Nuclear intron sequences for phylogenetics of closely related mammals: An example using the phylogeny of Mus

DNA sequence data from 2 nuclear introns (mitochondrial malate dehydrogenas e intron 7 and acid phosphatase type V intron 2) were collected fur 9 taxon omic units of rodents, 8 of which were in the genus Mus. Data were used to infer phylogenetic history of the 9 taxa, which was then compared with a co nsensus phylogeny taken from previous literature. In general, the nuclear i ntron data provided strong support (bootstrap proportions > 80) for relatio nships accepted in the consensus tree. The intron data disagreed with previ ous mitochondrial data in that 2 M. m. domesticus sequences were paraphylet ic with respect to M. m. castaneus and M. m. musculus. This paraphyly, if r eal, likely reflects the longer lineage-sorting time of the nuclear genome compared with the mitochondrial genome. Introns seem to provide an attracti ve source of nuclear DNA sequence data for phylogenetic analysis, but mitoc hondrial data an likely to be superior for very recent divergences.