Phylogenomic Analysis Reveals Evolutionary Relationships of Tropical Drosophilidae: From <i>Drosophila</i> to <i>Scaptodrosophila</i>

Species radiation in the family Drosophilidae has led to a diversity of species occupying a wide range of ecological niches. Despite the high diversity within this family, with over thousands of species and more than a hundred species recorded in Thailand and the Malay Peninsula, taxonomic classifications remain complicated due to morphological plasticity and inconsistent phylogenetic reconstructions based on limited genetic data. In this study, we assemble new mitochondrial genomes from <i>Drosophila</i> and <i>Scaptodrosophila</i> species collected in Thailand, expanding the genomic resources for these underexplored tropical regions. Phylogenetic analyses of 13 mitochondrial protein-coding genes revealed well-supported evolutionary relationships, with <i>Scaptodrosophila</i> forming a distinct lineage and several <i>Drosophila</i> subgroups, such as <i>ananassae</i>, <i>montium</i>, and <i>melanogaster</i>, exhibiting monophyly. Notable discrepancies were observed in the placement of the <i>suzukii</i> subgroup, which was not recovered as monophyletic, and the position of the <i>punjabiensis</i> subgroup, reflecting the complexities of lineage sorting and hybridization events. This comprehensive genomic analysis provides a more accurate understanding of evolutionary relationships within the family Drosophilidae's diversification in the tropics.