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Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different 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 profiles. The different mtDNA data sets have different amounts of information to reconstruct demographic events and phylogenetic trees with confidence. 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 different DNA regions to respond to different 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.

Fig 1 mtDNA map.tif (3098 kB)
Fig 1 mtDNA map.tif

Figure 2 D NJ 6-datasets.tif (3623 kB)
Figure 2 D NJ 6-datasets.tif

Figure 3 nmMDS and UPGMA RF 6-datasets.tif (575 kB)
Figure 3 nmMDS and UPGMA RF 6-datasets.tif

Figure 4 Saturation plots 6-datasets new.tif (4125 kB)
Figure 4 Saturation plots 6-datasets.tif

Figure 5 BSP 6-datasets.tif (852 kB)
Figure 5 BSP 6-datasets.tif

Figure 6 Profiles_net 6-datasets.tif (1033 kB)
Figure 6 Profiles_net 6-datasets.tif

supporting information table 1 modified.pdf (311 kB)
Supporting Information Table 1.pdf

Table 1.docx (15 kB)
Table 1.docx

Table 2.docx (16 kB)
Table 2.docx

supporting information table 2.pdf (252 kB)
Supporting information table 2.pdf

Supporting Information, Figure 1 nmMDS and UPGMA RF 6-datasets America.pdf (128 kB)
Supporting information figure 1.pdf

Supporting Information, Figure 2 BSP 6-datasets without aDNA.pdf (171 kB)
Supporting information figure 2.pdf