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A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations.

Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y, Tyler-Smith C - Mol. Biol. Evol. (2009)

Bottom Line: The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas.These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history.However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambs., United Kingdom.

ABSTRACT
We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d'Etude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

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Related in: MedlinePlus

Contour plot showing the posterior distribution of (A) TMRCA, (B) Expansion time, (C) Initial effective population size, and (D) Population growth rate. Each population is marked by a circle, centered on the sampling site and with a diameter proportional to its sample size. The sample sizes of different populations are shown in supplementary table S1, Supplementary Material online.
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fig2: Contour plot showing the posterior distribution of (A) TMRCA, (B) Expansion time, (C) Initial effective population size, and (D) Population growth rate. Each population is marked by a circle, centered on the sampling site and with a diameter proportional to its sample size. The sample sizes of different populations are shown in supplementary table S1, Supplementary Material online.

Mentions: Median values of the four demographic parameters were plotted according to the geographical location of the sample site in Figure 2A–D. A number of general features are apparent in the data. First, the parameters are correlated, with a tendency for populations with an older TMRCA to have an older expansion time and larger effective population size but a lower growth rate and vice versa.


A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations.

Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y, Tyler-Smith C - Mol. Biol. Evol. (2009)

Contour plot showing the posterior distribution of (A) TMRCA, (B) Expansion time, (C) Initial effective population size, and (D) Population growth rate. Each population is marked by a circle, centered on the sampling site and with a diameter proportional to its sample size. The sample sizes of different populations are shown in supplementary table S1, Supplementary Material online.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2806244&req=5

fig2: Contour plot showing the posterior distribution of (A) TMRCA, (B) Expansion time, (C) Initial effective population size, and (D) Population growth rate. Each population is marked by a circle, centered on the sampling site and with a diameter proportional to its sample size. The sample sizes of different populations are shown in supplementary table S1, Supplementary Material online.
Mentions: Median values of the four demographic parameters were plotted according to the geographical location of the sample site in Figure 2A–D. A number of general features are apparent in the data. First, the parameters are correlated, with a tendency for populations with an older TMRCA to have an older expansion time and larger effective population size but a lower growth rate and vice versa.

Bottom Line: The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas.These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history.However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambs., United Kingdom.

ABSTRACT
We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d'Etude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa.

Show MeSH
Related in: MedlinePlus