This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucl... more This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross‐tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.
Canadian Journal of Fisheries and Aquatic Sciences, Aug 1, 1994
Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to... more Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to determine the magnitude of intraspecific genetic differentiation among samples of striped marlin (Tetrapturus audax). Composite genotypes, representing information from 11 restriction endonucleases, were generated for samples of approximately 40 striped marlin each from Mexico, Ecuador, Australia, and Hawaii. Genotypic variation was relatively high in all samples: the pooled nucleon diversity was 0.82 (sample range 0.69–0.84), and the pooled nucleotide sequence diversity was 0.30% (sample range 0.20–0.32%). Values of corrected mean nucleotide sequence divergence between samples were low (0.01–0.06%, mean 0.03%). Despite low intersample divergences, significant heterogeneity was observed in the distribution of composite mtDNA genotypes among samples. Each location was characterized by the presence of unique genotypes at elevated frequencies. Samples taken from the same location 1 yr apart demonstrated temporal stability of the distribution of genotypes at that site. These results demonstrate significant spatial partitioning of genetic variation within striped marlin, a situation that sharply contrasts with similar studies of several species of tuna. Management should focus on units smaller than those currently used to conserve unique genetic variation within the species.
Different classes of molecular markers occasionally yield discordant views of population structur... more Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within ≈ 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single‐copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter‐ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex‐biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.
This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucl... more This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross‐tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.
Canadian Journal of Fisheries and Aquatic Sciences, Aug 1, 1994
Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to... more Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) was used to determine the magnitude of intraspecific genetic differentiation among samples of striped marlin (Tetrapturus audax). Composite genotypes, representing information from 11 restriction endonucleases, were generated for samples of approximately 40 striped marlin each from Mexico, Ecuador, Australia, and Hawaii. Genotypic variation was relatively high in all samples: the pooled nucleon diversity was 0.82 (sample range 0.69–0.84), and the pooled nucleotide sequence diversity was 0.30% (sample range 0.20–0.32%). Values of corrected mean nucleotide sequence divergence between samples were low (0.01–0.06%, mean 0.03%). Despite low intersample divergences, significant heterogeneity was observed in the distribution of composite mtDNA genotypes among samples. Each location was characterized by the presence of unique genotypes at elevated frequencies. Samples taken from the same location 1 yr apart demonstrated temporal stability of the distribution of genotypes at that site. These results demonstrate significant spatial partitioning of genetic variation within striped marlin, a situation that sharply contrasts with similar studies of several species of tuna. Management should focus on units smaller than those currently used to conserve unique genetic variation within the species.
Different classes of molecular markers occasionally yield discordant views of population structur... more Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within ≈ 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single‐copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter‐ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex‐biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.
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Papers by Jan McDowell