Abstract
Analysis of population genetics provides insights into the evolutionary processes, among which the sample size choice is per se a crucial issue in the analysis. Genome‐wide high‐throughput techniques based on RADseq have been increasingly used in studies on the population genomics of invasive species. However, there is little information available regarding optimal sample sizes for analyzing population genomics of invasive species. In this study, we first use type IIB endonucleases restriction site‐associated DNA (2b‐RAD) to mine thousands of single nucleotide polymorphisms (SNPs) for native and introduced populations in Q1 clade (SPB and 17JN) and Q2 clade (ISQ and UAS0601) of the whitefly, Bemisia tabaci (Gennadius) MED (also known as B. tabaci biotype Q). Then, we used resampling techniques to create simulated populations with a random subset of individuals and 3,000 SNPs to determine how many individuals should be sampled for accurate estimates of intra‐ and interpopulation genetic diversity. We calculated the intrapopulation genetic diversity parameters (unbiased expected heterozygosity, observed heterozygosity, and the number of effect alleles) and pairwise genetic differentiation F ST; finally, an ad hoc statistic, ΔK, was used to determine the optimal value. Our results showed that a sample size greater than four individuals (n ≥ 4) has little impact on estimates of genetic diversity within whitefly populations; moreover, precise estimate of F ST can be easily achieved at a very small simple size (n = 3 or 4). Our results will provide in‐depth understanding of the optimization of sampling schemes in population genomics of invasive species.
Highlights
Analysis of population genetics provides insights into the evolution‐ ary processes, among which the sample size selection is per se a crucial issue in the analysis (Hale, Burg, & Steeves, 2012; Nazareno, Bemmels, Dick, & Lohmann, 2017; Willing, Dreyer, & Oosterhout, 2012)
We evaluated the influence of rising sample sizes for intra‐ and inter‐ population genetic diversity valuation by resampling 2 to 8 samples from empirical data sets attained for the four B. tabaci populations
Genome‐wide high‐throughput techniques based on restriction site‐associated DNA sequencing (RADseq) have been widely used in ascertaining the population genomics of in‐ vasive species (Elfekih et al, 2018; Resh et al, 2018; Yi et al, 2018)
Summary
Analysis of population genetics provides insights into the evolution‐ ary processes, among which the sample size selection is per se a crucial issue in the analysis (Hale, Burg, & Steeves, 2012; Nazareno, Bemmels, Dick, & Lohmann, 2017; Willing, Dreyer, & Oosterhout, 2012). Recent studies have shown that analyzing population ge‐ netics can be conducted with small sample sizes when using a large number of single nucleotide polymorphisms (SNP; Jeffries et al, 2016; Nazareno et al, 2017). The RADseq technique has been widely used in the study of population genomics (Blanco‐Bercial & Bucklin, 2016; Wosula, Chen, Fei, & Legg, 2017), with the minimum sample size for population ge‐ nomics being evaluated based on simulation (Willing et al, 2012) or empirical analysis (Nazareno et al, 2017). By estimating the genetic differentiation (FST) a simulation analysis has shown that sample size can be reduced to four to six individuals when using a large number of SNPs (Willing et al, 2012). The ΔK means the sec‐ ond‐order rate of change in the likelihood function with respect to K; after the ΔK reaches the peak value, increasing the K value appeals to have little impact on the genetic diversity parameters
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