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

1991 ◽  
Vol 48 (9) ◽  
pp. 1724-1734 ◽  
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.

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

1989 ◽  
Vol 46 (8) ◽  
pp. 1446-1454 ◽  
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.

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

Genetics ◽  
1988 ◽  
Vol 118 (3) ◽  
pp. 509-518
Author(s):  
P Bentzen ◽  
W C Leggett ◽  
G G Brown
Keyword(s):  
Mitochondrial Dna ◽  
South Carolina ◽  
Nova Scotia ◽  
Length Polymorphism ◽  
Restriction Site ◽  
Restriction Endonuclease Analysis ◽  
American Shad ◽  
Length Variation ◽  
Alosa Sapidissima ◽  
Size Classes

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.

Anadromous Sturgeons: Habitats, Threats, and Management

2007 ◽  
Keyword(s):  
Large Scale ◽  
Atlantic Coast ◽  
The United States ◽  
Management Plan ◽  
Commercial Fishing ◽  
Atlantic Sturgeon ◽  
Coastal Fisheries ◽  
Number Of Factors ◽  
Acipenser Oxyrinchus ◽  
The U.S

<em>Abstract.</em>—Large-scale commercial fisheries for Atlantic sturgeon <em>Acipenser oxyrinchus</em> in the late 1880s eventually led to substantial reductions in the population size. The coastwide Atlantic sturgeon population of the United States has not recovered to the levels seen prior to the 1900s. A number of factors have contributed to the slow recovery or continued decline of Atlantic sturgeon populations, including continued commercial fishing and the targeting of females for caviar, bycatch in other fisheries, and changes in habitat due to dam construction and water quality degradation. The Atlantic States Marine Fisheries Commission (ASMFC) developed the first coastwide management plan for Atlantic sturgeon in 1990. In response to the shortcomings of that plan, the ASMFC applied new standards and the authority granted to it by the U.S. Congress to adopt a coastwide moratorium on all harvesting in 1998. A federal status review conducted in 1998 concluded that the continued existence of Atlantic sturgeon was not threatened given the situation at the time. Since then, monitoring programs have indicated varying levels of relative abundance in several water bodies along the Atlantic coast. The U.S. government is responsible for undertaking a status review to document any changes since the last review and determining whether those findings warrant a threatened or endangered listing for the species. The government’s findings may have far-reaching effects on many other Atlantic coastal fisheries.

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%.

Comparison of Logistic Regression and Discriminant Analyses for Stock Identification of Anadromous Fish, with Application to Striped Bass (Morone saxatilis) and American Shad (Alosa sapidissima)

1990 ◽  
Vol 47 (8) ◽  
pp. 1570-1577 ◽  
Author(s):  
Michael H. Prager ◽  
Mary C. Fabrizio
Keyword(s):  
Logistic Regression ◽  
Striped Bass ◽  
Logistic Model ◽  
Morone Saxatilis ◽  
Hudson River ◽  
American Shad ◽  
Stock Identification ◽  
Connecticut River ◽  
Alosa Sapidissima ◽  
Discriminant Analyses

We examined the applicability of logistic regression to stock identification studies and compared its performance on two data sets to that of linear and quadratic discriminant functions. Logistic regression can be used to model a categorical dependent variable associated with continuous or discrete independent variables, and is preferred to discriminant analyses when the explanatory variables are not multivariate normal. Our examples were American shad (Alosa sapidissima) from the Connecticut River and Hudson River estuaries, and striped bass (Morone Saxatilis) from the Hudson River, Chesapeake Bay, and Roanoke River estuaries. In the examples we used a resampling method to assess classification and allocation errors of the two methods on new data. For the shad data, the logistic model classified significantly more fish correctly, and provided a significantly better estimate of stock composition. For the striped bass data, the two methods classified about the same proportion of fish correctly, but the logistic model gave a significantly better estimate of stock composition.

Effect of Turbidity on the Temporal and Spatial Utilization of the Inner Bay of Fundy by American Shad (Alosa sapidissima) (Pisces: Clupeidae) and its Relationship to Local Fisheries

1983 ◽  
Vol 40 (S1) ◽  
pp. s322-s330 ◽  
Author(s):  
M. J. Dadswell ◽  
G. D. Melvin ◽  
P. J. Williams
Keyword(s):  
Light Intensity ◽  
Atlantic Coast ◽  
American Shad ◽  
Bay Of Fundy ◽  
Eastern Canada ◽  
Alosa Sapidissima ◽  
Migration Timing ◽  
Swimming Depth ◽  
Preference Zone ◽  
High Turbidity

Since 1750, a unique, directed fishery for American shad (Alosa sapidissima) has existed in shallow, turbid, mega-tidal embayments of the inner Bay of Fundy during summer and fall. Tagging experiments indicated that migrating shad consisting of intermixed, river populations from the entire Atlantic coast of North America occur there between June and October. Shad migration was counterclockwise around the Bay following the residual current structure. Presence and duration of the shad run in Cumberland Basin was a result of interaction between migration timing, turbidity, and temperature. Mean daytime swimming depth was related to tidal phase and turbidity. High turbidity (Secchi [Formula: see text]) of the mega-tidal embayments apparently extends the preference zone for light intensity of ocean-feeding shad into surface waters (2–10 m), making them accessible to the local fishery.Key words: drift gillnets, shad migration, light intensity preference, swimming depth, mega-tidal, eastern Canada

Usefulness of Meristic and Morphometric Characters in Discriminating Populations of American Shad (Alosa sapidissima) (Ostreichthyes:Clupeidae) Inhabiting a Marine Environment

1992 ◽  
Vol 49 (2) ◽  
pp. 266-280 ◽  
Author(s):  
Gary D. Melvin ◽  
Michael J. Dadswell ◽  
Joseph A. McKenzie
Keyword(s):  
North Carolina ◽  
Atlantic Coast ◽  
American Shad ◽  
Cape Cod ◽  
Bay Of Fundy ◽  
Morphometric Characters ◽  
Alosa Sapidissima ◽  
Linear Discriminant ◽  
Percent Correct ◽  
Spawning Run

American shad (Alosa sapidissima) concentrate each summer in the basins of the inner Bay of Fundy during their coastal migration. Tag returns from 6124 marked shad indicated that these fish return to every important shad spawning stream on the Atlantic coast. Ten meristic and 16 morphometric characters of shad collected from 14 rivers (range: Florida to Quebec) were used to develop linear discriminant functions (LDF). Variables which differed significantly (p < 0.05) between the sexes, year of sampling, and the time of collection during the spawning run were removed prior to LDF classification. The highest mean percent correct classification was achieved by the allocation of fish into regional groups, after classification into individual rivers, using pooled meristic and morphometric variables: 87.2% for males and 82.4% for females. The functions were then used to assign shad from a mixed populations (Cumberland Basin) to individual rivers and regions. Of these, 10.9% were assigned to rivers south of Cape Lookout, North Carolina, 38.1% to rivers between Cape Lookout and Cape Cod, 32.5% into rivers of the Bay of Fundy, and 18.5% into rivers in the Gulf of St. Lawrence. In-river tag returns were compared with LDF classification and were found to be similar.

Mitochondrial DNA divergence among popylations of American shad (Alosa sapidissima): how much variation is enough for mixed-stock analysis?

1995 ◽  
Vol 52 (8) ◽  
pp. 1688-1702 ◽  
Author(s):  
John M. Epifanio ◽  
Bonnie L. Brown ◽  
Peter E. Smouse ◽  
Carol J. Kobak
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Enzymes ◽  
American Shad ◽  
Data Set ◽  
Fourfold Increase ◽  
Mixed Stock Analysis ◽  
Haplotype Frequencies ◽  
Stock Analysis ◽  
Mtdna Diversity ◽  
Mixed Stock

We investigated the geographic distribution of the mitochondrial DNA (mtDNA) diversity of American shad from 15 North American rivers in 1992 with the intent of assessing sampling efficiency for future mixed-stock analysis. We observed 116 haplotypes among the 988 individuals assayed. Because no single or group of haplotypes completely discriminated river stocks or regional complexes, we investigated haplotype frequencies as stock descriptors. Analysis of four unique indices of haplotype divergence indicated that including rather than suppressing restriction site heteroplasmy increased resolution; however, the final results were not overwhelmingly dependent on this choice. A redundancy of variation among restriction enzymes diminished information returns rapidly after considering the six best enzymes, caused by physical linkage of restriction sites on the mtDNA molecule. Stock discriminatory power was tested by computing allocation efficiencies of mtDNA characters. When each individual was temporarily removed from the data set and reallocated to the various candidate populations on the basis of haplotypic similarity, 28% of the reallocations were correct, a fourfold increase over random success. We demonstrate that although the specific stock identity of individuals cannot be confidently established, the haplotypic arrays from baseline stocks can support stock identification and mixed-stock analysis for shad because rivers support stock-specific haplotype frequencies.

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