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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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Median-Joining Network generated from the compiled HVR-I sequences.The central lineage carries the mutations 16051G, 16223T, 16298C, 16325C, and 16327T. Yellow: fraction of the lineage carrying the 7697G→A mutation. Black: fraction of the lineage carrying the ancestral 7697G allele. White: fraction of the lineage lacking data on the state of np 7697.
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pone-0020978-g002: Median-Joining Network generated from the compiled HVR-I sequences.The central lineage carries the mutations 16051G, 16223T, 16298C, 16325C, and 16327T. Yellow: fraction of the lineage carrying the 7697G→A mutation. Black: fraction of the lineage carrying the ancestral 7697G allele. White: fraction of the lineage lacking data on the state of np 7697.

Mentions: The Median-Joining Network generated using the HVR-I sequences was comprised by a minimum of 5 MP trees, one of which is shown in Figure 2. Some of the sites providing multiple links (16209, 16223, 16298 and 16327) are documented as very mutable [15], [20]–[22], so they could be witnessing recurrent mutation. Nonetheless, they affect secondary branches: the primary branches (i.e., leading to the root) are highly consistent. Moreover, the exclusion of the five hypervariable sites 16093, 16129, 16189, 16311, and 16362 had the effect of drastically reducing the total number of back mutations necessary to explain the relationships between haplotypes, from 40 to 16 (data not shown).


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

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

Median-Joining Network generated from the compiled HVR-I sequences.The central lineage carries the mutations 16051G, 16223T, 16298C, 16325C, and 16327T. Yellow: fraction of the lineage carrying the 7697G→A mutation. Black: fraction of the lineage carrying the ancestral 7697G allele. White: fraction of the lineage lacking data on the state of np 7697.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020978-g002: Median-Joining Network generated from the compiled HVR-I sequences.The central lineage carries the mutations 16051G, 16223T, 16298C, 16325C, and 16327T. Yellow: fraction of the lineage carrying the 7697G→A mutation. Black: fraction of the lineage carrying the ancestral 7697G allele. White: fraction of the lineage lacking data on the state of np 7697.
Mentions: The Median-Joining Network generated using the HVR-I sequences was comprised by a minimum of 5 MP trees, one of which is shown in Figure 2. Some of the sites providing multiple links (16209, 16223, 16298 and 16327) are documented as very mutable [15], [20]–[22], so they could be witnessing recurrent mutation. Nonetheless, they affect secondary branches: the primary branches (i.e., leading to the root) are highly consistent. Moreover, the exclusion of the five hypervariable sites 16093, 16129, 16189, 16311, and 16362 had the effect of drastically reducing the total number of back mutations necessary to explain the relationships between haplotypes, from 40 to 16 (data not shown).

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