mountains of Virginia and West Virginia, USA

The disjunct distribution of Cambarus monongalensis has led to speculation about its taxonomic status. An Appalachian Plateau population occurs in northern and central West Virginia and Southwestern Pennsylvania, and a mountain population occurs in the Allegheny Mountains and Ridge and Valley physiographic provinces of the Virginias. Herein we describe the mountain population as Cambarus fetzneri sp. nov. The two species differ genetically and morphologically, and have different color patterns. Specifically, C. fetzneri sp. nov. chelae lack extensive red coloration on the distal end of the propodus and dactyl, possess rostral margins that lack any red coloration, compared to C. monongalensis , which has extensive red coloration on the dactyl and propodus, as well as red rostral margins. Morphologically, the rostrum of C. fetzneri sp. nov. is shorter and wider than that of C. monongalensis . Also, adult C. fetzneri sp. nov. are considerably smaller in body size than those of C. monongalensis .

Virginia, West Virginia↗

USGS2019

Cambarus loughmani, a new species of crayfish (Decapoda: Cambaridae) endemic to the pre-glacial Teays River Valley in West Virginia, USA

A new species of crayfish, Cambarus loughmani sp. nov., is described from the preglacial Teays River Valley of Cabell, Kanawha, Lincoln, Mason, and Putnam counties, West Virginia. The species was previously considered to be part of the Cambarus dubius complex. Loughman et al. restricted C. dubius to an orange colour morph found in central and northern portions of the Allegheny Mountains and Appalachian Plateau in central West Virginia, western Maryland, and south-central Pennsylvania. The new species described herein can be distinguished from all other members of Cambarus Erichson, 1846 by a double row of cristiform tubercles on the palm, an open areola with two rows of punctations, and a consistent blue colouration.

West Virginia↗

USGS2018

Genetic swamping and species collapse: Tracking introgression between the native Candy Darter and introduced Variegate Darter

Candy Darters ( Etheostoma osburni ) and Variegate Darters (E. variatum ) are both native to West Virginia and Virginia. The geographic ranges of these two species were historically separated by Kanawha Falls, a natural barrier to fish dispersal located at Glen Ferris, WV. In the early 1980s, Variegate Darters or putative hybrids ( E. osburni × E. variatum ) were first collected at locations upstream of Kanawha Falls, and have since undergone range expansion. Hybridization with the Variegate Darter was one of the threats that led to the Candy Darter being proposed for listing under the U.S. Endangered Species Act in 2017. Genetic and morphologic data were examined for individuals from the New, Gauley, and Greenbrier river drainages. Individuals were genotyped using a suite of 5 diagnostic microsatellite loci to investigate potential hybridization. Widespread hybridization was found throughout populations of Candy Darters, with the geographic range of hybridization expanding from 2004 to 2014. A hybrid zone was observed, with the highest levels of Variegate Darter introgression representing the kernel within this zone and the locations of first-generation (F1) hybrids at the periphery. F1 hybrids were morphologically intermediate within and across characters for parental species. Introgressive hybridization threatens the genetic integrity of the Candy Darter, and may lead to population extirpation or extinction.

West Virginia↗

USGS2018

Variation in DNA methylation is associated with migratory phenotypes of lake sturgeon (Acipenser fulvescens) in the St. Clair River

Lake sturgeon populations show a variety of movement patterns, but this variation is poorly understood. To compare two migratory phenotypes of lake sturgeon in the St. Clair River, multiple data types were analyzed. Individual fish were classified into migratory phenotypes based on acoustic telemetry data from 2012-2015. Lake sturgeon consistently showed movement from the St. Clair River upriver into Lake Huron or downriver into Lake St. Clair. The two migratory phenotypes were then compared for differences in morphometrics, genetics, and epigenetics. Morphological differences based on linear measurements were not detected between phenotypes. Microsatellite data from 11 loci suggested one population with no genetic differentiation between migratory phenotypes. Our epigenetic results indicated that the migratory phenotypes are differentially methylated (P=0.036), thus epigenetics may be associated with migratory differences in lake sturgeon. Only one restriction site was identified to be driving the differential methylation (P=0.012). While little evidence at neutral loci occurred for genetic differentiation of lake sturgeon, DNA methylation may play a role in the observed movement pattern variation. When combined with microsatellite and morphometric analyses, our results suggested that different migratory patterns may reflect phenotypic plasticity, allowing lake sturgeon to acclimate to short-term environmental variability. Without an integrated approach, the role of epigenetics in the migratory phenotype of lake sturgeon may have been overlooked. Further characterization of migratory phenotypes could be important for management to conserve behavioral variation across the distribution of lake sturgeon and for design of stocking guidelines.

Michigan↗

USGS2018

Population characteristics of Yellow Perch in a central Appalachia hydropower reservoir

Estimates of population characteristics of sport fishes inform fisheries management decisions and provide feedback on management strategies. Cheat Lake provides an unusual fishery in West Virginia because the hydropower reservoir supports a Yellow Perch Perca flavescens population. We estimated age structure, size structure, condition, total instantaneous mortality, growth, and summer diet for Cheat Lake Yellow Perch based on electrofishing collections in 2012. From 302 individuals, we observed a maximum age of 9 y. Maximum age, average size, and growth of females in the sample exceeded those of males. Cheat Lake Yellow Perch scored low on the relative weight index, but generally exhibited faster growth than other populations, even when compared by sex. Estimated annual survival was 0.63 (95% CI = 0.51–0.78), which is comparable to other exploited populations. These data support the presence of an ontogenetic diet shift from consumption of zooplankton to macroinvertebrates and fishes as Yellow Perch age. This study is the first evaluation we are aware of on Yellow Perch population characteristics in West Virginia, providing baseline data to enhance management decisions and direct future studies.

West Virginia↗

USGS2018

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

Connectivity among stream fish populations allows for exchange of genetic material and helps maintain genetic diversity, adaptive potential and population stability over time. Changes in species demographics and population connectivity have the potential to permanently alter the genetic patterns of stream fish, although these changes through space and time are variable and understudied in small‐bodied freshwater fish. As a spatially widespread, common species of benthic freshwater fish, the variegate darter ( Etheostoma variatum ) is a model species for documenting how patterns of genetic structure and diversity respond to increasing isolation due to large dams and how scale of study may shape our understanding of these patterns. We sampled variegate darters from 34 sites across their range in the North American Ohio River basin and examined how patterns of genetic structure and diversity within and between populations responded to historical population changes and dams within and between populations. Spatial scale and configuration of genetic structure varied across the eight identified populations, from tributaries within a watershed, to a single watershed, to multiple watersheds that encompass Ohio River mainstem habitats. This multiwatershed pattern of population structuring suggests genetic dispersal across large distances was and may continue to be common, although some populations remain isolated despite no apparent structural dispersal barriers. Populations with low effective population sizes and evidence of past population bottlenecks showed low allelic richness, but diversity patterns were not related to watershed size, a surrogate for habitat availability. Pairwise genetic differentiation ( F ST ) increased with fluvial distance and was related to both historic and contemporary processes. Genetic diversity changes were influenced by underlying population size and stability, and while instream barriers were not strong determinants of genetic structuring or loss of genetic diversity, they reduce population connectivity and may impact long‐term population persistence. The broad spatial scale of this study demonstrated the large spatial extent of some variegate darter populations and indicated that dispersal is more extensive than expected given the movement patterns typically observed for small‐bodied, benthic fish. Dam impacts depended on underlying population size and stability, with larger populations more resilient to genetic drift and allelic richness loss than smaller populations. Other darters that inhabit large river habitats may show similar patterns in landscape‐scale studies, and large river barriers may impact populations of small‐bodied fish more than previously expected. Estimation of dispersal rates and behaviours is critical to conservation of imperilled riverine species such as darters.

Freshwater Biology↗

USGS2018

Effects of an extreme flood event on federally endangered Diamond Darter abundances

Extreme flood events can substantially affect riverine systems, modifying instream habitat and influencing fish assemblages and densities. Rare species are especially vulnerable to these disturbance events because of their small population size and often reduced phenotypic heterogeneity. In June 2016 the lower Elk River in West Virginia experienced severe flooding, resulting in a peak discharge that exceeded the 0.005 annual exceedance probability (>200 y flood) in the main stem. We obtained pre-flood and postflood population count data and estimated abundances for one cohort of the federally endangered Diamond Darter ( Crystallaria cincotta ) at 15 sites. While both the total count data and total estimated abundance decreased following the flood, our analyses did not indicate the extreme flood event strongly impacted Diamond Darter abundance. This indicates individuals are able to withstand high velocities and resist displacement or mortality. In addition site-level abundances were estimated at three sentinel sites during 2015 and 2016 using a multinomial N -mixture model that accounted for variation in detectability resulting from water temperature. Mean estimated abundance varied among the three sites and between the 2 y. Our results suggest there is substantial variation in year-class strength between the two cohorts we sampled. It is suggested that survey efforts at established sentinel sites be continued on an annual basis in order to help determine factors influencing year-class strength.

The American Midland Naturalist↗

USGS2018

A multiscale investigation of habitat use and within-river distribution of sympatric sand darter species

The western sand darter Ammocrypta clara, and eastern sand darter Ammocrypta pellucida, are sand-dwelling fishes of conservation concern. Past research has emphasized the importance of studying individual populations of conservation concern, while recent research has revealed the importance of incorporating landscape scale processes that structure habitat mosaics and local populations. We examined habitat use and distributions of western and eastern sand darters in the lower Elk River of West Virginia. At the sandbar habitat use scale, western sand darters were detected in sandbars with greater area, higher proportions of coarse grain sand and faster bottom current velocity, while the eastern sand darter used a wider range of sandbar habitats. The landscape scale analysis revealed that contributing drainage area was an important predictor for both species, while sinuosity, which presumably represents valley type, also contributed to the western sand darter’s habitat suitability. Sandbar quality (area, grain size, and velocity) and fluvial geomorphic variables (drainage area and valley type) are likely key driving factors structuring sand darter distributions in the Elk River. This multiscale study of within-river species distribution and habitat use is unique, given that only a few sympatric populations are known of western and eastern sand darters.

West Virginia↗

USGS2017

Optimization of decision rules for hydroelectric operation to reduce both eel mortality and unnecessary turbine shutdown: A search for a win-win solution

Worldwide populations of freshwater eels have declined with one of the contributing causes related to mortality during passage through hydropower turbines. An inherent trade‐off underlies turbine management where the competing demand for more hydropower comes at the expense of eel survival. A win–win solution exists when an option performs better on all competing demands compared to other options. A predictive model for eel migration based on a recent telemetry study was used to develop decision rules for turbine management in the Shenandoah River system. The performance of alternative decision rules was compared to the status quo policy to search for win–win solutions. Decision rules were defined by the probability of eel movement and were evaluated by the probabilities of false positive and false negative errors. The exact value of the cut‐off probability used in the decision rule will need to be determined through negotiation between stakeholders, but a range of cut‐off probabilities resulted in a win–win situation with both reduced eel mortality and increased turbine operation relative to the current shutdown strategy. Monitoring the implementation is needed to evaluate and update the predictive model and to refine the decision rule. Although the decision is framed for the Shenandoah River system, the analytical approach could be used to develop decision rules for turbine shutdown policy in other areas.

Virginia, West Virginia↗

USGS2017

Effect of substrate size on sympatric sand darter benthic habitat preferences

The western sand darter, Ammocrypta clara , and the eastern sand darter, A. pellucida , are sand-dwelling fishes that have undergone range-wide population declines, presumably owing to habitat loss. Habitat use studies have been conducted for the eastern sand darter, but literature on the western sand darter remains sparse. To evaluate substrate selection and preference, western and eastern sand darters were collected from the Elk River, West Virginia, one of the few remaining rivers where both species occur sympatrically. In the laboratory, individuals were given the choice to bury into five equally available and randomly positioned substrates ranging from fine sand to granule gravel (0.12–4.0 mm). The western sand darter selected for coarse and medium sand, while the eastern sand darter was more of a generalist selecting for fine, medium, and coarse sand. Substrate selection was significantly different ( p = 0.02) between species in the same environment, where the western sand darter preferred coarser substrate more often compared to the eastern sand darter. Habitat degradation is often a limiting factor for many species of rare freshwater fish, and results from this study suggest that western and eastern sand darters may respond differently to variations in benthic substrate composition.

West Virginia↗