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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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Correlation between distance from East Africa with four demographic parameters in 51 populations. Strong negative correlations are seen between distance and (A) TMRCA, (B) expansion time, and (C) effective population size; a weak but significant positive correlation between distance and (D) population growth rate is also seen.
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fig3: Correlation between distance from East Africa with four demographic parameters in 51 populations. Strong negative correlations are seen between distance and (A) TMRCA, (B) expansion time, and (C) effective population size; a weak but significant positive correlation between distance and (D) population growth rate is also seen.

Mentions: Third, strong geographical patterns are seen on a continental scale. Sub-Saharan African populations tend to have the oldest TMRCAs, the largest Nes and the earliest expansion times, whereas the American populations have some of the most recent TMRCAs and expansion times and the smallest Nes (fig. 2A–C). The other continental populations fall in between. Walking distance from an origin in East Africa (conventionally set at Addis Ababa) has been found to correlate with several characteristics of human populations, for example, negatively with mean STR diversity (Prugnolle et al. 2005), so we tested the correlation of male demographic parameters with these distances. TMRCA, expansion time, and Ne were negatively correlated, and these correlations were highly significant (fig. 3A–C). In contrast, the correlation with growth rate was much weaker and positive but still reached significance (fig. 3D).


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)

Correlation between distance from East Africa with four demographic parameters in 51 populations. Strong negative correlations are seen between distance and (A) TMRCA, (B) expansion time, and (C) effective population size; a weak but significant positive correlation between distance and (D) population growth rate is also seen.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Correlation between distance from East Africa with four demographic parameters in 51 populations. Strong negative correlations are seen between distance and (A) TMRCA, (B) expansion time, and (C) effective population size; a weak but significant positive correlation between distance and (D) population growth rate is also seen.
Mentions: Third, strong geographical patterns are seen on a continental scale. Sub-Saharan African populations tend to have the oldest TMRCAs, the largest Nes and the earliest expansion times, whereas the American populations have some of the most recent TMRCAs and expansion times and the smallest Nes (fig. 2A–C). The other continental populations fall in between. Walking distance from an origin in East Africa (conventionally set at Addis Ababa) has been found to correlate with several characteristics of human populations, for example, negatively with mean STR diversity (Prugnolle et al. 2005), so we tested the correlation of male demographic parameters with these distances. TMRCA, expansion time, and Ne were negatively correlated, and these correlations were highly significant (fig. 3A–C). In contrast, the correlation with growth rate was much weaker and positive but still reached significance (fig. 3D).

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