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Bonnie L. Brown
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VCU Ecological Genetics Laboratory

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Mailing Address (P.O. Box):
Department of Biology
Virginia Commonwealth University
P.O. Box 842012
Richmond, Virginia 23284-2012 USA                      
Voice: 804-828-1562 
Fax: 801-858-9492 
e-mail: BLBROWN@vcu.edu
Physical Mailing Address (Samples):
Ecological Genetics Laboratory
Rooms 327-329
Life Sciences Building
1000 West Cary Street
Richmond, Virginia 23284-2012

Research interests: conservation, ecological, and aquaculture genetics; vertebrate and invertebrate strain evaluation for aquaculture


Metagenomics: The EGL has a long history of investigating genetic material obtained directly from environmental samples. Major efforts have included quantification and assessment of human DNA in dust, detection and quantification of predators, parasites, and disease-causing organisms in heterogenous environmental backgrounds. We currently are studying the occurrence and control of human pathogens and HAB species in James River, influenza from environmental isolates, and Stylochus predation on newly set oysters. Recent studies have documented Kudoa and parasitic amoebae on fishes, Dermo and MSX in oysters, determining fate of Bacillus in soils, and quantification of functional and taxonomic diversity of nitrifying and denitrifying bacteria in estuarine sediments. Major collaborators on these projects include: T Cruz, RB Franklin, KM Kester, GC Garman, C Keeler, W Watson.

Oyster Nutrient Trading : We are working with VaTech to quantitatively determine the basis for calculating nutrient assimilation credits associated with commercial scale oyster cultivation. Major collaborators on this project include: SK Stephenson, D Bosch, L Shabman, C Tobias, M Piehler, L Land, R Pelz.

Conservation genetics: The primary goal of these studies is to document the dynamic genetic processes that characterize populations of managed species and to employ this knowledge in resource enhancement. Recent projects have examined molecular indicators of genetic variation to discern anthropogenic impacts on supplemented populations of American shad (Alosa sapidissima), populations of the endangered blackbanded sunfish (Eneacanthus chaetodon), genetic variation of white-tailed deer (Odocoileus virginianus), and Nile tilapia (Oreochromis niloticus). Other studies have documented genetic variation in mammal populations (northern flying squirrel, Glaucomys sabrinus, and red-backed vole, Clethrionomys gapperi).  Major collaborators on these projects include: B Arbogast, RJ Dyer, JM Epifanio, TP Gunter, J Dolan, T Christensen, JM Pagels, P Smouse, T King, Y Saad, D Schwab.

Aquaculture genetics: The primary goal of these studies is to promote domestication of aquaculture species (intensify selection without unintentional inbreeding) and appropriate supplementation (maintain high levels of genetic variation). Recent projects have evaluated efficiency of propagation-assisted restoration of American shad (Alosa sapidissima), gene mapping and QTL identification in eastern oyster (Crassostrea virginica), and gene mapping and QTL identification in yellow perch (Perca flavescens). Major collaborators on these projects include: Y Gao, JM Epifanio, TP Gunter, HP Wang, J Waters

Aquaculture: Performance evaluation of fishes and pre-domestic strains of oysters in local environments has been a focus since 1992. Major collaborators on these project include: AJ Butt, D Meritt, S Newton, KT Paynter.

Services to the industry and government: The EGL provides a number of services including genetic mixed stock analysis for estimating harvest composition, genetic biodiversity asssessment, and ploidy analysis by flow cytometry for adult and larval fish and shellfish (grass carp, black carp, striped bass and oysters).

Detecting Influenza in the environment

Yellow Perch microsatellite genotypes


Stylochus predation

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Blue Ribbon aquacultured oysters


Recent EGL Graduate Students:

Aaron W. Aunins, PhD
Colleen B. Higgins, PhD
Devon Kersten, MS
Alaina Campbell, MS

Current EGL Graduate Students:

FNU Vishakha
April Piggott

Kensey Barker

Courses: Environmental Science
BIOL 103
(u/grad non-science majors)
Biotechniques Laboratory
BIOL 300
(DNA Sequencing lab)
Conservation Biology
BIOL 510
(senior u/grad and graduate)
Ecological Genetics
BIOL 550
(senior u/grad and graduate)
Conservation Genetics
BIOL 650
Conservation Applications
BIOL 610



Old Dominion University 1989 Ph.D. Biological Oceanography
University of Alabama in Birmingham 1981 B.S. Biology

Professional Positions 

Virginia Commonwealth University 2009-present Associate Chair of Biology
Virginia Commonwealth University 2008-present Professor
Virginia Commonwealth University 1997-2008 Associate Professor
Virginia Commonwealth University 1991-1997 Assistant Professor
East Carolina University 1990-1991 Adjunct Assistant Professor and Research Scientist
Chesapeake Bay Institute 1987-1991 Assistant Research Scientist
Old Dominion University 1986-1988 Associate Investigator

Selected Recent Publications

Ashe K, Chiu W-L, Khalifa AM, Nicolas AN, Brown BL, DeMartino RR, Alexander CP, Waggener CT, Fischer-Stenger K, Stewart JK. 2011. Vesicular monoamine transporter-1 (VMAT-1) mRNA and immunoreactive proteins in mouse brain. Neuroendocrinology Letters. 32: 253-258.

Campbell AH, Meritt DW, Franklin RB, Boone EL, Nicely CT, Brown BL. 2011. Effects of age and composition of field-produced biofilms on oyster larval setting. Biofouling 27: 255-265.

Franklin RB, Campbell AH, Higgins CB, Barker MK, Brown BL. 2011. Enumerating bacterial cells on bioadhesive coated slides. Journal of Microbial Methods 87: 154-160.

Higgins CB, Stephenson K, Brown BL. 2011. Nutrient bioassimilation capacity of aquacultured oysters: quantification of an ecosystem service. Journal of Environmental Quality. 40:0271-277.

Kester KM, Toothman MH, Brown BL, Street WS, Cruz T. 2010. Recovery of environmental human DNA by insects. Journal of Forensic Science 55: 1545-1551.

Wang HP, Li L, Wallat G, Brown B, Yao H, Gao Z, Tiu L, O’Bryant P, Rapp D & MacDonald R. 2009. Evaluation of relative growth performance and genotype by environment effects for cross-bred yellow perch families reared in communal ponds using DNA parentage analyses. Aquaculture Research. 2009: 1-11.

Zhan A, Wang Y, Brown B, and Wang HP. 2009. Isolation and Characterization of Novel Microsatellite Markers for Yellow Perch (Perca flavescens). International Journal of Molecular Sciences. 10: 18–27.

Shrinivas K, Kester KM, Mitchell ADSS, Martin PAW, & Brown BL. 2008. Molecular markers to determine ecological fate of Bacillus thuringiensis subsp. kurstaki. Molecular Ecology Resources. Molecular Ecology Resources 8: 1145-1148.

Toothman MH, KM Kester, J Champagne, T Dawson Cruz, WS Street IV, & BL Brown. 2008. Characterization of human DNA in environmental samples. Forensic Science International. 178(1): 7-15.

Brown BL, Li L, Givens CB, Wang HP, Wallat GK, & Tiu LG. 2007. Genetic evaluation of six yellow perch broodstock groups. Aquaculture: 271: 142-151.

Li L, Wang HP, Givens CB, Czesny S, & Brown BL. 2007. Isolation and characterization of microsatellites in yellow perch(Perca flavescens). Molecular Ecology Notes: 7: 600-603.

Brown BL, Butt AJ, Shelton SW, Meritt D, & Paynter KT. 2005. Resistance of Dermo in eastern oysters, Crassostrea virginica (Gmellin), of North Carolina but not Chesapeake Bay heritage. Aquaculture Research 36: 1391-1399.

Brown BL, Butt AJ, Meritt D, & Paynter KT. 2005. Evaluation of resistance to Dermo in eastern oyster strains tested in Chesapeake Bay. Aquaculture Research 36: 1544-1554.

Webb SR, Garman GC, McIninch SP, Nerad TA, Peglar MT, Gillevet PM, & Brown BL. 2005. Etiology of ulcerative lesions of Atlantic menhaden (Brevoortia tyrannus) from James Rier, Virginia .  Parasitology Research 97: 358-366.

Rudd ML, Nicolas AN, Brown BL, Fischer-Stenger K, & Stewart JK. 2005. Peritoneal macrophages express the serotonin transporter. Journal of Neuroimmunology. 159: 113-118.

Kester, KM, Brown BL, Jackman J, Theodore M, Le H & Shanholtz L. 2004. Methods and molecular tools for analysis ofBW agents delivered by insect sentinels. Proceedings of the 2003 Joint Service s Scientific Conference on Chemical and Biological Defense Research.

Busch W-D N, Brown BL & Mayer GF. (Eds) 2003. Strategic guidance for implementing an ecosystem-based approach to fisheries management.  United States Dept. of Commerce, National Oceanic and Atmospheric Administration, NMFS, Silver Spring , MD   62pp.

Brown BL & Epifanio JM. 2003. Nuclear DNA. Chapter 6 in Genetic Principles and Practices for Fisheries Scientists.pp. 101-123, E.M. Hallerman editor. American Fisheries Society. Bethesda , Maryland .

Hallerman EM, Brown B & Epifanio J. 2003. Introduction to Fisheries Genetics Principles. Chapter 1 in Genetic Principles and Practices for Fisheries Scientists. pp. 3-20 E.M. Hallerman editor. American Fisheries Society. Bethesda , Maryland .

Ettinger MR, Webb SR, Harris SA, McIninch SP, Garman GC, & Brown BL. 2003. Distribution of free-living amoebae in James River, Virginia, USA. Parasitology Research 89: 6-15.

Jensen MK, Kester KM, Kankare M & Brown BL. 2002. Characterization of microsatellite loci in the parasitoid, Cotesia congregata (Say) [Hymenoptera]. Molecular Ecology Notes 346-348.

Webb SR, Garman GC, McIninch SP & Brown BL. 2002. Amoebae associated with ulcerative lesions of fish from tidal freshwater of the James River, Virginia. Journal of Aquatic Animal Health. 14: 68-76.

Anderson J, Webb S, Fischer R, Kester K, & Brown B. 2001. Baseline and in vivo photoluminescence of endospore material using the parasitoid wasp C. congregata. Applied Spectroscopy, 55: 684-689.

Schultz SLW, Steinkoenig EL & Brown BL. 2001. Ploidy of feral grass carp in the Chesapeake Bay watershed. N. Amer. Jouranl of Fish Management 96-101.

Couch CR, Waters JM, Pagels JF & Brown BL. 2001. Genetic structuring of relict populations of the red-backed vole (Clethrionomys gapperi). J. Mammal. 82: 152-164.

Brown BL, Franklin DE, Gaffney P, Hong M, DenDanto D & Kornfield I. 2000. Characterization of microsatellite loci useful in ecological and aquaculture genetics of oysters. Molecular Ecology 9: 2217-2219.

Brown BL, Schultz SLW, & White FKH. 2000. A convenient field method of tissue preservation for flow cytometric ploidy assessment of grass carp. Transactions of the American Fisheries Society 129: 1354-1359.

Butt AJ & Brown BL. 2000. The cost of nutrient reduction: a case study of Chesapeake Bay. Coastal Management. 28: 175-185.

Day JM, Franklin DE & Brown BL. 2000. Use of competitive PCR to detect and quantify Haplosporidium nelsoni infection (MSX disease) in the eastern oyster, Crassostrea virginica. Molec. Mar. Biol. 2: 456-465.

Waters J, Epifanio J, Gunter T & Brown B. 2000. Homing behaviour facilitates subtle population differentiation among river populations of Alosa sapidissima: microsatellites and mtDNA. J. Fish Biol. 56: 622-636.

Brown B, Gunter T, Waters J, & Epifanio J. 2000. Evaluating genetic diversity associated with propagation-assisted restoration of American shad. Conservation Biology 14: 294-303.

Niculescu VA, Chinnici JP & Brown BL. 2000. Attitudes in physics education: an alternative approach to teaching physics to non-science college students. J. Math Sci. Collab. Explor. 3: 119-129.

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This page was last updated on   25 April 2012