Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction

Both mitochondrial and nuclear gene sequences have been employed in efforts to reconstruct deep-level phylogenetic relationships. A fundamental questi on in molecular systematics concerns the efficacy of different types of seq uences in recovering clades at different taxonomic levels. We compared the performance of four mitochondrial data sets (cytochrome b, cytochrome oxida se II, NADH dehydrogenase subunit I, 12S rRNA-tRNA(Val)-16S rRNA) and eight nuclear data sets (exonic regions of alpha -2B adrenergic receptor, aquapo rin, beta -casein, gamma -fibrinogen, interphotoreceptor retinoid binding p rotein, kappa -casein, protamine, von Willebrand Factor) in recovering deep -level mammalian clades. We employed parsimony and minimum-evolution with a variety of distance corrections for superimposed substitutions. In 32 diff erent pairwise comparisons between these mitochondrial and nuclear data set s, we used the maximum set of overlapping taxa. In each case, the variable- length bootstrap was used to resample at the size of the smaller data set. The nuclear exons consistently performed better than mitochondrial protein and rRNA-tRNA coding genes on a per-residue basis in recovering benchmark c lades. We also concatenated nuclear genes for overlapping taxa and made com parisons with concatenated mitochondrial protein-coding genes from complete mitochondrial genomes. The variable-length bootstrap was used to score the recovery of benchmark clades as a function of the number of resampled base pairs. In every case, the nuclear concatenations were more efficient than the mitochondrial concatenations in recovering benchmark clades. Among gene s included in our study, the nuclear genes were much less affected by super imposed substitutions. Nuclear genes having appropriate rates of substituti on should receive strong consideration in efforts to reconstruct deep-level phylogenetic relationships.