Genes and other samples of DNA sequence data for phylogenetic inference.

One of the most basic uses of DNA sequence data in the study of evolution is as a source of information for inferring evolutionary history. Where homology may be difficult to establish, particularly in comparisons of phylogenetic lineages that have diverged relatively early, DNA sequence data may offer distinct advantages over other data, such as morphology. However, DNA sequence data may present its own difficulties, and the sampling properties of DNA sequence data are not well characterized. To better understand the sampling properties of DNA sequence data in phylogenetic analysis, a series of computational experiments were performed using complete mitochondrial genomes from 10 vertebrate species. These taxa were cow, Bos taurus; carp, Cyprinus carpio; chicken, Gallus gallus; human, Homo sapiens; loach, Crossostoma lacustre; mouse, Mus musculus; rat, Rattus norvegicus; harbor seal, Phoca vitulina; fin whale, Balenoptera physalus; and frog, Xenopus laevis. For this study, the mitochondrial genome has some distinct advantages: