@article{cope_kwak_black_pacifici_harris_miller_raley_hallerman_2021, title={Genetic Structure and Diversity of the Endemic Carolina Madtom and Conservation Implications}, volume={41}, ISSN={["1548-8675"]}, url={https://doi.org/10.1002/nafm.10589}, DOI={10.1002/nafm.10589}, abstractNote={AbstractIdentification and conservation of genetic diversity within and among freshwater fish populations are important to better manage and conserve imperiled species. The Carolina Madtom Noturus furiosus is a small, nongame catfish that is endemic to the Tar and Neuse River basins of North Carolina. Genetic structure has not been studied in the species, and given recent population declines in both basins, identification of remaining genetic diversity within the species is vital for informing conservation efforts. To assess the status and trends of Carolina Madtom genetic structure, we analyzed genetic markers from 173 individuals to (1) define population genetic structure, (2) assess intra‐ and interbasin genetic differentiation in the Tar and Neuse River basins, and (3) present management implications to guide conservation efforts. Using 10 microsatellite primers developed for the related Yellowfin Madtom N. flavipinnis, we observed low genetic diversity in Carolina Madtoms. Genotype frequencies within samples were not in Hardy–Weinberg equilibrium, with a deficit of heterozygotes that could be due to family structure, inbreeding, or segregation of null alleles. Mean (±SD) M‐ratios for the Tar River (0.414 ± 0.117) and Neuse River (0.117 ± 0.102) basin collections indicated that both populations have experienced recent demographic bottlenecks, with that in the Neuse River basin population being more severe. Effective population size estimates for the respective populations were small, on the order of tens of individuals, driving low genetic diversity within populations. However, the multilocus population differentiation metrics  (mean ± SE = 0.135 ± 0.031) and DEST (0.125 ± 0.029) were significantly different from zero (P < 0.001), indicating significant genetic differentiation between the Tar and Neuse River basin populations. Our findings will inform managers on the status of genetic variation in the Carolina Madtom and will guide conservation toward protective listing and management decisions to maintain the viability of this important endemic species.}, number={S1}, journal={NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT}, publisher={Wiley}, author={Cope, W. Robert and Kwak, Thomas J. and Black, Tyler R. and Pacifici, Krishna and Harris, Sheila C. and Miller, Caitlin M. and Raley, Morgan E. and Hallerman, Eric M.}, year={2021}, month={Oct}, pages={S27–S41} }
 @article{raley_levine_bogan_2008, title={Hemolymph as a nonlethal and minimally invasive source for DNA for molecular systematic studies of freshwater mussels}, volume={14}, journal={Tentacle. The Newsletter of the IUCN/SSC Mollusc Specialist Group}, author={Raley, M. E. and Levine, J. F. and Bogan, A. E.}, year={2008}, pages={33–34} }
 @article{caldwell_raley_levine_2007, title={Mitochondrial Multiplex Real-Time PCR as a Source Tracking Method in Fecal-Contaminated Effluents}, volume={41}, ISSN={0013-936X 1520-5851}, url={http://dx.doi.org/10.1021/es062912s}, DOI={10.1021/es062912s}, abstractNote={Multiplex real-time PCR amplifying fecal mitochondrial DNA (mtDNA) combined with rapid, crude DNA preparations are promising additions to surface water source tracking methods. Amplification of eukaryotic mitochondrial DNA identifies the fecal source directly and can be used in conjunction with other intestinal microbial methods to characterize effluents. Species-specific primers and dual-labeled probes for human, swine, and bovine NADH dehydrogenase subunit 5 (ND5) genes were created for multiplex real-time PCR in feces and effluent slurries. The linear range of the multiplex assay was 10(2)-10(7) mtDNA copies for human, bovine, and swine effluent in combination (equal volumes). PCR amplification efficiencies for bovine, human, and swine mtDNA when assayed in combination were 93, 107, and 92% respectively. Linear regression correlation coefficients (r2) were 0.99 for all standard curves except for human mtDNA in combination (r2 = 0.95). Multiplex amplification of bovine, human, and swine mtDNA (ND5) exhibited no cross-reactions between the effluents from three species of interest. Also, no cross-reactions were observed with effluents of other vertebrates: sheep, goat, horse, dog, cat, Canada goose, broiler, layer, turkey, and tilapia. Performed as a blind test, the PCR operator was able to correctly identify all but two effluent challenge samples (10/12 or 83% correct) with no false positives (22/22 or 100% correct). The multiplex assay had a tendency to detect the species of highest mtDNA concentration only. Better detection of all three species in a combination of human, bovine, and swine effluents was accomplished by running each real-time PCR primer/ probe set singly. Real-time PCR detection limit was calculated as 2.0 x 10(6) mitochondrial copies or 0.2 g of human feces per 100 mL effluent. Some carry-over mtDNA PCR signal from consumed beef, but not pork, was found in feces of human volunteers.}, number={9}, journal={Environmental Science & Technology}, publisher={American Chemical Society (ACS)}, author={Caldwell, Jane M. and Raley, Morgan E. and Levine, Jay F.}, year={2007}, month={May}, pages={3277–3283} }
 @article{miller_fuller_gebreyes_lewbart_shchelkunov_shivappa_joiner_woolford_stone_dixon_et al._2007, title={Phylogenetic analysis of spring virema of carp virus reveals distinct subgroups with common origins for recent isolates in North America and the UK}, volume={76}, ISSN={["1616-1580"]}, DOI={10.3354/dao076193}, abstractNote={Genetic relationships between 35 spring viremia of carp virus (SVCV) genogroup Ia isolates were determined based on the nucleotide sequences of the phosphoprotein (P) gene and glycoprotein (G) genes. Phylogenetic analysis based on P gene sequences revealed 2 distinct subgroups within SVCV genogroup Ia, designated SVCV Iai and Iaii, and suggests at least 2 independent introductions of the virus into the USA in 2002. Combined P- and G-sequence data support the emergence of SVCV in Illinois, USA, and in Lake Ontario, Canada, from the initial outbreak in Wisconsin, USA, and demonstrate a close genetic link to viruses isolated during routine import checks on fish brought into the UK from Asia. The data also showed a genetic link between SVCV isolations made in Missouri and Washington, USA, in 2004 and the earlier isolation made in North Carolina, USA, in 2002. However, based on the close relationship to a 2004 UK isolate, the data suggest than the Washington isolate represents a third introduction into the US from a common source, rather than a reemergence from the 2002 isolate. There was strong phylogenetic support for an Asian origin for 9 of 16 UK viruses isolated either from imported fish, or shown to have been in direct contact with fish imported from Asia. In one case, there was 100% nucleotide identity in the G-gene with a virus isolated in China.}, number={3}, journal={DISEASES OF AQUATIC ORGANISMS}, author={Miller, O. and Fuller, F. J. and Gebreyes, W. A. and Lewbart, G. A. and Shchelkunov, I. S. and Shivappa, R. B. and Joiner, C. and Woolford, G. and Stone, D. M. and Dixon, P. F. and et al.}, year={2007}, month={Jul}, pages={193–204} }
 @inproceedings{cumbie_gerwig_lambeth_raley_mckeand_2004, title={Topgrafting loblolly pine to accelerate breeding and deployment of genetic gain in the southern US}, booktitle={Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future,  IUFRO Joint Conference of Division 2, Conference Proceedings}, author={Cumbie, W. P. and Gerwig, D. and Lambeth, C. C. and Raley, M. and McKeand, S.}, editor={Li, B. and McKeand, S.Editors}, year={2004}, pages={228} }