Figure 1.
Bayesian skyline plot for the mtDNA coding genome sequences.
The curve plots median Nef with its 95% CI indicated by the light gray lines. The calculated Nef assumes a generation time of 20 years following Hey [16]; alternatively, using a generation time of 25 years [55] would uniformly decrease all estimates of Nef by 20%. “X” marks the median coalescent time with its 95% CI given in brackets. The shaded regions highlight two periods of substantial population growth. This skyline plot provides the principal evidence for our three-stage model of New World colonization, i.e. the three stages that are depicted and labeled here.
Figure 2.
Bayesian skyline plot for the mtDNA HVR I+II datasets.
This plot follows the conventions of Figure 1. Its estimates of coalescent time and Nef at the coalescence and today are in agreement with the coding mtDNA skyline plot (Figure 1). In contrast, this HVRI+II plot provides little resolution for other population size changes, most likely because of mutational saturation in the non-coding control region (see text).
Figure 3.
Graph of IM results for the combined nuclear and mitochondrial coding DNA dataset.
The plot depicts mean Ne for the Amerind founder population (y-axis) as a product of increasing the constraint on the upper bound of the priors for the migration rates (x-axis). In these analyses, the prior on the lower bound of the divergence time was uniformly set to 15 kya on the basis of known archaeological materials for human occupation in the New World (see text). Each point is based on the average of the estimated medians for ten independent replicate analyses, with the bars corresponding to ± 1 standard deviation. These standard deviations are often small (with coefficients of variation less than 0.01), since their Markov chains were run for 100 million generations each.
Figure 4.
Maps depicting each phase of our three-step colonization model for the peopling of the Americas.
(A) Divergence, then gradual population expansion of the Amerind ancestors from their East Central Asian gene pool (blue arrow). (B) Proto-Amerind occupation of Beringia with little to no population growth for ≈20,000 years. (C) Rapid colonization of the New World by a founder group migrating southward through the ice free, inland corridor between the eastern Laurentide and western Cordilleran Ice Sheets (green arrow) and/or along the Pacific coast (red arrow). In (B), the exposed seafloor is shown at its greatest extent during the last glacial maximum at ≈20–18 kya [25]. In (A) and (C), the exposed seafloor is depicted at ≈40 kya and ≈16 kya, when prehistoric sea levels were comparable [24], [25]. Because of the earth's curvature, the km scale (which is based on the straight line distance at the equator) provides only an approximation of the same distance between two points on these maps. In addition, a scaled-down version of Beringia today (60% reduction of A–C) is presented in the lower left corner. This smaller map highlights the Bering Strait that has geographically separated the New World from Asia since ≈11–10 kya.