Unraveling the cryptic Bemisia tabaci species complex: Global phylogenomic analysis reveals evolutionary relationships and biogeographic patterns.

Bemisia tabaci is a complex of cryptic agro-economically important pest species characterized by diverse clades, substantial genetic diversity along with strong phylogeographic associations. However, a comprehensive phylogenomic analysis across the entire complex has been lacking, we thus conducted phylogenomic analyses and explored biogeographic patterns using 680 single-copy nuclear genes (SCNs) obtained from whole-genome sequencing data of 58 globally sourced B. tabaci specimens. We constructed both concatenation and coalescent trees using 680 SCNs, which produced highly supported bootstrap values and nearly identical topologies for all major clades. When comparing these concatenation trees with those constructed using mitochondrial cytochrome oxidase I (mtCOI) and mitochondrial genome, we found conflicting phylogenetic relationships, with the later trees recovering fewer major clades. In a separate comparison between concatenation and coalescent trees, particularly those generated using IQ-TREE, they were found to delineate population relationships more effectively than RaxML. In contrast, coalescent phylogenies were proficient in elucidating geographical dispersal patterns and the reorganization of biological species. Furthermore, we provided a strict consensus tree that clearly defines relationships within most clades, laying a solid foundation for future research on the evolution and taxonomy of B. tabaci. Ancestral range estimates suggested that the ancestral region of the complex is likely situated in equatorial Africa, the Middle East, and Mediterranean regions. Subsequently, the expansion occurred into part of the Palearctic and further into the Nearctic, Neotropical, Indomalayan, and Australasian regions. These findings challenge both previous classifications and origin hypotheses, offering a notably more comprehensive understanding of the global distribution, evolutionary history, diversification, and biogeography of B. tabaci.