Mitochondrial-DNA phylogenetic information and the reconstruction of human population history: The south american case

Abstract

Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the diffferences in the amount of information of diffferent mtDNA regions and their utility for the reconstruction of South American population history. We analyzed six data sets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), Control plus cytochrome b (cytb), and cytb plus 12S plus 16S. The amount of information in each data set was estimated employing several site-by-site and haplotype-based statistics, distances among sequences, neighbor-joining trees, distances among the estimated trees, Bayesian skyline plots, and phylogenetic informativeness profijiles. The diffferent mtDNA data sets have diffferent amounts of information to reconstruct demographic events and phylogenetic trees with confijidence. Whereas HVRI is not suitable for phylogenetic reconstruction of ancient clades, this region, as well as the Control data set, displays information for the demographic reconstruction during the Holocene period, probably because of the high rate of mutation of these regions. As expected, the Complete mtDNA and Coding data sets, displaying slower rates of mutation, present suitable information to estimate the founding subhaplogroups that populated South America and for the reconstruction of ancient demographic events. Our results point out the importance of evaluating the utility of diffferent DNA regions to respond to diffferent questions and problems in the human population studies, mainly considering the time scale of the phenomenon and the informativeness of the molecular region in a particular geographical area.