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Inferring human colonization history using a copying model.

Hellenthal G, Auton A, Falush D - PLoS Genet. (2008)

Bottom Line: We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006).They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native North [corrected] Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native South [corrected] Americans, implying multiple waves of migration into the Americas.A detailed depiction of the peopling of the world is available in animated form.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom.

ABSTRACT
Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single "Out-of-Africa" bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native North [corrected] Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native South [corrected] Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

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Summary of inferred history of the peopling of the world.The formation of 53 populations has been condensed into 38 frames, shown in full in Movie S1, by displaying the formation of each population as soon as all of its donors are present. When 2 or more populations are formed in the same frame, the connections from their donors are shown in different colors. (A) Africa subsequent to San, (B) initial colonization of central Eurasia, (C) initial colonization of Far East and Europe, (D) Americas and Pacific Islands. The thickness of each line is proportional to the mean estimated number of donor individuals from each source (numerical values provided in Table S2). Solid lines indicate that all or nearly all of the individuals in the population were used as donors. Dashed lines indicate that on average between four individuals and the number of available individuals minus two were used.
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pgen-1000078-g004: Summary of inferred history of the peopling of the world.The formation of 53 populations has been condensed into 38 frames, shown in full in Movie S1, by displaying the formation of each population as soon as all of its donors are present. When 2 or more populations are formed in the same frame, the connections from their donors are shown in different colors. (A) Africa subsequent to San, (B) initial colonization of central Eurasia, (C) initial colonization of Far East and Europe, (D) Americas and Pacific Islands. The thickness of each line is proportional to the mean estimated number of donor individuals from each source (numerical values provided in Table S2). Solid lines indicate that all or nearly all of the individuals in the population were used as donors. Dashed lines indicate that on average between four individuals and the number of available individuals minus two were used.

Mentions: We used the same approach to infer the order of birth and ancestral sources of the 53 populations in the Human Genome Diversity Panel using the data from 2,540 linked SNPs across 32 autosomal regions genotyped by Conrad et al [12]. The highest likelihood scenario is shown in Figure 4 and Movie S1. By visually inspecting these results, we have identified nine phases in the colonization of the world. This subdivision is subjective and the phases should not be thought of as occurring strictly in chronological order. For example, East Asia and Europe are peopled almost independently, making their relative position in the ordering nearly arbitrary. Furthermore, Melanesia has multiple sources that reflect ancient and recent migrations that introduced very distinct genetic material (see [16] for a review). Its inferred place in the ordering reflects the most recent of these migrations. Nevertheless, the phases do reflect progressive outward expansion, analogous to that implied by serial dilution models.


Inferring human colonization history using a copying model.

Hellenthal G, Auton A, Falush D - PLoS Genet. (2008)

Summary of inferred history of the peopling of the world.The formation of 53 populations has been condensed into 38 frames, shown in full in Movie S1, by displaying the formation of each population as soon as all of its donors are present. When 2 or more populations are formed in the same frame, the connections from their donors are shown in different colors. (A) Africa subsequent to San, (B) initial colonization of central Eurasia, (C) initial colonization of Far East and Europe, (D) Americas and Pacific Islands. The thickness of each line is proportional to the mean estimated number of donor individuals from each source (numerical values provided in Table S2). Solid lines indicate that all or nearly all of the individuals in the population were used as donors. Dashed lines indicate that on average between four individuals and the number of available individuals minus two were used.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2367454&req=5

pgen-1000078-g004: Summary of inferred history of the peopling of the world.The formation of 53 populations has been condensed into 38 frames, shown in full in Movie S1, by displaying the formation of each population as soon as all of its donors are present. When 2 or more populations are formed in the same frame, the connections from their donors are shown in different colors. (A) Africa subsequent to San, (B) initial colonization of central Eurasia, (C) initial colonization of Far East and Europe, (D) Americas and Pacific Islands. The thickness of each line is proportional to the mean estimated number of donor individuals from each source (numerical values provided in Table S2). Solid lines indicate that all or nearly all of the individuals in the population were used as donors. Dashed lines indicate that on average between four individuals and the number of available individuals minus two were used.
Mentions: We used the same approach to infer the order of birth and ancestral sources of the 53 populations in the Human Genome Diversity Panel using the data from 2,540 linked SNPs across 32 autosomal regions genotyped by Conrad et al [12]. The highest likelihood scenario is shown in Figure 4 and Movie S1. By visually inspecting these results, we have identified nine phases in the colonization of the world. This subdivision is subjective and the phases should not be thought of as occurring strictly in chronological order. For example, East Asia and Europe are peopled almost independently, making their relative position in the ordering nearly arbitrary. Furthermore, Melanesia has multiple sources that reflect ancient and recent migrations that introduced very distinct genetic material (see [16] for a review). Its inferred place in the ordering reflects the most recent of these migrations. Nevertheless, the phases do reflect progressive outward expansion, analogous to that implied by serial dilution models.

Bottom Line: We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006).They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native North [corrected] Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native South [corrected] Americans, implying multiple waves of migration into the Americas.A detailed depiction of the peopling of the world is available in animated form.

View Article: PubMed Central - PubMed

Affiliation: Department of Statistics, University of Oxford, Oxford, United Kingdom.

ABSTRACT
Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single "Out-of-Africa" bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native North [corrected] Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native South [corrected] Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

Show MeSH