Pacific salmon and the coalescent effective population size

Abstract

Pacific salmon include several species that are both commercially important and endangered. Understanding the causes of loss in genetic variation is essential for designing better conservation strategies. Here we use a coalescent approach to analyze a model of the complex life history of salmon, and derive the coalescent effective population (CES). With the aid of Kronecker products and a convergence theorem for Markov chains with two time scales, we derive a simple formula for the CES and thereby establish its existence. Our results may be used to address important questions regarding salmon biology, in particular about the loss of genetic variation. To illustrate the utility of our approach, we consider the effects of fluctuations in population size over time. Our analysis enables the application of several tools of coalescent theory to the case of salmon. © 2010 Cenik, Wakeley.