title: Control region variability of haplogroup C1d and the tempo of the peopling of the Americas.
abstract: BACKGROUND
  Among 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.
  
  
  RESULTS
  HVR-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
  The 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.
authors.affiliation: Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. vazfigue@gmail.com
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Figueiro
authors.forename: Pedro C
authors.initials: PC
authors.lastname: Hidalgo
authors.forename: Mónica
authors.initials: M
authors.lastname: Sans
mesh_terms: D000569:Americas; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D040481:Genome Components / Q000235:genetics*; D005843:Geography; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data