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, 79 (2), 230-7

A Geographically Explicit Genetic Model of Worldwide Human-Settlement History

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A Geographically Explicit Genetic Model of Worldwide Human-Settlement History

Hua Liu et al. Am J Hum Genet.

Abstract

Currently available genetic and archaeological evidence is generally interpreted as supportive of a recent single origin of modern humans in East Africa. However, this is where the near consensus on human settlement history ends, and considerable uncertainty clouds any more detailed aspect of human colonization history. Here, we present a dynamic genetic model of human settlement history coupled with explicit geographical distances from East Africa, the likely origin of modern humans. We search for the best-supported parameter space by fitting our analytical prediction to genetic data that are based on 52 human populations analyzed at 783 autosomal microsatellite markers. This framework allows us to jointly estimate the key parameters of the expansion of modern humans. Our best estimates suggest an initial expansion of modern humans approximately 56,000 years ago from a small founding population of approximately 1,000 effective individuals. Our model further points to high growth rates in newly colonized habitats. The general fit of the model with the data is excellent. This suggests that coupling analytical genetic models with explicit demography and geography provides a powerful tool for making inferences on human-settlement history.

Figures

Figure  1.
Figure 1.
Schematic representation of the colonization model. At generation t0, the entire population consists of a single ancestral deme at the border of the stepping-stone. This initial founding population has a carrying capacity K0 and is at mutation-drift equilibrium. At each generation, this population sends a proportion of m/2 migrants to the neighboring site (deme 2). Thus, at generation t1, deme 2 comprises (m/2)K0 individuals. The individuals in deme 2 reproduce randomly and produce a number of offspring determined by the growth rate parameter r. Once deme 2 has reached its carrying capacity K (at times tk), it starts sending migrants to its two neighboring sites. This process of migration and population growth of newly colonized demes continues until all demes are full.
Figure  2.
Figure 2.
Shortest colonization routes from East Africa (Addis Ababa) along landmasses and high mountain ranges (areas with average elevation >2,000 m) to the populations from the CEPH human genetic–diversity panel. Small blue dots represent populations, the hypothetical origin of modern humans is represented as a large red dot, colonization routes are shown in red, and uncrossable areas with average altitude >2,000 m are brown.
Figure  3.
Figure 3.
Contour plot of the fit between simulated and empirical data (R2) for the size of the initial founding population K0 and the growth rate within demes (r). Lighter areas represent better fits between simulations and actual data. The black area represents unrealistic regions of the parameter space, corresponding to a colonization of the world achieved in <1,500 generations. The red line delineates the 95% CI. The best fit between simulations and empirical data (R2>0.72) is obtained for high values of r (∼0.7–1.0) and a founding population, K0, of 800–1,200 individuals.
Figure  4.
Figure  4.
Illustration of coalescence times (A) and gene diversities (B) plotted against geographic distance from East Africa, computed through landmasses. The continuous lines represent analytical expectations from the model, and the unblackened circles represent actual values for 52 populations from the CEPH human genetic–diversity panel. In this figure, parameter values for the simulations are as follows: K0=1,000, r=0.85, K=800, Km=150, and the number of generations=2,392.

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