Understanding the genetic basis of adaptation to novel environments remains one of the major challenges confronting evolutionary biologists. While newly developed genomic approaches hold considerable promise for addressing this overall question, the relevant tools have not often been available in the most ecologically interesting organisms, until now (Matzkin 2013).

One of our core study organisms are a pair of sibling species, Drosophila mojavensis and D. arizonae.  These cactophilic Sonoran Desert endemic species are members of the Repleta group and its well studied ecology makes them an excellent system to study the genetic basis of adaptation and speciation. As a cactophile, D. mojavensis and D. arizonae oviposits in the necrotic tissues of cacti, therefore exposing larvae and even adults to the varied and sometimes toxic compounds of rotting cacti. Drosophila mojavensis is composed of four host races (Mainland Sonoran, Baja California, Mojave and Catalina Is.), each with its own specific cactus host (Organpipe, Agria, Barrel, and Prickly Pear, respectively).  Drosophila arizonae is more of a cactus generalist and has been associated with several cactus species.  We use and developed several genetic and genomic tools, such as next-gen sequencing (DNA and RNAseq) as well as genome editing approaches (CRISPR), to investigate the genetics of adaptation and speciation in these and other related Drosophila species.