Molecular Phylogenetics and Evolution xxx (2005) xxx–xxx www.elsevier.com/locate/ympev 1055-7903/$ - see front matter  2005 Published by Elsevier Inc. doi:10.1016/j.ympev.2005.02.018 ARTICLE IN PRESS The phylogeny of the subgroups within the melanogaster species group: Likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny Rebecca L. Lewis, Andrew T. Beckenbach, Arne Ø. Mooers ¤ Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada V5A 1S6 Received 4 September 2004; revised 12 January 2005 Abstract The relationships among the majority of the subgroups in the Drosophila melanogaster species group remain unresolved. We pres- ent a 2223 basepair dataset for mitochondrial cytochrome oxidase I and cytochrome oxidase II for 43 species (including new data from 11 species), sampled to include the major subgroups. After a brief review of competing hypotheses for the ananassae, montium, suzukii, and takahashii subgroups, we combine the two genes based on a new use of the SH test and present KH and SH likelihood comparisons (Kishino and Hasegawa, 1989. J. Mol. Evol. 29, 170–179; Shimodaira and Hasegawa, 1999) to test the monophyly and placement of these subgroups within the larger species group. Although we Wnd insigniWcant diVerences between the two suggested placements for the ananassae subgroup, the ananassae is sister to the rest of the subgroups in the melanogaster species group in every investigation. For the takahashii subgroup, although we cannot reject monophyly, the species are so closely related to the suzukii sub- group for these data that the two subgroups often form one clade. Finally, we present a Bayesian estimate of the phylogeny for both genes combined, utilizing a recently published method that allows for diVerent models of evolution for diVerent sites.  2005 Published by Elsevier Inc. Keywords: Drosophila melanogaster; Takahashii; Suzukii; Ananassae; Montium; COI; COII; Phylogeny; Likelihood; Ratchet; Bayesphylogenies 1. Introduction Drosophila melanogaster, a member of the order Dip- tera (two-winged Xies), is a diversely studied species in many Welds of biology and has served as a model organ- ism in, for example, both developmental biology and evolutionary genetic analysis (see, e.g., Presgraves et al., 2003; Sempere et al., 2003). This species was also the sec- ond metazoan to have its genome completely sequenced (Adams et al., 2000), and is also a model species for many behavioral investigations (see, e.g., Dukas and Mooers, 2003; Friberg and Arnqvist, 2003). However, D. melanogaster is not the only member of the Drosophila genus to be extensively studied: Drosophila yakuba was the Wrst species to have its mitochondrion completely sequenced (Clary and Wolstenholme, 1985) and now serves as the standard for comparison when sequencing and aligning mitochondrial sequences. Extensive studies into the phylogenies of the obscura (Beckenbach et al., 1993; Gleason et al., 1997), saltans (O’Grady et al., 1998), and willistoni (Gleason et al., 1998) species groups (which are all members of the Sophophora subgenus) have been reported over the years; however, as of yet, there is no complete phylogeny for melanogaster species group. Here, we examine four subgroups within the melano- gaster species group whose placement and clade status is the subject of ongoing work: the ananassae, montium, * Corresponding author. E-mail address: amooers@sfu.ca (A.Ø. Mooers).