Conservation Genetics

Abstract

This chapter reviews some of the statistical methodologies used in the genetic analysis of endangered and managed populations. The topics covered include the estimation of effective population size, N e , the detection of past changes in population size, the estimation of admixture proportions, and the detection of immigrant and hybrid individuals. The reasons why it may be useful to measure N e are discussed. Using genetic information it is possible to estimate N e from changes in gene frequencies between samples taken at different times, or from genotypic disequilibria in one sample, or from differences in gene frequencies between two recently descended populations. The different statistical methodologies that have been applied are discussed in some detail. The ability to detect past changes in population size may also be useful in conservation management, and some of the more recent approaches are described. Another area of concern in conservation biology is introgressive hybridization. At the population level it is possible to infer admixture proportions by comparing the gene frequencies in the admixed and non‐admixed populations, providing they are available, and the different statistical approaches to analysing this problem are reviewed. Very recently statistical methods have been developed to detect immigrant and hybrid individuals from their multilocus genotype, and the main methods developed in this area are described.

Genetic equilibrium despite habitat fragmentation in an Afrotropical bird

“…Recently, a method has become available that tests exactly whether an equilibrium between gene flow and drift has been reached (Ciofi et al . 1999; Beaumont 2001; Goodman et al . 2001; Palo et al .…”

“…This Bayesian method explores the most probable demographic and genealogical histories consistent with the sample of chromosomes typed (Ciofi et al . 1999; Beaumont 2001). Its main assumption is a negligible mutation rate.…”

“…Equilibrium testing. We tested for migration–drift equilibrium with the program 2 mod (http://www.rubic.rdg.ac.uk/~mab/software.html; Beaumont 2001). This program identifies populations subjected to genetic drift and gene flow as opposed to those under genetic drift only, through estimation of the relative likelihood of the two models using a MCMC procedure (Ciofi et al .…”

Genetics of a reintroduced swift fox population highlights the need for integrated conservation between neighbouring countries

“…To test whether the system is in drift‐migration equilibrium, we used 2 mod (Beaumont, ). This application assesses whether the gene frequencies observed among clusters are explained by the drift‐migration equilibrium or a model of drift alone, using a relative likelihood approach (Ciofi et al ., ).…”

“…Population substructure may result from non‐equilibrium population dynamics that have resulted from two separate founding locations (Latch & Rhodes, ; Brekke et al ., ; Moraes et al ., ) or from natural barriers to dispersal (Schwalm, Waits & Ballard, ). We examine equilibrium dynamics through mutation‐drift and migration‐drift equilibrium tests (Piry, Luikart & Cornuet, ; Beaumont, ) to understand whether the population substructure is more likely the result of founding effects and non‐equilibrium dynamics. To determine whether there are habitat effects on dispersal, we calculate the amount of spatial genetic structure across the study area (Galpern et al ., ) and use landscape genetics to identify dispersal barriers (McRae & Beier, ).…”