PHRforJan13 - Molecular Ecology(2003 12 2511 2523 doi...

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Molecular Ecology (2003) 12 , 2511–2523 doi: 10.1046/j.1365-294X.2003.01928.x © 2003 Blackwell Publishing Ltd Blackwell Publishing Ltd. INVITED REVIEW Methods of parentage analysis in natural populations ADAM G. JONES * and WILLIAM R. ARDREN * School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332 USA, Conservation Genetics Laboratory, Abernathy Fish Technology Center, US Fish and Wildlife Service, 1440 Abernathy Creek Road, Longview, WA 98632, USA Abstract The recent proliferation of hypervariable molecular markers has ushered in a surge of tech- niques for the analysis of parentage in natural and experimental populations. Conse- quently, 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. Keywords : exclusion, fractional allocation, likelihood, microsatellites, parentage analysis, paternity Received 12 February 2003; revision received 8 May 2003; accepted 11 June 2003 Introduction An appreciation that molecular techniques can resolve issues of uncertain parentage arose from some of the earliest studies of genetic polymorphisms in populations. Since then, genetic studies of parentage have played a major role in the study of evolution and behavioural ecology and have become one of the central themes in the new field of molecular ecology (Avise 1994; Hughes 1998). Here we focus on the study of parentage in natural populations, which started slowly with the utilization first of chromosomal polymor- phisms (Anderson 1974; Milkman & Zeitler 1974; Levine et al . 1980) and later with allozyme electrophoresis (Hanken & Sherman 1981; Ellstrand 1984; Meagher 1986). The advent of DNA fingerprinting in the 1980s led to an explosion of parentage analyses, primarily in birds, that first revealed the power of such studies to overturn existing paradigms in behavioural ecology (Gibbs et al . 1990; Westneat 1990; Birkhead & Møller 1992). At the same time, statistical tech- niques were being developed for the analysis of parentage using single-locus polymorphisms, such as allozymes (Chakraborty & Hedrick 1983; Meagher & Thompson 1986). The multilocus nature of DNA fingerprinting data precluded simple statistical analysis, so parentage analysis in theory began a noticeable departure from parentage analysis in practice (Pena & Chakraborty 1994). It was the discovery of microsatellite markers that reunited theory and practice, resulting in a flood of empirical studies of parentage and a profusion of statistical methods for the analysis of such studies (Luikart & England 1999).
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