The genus Alasmidonta currently contains 12 species with 3 species presumed extinct. Six species ... more The genus Alasmidonta currently contains 12 species with 3 species presumed extinct. Six species of Alasmidonta occur in North Carolina, including the presumed extinct Alasmidonta robusta. Tissue samples from all taxa of living Alasmidonta species were included in a test of the monophyly of the genus and the relationships of the species using mitochondrial DNA sequences from cytochrome oxidase c subunit 1 (COI) and NADH dehydrogenase subunit (ND1). Alasmidonta (Prolasmidonta) heterodon and Alasmidonta (Pressodonta) viridis are significantly different from the rest of Alasmidonta and the two subgenera are elevated to generic level. Alasmidonta varicosa is split into two separate species as is A. viridis. Alasmidonta raveneliana is represented by two separate conservation units corresponding to the French Broad and Little Tennessee River drainages. Further work is needed to understand the variation in A. marginata between the upper Mississippi River basin and the Ohio River drainage p...
Blueback Herring Alosa aestivalis populations throughout the East Coast have declined precipitous... more Blueback Herring Alosa aestivalis populations throughout the East Coast have declined precipitously since the late 1980s and were listed as a Species of Concern in 2006 by the National Oceanic and Atmospheric Administration. Natural resource agencies are attempting to restore this species to viable and sustainable levels with fry stockings cultured in hatcheries. To evaluate the long-term contribution of stockings to populations, agencies need an accurate method to track these stocking efforts. Genetic parentage-based tagging is recognized as a feasible means of assessing hatchery contribution of stocked fish to rivers of interest. However, Blueback Herring lack a reliable set of genetic markers to conduct parentage-based tagging. To this end, we analyzed previously described microsatellites as well as new microsatellite markers identified through NextGeneration sequencing to create a suite of 14 Blueback Herring markers useful for parentage-based tagging. The markers were successfu...
Molecular phylogenetics and evolution, Jan 9, 2016
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsi... more Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. The present study presents the most comprehensive phylogeny of the most species rich Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Mol...
North American Journal of Fisheries Management, 2021
Identification and conservation of genetic diversity within and among freshwater fish populations... more Identification 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
Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Ouachit... more Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Ouachita River system in the Ouachita Highlands of Arkansas. Bruce Thompson first noted the distinctiveness of the new species from the nominal P. nasuta distributed in the White River and Arkansas River basins in his 1977 doctoral dissertation. The new species is delimited through morphological comparisons with P. nasuta and a phylogenetic analysis of the Percina subclade Swainia using two mitochondrial genes. More than 385 specimens were examined for the morphological comparisons, and 54 specimens were sampled for mitochondrial DNA sequencing. Percina brucethompsoni is distinguished from P. nasuta by a shorter snout, a broader and deeper head, six versus seven branchiostegal rays and specific patterns of lateral pigmentation on the side of the body. Phylogenetic analysis of DNA sequences sampled from two regions of the mitochondrial genome indicate that P. brucethompsoni is the sister species of P. nasuta populations in the White River drainage. Neither P. nasuta nor P. phoxocephala are monophyletic in the mitochondrial DNA gene tree. Specimens of P. phoxocephala from the Red River drainage are resolved as the sister lineage of a clade containing all other sampled populations of P. phoxocephala, P. brucethompsoni and P. nasuta. Percina nasuta and P. phoxocephala sampled from the Arkansas River drainage form a clade that is the sister lineage of a clade containing P. brucethompsoni and P. nasuta from the White River drainage.
North American Journal of Fisheries Management, 2021
Identification and conservation of genetic diversity within and among freshwater fish populations... more Identification 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 collec- tions 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 G0ST (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 conserva- tion toward protective listing and management decisions to maintain the viability of this important endemic species.
The “Carolina” Redhorse is a rare, undescribed member of genus Moxostoma (Catostomidae) restricte... more The “Carolina” Redhorse is a rare, undescribed member of genus Moxostoma (Catostomidae) restricted to the Pee Dee and Cape Fear drainages in North and South Carolina. R. E. Jenkins recognized the species in 1995 and proposed it as sister to the Golden Redhorse, M. erythrurum, a widely distributed species occurring in the Mobile, Mississippi, Great Lakes, and Hudson Bay drainages, as well as on the Atlantic slope in the James and Roanoke drainages with a probable introduction in the Potomac drainage. No similar form was known south of the Roanoke drainage prior to 1995. While the “Carolina” Redhorse shares several features allying it to the Golden Redhorse (e.g., shape of lips, breeding tuberculation, nuptial and non-nuptial colorations, and spawning behavior), several anatomical and fixed genetic differences attest to its distinctiveness and validity as a separate taxon. Since 1996, periodic intensive electroshocking surveys were conducted to refine knowledge of the range and age st...
This study illustrates the importance of identification of putative species or populations in the... more This study illustrates the importance of identification of putative species or populations in the process of speciation using both molecular and morphometric techniques. Despite apparent genetic divergence across the drainages, we have shown that our groupings do not hold distinct morphotypes. Even using CVA to try to determine which morphological features might be important for group identification did not elucidate any patterns. A lack of morphological distinction in the presence of genetic divergence could indicate evidence of one or more cryptic species or that stabilizing selection is driving the morphology of this group while the genes are becoming more and more divergent across these populations.
The genus Alasmidonta currently contains 12 species with 3 species presumed extinct. Six species ... more The genus Alasmidonta currently contains 12 species with 3 species presumed extinct. Six species of Alasmidonta occur in North Carolina, including the presumed extinct Alasmidonta robusta. Tissue samples from all taxa of living Alasmidonta species were included in a test of the monophyly of the genus and the relationships of the species using mitochondrial DNA sequences from cytochrome oxidase c subunit 1 (COI) and NADH dehydrogenase subunit (ND1). Alasmidonta (Prolasmidonta) heterodon and Alasmidonta (Pressodonta) viridis are significantly different from the rest of Alasmidonta and the two subgenera are elevated to generic level. Alasmidonta varicosa is split into two separate species as is A. viridis. Alasmidonta raveneliana is represented by two separate conservation units corresponding to the French Broad and Little Tennessee River drainages. Further work is needed to understand the variation in A. marginata between the upper Mississippi River basin and the Ohio River drainage p...
Blueback Herring Alosa aestivalis populations throughout the East Coast have declined precipitous... more Blueback Herring Alosa aestivalis populations throughout the East Coast have declined precipitously since the late 1980s and were listed as a Species of Concern in 2006 by the National Oceanic and Atmospheric Administration. Natural resource agencies are attempting to restore this species to viable and sustainable levels with fry stockings cultured in hatcheries. To evaluate the long-term contribution of stockings to populations, agencies need an accurate method to track these stocking efforts. Genetic parentage-based tagging is recognized as a feasible means of assessing hatchery contribution of stocked fish to rivers of interest. However, Blueback Herring lack a reliable set of genetic markers to conduct parentage-based tagging. To this end, we analyzed previously described microsatellites as well as new microsatellite markers identified through NextGeneration sequencing to create a suite of 14 Blueback Herring markers useful for parentage-based tagging. The markers were successfu...
Molecular phylogenetics and evolution, Jan 9, 2016
Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsi... more Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. The present study presents the most comprehensive phylogeny of the most species rich Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Mol...
North American Journal of Fisheries Management, 2021
Identification and conservation of genetic diversity within and among freshwater fish populations... more Identification 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
Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Ouachit... more Percina brucethompsoni, the Ouachita Darter, is described as a new species endemic to the Ouachita River system in the Ouachita Highlands of Arkansas. Bruce Thompson first noted the distinctiveness of the new species from the nominal P. nasuta distributed in the White River and Arkansas River basins in his 1977 doctoral dissertation. The new species is delimited through morphological comparisons with P. nasuta and a phylogenetic analysis of the Percina subclade Swainia using two mitochondrial genes. More than 385 specimens were examined for the morphological comparisons, and 54 specimens were sampled for mitochondrial DNA sequencing. Percina brucethompsoni is distinguished from P. nasuta by a shorter snout, a broader and deeper head, six versus seven branchiostegal rays and specific patterns of lateral pigmentation on the side of the body. Phylogenetic analysis of DNA sequences sampled from two regions of the mitochondrial genome indicate that P. brucethompsoni is the sister species of P. nasuta populations in the White River drainage. Neither P. nasuta nor P. phoxocephala are monophyletic in the mitochondrial DNA gene tree. Specimens of P. phoxocephala from the Red River drainage are resolved as the sister lineage of a clade containing all other sampled populations of P. phoxocephala, P. brucethompsoni and P. nasuta. Percina nasuta and P. phoxocephala sampled from the Arkansas River drainage form a clade that is the sister lineage of a clade containing P. brucethompsoni and P. nasuta from the White River drainage.
North American Journal of Fisheries Management, 2021
Identification and conservation of genetic diversity within and among freshwater fish populations... more Identification 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 collec- tions 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 G0ST (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 conserva- tion toward protective listing and management decisions to maintain the viability of this important endemic species.
The “Carolina” Redhorse is a rare, undescribed member of genus Moxostoma (Catostomidae) restricte... more The “Carolina” Redhorse is a rare, undescribed member of genus Moxostoma (Catostomidae) restricted to the Pee Dee and Cape Fear drainages in North and South Carolina. R. E. Jenkins recognized the species in 1995 and proposed it as sister to the Golden Redhorse, M. erythrurum, a widely distributed species occurring in the Mobile, Mississippi, Great Lakes, and Hudson Bay drainages, as well as on the Atlantic slope in the James and Roanoke drainages with a probable introduction in the Potomac drainage. No similar form was known south of the Roanoke drainage prior to 1995. While the “Carolina” Redhorse shares several features allying it to the Golden Redhorse (e.g., shape of lips, breeding tuberculation, nuptial and non-nuptial colorations, and spawning behavior), several anatomical and fixed genetic differences attest to its distinctiveness and validity as a separate taxon. Since 1996, periodic intensive electroshocking surveys were conducted to refine knowledge of the range and age st...
This study illustrates the importance of identification of putative species or populations in the... more This study illustrates the importance of identification of putative species or populations in the process of speciation using both molecular and morphometric techniques. Despite apparent genetic divergence across the drainages, we have shown that our groupings do not hold distinct morphotypes. Even using CVA to try to determine which morphological features might be important for group identification did not elucidate any patterns. A lack of morphological distinction in the presence of genetic divergence could indicate evidence of one or more cryptic species or that stabilizing selection is driving the morphology of this group while the genes are becoming more and more divergent across these populations.
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Papers by Morgan Raley