Ecology and Evolution (2020) 10, 38-49

Wan-Mei Qu, Ni Liang, Zi-Ku Wu, You-Gang Zhao and Dong Chu (2020)
Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly
Ecology and Evolution 10 (1), 38-49
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.
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Database assignments for author(s): Dong Chu

Research topic(s) for pests/diseases/weeds:
molecular biology - genes

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Pest and/or beneficial records:

Beneficial	Pest/Disease/Weed	Crop/Product	Country	Quarant.
	Bemisia tabaci biotype MED