A comprehensive phylogenomic approach to resolve the relationships among three major Diptera clades: Drosophilidae, Calyptratae, and Tephritidae

This study uses a phylogenomic approach to resolve the relationship between three major Diptera clades, Drosophilidae, Calyptratae (including Muscidae), and Tephritidae. The phylogeny was inferred using different methodological approaches, in order to investigate the robustness of the results. In particular, amino acid, nucleotide and codon datasets were used, and both concatenation-based (supermatrix) and coalescence-based (supertree) approaches were employed. We also tested the effects of taxon sampling, gene sampling, and the removal of problematic genes, as well as the impact of using different tools, including IQ-TREE, RAxML-NG and ASTRAL. Our study revealed pervasive discordance between gene and species trees and differing topologies when using different datasets. However, amino acid datasets consistently resolved the relationship ((Drosophilidae, Calyptratae), Tephritidae), i.e. placing Drosophilidae and Calyptratae as sister groups, and Tephritidae as more distantly related. The observed discordance between the gene and species trees suggests Incomplete Lineage Sorting (ILS), hybridisation, and introgression, as expected given the short internal branches that characterize the split of the three clades, which are typical of rapid radiation events. Our results reinforce the hypothesis that Diptera species have undergone episodic rapid radiation events throughout their history. These events lead to phylogenetic conflict and complications when attempting to resolve the phylogeny of this order. The findings of this study emphasise the importance of using a rich and informative dataset, of using amino acid datasets, as well as integrating coalescent-based approaches when reconstructing the phylogeny of species with a complex evolutionary history such as those of Diptera.