Heterogeneity in effective population size and its implications in conservation genetics and animal breeding

Abstract

Effective population size (N e ) is defined as the size of an idealized population undergoing the same rate of genetic drift as the population under study. It is a central concept in population genetics and used extensively in the design and monitoring of conservation and breeding programs. It is most often assumed that genetic drift effects are homogeneous across the genome and thus, so is N e . However, theory predicts that various processes can modify rates of genetic drift experienced by a locus in the genome. In particular, selection affecting linked neutral sites and rates of recombination can modulate the intensity of genetic drift throughout the genome. The increasing availability of sequence data has made it possible to test whether a single N e can account for the evolution of the genome. In this article, we discuss reasons why a heterogeneous N e can be expected theoretically and review what evidence is available from empirical studies. We finish by discussing potential implications for conservation and breeding practices. The evidence suggests that heterogeneity in N e can be just as important as heterogeneity in mutation rates in determining levels of genetic diversity throughout the genome.

Next‐generation metrics for monitoring genetic erosion within populations of conservation concern

“…Without the counteracting action of forces such as migration and mutation, genetic drift can lead to the fixation of one allele and the loss of all other alleles at a locus at a rate dependent on the effective population size (i.e., complete loss of genetic variation or fixation). The mean rate of erosion of genetic variation due to drift is expected to be the same for all neutral loci in the nuclear genome, although actual values will vary, for example, due to genetic hitchhiking (Jiménez‐Mena & Bataillon, ) and background selection. The level of genetic drift in a population can be monitored by estimating the variance effective population size.…”

One size fits all? Direct evidence for the heterogeneity of genetic drift throughout the genome

“…If the variation in N e we uncover is typical, caution should be used when interpreting mean values of N e , as genomic regions can drift and accumulate consanguinity at a much higher rate than would be predicted if N e was homogeneous (see [15] for a review in the topic).…”

Geno‐Diver: A combined coalescence and forward‐in‐time simulator for populations undergoing selection for complex traits

“…The heterogeneity of genetic diversity across the genome has been recently discussed by Jim enez-Mena, Hospital, and Bataillon (2016) and Howard et al (2016). Jim enez- Mena et al (2016) found the effective population size (Ne) to vary considerably across the genome (Ne: 40-250) in a Danish Holstein population, implying the accumulation of inbreeding is heterogeneous across the genome. Heterogeneous accumulation of inbreeding results in certain regions of the genome being inbred at a faster rate than others.…”