Length and restriction site heteroplasmy in the mitochondrial DNA of american shad (alosa sapidissima).

Abstract Restriction endonuclease analysis was used to assess mitochondrial DNA (mtDNA) variation in American shad (Alosa sapidissima) collected from 14 rivers ranging from Florida to Quebec. Two types of heteroplasmy were observed, one involving a major length polymorphism and the other a single restriction site. Shad mtDNA occurred in two principal size classes, 18.3 and 19.8 kb. Of 244 shad examined, 30 were heteroplasmic and carried both size classes of mtDNA in varying proportions; the remainder were homoplasmic for the smaller size class of mtDNA. The large mtDNA variant occurred most frequently at the southern end of the range, and except for two individuals from Nova Scotia, was not detected among shad from rivers north of the Delaware. In contrast, ten shad heteroplasmic for a SalI restriction site originated from rivers ranging from South Carolina to Nova Scotia. DNA mapping and hybridization experiments indicated that the length polymorphism is in the D-loop-containing region and consists of a tandemly repeated 1.5-kb DNA sequence occurring in two and three copies, respectively, in the two major size classes of shad mtDNA. Continuous length variation up to approximately 40 bp occurs among copies of the repeat both within and among individuals. Restriction site data support the conclusion that both forms of heteroplasmy in shad mtDNA have originated more than once.

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Discrimination among Atlantic Coast Populations of American Shad (Alosa sapidissima) Using Mitochondrial DNA

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f91-204 ◽

1991 ◽

Vol 48 (9) ◽

pp. 1724-1734 ◽

Cited By ~ 19

Author(s):

Kathleen Nolan ◽

Joseph Grossfield ◽

Isaac Wirgin

Keyword(s):

Mitochondrial Dna ◽

Atlantic Coast ◽

Restriction Enzymes ◽

Hudson River ◽

Restriction Endonuclease Analysis ◽

The United States ◽

American Shad ◽

Alosa Sapidissima ◽

Coastal Fisheries ◽

Latitudinal Clines

We used restriction endonuclease analysis of mitochondrial DNA (mtDNA) to differentiate among spawning stocks of American shad (Alosa sapidissima). Highly purified mtDNA was isolated from shad from four major spawning rivers: the St. John's (Florida), the Delaware, and the Hudson in the United States and the Miramichi in New Brunswick, Canada. Primarily four-and-five-base-cutting restriction enzymes were used to prepare both individual enzyme profiles and composite genotypes. Three separate spawning stocks, St. John's, Delaware–Hudson, and Miramichi, could be distinguished based on frequency differences in mtDNA genotypes generated by single restriction enzyme digests. We could not distinguish Delaware from Hudson River shad. Only a single definitive restriction site polymorphism was observed among all samples, but polyacrylamide gel electrophoretic mobility variants were common. Eco RI, Dde I, and Rsa I revealed stock-specific mtDNA genotypes. The frequencies of some genotypes occurred in latitudinal clines. Fifty-seven of 81 fish showed individual-specific composite genotypes. Geographic partitioning of genotypes suggests that mtDNA analysis may be useful for the identification of some American shad stocks and their relative contributions to mixed coastal fisheries.

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Mitochondrial DNA Polymorphism, Population Structure, and Life History Variation in American Shad (Alosa sapidissima)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f89-184 ◽

1989 ◽

Vol 46 (8) ◽

pp. 1446-1454 ◽

Cited By ~ 47

Author(s):

Paul Bentzen ◽

Gregory C. Brown ◽

William C. Leggett

Keyword(s):

Mitochondrial Dna ◽

Population Structure ◽

Reproductive Traits ◽

Restriction Endonuclease Analysis ◽

American Shad ◽

Life History Variation ◽

Alosa Sapidissima ◽

Mitochondrial Dna Polymorphism ◽

Mtdna Variation ◽

Mtdna Sequence

Restriction endonuclease analysis of mitochondrial DNA (mtDNA) variation was used to assess genetic differentiation and population structure in American shad (Alosa sapidissima) sampled from 14 rivers spanning the native range of the species (Florida to Quebec). Estimated mtDNA sequence divergences among 52 shad surveyed with 16 endonucleases were relatively low (mean 0.2%). The low level of mtDNA variation in shad may be a consequence of population bottlenecks that occurred during Pleistocene glacial maxima. A survey of 243 shad with four enzymes revealed several genotypes that were distributed across the range of the species. Three genotypes, a length variant and two single-enzyme genotypes, exhibited nonrandom, geographically clumped distributions. The distributions of shad mtDNA genotypes may have been influenced primarily by founder effects in the northern (glaciated) part of the range, and gene flow in the southern part of the range. The mtDNA data suggest that differences in the reproductive traits of northern and southern populations of shad, if genetically mediated, are likely to have evolved since the Pleistocene. The results of this study support theoretical predictions that mtDNA analysis is a highly sensitive means of examining population structures.

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Genetics of Cronartium ribicola. II. Variation in the ribosomal gene cluster

Canadian Journal of Botany ◽

10.1139/b96-057 ◽

1996 ◽

Vol 74 (3) ◽

pp. 461-468 ◽

Cited By ~ 9

Author(s):

E. E. White ◽

B. M. Foord ◽

B. B. Kinloch Jr.

Keyword(s):

Restriction Site ◽

Intergenic Spacer ◽

Fungal Species ◽

Ribosomal Gene ◽

Length Variation ◽

Cronartium Ribicola ◽

Western North America ◽

Size Classes ◽

Restriction Site Variation ◽

Site Variation

The ribosomal gene repeat in Cronartium ribicola J.C. Fisch is highly variable among spore samples from British Columbia, Canada. Both restriction site variation and length variation occur. Length heterogeneity results from differences in the number of subrepeats in the intergenic spacer (IGS). The number of IGS size classes in haploid cultures is limited but is very large and highly variable in aeciospores from single cankers. The proportions of different size classes vary among cankers on different trees, and among subsamples taken around the periphery of large old cankers. The results are consistent with the fungus having a haploid infective mycelium that produces functional pycnia that result in localized dikaryotic areas following fusion between flexuous hyphae and pycnia. Restriction site variation appears lower than has been reported in range-wide samples of endemic fungal species, consistent with the hypothesis that introduction of C. ribicola to western North America was limited and does not represent the full genetic range of the species. No particular restriction site variants or IGS size classes characterize samples from particular geographic areas. No evidence for geographic races of the fungus was obtained. Keywords: rusts, rust races, ribosomal DNA, intergenic spacer, population structure, RFLP.

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Mitochondrial DNA Sequence Similarity of Atlantic and Pacific Albacore Tuna (Thunnus alalunga)

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f89-110 ◽

1989 ◽

Vol 46 (5) ◽

pp. 870-873 ◽

Cited By ~ 34

Author(s):

John E. Graves ◽

Andrew E. Dizon

Keyword(s):

Mitochondrial Dna ◽

Restriction Site ◽

Sequence Similarity ◽

Restriction Endonuclease Analysis ◽

Albacore Tuna ◽

Restriction Sites ◽

Site Variation ◽

Thunnus Alalunga ◽

Pooled Sample ◽

Endonuclease Analysis

Restriction endonuclease analysis of mitochondrial DNA purified from 11 south Atlantic (Capetown, South Africa) and 12 north Pacific (San Diego, USA) albacore tuna (Thunnus alalunga) revealed no restriction sites which could distinguish an Atlantic from a Pacific albacore. Although restriction site variation was found within the pooled sample, variants were found only in single fish. These results suggest either recent isolation of Atlantic and Pacific albacore or, more likely, at least a small amount of migration between the two ocean basins.

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Evolutionary dynamics of mitochondrial DNA duplications in parthenogenetic geckos, Heteronotia binoei.

Genetics ◽

10.1093/genetics/129.1.221 ◽

1991 ◽

Vol 129 (1) ◽

pp. 221-230

Author(s):

C Moritz

Keyword(s):

Mitochondrial Dna ◽

Geographic Distribution ◽

Evolutionary Dynamics ◽

Restriction Site ◽

Restriction Endonucleases ◽

Length Variation ◽

Mtdna Sequences ◽

Coding Sequences ◽

Recent Origin

Abstract Mitochondrial DNA (mtDNA) from triploid parthenogenetic geckos of the Heteronotia binoei complex varies in size from 17.2 to 27.6 kilobases (kb). Comparisons of long vs. short genomes using restriction endonucleases revealed a series of tandem direct duplications ranging in size from 1.2 to 10.4 kb. This interpretation was supported by transfer-hybridization experiments which also demonstrated that coding sequences were involved. Some of the duplications have been modified by deletion and restriction site changes, but no other rearrangements were detected. Analysis of the phylogenetic and geographic distribution of length variation suggests that duplications have arisen repeatedly within the parthenogenetic form of H. binoei. The parthenogens, and thus the duplications, are of recent origin; modifications of the duplicated sequences, particularly by deletion, has therefore been rapid. The absence of duplications from the mtDNA of the diploid sexual populations of H. binoei reinforces the correlation between nuclear polyploidy and duplication of mtDNA sequences reported for other lizards. In comparison to the genomes of sexual H. binoei and of most other animals, the mtDNA of these parthenogenetic geckos is extraordinarily variable in length and organization.

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Intraspecific and interspecific variation at the y-ac-sc region of Drosophila simulans and Drosophila melanogaster.

Genetics ◽

10.1093/genetics/130.4.805 ◽

1992 ◽

Vol 130 (4) ◽

pp. 805-816 ◽

Cited By ~ 2

Author(s):

J M Martín-Campos ◽

J M Comerón ◽

N Miyashita ◽

M Aguadé

Keyword(s):

Drosophila Melanogaster ◽

X Chromosome ◽

Length Polymorphism ◽

Restriction Site ◽

Natural Populations ◽

Restriction Enzymes ◽

Drosophila Simulans ◽

Population Subdivision ◽

Telomeric Region ◽

Length Variation

Abstract A 2.2-kb region including the ac gene of Drosophila simulans has been sequenced. Interspecific divergence between Drosophila melanogaster and D. simulans was estimated as 0.0695 and 0.0558 for silent and for all sites, respectively. Estimated silent site divergence for the ac region is comparable to that estimated for other regions of the genome between these species, indicating that silent sites of the ac region are not under significantly stronger functional constraint. Intraspecific variation in both species was also investigated. Restriction-site and length polymorphism in the ac region of D. simulans has been investigated for 103 X chromosome lines sampled from three natural populations in Spain using eight four-cutter restriction enzymes. Neither restriction-site nor length variation was detected in the three populations surveyed. In D. melanogaster restriction-site and length polymorphism in all major transcription units of the y-ac-sc region (23.1-kb region) has been studied using four four-cutter restriction enzymes for 245 X chromosome lines sampled from 10 natural populations (seven from Europe, two from North America and one from Japan). Fourteen restriction-site and 28 length polymorphisms were detected. There was some indication of population subdivision for North American vs. European samples of D. melanogaster. The frequency spectrum of restriction-site polymorphisms in European populations was skewed toward rarer frequencies than predicted by the neutral theory. Comparison of silent site variation at this telomeric region with that in the Adh 5'-flanking region showed a reduced level of heterozygosity in the y-ac-sc region. Since interspecific silent divergence is not reduced in the y-ac-sc region as compared to other regions, the reduction in standing levels of variation at this telomeric locus in both D. simulans and D. melanogaster is most easily explained by a hitchhiking effect of linked selected substitutions.

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Fidelity of American Shad, Alosa sapidissima (Gupeidae), to its River of Previous Spawning

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f86-077 ◽

1986 ◽

Vol 43 (3) ◽

pp. 640-646 ◽

Cited By ~ 49

Author(s):

Gary D. Melvin ◽

Michael J. Dadswell ◽

James D. Martin

Keyword(s):

Nova Scotia ◽

Marine Environment ◽

American Shad ◽

Geographical Range ◽

Bay Of Fundy ◽

Alosa Sapidissima ◽

St Lawrence River

Of 5074 adult American shad, Alosa spidissima, tagged in the Annapolis River, Nova Scotia, during the 1981 and 1982 spawning runs, 292 (5.8%) were recaptured, 180 in the river during the same year, 56 in the river in subsequent years, 53 at distant marine sites, and 1 in another Nova Scotia river. Recovery from 6124 adult shad tagged in a marine environment (Cumberland Basin, Bay of Fundy) was similar (395 recaptures, 6.5%) but distribution was markedly different. Thirty-five were taken in the Basin during the same year, but only 7 in subsequent years. Conversely, 139 were recaptured at distant marine sites, and 214 in rivers from the St. Lawrence River, Quebec, to the St. John's River, Florida. Assuming equal probabilities for recapture within this species' geographical range, Annapolis River freshwater recaptures were specific for the Annapolis River but Cumberland freshwater recaptures were nonspecific. Except for two returns, possible strays, fidelity to the Annapolis was 97%.

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