Accurate characterization of members of the Bemisia tabaci cryptic species group requires combined genomic and morphological approaches. Both mitochondrial (mtDNA) [namely, cytochrome oxidase I gene (COI)] and nuclear DNA (nDNA) markers have been explored for taxonomic classification and to study population dynamics. However, careful consideration is essential when selecting these markers. The mtDNA exhibits a high mutation rate, and the presence of nuclear mitochondrial pseudogenes (numts) can confound accurate identification, while nDNA sequences show low intraspecific divergence, heterogeneous mutation rate, and recombination. Here, a nuclear loci dataset was validated for phylogenetic informativeness for select populations of B. tabaci available in a global whitefly collection. Three nuclear markers yielded phylogenies that mirror those of the mitochondrial COI, and one of them, the ribosomal protein-15 (RP15) was instrumental in identifying intraspecific hybridization patterns. The RP15 marker was used to analyze B. tabaci groups associated with cassava in Sub-Saharan Africa (SSA). The RP15 allelic frequencies of the predominant ‘super-abundant’ B. tabaci group SSA-SG1 suggest it resulted from intraspecific hybridization between SSA2 and SSA1-SG3 groups. The variation in RP15 allele frequencies among SSA-SG1 individuals indicates contemporary hybridization, with hybrids varying in genome composition due to repeated introductions of parental chromosomal segments. These results underscore the importance of historical and ongoing hybridization events that shape the evolution of the B. tabacicryptic species group. Understanding the consequences of hybridization is integral to developing effective pest management strategies and biosecurity measures for agricultural crops.
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