A method to bin alleles of genetic loci that maintains population heterogeneity

2005 ◽  
Vol 62 (7) ◽  
pp. 1570-1579 ◽  
Author(s):  
Jeffrey F Bromaghin ◽  
Penelope A Crane
Keyword(s):  
Chum Salmon ◽  
Genetic Relationships ◽  
Population Heterogeneity ◽  
Oncorhynchus Keta ◽  
Objective Method ◽  
Yukon River ◽  
Dolly Varden Salvelinus Malma ◽  
Rare Alleles ◽  
Mixed Stock ◽  
High Degree

Fishery resources are often studied when individuals from multiple stocks are aggregated. For that reason, mixed-stock analysis (MSA), i.e., estimation of the stock composition of a mixture of individuals, is an important component of many research programs. Although many characteristics can be used in MSA, DNA loci, particularly microsatellites, have become extremely common. Microsatellite loci usually have a greater number of potential expressions, or alleles, than other marker types. A high degree of polymorphism can enhance the power of MSA, but allele proportions are estimated less precisely and rare alleles are absent or observed in very small numbers in typically sized samples. The reduced precision and presence of rare alleles can degrade the performance of some analytic methods. Although the effect can be reduced by binning alleles, which is common, an objective method of doing so has not been available previously. We present a method for binning alleles that reduces the number of rare alleles, largely preserves the genetic relationships observed among stocks, and modestly improves the performance of mixed-stock and individual-assignment analyses. The method is illustrated with data from Yukon River chum salmon (Oncorhynchus keta) and western Alaska Dolly Varden (Salvelinus malma).

Genetic Relationships Among Chum Salmon Populations in Southeast Alaska and Northern British Columbia

1994 ◽  
Vol 51 (S1) ◽  
pp. 50-64 ◽  
Author(s):  
C. M. Kondzela ◽  
C. M. Guthrie ◽  
S. L. Hawkins ◽  
C. d. Russell ◽  
J. H. Helle ◽  
...  
Keyword(s):  
British Columbia ◽  
Chum Salmon ◽  
Genetic Relationships ◽  
The United States ◽  
Oncorhynchus Keta ◽  
Significant Heterogeneity ◽  
Southeast Alaska ◽  
Queen Charlotte Islands ◽  
Spawning Time ◽  
Mixed Stock

Allozymes from 46 loci were analyzed from chum salmon (Oncorhynchus keta) collected at 61 locations in southeast Alaska and northern British Columbia. Of the 42 variable loci, 21 had a common allele frequency <0.95. We observed significant heterogeneity within and among six regional groups: central southeast Alaska, Prince of Wales Island area, southern southeast Alaska – northern British Columbia, north-central British Columbia, and two groups in the Queen Charlotte Islands. Genetic variation among regions was significantly greater than within regions. The three island groups were distinct from each other and from the mainland populations. Allele frequencies were stable over time in 14 of 15 locations sampled for more than 1 yr. The geographic basis for heterogeneity among regions is confounded in part by spawning-time differences. The Prince of Wales and Queen Charlotte populations spawn in the fall; the mainland populations spawn mainly in the summer, although some overlap exists. Overall, most genetic diversity (97%) occurred within sampling locations; the remaining diversity was distributed almost equally within and among regions. Our genetic data may provide fishery managers a means to estimate stock composition in the mixed-stock fisheries near this boundary between the United States and Canada.

DNA and allozyme markers provide concordant estimates of population differentiation: analyses of U.S. and Canadian populations of Yukon River fall-run chum salmon (Oncorhynchus keta)

1998 ◽  
Vol 55 (7) ◽  
pp. 1748-1758 ◽  
Author(s):  
Kim T Scribner ◽  
Penelope A Crane ◽  
William J Spearman ◽  
Lisa W Seeb
Keyword(s):  
Genetic Markers ◽  
Population Differentiation ◽  
Chum Salmon ◽  
Allele Frequencies ◽  
Border Region ◽  
Oncorhynchus Keta ◽  
Mitochondrial Haplotype ◽  
Chum Salmon Oncorhynchus Keta ◽  
Yukon River ◽  
Mixed Stock

Although the number of genetic markers available for fisheries research has steadily increased in recent years, there is limited information on their relative utility. In this study, we compared the preformance of different "classes" of genetic markers (mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and allozymes) in terms of estimating levels and partitioning of genetic variation and of the relative accuracy and precision in estimating population allocations to mixed-stock fisheries. Individuals from eight populations of fall-run chum salmon (Oncorhynchus keta) from the Yukon River in Alaska and Canada were assayed at 25 loci. Significant differences in mitochondrial haplotype and nuclear allele frequencies were observed among five drainages. Populations from the U.S.-Canada border region were not clearly distinguishable based on multilocus allele frequencies. Although estimates of total genetic diversities were higher for the DNA loci (Ht = 0.592 and h = 0.647 for nDNA and mtDNA, respectively) compared with protein allozymes (Ht = 0.250), estimates of the extent of population differentiation were highly concordant across marker classes (mean theta = 0.010, 0.011, and 0.016 for allozymes, nDNA, and mtDNA, respectively). Simulations of mixed-stock fisheries composed of varying contributions of U.S. and Canadian populations revealed a consistent bias for overallocation of Canadian stocks when expected Canadian contributions varied from 0 to 40%, due primarily to misallocations among genetically similar border populations. No single marker class is superior for differentiating populations of this species at the spatial scale examined.

Population Structure and Identification of North Pacific Ocean Chum Salmon (Oncorhynchus keta) Revealed by an Analysis of Minisateliite DNA Variation

1994 ◽  
Vol 51 (6) ◽  
pp. 1430-1442 ◽  
Author(s):  
Eric B. Taylor ◽  
Terry D. Beacham ◽  
Masahide Kaeriyama
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
North Pacific ◽  
Chum Salmon ◽  
North Pacific Ocean ◽  
Oncorhynchus Keta ◽  
The North ◽  
Yukon River ◽  
Regional Population ◽  
The North Pacific

We examined geographic variability in minisatellite DNA in chum salmon (Oncorhynchus keta) from 42 populations from the North Pacific Ocean to (1) determine the extent of regional population structure at minisatellite loci and (2) assess the ability of minisatellite variability to determine the geographic origin in individual chum salmon. Restriction fragments from 1.6 to 13.6 kilobase pairs in molecular weight were resolved with a minisatellite probe. The fragments were inherited from parent to offspring and appeared to represent segregation at two linked loci. Minisateliite DNA variability was negligible between annual samples from the same rivers, and chum salmon fell into three regional population groupings: (i) Japanese, (ii) Russian/Yukon River, and (iii) southeastern Alaska/British Columbia salmon. These regional groupings probably reflect historical patterns of postglacial dispersal of chum salmon from three distinct refugia in the North Pacific. We used restriction fragment counts as input to linear discriminant and neural network classification of independent test samples of salmon. Accuracies of 90–95, 81–86, and 72–80% were achieved when classifying fish as of either Japan/Russia/Yukon River versus southeastern Alaska/British Columbia origin, Japan versus Russia/Yukon River origin, or Russia versus Yukon River origin, respectively.

Population structure and stock identification of chum salmon (Oncorhynchus keta) from British Columbia determined with microsatellite DNA variation

2008 ◽  
Vol 86 (9) ◽  
pp. 1002-1014 ◽  
Author(s):  
Terry D. Beacham ◽  
Brian Spilsted ◽  
Khai D. Le ◽  
Michael Wetklo
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Chum Salmon ◽  
Oncorhynchus Keta ◽  
Stock Identification ◽  
Dna Variation ◽  
Coastal Fisheries ◽  
Chum Salmon Oncorhynchus Keta ◽  
Regional Estimates ◽  
Mixed Stock

Variation at 14 microsatellite loci was surveyed in 205 populations of chum salmon ( Oncorhynchus keta (Walbaum in Artedi, 1792)) from British Columbia to determine population structure and the possible application of microsatellites to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (FST) over all populations and loci was 0.016, with individual locus values ranging from 0.006 to 0.059. Sixteen regional stocks were defined in British Columbia for stock identification applications. Analysis of simulated fishery samples suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. The main stocks that constitute the October 2007 samples of migrating chum salmon through Johnstone Strait in southern British Columbia were Fraser River (45%–64%), southern British Columbia mainland (22%), and east coast Vancouver Island (13%–28%), within the range of those to be expected in samples from Johnstone Strait. Microsatellites have the ability to provide fine-scale resolution of stock composition in British Columbia coastal fisheries.

scholarly journals Genetic Characterization of Juvenile Chum Salmon (Oncorhynchus keta) Migrating out of the Yukon River Delta

2019 ◽  
pp. 51-53
Author(s):  
Genevieve Johnson ◽  
Christine Kondzela ◽  
Jacqueline Whittle ◽  
Katharine Miller ◽  
Jeffrey Guyon
Keyword(s):  
Chum Salmon ◽  
Genetic Characterization ◽  
River Delta ◽  
Oncorhynchus Keta ◽  
Chum Salmon Oncorhynchus Keta ◽  
Yukon River ◽  
Juvenile Chum Salmon

The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta)

2008 ◽  
Vol 65 (9) ◽  
pp. 2026-2042 ◽  
Author(s):  
Jeffrey B. Olsen ◽  
Blair G. Flannery ◽  
Terry D. Beacham ◽  
Jeffrey F. Bromaghin ◽  
Penelope A. Crane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Chum Salmon ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Population Connectivity ◽  
Oncorhynchus Keta ◽  
Chum Salmon Oncorhynchus Keta ◽  
Yukon River ◽  
Run Timing

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon ( Oncorhynchus keta ) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling for geographic distance, supported the hypothesis that genetic divergence in Yukon River chum salmon is influenced by seasonal run timing. However, evidence of isolation-by-distance, when controlling for season run timing, indicated the populations are not sufficiently isolated, spatially or temporally, to prevent gene flow. Dispersal among summer- and fall-run populations may play a role in maintaining genetic diversity.

Estimating Stock Composition in Mixed Stock Fisheries Using Morphometric, Meristic, and Electrophoretic Characteristics

1984 ◽  
Vol 41 (3) ◽  
pp. 400-408 ◽  
Author(s):  
D. A. Fournier ◽  
T. D. Beacham ◽  
B. E. Riddell ◽  
C. A. Busack
Keyword(s):  
Maximum Likelihood ◽  
Chum Salmon ◽  
Vancouver Island ◽  
Oncorhynchus Keta ◽  
Morphometric Data ◽  
Conditional Maximum Likelihood ◽  
Chum Salmon Oncorhynchus Keta ◽  
Maximum Likelihood Procedure ◽  
Conditional Maximum ◽  
Mixed Stock

We describe a conditional maximum likelihood procedure for estimating stock composition in a mixed-stock fishery, provided that samples can be collected from the contributing stocks in isolation from each other and that characters exist that differ significantly between stocks. The procedure presented can use discrete (electrophoretic, meristic) or continuous (morphometric) data or any combination of these data. The procedure is tested by simulations and is used to estimate stock compositions of chum salmon (Oncorhynchus keta) sampled in a test fishery near Vancouver Island, B.C., in 1981. The estimated composition in the test fishery agreed closely with the results of previous tagging studies in the same area.

Genetic Stock Structure of Western Alaska Chum Salmon and a Comparison with Russian Far East Stocks

1994 ◽  
Vol 51 (S1) ◽  
pp. 84-94 ◽  
Author(s):  
Richard L. Wilmot ◽  
Rebecca J. Everett ◽  
William J. Spearman ◽  
Ramone Baccus ◽  
Natalya V. Varnavskaya ◽  
...  
Keyword(s):  
Chum Salmon ◽  
Gene Diversity ◽  
Russian Far East ◽  
Far East ◽  
Geographic Region ◽  
Oncorhynchus Keta ◽  
Genetic Stock ◽  
Alaska Peninsula ◽  
Bay Area ◽  
Yukon River

Substantial genetic divergence was found among chum salmon (Oncorhynchus keta) populations collected from North America and Russia. Five major groups of populations can be identified by geographic region: (1) lower Yukon River summer run; (2) upper Yukon River fall run; (3) Bristol Bay area; (4) Alaska Peninsula; and (5) Russia. Mean heterozygosities were 0.064, 0.062, 0.065, 0.064, and 0.063, respectively; and the percent polymorphic loci values at the 0.99 level were 33.7, 31.3, 32.6, 30.6, and 30.9%, respectively. The hierarchical gene diversity analysis showed that 95.42% of the diversity can be explained by heterogeneity within sites, 1.36% among sites, 0.49% between Yukon River run timing, 1.69% among areas, and 1.04% among countries. The Alaska Peninsula populations are genetically more similar to populations from Russia than to those from western Alaska, and two populations from the upper Yukon River are distinct from other nearby populations. Possible reasons for these findings concern the complex glacial histories of the watersheds.

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