Linda R. Richardson

Polymorphic microsatellite DNA markers in red drum (Sciaenops ocellatus)

The red drum (Sciaenops ocellatus, family Sciaenidae) is a marine fish species that is distributed in estuaries and nearshore habitats along the northern Gulf of Mexico and southeastern Atlantic coasts of the USA. Successful recruitment of red drum and co-occurring sciaenid fish species depends on estuarine habitats that serve as nursery areas for larvae. One goal of our research program is to determine whether finescale genetic structure of larvae is associated with heterogeneity in nursery habitat. Resolution of fine-scale structure in this case will require several highly polymorphic DNA markers that can be reliably scored from larvae.

Genetic studies in marine fishes. IV : An analysis of population structure in the red drum (Sciaenops ocellatus) using mitochondrial DNA

Abstract Variation in mitochondrial DNA (mtDNA) was examined among 397 individuals representing 13 geographic samples of red drum ( Sciaenops ocellatus ). Five of the samples were from the Atlantic coast of the southeastern United States, and eight were from the northern Gulf of Mexico. Seventy-six mtDNA haplotypes were found: eight haplotypes were found in 13 or more individuals, ten were found in four to 12 individuals, 22 were found in two to three individuals, and 36 were found in only one individual each. Mitochondrial DNA nucleon diversity values within samples ranged from 0.850 to 1.000; the value over all fish surveyed was 0.943. These data indicate that red drum have at least “normal” levels of genetic variability. Estimates of the percentage nucleotide sequence divergence among the 76 mtDNA haplotypes ranged from 0.137 to 1.962, with a mean (±SE) of 0.803 ± 0.006. Heterogeneity in the frequencies of four haplotypes was detected between pooled samples from the Atlantic vs. pooled samples from the Gulf. No heterogeneity was detected among samples from the Atlantic or among samples from the Gulf. F ST values (a measure of the variance in mtDNA haplotype frequencies) over the four heterogeneous haplotypes ranged from 0.019 to 0.137 (mean F ST = 0.057), and the effective number of female migrants ( N e m ) per generation using Wrights island model ranged from 1.58 to 12.91 (mean N e m = 4.14). The average percentage nucleotide sequence divergence within samples ranged from 0.494 to 0.734, with a mean (±SE) of 0.574 ± 0.021. The percentage nucleotide sequence divergence among pairwise comparisons of samples ranged from 0.498 to 0.713, with a mean (±SE) of 0.571 ± 0.005. Parsimony and phenetic analyses of individuall mtDNA haplotypes and of sample localities revealed no strong evidence for geographic cohesion of haplotype or sample groupings. A matrix correlation (Mantel) test also revealed no significant association between matrices of mtDNA sequence divergence and geographic distance among sample localities. Collectively, these data indicate that the red drum population is weakly subdivided, with semi-isolated subpopulations occurring along the southeastern Atlantic coast and in the northern Gulf of Mexico. The large number of rare or unique mtDNA haplotypes found in the study may prove useful in evaluating the success of red drum stocking programs.

Temporal genetic variation of mitochondrial DNA and the female effective population size of red drum (Sciaenops ocellatus) in the northern Gulf of Mexico.

We studied genetic drift of mitochondrial DNA (mtDNA) haplotype frequencies in a natural population of red drum (Sciaenops ocellatus) from the northern Gulf of Mexico (Gulf). The amount of genetic drift observed across temporally adjacent year classes (1986–89) was used to estimate variance effective (female) population size (Nef). Nef was estimated to be 14 308 and the ratio of female effective size to adult female census size was approximately 0.004, which is among the lowest value reported for vertebrate animals. Low effective size relative to census size among red drum in the northern Gulf may result from yearly fluctuations in the number of breeding females, high variance in female reproductive success, or both. Despite low genetic effective size relative to census size, the genetic effective population size of red drum in the northern Gulf appears sufficiently large to preclude potentially deleterious effects of inbreeding.

Microsatellite variation among red snapper (Lutjanus campechanus) from the Gulf of Mexico

Abstract: Allelic variation at a total of 20 nuclear-encoded microsatellites was examined among adult red snapper (Lutjanus campechanus) sampled from 4 offshore localities in the Gulf of Mexico. The number of alleles at the 20 microsatellites ranged from 5 to 20; average (± SE) direct count heterozygosity values ranged from 0.148 ± 0.025 to 0.902 ± 0.008. No significant departures from expectations of Hardy-Weinberg equilibrium were found for any locus within samples, and genotypes at pairs of microsatellites appeared to be randomly associated, i.e., in genotypic equilibrium. Tests of homogeneity in allele distributions among the 4 localities were nonsignificant for 19 of the microsatellites. Allele distribution at microsatellite Lca 43 was heterogeneous among localities before (but not after) Bonferroni corrections for multiple tests executed simultaneously. Tests of homogeneity in the distribution of individual alleles at Lca 43 gave similar results: one low frequency allele was distributed heterogeneously among samples before, but not after, Bonferroni correction. Molecular analysis of variance indicated that more than 99% of variation at each microsatellite was distributed within sample localities. These results generally are consistent with the hypothesis of a single population (stock) of red snapper in the northern Gulf of Mexico.

Mitochondrial DNA differentiation and population structure in red drum (Sciaenops ocellatus) from the Gulf of Mexico and Atlantic Ocean

Variation in mitochondrial (mt)DNA was examined among 473 red drum (Sciaenops ocellatus) sampled in 1988 and 1989 from nearshore localities in the northern Gulf of Mexico (Gulf) and the Atlantic coast of the southeastern United States (Atlantic). Data were combined with those from a previous study to generate a total of 871 individuals sampled from 11 localities in the Gulf and 5 localities in the Atlantic. Individuals assayed were from the 1986 and 1987 year-classes. A total of 118 composite mtDNA genotypes (haplotypes) was found. The percentage nucleotide sequence divergence among the 118 haplotypes ranged from 0.184 to 1.913, with a mean (±SE) of 0.878±0.004. MtDNA nucleon diversities and intrapopulational nucleotide-sequence divergence values were similar over all Gulf and Atlantic localities, and were high relative to most fish species surveyed to date. These data indicate that the perceived decline in red drum abundance appears not to have affected the genetic variability base of the species. Significant heterogeneity in the frequencies of at least four haplotypes was detected between pooled samples from the Gulf vs pooled samples from the Atlantic. No heterogeneity was found among localities from the Gulf or localities from the Atlantic. High levels of gene flow among all localities were inferred from FST values (a measure of the variance in mtDNA haplotype frequencies) and from Slatkins qualitative and quantitative analyses. Parsimony and phenetic analyses revealed no strong evidence for phylogeographic cohesion of localities, although there was weak support for cohesion of four of five localities from the Atlantic. These data indicate that the red drum population is subdivided, with weakly differentiated subpopulations (stocks) occurring in the northern Gulf and along the Atlantic coast of southeastern USA. Spatial autocor-relation analysis and heterogeneity tests of haplotype frequencies among regions within the Gulf supported the hypothesis of increased gene flow among neighboring localities; i.e., migration of individuals within the Gulf may be inversely related to geographic distance from an estuary or bay of natal origin. Estimates of evolutionary effective female-population size indicate that the red drum subpopulations may be large.

Population Structure of Red Snapper from the Gulf of Mexico as Inferred from Analysis of Mitochondrial DNA

Abstract Variation in mitochondrial DNA (mtDNA) was examined among 707 red snapper Lutjanus campechanus representing 16 samples taken during 3 years from localities in the northern and western Gulf of Mexico. Ninety-two composite mtDNA haplotypes were revealed by 13 restriction enzymes (representing 93 inferred restriction sites). Significant heterogeneity (P = 0.042) in mtDNA haplotype frequencies was detected among the 16 samples; however, homogeneity tests of mtDNA haplotype frequencies between or among samples taken in different years at the same locality and among samples at different localities within the same year, were not significant. No phylogeographic structure of haplotypes was evident, nor were rare haplotypes clustered geographically. Spatial autocorrelations did not differ significantly from those expected when no correlation exists. These findings are consistent with the hypothesis that a single breeding population of red snapper inhabits the northern Gulf of Mexico. Intrapopulational mtDN...

Evolution of the Cyprinella lutrensis species group. III. Geographic variation in the mitochondrial DNA of Cyprinella lutrensis— the influence of Pleistocene glaciation on population dispersal and divergence

We employed restriction site variation in mitochondrial (mt)DNA to determine if significant phylogeographic structure occurs in the North American cyprinid fish Cyprinella lutrensis. Digestion patterns from 16 restriction endonucleases identified fifty mtDNA haplotypes among 127 individuals of Cyprinella lutrensis assayed from localities in the Gulf Coastal Plain, the Great Plains, and the Central Lowlands. Nucleotide sequence divergence among haplotypes was highly variable (mean ± SE: 2.87%± 0.08; range: 0.14–9.24%). Maximum‐parsimony analysis and the neighbour joining method of tree construction revealed three major groupings (clades) of haplotypes that differed in geographic distribution. Divergence estimates between the basal clade, comprised of haplotypes primarily from the Brazos River in east Texas, and the remaining two clades, place C. lutrensis in the western Gulf Coastal Plain prior to Pleistocene glaciation. Nucleotide sequence divergence between the second clade, comprised of haplotypes from the Trinity and Calcasieu rivers in east Texas and southwestern Louisiana, respectively, and the third clade (comprised primarily of haplotypes from localities north of Texas and affected directly by Pleistocene glaciation), suggest that C. lutrensis colonized gladated regions to the north during the mid‐ to late Pleistocene. This hypothesis is supported by levels of intrapopulational nucleotide diversity in geographic localities outside of Texas and by geological evidence. Despite marked geographic variation in morphometries, meristics, and nuptial coloration, mtDNA variation in glaciated regions was not geographically structured, and subspecies of C. lutrensis were not identifiable by phylogenetic analysis of mtDNA.

Evolution of the Cyprinella lutrensis Species-Complex. II. Systematics and Biogeography of the Edwards Plateau Shiner, Cyprinella lepida

We examined geographic samples of the Edwards Plateau shiner, Cyprinella lepida, for restriction site variation of mitochondrial (mt)DNA. Sixteen restriction endonucleases were used to assay mtDNAs from 32 individuals of C. lepida sampled from the three rivers (Nueces, Frio, and Sabinal) of the Nueces River basin. Maximum-parsimony analysis using Cyprinella lutrensis as the outgroup and Cyprinella venusta as the root revealed that C. lepida in the Frio and Sabinal rivers is distinct from C. lepida in the Nueces River. A tree generated from a matrix of genetic distance using the Fitch-Margoliash method also revealed the same two distinct lineages of Cyprinella within the Nueces River basin. Percentage nucleotide sequence divergence estimates (? SE) between pairwise comparisons of the two evolutionary lineages of Cyprinella in the Nueces River basin and C. lutrensis were as follows: 8.36 ? 0.01 (Cyprinella in the Frio and Sabinal rivers vs C. lutrensis), 9.04 ? 0.03 (Cyprinella in the Frio and Sabinal rivers vs Cyprinella in the Nueces River), and 9.52 ? 0.03 (Cyprinella in the Nueces River vs C. lutrensis). Assuming mtDNA mutation-rate equivalency within Cyprinella, the two lineages (species) of Cyprinella in the Nueces River basin could have evolved nearly instantaneously in geological time. The estimates of mtDNA nucleotide sequence divergence, in concert with geographic considerations and the assumption that the genus Cyprinella originated north of the Coastal Plain, are consistent with the hypothesis that the ancestor(s) to the lineages of Cyprinella in the Nueces River basin entered the western (Gulf) Coastal Plain preglacially and from the northwest.

Temporal Stability of Nuclear Gene (Allozyme) and Mitochondrial DNA Genotypes among Red Drums from the Gulf of Mexico

Abstract Allelic variation in nine polymorphic nuclear genes and restriction-site variation in mitochondrial DNA (mtDNA) were assayed among 194 adult red drums Sciaenops ocellatus from the northern Gulf of Mexico, Data were combined with those of previous studies in order to examine patterns of temporal genetic variation among four year-classes (1984–1987) and individuals spawned prior to 1984, Tests of heterogeneity among year-classes in both nuclear gene allele frequencies and mtDNA haplotype frequencies were nonsignificant, and estimated fixation (F ST) values were 0.009 (nuclear genes) and 0.002 (mtDNA). Estimates of Neis unbiased genetic distance (nuclear genes) and nucleotide sequence divergence (mtDNA) among year-classes also indicated the absence of temporal genetic differentiation, Estimates of average heterozygosity (nuclear genes) and nucleon and nucleotide sequence diversities (mtDNA) indicated that levels of genome-wide variation within and among year-classes of red drum are equivalent to (o...

Mitochondrial DNA variation among ‘red’ fishes from the Gulf of Mexico

Abstract Restriction-site variation in mitochondrial (mt) DNA was used to assess population (stock) structure in three species of ‘red’ fishes from the Gulf of Mexico (Gulf): red drum ( Sciaenops ocellatus ), red snapper ( Lutjanus campechanus ), and red grouper ( Epinephelus morio ). MtDNA haplotype frequencies among geographic samples of all three species were statistically homogeneous, and phylogenetic analysis and phenetic clustering of mtDNA haplotypes or of geographic samples in each species revealed no evidence of phylogeographic cohesion. These findings are consistent with the hypothesis that each species is composed of a single, panmictic population in the Gulf. Autocorrelations of mtDNA haplotype frequencies in red drum were positive in proximal distance classes and negative in distal distance classes, indicating that migration of red drum within the Gulf is inversely related to geographic distance from an estuary or bay of natal origin. Estimates of intrapopulational mtDNA nucleotide sequence diversity differed significantly among geographic samples in all three species. The differences were especially pronounced among samples of red snapper and red grouper. In red drum and red snapper, intrapopulational mtDNA diversities appear temporally stable. Spatial differences in intrapopulational mtDNA diversity imply geographic differences in effective female population size and may signal relevant units for management of fishery resources.