This model depicts (a) an early divergence of an African (represented by Yoruba) and Asian/Australasian populations. These mix with first Neandertals and then (for the Australian/New Guinea/Mamanwa populations) with Denisova-like people. Later (b), after the initial habitation of the Philippines by the ancestors of Mamanwa, a population like Andamanese Onge pushes into the islands, mixing with the ancestors of New Guinea and Australian populations. Later still (c), a population ancestral to today's Chinese people mixes with Philippines and other Southeast Asian people.
This is not really particularly new, however. A 2006 analysis of mtDNA in Malaysia concluded that: "Phylogeographic analysis suggests at least 4 detectable colonization events . . .respectively dated to over 50,000 years ago, ∼10,000 years ago, the middle Holocene, and the late Holocene." Similarly, a 2008 paper on Y-DNA lineages in Asia also suggested multiple waves of migration.
What the Denisovian ancestry data most help establish is the order of the layers and their geographic extent. This data set suggests that the wave associated in Papuans and Australians and earliest Philippino Negritos preceded the wave that brought the ancestors of the Andamanese, Malaysian Negritos and probably the Ainu as well (associated in part with Y-DNA haplogroup D). At least one other major wave of migration followed these two waves in Asia prior to the Neolithic era.
The first wave in Asia is distinctively non-African. The second, associated as it is to some extent with Y-DNA haplogroup D, might be more closely related to the the dominant Y-DNA haplogroup of much of Africa which is E, than the first wave. The third pre-Neolithic wave in Asia, however, which is the greatest ancestral contribution to the Chinese, is also distinctly non-African.
Genetics points to both Neanderthal admixture at a point in time shared by all non-Africans, and subsequent to them Denisovian admixture with first wave Asians - although it isn't entirely clear which extinct species of hominin to associate with the Denisovians. And, the exact place of Homo Florensis, a hominin species that co-existed with modern humans until 18,000 years ago or perhaps even more recently in Flores, Indonesia, is not entirely clear. Recent inferences from African genetics, meanwhile, are suggestive of admixture with probably two archaic African populations with Khoisan and Pygmy peoples in Africa, quite possibly as recently as the dawn of the Holocene. So, there may be evidence for as many as five different populations of archaic hominins co-existing with and admixing with modern humans in the last 100,000 years or so.
The Major Continental Divisions
European population genetics show a narrower range of lineages than seen in Asia that reflect a subset of ancestral South Asian genetic diversity. It has two of the three main non-African Y-DNA types and one of the two main non-African mtDNA types.
The relatively full fledged mix of Y-DNA and mtDNA haplogroups that made it to Asutralia and Papua also suggest either considerable time for the development of this DNA structure in India or elsehwere in Eurasia, after the population emerged from a common L3* group before dispersing widely in which Neanderthall genes were also acquired.
The Major Divisions of mtDNA
All ancestral non-Africans have mtDNA from macrohaplogroups M or N (which includes R) which are likely to have originated in South Asia, and both of which derive from African haplogroup L3*, with roots probably in East Africa.
But, all of the West Eurasian mtDNA haplogroups (with the exception of a couple like M1 that show signs of early Holocene or later back migration) derive only from mtDNA macrohaplogroup N which is found in both Europe and Asia.
The second wave of Asian migration associated with the Andamanese, Malaysian Negritos, Paleo-Tibetans and Ainu appear from strong circumstantial evidence to have comprised predominantly or exclusively of people belonging to mtDNA macrohaplogroup M.
The largely private mtDNA haplogroups of Africa are lumped into macrohaplogroup L. L2 and L3 are the predominant mtDNA haplogroups of black Africans, with L2 having a more West African, and L3 having a more East African orientation. L0 is roughly associated with the Khoisan, and L1 is roughly associated with the Pygmies. L4 has a strongly East African affinity. L5, which is a lineage more basal than L2 but less so than L1, is particularly to minorities in Sudan, Ethiopia, and the Congo. L4, a siser clade to L3, has an East African distribution from Sudan to a maxmium concentration in Angola.
The Major Y-DNA Divisions
Y-DNA macrohaplogroups C and D are likewise found in Asia, but not in West Eurasian populations where all Y-DNA haplogroups (with exceptions for relatively recent migration) seem to derive from Y-DNA macrohaplogroup F, which probably originated in South Asia, which is found in both West and East Eurasia, from which Europe was a "receiver." Haplogroup C probably originated somewhere in Asia. Haplogroup D's place of origin, given its erratic Asian distribution, is more obscure as its sister Haplogroup E shows strong signs of African origins.
As noted before, C and F are distinctively non-African lineages somewhat more closely related to each than they are to D and E, the former Asian and the latter African, with the former associated with a second wave of Asian migration. A few subtypes of Y-DNA haplogroup E, which is found across Africa and is dominant in much of sub-Saharan African, particularly in West African and Bantu populations, are also found in Southwest Asia and Southern Europe, but the phylogeny clearly indicates that these are isolated migrants to neighboring regions.
Macrohaplogroups A and B, the most basal Y-DNA types, are associated with the preagriculture peopling of sub-Saharan African according to a 2011 paper, The C, D, E and F lineages all break off from the B branch of Y-DNA phylogeny.
[W]e carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. . . . [T]heir subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent.
The Americas, of course, we peopled from Asia via the Bering Straight ca. 17,000 years ago when there was a land bridge, possibly by a population with an initial effective size as small as 70 reproducing adults, who may have spent a period of time in isolated in Beringia from later arrivals. This group origins was mostly from the general direction of China, although a minority of Paleosiberian ancestry was also present. There were at least a couple of subsequent waves of major population upheaval in the circumpolar area of the Americans after the initial peopling of the Americans, and genetic diversity was considerably reduced in what would become Latin America by serial founder effects relative to North America.
All of this, moreover, fails to reflect the massive reshufflings that would take place in the Neolithic.