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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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Description and results for simulations with recent admixture.(a) and (c) A graphical representation of the simulation parameters, comparable to Figure 2-a, with the addition of recent migration from population A into C and recent back migration from population D into C, respectively. (b) and (d) A graphical representation, as described in Figure 2, of typical examples of the results of our model applied to the simulated data. The recent back migration from population D into C does not significantly alter inference, while recent migration from population A into C results in mistakingly inferring that population C is a source for B in this example.
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pgen-1000078-g003: Description and results for simulations with recent admixture.(a) and (c) A graphical representation of the simulation parameters, comparable to Figure 2-a, with the addition of recent migration from population A into C and recent back migration from population D into C, respectively. (b) and (d) A graphical representation, as described in Figure 2, of typical examples of the results of our model applied to the simulated data. The recent back migration from population D into C does not significantly alter inference, while recent migration from population A into C results in mistakingly inferring that population C is a source for B in this example.

Mentions: Complex patterns of admixture might considerably complicate inference. We modified the scenarios shown in Figure 2-a and Figure 2-c by adding recent admixture, either from D to C or from A to C. Examples are shown in Figures 3-a and 3-c. A genetic contribution from population D to C had little effect on inference in 10 different simulations (Figure 3-d). These results show that “back admixture”, for example migrations into Africa, will generally not be detectable by our method. In this simulated example at least, the back admixture did not affect the rest of the inference. The effect of a recent contribution from population A to population C was more substantial. In 5/10 cases (four for the scenario shown in Figure 3-a) the inferred order of populations B and C were swapped (Figure 3-b). The swapping of the populations leaves the genetic connections between the populations correct but inferences on which are sources and which are sinks are confused by the multi-layered migrational history.


Inferring human colonization history using a copying model.

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

Description and results for simulations with recent admixture.(a) and (c) A graphical representation of the simulation parameters, comparable to Figure 2-a, with the addition of recent migration from population A into C and recent back migration from population D into C, respectively. (b) and (d) A graphical representation, as described in Figure 2, of typical examples of the results of our model applied to the simulated data. The recent back migration from population D into C does not significantly alter inference, while recent migration from population A into C results in mistakingly inferring that population C is a source for B in this example.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000078-g003: Description and results for simulations with recent admixture.(a) and (c) A graphical representation of the simulation parameters, comparable to Figure 2-a, with the addition of recent migration from population A into C and recent back migration from population D into C, respectively. (b) and (d) A graphical representation, as described in Figure 2, of typical examples of the results of our model applied to the simulated data. The recent back migration from population D into C does not significantly alter inference, while recent migration from population A into C results in mistakingly inferring that population C is a source for B in this example.
Mentions: Complex patterns of admixture might considerably complicate inference. We modified the scenarios shown in Figure 2-a and Figure 2-c by adding recent admixture, either from D to C or from A to C. Examples are shown in Figures 3-a and 3-c. A genetic contribution from population D to C had little effect on inference in 10 different simulations (Figure 3-d). These results show that “back admixture”, for example migrations into Africa, will generally not be detectable by our method. In this simulated example at least, the back admixture did not affect the rest of the inference. The effect of a recent contribution from population A to population C was more substantial. In 5/10 cases (four for the scenario shown in Figure 3-a) the inferred order of populations B and C were swapped (Figure 3-b). The swapping of the populations leaves the genetic connections between the populations correct but inferences on which are sources and which are sinks are confused by the multi-layered migrational history.

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