2 evolutionary history of the Drosophila 3 buzzatii cluster (repleta group) 4 5 Nicolás NAbstract 18The Drosophila repleta group is an array of more than 100 cactophilic species endemic to the 19 "New World". The acquisition of the ability to utilize decaying cactus tissues as breeding and 20 feeding sites is a key aspect that allowed the successful diversification of the repleta group in the 21 American deserts. Within this group, the Drosophila buzzatii cluster is a South American clade of 22 seven cactophilic closely related species in different stages of divergence, a feature that makes it a 2 23 valuable model system for evolutionary research. However, even though substantial effort has been 24 devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, the 25 issue is still controversial. In effect, molecular phylogenetic studies performed to date generated 26 ambiguous results since tree topologies depend on the kind of molecular marker employed.27 Curiously, even though mitochondrial DNA has become a popular marker in evolutionary biology 28 and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far 29 belongs to this cluster. In this work we report the assembly of six complete mitogenomes of five 30 species: D. antonietae, D. borborema, D. buzzatii, D. seriema and two strains of D. koepferae, with 31 the aim to revisit the phylogenetic relationships and divergence times by means of a mitogenomic 32 approach. The recovered topology using complete mitogenomes gives support to the hypothesis of 33 the monophyly of that the D. buzzatii cluster and shows two main clades, one including D. buzzatii 34 and D. koepferae (both strains) and the other the remaining species. These results are in agreement 35 with previous reports based on a few mitochondrial and/or nuclear genes but in conflict with the 36 results of a recent large-scale nuclear phylogeny, suggesting that nuclear and mitochondrial 37 genomes depict different evolutionary histories. 38 Introduction 39 Nowadays, almost every mitochondrial genome, called mitogenome, can be assembled 40 directly from genome or even transcriptome sequencing datasets [1, 2]. The exponential 41 development of next-generation sequencing (NGS) technologies, together with efficient 42 bioinformatic tools for the analysis of genomic information make possible the fast and cheap 43 assembly of mitochondrial genomes, giving rise to the emergence of the mitogenomics era [3]. 44 Mitogenomics has been very useful in illuminating phylogenetic relationships at various depths of 45 the Tree of Life, e.g. among early branching of metazoan phyla [4], among crocodilians and their 46 survival in the Cretaceous-Tertiary boundary [5], Primates [6], the largest clade of freshwater 47 actynopterigian fishes [7] and Anura, the largest living Amphibian group [8]. Also, mitogenomic 3 48 approaches have been used to investigate evolutionary relationships in groups of closely related 49 species (e.g. [9]). In animals, the mitocho...