When One Is Not Enough: Introgression of Mitochondrial DNA in Drosophila

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Abstract
The specific purpose of this study is to investigate alternate processes that may have resulted in the formation of the two distinct mitochondrial haplotypes (maI and maII) of Drosophila mauritiana. The most plausible explanation for the observed data is that there has been introgression of Drosophila simulans mtDNA into D. mauritiana. More generally, this article addresses three important issues concerning resolution of species relationships. First, pooling data from distinct process partitions has the potential to obscure biologically informative patterns of substitution (Bull et al. 1993 ; Ballard et al. 1998 ). Second, hypothesizing a species phylogeny from a single linkage partition may be problematic (reviewed by Doyle 1992 ; Avise 1994 ). Third, phylogenetic hypotheses may be influenced by the inclusion of a single representative of a terminal taxon (Omland, Lanyon, and Fritz 1999 ). Multiple unlinked loci and multiple individuals from within species that exhibit extensive population subdivision should be included to maximize the potential to fully resolve species relationships.