Description and Power Analysis of Two Tests for Detecting Recent Population Bottlenecks From Allele Frequency Data

Abstract

When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.

Shifting Quaternary migration patterns in the Bahamian archipelago: Evidence from theZamia pumilacomplex at the northern limits of the Caribbean island biodiversity hotspot

“…For this analysis, we followed the recommendations given by Meirmans (2014) . Th e program BOTTLENECK 1.2.02 ( Cornuet and Luikart, 1996 ) was used to test for recent genetic bottlenecks under the IAM model using the Wilcoxon sign-ranked test. ).…”

Large-scale geography survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

“…We tested whether a bottleneck occurred during the range expansion of each population with the method implemented in BOTTLENECK (Cornuet & Luikart, 1996; Piry, Luikart, & Cornuet, 1999). Inferences regarding historical changes in population size are based on the principle that the expected heterozygosity estimated from allele frequencies decreases faster than the expected heterozygosity estimated under a given mutation model at mutation-drift equilibrium in populations that have experienced a recent reduction in size.…”

No severe genetic bottleneck in a rapidly range-expanding bumblebee pollinator

“…Using single workers randomly selected from each of 89 independent clusters among the worker genotypic data identified with COLONY v. 2 [50] (see the electronic supplementary material), two different methods were employed to test for a bottleneck in the B. hypnorum study population. The first was a sign test implemented in the programme BOTTLENECK 1.2.02 [51], in which an excess of expected heterozygosity over that expected under mutation-drift equilibrium suggests that a recent reduction in population size has occurred [52]. The second test calculated the M-ratio [53] across loci for the B. hypnorum study population.…”

“…putative bottleneck [52]. Therefore, the sign test should have detected a bottleneck of 6-60 diploid individuals (15 generations/2.5 = 6, and 15 generations/0.25 = 60).…”