Progress 04/01/14 to 03/31/19
Outputs
Target Audience:The direct target audiences for this work are: - Professionals at public agencies that manage game fishes and non-game species or their critical habitats, including the Virginia Department of Game and Inland Fisheries, other state fisheries and wildlife management agencies, the Virginia Department of Transportation, U.S. Fish and Wildlife Service, and U.S.D.A.-Forest Service. - Fish and mussel geneticists, environmental non-governmental organizations. - The general public. Changes/Problems:None What opportunities for training and professional development has the project provided?M.S. candidate Sheila Harris and undergraduates Caitlin Miller and Maddie Johnson were trained in the project on population genetics of Striped Bass and Walleye. M.S. candidate Katie McBaine is receiving training in population genetics of Candy Darter. Ph.D. candidates Miluska Hyde and Alissa Ganser are receiving training on population genetics and evolution of several freshwater mussel species. Rebecca Bourquin received training on population genetics of Clinch Dace. How have the results been disseminated to communities of interest?The findings of these studies led to direct interactions with the Virginia Department of Game and Inland Fisheries, other state fisheries and wildlife management agencies, U.S. Fish and Wildlife Service, U.S.D.A.-Forest Service, and other aquatics professionals. The results of this body of research have been reported in scientific publications in peer-reviewed scientific journals - which this year includes Conservation Genetics. The publication audience is fisheries scientists and managers. Colleagues and I have made numerous presentations at meetings of scientists and fishery managers. I made presentations on finding regarding population genetics of Brook Trout in the southern Appalachian Mountains at the Eastern Trout VI workshop in Frostburg, MD in June, 2019 and at the meeting of the Virginia, West Virginia and Virginia Tech Chapters of the American Fisheries Society in Blacksburg, VA in February, 2019. Mentees or colleague Jess Jones made four presentations on population genetics and evolution of freshwater mussels with implications for management at the Biennial Symposium of the Freshwater Mollusk Conservation Society in San Antonio, TX in April, 2019, at the meeting of the Virginia, West Virginia and Virginia Tech Chapters of the American Fisheries Society in Blacksburg, VA, in February, 2019. Mentee Sheila Harris spoke about population genetic analysis of Striped Bass in the Roanoke River basin and mentee Rebecca Bourquin about fragmentation and genetic diversity in Clinch Dace at the meeting of the Virginia, West Virginia and Virginia Tech Chapters of the American Fisheries Society in Blacksburg, VA, February, 2019. A mentee of collaborator Tom Kwak spoke on work that he did in my laboratory on genetics of the endemic Carolina Madtom at the 148th Annual Meeting of the American Fisheries Society in Atlantic City, NJ in August, 2018. What do you plan to do during the next reporting period to accomplish the goals?While this is a final report for the current project, considerable work is ongoing. Next year, I expect to report the publication of several manuscripts in peer-reviewed scientific journals. Clinch Dace Chrosomus sp. cf. saylori is an undescribed species endemic to the Upper Clinch River Basin in Virginia. A graduate student co-supervised by colleague Don Orth and me is using genetic markers to characterize population genetic differentiation and to estimate the genetically effective sizes of several populations. Colleague Jess Jones and I have completed work with two of our graduate students describing discovery of cryptic mussel biodiversity in the genera Fusconaia, Pleurobema, and Pleuronaia using molecular phylogenetics and morphology. With colleagues Dave Hata (Virginia Tech) and Mike Eackles and Tim King (U.S. Geological Survey - Biological Resources Division), I expect to report data on population genetics and movement showing dispersal dynamics of Delaware Bay region horseshoe crabs. With a dozen colleagues in state and federal fisheries management agencies, I expect to report on patterns of regional population genetic differentiation in brook trout. With colleague Paul Angermeier (U.S. Geological Survey - Biological Resources Division), I expect to report results of a study using molecular genetic tools to identify larval fishes, with implications for identifying critical habitat for the threatened Roanoke logperch, Percina rex. One of my graduate students and I expect to product manuscripts describing population genetic differentiation for Walleye and Striped Bass, with implications for management of the species.
Impacts
What was accomplished under these goals?
The Commonwealth of Virginia has a rich aquatic fauna. While many of Virginia's aquatic species have stable populations, habitat alteration, invasive species, pollution, and other factors have led certain species to decline. The Virginia Department of Game and Inland Fisheries (VDGIF, 2011) listed 21 fishes, four amphibians, 50 mollusks, and four crustaceans as threatened or endangered within the Commonwealth. Conservation of Virginia's aquatic biodiversity in the face of development pressures (including dams, agricultural and industrial impacts, and water withdrawal) will require the development and implementation of scientifically justified management plans, a developmental process that often includes consideration of the results of genetic studies. The goal of this Hatch project was to develop and apply the tools of molecular genetics to resolve key issues facing the conservation of aquatic biodiversity in the Commonwealth of Virginia and the American southeast. The freshwater mussel Cumberland bean Venustaconcha troostensis and the Tennessee bean V. trabalis are endangered freshwater mussel species endemic to the Cumberland and Tennessee river basins, respectively. These species are closely related and very similar in appearance, and now exist only in small, fragmented populations relative to their historical abundances and distributions throughout the southeastern United States. Managers need to understand genetic differences among populations, so that informed decisions can be made to promote demographic and genetic viability of remaining populations. We conducted a population genetic analysis by assessing variation at eight nuclear DNA markers across 127 individuals. Our results showed five clusters of significantly differentiated clusters of populations across five rivers: V. trabalis in the Clinch, Obed-Emory, Holston, and Hiwassee rivers; and V. troostensis in the Cumberland river. Analyses of allele frequencies suggest that all populations likely have lost genetic diversity and are bottlenecked to various degrees. Estimates of recent-current genetically 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. The inferences we 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, we do not recommend interspecific mixing of individuals between the Cumberland and Tennessee River basins. Ongoing projects address population genetics of Walleye, Striped Bass, Candy Darter, and molecular genetic identification of larval darters.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Lane, T.W., E.M. Hallerman, and J.W. Jones. 2019. Population genetic assessment of two critically endangered freshwater mussel species, Tennessee bean Venustaconcha trabilis and Cumberland bean Venustaconcha troostensis. Conservation Genetics 20:759779.
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The direct target audiences for this work are professionals and fellow scientists that work at agencies that manage game fishes and non-game fishes and freshwater mussels or their critical habitats, including the Virginia Department of Game and Inland Fisheries, other state fisheries and wildlife management agencies, U.S. Fish and Wildlife Service, and U.S.D.A.-Forest Service. The results are of wider interest to fish and mussel geneticists, environmental non-governmental organizations, and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Joanne Davis Printz was trained under the Brook Trout project, and her work provided the basis for both her M.S. thesis and the related publication. Ph.D. candidate Corbin Hilling and undergraduate Skylar Wolf were trained in molecular genetics identification of non-indigenous suckers in the New River; S. Wolf received additional training on molecular genetic identification of larval darters. Ph.D. candidate Jane Argentina was trained in population genetics of variegate darter. M.S. candidates Bobby Cope (North Carolina State University) and Sheila Harris (Virginia Tech) and undergraduate Caitlin Miller (Virginia Tech) were trained in the project on population genetics of Carolina Madtom. M.S candidate Sheila Harris continues to work on population genetics of Walleye and Striped Bass. M.S. candidate Katie McBaine is receiving training in population genetics of Candy Darter. How have the results been disseminated to communities of interest?The findings of these studies led to direct interactions with the Virginia Department of Game and Inland Fisheries, other state fisheries and wildlife management agencies, U.S. Fish and Wildlife Service, U.S.D.A.-Forest Service, and other aquatics professionals. The results of this body of research have been reported in scientific publications in peer-reviewed scientific journals - which include Northeastern Naturalist, Invertebrate Systematics, and Freshwater Biology - and in a book, Biological Resources of Water. The publication audience is fisheries scientists and managers. Bobby Cope, a North Carolina State University M.S. candidate who worked in my laboratory, made oral presentations on the status, habitat, and genetics of the endemic Carolina Madtom at meetings of the North Carolina Chapter, Southern Division, and national American Fisheries Society. I made an oral presentation on timing of appearance and habitat use of larval darters in the upper Roanoke River basin at the Annual Meeting of the Virginia Chapter, American Fisheries Society, Fredericksburg, VA, February 20-22, 2018. Mentee Sheila Harris made an oral presentation on population genetics of Virginia walleye and mentee Katie McBaine on a preliminary assessment of within-stream movement patterns of Candy Darter in Virginia at that same meeting. I have had numerous discussions with fisheries scientists and managers in informal meetings at agency offices, at regional fisheries meetings, and elsewhere. What do you plan to do during the next reporting period to accomplish the goals?Considerable work is ongoing, and next year, I expect to report the publication of several manuscripts in peer-reviewed scientific journals. Clinch Dace Chrosomus sp. cf. saylori is an undescribed species endemic to the Upper Clinch River Basin in Virginia. A graduate student co-supervised by colleague Don Orth and me is using genetic markers to characterize population genetic differentiation and to estimate the genetically effective sizes of several populations. Colleague Jess Jones and I have completed work with two of our graduate students describing discovery of cryptic mussel biodiversity in the genera Fusconaia, Pleurobema, and Pleuronaia using molecular phylogenetics and morphology. We will also report results of a population genetic assessment of two critically endangered freshwater mussel species, Tennessee bean Venustaconcha trabilis and Cumberland bean V. troostensis. With colleagues Dave Hata (Virginia Tech) and Mike Eackles and Tim King (U.S. Geological Survey - Biological Resources Division), I expect to report data on population genetics and movement showing dispersal dynamics of Delaware Bay region horseshoe crabs.
Impacts
What was accomplished under these goals?
The New River in Virginia has a unique native fish community, with eight endemic species and several notable absences, including large suckers (Family Catostomidae) that occur elsewhere in the Ohio River basin. Two catostomid fishes were recently discovered in the New River. Using morphological and genetic characters, we identified these fishes as Quillback Carpsucker and Notchlip Redhorse. These fishes are seemingly established in Claytor Lake and dispersing into other reaches of the mainstem New River. We suspect that these species became established following bait-bucket introductions or incidentally during gamefish stockings. A widespread, common species, Variegate Darter 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 35 sites across their range in the 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. The pattern of population structuring suggests that 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. Instream barriers such as dams were not strong determinants of genetic structuring across the landscape or loss of genetic diversity, but reduce population connectivity and may impact long-term population persistence. The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of the freshwater mussels in North America. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined mitochondrial cytochrome oxidase I sequences from 110 currently recognized species to assess evolutionary relationships among pleurobeminid species. The results supported the evolutionary distinctiveness of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Further, the results revealed multiple instance where two species may actually be one, 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. There also may be unrecognized species, 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 formalized. Population genetic suggests distinct evolutionary significant units among southern and northern Appalachian Brook Trout. Before this was recognized, Brook Trout of northern origin were stocked throughout the southeast. We screened established allozyme markers among 56 southwest Virginia populations, and found 19 populations of southern, 5 of northern, and 32 of mixed genetic origin. Data compiled among published studies showed a sharp southern/northern break at the New/Roanoke-James watershed divide. We recommend that management of southern Appalachian Brook Trout include: 1) genetically cognizant planning of stocking, 2) management on a stream-by-stream basis, and 3) prioritized conservation of pure southern populations. Ongoing projects address population genetics of Walleye, Striped Bass, Carolina Madtom, Candy Darter, and molecular genetic identification of larval darters.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Hilling, C.D., S.L. Wolf, J.R. Copeland, D.J. Orth, and E.M. Hallerman. 2018. Occurrence of two non-indigenous catostomid fishes in the New River, Virginia. Northeastern Naturalist 25:215-221.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Inoue, K., D.M. Hayes, J.L. Harris, N.A. Johnson, C.L. Morrison, M.S. Eackles, T.L. King, J.W. Jones, E.M. Hallerman, A.D. Christian, and C.R. Randklev. 2018. The Pleurobemini (Bivalvia: Unionoida) revisited: DNA barcoding approaches reveal multiple undescribed species. Invertebrate Systematics 32:689-702.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Argentina, J.E., P.L. Angermeier, E.M. Hallerman, S.A. Welsh, and T.L. King. 2018. Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae). Freshwater Biology 63:1185-1198.
- Type:
Book Chapters
Status:
Published
Year Published:
2018
Citation:
Printz, J.E., J. Williams, and E.M. Hallerman. 2018. Genetic characterization of brook trout (Salvelinus fontinalis) populations at the zone of contact between southern and northern Appalachian lineages. Pages 55-73 in S. Ray, ed. Biological Resources of Water. InTech Publishing, Rijeka, Croatia. ISBN 978-1-78923-080-2.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:The direct target audiences for this work are professionals that work at agencies that manage game fishes and non-game fishes and freshwater mussels or their critical habitats, including the Virginia Department of Game and Inland Fisheries, Tennessee Wildlife Resources Agency, Kentucky Department of Fish and Wildlife Resources, U.S. Fish and Wildlife Service, and U.S.D.A.-Forest Service. The results are of wider interest to fish and mussel geneticists, environmental non-governmental organizations, and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Joanne Davis Printz was trained under the Brook Trout project, and her work provided the basis for both her M.S. thesis and the related publication. Undergraduate Pearce Cooper conducted the laboratory assays and gained molecular genetics experience in the study of chub nest associates, which contributed to the doctoral dissertation research of Brandon Peoples, who was supervised by colleague Dr. Emmanuel Frimpong. The survey of freshwater mussels was part of the M.S. thesis research of Daniel Schilling, whom I co-advised with Dr. Jess Jones. Field work for that study and for the toxicogenomic study was contributed by M.S. candidate Andrew Phipps. The findings of these studies led to direct interactions with the Virginia Department of Game and Inland Fisheries, the Tennessee Wildlife Resources Agency, the U.S. Fish and Wildlife Service, and other aquatics professionals. How have the results been disseminated to communities of interest?The results of this body of research have been reported in scientific publications in peer-reviewed scientific journals - which include Transactions of the American Fisheries Society and Southeastern Naturalist - and in two books, Freshwater Fish - Biology and Conservation (Y. Bozkurt, ed.) and Organismal and Molecular Malacology (S. Ray, ed.). The publication audience is fisheries scientists and managers. Former undergraduate research mentee Zach Moran made an oral presentation of "Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes" at the 147th Annual Meeting of the American Fisheries Society, Tampa, FL, August 20-24, 2017 and a poster presentation of that material at the 146th Annual Meeting of the American Fisheries Society, Kansas City, MO, August 21-25, 2016. Master's degree candidate and mentee Sheila Harris made an oral presentation, "Marker-assisted restoration of native New River walleye", and doctoral candidate (and mentee of colleague Dr. Don Orth) Corbin Hilling an oral presentation, "Catostomidae: The importance and challenges facing a forgotten family in the New River" at the New River Symposium, Radford, VA, May 16, 2017. I made an oral presentation, "Freshwater mussels exposed to arsenic and sulfate show contrasting patterns of gene expression" at the annual meeting of the Virginia and Virginia Tech Chapters of the American Fisheries Society, Lexington, VA, February 21-23, 2017. Doctoral mentee Miluska Hyde presented a poster, "Phylogenetic and experts' identification of "look-alike" freshwater mussel species belonging to the genera Fusconaia and Pleurobema in the Green River, Kentucky" at the annual meeting of the Freshwater Mussel Conservation Society, Cleveland, OH, March 26-30, 2017. I have had numerous discussions with fisheries scientists and managers in informal meetings at agency offices, at regional fisheries meetings, and elsewhere. What do you plan to do during the next reporting period to accomplish the goals?Considerable work is ongoing, and next year, I expect to report the publication of several manuscripts in peer-reviewed scientific journals. Clinch Dace Chrosomus sp. cf. saylori is an undescribed species endemic to the Upper Clinch River Basin in Virginia. A graduate student co-supervised by colleague Don Orth and me is using genetic markers to characterize population genetic differentiation and to estimate the genetically effective sizes of several populations. The New River in Virginia has a unique native fish community, with eight endemic species and several notable absences, including large suckers (Family Catostomidae) that occur elsewhere in the Ohio River basin. Two catostomid fishes were recently discovered in the New River. Using morphological and genetic characters, we identified these fishes as Quillback Carpsucker and Notchlip Redhorse. These fishes are seemingly established in Claytor Lake and dispersing into other reaches of the mainstem New River. We suspect that these species became established following bait-bucket introductions or incidentally during gamefish stockings. Freshwater mussels in the genera Fusconaia, Pleurobema, and Pleuronaia are similar in their external shell morphology, making classification of species within these genera difficult and leading to many taxonomic revisions. We collected mussels in these genera in the upper Tennessee River basin and analyzed mitochondrial ND1 and nuclear ITS1 DNA sequences to assess phylogenetic relationships. Nine species were phylogenetically distinct at ND1, including three unrecognized or cryptic species. Most species were distinct at the ITS1 region. Among morphological traits, differences in foot- color and gravidity characters showed differences between recognized species.
Impacts
What was accomplished under these goals?
Population genetic suggests distinct evolutionary significant units among southern and northern Appalachian Brook Trout. Before this was recognized, Brook Trout of northern origin were stocked throughout the southeast. We screened established allozyme markers among 56 southwest Virginia populations, and found 19 populations of southern, 5 of northern, and 32 of mixed genetic origin. Data compiled among published studies showed a sharp southern/northern break at the New/Roanoke-James watershed divide. We recommend that management of southern Appalachian Brook Trout include: 1) genetically cognizant planning of stocking, 2) management on a stream-by-stream basis, and 3) prioritized conservation of pure southern populations. Chubs (Family Cyprinidae, Genus Nocomis) build gravel mounds upon which they and other cyprinids spawn. We used visual surveys and DNA barcoding to identify cyprinids associated with chub nests in Catawba Creek in the James River system. We sequenced the mitochondrial cytochrome oxidase I - region 3 gene of individual larvae and compared DNA sequences to entries in GenBank. Central Stoneroller and Rosyside Dace had not been witnessed spawning on those nests. While Central Stoneroller was a known egg predator, identification of its larvae indicates spawning activity as well. We surveyed the freshwater mussels of Little River, Tennessee, to determine species diversity and relative abundances. Among the extant mussels were two federally endangered species, Fusconaia cuneolus, and Pleuronaia dolabelloides, and other mussels considered imperiled globally. We collected 319 individuals of a putative new species, Pleurobema sp. cf. oviforme, at nine sites, and 857 individuals of a putative new species, Villosa sp. cf. iris, at nine sites. These putative species may be endemic to the Little River. The Clinch and Powell rivers of Virginia have been heavily impacted by coal mining, processing, and use. We exposed Pheasantshells Actinonaias pectorosa to arsenate (As(V)) or sulphate for 28 days and compared gene expression in digestive gland among control and contaminant-exposed individuals. Arsenate and sulfate induced statistically significant up- or down-expression of different suites of 50-100 genes, showing proof-of-principle for using "RNAseq" technology to study toxicogenomics in freshwater mussels.
Publications
- Type:
Book Chapters
Status:
Accepted
Year Published:
2017
Citation:
Printz, J.E., J. Williams, and E.M. Hallerman. In press. Genetic characterization of brook trout (Salvelinus fontinalis) populations at the zone of contact between southern and northern Appalachian lineages. In Y. Bozkurt, ed. Freshwater Fish - Biology and Conservation. InTech Publishing, Rijeka, Croatia. ISBN 978-953-51-5600-0.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Peoples, B.K., P. Cooper, E. Hallerman, and E.A. Frimpong. 2017. DNA barcoding elucidates cyprinid reproductive interactions in a southwest Virginia stream. Transactions of the American Fisheries Society 146:84-91.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Schilling, D.E., J.W. Jones, E.M. Hallerman, and A.T. Phipps. 2017. A survey of freshwater mussels (Unionidae) in Little River, Blount County, Tennessee. Southeastern Naturalist 16:105-116.
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Michalak, P., L. Kang, S. Ciparis, W. Henley, J. Jones, A. Phipps, and E. Hallerman. 2017. Freshwater mussels exposed to arsenic and sulfate show contrasting patterns of gene expression. Pages 99-117 in: S. Ray, ed., Organismal and Molecular Malacology, InTech Publishing, Rijeka, Croatia. ISBN 978-953-3305-6.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:The direct target audiences for this work are professionals that work at agencies that manage game fishes and non-game fishes and freshwater mussels or their critical habitats, including the Virginia Department of Game and Inland Fisheries, Tennessee Wildlife Resources Agency, Kentucky Department of Fish and Wildlife Resources, U.S. Fish and Wildlife Service, and U.S.D.A.-Forest Service. The results are of wider interest to fish and mussel geneticists, environmental non-governmental organizations, and the general public. Changes/Problems:None. What opportunities for training and professional development has the project provided?M.S. graduate Michael Moore was trained on the Clinch dace project, and his work was the basis for his M.S. thesis, and several scientific manuscripts. M.S. candidate Tim Lane was trained on the Cumberland and purple bean project; his thesis and two other manuscripts are in progress. Ph.D. graduate Jamie Roberts was trained on the Roanoke logperch project, resulting in his dissertation and several scientific papers. Ph.D. graduate Anne Timm was trained on the brook trout project, resulting in her dissertation and several scientific papers. The DNA barcoding project resulted in the training of undergraduate Zach Moran, M.S. candidate Jason Emmel, and Ph.D. candidate Joe Schmidt, resulting in two scientific papers and contributing to Joe's dissertation research. All of these projects led to interactions with state agencies (most notably the Virginia Department of Game and Inland Fisheries) and federal agencies (U.S. Fish and Wildlife Service, USDA-Forest Service). How have the results been disseminated to communities of interest?The results of this body of research have been reported in scientific publications in Conservation Genetics, Ecology of Freshwater Fish, and two in Environmental Biology of Fish. The publication audience is fisheries scientists and managers. M.S. degree candidate Michael Moore made an oral presentation, "The onion or the silver bullet: eDNA trials for Clinch Dace detection" at the U.S. Forest Service Southern Division Aquatics Meeting in Asheville, NC on November 4, 2015. He also presented a poster, "Development of environmental DNA protocols for detecting occurrence of imperiled daces (Genus Chrosomus) in Virginia", at the meeting of the Virginia and North Carolina Chapters of the American Fisheries Society in Danville, VA, March 15-17, 2016. Undergraduate Zach Moran presented a poster, "Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes" at the 146th Annual Meeting of the American Fisheries Society in Kansas City, MO, August 21-25, 2016. I have had numerous informal discussions with fisheries scientists and managers at regional fisheries meetings and elsewhere. What do you plan to do during the next reporting period to accomplish the goals?Considerable work is ongoing, and next year, I expect to report the publication of several manuscripts in peer-reviewed scientific journals. Two projects pertain to use of DNA barcoding and will be used to determine the species of hard-to-identify material.Colleague Emmanuel Frimpong and I are supervising twostudents, whocollect impossible-to-identify larval fishes from the gravel nests of chubs in a southwest Virginia stream. The resultsshow that in addition to the offspring of the male chub that built the nest, there arelarvae of several other species, including some that are not observed spawning there. In another study, colleague Don Orth and I are supervising threestudents who collected partially digested stomach contents from a now-larger number of invasive catfishes in the Atlantic slope Rivers of Virginia. We are applying DNA barcoding to identify the species that the catfishes preyed upon and determining whetherthese invasive catfishes are likely to have an adverse impact upon native fishes. While it is known that the freshwater mussel fauna of the Southeast is highly diverse, we still have not fully characterized it. Colleague Jess Jones and I are supervising two graduate students who are carryingout a survey of freshwater mussels (Unionidae) in the Little River in Blount County, Tennessee. Among the mussels collected are two putatively new species, Pleurobema sp. cf. oviforme and Villosa sp. cf. iris; observation of genetic differentiation from known species is critical in recognizing their novelty. Clinch Dace, Chrosomus sp. cf. saylori is an undescribed species endemic to the Upper Clinch River Basin in Virginia. A graduate student supervised by colleague Don Orth andI are usinggenetic markers to estimate the genetically effective sizes of several populations, noting that at least some populatiosare likely too small to prove viable over the long term.
Impacts
What was accomplished under these goals?
Colleague Don Orth and I supervised a Master's degree candidate who developed and tested protocols for indirectly detecting the occurrence of the imperiled Clinch Dace Chrosomus sp. cf. saylori and Tennessee Dace C. tennesseensis based on the presence of their DNA within water samples collected from streams of interest. The set of assays amplifies the mitochondrial cytochrome b and cytochrome oxidase I genes. The amplified DNA is subjected to DNA sequencing to confirm and identify the Chrosomus species present in the stream of interest. Our primers and eDNA protocols showed high sensitivity of detection (to 7.9 x 10-4 nanograms per microliter) in laboratory serial dilution studies. Assays of water samples from Southwest Virginia streams showed true-positive detection in 73% of cases for Clinch dace, but only 33% for Tennessee Dace. Inadequate understanding of the species-level diversity and distributions of two critically imperiled freshwater mussels, Cumberland bean and purple bean, has hindered management and recovery actions. Colleague Jess Jones and I supervised a Master's degree candidate student who analyzed variation among 140 individuals collected from 10 streams in Virginia, Tennessee, and Kentucky, representing all known extant populations of each species. A section of the mitochondrial ND1 gene was sequenced. Results showed two distinct species, one in the Cumberland River basin and one in the Tennessee River basin. Updates to scientific names and recovery plans for the species are needed. A doctoral candidate, supervised by colleague Paul Angermeier and myself, used microsatellite DNA marker data to characterize dispersal patterns and genetically effective population size (Ne) for a population of Roanoke logperch, an endangered darter. Juveniles and candidate parents were sampled for two years at sites throughout the Roanoke River watershed. Estimates of Ne varied from 105 to 1218 individuals, depending on the estimation method. Model-based estimates of median lifetime dispersal distance (6-24 km, depending on assumptions) suggest that darters and other small benthic stream fishes are unexpectedly mobile. Monitoring and management of such populations should encompass entire watersheds to fully capture population dynamics. The effects of barriers to fish movement and human-mediated passage have not been investigated empirically at a landscape scale. We screened variation at eight microsatellite DNA loci within and among brook trout populations above and below putative natural barriers ranging in height from 1.4 to 61.0 meters, in 10 streams. We observed significant relationships between barrier height and metrics of inter-individual relatedness and population genetic differentiation. Gene flow was apparent across greater height barriers than the previously documented 0.74 m. This finding will affect prioritization of which culverts and stream crossings require replacement. In work done to develop molecular genetic tools for applications in fisheries management, colleague Don Orth and I supervised three students who evaluated DNA barcoding to identify piscine prey in the stomachs of invasive catfishes in Virginia's Atlantic slope rivers. Prey items of non-native blue and flathead catfishes were obtained by forcing the catfish to regurgitate them. We amplified the cytochrome oxidase I mitochondrial DNA gene, sequenced it, and compared the results to entries in GenBank. DNA barcoding resulted in identification of 88% of fish prey items overall. Diet items included anadromous striped bass, herrings, and shads that are the focus of fishery restoration programs in these rivers.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Lane, T.W., E.M. Hallerman, and Jess W. Jones. 2016. Phylogenetic assessment of the federally endangered Cumberland bean Villosa trabalis and purple bean Villosa perpurpurea. Conservation Genetics 17:1109-1124.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Roberts, J., P. Angermeier, E. Hallerman. 2016. Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data. Ecology of Freshwater Fish 25:1-16.
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Timm, A., E. Hallerman, C.A. Dolloff, M. Hudy, and R. Kolka. 2016. Identification of a barrier height threshold where brook trout population genetic diversity, differentiation, and relatedness are affected. Environmental Biology of Fishes 99:195-208.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Moran, Z., D. J. Orth, J. D. Schmitt, E.M. Hallerman, and R. Aguilar. 2015. Effectiveness of DNA barcoding for identifying piscine prey items in stomach contents of piscivorous catfishes. Environmental Biology of Fishes 99:161-167.
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:The direct target audiences for this work are agencies that manage rough pigtoe populations or their critical habitats, including the Kentucky Department of Fish and Wildlife Resources, Tennessee Wildlife Resources Agency, Alabama Department of Conservation, and the U.S. Fish and Wildlife Service. The results are of wider interest to fish and mussel geneticists, environmental non-governmental organizations, and the general public. Changes/Problems:With the help of colleagues with local knowledge, we were able to make collections of these rare species. Other colleagues allowed us access to unpublished information that proved useful for cost-effective genetic characterization of population genetic variation in the target species. The laboratory work went forward smoothly, as did the data analysis. What opportunities for training and professional development has the project provided?Two Master's degree candidatesworked on this project and gained valuable training in molecular tools for analyses and information literacy. How have the results been disseminated to communities of interest?The results were communicated directly to key people at the U.S. Fish and Wildlife Service and states fisheries and wildlifemanagement agencies in thestates that have the species at issue. We have a manuscript in press in a peer-reviewed scientific journal. What do you plan to do during the next reporting period to accomplish the goals?We have a follow-up project on inference of the evolutionary history and identification of management units for other mussels in the Cumberlandian region of eastern North America.
Impacts
What was accomplished under these goals?
Conservation aims to protect the adaptive potential of a species in a changing ecological context; hence, focusing on the unit of evolution is critical. Accurate knowledge of spatial population structure is fundamental to understanding the demography and evolution of a species. We particularly need to understand the spatial scales over which populations are connected through dispersal and gene flow, the landscape features that regulate connectivity, and the resulting population boundaries. This knowledge informs management tasks including delineation of conservation units, assessment of population and metapopulation viability, and enhancement of landscape connectivity. This information is lacking for many freshwater mussels. The rough pigtoe Pleurobema plenum was listed as an endangered species in 1976. P. plenum is known to occur in only three locations in the United States: 1) the Green River and its tributary Barren River, Kentucky, 2) in the Tennessee River in Alabama and Tennessee, and 3) in the Clinch River, Tennessee. The species belongs to a complex of four morphologically similar-looking species, including Ohio pigtoe (Pleurobema cordatum), P. plenum, pyramid pigtoe (Pleurobema rubrum), and round pigtoe (Pleurobema sintoxia). A genetic study of the two largest remaining populations of P. plenum in the Green and Clinch rivers was initiated to answer two main questions: 1) within the P. cordatum species complex, are these species with highly similar shells phylogenetically distinct, and 2) are the two largest populations of P. plenum genetically differentiated? Answering the first question is central to resolving the conservation status of P. plenum; for example, if one or more members of the P. cordatum species complex are found to be genetically indistinguishable from P. plenum, conservation status may not be warranted. However, if P. plenum is a valid species, determining whether the two largest populations are genetically differentiated is important for recovery planning. Implementation of certain recovery strategies for P. plenum, such as release of propagated juvenile mussels and translocation of adult mussels to protected habitats, is contingent upon achieving a thorough understanding of the species' life history and population genetics. Together with biologists from the Kentucky Department of Fish and Wildlife Resources, U.S. Fish and Wildlife Service, and U.S. Geological Survey-Biological Resources Division (USGS BRD), we non-lethally collected mussel mantle tissue samples. Mitochondrial DNA (mtDNA) sequences from the first subunit of NADH dehydrogenase (ND1) were amplified by polymerase chain reaction (PCR) and sequenced. Phylogenetic analysis was conducted to assess genetic distinctiveness of DNA sequence haplotypes of P. plenum relative to those of P. cordatum, P. rubrum, and P. sintoxia. PCR amplification products containing microsatellite loci were examined for size polymorphism using an automated DNA sequencer. Genetic variability across microsatellite loci for populations of P. plenum and P. cordatum was quantified and patterns of genetic differentiation assessed. Phylogenetic analysis of mitochondrial ND1 DNA sequences showed that all investigated species of Pleurobema are genetically distinct. Our results indicated that P. cordatum, P. plenum, P. rubrum, and P. sintoxia each represent distinct evolutionary lineages; however, the latter two species were closely related, separated by only one to three nucleotide differences. Further, DNA sequence variants from both populations of P. plenum grouped together into one evolutionary lineage, which did not support characterization of the two populations as separate species. Thus, our phylogenetic analysis confirms that populations of P. plenum in the Clinch and Green rivers are the same species. We assessed genetic differentiation between P. plenum populations in each river by analyzing variation at eight nuclear DNA microsatellite loci, and metrics of population-level differences indicated genetically differentiated populations. Because these populations are geographically and demographically independent, and differentiated at nuclear microsatellite loci, we recommend their recognition as distinct management units. Additional studies are needed to determine whether there are differences at adaptive or life-history traits, such as fish host usage, shell morphology, and soft anatomy between populations, and to further investigate the phylogenetic relationship of P. rubrum and P. sintoxia.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2015
Citation:
Jones, J.W., N. Johnson, P. Grobler, D. Schilling, R.J. Neves, and E.M. Hallerman. 2015. Assessment of phylogenetic status and genetic differentiation of two geographically isolated populations of the endangered rough pigtoe pearlymussel in the Ohio River Basin, U.S.A. Journal of Fish and Wildlife Management, in press.
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Progress 04/01/14 to 09/30/14
Outputs
Target Audience: The direct target audiences for this work are agencies that manage Roanoke logperch populations or their critical habitats, including the Virginia Department of Game and Inland Fisheries, the North Carolina Wildlife Resources Commission, the U.S. Fish and Wildlife Service and the U.S. Forest Service. The results are of wider interest to fish geneticists, environmental non-governmental organizations, and the general public. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? James Roberts was a post-doctoral fellow whose population genetics work within this study was supervised jointly by Dr. Angermeier and myself. Dr. Roberts is now a faculty member at Georgia Southern University. How have the results been disseminated to communities of interest? The report was published in the peer-reviewed literature and associated reports were diseminated to the Virginia Department of Game and Inland Fisheries, the North Carolina Wildlife Resources Commission, the U.S. Fish and Wildlife Service, and the U.S. Forest Service. Presentations were made at relevant scientific meetings of the American Fisheries Society and the Southeastern Fishes Council. What do you plan to do during the next reporting period to accomplish the goals? Other reports are in pending preparation forRoanoke logperch, other freshwater fishes, and freshwater molluscs.
Impacts
What was accomplished under these goals?
Conservation aims to protect the adaptive potential of a species in a changing ecological context; hence, focusing on the unit of evolution is critical. Accurate knowledge of spatial population structure is fundamental to understanding the demography and evolution of a species. We particularly need to understand the spatial scales over which populations are connected through dispersal and gene flow, the landscape features that regulate connectivity, and the resulting population boundaries. This knowledge informs management tasks including delineation of conservation units, assessment of population and metapopulation viability, and enhancement of landscape connectivity. This information is lacking for many stream-dwelling fish species. Against this background, we investigated the spatial scale and environmental determinants of population structure in Roanoke logperch Percina rex, an endangered, warmwater stream fish. Its dispersal and spatial population structure are poorly understood, which typifies members of the darter subfamily, a disproportionately imperiled group of fishes. P. rex is endemic to the Roanoke, Dan and Nottoway river basins of Virginia and North Carolina. Occupied watershed are separated by long, unoccupied and potentially uninhabitable stream reaches, major hydroelectric projects, or both. Recovery goals focus on monitoring and increasing population sizes, ensuring evolutionary viability and restoring population connectivity. Our objectives were to estimate the spatial scales over which P. rex populations are structured; test hypotheses about the environmental factors most responsible for generating structure, including geographic distance, fragmentation by hydroelectric projects and genetic drift; and discuss the implications for the ecology and conservation of stream fishes. Together with biologists from the Virginia Department of Game and Inland Fisheries and the North Carolina Wildlife Resources Commission, we made field collections of P. rex. DNA samples were collected from 578 fish across 35 sites; we genotyped samples at 11 microsatellite DNA loci. We conducted a thorough statistical analysis of genetic variation, including testing for departures from Hardy-Weinberg equilibrium and applying both classical and Bayesian clustering-based analyses of population structure. We used Bayesian generalized linear mixed models (BGLMMs) to test alternative hypotheses about the factors most responsible for generating spatial patterns of genetic differentiation among sites. Models employing clustering algorithms delineated seven discrete populations, whose boundaries coincided with agents of fragmentation, including hydroelectric dams and associated tailwaters. In the absence of hydrological barriers, gene flow was extensive throughout watersheds, while there was no evidence for contemporary dispersal between watersheds across such barriers. In the best-supported BGLMM, genetic differentiation was positively related to the spatial distance and degree of hydrological alteration between sites and negatively related to genetic diversity within sites. While the effect of tailwaters was equivocal, dams strongly influenced differentiation; the effect of a dam on genetic differentiation was comparable to that of a distance of over 750 miles of unimpounded river. Overall, the effect of distance-mediated dispersal was negligible compared to the combined effects of fragmentation and genetic drift. The contemporary population structure of P. rex comprises a few geographically extensive 'islands' that are fragmented by hydroelectric projects. This information clarifies the importance of a watershed-scale perspective on conserving the species and suggests that its recovery may require genetic and demographic reconnection of presently isolated populations. Our results inform management planning for P. rex by responsible public agencies. P. rex populations comprise seven management units. Should the species continue to decline, managers may want to target habitat improvements in some critical areas or promote gene flow into populations that have lost genetic variation, perhaps by translocation of individuals from other nearby populations. More generally, our results for P. rex suggest that, in the absence of hydrological barriers, benthic, non-migratory species can undertake surprisingly extensive gene flow. Conceptual models presuming restricted movement of such species need to be critically reexamined and further tested, and the spatial scale of monitoring and management activities adjusted accordingly. We also found that hydroelectric dams drastically accelerated genetic differentiation relative to historical, riverine connections; given the global ubiquity of hydroelectric projects, this finding has profound implications for fish conservation. We encourage others to conduct analogous analyses of population structure in other species, assess the influences of fragmentation agents such as dams and inhospitable habitat; and assess the consequences for persistence and evolution of stream fishes.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Roberts, J.H., D.J. Dutton, P.L. Angermeier, and E.M. Hallerman. 2013. Distance, dams, and drift: What structures populations of an endangered, benthic stream fish? Freshwater Biology 58:2050-2064.
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