Mitochondrial DNA diversity among populations of striped bass in the southeastern United States

1989 ◽  
Vol 67 (4) ◽  
pp. 891-907 ◽  
Author(s):  
Isaac I. Wirgin ◽  
Rui Proenca ◽  
Joseph Grossfield
Keyword(s):  
Mitochondrial Dna ◽  
South Carolina ◽  
Striped Bass ◽  
Gulf Coast ◽  
Sequence Divergence ◽  
River System ◽  
Restriction Enzymes ◽  
Mtdna Sequence ◽  
Apalachicola River ◽  
Atlantic Coastal

Mitochondrial DNA (mtDNA) genotypes were determined for Atlantic striped bass from the St. Johns River in northeastern Florida and several hatchery reared individuals from Monck's Corner, South Carolina. Adults and hatchery-reared descendants of striped bass with high lateral line scale counts were sampled from several sites in the Apalachicola River system along the Gulf coast of Florida. In addition, naturally reproduced 1985 year class juveniles from the Apalachicola system were sampled. All mtDNA genotypes were compared with those observed in our sample of approximately 200 fish from the Atlantic coastal migratory stock. Ten different restriction endonucleases were used, generating 169 mtDNA fragments in most individuals. Heteroplasmy was observed in striped bass from both the St. Johns River and the Apalachicola system. Base sequence divergence among the populations surveyed was extremely low (maximum p = 0.0004), among the lowest reported for any animal species to date. However, the restriction enzymes RsaI and XbaI both revealed base substitutions unique to populations of Gulf Coast striped bass. Approximately 57% of striped bass from the Apalachicola system displayed an XbaI genotype not seen in any of our Atlantic collections. Four discrete mtDNA size classes were detected, differing by approximately 200, 300, and 400 base pairs from the smallest mtDNA molecule observed. The largest genotype was only seen in the Apalachicola system. The smallest genotype, while restricted to Gulf Coast striped bass sampled for this study, has been frequently observed in the Atlantic coastal migratory stock. The presence of mtDNA genotypes unique to the Apalachicola systems suggests the continued existence of a maternal lineage of striped bass of Gulf ancestry and points to the use of mtDNA as a valuable tag in the management of these populations. The lack of mtDNA sequence divergence in striped bass suggests a very recent origin for these populations.

Intra- and inter-specific mitochondrial DNA sequence divergence in Salmo: rainbow, steelhead, and cutthroat trouts

1985 ◽  
Vol 63 (9) ◽  
pp. 2088-2094 ◽  
Author(s):  
Gary M. Wilson ◽  
W. Kelley Thomas ◽  
Andrew T. Beckenbach
Keyword(s):  
Mitochondrial Dna ◽  
Rainbow Trout ◽  
Life Histories ◽  
Sequence Divergence ◽  
Cutthroat Trout ◽  
Restriction Enzymes ◽  
Restriction Endonuclease Analysis ◽  
Salmo Gairdneri ◽  
Intraspecific Divergence ◽  
Clonal Lines

Two forms of Salmo gairdneh with different life histories (steelhead and rainbow trout) were compared using restriction endonuclease analysis of mitochondrial DNA. A total of 19 individuals from four populations were studied for each of the two forms, using 14 restriction enzymes. In addition, five cutthroat trout samples were included as an interspecific comparison. These enzymes revealed a total of 81 cut sites, representing a sample of more than 400 nucleotides per fish. Of these sites, 25 were phylogenetically informative, dividing the 43 fish into 10 clonal lines, 8 Salmo gairdneri and 2 Salmo clarki. Results indicated detectable divergence between all geographic populations of steelhead and rainbow trout except Pennask rainbow trout, Coquihalla steelhead, and Wampus Creek rainbow trout. Other steelhead populations analysed showed a closer phylogenetic relationship to each other than to rainbow trout populations analysed. Intraspecific divergence was in most cases 1% or less, with a 1.5% maximum. Interspecific divergence between S. gairdneri and S. clarki was between 2% and 3.5%.

scholarly journals EVOLUTIONARY RELATIONSHIPS AMONG FIVE SUBSPECIES OF MUS MUSCULUS BASED ON RESTRICTION ENZYME CLEAVAGE PATTERNS OF MITOCHONDRIAL DNA

Genetics ◽  
1981 ◽  
Vol 98 (4) ◽  
pp. 801-816
Author(s):  
Hiromichi Yonekawa ◽  
Kazuo Moriwaki ◽  
Osamu Gotoh ◽  
Jun-Ichi Hayashi ◽  
Junko Watanabe ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Sequence ◽  
Restriction Enzyme ◽  
Mus Musculus ◽  
Sequence Divergence ◽  
Restriction Enzymes ◽  
Genetic Distances ◽  
The Other ◽  
Enzyme Cleavage ◽  
The Times

ABSTRACT The intra- and intersubspecific genetic distances between five subspecies of Mus musculus were estimated from restriction enzyme cleavage patterns or maps of mitochondrial DNA (mtDNA). The European subspecies, M. m. domesticus and Asian subspecies, M. m. bactrianus, M. m. castaneus, M. m. molossinus and M. m. urbanus were examined. For each subspecies, except M. m. urbanus, at least two local races from widely separated localities were examined. Intrasubspecific heterogeneity was found in the mtDNA cleavage patterns of M. m. bactrianus and M. m. castaneus. M. m. molossinus and M. m. domesticus, however, revealed no intrasubspecific heterogeneity. Four of the subspecies had distinct cleavage patterns. The fifth, M. m. urbanus, had cleavage patterns identical to those of M. m. castaneus with several enzymes. Estimates of genetic distances between the various races and subspecies were obtained by comparing cleavage maps of the mtDNAs with various restriction enzymes. Nucleotide sequence divergences of mtDNA between local races were estimated to be less than 0.4% in M. m. bactrianus and less than 0.3% in M. m. castaneus. The times of divergence of both subspecies were calculated to be 0.1-0.2 × 106 years. These values suggest that the intrasubspecific divergence began some 0.1-0.2 × 106 years ago. On the other hand, nucleotide sequence divergences between European subspecies M. m. domesticus and Asian subspecies M. m. bactrianus and M. m. castaneus were 7.1% and 5.8%, respectively. The times of divergence were calculated to be 2.1-2.6 × 106 years. Further, the nucleotide sequence divergence and time of divergence between M. m. molossinus and the other two Asian subspecies were comparable to those between M. m. molossinus and M. m. domesticus (about 3% and 1 × 106 years, respectively). These results suggest that M. m. molossinus is situated in a unique evolutionary position among Asian subspecies.

scholarly journals GENETIC VARIATION AND GEOGRAPHIC DIFFERENTIATION IN MITOCHONDRIAL DNA OF THE HORSESHOE CRAB, LIMULUS POLYPHEMUS

Genetics ◽  
1986 ◽  
Vol 112 (3) ◽  
pp. 613-627
Author(s):  
Nancy C Saunders ◽  
Louis G Kessler ◽  
John C Avise
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Horseshoe Crab ◽  
Gulf Coast ◽  
Sequence Divergence ◽  
Clonal Diversity ◽  
Limulus Polyphemus ◽  
Site Variation ◽  
Horseshoe Crabs ◽  
Or Gene

ABSTRACT Restriction site variation in mitochondrial DNA (mtDNA) of the horseshoe crab (Limulus polyphemus) was surveyed in populations ranging from New Hampshire to the Gulf Coast of Florida. MtDNA clonal diversity was moderately high, particularly in southern samples, and a major genetic "break" (nucleotide sequence divergence approximately 2%) distinguished all sampled individuals which were north vs. south of a region in northeastern Florida. The area of genotypic divergence in Limulus corresponds to a long-recognized zoogeographic boundary between warm-temperate and tropical marine faunas, and it suggests that selection pressures and/or gene flow barriers associated with water mass differences may also influence the evolution of species widely distributed across such transition zones. On the other hand, a comparison of the mtDNA divergence patterns in Limulus with computer models involving stochastic lineage extinction in species with limited gene flow demonstrates that deterministic explanations need not necessarily be invoked to account for the observations. Experiments to distinguish stochastic from deterministic possibilities are suggested. Overall, the pattern and magnitude of mtDNA differentiation in horseshoe crabs is very similar to that typically reported for freshwater and terrestrial species assayed over a comparable geographic range. Results demonstrate for the first time that, geographically, at least some continuously distributed marine organisms can show considerable mtDNA genetic differentiation.

Biology and Management of Inland Striped Bass and Hybrid Striped Bass

2013 ◽  
Keyword(s):  
Gulf Of Mexico ◽  
Striped Bass ◽  
Nuclear Dna ◽  
Atlantic Coast ◽  
Relative Survival ◽  
River System ◽  
Thermal Refuge ◽  
Natural Reproduction ◽  
Apalachicola River ◽  
Flint River

<em>Abstract</em>.—Since the 1970s, the only known naturally reproducing population of native Gulf of Mexico (Gulf ) striped bass <em>Morone saxatilis</em> occurs in the Apalachicola–Chattahoochee–Flint River system (ACF) in Florida, Georgia, and Alabama.To augment its depleted population, low numbers of fry and fingerlings of Atlantic coast ancestry were released into the ACF between 1965 and 1976.Restoration of Gulf striped bass was initiated in 1980 when putative Gulf fingerlings spawned from Apalachicola River (Gulf ) broodfish were stocked back into the ACF. Since the initial stocking, approximately 10 million phase-I (25–50 mm) and 900,000 phase-II (150–250 mm) fingerlings have been released into Lake Seminole and the Apalachicola River, with hundreds of thousands more released into upstream reservoirs. Low levels of successful natural reproduction in the ACF were documented in 9 of the 10 years that natural reproduction was evaluated. Marked stocked fish have typically comprised 75–100% of fall age-0 samples. After stocking was initiated, striped bass harvest estimates increased as much as 10-fold during peak-season creel surveys conducted in the tailrace of Jim Woodruff Lock and Dam. A comparison of Atlantic-origin and Gulf striped bass co-stocked into an adjacent river-reservoir system over a 5-year period indicated no consistent differences in relative survival or growth through age 4. Gulf striped bass occupied coolwater thermal refuges during summer. Enhancement of thermal refuge habitats was successful, but results were short-lived. Small populations of Gulf striped bass, dependent on stocking of hatchery fish, now exist in several Gulf of Mexico tributary systems where adequate habitat is present.Genetic analysis of both mitochondrial and nuclear genomes revealed that a high percentage of fish from the ACF exhibit mitochondrial DNA (mtDNA) haplotypes and nuclear DNA (nDNA) alleles that are absent in Atlantic populations.However, significant introgression of Atlantic nDNA alleles was documented in the extant population. Knowledge of the life history of Gulf striped bass was improved as a result of this multi-state collaboration as well as a large stocking program, new Gulf broodfish repositories, extensive genetic cataloged database,and expanded trophy fisheries. ACF Gulf striped bass restoration goals and objectives were defined, adjusted, and revised throughout the collaborative process to meet the concerns and management needs of all participating agencies.

Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

1993 ◽  
Vol 50 (10) ◽  
pp. 2112-2118 ◽  
Author(s):  
S. Fournier Lockwood ◽  
Robert E. Dillinger Jr. ◽  
Tim P. Birt ◽  
John M. Green ◽  
Thomas P. Snyder
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Cladistic Analysis ◽  
Sequence Divergence ◽  
Amino Acid Replacement ◽  
Mitochondrial Cytochrome B ◽  
Mtdna Sequence ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

scholarly journals POLYMORPHIC SITES AND THE MECHANISM OF EVOLUTION IN HUMAN MITOCHONDRIAL DNA

Genetics ◽  
1984 ◽  
Vol 106 (3) ◽  
pp. 479-499
Author(s):  
Rebecca L Cann ◽  
Wesley M Brown ◽  
Allan C Wilson
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Proteins ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Mitochondrial Genes ◽  
Rrna Genes ◽  
Exact Nature ◽  
Sequence Comparisons ◽  
Functional Regions ◽  
Mtdna Sequence

ABSTRACT Twelve restriction enzymes were used to screen for the presence or absence of cleavage sites at 441 locations in the mitochondrial DNA of 112 humans from four continents. Cleavage maps were constructed by comparison of DNA fragment sizes with those expected from the published sequence for one human mtDNA. One hundred and sixty-three of the sites were polymorphic, i.e., present in some individuals but absent from others, 278 sites being invariant. These polymorphisms probably result from single base substitutions and occur in all functional regions of the genome.—In 77 cases, it was possible to specify the exact nature and location (within a restriction site) of the mutation responsible for the absence of a restriction site in a known human mtDNA sequence and its presence in another human mtDNA. Fifty-two of these 77 gain mutations occur in genes coding for proteins, 34 being silent and 18 causing amino acid replacements; moreover, nine of the replacements are radical.—Notable also is the anomalous ratio of transitions to transversions required to account for these 77 restriction site differences between the known human mtDNA sequences and other human mtDNAs. This ratio is lower for most groups of restriction sites than has been reported from sequence comparisons of limited parts of the mtDNA genome in closely related mammals, perhaps indicating a special functional role or sensitivity to mutagenesis for palindromic regions containing high levels of guanine and cytosine.—From the genomic distribution of the 163 polymorphic sites, it is inferred that the level of point mutational variability in tRNA and rRNA genes is nearly as high as in protein-coding genes but lower than in noncoding mtDNA. Thus, the functional constraints operating on components of the protein-synthetic apparatus may be lower for mitochondria than for other systems. Furthermore, the mitochondrial genes for tRNAs that recognize four codons are more variable than those recognizing only two codons.—Among the more variable of the human mitochondrial genes coding for proteins is that for subunit 2 of cytochrome oxidase; this polypeptide appears to have been evolving about five times faster in primates than in other mammals. Cytochrome c, a nuclearly encoded protein that interacts directly with the oxidase 2 subunit in electron transport, has also evolved faster in primates than in rodents or ungulates. This example, along with that for the mitochondrial rRNA genes and the nuclear genes coding for mitochondrial ribosomal proteins, provides evidence for coevolution between specific nuclear and mitochondrial genes.

scholarly journals Mitochondrial DNA variation and the evolution of Robertsonian chromosomal races of house mice, Mus domesticus.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 1105-1120 ◽  
Author(s):  
M W Nachman ◽  
S N Boyer ◽  
J B Searle ◽  
C F Aquadro
Keyword(s):  
Mitochondrial Dna ◽  
Western Europe ◽  
Sequence Divergence ◽  
Mus Domesticus ◽  
Sequence Evolution ◽  
Ancestral Polymorphism ◽  
Chromosomal Races ◽  
Mtdna Sequence ◽  
Average Sequence Divergence ◽  
Standard Karyotype

Abstract The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time.

Biology and Management of Inland Striped Bass and Hybrid Striped Bass

2013 ◽  
Keyword(s):  
South Carolina ◽  
Striped Bass ◽  
Colorado River ◽  
River System ◽  
The United States ◽  
High Survival ◽  
Natural Reproduction ◽  
Boom And Bust ◽  
Catch Rates ◽  
Boom And Bust Cycle

<em>Abstract</em>.—The discovery of landlocked populations of striped bass <em>Morone saxatilis</em> in Santee–Cooper Reservoir, South Carolina and Kerr Reservoir, Virginia prompted a rush to stock striped bass in other inland waters of the United States, including impoundments in the Colorado River. Fisheries managers responsible for Colorado River waters studied existing literature and predicted that it would be unlikely for successful natural reproduction of striped bass in these systems. Striped bass population development proved unique in the Colorado River system, which is marked by nutrient-poor, well-oxygenated waters with limited forage. Natural reproduction did occur in these reservoirs despite the lack of current previously thought to be essential for successful reproduction, resulting in high survival. Developing populations were sometimes overabundant to the point of forage elimination from pelagic zones. Lack of prey limited growth and temporarily reduced reproduction. Eventually forage returned, increasing striped bass growth and maturity, which led to more reproduction (a “boom and bust”cycle). Planned low-impact, low-abundance adult trophy fisheries produced by managed stocking were replaced by high-abundance juvenile fisheries with high catch rates produced by natural reproduction. In most years, juvenile striped bass living in warm surface waters proved to have the competitive advantage over adults for limited forage.

Mitochondrial and nuclear DNA variation, genotype fingerprinting and genetic relationships in lentil (Lens culinaris Medik.)

1997 ◽  
Vol 77 (4) ◽  
pp. 515-521 ◽  
Author(s):  
Om P. Rajora ◽  
John D. Mahon
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Lens Culinaris ◽  
Nuclear Dna ◽  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Dna Variation ◽  
Apocytochrome B ◽  
Nuclear Dna Variation ◽  
Mean Similarity

Mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) variations were examined in six cultivars of Lens culinaris ssp. culinaris and two (mtDNA) or one (nuDNA) accession(s) of L. culinaris ssp. orientalis. Total leaf DNA was digested with up to 15 restriction endonucleases, separated by agarose gel electrophoresis and trasferred to nylon membranes. To examine mtDNA variation, blots were probed with mtDNA coding for cytochrome c oxidase I (coxI) and ATPase 6 (atp6) of both wheat and maize as well as apocytochrome b (cob) and Orf25 (orf25) of wheat. Sixteen combinations of mtDNA probes and restriction enzymes revealed 34 fragments that discriminated between at least two lentil accessions. For nuDNA analysis, probes from cDNA and genomic DNA clones of lentil were used to probe the same blots, and identified 46 diagnostic fragments from 19 probe/enzyme combinations. Each lentil accession could be unequivocably distinguished from all others on the basis of both mitochondrial and nuclear DNA fragment patterns. The mitochondrial restriction fragment similarities ranged from 0.944 to 0.989, with a mean of 0.970 but nuclear restriction fragment similarities varied from 0.582 to 0.987, with a mean of 0.743. The apparent genetic relationships among accessions differed according to the source of DNA examined, although the commercial varieties Laird, Brewer and Redchief showed similarly high levels of mean similarity with both nuclear (0.982) and mitochondrial DNA (0.983). Key words: Lens culinaris Medik., genetic variation, mitochondrial, nuclear, DNA, lentil

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