Abstract
BackgroundAmong the founding mitochondrial haplogroups involved in the peopling of the Americas, haplogroup C1d has been viewed as problematic because of its phylogeny and because of the estimates of its antiquity, apparently being much younger than other founding haplogroups. Several recent analyses, based on data from the entire mitochondrial genome, have contributed to an advance in the resolution of these problems. The aim of our analysis is to compare the conclusions drawn from the available HVR-I and HVR-II data for haplogroup C1d with the ones based on whole mitochondrial genomes.Methodology/Principal FindingsHVR-I and HVR-II sequences defined as belonging to haplogroup C1d by standard criteria were gathered from the literature as well as from population studies carried out in Uruguay. Sequence phylogeny was reconstructed using median-joining networks, geographic distribution of lineages was analyzed and the age of the most recent common ancestor estimated using the ρ-statistic and two different mutation rates. The putative ancestral forms of the haplogroup were found to be more widespread than the derived lineages, and the lineages defined by np 194 were found to be widely distributed and of equivalent age.Conclusions/SignificanceThe analysis of control region sequences is found to still harbor great potential in tracing microevolutionary phenomena, especially those found to have occurred in more recent times. Based on the geographic distributions of the alleles of np 7697 and np 194, both discussed as possible basal mutations of the C1d phylogeny, we suggest that both alleles were part of the variability of the haplogroup at the time of its entrance. Moreover, based on the mutation rates of the different sites stated to be diagnostic, it is possible that the anomalies found when analyzing the haplogroup are due to paraphyly.
Highlights
The estimation of the antiquity of the human peopling of the Americas has relied heavily on the coalescence ages of the four major founding mitochondrial DNA haplogroups A, B, C and D [1], with various ages and mechanisms of entrance proposed
Published sequences North, Central and South American hypervariable region I (HVR-I) (N = 170) and Hypervariable regions (HVR)-II (N = 101) sequences belonging to haplogroup C1d as defined by the 16051G mutation plus at least three of the four HVR-I mutations found in haplogroup C1 (16223T, 16298C, 16325C, and 16327T) were collected from the literature (Figure 1; Supporting information, Table S1)
Variability and distribution of haplogroup C1d The geographic distributions of the HVR-I 16051G motif (Figure 4A) on one hand, and of the 194T and 194C lineages (Figure 4B) on the other are wide enough to make it reasonable to assume that haplogroup C1d entered the continent as a part of the initial peopling of the Americas
Summary
The estimation of the antiquity of the human peopling of the Americas has relied heavily on the coalescence ages of the four major founding mitochondrial DNA (mtDNA) haplogroups A, B, C and D [1] (the American variants of which are named A2, B2, C1, and D1 [2]), with various ages and mechanisms of entrance proposed. When using mtDNA data, the accuracy of the estimation is based on the resolution of the data and on the assumption that the Time to the Most Recent Common Ancestor (TMRCA) of the haplogroup in question is as close as possible to the time of arrival of its carriers. Several recent analyses, based on data from the entire mitochondrial genome, have contributed to an advance in the resolution of these problems. The aim of our analysis is to compare the conclusions drawn from the available HVR-I and HVR-II data for haplogroup C1d with the ones based on whole mitochondrial genomes
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