Evaluating methods for estimating local effective population size with and without migration

Evolution. 2015 Aug;69(8):2154-66. doi: 10.1111/evo.12713. Epub 2015 Jul 21.

Abstract

Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed that take advantage of various approaches for inferring Ne . The ability of these methods to accurately estimate Ne , however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of Ne can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves Ne estimates.

Keywords: Effective population size; gene flow; genetic drift; population genetics; population structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Migration*
  • Animals
  • Biological Evolution
  • Computer Simulation
  • Conservation of Natural Resources / methods
  • Genetics, Population
  • Islands
  • Population Density
  • Population Dynamics

Associated data

  • Dryad/10.5061/dryad.3R651