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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.

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Isolation with Migration Models(A) The basic IM model. The demographic terms are effective population sizes (N1, N2, and NA), gene flow rates (m1 and m2), and population splitting time (t). Also shown are parameters scaled by the neutral mutation rate (u), as they are actually used in the model fitting. Terms for basic demographic parameters, including N, m, t, and u, are not italicized. Note that the migration parameters are identified by the source of migrants as time goes backward in the coalescent. In other words, the migration rate from population 1 to population 2 (i.e., m1) actually corresponds to the movement of genes from population 2 to population 1 as time moves forward.(B) The IM model with changing population size. An additional parameter, s, is the fraction of NA that forms N1 (i.e., the fraction 1 − s gives rise to N2)
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pbio-0030193-g001: Isolation with Migration Models(A) The basic IM model. The demographic terms are effective population sizes (N1, N2, and NA), gene flow rates (m1 and m2), and population splitting time (t). Also shown are parameters scaled by the neutral mutation rate (u), as they are actually used in the model fitting. Terms for basic demographic parameters, including N, m, t, and u, are not italicized. Note that the migration parameters are identified by the source of migrants as time goes backward in the coalescent. In other words, the migration rate from population 1 to population 2 (i.e., m1) actually corresponds to the movement of genes from population 2 to population 1 as time moves forward.(B) The IM model with changing population size. An additional parameter, s, is the fraction of NA that forms N1 (i.e., the fraction 1 − s gives rise to N2)

Mentions: Figure 1A shows the basic IM model, in which the ancestral and descendant populations each have a constant size. Each of the terms in the model is explained in Table 1. Basic limitations of this model are that it cannot provide details on how descendant populations were founded or whether population sizes have changed. Certainly for human populations there is considerable genetic evidence that population sizes have grown [34–37], and it would be helpful if it were possible to capture information on the sizes of descendant populations as they are formed. For example, if one descendant population formed as a small founder population that later grew to a large size, such dynamics would not be revealed in the fitting of the basic IM model. To allow the study of such histories, an additional parameter has been added to the IM model. Figure 1B shows a model in which an ancestral population splits in two, with the relative sizes of those two new populations reflected in the parameter s, where 0 < s < 1. At the time of the split, descendant population 1 has size sNA from which it moves to size N1 at the time of sampling. Similarly, population 2 begins with size (1 − s)NA from which it moves to size N2 at the time of sampling. Figure 1B depicts one population growing and the other shrinking, but in fact either population is free to either grow or shrink under this model.


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

Hey J - PLoS Biol. (2005)

Isolation with Migration Models(A) The basic IM model. The demographic terms are effective population sizes (N1, N2, and NA), gene flow rates (m1 and m2), and population splitting time (t). Also shown are parameters scaled by the neutral mutation rate (u), as they are actually used in the model fitting. Terms for basic demographic parameters, including N, m, t, and u, are not italicized. Note that the migration parameters are identified by the source of migrants as time goes backward in the coalescent. In other words, the migration rate from population 1 to population 2 (i.e., m1) actually corresponds to the movement of genes from population 2 to population 1 as time moves forward.(B) The IM model with changing population size. An additional parameter, s, is the fraction of NA that forms N1 (i.e., the fraction 1 − s gives rise to N2)
© Copyright Policy
Related In: Results  -  Collection

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

pbio-0030193-g001: Isolation with Migration Models(A) The basic IM model. The demographic terms are effective population sizes (N1, N2, and NA), gene flow rates (m1 and m2), and population splitting time (t). Also shown are parameters scaled by the neutral mutation rate (u), as they are actually used in the model fitting. Terms for basic demographic parameters, including N, m, t, and u, are not italicized. Note that the migration parameters are identified by the source of migrants as time goes backward in the coalescent. In other words, the migration rate from population 1 to population 2 (i.e., m1) actually corresponds to the movement of genes from population 2 to population 1 as time moves forward.(B) The IM model with changing population size. An additional parameter, s, is the fraction of NA that forms N1 (i.e., the fraction 1 − s gives rise to N2)
Mentions: Figure 1A shows the basic IM model, in which the ancestral and descendant populations each have a constant size. Each of the terms in the model is explained in Table 1. Basic limitations of this model are that it cannot provide details on how descendant populations were founded or whether population sizes have changed. Certainly for human populations there is considerable genetic evidence that population sizes have grown [34–37], and it would be helpful if it were possible to capture information on the sizes of descendant populations as they are formed. For example, if one descendant population formed as a small founder population that later grew to a large size, such dynamics would not be revealed in the fitting of the basic IM model. To allow the study of such histories, an additional parameter has been added to the IM model. Figure 1B shows a model in which an ancestral population splits in two, with the relative sizes of those two new populations reflected in the parameter s, where 0 < s < 1. At the time of the split, descendant population 1 has size sNA from which it moves to size N1 at the time of sampling. Similarly, population 2 begins with size (1 − s)NA from which it moves to size N2 at the time of sampling. Figure 1B depicts one population growing and the other shrinking, but in fact either population is free to either grow or shrink under this model.

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