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P473052-Prelims.qxd 10/1/05 5:18 PM Page vii Preface When you say “Drosophila” to most people, they think of Drosophila melanogaster, the laboratory workhorse that for nearly 100 years has been the premier genetic model system in biology. Many remember the smell of ether while handling flies in their undergraduate biology classes, while others recall curly wings and white eyes and Punnet squares. T. H. Morgan and his students C. Bridges, H. J. Muller, and A. H. Sturtevant pioneered the field of Drosophila genetics during the first half of the twentieth century. Their work has been carried on by countless “drosophilists” and, in some ways, culminated with the publication of the full genome sequence of Drosophila melanogaster in 2000. Now Drosophila biology is entering a new era. The genome of a second species, Drosophila pseudoobscura, has recently been completed and more are surely to come. Increasingly, when researchers state that they work on Drosophila they are met with the following question: “What species?” Scientists in the fields of ecology and evolu- tionary biology are beginning to co-opt various members of the genus Drosophila to serve as a model system for their own research, largely because of the ease of obtain- ing molecular markers from these species. As we were preparing this book for publi- cation, the National Human Genome Research Institute approved whole genome sequencing of 10 additional Drosophila species, and the creation of BAC libraries for 20. We feel that this initiative will invigorate Drosophila research for the next 100 years. The genus Drosophila represents an unprecedented model system not only for understanding genome evolution, but also for comparative experimental research. No other group has such a well-defined phylogeny and an extensive literature on genetics, development, neurobiology and behavior, physiology, and ecology. A. H. Sturtevant, one of the pioneers of Drosophila genetics, was clearly aware of the importance of the evolutionary context in which D. melanogaster is embedded. He described many new Drosophila species, studied their behavior and genetic relationships, and published his 1921 monograph, The North American Species of Drosophila. A number of excellent resources exist in which the primary literature concerning the distribution, evolutionary relationships, and ecology for most of the known Drosophila species is summarized. In 1952, J. T. Patterson and W. Stone published their still indispensable Evolution in the Genus Drosophila, which, while drawing heavily on work generated from their own activities and those of their students, pro- vided the first overview of the evolutionary relationships and distributions of all known Drosophila species. The international Drosophila community has since con- tributed its expertise to five volumes of the The Genetics and Biology of Drosophila series, edited by Ashburner, Carson and Thompson between 1981 and 1986. Michael Ashburner (1990, 2004) and Jeff Powell (1997) have both compiled encyclopedic works that effectively summarize decades of basic Drosophila research. A wide range P473052-Prelims.qxd 10/1/05 5:18 PM Page viii viii Preface of data for many Drosophila species now can be accessed through web-based resources such as Flybase and Taxodros. As the number of investigators taking advantage of Drosophila diversity grows, the need for a portable resource for identifying and using the different species becomes increasingly critical. In 2001, the Tucson Stock Center began offering the now annual Drosophila Species Identification Workshop to teach basic approaches to keying out flies and maintaining non-melanogaster species in laboratory culture. The over- whelming interest of the research community in attending this workshop and in becoming comfortable with using species in addition to D. melanogaster has led us to create this guide. We have had the amazing good fortune of having the participation in these workshops of many colleagues who were responsible for the original collections and descriptions of diverse Drosophila species: Wyatt Anderson, Michael Ashburner, Hampton Carson, David Foote, Nicolas Gompel, William Heed, Kenneth Kaneshiro, Thom Kaufman, Margaret Kidwell, Kathy Matthews, Bryant McAllister, Stephen Schaeffer, Valerie Schaworoch, Marvin Wasserman, and Marshall Wheeler. To all of them we express our gratitude for their unselfish sharing of their time and expertise with us and with the students in the workshops. Activities associated with the annual workshops, including input from the attendees, have been instrumental in shaping the contents of this guide. Space limitations prevent us from including all Drosophila species in this guide. We have chosen to focus upon the several hundred species maintained at the Tucson Stock Center, as these are readily available to the community and the demand for them is increasing. Conditions for the successful rearing of these species have been worked out and the life history differences critical to their meaningful use in comparative experimental work have been well documented for a number of them. We hope that this guide encourages and enables researchers to exploit the wealth of diversity offered by Drosophila in their investigations. Therese Ann Markow Patrick O’Grady P473052-Ch01.qxd 10/1/05 5:19 PM Page 3 CHAPTER 1 Phylogenetic relationships of Drosophilidae Contents • The origin of the family Drosophilidae • Drosophilidae: relationships among genera • Steganinae • Drosophilinae • Conclusions • Acknowledgements • References The origin of the family Drosophilidae The Drosophilidae is an acalyptrate family in the superfamily Ephydroidea (McAlpine, 1989). This superfamily contains two large families, Ephydridae and Drosophilidae, as well as several smaller families, such as Camilidae, Diastatidae, and Curtonotidae. Throckmorton (1975) suggested that Diastatidae was the closest relative of the Drosophilidae, based largely on the fact that diastatids are saprophagous in leaf mold (Oldroyd, 1964; Hennig, 1965). Even though Okada (1962) suggested that the ances- tral drosophilid substrate was bleeding tree sap, Throckmorton (1975) believed that the current diversity of substrates was the result of opportunism centering on the saprophagous leaf-mold habit. Grimaldi (1990) examined the phylogenetic relationships of Ephydroidea using mor- phological characters. Of the three most parsimonious trees his search recovered, he selected a “preferred phylogeny”. The strict consensus of all three trees gives the more conservative hypothesis (Figure 1.1a). McAlpine (1989) presents an alternative view of evolution in the superfamily Ephydroidea (Figure 1.1b). These two phylogenetic hypothe- ses differ mainly in the placement of Drosophilidae. The strict consensus of Grimaldi’s (1990) trees is unable to resolve the sister group of the Drosophilidae (his preferred tree favored the Curtonotidae as the sister family of Drosophilidae). McAlpine’s (1989) phylogeny, however, suggests that the Camilidae is the sister clade of Drosophilidae. The exact placement of Drosophilidae remains an open question, as few ephydroid taxa out- side of Drosophilidae and a small number of Ephydridae are well known. Throckmorton (1975) placed the origin of the Drosophilidae in the tropics, based primarily on the pan-tropical distribution of the Lissocephala, a group he considered P473052-Ch01.qxd 10/1/05 5:19 PM Page 4 4 How to look at flies Drosophilinae Steganinae Camilidae Risidae Ephydridae Diastatidae Campichoetidae Curtonotidae (a) (b) Figure 1.1. (a) Phylogeny of Ephydroidea based on Grimaldi (1990); (b) Phylogeny of Ephydroidea from McAlpine (1989). to be basal within the Drosophilidae. The fossil genus Electrophortica, described from Baltic amber (Hennig, 1965), suggests that the Drosophilidae predate the Eocene and may be 50 million years old or older. Drosophilidae: relationships among genera Throckmorton (1962, 1975) was the first to propose a higher-level phylogenetic frame- work for the family Drosophilidae (Figure 1.2). He proposed a number of radiations, meant to represent multiple speciation events with subsequent diversification, based on morphological characters. There have been two major criticisms of Throckmorton’s work: first, his analyses were not based on any explicit cladistic algorithm and are there- fore not repeatable; and second, he did not attempt to maintain any concept of monophyly in his study. As a result, species groups of the genus Drosophila are more closely related to other genera than they are to other species groups in their genera. In spite of these criticisms, it is still useful to review Throckmorton’s work as it agrees quite well with recent phylogenetic analyses based on molecular data (e.g. Remsen and O’Grady, 2002). The basal radiation in this family is the Steganinae radiation, which includes all the members of the subfamily Steganinae. A derivative of this radiation led to the Scapto- drosophila radiation, and the diversification of the basal Drosophilidae species. The Sophophoran radiation led to the present day subgenus Sophophora, and some related genera such as Chymomyza (Figure 1.2). The Drosophila radiation is divided into three major parts: 1. A basal radiation containing the funebris species group and related taxa 2. The virilis-repleta radiation 3. The immigrans-Hirtodrosophila radiation. P473052-Ch01.qxd 10/1/05 5:19 PM Page 5 Phylogenetic relationships of Drosophilidae 5 Figure 1.2. Genus-level phylogeny of Drosophilidae based on Throckmorton (1975). The virilis-repleta

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