The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.

Estimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.

Population supplementation programs that release captive-bred offspring into the wild to boost the size of endangered populations are now in place for many species. The use of hatcheries for supplementing salmonid populations has become particularly popular. Nevertheless, whether such programs actually increase the size of wild populations remains unclear, and predictions that supplementation fish drag down the fitness of wild fish remain untested. To address these issues, we performed DNA-based parentage analyses on almost complete samples of anadromous steelhead (Oncorhynchus mykiss) in the Hood River in Oregon (U.S.A.). Steelhead from a supplementation hatchery (reared in a supplementation hatchery and then allowed to spawn naturally in the wild) had reproductive success indistinguishable from that of wild fish. In contrast, fish from a traditional hatchery (nonlocal origin, multiple generations in hatcheries) breeding in the same river showed significantly lower fitness than wild fish. In addition, crosses between wild fish and supplementation fish were as reproductively successful as those between wild parents. Thus, there was no sign that supplementation fish drag down the fitness of wild fish by breeding with them for a single generation. On the other hand, crosses between hatchery fish of either type (traditional or supplementation) were less fit than expected, suggesting a possible interaction effect. These are the first data to show that a supplementation program with native brood stock can provide a single-generation boost to the size of a natural steelhead population without obvious short-term fitness costs. The long-term effects of population supplementation remain untested.

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