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Control region variability of haplogroup C1d and the tempo of the peopling of the Americas.

Figueiro G, Hidalgo PC, Sans M - PLoS ONE (2011)

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. vazfigue@gmail.com

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.

Methodology/principal findings: 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/significance: 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.

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Distribution of C1d lineages in the Americas.A: Distribution of the ancestral and derived lineages as defined using HVR-I only. B: Distribution of lineages carrying the 194C and 194T alleles. C: Distribution of lineages with and without the 7697G→A mutation.
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pone-0020978-g004: Distribution of C1d lineages in the Americas.A: Distribution of the ancestral and derived lineages as defined using HVR-I only. B: Distribution of lineages carrying the 194C and 194T alleles. C: Distribution of lineages with and without the 7697G→A mutation.

Mentions: The distribution of the ancestral (16051G-16223T-16298C-16325C-16327T) and derived lineages for the HVR-I analysis is shown in Figure 4A. Both types of lineages can be found throughout the Americas. The ancestral lineage has a large geographic distribution, with a mean interpopulation distance of 4,762 Km and 10% of the distances below 1,000 Km. In contrast to the ancestral lineage, populations sharing a same derived lineage are located on average 2,786 Km away, with 28% of the distances being less than 1,000 Km. The difference between the distance distributions is statistically significant (U = 14,027, Z = 5.63, p<.0001).


Control region variability of haplogroup C1d and the tempo of the peopling of the Americas.

Figueiro G, Hidalgo PC, Sans M - PLoS ONE (2011)

Distribution of C1d lineages in the Americas.A: Distribution of the ancestral and derived lineages as defined using HVR-I only. B: Distribution of lineages carrying the 194C and 194T alleles. C: Distribution of lineages with and without the 7697G→A mutation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3113844&req=5

pone-0020978-g004: Distribution of C1d lineages in the Americas.A: Distribution of the ancestral and derived lineages as defined using HVR-I only. B: Distribution of lineages carrying the 194C and 194T alleles. C: Distribution of lineages with and without the 7697G→A mutation.
Mentions: The distribution of the ancestral (16051G-16223T-16298C-16325C-16327T) and derived lineages for the HVR-I analysis is shown in Figure 4A. Both types of lineages can be found throughout the Americas. The ancestral lineage has a large geographic distribution, with a mean interpopulation distance of 4,762 Km and 10% of the distances below 1,000 Km. In contrast to the ancestral lineage, populations sharing a same derived lineage are located on average 2,786 Km away, with 28% of the distances being less than 1,000 Km. The difference between the distance distributions is statistically significant (U = 14,027, Z = 5.63, p<.0001).

Bottom Line: 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.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.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.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, Montevideo, Uruguay. vazfigue@gmail.com

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.

Methodology/principal findings: 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/significance: 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.

Show MeSH
Related in: MedlinePlus