The human lineage two million years ago was a population with ape-sized brains limited to sub-Saharan Africa. The human lineage expanded into Eurasia around 1.85 million years ago, and our brain size increased throughout the Pleistocene. Anatomically modern humans first appeared in Africa about 200,000 years ago, with anatomically modern forms appearing outside of Africa at more recent dates. [. . .]
One powerful way of extracting this information about past evolution is through multilocus nested clade analysis (MLNCA). This method converts the evolutionary history of a DNA region with little to no recombination into a series of nested branches (clades), which captures time (the deeper the branch in a nested series, the older the time), and then overlays the spatial distribution of the currently observed genetic variation upon the nested series. In this manner, we can estimate the evolutionary history of current variation through both space and time. [. . .]
MLNCA does not require a prespecified model of evolution; rather, the model emerges naturally out of the cross-validated statistically significant inferences. Thus, there is no inherent bias toward any a priori model of human evolution. The cross-validated MLNCA inferences produced a model of human evolution that had some features of previous models, but unique features as well (Figure).
Moving Out of Africa
The first detected event is an expansion out-of-Africa into Eurasia dated to 1.9 million years ago using a molecular clock—an inference confirmed by the fossil record. Unlike any other model of human evolution at the time, a second expansion of nonmodern humans out-of-Africa into Eurasia occurs about 650,000 years ago, which corresponds well to the expansion of the Acheulean tool culture out of Africa.
These Acheulean populations did not replace the Eurasian populations they encountered, but rather admixed with them. Moreover, after Acheulean expansion, there was significant, albeit limited, recurrent gene flow between Eurasia and sub-Saharan Africa.
Next, there was a third major expansion of humans out-of-Africa into Eurasia at 130,000 years ago, corresponding to the fossil record of the spread of anatomically modern humans out-of-Africa beginning 130,000 to 125,000 years ago and reaching far Eastern Asia by 110,000 years before present.
Like the earlier Acheulean expansion, this third expansion out of Africa resulted in low levels of admixture with Eurasian populations, not complete replacement. Indeed, the hypothesis of replacement (zero admixture) was rejected with a 10-17 probability level, making this the most definitive conclusion of the analysis.
After this third out-of-Africa expansion, human populations subsequently expanded into Northern Eurasia (including northern Europe), the Americas, and the Pacific. Wherever humans went, patterns of genetic interchange were soon established (Templeton, 2005).
These results were extremely controversial when first published because of their strong rejection of the out-of-Africa replacement model, which posited that anatomically modern humans, when they expanded out of Africa into Eurasia, drove all the native Eurasian populations to complete extinction with no admixture. Even a mostly out-of-Africa expansion was anathema to the replacement advocates because a low level of admixture can still have strong evolutionary consequences.
Interestingly, the out-of-Africa replacement hypothesis rose in popularity due to a genetic analysis based on mitochondrial DNA (Cann et al., 1987). [. . .]
The fact that the mtDNA evolutionary history had no deep divergences and coalesced to a common, ancestral mtDNA molecule about 200,000 years ago certainly falsified the candelabra model. Unfortunately, the original paper reporting this mitochondrial evolutionary history falsely equated the candelabra and multiregional models, thereby leaving only the replacement model. [. . .]
However, the mitochondrial evolutionary history was also compatible with the multiregional model. Indeed, there has never been a genetic dataset or analysis that favored the replacement model over alternatives in a statistically significant fashion (Templeton, 2007). Nevertheless, the replacement model became the standard model of human evolution through the 1990s onward.
Now that ancient DNA studies offer direct confirmation of the MLNCA inference that there was admixture, this major controversy in human evolution can now be regarded as settled—at least, as settled as any scientific debate can be.
The future of human evolution studies is particularly bright due to genetics. As techniques become more refined, we can anticipate more ancient DNA studies that allow us a direct glimpse into our evolutionary past.