Geography predicts neutral genetic diversity of human populations

A leading theory for the origin of modern humans, the 'recent African origin' (RAO) model [1], postulates that the ancestors of all modern humans originated in East Africa and that, around 100,000 years ago, some modern humans left the African continent and subsequently colonised the entire world, displacing previously established human species such as Neanderthals in Europe [2,3]. This scenario is supported by the observation that human populations from Africa are genetically the most diverse [2] and that the genetic diversity of non-African populations is negatively correlated with their genetic differentiation towards populations from Africa [3]. Here we add further compelling evidence supporting the RAO model by showing that geographic distance — not genetic distance as in [3] — from East Africa along likely colonisation routes is an excellent predictor for genetic diversity of human populations (R 2 = 85%). Our results point to a history of colonisation of the world characterised by a very large number of small bottlenecks [4] and limited subsequent gene flow. The pattern of decrease in genetic diversity along colonisation routes is very smooth and does not provide evidence for major genetic discontinuities that could be interpreted as evidence for human 'races' [2,5]. In order to characterise the fine patterns in the decrease of genetic diversity in human populations along likely colonisation routes, we analysed a dataset comprising 51 populations distributed worldwide (Figure 1) that have been typed at 377 autosomal microsatellite loci [6] (freely downloadable from: http://research.marshfieldclinic. org/genetics/Freq/FreqInfo.htm). We first computed geographic distances in a way that is meaningful in the context of modern human settlement history. The point of origin for modern humans was set in Ethiopia, a location where the oldest remains of modern humans have been found [7]. Using graph theory, we then computed the shortest path between this origin and the 51 populations through landmasses wherever possible (see Supplemental data for details). This generated migration routes (Figure 1) compatible with the ones proposed by Cavalli-Sforza and colleagues [8], with the exception of the route to America, where the algorithm suggested a scenario with a long stretch at very high latitudes in Asia. To avoid this unrealistic northern migration path, we forced the route to first reach Eastern Asia before veering to high latitudes to move through the Bering Strait (Figure 1). In a second step, we estimated the genetic diversity for each of the 51 human populations as the unbiased …