The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex

A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group

Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.

Morphology-based identification of Bemisia tabaci cryptic species puparia via embedded group-contrast convolution neural network analysis

The Bemisia tabaci species complex is a group of tropical–subtropical hemipterans, some species of which have achieved global distribution over the past 150 years. Several species are regarded currently as among the world’s most pernicious agricultural pests, causing a variety of damage types via direct feeding and plant-disease transmission. Long considered a single variable species, genetic, molecular and reproductive compatibility analyses have revealed that this “species” is actually a complex of between 24 and 48 morphologically cryptic species. However, determinations of which populations represent distinct species have been hampered by a failure to integrate genetic/molecular and morphological species–diagnoses. This, in turn, has limited the success of outbreak-control and eradication programs. Previous morphological investigations, based on traditional and geometric morphometric procedures, have had limited success in identifying genetic/molecular species from patterns of morphological variation in puparia. As an alternative, our investigation focused on exploring the use of a deep-learning convolution neural network (CNN) trained on puparial images and based on an embedded, group-contrast training protocol as a means of searching for consistent differences in puparial morphology. Fifteen molecular species were selected for analysis, all of which had been identified via DNA barcoding and confirmed using more extensive molecular characterizations and crossing experiments. Results demonstrate that all 15 species can be discriminated successfully based on differences in puparium morphology alone. This level of discrimination was achieved for laboratory populations reared on both hairy-leaved and glabrous-leaved host plants. Moreover, cross-tabulation tests confirmed the generality and stability of the CNN discriminant system trained on both ecophenotypic variants. The ability to identify B. tabaci species quickly and accurately from puparial images has the potential to address many long-standing problems in B. tabaci taxonomy and systematics as well as playing a vital role in ongoing pest-management efforts. [Aleyrodidae; entomology; Hemiptera; machine learning; morphometrics; pest control; systematics; taxonomy; whiteflies.]

A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey

Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multi-primer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the 'tabaci' species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multi-primer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multi-primer HTS metabarcoding method incorporated two over-lapping amplicons of 472bp and 518bp that spanned the entire 657bp 3' barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.

Phylogeographic and SNPs Analyses of Bemisia tabaci B Mitotype Populations Reveal Only Two of Eight Haplotypes Are Invasive

Simple Summary

The whitefly Bemisia tabaci taxon consists of an undefined number of morphologically identical genetic variants of which only a few, including the B, harbor invasive haplotypes. These haplotypes have potential to upsurge and become important pests and plant virus vectors in irrigated agroecosystems worldwide. In the 1980s, unprecedented outbreaks associated with the B variant were reported worldwide, however, the precise origin(s) of the invasive haplotypes has not been determined. In this study, available B. tabaci mitochondrial gene sequences were examined for patterns of conserved single nucleotide changes (SNPs). The whitefly sequence records represented North Africa-Middle Eastern habitats, the proposed B variant center of origin, and distant locales recently invaded by haplotype(s) of the B variant. Unexpectedly, the analysis revealed eight SNPs groups (haplotypes) demonstrating that the genetic architecture of the B mitoype is more complex than previously recognized. Also, the distribution patterns of the eight B haplotypes were tightly linked to well-defined eco-geographic regions, suggesting the different groups have diversified by geographic isolation. Contrary to claims that collectively, the B variant is invasive, only two of the eight haplotypic groups have established in geographical locations outside of their zone of endemism.

Abstract

The Bemisia tabaci cryptic species contains 39 known mitotypes of which the B and Q are best recognized for having established outside their extant endemic range. In the 1980s, previously uncharacterized haplotype(s) of the B mitotype rapidly established in tropical and subtropical locales distant from their presumed center of origin, leading to displacement of several native mitotypes and extreme damage to crops and other vegetation particularly in irrigated agroecosystems. To trace the natural and evolutionary history of the invasive B haplotypes, a phylo-biogeographic study was undertaken. Patterns of single nucleotide polymorphisms (SNPs) and signatures potentially indicative of geographic isolation were investigated using a globally representative mitochondrial cytochrome oxidase I gene (mtCOI) sequence database. Eight haplotype groups within the North Africa-Middle East (NAFME) region were differentiated, NAFME 1–8. The NAFME 1–3 haplotypes were members of the same population that is associated with warm desert climate niches of the Arabian Peninsula and east coastal Africa-Ethiopia. The NAFME 4 and 5 haplotypes are endemic to warm and cold semi-arid niches delimited by the Irano-Turanian floristic region, itself harboring extensive biodiversity. Haplotypes 6 and 7 co-occurred in the Middle East along eastern Mediterranean Sea landmasses, while NAFME 8 was found to be endemic to Cyprus, Turkey, and desert micro-niches throughout Egypt and Israel. Contrary to claims that collectively, the B mitotype is invasive, NAFME 6 and 8 are the only haplotypes to have established in geographical locations outside of their zone of endemism.

Whole-genome sequencing to detect mutations associated with resistance to insecticides and Bt proteins in Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a major pest native to the Americas that has recently invaded the Old World. Point mutations in the target-site proteins acetylcholinesterase-1 (ace-1), voltage-gated sodium channel (VGSC) and ryanodine receptor (RyR) have been identified in S. frugiperda as major resistance mechanisms to organophosphate, pyrethroid and diamide insecticides respectively. Mutations in the adenosine triphosphate-binding cassette transporter C2 gene (ABCC2) have also been identified to confer resistance to Cry1F protein. In this study, we applied a whole-genome sequencing (WGS) approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China, Malawi, Uganda and Brazil. This approach revealed three amino acid substitutions (A201S, G227A and F290V) of S. frugiperda ace-1, which are known to be associated with organophosphate resistance. The Brazilian population had all three ace-1 point mutations and the 227A allele (mean frequency = 0.54) was the most common. Populations from China, Malawi and Uganda harbored two of the three ace-1 point mutations (A201S and F290V) with the 290V allele (0.47-0.58) as the dominant allele. Point mutations in VGSC (T929I, L932F and L1014F) and RyR (I4790M and G4946E) were not detected in any of the 150 individuals. A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations. Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations, but also provide insights for improvement of resistance management tactics in S. frugiperda.

On species delimitation, hybridization and population structure of cassava whitefly in Africa

The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.

Genetic diversity of whitefly (Bemisia spp.) on crop and uncultivated plants in Uganda: implications for the control of this devastating pest species complex in Africa

Over the past three decades, highly increased whitefly (Bemisia tabaci) populations have been observed on the staple food crop cassava in eastern Africa and associated with ensuing viral disease pandemics and food insecurity. Increased whitefly numbers have also been observed in other key agricultural crops and weeds. Factors behind the population surges on different crops and their interrelationships are unclear, although in cassava they have been associated with specific populations within the Bemisia tabaci species complex known to infest cassava crops in Africa. This study carried out an in-depth survey to understand the distribution of B. tabaci populations infesting crops and uncultivated plant hosts in Uganda, a centre of origin for this pest complex. Whitefly samples were collected from 59 identified plant species and 25 unidentified weeds in a countrywide survey. Identities of 870 individual adult whiteflies were determined through mitochondrial cytochrome oxidase 1 sequences (651 bp) in the 3' barcode region used for B. tabaci systematics. Sixteen B. tabaci and five related whitefly putative species were identified based on > 4.0% nucleotide divergence, of which three are proposed as novel B. tabaci putative species and four as novel closely related whitefly species. The most prevalent whiteflies were classified as B. tabaci MED-ASL (30.5% of samples), sub-Saharan Africa 1 (SSA1, 22.7%) and Bemisia Uganda1 (12.1%). These species were also indicated to be the most polyphagous occurring on 33, 40 and 25 identified plant species, respectively. Multiple (≥ 3) whitefly species occurred on specific crops (bean, eggplant, pumpkin and tomato) and weeds (Sida acuta and Ocimum gratissimum). These plants may have increased potential to act as reservoirs for mixed infections of whitefly-vectored viruses. Management of whitefly pest populations in eastern Africa will require an integration of approaches that consider their degree of polyphagy and a climate that enables the continuous presence of crop and uncultivated plant hosts.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10340-021-01355-6.

Improving climate suitability for Bemisia tabaci in East Africa is correlated with increased prevalence of whiteflies and cassava diseases

Projected climate changes are thought to promote emerging infectious diseases, though to date, evidence linking climate changes and such diseases in plants has not been available. Cassava is perhaps the most important crop in Africa for smallholder farmers. Since the late 1990’s there have been reports from East and Central Africa of pandemics of begomoviruses in cassava linked to high abundances of whitefly species within the Bemisia tabaci complex. We used CLIMEX, a process-oriented climatic niche model, to explore if this pandemic was linked to recent historical climatic changes. The climatic niche model was corroborated with independent observed field abundance of B. tabaci in Uganda over a 13-year time-series, and with the probability of occurrence of B. tabaci over 2 years across the African study area. Throughout a 39-year climate time-series spanning the period during which the pandemics emerged, the modelled climatic conditions for B. tabaci improved significantly in the areas where the pandemics had been reported and were constant or decreased elsewhere. This is the first reported case where observed historical climate changes have been attributed to the increase in abundance of an insect pest, contributing to a crop disease pandemic.

KASP Genotyping as a Molecular Tool for Diagnosis of Cassava-Colonizing Bemisia tabaci

Bemisia tabaci is a cryptic species complex that requires the use of molecular tools for identification. The most widely used approach for achieving this is the partial sequencing of the mitochondrial DNA cytochrome oxidase I gene (COI). A more reliable single nucleotide polymorphism (SNP)-based genotyping approach, using Nextera restriction-site-associated DNA (NextRAD) sequencing, has demonstrated the existence of six major haplogroups of B. tabaci on cassava in Africa. However, NextRAD sequencing is costly and time-consuming. We, therefore, developed a cheaper and more rapid diagnostic using the Kompetitive Allele-Specific PCR (KASP) approach. Seven sets of primers were designed to distinguish the six B. tabaci haplogroups based on the NextRAD data. Out of the 152 whitefly samples that were tested using these primer sets, 151 (99.3%) produced genotyping results consistent with NextRAD. The KASP assay was designed using NextRAD data on whiteflies from cassava in 18 countries across sub-Saharan Africa. This assay can, therefore, be routinely used to rapidly diagnose cassava B. tabaci by laboratories that are researching or monitoring this pest in Africa. This is the first study to develop an SNP-based assay to distinguish B. tabaci whiteflies on cassava in Africa, and the first application of the KASP technique for insect identification.

Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Colonizing Sweet Potato and Cassava in South Sudan

Bemisia tabaci (Gennadius) is a polyphagous, highly destructive pest that is capable of vectoring viruses in most agricultural crops. Currently, information regarding the distribution and genetic diversity of B. tabaci in South Sudan is not available. The objectives of this study were to investigate the genetic variability of B. tabaci infesting sweet potato and cassava in South Sudan. Field surveys were conducted between August 2017 and July and August 2018 in 10 locations in Juba County, Central Equatoria State, South Sudan. The sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) were used to determine the phylogenetic relationships between sampled B. tabaci. Six distinct genetic groups of B. tabaci were identified, including three non-cassava haplotypes (Mediterranean (MED), Indian Ocean (IO), and Uganda) and three cassava haplotypes (Sub-Saharan Africa 1 sub-group 1 (SSA1-SG1), SSA1-SG3, and SSA2). MED predominated on sweet potato and SSA2 on cassava in all of the sampled locations. The Uganda haplotype was also widespread, occurring in five of the sampled locations. This study provides important information on the diversity of B. tabaci species in South Sudan. A comprehensive assessment of the genetic diversity, geographical distribution, population dynamics, and host range of B. tabaci species in South Sudan is vital for its effective management.

Nuclear Orthologs Derived from Whole Genome Sequencing Indicate Cryptic Diversity in the Bemisia tabaci (Insecta: Aleyrodidae) Complex of Whiteflies

The Bemisia tabaci complex of whiteflies contains globally important pests thought to contain cryptic species corresponding to geographically structured phylogenetic clades. Although mostly morphologically indistinguishable, differences have been shown to exist among populations in behavior, plant virus vector capacity, ability to hybridize, and DNA sequence divergence. These differences allow for certain populations to become invasive and cause great economic damage in a monoculture setting. Although high mitochondrial DNA divergences have been reported between putative conspecifics of the B. tabaci species complex, there is limited data that exists across the whole genome for this group. Using data from 2184 orthologs obtained from whole genome sequencing (Illumina), a phylogenetic analysis using maximum likelihood and coalescent methodologies was completed on ten individuals of the B. tabaci complex. In addition, automatic barcode gap discovery methods were employed, and results suggest the existence of five species. Although the divergences of the mitochondrial cytochrome oxidase I gene are high among members of this complex, nuclear divergences are much lower in comparison. Single-copy orthologs from whole genome sequencing demonstrate divergent population structures among members of the B. tabaci complex and the sequences provide an important resource to aid in future genomic studies of the group.

Going global - genomic insights into insect invasions

The spread of invasive insect pests is becoming an increasing problem for agriculture globally. We discuss a number of invasive insects, already of major economic significance that have recently expanded their range to become truly global threats. These include the noctuid moths Helicoverpa and Spodoptera, whose caterpillars have long been among the worst pests in their native Old and New World habitats, respectively, and the whitefly Bemisia, a major vector of plant virus diseases. Importantly, genomic resources for these species have recently become available, allowing research to move beyond the restrictions imposed by earlier approaches limited to a single or few mitochondrial and nuclear markers, to employ genome-wide genotyping and resequencing protocols. These studies have shown hybridisation within the various species complexes, identified regions under selection in agricultural environments, and enable monitoring of genes important as biosecurity risks through introgression into established populations free of the genes. In all cases studied, global trade has emerged as the probable cause of insect spread, making it ever more important that biosecurity protocols and agencies work with researchers to make the most effective use of emerging genomic resources and tools.

Distribution and phylogenetics of whiteflies and their endosymbiont relationships after the Mediterranean species invasion in Brazil

The Bemisia tabaci is a polyphagous insect and a successful vector of plant viruses. B. tabaci is a species complex and in Brazil native species from the New World (NW) group, as well as the invasive species, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) were reported. For better understanding the distribution of the different species four years after the Mediterranean species invasion in Brazil, whiteflies were collected from 237 locations throughout the country between the years of 2013 and 2017, species were identified and the facultative endosymbionts detected. The survey revealed that MEAM1 was the prevalent species found on major crops across Brazil. It is the only species present in North, Northwestern and Central Brazil and was associated with virus-infected plants. MED was found in five States from Southeast to South regions, infesting mainly ornamental plants and was not associated with virus-infected plants. The prevalent endosymbionts identified in MEAM1 were Hamiltonella and Rickettsia; and the mtCOI analysis revealed low genetic diversity for MEAM1. In contrast, several different endosymbionts were identified in MED including Hamiltonella, Rickettsia, Wolbachia and Arsenophonus; and two distinct genetic groups were found based on the mtCOI analysis. Monitoring the distribution of the whiteflies species in Brazil is essential for proper management of this pest.

Whitefly-transmitted viruses threatening cassava production in Africa

Emerging plant viruses are one of the greatest problems facing crop production worldwide, and have severe consequences in the developing world where subsistence farming is a major source of food production, and knowledge and resources for management are limited. In Africa, evolution of two viral disease complexes, cassava mosaic begomoviruses (CMBs) (Geminiviridae) and cassava brown streak viruses (CBSVs) (Potyviridae), have resulted in severe pandemics that continue to spread and threaten cassava production. Identification of genetically diverse and rapidly evolving CMBs and CBSVs, extensive genetic variation in the vector, Bemisia tabaci (Hemiptera: Aleyrodidae), and numerous secondary endosymbiont profiles that influence vector phenotypes suggest that complex local and regional vector-virus-plant-environment interactions may be driving the evolution and epidemiology of these viruses.

Comparative transcriptome analysis reveals genetic diversity in the endosymbiont Hamiltonella between native and exotic populations of Bemisia tabaci from Brazil

The whitefly, Bemisia tabaci, is a species complex of more than 40 cryptic species and a major agricultural pest. It causes extensive damage to plants mainly by transmitting plant viruses. There is still a lack of genomic data available for the different whitefly species found in Brazil and their bacterial endosymbionts. Understanding the genetic and transcriptomic composition of these insect pests, the viruses they transmit and the microbiota is crucial to sustainable solutions for farmers to control whiteflies. Illumina RNA-Seq was used to obtain the transcriptome of individual whiteflies from 10 different populations from Brazil including Middle East-Asia Minor 1 (MEAM1), Mediterranean (MED) and New World 2 (NW2). Raw reads were assembled using CLC Genomics Workbench and subsequently mapped to reference genomes. We obtained whitefly complete mitochondrial genomes and draft genomes from the facultative bacterial endosymbiont Hamiltonella for further phylogenetic analyses. In addition, nucleotide sequences of the GroEL chaperonin gene from Hamiltonella from different populations were obtained and analysed. There was concordance in the species clustering using the whitefly complete mitogenome and the mtCOI gene tree. On the other hand, the phylogenetic analysis using the 12 ORF's of Hamiltonella clustered the native species NW2 apart from the exotics MEAM1 and MED. In addition, the amino acid analysis of GroEL chaperonin revealed a deletion only in Hamiltonella infecting NW2 among whiteflies populations analysed which was further confirmed by PCR and Sanger sequencing. The genomic data obtained in this study will aid understanding the functions that Hamiltonella may have in whitefly biology and serve as a reference for further studies regarding whiteflies in Brazil.

An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the "ASL" does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.

African ancestry of New World, Bemisia tabaci-whitefly species

Bemisia tabaci whitefly species are some of the world’s most devastating agricultural pests and plant-virus disease vectors. Elucidation of the phylogenetic relationships in the group is the basis for understanding their evolution, biogeography, gene-functions and development of novel control technologies. We report here the discovery of five new Sub-Saharan Africa (SSA) B. tabaci putative species, using the partial mitochondrial cytochrome oxidase 1 gene: SSA9, SSA10, SSA11, SSA12 and SSA13. Two of them, SSA10 and SSA11 clustered with the New World species and shared 84.8‒86.5% sequence identities. SSA10 and SSA11 provide new evidence for a close evolutionary link between the Old and New World species. Re-analysis of the evolutionary history of B. tabaci species group indicates that the new African species (SSA10 and SSA11) diverged from the New World clade c. 25 million years ago. The new putative species enable us to: (i) re-evaluate current models of B. tabaci evolution, (ii) recognise increased diversity within this cryptic species group and (iii) re-estimate divergence dates in evolutionary time.

Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO). Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.

Updated mtCOI reference dataset for the Bemisia tabaci species complex

Members of the whitefly Bemisia tabaci species complex cause millions of dollars of damage globally and are considered one of the world's most invasive species. They are capable of causing extensive damage to major vegetable, grain legume and fiber crops. All member of the species complex are morphologically identical therefore, data from the partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene sequence has been used to identify the various species. The current reference dataset that is widely used is found on the CSIRO data portal. However, the reference set stored on the CSIRO data does not include newly added sequences (2013-2017), therefore an updated reference dataset is needed.  All mtCOI data for the Bemisia tabaci species complex were downloaded on 22 May 2017 from GenBank and after quality checking, a dataset of 1,071 unique sequences and 696 base pairs was generated (https://doi.org/10.6084/m9.figshare.5437420.v1).