Genetic variation and divergence among samples of Chilean hake Merluccius gayi, from three locali... more Genetic variation and divergence among samples of Chilean hake Merluccius gayi, from three localities off the coast of Chile and one locality off the coast of northern Peru, were assessed using sequences from the control region of mitochondrial DNA. Homogeneity tests revealed occurrence of at least three distinct genetic stocks of M. gayi within the region sampled. Factors potentially contributing to genetic divergence among M. gayi probably include hydrodynamics and behaviour.
-Genome sizes (nuclear DNA contents) were documented spectrophotometrically for 29 species of Nor... more -Genome sizes (nuclear DNA contents) were documented spectrophotometrically for 29 species of North American cyprinid fishes. The data were then merged with comparable genome size data (published previously) from an additional 20 North American cyprinid species. The distributions of DNA values within populations of the 49 cyprinid species were essentially continuous and normal. The proportion of DNA which apparently is free to vary quantitatively within cyprinid populations appears to be between 4 and 5 % of the genome. The distribution of DNA values among cyprinid species was more-or-less continuous, with considerable overlap among species with intermediate DNA values. Analysis of the average genome size difference (distance) between individuals drawn from successive levels of evolutionary divergence indicated that: (i) the majority of genome size divergence in North American c prinids has occurred above the level of individuals within populations of species, and (ii) the degree of genome size divergence in the extremely speciose cyprinid genus Notropis is greater than that between species in other, less speciose cyprinid genera. The hypothesis that genome size change might be concentrated in speciation episodes was tested by comparing the means and variances of genome size difference (distance) between species in the cyprinid genus Notropis (a species-rich phylad) and the centrarchid (sunfish) genus Lepomis (a species-poor phylad). The ratios of mean distances and variances in the Notropis versus Lepomis comparisons were greater than unity, suggesting that changes in genome size in cyprinids may be correlated with speciation episodes. Whether or not genome size change in cyprinids occurs at speciation sensu strictu is problematic. The data suggest that separate facets or levels of the cyprinid genome may follow independent evolutionary paths. genome size (DNA content) / cyprinid fish / natural selection / speciation Résumé-Variation et évolution de la taille du génome chez les cyprinidés d'Amérique du Nord-La taille du génome (estimée par la quantité d'ADN nucléaire) de 29 espèces * Correspondence and reprints taille du génome (quantité d'ADN) / cyprinidés / sélection naturelle / spéciation
Spatial and temporal variation in recovery of hatchery-released red drum (Sciaenops ocellatus) wa... more Spatial and temporal variation in recovery of hatchery-released red drum (Sciaenops ocellatus) was assessed in nine bays and estuaries along the Texas coast. Sixteen nuclear-encoded microsatellites were used to identify a total of 167 hatchery-released fish among 4325 red drum sampled between the fall of 2006 and the spring of 2009; these were added to 41 recovered hatchery-released fish identified in a prior study of 1332 red drum sampled from Galveston and Aransas bays in the fall of 2005 and spring of 2006. Recovery of hatchery releases across bays and years ranged from 0.28% to 17.65%. Of the 208 recovered hatchery-released fish, 158 were age 0-1, 46 were age 1-2, and four fish were age 2-3. The distribution of recovered hatchery-released fish and wild fish differed significantly across sampling periods within and among bays or estuaries. Allelic richness in recovered hatchery-released fish was significantly lower than in both hatchery brood fish and wild fish. In addition, recovered hatchery-released fish were produced by fewer dams, sires, and dam × sire combinations in 2005 and 2006 and by fewer dams and sires in 2007 than would be expected if reproductive success was distributed randomly among brood fish. The spatial distributions of recovered hatchery-released and wild fish deviated from random expectations for samples from the Upper Laguna Madre in the fall of 2006 and spring of 2007 and from West Matagorda Bay in the spring and fall of 2008. Correlation and principal components analysis identified a significant, positive relationship between annual average CPUE and relative annual mortality. No relationship was observed between the number of fish released per hectare and the percentage of recovered hatchery-released fish. Comparisons to other studies of red drum stock enhancement are discussed.
... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special ... more ... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special concern (Texas Wildlife Action Plan, http://www.tpwd.state.tx.us/publications/pwdpubs/ pwd_pl_w7000_1187a/) and is believed to be endemic to the Devils River, San Felipe Creek, ...
... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special ... more ... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special concern (Texas Wildlife Action Plan, http://www.tpwd.state.tx.us/publications/pwdpubs/ pwd_pl_w7000_1187a/) and is believed to be endemic to the Devils River, San Felipe Creek, ...
A total of 313 young-of-the-year red snapper (Lutjanus campechanus) belonging to the 1999 year cl... more A total of 313 young-of-the-year red snapper (Lutjanus campechanus) belonging to the 1999 year class were sampled from three geographic regions in the northern Gulf of Mexico and assayed for haplotype variation in mitochondrial (mt)DNA. Analysis of molecular variance revealed that only a small proportion (0.24%) of the genetic variance was distributed among regions; accordingly, the corresponding !lJ ST value did not differ significantly from zero. Exact tests of homogeneity of haplotype distributions also were non-significant. Tests for departure from a neutral Wright-Fisher model of genetic polymorphism, however, were significant, and a 'mismatch' distribution of nucleotide-site differences in mtDNA indicated that the departure from neutrality could be due to population expansion.
We have examined the chromosomes of four darter species (Percidae) from Texas and Louisiana: Perc... more We have examined the chromosomes of four darter species (Percidae) from Texas and Louisiana: Percina caprodes, P. nigrofasciata, P. sciera and Ammocrypta vivax. All four have diploid complements of 48 chromosomes. Estimates of diploid chromosome arm number among the four species varied from 80 (P. sciera) to 92 (P. caprodes and A. vivax) to 94 (P. nigrofasciata); but between two to five chromosome pairs in each species could not be unequivocally classified as either uni-armed or hi-armed. Percina sciera, which was scored as having the highest number (16) of uni-armed chromosomes, probably differs in gross karyotype from the other three, but the magnitude of difference may be less than indicated by our measurements.
A total of 2,206 base pairs of coding sequences of mitochondrial DNA from nine of 10 lutjanine (L... more A total of 2,206 base pairs of coding sequences of mitochondrial DNA from nine of 10 lutjanine (Lutjanidae) species endemic to the eastern Pacific Ocean were used in a phylogenetic analysis to infer species relationships among lutjanines on either side of the Isthmus of Panama. Monotypic Hoplopagrus (guentherii) appears to be at the base of all lutjanines assayed to date and represents the first of five, eastward dispersal events of lutjanines from the Indo-Pacific to the Americas. Diversification of lutjanines in the Americas appears to have occurred primarily in the western Atlantic Ocean (Caribbean Sea) and been aided by an early Miocene eastward-flowing current and by more optimal lutjanine habitat in the warmer Caribbean waters. Five geminate species pairs in five, strongly supported clades were identified. In three, the trans-isthmian geminate species in the eastern Pacific belonged to clades in which basal and other members of the clade are endemic to the western Atlantic, suggesting that the ancestor to each species geminate pair dispersed westward into the eastern Pacific prior to closure of connections between the two oceans; the opposite occurred in one of the clades. The fifth clade contained only two species, one on either side of the Isthmus. Diversification in life-history and other traits in each geminate species pair appears to have been slight. Five lutjanine species possessing horizontal blue stripes (the blue-lined complex) and distributed from the western Indian Ocean to the eastern Pacific formed a strongly supported monophyletic clade. The lone blue-lined species in the eastern Pacific (Lutjanus viridis) could be conspecific with its highly dispersive sister species (Lutjanus kasmira) from the Indo-Pacific. The chronology of lutjanine diversification and closure of seawater exchange between the two oceans is briefly discussed.
Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and ... more Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and recreational fisheries in U.S. waters, but has been overfished for at least the last 25 years. Successful rebuilding efforts and future management of these fisheries depend on accurate knowledge of genetic structure and connectivity among subpopulations or stocks. Failure to recognize existing genetic structure may lead to localized stock depletion, while defining patterns of connectivity is critical to understanding metapopulation dynamics and recruitment potential. The advent of next-generation sequencing technology has transcended fishery genetics from a simple approach (survey of a handful of genetic markers) to a complex genomics approach where thousands of loci across the genome can be assayed. Using restriction-site associated DNA tags (RAD tags), we surveyed variation in >3,000 single nucleotide polymorphisms (SNPs) from red snapper sampled at five geographic localities: three...
A genetic linkage map of anonymous and gene-linked microsatellites was generated for red drum, an... more A genetic linkage map of anonymous and gene-linked microsatellites was generated for red drum, an economically important sciaenid fish cultured for both restoration enhancement and commercial food-fish production. The consensus map, based on linkage data combined from two full-sib families, consisted of 486 total microsatellites (440 anonymous, 46 gene-linked), and spanned 24 linkage groups corresponding to the 24 (haploid) red drum chromosomes. The linkage map generated was used to identify regions of shared synteny between red drum and four other percomorph species for which genome assemblies are available. Considerable synteny was observed between red drum and all four comparison species, and a synteny-based mapping approach was used to putatively localize an additional 80 genes and monomorphic, gene-linked microsatellites within the red drum genome. The genetic linkage map will be a valuable resource for red drum aquaculture, particularly for candidate-gene approaches to identify and map quantitative trait loci.
Twenty-seven nuclear-encoded microsatellites were isolated from an enriched genomic library of ye... more Twenty-seven nuclear-encoded microsatellites were isolated from an enriched genomic library of yellowfin grouper, Mycteroperca venenosa, and characterized in 24 individuals. The microsatellites include 17 dinucleotide repeats, eight trinucleotide repeats (one imperfect), one tetranucleotide repeat, and one pentanucleotide repeat. Yellowfin grouper are susceptible to fishing pressure targeted towards their spawning aggregations; data pertaining to stock structure and levels of genetic variability will aid in future management of this species. KeywordsMicrosatellites–Yellowfin grouper– Mycteroperca venenosa
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for... more Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, wide...
Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-s... more Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-strand replication, displacing the parental H-strand as it proceeds along the molecule. The H-strand remains single stranded until light (L)-strand replication is initiated from a second origin of replication. It has been suggested that single-stranded H-strand DNA is more sensitive to mutational damage, giving rise to substitutional rate differences between the two strands and among genes in mammalian mitochondrial DNA. In this study, we analyzed sequences of the cytochrome b, ND4, ND4L, and COI genes of cyprinid fishes to investigate rates and patterns of nucleotide substitution in the mitochondrial genome. To test for strand-asymmetric mutation pressure, a likelihood-ratio test was developed and applied to the cyprinid sequences. Patterns of substitution and levels of strand-asymmetric mutation pressure were largely consistent with a mutation gradient between the H- and L-strand origin...
Genetic variation at ten microsatellite loci and one anonymous-nuclear locus was assayed for thre... more Genetic variation at ten microsatellite loci and one anonymous-nuclear locus was assayed for three geographic samples of the critically endangered North American cyprinid Notropis mekistocholas (Cape Fear shiner). Despite low abundance of this species, there was little suggestion of small population effects; allele diversity and hetero- zygosity were relatively high, FIS values within samples were non-significant, and genotypes were distributed
Twenty-six nuclear-encoded microsatellites were isolated from an enriched genomic library of sout... more Twenty-six nuclear-encoded microsatellites were isolated from an enriched genomic library of southern hake, Merluccius australis, and characterized in 30 individuals. The microsatellites include 18 dinucleotide repeats, seven trinucleotide repeats (two imperfect), and one pentanucleotide repeat. Southern hake support important industrial and artisanal fisheries in Chile, Argentina, and New Zealand.
The blacknose shark, Carcharhinus acronotus, is distributed in coastal waters of the western Atla... more The blacknose shark, Carcharhinus acronotus, is distributed in coastal waters of the western Atlantic Ocean from North Carolina to Brazil and is a component of both commercial and recreational fisheries throughout its range. In waters off of the United States, the species is managed as a component of the small coastal shark (SCS) complex. Concerns recently have arisen that blacknose
A total of 32 nuclear-encoded microsatellites, including 15 polymorphic and 13 monomorphic micros... more A total of 32 nuclear-encoded microsatellites, including 15 polymorphic and 13 monomorphic microsatellites, isolated from an enriched genomic library of the triakid shark, Mustelus canis (dusky smoothhound), and four microsatellites previously isolated from two other triakid sharks were characterized in 91 individuals of M. canis. Polymorphic repeat motifs included 12 dinucleotide, two trinucleotide and one pentanucleotide repeat(s). Mustelus canis supports
Genetic variation and divergence among samples of Chilean hake Merluccius gayi, from three locali... more Genetic variation and divergence among samples of Chilean hake Merluccius gayi, from three localities off the coast of Chile and one locality off the coast of northern Peru, were assessed using sequences from the control region of mitochondrial DNA. Homogeneity tests revealed occurrence of at least three distinct genetic stocks of M. gayi within the region sampled. Factors potentially contributing to genetic divergence among M. gayi probably include hydrodynamics and behaviour.
-Genome sizes (nuclear DNA contents) were documented spectrophotometrically for 29 species of Nor... more -Genome sizes (nuclear DNA contents) were documented spectrophotometrically for 29 species of North American cyprinid fishes. The data were then merged with comparable genome size data (published previously) from an additional 20 North American cyprinid species. The distributions of DNA values within populations of the 49 cyprinid species were essentially continuous and normal. The proportion of DNA which apparently is free to vary quantitatively within cyprinid populations appears to be between 4 and 5 % of the genome. The distribution of DNA values among cyprinid species was more-or-less continuous, with considerable overlap among species with intermediate DNA values. Analysis of the average genome size difference (distance) between individuals drawn from successive levels of evolutionary divergence indicated that: (i) the majority of genome size divergence in North American c prinids has occurred above the level of individuals within populations of species, and (ii) the degree of genome size divergence in the extremely speciose cyprinid genus Notropis is greater than that between species in other, less speciose cyprinid genera. The hypothesis that genome size change might be concentrated in speciation episodes was tested by comparing the means and variances of genome size difference (distance) between species in the cyprinid genus Notropis (a species-rich phylad) and the centrarchid (sunfish) genus Lepomis (a species-poor phylad). The ratios of mean distances and variances in the Notropis versus Lepomis comparisons were greater than unity, suggesting that changes in genome size in cyprinids may be correlated with speciation episodes. Whether or not genome size change in cyprinids occurs at speciation sensu strictu is problematic. The data suggest that separate facets or levels of the cyprinid genome may follow independent evolutionary paths. genome size (DNA content) / cyprinid fish / natural selection / speciation Résumé-Variation et évolution de la taille du génome chez les cyprinidés d'Amérique du Nord-La taille du génome (estimée par la quantité d'ADN nucléaire) de 29 espèces * Correspondence and reprints taille du génome (quantité d'ADN) / cyprinidés / sélection naturelle / spéciation
Spatial and temporal variation in recovery of hatchery-released red drum (Sciaenops ocellatus) wa... more Spatial and temporal variation in recovery of hatchery-released red drum (Sciaenops ocellatus) was assessed in nine bays and estuaries along the Texas coast. Sixteen nuclear-encoded microsatellites were used to identify a total of 167 hatchery-released fish among 4325 red drum sampled between the fall of 2006 and the spring of 2009; these were added to 41 recovered hatchery-released fish identified in a prior study of 1332 red drum sampled from Galveston and Aransas bays in the fall of 2005 and spring of 2006. Recovery of hatchery releases across bays and years ranged from 0.28% to 17.65%. Of the 208 recovered hatchery-released fish, 158 were age 0-1, 46 were age 1-2, and four fish were age 2-3. The distribution of recovered hatchery-released fish and wild fish differed significantly across sampling periods within and among bays or estuaries. Allelic richness in recovered hatchery-released fish was significantly lower than in both hatchery brood fish and wild fish. In addition, recovered hatchery-released fish were produced by fewer dams, sires, and dam × sire combinations in 2005 and 2006 and by fewer dams and sires in 2007 than would be expected if reproductive success was distributed randomly among brood fish. The spatial distributions of recovered hatchery-released and wild fish deviated from random expectations for samples from the Upper Laguna Madre in the fall of 2006 and spring of 2007 and from West Matagorda Bay in the spring and fall of 2008. Correlation and principal components analysis identified a significant, positive relationship between annual average CPUE and relative annual mortality. No relationship was observed between the number of fish released per hectare and the percentage of recovered hatchery-released fish. Comparisons to other studies of red drum stock enhancement are discussed.
... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special ... more ... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special concern (Texas Wildlife Action Plan, http://www.tpwd.state.tx.us/publications/pwdpubs/ pwd_pl_w7000_1187a/) and is believed to be endemic to the Devils River, San Felipe Creek, ...
... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special ... more ... Correspondent: evan.carson@tamu ... one of the species of Dionda considered to be of special concern (Texas Wildlife Action Plan, http://www.tpwd.state.tx.us/publications/pwdpubs/ pwd_pl_w7000_1187a/) and is believed to be endemic to the Devils River, San Felipe Creek, ...
A total of 313 young-of-the-year red snapper (Lutjanus campechanus) belonging to the 1999 year cl... more A total of 313 young-of-the-year red snapper (Lutjanus campechanus) belonging to the 1999 year class were sampled from three geographic regions in the northern Gulf of Mexico and assayed for haplotype variation in mitochondrial (mt)DNA. Analysis of molecular variance revealed that only a small proportion (0.24%) of the genetic variance was distributed among regions; accordingly, the corresponding !lJ ST value did not differ significantly from zero. Exact tests of homogeneity of haplotype distributions also were non-significant. Tests for departure from a neutral Wright-Fisher model of genetic polymorphism, however, were significant, and a 'mismatch' distribution of nucleotide-site differences in mtDNA indicated that the departure from neutrality could be due to population expansion.
We have examined the chromosomes of four darter species (Percidae) from Texas and Louisiana: Perc... more We have examined the chromosomes of four darter species (Percidae) from Texas and Louisiana: Percina caprodes, P. nigrofasciata, P. sciera and Ammocrypta vivax. All four have diploid complements of 48 chromosomes. Estimates of diploid chromosome arm number among the four species varied from 80 (P. sciera) to 92 (P. caprodes and A. vivax) to 94 (P. nigrofasciata); but between two to five chromosome pairs in each species could not be unequivocally classified as either uni-armed or hi-armed. Percina sciera, which was scored as having the highest number (16) of uni-armed chromosomes, probably differs in gross karyotype from the other three, but the magnitude of difference may be less than indicated by our measurements.
A total of 2,206 base pairs of coding sequences of mitochondrial DNA from nine of 10 lutjanine (L... more A total of 2,206 base pairs of coding sequences of mitochondrial DNA from nine of 10 lutjanine (Lutjanidae) species endemic to the eastern Pacific Ocean were used in a phylogenetic analysis to infer species relationships among lutjanines on either side of the Isthmus of Panama. Monotypic Hoplopagrus (guentherii) appears to be at the base of all lutjanines assayed to date and represents the first of five, eastward dispersal events of lutjanines from the Indo-Pacific to the Americas. Diversification of lutjanines in the Americas appears to have occurred primarily in the western Atlantic Ocean (Caribbean Sea) and been aided by an early Miocene eastward-flowing current and by more optimal lutjanine habitat in the warmer Caribbean waters. Five geminate species pairs in five, strongly supported clades were identified. In three, the trans-isthmian geminate species in the eastern Pacific belonged to clades in which basal and other members of the clade are endemic to the western Atlantic, suggesting that the ancestor to each species geminate pair dispersed westward into the eastern Pacific prior to closure of connections between the two oceans; the opposite occurred in one of the clades. The fifth clade contained only two species, one on either side of the Isthmus. Diversification in life-history and other traits in each geminate species pair appears to have been slight. Five lutjanine species possessing horizontal blue stripes (the blue-lined complex) and distributed from the western Indian Ocean to the eastern Pacific formed a strongly supported monophyletic clade. The lone blue-lined species in the eastern Pacific (Lutjanus viridis) could be conspecific with its highly dispersive sister species (Lutjanus kasmira) from the Indo-Pacific. The chronology of lutjanine diversification and closure of seawater exchange between the two oceans is briefly discussed.
Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and ... more Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and recreational fisheries in U.S. waters, but has been overfished for at least the last 25 years. Successful rebuilding efforts and future management of these fisheries depend on accurate knowledge of genetic structure and connectivity among subpopulations or stocks. Failure to recognize existing genetic structure may lead to localized stock depletion, while defining patterns of connectivity is critical to understanding metapopulation dynamics and recruitment potential. The advent of next-generation sequencing technology has transcended fishery genetics from a simple approach (survey of a handful of genetic markers) to a complex genomics approach where thousands of loci across the genome can be assayed. Using restriction-site associated DNA tags (RAD tags), we surveyed variation in >3,000 single nucleotide polymorphisms (SNPs) from red snapper sampled at five geographic localities: three...
A genetic linkage map of anonymous and gene-linked microsatellites was generated for red drum, an... more A genetic linkage map of anonymous and gene-linked microsatellites was generated for red drum, an economically important sciaenid fish cultured for both restoration enhancement and commercial food-fish production. The consensus map, based on linkage data combined from two full-sib families, consisted of 486 total microsatellites (440 anonymous, 46 gene-linked), and spanned 24 linkage groups corresponding to the 24 (haploid) red drum chromosomes. The linkage map generated was used to identify regions of shared synteny between red drum and four other percomorph species for which genome assemblies are available. Considerable synteny was observed between red drum and all four comparison species, and a synteny-based mapping approach was used to putatively localize an additional 80 genes and monomorphic, gene-linked microsatellites within the red drum genome. The genetic linkage map will be a valuable resource for red drum aquaculture, particularly for candidate-gene approaches to identify and map quantitative trait loci.
Twenty-seven nuclear-encoded microsatellites were isolated from an enriched genomic library of ye... more Twenty-seven nuclear-encoded microsatellites were isolated from an enriched genomic library of yellowfin grouper, Mycteroperca venenosa, and characterized in 24 individuals. The microsatellites include 17 dinucleotide repeats, eight trinucleotide repeats (one imperfect), one tetranucleotide repeat, and one pentanucleotide repeat. Yellowfin grouper are susceptible to fishing pressure targeted towards their spawning aggregations; data pertaining to stock structure and levels of genetic variability will aid in future management of this species. KeywordsMicrosatellites–Yellowfin grouper– Mycteroperca venenosa
Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for... more Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, wide...
Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-s... more Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-strand replication, displacing the parental H-strand as it proceeds along the molecule. The H-strand remains single stranded until light (L)-strand replication is initiated from a second origin of replication. It has been suggested that single-stranded H-strand DNA is more sensitive to mutational damage, giving rise to substitutional rate differences between the two strands and among genes in mammalian mitochondrial DNA. In this study, we analyzed sequences of the cytochrome b, ND4, ND4L, and COI genes of cyprinid fishes to investigate rates and patterns of nucleotide substitution in the mitochondrial genome. To test for strand-asymmetric mutation pressure, a likelihood-ratio test was developed and applied to the cyprinid sequences. Patterns of substitution and levels of strand-asymmetric mutation pressure were largely consistent with a mutation gradient between the H- and L-strand origin...
Genetic variation at ten microsatellite loci and one anonymous-nuclear locus was assayed for thre... more Genetic variation at ten microsatellite loci and one anonymous-nuclear locus was assayed for three geographic samples of the critically endangered North American cyprinid Notropis mekistocholas (Cape Fear shiner). Despite low abundance of this species, there was little suggestion of small population effects; allele diversity and hetero- zygosity were relatively high, FIS values within samples were non-significant, and genotypes were distributed
Twenty-six nuclear-encoded microsatellites were isolated from an enriched genomic library of sout... more Twenty-six nuclear-encoded microsatellites were isolated from an enriched genomic library of southern hake, Merluccius australis, and characterized in 30 individuals. The microsatellites include 18 dinucleotide repeats, seven trinucleotide repeats (two imperfect), and one pentanucleotide repeat. Southern hake support important industrial and artisanal fisheries in Chile, Argentina, and New Zealand.
The blacknose shark, Carcharhinus acronotus, is distributed in coastal waters of the western Atla... more The blacknose shark, Carcharhinus acronotus, is distributed in coastal waters of the western Atlantic Ocean from North Carolina to Brazil and is a component of both commercial and recreational fisheries throughout its range. In waters off of the United States, the species is managed as a component of the small coastal shark (SCS) complex. Concerns recently have arisen that blacknose
A total of 32 nuclear-encoded microsatellites, including 15 polymorphic and 13 monomorphic micros... more A total of 32 nuclear-encoded microsatellites, including 15 polymorphic and 13 monomorphic microsatellites, isolated from an enriched genomic library of the triakid shark, Mustelus canis (dusky smoothhound), and four microsatellites previously isolated from two other triakid sharks were characterized in 91 individuals of M. canis. Polymorphic repeat motifs included 12 dinucleotide, two trinucleotide and one pentanucleotide repeat(s). Mustelus canis supports
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