The figure to the left is from Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry. It is a graph which captures general features of human population historical relationships as we understand them today. Or at least the model fits the data (remember, many models may fit the data!). The graph is complex…but even within the text of the preprint, the author admits that it is characterized by simplifying assumptions, which nevertheless are informative of some general dynamics and processes (e.g., pulse admixtures).
To some extent, the whole last generation or so has been characterized by the victory of a simplifying assumption that captures general truths about the past, with the accumulation of modifications on the margins as more nuanced results enter the picture. The simplifying assumption I am talking about here is the “out of Africa” 50,000 years ago with a total replacement of all other human lineages framework.
By the last quarter of the 20th century, a combination of archaeological and genetic evidence pointed to the likelihood of a massive bottleneck and expansion of humans outside of Africa in the relatively recent past. In the pre-genomic era, the tools were coarse, from uniparental lineages, classical markers, microsatellites, morphometric analyses, as well as archaeological surveys. But, they strongly pointed to massive expansion and population turnover ~50,000 years ago. This, combined with a line of thinking which suggested that Neanderthals were “evolutionary dead-ends” led to the thesis that there was a total replacement.
To a great extent, this model seems to hold up in the broad sketch. But not to an absolute and total degree. Some paleoanthropologists and geneticists were pointing out for decades that the tools we had could not exclude the possibility of admixture at lower fractions with earlier lineages in Eurasia on purely statistical grounds. These scholars were correct, as it turns out. There is now high confidence that in the range of 1-5% of the ancestry of non-Africans derives from highly diverged “archaic” lineages, Neanderthals and Denisovans. The fraction is low enough that more coarse methods did not definitively pick them up, and without ancient genomes, the “game of inference” was not dispositive in either direction. This, despite the fact that these Eurasian hominins’ ancestors seem to have diverged from those of modern humans ~750,000 years ago. Ultimately, scientists needed a physical ancient genome which they could compare to modern populations to come to this conclusion (before the Denisovan result, scientists had been noticing anomalies in Oceanian data for a decade or so but generally ignored it as beneath comment…a presentation was given an anthropology conference on archaic admixture in Oceania right before the Denisova cave paper).
The second major issue is that the massive expansion and bottleneck that occurred ~50,000 years ago may not explain all of the remaining ancestry that is not “archaic.” That is, there were many modern human lineages present 50,000 years ago. The major lacunae in the current model is a huge one: populations within Sub-Saharan Africa maintained larger population sizes throughout this event. And, anatomically modern humans predate this expansion by hundreds of thousands of years. From an archaeological perspective, a lower limit is 200,000 years ago, and an upper limit probably exceeds 300,000 years ago. Additionally, there are “deep lineages” within Africa which clearly predate the expansion 50,000 years ago. There is a strong consensus that the Khoisan people have at least some substantial ancestry that diverged more than 150,000 years ago from other humans, and tentative suggestions from several different research groups suggest that there are even more “basal” (deep divergence) lineages in parts of West Africa that the component within the Khoisan.
This does not even address the likelihood that some “archaic” ancestry persists within Sub-Saharan Africa just as it does outside of Sub-Saharan Africa.