The above model of the settlement of the Americas is from a new paper which utilized ancient mtDNA, Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas (open access):
The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.
The key here is that looked at whole mitochondrial genomes, which gives them more information to work with. Earlier work often focused on a particular variable region of the mitochondrial genome. And, mtDNA is copious, so they got good quality data from all of their samples (really 5x is decent for population genomic work, and that was the worst). Combined with the fact that they had ancient genomes, which allow them to investigate the phylogeny in a more precise manner temporally, and have you the potential to make some really strong inferences.
Figure 3 in the paper makes everything really clear. The last common ancestors between Native American mtDNA lineages and those of Siberians is >20,000 years before the present. That is, before the Last Glacial Maximum. The next major feature you see is an explosion of lineages aroun ~15-16 thousand years ago. This is the hallmark of a rapid population expansion. But after the initial period of diversification you see the persistence of a lot of deeply divergent lineages. Additionally, further population genomic modeling indicate that there was a major extinction event ~500 years ago, no doubt due to the Columbian Exchange and the arrival of Old World populations and their diseases.
This paper is fundamentally about Native American historical genetics. It is another nail in the coffin of the “Clovis first” model of Amerindian origins. Basically, that the Clovis group of megafaunal hunters were the First Americans. No, it does seem likely now that modern humans were present in portions of the New World thousands of years before Clovis. The Monte Verde site’s occupation on the Chilean coast less than two thousand years after the opening of a coastal route from Beringia indicates that perhaps there was a strong focus on marine environments for a significant period of time. Once the New World was settled there seems to have been a lot of persistent population structure, until the arrival of Europeans, at least in comparison to what ancient DNA has told us about Europe. Additionally, the long isolation of the Beringians is also significant in my opinion.
In a world of billions of humans it may be that we lack proper intuition for how little gene flow may have occurred between populations in a sparsely populated globe. The Beringians were separated from Siberians for on the order of ~5,000 years. It only takes ~1 migrant between two populations per generation to prevent them from drifting apart in allele frequencies, so the gene flow was very low (this is mtDNA, so not strictly applicable, but the same logic holds). But it is possible that in much of northern Eurasia during the Last Glacial Maximum humans retreated to zones of survival, and vast swaths of territory became empty. This would result in islands of human habitation diverging and become very different over several thousands of years. In sharp contrast, the world over the past 4,000 years or so has been characterized by the ability of humans to travel long distances over inclement territory, and settle amongst strangers, usually through conquest. Partially this is due to the domestication of the horse, but partially it is probably due to the emergence of high density complex societies which can incubate specialist castes whose role arose initially as defense, but who often engage in offense whenever the opportunity arises.