We screen molecular genetic markers – mostly mitochondrial DNA sequences and nuclear microsatellite DNA markers and analyze the frequencies of the variants within the context of applied population genetics, informing the management of fished or imperiled organisms. We work mostly with freshwater fishes and mussels, and sometimes also marine or terrestrial organisms as the opportunities arise. To gain a sense of what we are up to, here are profiles of our lab group members and their projects.


Developing tilapia broodstock for use in Ghana.
Gifty Anane-Taabeah is a doctoral candidate under the direction of Professor Emmanuel Frimpong and myself. Nile tilapia Oreochomis niloticus is the major aquaculture species of Ghana and West Africa. However, the aquaculture performance of regional strains has not been evaluated. Gifty will evaluate the performance regional stocks with regard to tolerance of high temperature, salinity, low dissolved oxygen, and growth rate. Review of the literature suggests that these targeted traits can be improved by selective breeding.

Alissa Ganser is a doctoral degree candidate under the direction of Jess Jones and myself. Alissa is  assessing the distribution, abundance, and genetic diversity of imperiled mussel species, Tennessee heelsplitter Lasmigona holstonia, Cumberland moccasinshell Medionidus conradicus and fluted kidneyshell Ptychobranchus subtentum. For conservation planning, we need information on the abundance and distribution of remaining populations, as well as genetic diversity within and genetic differentiation among them. With this information, we can identify ideal source populations within each basin and locations for conducting population management activities. The data also will help determine the status of L. holstonia and M. conradicus and assess the need for listing.

Miluska Olivera-Hyde is a doctoral degree candidate working under the direction of Jess Jones and myself. Her research relates to assessment of morphological and molecular genetic variation of difficult-to-identify mussel species belonging to the genera Fusconaia and Pleurobema in the Green River, Kentucky and other nearby tributaries of the Ohio River.  Morphological and genetic data are needed to improve accuracy of field survey identifications and make population genetic management decisions on augmentation, reintroduction and monitoring activities for these mussels, especially two federally listed endangered species, rough pigtoe (Pleurobema plenum) and clubshell (Pleurobema clava). Further, data will be used to help determine whether unrecognized or cryptic species reside in the river.

Clinch dace2
Miluska also is working on a collaborative project with Dr. Alex Silvis and Professor Mark Ford. The northern bat Myotis septentrionalis is an imperiled species. Females and young live in communal roosts, but little is known about them. Are the females related or unrelated. Were the young fathered by males nearby, or by males from the hibernacula from which the bats dispersed in the spring? We seek to answer these questions using molecular genetic markers from both the (maternally transmitted) mitochondrial and (biparentally transmitted) nuclear genomes.

 

Katie Ortiz is a Laboratory Technician working under the direction of Jess Jones and myself. The objective of his project is to develop captive spawning and long-term culture protocols for freshwater mussels in the genus Epioblasma. Genetic and reproductive behavior data are needed to adequately understand the conditions required to successfully condition and spawn Epioblasma mussels in captivity, as well as the genetic implications associated with long-term captive culture programs. In work done in the genetics lab, he will compare genetic variation of Epioblasma mussels among natal river populations, parental broodstock, and subsequent progeny.

Bourquin

Rebecca Bourquin is a master’s degree candidate coadvised by Professor Don Orth and myself. Clinch dace Chrosomus sp. cf. sailor is a colorful member of the minnow family that was discovered in 1998 in the Clinch drainage of Virginia. Clinch dace populations are small, and fragmented. Rebecca will characterize the ecology and population genetic differentiation of Clinch dace. The thrust of the project is to evaluate conservation options for actions including habitat protection/enhancement, translocations, and demographic enhancement.


Lab member Skylar Wolf  worked closely with Rebecca; his work with mitochondrial DNA markers will complement her work using microsatellite markers. Analysis of both datasets will contribute to definition of management units for this imperiled species.

Clinch dace2

Which fishes use chub mounds to spawn?
Stephen Floyd is a Master’s degree candidate working in my laboratory on the genetic portion of his research directed by Emmanuel Frimpong. Nest association is a communal spawning behavior among fishes in which individuals of one species (nest associates) deposit eggs in nests constructed by another species (the host). We are screening variation at the mitochondrial COI-3 gene marker to identify which minnow species spawn on the mounds built by chubs.

Sheila Harris is a master’s degree candidate working under my direction. Application of population genetics at the regional scale can define the most appropriate units for management of sportfishes. Sheila is conducting a baseline genetic assessment of striped bass populations in the Roanoke River drainage to inform genetically cognizant management of the species. She is assessing genetic differentiation among Walleye populations across the southeast.

Caitlin Miller is a freshman learning about population genetics while helping Sheila with her work.

Katie McBaine is a master’s degree candidate under the direction of Professor Paul Angermeier and myself. Candy darter Etheostomoa osburni is an imperiled New River drainage endemic. Her project evaluates population dynamics and population genetic differentiation to inform conservation planning; i.e., which populations might be sources or recipients for translocations or hatchery-based enhancement.

Candy Darter

Dr. Bruce J. Turner is Associate Professor Emeritus in Biology here at Virginia Tech. A member of the Virginia Tech community since 1978, Turner has published more than 80 peer-reviewed articles and book chapters on fish genetics in national and international journals. His focus is on evolutionary genetics, especially speciation and isolating mechanisms in fish populations, as well as genetics of clonal and self-fertilizing fishes. Through his retirement in 2011, he taught biological sciences courses that ranged from the sophomore to the graduate level. He mentored many undergraduate students in their individual research projects and served as major professor for nine doctoral students and eight master’s degree students.

Annual fish

Picture of Joe Buckwalter

Joe Buckwalter is a research scientist working with Paul Angermeier and me on ecology of imperiled stream fishes. A part of his work involves identifying stream reaches where the threatened Roanoke logperch spawns and the larval fish have their nursery areas. He collects larval percids with drift nets, and sequences the mitochondrial COI gene to identify them, an application of “DNA barcoding”. This work will contribute to conservation of the species and to better understanding of larval fish ecology.

Roanoke Logperch

Picture of Emily Thorne

Emily Thorne is a Mark Ford mentee who is studying the ecology of spotted skunks. She is executing a portion of her dissertation research on landscape genetics of the skunks in my lab.

Spotted Skunk

Picture of Brandon Semel

Brandon Semel is a doctoral candidate working with Sarah Karpanty on ecology of sifakas, a species of lemur living in northeastern Madagascar. Part of his work addresses the mating dynamics of the sifakas. Brandon isolates DNA from their scats and screens microsatellite DNA markers to assess relatedness within troops.

Caitlin Carey

Caitlin Carey is a research associate at the Conservation Management Institute who also works in our laboratory, especially on mussel-related projects. Ongoing work pertains to population genetic assessments of yellow lampmussel Lampsilis cariosa and alewife floater Utterbackia implicata.

Mussels

Hata

Horseshoe crab trawl survey.
Dr. David Hata is a research scientist working under my direction. In order to properly manage the horseshoe crab fishery, we need accurate information on the relative abundance levels and demographic trends of crab populations. This trawl survey project provides relative population abundance information required for proper multi-regional and multi-species management of the Mid-Atlantic horseshoe crab population.

Córrego Baixo - me collecting mussels

Eric Hallerman. Although I mostly administer research, I still enjoy the research itself, and get my hands dirty, both in the field (here collecting freshwater mussels in Brazil) and in the lab. I also do work on animal biotechnology policy.


Recent Work

Here are citations for recent publications to give you a sense of some of our recently completed projects involving lab alumni:

  • Moore, M.J., D.J. Orth, and E.M. Hallerman. 2018. Multi-metric conservation assessment for imperiled Clinch dace. Southeastern Fishes Council Proceedings. In press.
  • Bi, R., Y. Jiao, C. Zhou, and E. Hallerman. 2018. A Bayesian spatiotemporal approach to inform management unit appropriateness. Canadian Journal of Fisheries and Aquatic Sciences, in press. https://doi.org/10.1139/cjfas-2017-0526
  • Argentina, J.E., P.L. Angermeier, E.M. Hallerman, S.A. Welsh, and T.L. King. Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae). Freshwater Biology, in press. DOI: 10.1111/fwb.13106
  • Holliday, J.A., E. Hallerman, and D. Haak. Genotyping and sequencing technologies in population genomics. In: O.M. Rajora, ed. Population Genomics Concepts, Strategies, and Approaches. Springer, Berlin, in press.
  • 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 978-1-78923-081-9.<
  • Huang, Z., X. Song, E. Hallerman, D. Dong, T. Mao, and J. Zhai. 2018. Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system. Applied Microbiology and Biotechnology Express 8:17. doi: 10.1186/s13568-018-0551-1.
  • Li, Y., E.M. Hallerman, and Y. Peng. 2018. How can China prepare for the domestic cultivation of Bt maize? Trends in Food Science and Technology 73:87-88.
  • 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.
  • 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.
  • 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.
  • Cheng, F., S.B. Zhao, B.V. Schmidt, E.M. Hallerman, and S.G. Xie. 2017. Morphological but no genetic differentiation among fragmented populations of Hemiculter leucisculus (Actinopterygii, Cyprinidae) from a lake complex in the middle Yangtze, China. Hydrobiologia 809(1):185-200.
  • Moncrief, N.D., *J.H. Roberts, E.M. Hallerman, R.A. Van Den Bussche, and R.D. Dueser. 2017. Genetics of raccoons (Procyon lotor) in a naturally fragmented coastal landscape: evidence from mitochondrial and microsatellite DNA markers. Journal of Mammalogy 98(4):1137-1155.
  • Fonseca, F.S., R.R. Domingues, E.M. Hallerman, and A.W.S. Hilsdorf. 2017. Assessment of genetic diversity of imperiled Neotropical catfish and restoration genetics to prevent its extinction. Frontiers in Genetics 8:196. doi: 10:2289/gene2017.00196.
  • Okazaki, T.I., E. Hallerman, E. Kawakami de Resende, and A.W.S. Hilsdorf. 2017. Genetic characterization of Brycon hilarii (Characiformes) populations within the Pantanal, upper Paraguay River basin, Brazil using microsatellite markers. Journal of Ichthyology 57(3):434-444.