Some methods for analysing genetic marker data in a biodiversity setting - example of the pigbiodiv data

Biodiversity is an important factor to consider when establishing conservation programmes. The PigBioDiv project aimed to assess the genetic diversity of the European pig by using genetic markers. This chapter presents some methods available for analysing such data. The two marker technologies used in PigBioDiv, namely microsatellites and AFLP (described in chapters 3 and 4 by Groenen et al., 2003 and Plastow et al., 2003), allow a fairly precise evaluation of the withinbreed and the between-breed variation. The meanings of the Reynolds and standard Nei genetic distances are given under some population genetics models. Various ways are shown for exploiting the information those distances provide, such as comparisons between distances, tree building and analysis of breed diversity. The need to combine within- and between-breed diversity is emphasised and ways of combining those two components of biodiversity are discussed