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

• Published in: Canadian Journal of Fisheries and Aquatic Sciences
• Main Authors: Bromaghin, Jeffrey F, Crane, Penelope A
• Format: Article in Journal/Newspaper
• Language: English
• Published: Canadian Science Publishing 2005
• Subjects: Aquatic Science; Ecology, Evolution, Behavior and Systematics; Yukon; Keta; Varden; Yukon river; Alaska
• Online Access: http://dx.doi.org/10.1139/f05-093; http://www.nrcresearchpress.com/doi/pdf/10.1139/f05-093

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).