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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.

Show MeSH
Formation of a new population using its donor pool.The donor pool for population D consists of the red, blue and green haploids from populations A, B and C. Gray haploids are not used as donors. Haploids within population D are created in order, and previously created haploids from population D can be used in the formation of each new one (magenta). For example, haploid D1a is copied from A1a, C2b and B2b, while haploid D1b is copied from C1b, B2b, C1a and D1a. One of the two alleles at each locus is indicated by a black cross, with differences from the copied haploid, i.e. mutations, indicated by a white box around the mutated nucleotide.
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pgen-1000078-g001: Formation of a new population using its donor pool.The donor pool for population D consists of the red, blue and green haploids from populations A, B and C. Gray haploids are not used as donors. Haploids within population D are created in order, and previously created haploids from population D can be used in the formation of each new one (magenta). For example, haploid D1a is copied from A1a, C2b and B2b, while haploid D1b is copied from C1b, B2b, C1a and D1a. One of the two alleles at each locus is indicated by a black cross, with differences from the copied haploid, i.e. mutations, indicated by a white box around the mutated nucleotide.

Mentions: In addition to the order in which populations were founded, we would also like to learn about patterns of ancestry. For each new population, a subset of individuals from the previously formed populations is designated as a “donor pool.” In the model, each new haploid genome or “haploid” is formed by copying chromosomal segments from the donor pool or from previously created haploids in the same population (for notational simplicity we assume that every individual consists of two haploids that each contain one of the two copies of the 22 autosomes). The model allows different donor pool combinations to be compared according to the likelihood of generating all the chromosomes in the new population. The number of individuals from each population in the donor pool with the highest likelihood provides an indication of the relative importance of different ancestral sources. For convenience, we refer to the donors using the labels of the modern populations they come from, but they in fact represent surrogates for the shared common ancestors of the donor and recipient populations. The generation of individuals from a single population is illustrated for a hypothetical example in Figure 1.


Inferring human colonization history using a copying model.

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

Formation of a new population using its donor pool.The donor pool for population D consists of the red, blue and green haploids from populations A, B and C. Gray haploids are not used as donors. Haploids within population D are created in order, and previously created haploids from population D can be used in the formation of each new one (magenta). For example, haploid D1a is copied from A1a, C2b and B2b, while haploid D1b is copied from C1b, B2b, C1a and D1a. One of the two alleles at each locus is indicated by a black cross, with differences from the copied haploid, i.e. mutations, indicated by a white box around the mutated nucleotide.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000078-g001: Formation of a new population using its donor pool.The donor pool for population D consists of the red, blue and green haploids from populations A, B and C. Gray haploids are not used as donors. Haploids within population D are created in order, and previously created haploids from population D can be used in the formation of each new one (magenta). For example, haploid D1a is copied from A1a, C2b and B2b, while haploid D1b is copied from C1b, B2b, C1a and D1a. One of the two alleles at each locus is indicated by a black cross, with differences from the copied haploid, i.e. mutations, indicated by a white box around the mutated nucleotide.
Mentions: In addition to the order in which populations were founded, we would also like to learn about patterns of ancestry. For each new population, a subset of individuals from the previously formed populations is designated as a “donor pool.” In the model, each new haploid genome or “haploid” is formed by copying chromosomal segments from the donor pool or from previously created haploids in the same population (for notational simplicity we assume that every individual consists of two haploids that each contain one of the two copies of the 22 autosomes). The model allows different donor pool combinations to be compared according to the likelihood of generating all the chromosomes in the new population. The number of individuals from each population in the donor pool with the highest likelihood provides an indication of the relative importance of different ancestral sources. For convenience, we refer to the donors using the labels of the modern populations they come from, but they in fact represent surrogates for the shared common ancestors of the donor and recipient populations. The generation of individuals from a single population is illustrated for a hypothetical example in Figure 1.

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