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On the number of New World founders: a population genetic portrait of the peopling of the Americas.

Hey J - PLoS Biol. (2005)

Bottom Line: The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow.The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population.Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA. hey@biology.rutgers.edu

ABSTRACT
The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Show MeSH
Marginal Posterior Probability DensitiesProbability densities for each of the parameters described in Figure 1 are shown, as follows: (A) θ1; (B) θ2; (C) θA; (D) t (i.e., t/u); (E) t shown on a scale of years over the range corresponding to a maximum t value of 0.2; (F) s; (G) m1; and (H) m2. The analysis in which a high upper limit on the prior distribution for t was used is identified as “high tupper,” while those analyses with a smaller upper limit on the prior distribution of t are identified as “low tupper.” Each curve is based upon the results of multiple simulations over millions of Markov chain updates (see Materials and Methods), and is plotted over the specified prior range of that parameter.
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pbio-0030193-g003: Marginal Posterior Probability DensitiesProbability densities for each of the parameters described in Figure 1 are shown, as follows: (A) θ1; (B) θ2; (C) θA; (D) t (i.e., t/u); (E) t shown on a scale of years over the range corresponding to a maximum t value of 0.2; (F) s; (G) m1; and (H) m2. The analysis in which a high upper limit on the prior distribution for t was used is identified as “high tupper,” while those analyses with a smaller upper limit on the prior distribution of t are identified as “low tupper.” Each curve is based upon the results of multiple simulations over millions of Markov chain updates (see Materials and Methods), and is plotted over the specified prior range of that parameter.

Mentions: The estimated posterior distributions are shown in Figure 3. For the initial analysis, allowing for exponential population size changes, the posterior distribution for t yielded both a major and a minor peak (the curve for t with a high tupper, Figure 3D). Given the mutation rate estimates (see Table 1), the location of the major peak (t = 0.032) corresponds to 7,130 y, whereas the location of the minor peak (t = 0.27) corresponds to 44,400 y. Given the remote possibility of such an ancient time as the latter, analyses were also done with a smaller upper bound on t of 0.2 (identified as “low tupper” in Figure 3), which corresponds to 33,000 y. Analyses were done with this reduced upper limit for t for both models in Figure 1, allowing for population size change and for the case of fixed population sizes. In the case of constant population sizes, the distribution for t shows a peak (t = 0.038) very near those for the analyses under population size change; however, the highest posterior density is found at the upper limit of t. When the constant population size model was run with a higher upper limit on t, the posterior distribution showed the same low value peak as well as a steadily rising curve for higher values of t (unpublished data).


On the number of New World founders: a population genetic portrait of the peopling of the Americas.

Hey J - PLoS Biol. (2005)

Marginal Posterior Probability DensitiesProbability densities for each of the parameters described in Figure 1 are shown, as follows: (A) θ1; (B) θ2; (C) θA; (D) t (i.e., t/u); (E) t shown on a scale of years over the range corresponding to a maximum t value of 0.2; (F) s; (G) m1; and (H) m2. The analysis in which a high upper limit on the prior distribution for t was used is identified as “high tupper,” while those analyses with a smaller upper limit on the prior distribution of t are identified as “low tupper.” Each curve is based upon the results of multiple simulations over millions of Markov chain updates (see Materials and Methods), and is plotted over the specified prior range of that parameter.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1131883&req=5

pbio-0030193-g003: Marginal Posterior Probability DensitiesProbability densities for each of the parameters described in Figure 1 are shown, as follows: (A) θ1; (B) θ2; (C) θA; (D) t (i.e., t/u); (E) t shown on a scale of years over the range corresponding to a maximum t value of 0.2; (F) s; (G) m1; and (H) m2. The analysis in which a high upper limit on the prior distribution for t was used is identified as “high tupper,” while those analyses with a smaller upper limit on the prior distribution of t are identified as “low tupper.” Each curve is based upon the results of multiple simulations over millions of Markov chain updates (see Materials and Methods), and is plotted over the specified prior range of that parameter.
Mentions: The estimated posterior distributions are shown in Figure 3. For the initial analysis, allowing for exponential population size changes, the posterior distribution for t yielded both a major and a minor peak (the curve for t with a high tupper, Figure 3D). Given the mutation rate estimates (see Table 1), the location of the major peak (t = 0.032) corresponds to 7,130 y, whereas the location of the minor peak (t = 0.27) corresponds to 44,400 y. Given the remote possibility of such an ancient time as the latter, analyses were also done with a smaller upper bound on t of 0.2 (identified as “low tupper” in Figure 3), which corresponds to 33,000 y. Analyses were done with this reduced upper limit for t for both models in Figure 1, allowing for population size change and for the case of fixed population sizes. In the case of constant population sizes, the distribution for t shows a peak (t = 0.038) very near those for the analyses under population size change; however, the highest posterior density is found at the upper limit of t. When the constant population size model was run with a higher upper limit on t, the posterior distribution showed the same low value peak as well as a steadily rising curve for higher values of t (unpublished data).

Bottom Line: The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow.The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population.Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA. hey@biology.rutgers.edu

ABSTRACT
The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.

Show MeSH