Leetown Science Center

Kearneysville, WV, United States

Leetown Science Center

Kearneysville, WV, United States

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Kanno Y.,Clemson University | Pregler K.C.,Clemson University | Hitt N.P.,Leetown Science Center | Letcher B.H.,Silvio O Conte Anadromous Fish Research Branch | And 2 more authors.
Freshwater Biology | Year: 2016

Abundance of the young-of-the-year (YOY) fish can vary greatly among years and it may be driven by several key biological processes (i.e. adult spawning, egg survival and fry survival) that span several months. However, the relative influence of seasonal weather patterns on YOY abundance is poorly understood. We assessed the importance of seasonal air temperature (a surrogate for stream temperature) and precipitation (a surrogate for stream flow) on brook trout (Salvelinus fontinalis) YOY summer abundance using a 29-year data set from 115 sites in Shenandoah National Park, Virginia, U.S.A. We used a Bayesian hierarchical model that allowed the effect of seasonal weather covariates to vary among sites and accounted for imperfect detection of individuals. Summer YOY abundance was affected by preceding seasonal air temperature and precipitation, and these regional-scale drivers led to spatial synchrony in YOY abundance dynamics across the 170-km-long study area. Mean winter precipitation had the greatest effect on YOY abundance and the relationship was negative. Mean autumn precipitation, and winter and spring temperature had significantly positive effects on YOY abundance, and mean autumn temperature had a significant negative effect. In addition, the effect of summer precipitation differed along a latitudinal gradient, with YOY abundance at more northern sites being more responsive to inter-annual variation in summer precipitation. Strong YOY years resulted in high abundance of adults (>age 1 + fish) in the subsequent year at more than half of sites. However, higher adult abundance did not result in higher YOY abundance in the subsequent year at any of the study sites (i.e. no positive stock-recruitment relationship). Our results indicate that YOY abundance is a key driver of brook trout population dynamics that is mediated by seasonal weather patterns. A reliable assessment of climate change impacts on brook trout needs to account for how alternations in seasonal weather patterns impact YOY abundance and how such relationships may differ across the range of brook trout distribution. © 2016 John Wiley & Sons Ltd.


Kanno Y.,Clemson University | Letcher B.H.,Silvio O Conte Anadromous Fish Research Branch | Hitt N.P.,Leetown Science Center | Boughton D.A.,National Oceanic and Atmospheric Administration | And 2 more authors.
Global Change Biology | Year: 2015

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark-recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage-structured population model. The data were a 15-year record of brook trout abundance from 72 sites distributed across a 170-km-long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site-specific conditions. Specifically, young-of-year survival was most strongly affected by spring temperature, adult survival by elevation and per-capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel-scouring flows on eggs and newly hatched individuals. However, high-elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density-dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage-structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics. © 2014 John Wiley & Sons Ltd.


Cornman R.S.,Leetown Science Center | Robertson L.S.,Leetown Science Center | Galbraith H.,Northern Appalachian Research Branch Leetown Science Center | Blakeslee C.,Northern Appalachian Research Branch Leetown Science Center
PloS one | Year: 2014

Mussels are useful indicator species of environmental stress and degradation, and the global decline in freshwater mussel diversity and abundance is of conservation concern. Elliptio complanata is a common freshwater mussel of eastern North America that can serve both as an indicator and as an experimental model for understanding mussel physiology and genetics. To support genetic components of these research goals, we assembled transcriptome contigs from Illumina paired-end reads. Despite efforts to collapse similar contigs, the final assembly was in excess of 136,000 contigs with an N50 of 982 bp. Even so, comparisons to the CEGMA database of conserved eukaryotic genes indicated that ∼ 20% of genes remain unrepresented. However, numerous candidate stress-response genes were present, and we identified lineage-specific patterns of diversification among molluscs for cytochrome P450 detoxification genes and two saccharide-modifying enzymes: 1,3 beta-galactosyltransferase and fucosyltransferase. Less than a quarter of contigs had protein-level similarity based on modest BLAST and Hmmer3 statistical thresholds. These results add comparative genomic resources for molluscs and suggest a wealth of novel proteins and noncoding transcripts.


PubMed | Leetown Science Center and Northern Appalachian Research Branch Leetown Science Center
Type: Journal Article | Journal: PloS one | Year: 2014

Mussels are useful indicator species of environmental stress and degradation, and the global decline in freshwater mussel diversity and abundance is of conservation concern. Elliptio complanata is a common freshwater mussel of eastern North America that can serve both as an indicator and as an experimental model for understanding mussel physiology and genetics. To support genetic components of these research goals, we assembled transcriptome contigs from Illumina paired-end reads. Despite efforts to collapse similar contigs, the final assembly was in excess of 136,000 contigs with an N50 of 982 bp. Even so, comparisons to the CEGMA database of conserved eukaryotic genes indicated that 20% of genes remain unrepresented. However, numerous candidate stress-response genes were present, and we identified lineage-specific patterns of diversification among molluscs for cytochrome P450 detoxification genes and two saccharide-modifying enzymes: 1,3 beta-galactosyltransferase and fucosyltransferase. Less than a quarter of contigs had protein-level similarity based on modest BLAST and Hmmer3 statistical thresholds. These results add comparative genomic resources for molluscs and suggest a wealth of novel proteins and noncoding transcripts.


King T.L.,U.S. Geological Survey | Henderson A.P.,U.S. Geological Survey | Kynard B.E.,University of Massachusetts Amherst | Kieffer M.C.,U.S. Geological Survey | And 3 more authors.
PLoS ONE | Year: 2014

The shortnose sturgeon, Acipenser brevirostrum, oft considered a phylogenetic relic, is listed as an "endangered species threatened with extinction" in the US and "Vulnerable" on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.


Robertson L.S.,Leetown Science Center | Robertson L.S.,Shepherd University | Cornman R.S.,Leetown Science Center
Molecular Ecology Resources | Year: 2014

We developed genetic resources for two North American frogs, Lithobates clamitans and Pseudacris regilla, widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. De novo assemblies with Mira3 resulted in 50 238 contigs (N50 = 687 bp) and 48 213 contigs (N50 = 686 bp) for L. clamitans and P. regilla, respectively, after clustering with CD-Hit-EST and purging contigs below 200 bp. We performed BLASTX similarity searches against the Xenopus tropicalis proteome and, for predicted ORFs, HMMER similarity searches against the Pfam-A database. Because there is broad interest in amphibian immune factors, we manually annotated putative antimicrobial peptides. To identify conserved regions suitable for amplicon resequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus Rana and identified reciprocal best TBLASTX matches among all assemblies. Although P. regilla, a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow nondegenerate primer design with Primer3. In addition to providing a foundation for comparative genomics and quantitative gene expression analysis, our results enable quick development of nuclear sequence-based markers for phylogenetics or population genetics. © 2014 John Wiley & Sons Ltd 141 January 2014 10.1111/1755-0998.12164 Resource Article RESOURCE ARTICLES Permanent Genetic Resources Published 2013. This article is a U.S. Government work and is in the public domain in the USA.


Cornman R.S.,Leetown Science Center | Robertson L.S.,Leetown Science Center | Robertson L.S.,Shepherd University | Galbraith H.,Northern Appalachian Research Branch | Blakeslee C.,Northern Appalachian Research Branch
PLoS ONE | Year: 2014

Mussels are useful indicator species of environmental stress and degradation, and the global decline in freshwater mussel diversity and abundance is of conservation concern. Elliptio complanata is a common freshwater mussel of eastern North America that can serve both as an indicator and as an experimental model for understanding mussel physiology and genetics. To support genetic components of these research goals, we assembled transcriptome contigs from Illumina paired-end reads. Despite efforts to collapse similar contigs, the final assembly was in excess of 136,000 contigs with an N50 of 982 bp. Even so, comparisons to the CEGMA database of conserved eukaryotic genes indicated that, 20% of genes remain unrepresented. However, numerous candidate stress-response genes were present, and we identified lineagespecific patterns of diversification among molluscs for cytochrome P450 detoxification genes and two saccharide-modifying enzymes: 1,3 beta-galactosyltransferase and fucosyltransferase. Less than a quarter of contigs had protein-level similarity based on modest BLAST and Hmmer3 statistical thresholds. These results add comparative genomic resources for molluscs and suggest a wealth of novel proteins and noncoding transcripts.


Aunins A.W.,Leetown Science Center | Petty J.T.,West Virginia University | King T.L.,U.S. Geological Survey | Schilz M.,West Virginia University | Mazik P.M.,U.S. Geological Survey
Conservation Genetics | Year: 2014

Brook trout (Salvelinus fontinalis) often exist as highly differentiated populations, even at small spatial scales, due either to natural or anthropogenic sources of isolation and low rates of dispersal. In this study, we used molecular approaches to describe the unique population structure of brook trout inhabiting the Shavers Fork watershed, located in eastern West Virginia, and contrast it to nearby populations in tributaries of the upper Greenbrier River and North Fork South Branch Potomac Rivers. Bayesian and maximum likelihood clustering methods identified minimal population structuring among 14 collections of brook trout from throughout the mainstem and tributaries of Shavers Fork, highlighting the role of the cold-water mainstem for connectivity and high rates of effective migration among tributaries. In contrast, the Potomac and Greenbrier River collections displayed distinct levels of population differentiation among tributaries, presumably resulting from tributary isolation by warm-water mainstems. Our results highlight the importance of protecting and restoring cold-water mainstem habitats as part of region-wide brook trout conservation efforts. In addition, our results from Shavers Fork provide a contrast to previous genetic studies that characterize Appalachian brook trout as fragmented isolates rather than well-mixed populations. Additional study is needed to determine whether the existence of brook trout as genetically similar populations among tributaries is truly unique and whether connectivity among brook trout populations can potentially be restored within other central Appalachian watersheds. © 2014, Springer Science+Business Media Dordrecht.


McCormick P.V.,Leetown Science Center | McCormick P.V.,South Florida Water Management District
Wetlands Ecology and Management | Year: 2011

Surface soils and periphyton communities were sampled across an oligotrophic, soft-water wetland to document changes associated with pulsed inputs of nutrient- and mineral-rich canal drainage waters. A gradient of canal-water influence was indicated by the surface-water specific conductance, which ranged between 743 and 963 μS cm-1 in the canals to as low as 60 μS cm-1 in the rainfall-driven wetland interior. Changes in soil chemistry and periphyton taxonomic composition across this gradient were described using piecewise regressions models. The greatest increase in soil phosphorus (P) concentration occurred at sites closest to the canal while soil mineral (sulfur, calcium) concentrations increased most rapidly at the lower end of the gradient. Multiple periphyton shifts occurred at the lower end of the gradient and included; (1) a decline in desmids and non-desmid filamentous chlorophytes, and their replacement by a diatom-dominated community; (2) the loss of soft-water diatom indicator species and their replacement by hard-water species. Increased dominance by cyanobacteria and eutrophic diatom indicators occurred closer to the canals. Soil and periphyton changes indicated four zones of increasing canal influence across the wetland: (1) a zone of increasing mineral concentrations where soft-water taxa remained dominant; (2) a transition towards hard-water, oligotrophic diatoms as mineral concentrations increased further; (3) a zone of dominance by these hard-water species; (4) a zone of rapidly increasing P concentrations and dominance by eutrophic taxa. In contrast to conclusions drawn from routine water-chemistry monitoring, measures of chemical and biological change presented here indicate that most of this rainfall-driven peatland receives some influence from canal discharges. These changes are multifaceted and induced by shifts in multiple chemical constituents. © 2010 US Government.


PubMed | Leetown Science Center
Type: Journal Article | Journal: Molecular ecology resources | Year: 2013

We developed genetic resources for two North American frogs, Lithobates clamitans and Pseudacris regilla, widespread native amphibians that are potential indicator species of environmental health. For both species, mRNA from multiple tissues was sequenced using 454 technology. De novo assemblies with Mira3 resulted in 50238 contigs (N50=687bp) and 48213 contigs (N50=686bp) for L.clamitans and P.regilla, respectively, after clustering with CD-Hit-EST and purging contigs below 200bp. We performed BLASTX similarity searches against the Xenopus tropicalis proteome and, for predicted ORFs, HMMER similarity searches against the Pfam-A database. Because there is broad interest in amphibian immune factors, we manually annotated putative antimicrobial peptides. To identify conserved regions suitable for amplicon resequencing across a broad taxonomic range, we performed an additional assembly of public short-read transcriptome data derived from two species of the genus Rana and identified reciprocal best TBLASTX matches among all assemblies. Although P.regilla, a hylid frog, is substantially more diverged from the ranid species, we identified 56 genes that were sufficiently conserved to allow nondegenerate primer design with Primer3. In addition to providing a foundation for comparative genomics and quantitative gene expression analysis, our results enable quick development of nuclear sequence-based markers for phylogenetics or population genetics.

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