Linkage Analysis and Coalescents

Abstract I’he number of chapters in this volume, and in the research literature generally, that discuss the coalescent attests to the importance of this concept, both in theoretical and in applied population genetics. This chapter discusses applications of the coalescent to linkage analysis. The disease genes in a sample of affected individuals can often be traced back to a most recent common ancestor disease gene, thus forming a natural coalescent process. However, the genetic information available to the investigator concerns marker genes, which if linked to the disease gene share some but not all aspects of this coalescent. Thus, since the observations concern a locus different from that relating to the relevant coalescent process, an analysis more complex than that associated with the standard coalescent process is needed.