An empirical examination of sample size effects on population demographic estimates in birds using single nucleotide polymorphism (SNP) data

Abstract

Sample size is a critical aspect of study design in population genomics research, yet few empirical studies have examined the impacts of small sample sizes. We used datasets from eight diverging bird lineages to make pairwise comparisons at different levels of taxonomic divergence (populations, subspecies, and species). Our data are from loci linked to ultraconserved elements and our analyses used one single nucleotide polymorphism per locus. All individuals were genotyped at all loci, effectively doubling sample size for coalescent analyses. We estimated population demographic parameters (effective population size, migration rate, and time since divergence) in a coalescent framework using Diffusion Approximation for Demographic Inference, an allele frequency spectrum method. Using divergence-with-gene-flow models optimized with full datasets, we subsampled at sequentially smaller sample sizes from full datasets of 6–8 diploid individuals per population (with both alleles called) down to 1:1, and then we compared estimates and their changes in accuracy. Accuracy was strongly affected by sample size, with considerable differences among estimated parameters and among lineages. Effective population size parameters (ν) tended to be underestimated at low sample sizes (fewer than three diploid individuals per population, or 6:6 haplotypes in coalescent terms). Migration (m) was fairly consistently estimated until <2 individuals per population, and no consistent trend of over-or underestimation was found in either time since divergence (T) or theta (Θ = 4Nrefμ). Lineages that were taxonomically recognized above the population level (subspecies and species pairs; that is, deeper divergences) tended to have lower variation in scaled root mean square error of parameter estimation at smaller sample sizes than population-level divergences, and many parameters were estimated accurately down to three diploid individuals per population. Shallower divergence levels (i.e., populations) often required at least five individuals per population for reliable demographic inferences using this approach. Although divergence levels might be unknown at the outset of study design, our results provide a framework for planning appropriate sampling and for interpreting results if smaller sample sizes must be used.

Signals of adaptation to agricultural stress in the genomes of two European bumblebees

“…A second potential caveat to our study may be the rather limited population sizes (n≥3). While performing a population genetic study with populations represented by only three specimens was previously and usually considered too small, recent studies have shown that accurate population parameters such as F st-values or genetic diversity measurements can be obtained when a large number of SNPs are used to compensate for such low population sizes ( Nazareno et al, 2017 ; McLaughlin and Winker, 2020 ). Here, by conducting a genomic study with approximately 14,000 SNPs per species after filtering, we met the latter criteria.…”

Genetic depletion does not prevent rapid evolution in island‐introduced lizards

“…To assess the potential effect of our sample sizes, we performed a rarefaction analysis, which showed that good estimates of H e and pairwise F ST can be obtained from subsample sizes as small as four diploid individuals (Figure S1 ), supporting the robustness of genetic diversity and differentiation estimates when a large number of SNPs are available (Nazareno et al., 2017 ). Although desirable, we were unable to perform robust estimations of past and contemporary effective population size, as both the sample size (between 14 and 16 gene copies) and the short time‐scale at which the demographic events occurred (~30 generations) limit the use of both linkage and coalescent approaches (McLaughlin & Winker, 2020 ; Nunziata & Weisrock, 2018 ; Robinson et al., 2014 ; van der Zee et al., 2022 ). Nevertheless, the frequency distribution of polymorphisms within a population still carries information about recent processes.…”

Limited Introgression between Rock-Wallabies with Extensive Chromosomal Rearrangements

“…However, approaches are now available to test for introgression separate from incomplete lineage sorting, using both population and phylogenomic approaches (e.g., Pickrell and Pritchard 2012 ; Pease and Hahn 2015 ; Wen et al 2018 ). How taxa are sampled can also affect the ability to resolve recent population divergence with gene flow; sampling of multiple geographically dispersed individuals per taxon should result in improved parameter estimates compared with just one or two individuals ( Robinson et al 2014 ; McLaughlin and Winker 2020 ; e.g., Teng et al 2017 ; Linck et al 2019 ).…”