CONSTRAINED LEAST-SQUARES ESTIMATION OF MIXED POPULATION STOCK COMPOSITION FROM MTDNA HAPLOTYPE FREQUENCY DATA

Nuclear allozymes have provided the markers of choice for genetic stoc k identification, especially for Pacific salmonids. For other species, a dearth of allozyme variation has led workers to pursue mtDNA marker s. Haploid mtDNA markers obviate methods based on Hardy-Weinberg equil ibrium; all mtDNA markers are rigidly linked, violating the independen ce assumption; and mtDNA sample sizes are small. Based on a conditiona l weighted least squares approach for the case of known source populat ion genotype frequencies, we develop an unconditional method for estim ated genotype frequencies. We compare the methods with Monte Carlo sim ulation, evaluating effects of source population and mixed harvest sam ple sizes and those of source population divergence and mixture compos ition. When genetic resolution is poor or sample sizes are inadequate, the conditional method works better, but with larger sample sizes and reasonable population resolution, the unconditional method is superio r.