Mixed-Stock Analysis of Yukon River Chum Salmon: Application and Validation in a Complex Fishery

2010 ◽  
Vol 30 (5) ◽  
pp. 1324-1338 ◽  
Author(s):  
Blair G. Flannery ◽  
Terry D. Beacham ◽  
John R. Candy ◽  
Russell R. Holder ◽  
Gerald F. Maschmann ◽  
...  
Keyword(s):  
Chum Salmon ◽  
Mixed Stock Analysis ◽  
Yukon River ◽  
Stock Analysis ◽  
Mixed Stock

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.

scholarly journals Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5651
Author(s):  
Karina Jones ◽  
Michael Jensen ◽  
Graham Burgess ◽  
Johanna Leonhardt ◽  
Lynne van Herwerden ◽  
...  
Keyword(s):  
Great Barrier Reef ◽  
Spatial Ecology ◽  
New Caledonia ◽  
Relative Proportion ◽  
Chelonia Mydas ◽  
Barrier Reef ◽  
Green Turtles ◽  
Mixed Stock Analysis ◽  
Stock Analysis ◽  
Mixed Stock

A solid understanding of the spatial ecology of green turtles (Chelonia mydas) is fundamental to their effective conservation. Yet this species, like many marine migratory species, is challenging to monitor and manage because they utilise a variety of habitats that span wide spatio-temporal scales. To further elucidate the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 278 turtles across three foraging sites from the northern Great Barrier Reef (GBR) spanning more than 330 km: Cockle Bay, Green Island and Low Isles. This was performed with a newly developed assay, which targets a longer fragment of mtDNA than previous studies. We used a mixed stock analysis (MSA), which utilises genetic data to estimate the relative proportion of genetically distinct breeding populations found at a given foraging ground. Haplotype and nucleotide diversity was also assessed. A total of 35 haplotypes were identified across all sites, 13 of which had not been found previously in any rookery. The MSA showed that the northern GBR (nGBR), Coral Sea (CS), southern GBR (sGBR) and New Caledonia (NC) stocks supplied the bulk of the turtles at all three sites, with small contributions from other rookeries in the region. Stock contribution shifted gradually from north to south, although sGBR/CS stock dominated at all three sites. The major change in composition occured between Cockle Bay and Low Isles. Our findings, together with other recent studies in this field, show that stock composition shifts with latitude as a natural progression along a coastal gradient. This phenomenon is likely to be the result of ocean currents influencing both post-hatchling dispersal and subsequent juvenile recruitment to diverse coastal foraging sites.

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).

Mixed stock analysis of a resident green turtle, Chelonia mydas, population in New Caledonia links rookeries in the South Pacific

2015 ◽  
Vol 42 (6) ◽  
pp. 488 ◽  
Author(s):  
Tyffen C. Read ◽  
Nancy N. FitzSimmons ◽  
Laurent Wantiez ◽  
Michael P. Jensen ◽  
Florent Keller ◽  
...  
Keyword(s):  
New Caledonia ◽  
South Pacific ◽  
Chelonia Mydas ◽  
Marine Conservation ◽  
Published Data ◽  
The South ◽  
Mixed Stock Analysis ◽  
Coral Sea ◽  
Stock Analysis ◽  
Mixed Stock

Context Migratory species are known to pose a challenge for conservation because it is essential to understand their complex life history in order to implement efficient conservation actions. Aims In New Caledonia, large seagrass habitats in the Grand Lagon Sud (GLS) are home to resident green turtles (Chelonia mydas) of unknown origins. To assess the stock composition in the GLS, 164 foraging turtles were sampled for genetic analysis of ~770 base pairs of the mitochondrial DNA (mtDNA) control region. Methods Foraging turtles ranging in size from 48.0 to 108.4 cm curved carapace length were captured at five different sites within the GLS between September 2012 and December 2013. To provide baseline data for mixed stock analysis, published data from rookeries were used in addition to 105 samples collected at rookeries in the d’Entrecasteaux Islands and Chesterfield Islands in New Caledonia and at Malekula Island in Vanuatu. Exact tests of population differentiation and pairwise FST estimates were used to test for differences in mtDNA haplotype frequencies. Key results These analyses indicated that rookeries in the d’Entrecasteaux Islands and Vanuatu form unique management units and that the Chesterfield Islands rookeries are linked to the Coral Sea management unit. Mixed stock analysis indicated the highest proportion (mean = 0.63) of foraging turtles originate from the d’Entrecasteaux stock. Conclusions The larger contribution is estimated to be from a large rookery from New Caledonia, but smaller contributions are suggested from other rookeries in the South Pacific. Implications Marine conservation policies in New Caledonia need to consider the links between the foraging and nesting populations of C. mydas in New Caledonia and other rookeries and foraging grounds in the Coral Sea.

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