Mitochondrial Genome Variations and Possible Adaptive Implications in Some Tephritid Flies (Diptera, Tephritidae)

Tephritidae is an economically important family among Diptera that also exhibits high diversity, biogeographical distribution, and different lifestyles. Despite the recent release of genomes and mitochondrial genome sequences of various species of the family, the evolutionary history of the group and the origin of host adaptation within it remain poorly understood. We undertook a whole-mitochondrial-genome study covering molecular variation at the mitochondrial level by analyzing 10 new mitochondrial genomes obtained from genomic data reported and downloaded from the SRA database from NCBI, analyzed in FastQC and assembled through MITGARD, and 44 mitogenomes available in the Organelle-Refseq database, in total representing 4 subfamilies, 9 tribes, 13 genera, and 54 species. We determined compositional asymmetry and codon usage patterns across the different subfamilies analyzed by using DNASp6 and CAICal. We found high evolutionary rates in the NADH genes, which could play an important role in the adaptation of species to different hosts and environmental variation. By using maximum likelihood phylogenetic reconstruction obtained by IQTREE and ModelFinder, and lifestyle and distribution data of the included species, we considered a generalist feature, explained as possible predominant adaptation in some members of the family. This study in Tephritidae tries to demonstrate possible patterns among molecular variability in mitogenomes, adaptations, and lifestyles. Our findings suggest that selection pressures on certain NADH genes may be linked to host specificity in some Tephritidae species, providing evolutionary insights into how molecular evolution drives ecological adaptation or biogeographical diversity, probably in response to changing environmental conditions and host-parasite co-evolution across taxa.