Evaluating sample size to estimate genetic management metrics in the genomics era

• Published in: Molecular ecology resources Vol. 18; no. 5; pp. 1077 - 1091
• Main Authors: Flesch, Elizabeth P., Rotella, Jay J., Thomson, Jennifer M., Graves, Tabitha A., Garrott, Robert A.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.09.2018
• Subjects: Data processing; Empirical analysis; Estimates; Filtration; Genomics; Genotypes; Inbreeding; kinship; Ovis canadensis; Ovis canadensis canadensis; Population differentiation; Population genetics; Populations; sampling; Sheep; Simulation; Single-nucleotide polymorphism; Ovis canadensis canadensis; single nucleotide polymorphism; kinship; sampling
• DOI: 10.1111/1755-0998.12898
• ISSN: 1755-098X

Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free‐ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross‐species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra‐ and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.