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  • Jody Hey

    Affiliation Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, United States of America


  • Jody Hey








Figure 1. 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)


Figure 2. Approximate Geographic Locations, and Sample Sizes per location, for Each Locus Listed in Table 1

In some cases locations are based on actual geographic locations, in other cases the locations are the approximate center of the geographic region occupied by ethnic groups identified in the original references (Table 1).






Figure 3. Marginal Posterior Probability Densities

Probability 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.













Materials and Methods

Selected loci and samples.



Model development.






and for population 2,



and for migration in the reverse direction it is






Figure 4. The Marginal Densities Obtained by Fitting the Model with Population Size Change to Simulated Data

The input parameters for the simulations were as follows: (A) θ1 = 10; (B) θ2 = 10; (C) θA = 10; (D) t =2.5, (E) s = 0.2, (F) m1= 0.04; (G) m2= 0.2 ; and t = 5 (t/2NA = 0.5). For each simulated dataset, coalescent simulations were done for each of 20 loci with identical mutation rates under an infinite sites mutation model, each with sample sizes of 10 for each of the two populations. Each simulated dataset was analyzed using wide uniform prior distributions for each parameter. Each analysis began with a burn-in period of 300,000 steps followed by a primary chain of 3 million to 10 million steps. The curves for parameters θ1 through m2 are shown in (A) through (G), respectively. For each figure, the true parameter value used in the simulations is shown as a black vertical bar, and the mean of the estimates for the 20 simulations (based on peak locations) is shown as a gray vertical bar.








Supporting Information

Dataset S1. Peopling of Americas Data File: Nine Loci



(582 KB TXT).

Protocol S1. Additional Simulations and List of Sample Locations


(92 KB DOC).



Author Contributions



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