Genome Evolution in Three Species of Cactophilic Drosophila

We report genomes of two species of cactophilic Drosophila, Drosophila arizonae and Drosophila navojoa. These two are the closest relatives of Drosophila mojavensis, forming the mojavensis cluster. Drosophila mojavensis and D. arizonae diverged from D. navojoa approximately 5.8 Mya, while the split between D. arizonae and D. mojavensis is more recent, at 1.5 Mya. Together the three genomes provide opportunities to examine genomic changes associated with speciation and host shifts in this ecologically defined group of flies. The three species also are separated by fixed inversion differences in three of their six chromosomes. While the levels of nucleotide divergence in the colinear chromosomes are significantly lower than in the inverted chromosomes, consistent with a role of the inversions in preventing gene flow in the past, the patterns differ among the inverted chromosomes when the locations of nucleotides inside or outside of the inversions are considered. For Muller element E, there is greater divergence external to the inversion breakpoints. For Muller A, the divergence is slightly higher inside the inversions, while for Muller B, the breakpoints and hence the difference in substitutions in relation to the inversions could not be determined. The differences among the inverted chromosomes, especially once the breakpoints are clearly established, could aid in dating the origins of the inversions.

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