Minimum sample sizes for invasion genomics: Empirical investigation in an invasive whitefly

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 FST; 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 FST 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.

Effect of the Central American Isthmus on gene flow and divergence of the American crocodile ( Crocodylus acutus )

“…2017; Qu et al. 2020). Wild populations of C. acutus in Panama are scarce due to habitat destruction, and the populations sampled were the most adjacent to the Panama Canal.…”

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

“…However, empirical studies have denoted that high throughput DNA sequencing have compensated smaller sample size with large number of generated SNP loci, to ensure high accuracy in estimating population genetic parameters [ 80 , 81 , 82 ]. Sample size as low as four individuals have been documented to be efficient in providing a precise estimate of FST values [ 83 , 84 ]. Indeed, a universal sample size rule may not be feasible to address the complexities in genomic kinship estimates [ 85 ].…”

What Is the Spatial Extent of a Bemisia tabaci Population?

“…While some sampled populations appear to have undergone a population bottleneck, perhaps due to founder events typical of invasive populations or strong population suppression from insecticides [13,55,57], the majority of populations instead exhibit some degree of heterozygote deficit. [13,16,17,54,[56][57][58]60,61,65,66,70]. "MEAM 1" stands for Middle East-Asia Minor 1; "MED" stands for Mediterranean; "IO" stands for Indian Ocean; "SSA 1" stands for Sub-Saharan Africa 1.…”

“…This might follow from an absence of gene flow among divergent populations, suggesting that localized B. tabaci movements over the landscape may predominate, but could also arise if sampling schemes result in high rates of sibling sampling. Additional evidence of inbreeding in microsatellite datasets is strong linkage disequilibrium among loci, wherein allele frequencies among loci are correlated because they share a very recent common ancestor and are still being [13,16,17,54,[56][57][58]60,61,65,66,70]. "MEAM 1" stands for Middle East-Asia Minor 1; "MED" stands for Mediterranean; "IO" stands for Indian Ocean; "SSA 1" stands for Sub-Saharan Africa 1.…”

“…These studies are global in coverage, focus largely on populations of MEAM 1 and MED, and span collections from 1991−2018 ( Figure 1 , Table S1 ). Studies leverage a variety of genetic marker types [ 27 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 ], but, while the majority use microsatellites [ 13 , 16 , 17 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 ], use of single nucleotide polymorphisms is beginning to become more common [ 15 , 69 , 70 , 71 ] ( Figure 1 ). We organize our synthesis around insights gained from three common marker types (cytochrome oxidase I, microsatellites, single nucleotide polymorphisms) and associated measures of genetic diversity and differentiation, interpreting emergent patterns in light of potential underlying ecological and evolutionary processes.…”