Clayton Raines, PhD
Clay is a Fish Biologist at the USGS Eastern Ecological Science Center, National Fish Health Research Laboratory in Kearneysville, WV.
I am currently serving as Fish Biologist at the USGS National Fish Health Research Laboratory. I previously worked as a biologist with the WV DNR, as well as the Tennessee Aquarium Conservation Institute where I oversaw restoration and monitoring efforts for threatened and endangered freshwater species as well as conducted research on a variety of fisheries management topics. Additionally, I studied Southeast reservoir fish ecology and physiology as a graduate research assistant at Mississippi State University. I also completed a GIS internship with Jefferson County Planning and Zoning, as well as conducting research at The Conservation Fund’s Freshwater Institute and USDA Appalachian Fruit Research Station.
Professional Experience
October 2023-Current Employer: USGS - National Fish Health Research Lab Job Title: Fish Biologist
August 2019-Current Employer: USGS - National Fish Health Research Lab Job Title: Research Technician
February 2018-August 2019 Employer: West Virginia Division of Natural Resources Job Title: Fisheries Biologist
October 2017-January 2018 Employer: Critter Control Job Title: Wildlife Biologist
Education and Certifications
2020-2025: PhD, Fisheries Resource Management University: West Virginia University Morgantown, WV
2014-2017 Degree: MS Wildlife, Fisheries, and Aquaculture Sciences University: Mississippi State University Starkville, MS
2008-2013 Degree: Honors BS, Biology-Ecological Science University: Shepherd University Shepherdstown, WV
Affiliations and Memberships*
WV Chapter of the American Fisheries Society- Secretary/Treasurer
WV Health Science and Technology Academy- Research Coordinator
American Fisheries Society (AFS) – member
Early Career Professional Section- member
Marine Fisheries Subsection -member
AFS Fish Culture Subsection- member
AFS Fish Health Subsection -member
Science and Products
Filter Total Items: 19
Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago
Here, we announce the complete genome of a previously undescribed papillomavirus from a betta fish, Betta splendens. The genome is 5,671 bp with a GC content of 38.2%. Variants were detected in public databases. This genome is most similar to papillomaviruses that infect sea bass (52.9 % nucleotide identity).
Authors
Lemar Blake, A. Carla Phillips-Savage, Esteban Soto, Christopher Oura, Arianne Brown-Jordan, Clayton D. Raines, Christopher B. Buck, Luke R. Iwanowicz
Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics
Current pollinator survey methods exhibit bias, require highly-trained practitioners, and are difficult to scale to large sample sizes. High-throughput sequencing of terrestrial eDNA could provide a complementary tool for studying pollinator communities, but eDNA methods have not been extensively evaluated. We conducted metagenetic analysis of whole arthropod community eDNA from 20...
Authors
Grace Avalos, Regina Trott, John Ballas, Chia Hua Lin, Clayton D. Raines, Deborah D. Iwanowicz, Karen Goodell, Rodney T. Richardson
Effects of hard water precipitates on early life stage brook trout Effects of hard water precipitates on early life stage brook trout
Brook trout (Salvelinus fontinalis) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an impediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if brook...
Authors
John Davidson, Brandon J. Keplinger, Clayton D. Raines, Curtis Crouse, CHristopher Goodchild
Evaluating brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation Evaluating brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation
Brook trout (Salvelinus fontinalis) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an im- pediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if...
Authors
John. Davidson, Clayton D. Raines, Curtis Crouse, CHristopher Goodchild, Brandon J. Keplinger
Comparison of microscopy and metabarcoding to identify pollen used by the critically endangered rusty patched bumble bee, Bombus affinis Comparison of microscopy and metabarcoding to identify pollen used by the critically endangered rusty patched bumble bee, Bombus affinis
Taxonomic analysis of pollen collected by bees can provide insights into their host plant use, providing information about the plant species selected for targeted conservation strategies. The two main identification approaches used are morphological analysis of pollen samples affixed to microscope slides (i.e., microscopic palynology) and molecular analysis of samples. Both methods are...
Authors
Michael P. Simanonok, Deborah D. Iwanowicz, Clayton D. Raines, Thomas J. Wood, Rufus Isaacs, Robert S. Cornman, Clint Otto
Reservoir diel water quality patterns relative to riparian shade Reservoir diel water quality patterns relative to riparian shade
Investigations into the effects of riparian shade on water quality have focused on streams, with less emphasis on natural lakes, and almost no attention given to reservoirs. In view of this gap, our objective was to assess diel water quality patterns in the nearshore zone of a reservoir and test whether diel patterns differed relative to the presence or absence of riparian shade. Light...
Authors
Leandro E. Miranda, C.D. Raines
Role of riparian shade on the fish assemblage of a reservoir littoral Role of riparian shade on the fish assemblage of a reservoir littoral
Research into the effects of shade on reservoir fish assemblages is lacking, with most investigations focused on streams. Unlike many streams, the canopy in a reservoir shades only a narrow fringe of water adjacent to the shoreline, and may not have the influential effect on the aquatic environment reported in streams. We compared fish assemblages between shaded and unshaded sites in a...
Authors
C. D. Raines, Leandro E. Miranda
Science and Products
Filter Total Items: 19
Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago Complete genome sequence of a novel papillomavirus in Siamese fighting fish (Betta splendens) from Trinidad and Tobago
Here, we announce the complete genome of a previously undescribed papillomavirus from a betta fish, Betta splendens. The genome is 5,671 bp with a GC content of 38.2%. Variants were detected in public databases. This genome is most similar to papillomaviruses that infect sea bass (52.9 % nucleotide identity).
Authors
Lemar Blake, A. Carla Phillips-Savage, Esteban Soto, Christopher Oura, Arianne Brown-Jordan, Clayton D. Raines, Christopher B. Buck, Luke R. Iwanowicz
Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics Prospects of pollinator community surveillance using terrestrial environmental DNA metagenetics
Current pollinator survey methods exhibit bias, require highly-trained practitioners, and are difficult to scale to large sample sizes. High-throughput sequencing of terrestrial eDNA could provide a complementary tool for studying pollinator communities, but eDNA methods have not been extensively evaluated. We conducted metagenetic analysis of whole arthropod community eDNA from 20...
Authors
Grace Avalos, Regina Trott, John Ballas, Chia Hua Lin, Clayton D. Raines, Deborah D. Iwanowicz, Karen Goodell, Rodney T. Richardson
Effects of hard water precipitates on early life stage brook trout Effects of hard water precipitates on early life stage brook trout
Brook trout (Salvelinus fontinalis) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an impediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if brook...
Authors
John Davidson, Brandon J. Keplinger, Clayton D. Raines, Curtis Crouse, CHristopher Goodchild
Evaluating brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation Evaluating brook trout egg and alevin survival at different temperatures in simulated karst environments with marl sedimentation
Brook trout (Salvelinus fontinalis) have been extirpated from many karst-geology streams in West Virginia; however, the causes are not fully understood. Specifically, the impact of calcareous precipitate (marl), which is common in hard-water environments, has not been evaluated as an im- pediment to juvenile survival. Accordingly, two lab-based studies were conducted to determine if...
Authors
John. Davidson, Clayton D. Raines, Curtis Crouse, CHristopher Goodchild, Brandon J. Keplinger
Comparison of microscopy and metabarcoding to identify pollen used by the critically endangered rusty patched bumble bee, Bombus affinis Comparison of microscopy and metabarcoding to identify pollen used by the critically endangered rusty patched bumble bee, Bombus affinis
Taxonomic analysis of pollen collected by bees can provide insights into their host plant use, providing information about the plant species selected for targeted conservation strategies. The two main identification approaches used are morphological analysis of pollen samples affixed to microscope slides (i.e., microscopic palynology) and molecular analysis of samples. Both methods are...
Authors
Michael P. Simanonok, Deborah D. Iwanowicz, Clayton D. Raines, Thomas J. Wood, Rufus Isaacs, Robert S. Cornman, Clint Otto
Reservoir diel water quality patterns relative to riparian shade Reservoir diel water quality patterns relative to riparian shade
Investigations into the effects of riparian shade on water quality have focused on streams, with less emphasis on natural lakes, and almost no attention given to reservoirs. In view of this gap, our objective was to assess diel water quality patterns in the nearshore zone of a reservoir and test whether diel patterns differed relative to the presence or absence of riparian shade. Light...
Authors
Leandro E. Miranda, C.D. Raines
Role of riparian shade on the fish assemblage of a reservoir littoral Role of riparian shade on the fish assemblage of a reservoir littoral
Research into the effects of shade on reservoir fish assemblages is lacking, with most investigations focused on streams. Unlike many streams, the canopy in a reservoir shades only a narrow fringe of water adjacent to the shoreline, and may not have the influential effect on the aquatic environment reported in streams. We compared fish assemblages between shaded and unshaded sites in a...
Authors
C. D. Raines, Leandro E. Miranda
*Disclaimer: Listing outside positions with professional scientific organizations on this Staff Profile are for informational purposes only and do not constitute an endorsement of those professional scientific organizations or their activities by the USGS, Department of the Interior, or U.S. Government