Estimating the optimal number of samples to determine the effective population size in livestock

Abstract

Effective population size (Ne) is a key parameter in various biological disciplines, including evolutionary biology, conservation genetics, and livestock breeding programs. When applying genomic approaches to estimate Ne or other indicators of genetic variation, sample size is among the critical factors that directly affect the balance between cost and precision. In this study, we investigated the impact of sample size on Ne estimates by analyzing data from previous genotyping studies and simulations. Our results suggest that a sample size of 50 animals is a reasonable approximation of the "true" ("unbiased") Ne value within the populations analyzed. While estimating the Ne value is an important starting point in population genetics, additional factors, such as the degree of inbreeding, population structure, and admixture, must be taken into account to obtain a comprehensive genetic evaluation and avoid misinterpretation. We conclude that linkage disequilibrium (LD)-based approaches are well suited for the estimation of Ne in livestock populations. However, careful interpretation of results is essential as current bioinformatics tools may introduce potential biases due to methodological assumptions, marker density, or population-specific factors.

Keywords: SNP arrays; conservation; effective population size; simulation; small ruminants.

FIGURE 1

Ne estimates calculated for the four breeds of the two species over a range of sizes: 20, 50, and 100 animals. (A) Solid circles represent the estimates from 100 independent iterations and (B) each black point corresponds to the mean value of 100 estimates with the CI. The “true” effective size, the value of which was calculated based on the entire dataset, is indicated by the red horizontal line.

FIGURE 2

Simulated scenarios. The Ne estimates of 20, 50, and 100 subsampled individuals for every population are plotted against the effective sizes calculated for the whole population (indicated by the red horizontal line whose value can be retrieved in Supplementary Table S2). (A) Solid circles represent the estimates from 100 independent iterations and (B) each black point corresponds to the averaged value of 100 estimates. The black point shows the harmonic mean of 100 estimates.