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.
Finding optimal sample sizes is critical for the accurate estimation of genetic diversity of large invasive populations. Based on previous studies, we hypothesized that a minimal sample size of 3–8 individuals is sufficient to dissect the population architecture of the harlequin lady beetle, Harmonia axyridis, a biological control agent and an invasive alien species. Here, equipped with a type IIB endonuclease restriction site-associated (2b-RAD) DNA sequencing approach, we identified 13,766 and 13,929 single nucleotide polymorphisms (SNPs), respectively, among native and invasive H. axyridis populations. With this information we simulated populations using a randomly selected 3000 SNPs and a subset of individuals. From this simulation we finally determined that six individuals is the minimum sample size required for the accurate estimation of intra- and inter-population genetic diversity within and across H. axyridis populations. Our findings provide an empirical advantage for population genomic studies of H. axyridis in particular and suggest useful tactics for similar studies on multicellular organisms in general.
An unwelcome side effect of the globalization of the world's economy and dramatic increase in human mobility and trade has been a marked increase in species invasions that have posed severe threats to the ecological, economic, and/or social stability of the introduced regions. In this review, we analyzed the application of molecular markers in invasion genetics of invasive alien insect pests (IAIPs) in China based on a bibliometric survey. Our report discusses the considerable progress that has been made during the past two decades in understanding the invasion genetics of IAIPs in China. We reviewed the major findings in the main topics including the effects of origin and routes of invasion on genetic structure, spatial and temporal genetic changes, factors contributing to the genetic changes of IAIPs, and genetic mechanisms involved in IAIPs' invasions. On the other hand, some of these research areas remain relatively unexplored in China, especially those pertaining to spatial and temporal genetic changes of IAIPs and genetic mechanisms of IAIPs' invasions. Finally, the future research prospects of IAIPs in China are discussed. We hope this review will stimulate an interest in and provide an increased understanding of the field of invasion genetics of IAIPs in China, and provide a basis for future research in this area.
AimThe sweet potato whitefly, Bemisia tabaci MED is a globally invasive species that causes serious economic damage to agroecosystems. Despite the significant threat it poses to agricultural and economic crops worldwide, the global perspective of the invasion patterns and genetic mechanisms contributing to the success of this notorious pest is still poorly understood. The objective of this research was to enhance genome and population genetic analyses to better understand the intricate invasion patterns of B. tabaci MED.LocationSamples were collected in native (Spain, Croatia, Bosnia and Herzegovina, Cyprus, and Israel) and invaded regions (China, South Korea and North America).MethodsWe first assembled a chromosome‐scale reference genome of B. tabaci MED and then employed the restriction site‐associated 2b‐RAD method to genotype over 20,000 high‐quality single‐nucleotide polymorphisms from 29 geographical populations.ResultsA reference genome of B. tabaci MED, with a size of 637.47 Mb, was available. The majority of the assembled sequences (99%) were anchored onto 10 linkage groups, with an N50 size of 58.76 Mb, representing a significant improvement over previous whitefly genome assemblies. We identified rapidly expanded gene families and positively selected genes, probably contributing to successful invasion and rapid adaptation to the new environment. Population genomics analysis showed that three highly differentiated genetic groups were formed, and complex and extensive gene flow occurred across the Mediterranean populations. The genetic admixture patterns in East Asia populations were distinct from those in North America, indicating that they had different source populations.ConclusionsThe high‐quality, chromosome‐scale genome of B. tabaci MED offered opportunities for more comprehensive genome‐wide studies and provided solid foundation to the complex introduction events and the differential invasiveness of B. tabaci MED worldwide.
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