[W]e genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526.From Tatiana M Karafet, Fernando L Mendez, Herawati Sudoyo, J Stephen Lansing and Michael F Hammer, "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia", European Journal of Human Geneticas (June 4, 2014).
Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R.
Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.
Y-DNA R and Q have origins in SE Asia Probably Between 45 kya and 70 kya.
The most common Y-DNA haplogroup type in Europe is R (specifically, R1a and R1b), although this distribution probably didn't arise for most of Europe until the second wave of farmer/herder migrations to Europe, a thousand to two thousand years or so after the first farmers brought the Neolithic Revolution to Europe.
R1a is associated with Indo-European settlement starting as far back as the Corded Ware culture or earlier in Central to Eastern Europe and Central Europe with ancient DNA evidence of the population's genotype extended all of the way to the Tarim Basin in far Western China at its greatest extent for essentially all of the Bronze Age and into the 7th century CE or so, when Uygur populations emerge in the region.
R1b is the predominant Y-DNA haplogroup of Western Europe and a very basal branch of it (R1b-V88) is common among the mostly pastoralist speakers of the Chadic languages in the African Sahel, a branch that probably arrived around 5,200 years ago based on archaeological evidence. A migration probably brought this Y-DNA haplogroup into Western Europe at high frequencies sometime after that, although the precise archaeological culture associated with the predominance of R1b in Western Europe isn't entirely clear. I've advanced that hypothesis that the Bell Beaker culture (the earliest to have R1b ancient DNA discovered so far) was responsible (for lack of any better candidates), but other evidence points to the prior Megalithic culture members who were first farmers in much of Western Europe, but with very fragile evidence, mostly from archaeologically inferred population booms and busts and no ancient DNA at all, to support that hypothesis.
Y-DNA haplogroup R2 has a largely South Asian distribution with concentrations highest in the Indus River Valley. Ancient DNA reveals an Y-DNA R* individual, Ma'lta boy ca. 24,000 years ago, with significant autosomal genetic affinity to modern Native Americans near the Altai region of Southern Siberia.
Y-DNA haplogroup Q is the most common Y-DNA haplogroup of Native Americans and is also found in Siberia.
Thus, the Y-DNA P clade within newly redesignated Y-DNA K2b is the leading Y-DNA clade of the Northern part of the Northern hemisphere. The latest study cited above indicates that the Y-DNA P clade that includes R and Q probably arose in Southeast Asia, coincident with the expansion of Y-DNA K2, in general, and then migrated West together before expanding into their current range, from an intermediate source somewhere in the region from India to Iran to Central Asia.
More On The Expansion of K2 into SE Asia
Both Y-DNA haplogroup C (whose Asian specific break from other Eurasian Y-DNA haplogroups is more basal than K) and Y-DNA haplogroup P (which is part of K2) haplogroups are found in Australian aboriginal men and indigeneous Papuan peoples. So, the rapid expansion of K2 giving rise to sub-haplogroups had to have taken place before about 45,000 years ago, the earliest securely dated archaeological evidence of modern human presences in those places.
It isn't clear if C and K arrived in Southeast Asia in a single migration of a genetically mixed population, or if they were two separate waves of migration that only started to produce a Y-DNA haplogroup mixed population in SE Asia prior to migrations to Australia and Papua New Guinea.
Suggestive evidence, but no smoking evidence, suggests that modern humans most likely reached Southeast Asia from South Asia around the time of the Toba volcanic eruption ca. 74,000 years ago. The 74,000 years ago date would also fit an mtDNA mutation rate estimated expansion of mtDNA haplogroups N and R out of India.
This time span (from 45,000 years ago to 74,000 years ago) is long enough to accommodate either a one wave or two wave scenario. Time ranges from 100,000 years ago to about 55,000 years ago could be squared with hypothesis proving interpretations of the archaeological evidence.
My weak personal bias is an expectation that these waves of migration were separate, with C expanding first (probably around 74,000 years ago), based mostly upon the phylogeny of the Y-DNA C haplogroup expanded in Asia, which seems to show a rapid "race across the coastal route" path from India that differs quite a bit from the pattern seen in haplogroup K. Haplogroup K2 would then migration to SE Asia in a separate wave perhaps 5,000 to 10,000 years later.
Also, sometime between 45,000 and 74,000 years ago, somewhere between India and the island of Flores, these early modern human migrants to Asia admixed with archaic hominins whose Denisovan-like genetic traces are present in modern Australian Aborigines, Melanesians and Phillipino Negrito populations at significant levels. The peak admixture percentage in the source population for these groups is estimated to have been around 8%. My weak personal bias that this admixture took place mostly on the island of Flores with H. Florensis who would have Denisovan DNA in that scenario, but I'm less confident of any particular scenario for Denisovan admixture than I once was, mostly because of (1) possible evidence of a low but non-zero level of mainland Asian Denisovan admixture that is highly diluted but was not eliminated that is unlikely to be due to Melanesian back migration, and (2) physical anthropology and archaeology suggestions that H. Florensis may have been Homo Erectus that evolved to a smaller size due to island dwarfism. But, I have not yet seen really solid evidence of either point.
Homo Erectus was the first hominin species to leave Africa and arrived in Asia including South East Asia around 1,800,000 years ago. It isn't clear if Homo Erectus was still in SE Asia at the time and went extinct as part of the same Toba/migration event, or if this hominin species went extinct in the region at an earlier time, because the archaeological record of them more recently than 100,000 years ago is pretty much non-existent. The genetic evidence related to Denisovan admixture, strongly supports the concluding that the Archaic Denisovan admixture seen in modern humans is from a hominin species that probably was not a direct decedent of Asian Homo Erectus.
The species with Denisovan genetics might have replaced Homo Erectus before modern humans reached Southeast Asia from South Asia, or might have co-existed with Homo Erectus in Asian until modern humans brought about the extinction of Homo Erectus. In either case, the extinction of Homo Erectus could have happened either directly, via genocide, or indirectly, for example, through impacts on food supply and habitat. An extinction of Homo Erectus entirely, without a strong role in that process from another hominin species, seems unlikely for an archaic hominin species that had already managed to persist for 1,700,000 years or so in Asia.
A Toba/modern human migration model of Homo Erectus extinction seems more parsimonious.
There is no meaningful archaeological evidence of an intermediate archaic homin species other than Homo Flores (which seems like a poor candidate to wipe out a continent wide Homo Erectus population) apart from Denisovan admixture in the populations mentioned above, but we really don't have much solid evidence one way or the other to discriminate between different models of Homo Erectus extinction.
Footnote on Y-DNA Haplogroup D
Y-DNA haplogroup D is the other main Y-DNA haplogroup, in addition to C and K2 that is found in East Eurasia. It is very common in Japan and is also found in a swath of land from the Anadaman Islands, across South Asia to Tibet and into the steppe to the North of Tibet. The Japan v. non-Japan split in the phylogeny is more basal than the splits within each category and is almost complete (i.e. only Japanese D is found in Japan, and only non-Japanese D is found in South Asia).
The details of a DE split are controversial and beyond the scope of this post, but the question with Y-DNA haplogroup D is whether its island-like distribution is a result of a much wider range that was split up by subsequent migration, or whether it migrated to Asia after Y-DNA C and K2, perhaps seeking out niches not already occupied by modern humans in Asia ca. 30-40 kya. I tend to favor the later scenario, because there is so little evidence of Y-DNA D anywhere else in Asia, and because the later scenario is still consistent with the evidence on the earliest migrations of modern humans to Japan. I also tend to favor a scenario in which the Japanese Y-DNA D carriers arrive via a Northern route from somewhere North of Tibet, rather than a Southern Coastal route.
On the other hand, mutation rate data tend to favor a spit between Y-DNA D and Y-DNA E around the same time as the split between Y-DNA K1 and Y-DNA K2, for which the archaelogically favored date would be around 70,000 years ago, or perhaps a few thousand years earlier. It could be that Y-DNA D expanded on a Northern route from Central Asia to Korea and then trickled down into India and the Andaman Islands from Tibet, prior to the LGM ca. 20,000 years ago, while Y-DNA C and K2 expanded along a Southern route from India into South East Asia, but that the LGM ice age wiped out all but a few relict populations with Y-DNA D, thus breaking up its range.
Another factor favoring Y-DNA haplogroup D as a post-Y-DNA C and K2 wave is that none of the Y-DNA haplogroup D populations has any significant non-Neanderthal archaic hominin admixture.
The New Y-DNA Haplogroup K1.
The Y-DNA haplogroups known as L (mostly South Asian and especially the Indus River Valley) and T (geographically broad early Neolithic and/or Epipaleolithic expansion from around Mesopotamia into Europe and parts of Africa and since diluted in many places), have been included in a newly designated Y-DNA K1 haplogroup.
It would appear that K1, which stayed in West Eurasia (probably in Iran or South Asia) before it split from K2, which continued on to SE Asia around 70 kya, if not earlier.
K1 could also have backmigrated from Southeast Asia around the same time as Y-DNA haplogroups Q and R, but that seems much less likely as there are few traces of Y-DNA haplogroup L or T in Southeast Asia that can't be much more easily explained by later migrations.