Phylogenetic Analysis of the repleta Species Group of the Genus Drosophila Using Multiple Sources of Characters Celeste M. Durando,* , † Richard H. Baker,† , ‡ ,1 William J. Etges,§ William B. Heed, ¶ Marvin Wasserman,* and Rob DeSalle† * Department of Biology, City University of New York, New York, New York 10036; †Department of Entomology, American Museum of Natural History, 79th Street at Central Park West, New York, New York 10024; ‡Department of Biology, Yale University, New Haven, Connecticut 06511; §Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701; and ¶ Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 05721 Received September 14, 1999, revised April 7, 2000 The species in the repleta group of the genus Dro- sophila have been placed into five subgroups—the mulleri, hydei, mercatorum, repleta, and fasciola sub- groups. Each subgroup has been further subdivided into complexes and clusters. Extensive morphological and cytological analyses of the members of this species group have formed the foundation for the proposed relationships among the members of the repleta spe- cies group. Fifty-four taxa, including 46 taxa belong- ing to the repleta species group, were sequenced for fragments of four genes—16S ribosomal DNA (16S), cytochrome oxidase II (COII), and nitrogen dehydro- genase 1 (ND1) of the mitochondrial genome and a region of the hunchback (hb) nuclear gene. We also generated a partial data set of elongation factor 1-al- pha (Ef1) sequences for a subset of taxa. Our analysis used both DNA characters and chromosomal inversion data. The phylogenetic hypothesis we obtained sup- ports many of the traditionally accepted clades within the mulleri subgroup, but the monophyly of taxonomic groups outside of this subgroup appears not to be sup- ported. Phylogenetic analysis revealed one well-sup- ported, highly resolved clade that consists of closely related members of the mulleri and buzzatii com- plexes. The remaining taxa, a wide assortment of tax- onomic groups, ranging from members of other spe- cies groups to members of several subgroups and members of three species complexes from the mulleri subgroup are found in poorly supported arrangements at the base of the tree. © 2000 Academic Press INTRODUCTION The Drosophila repleta species group is among the largest of all species groups in the genus Drosophila. Part of the virilis–repleta radiation (Throckmorton, 1982a), it is considered one of the most important and successful radiations in the genus Drosophila. For the most part the members of the repleta species group are found in the arid or semiarid deserts of the New World where they live on various species of cactus (Wasser- man, 1992). The species in this group have been placed into five subgroups—the D. mulleri subgroup, the D. hydei subgroup, the D. mercatorum subgroup, the D. repleta subgroup, and the D. fasciola subgroup—and each subgroup has been further subdivided into com- plexes, clusters, and subclusters. Current knowledge of the phylogeny of this species group is based on the morphological work of Throck- morton (1982a) and Vilela (1983) and the cytological work of Wasserman (1982, 1992 for reviews). In addi- tion, several allozyme studies (Zouros, 1973; Richard- son et al., 1975; Richardson and Smouse, 1976; Rich- ardson et al., 1977; Heed et al., 1990) and some molecular studies (Sullivan et al., 1990; Russo et al., 1995; Spicer, 1995, 1996) have contributed to our knowledge of relationships among members of subsets of this species group. However, none of the allozyme or molecular studies has attempted to address the phylo- genetic relationships of the repleta species group as a whole. Detailed polytene chromosome maps have been con- structed for 70 of the 91 species in this group, and more than 296 inversions have been mapped, of which 118 constitute fixed differences between species. Ninety- four of these 118 fixed chromosomal inversions are autapomorphic and diagnostic for various single spe- cies. Several of the chromosomal inversions that have been studied so far are variable among closely related species indicating the possible utility of inversions as phylogenetic tools at this level, yet the degree of reso- lution from the inversion data within species com- plexes and clusters is low (Wasserman, 1992). In addi- tion, although these data have been used to infer relationships among species, they tell us little about 1 Present address: The Galton Laboratory, University College Lon- don, 4 Stephenson Way, London NW1 2HE, UK. Molecular Phylogenetics and Evolution Vol. 16, No. 2, August, pp. 296 –307, 2000 doi:10.1006/mpev.2000.0824, available online at http://www.idealibrary.com on 1055-7903/00 $35.00 Copyright © 2000 by Academic Press All rights of reproduction in any form reserved. 296