Sampling properties of DNA sequence data in phylogenetic analysis

We inferred phylogenetic trees from individual genes and random samples ofnucleotides from the mitochondrial genomes of 10 vertebrates and comparedthe results to those obtained by analyzing the whole genomes. Individualgenes are poor samples in that they infrequently lead to the whole-genometree. A large number of nucleotide sites is needed to exactly determine thewhole-genome tree. A relatively small number of sites, however, oftenresults in a tree close to the whole-genome tree. We found that blocks ofcontiguous sites were less likely to lead to the whole-genome tree thansamples composed of sites drawn individually from throughout the genome.Samples of contiguous sites are not representative of the entire genome, acondition that violates a basic assumption of the bootstrap method as it isapplied in phylogenetic studies.