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.
... 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, ...
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...
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.
... 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, ...
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...
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
Uploads
Papers by john gold