Review of population history reconstruction methods in conservation biology

Abstract

Demographic history reconstruction is based on the estimation of effective population size (Ne), which is inferred and interpreted in various fields of evolutionary and conservation biology. Interest in Ne estimation is growing, as the key evolutionary forces and their are linked to Ne, and genetic data become increasingly accessible. However, what is effective population size, and how can we obtain an estimate of effective population size? In this review, we describe the history of the term Ne and explore existing methods for obtaining historical and contemporary estimates of changes in effective population size. We provide a detailed overview of methods based on sequential Markovian coalescence (SMC), generalized phylogenetic coalescence (G-PhoCS), identity by descent (IBD) and identity by state (IBS) similarity, as well as methods using allele frequency spectrum (AFS). For each method, we briefly summarize the underlying theory and note its advantages and disadvantages. In the final section of the review, we present examples of the use of these methods for various non-model species with conservation status.