Thursday, June 21, 2012

Y-DNA E Didn't Back Migrate To Africa

One theory held by Dienekes and a few others (and a minority of archaegeneticists) is that Y-DNA haplogroup E, the predominant Y-DNA type in Africa (with most of the remainign men having Y-DNA haplogroups A, B, T or R1b-V88) is a back migration to Africa from Eurasia. The points below, originally composed and somewhat edited since, as a comment to a post on his blog that reiterates this claim, sets out the arguments against this conclusion.

Significant Back Migration To Africa Did Happen

There is no real dispute that there has been some back migration from Eurasia to Africa. Y-DNA haplogroups T and R1b-V88 and mtDNA haplogroups M1 and U6, as well as autosomal data for North Africa, Ethiopia and Somolia, for example, all make a very strong case for back migration having taken place. North Africans, generally speaking have automsomal DNA which 80%-90% or so derived from West Eurasia. Most Ethiopian and Somolians have autosomal DNA which is 40%-50% derived from West Eurasia. The Maasai have a lower but significant share of West Eurasian autosomal genetic contributions. Most other sub-Saharan Africans have almost no West Eurasian source autosomal DNA.

The vast majority of Africans with significant back migrating uniparental and autosomal genetic traces (apart from the people of Madagascar who have quite recent Asian genetic origins in addition to their African roots and cases of recent European admixture such as colored South Africans), speak an Afro-Asiatic language, and most of the rest speak a Nilo-Saharan language. Prehistoric Eurasian admixture is almost completely absent in Paleo-African populations (Khoisan, Pygmies, San, etc.), and populations that speak Niger-Congo languages, apart from some small communities near the outer boundaries of the Niger-Congo linguistic region like the Fulani of Northern Cameroon.

There is also good evidence to suggest that there was at least, a relatively recent back migration that gave rise to the Ethio-semitic languages, and a probably also a more ancient back migration. Ancient DNA and the mtDNA mutation rate data (for mtDNA haplogroupds M1 and U6 which have roughly the same age) suggest that this back migration probably sometime in the late Upper Paleolithic or early Neolithic. A good guess might be around 12,000 years ago when North Africa was repopulated in the Mesolithic at the start of a "wet" Sahara period.

A recent study of autosomal genetics in Ethiopia, however, estimates the Eurasian contribution at ca. 3000 years ago, around the time of the Ethiosemitic language subfamily's arrival there as estimated from linguistic evidence.

But, this most recent study but does not show much difference in Eurasian genetic contributions between Ethiosemitic language speakers and populations such as Cushitic language speakers who are known to have preceded Ethiosemitic language speakers in the region, despite an expectation that a three thousand year old contibution of 40%-50% of Ethiopian autosomal genes would show greater percentage contributions in Ethiosemitic language speakers than in earlier Cushitic language family speakers as earlier uniparental genetic studies had suggested might be the case, particularly on the Y-DNA side (suggesting a male dominanted Ethiosemitic colonization event).

When Did The Out of Africa Migration Happen?

There is archaeological evidence for an Out of Africa and into the Near East migration from somewhere around Sudan to Arabia via the Sinai Pennisula around 104,000 years ago. Modern humans aren't found in Eurasia outside the Middle East (at that time, in South Asia) before about 74,000 years ago, however, and there is a gap in the record of modern humans in the Levant from about 75,000 years ago until about 50,000 years ago. At that time modern humans could have retreated to non-Levantine refugia in Eurasia, or could have simply failed only to be demically replaced by a sceond wave of modern human migration.

The case for a Eurasian refugia during modern human's absence from the Levant is the stronger one.

The flat phylogeny (i.e. with many contemporaneous branches dispersed over a very great geographic area) of mtDNA haplogroup M suggests a rapid Southern route expansion when modern humans finally burst into East Eurasia. The youngest archaic hominin remains on the mainland side of the Wallace line in East Eurasia appear to date from around 100,000 years ago, and the well dated appearance of modern humans in Australia and Melanesia around 45,000 years ago bounds the modern human expansion into East Eurasia from South Asia to sometime before that date. An expansion of modern humans into East Eurasia from South Asia around the time of the Toba explosion, 74,000 years ago, would be a fairly good match to the available genetic based dates from the Y-DNA CF branch, and from the mtDNA M and N derived haplogroups found in East Eurasia, and would also be consistent with the rather thin early archaeological record in East Eurasia from that time period.

As I explain at greater depth below, the distribution of Y-DNA haplogroup D suggests that it was a maritime secondary Out of Africa wave, rather than being part of the initial Southern route expansion Out of Africa, or the migration of modern humans into Europe.

Y-DNA Haplogroup E is not derived from a back migration to Africa

The case for a back migration of Y-DNA haplogroup E, the African branch of Y-DNA clade DE, is not well supported, however.

Y-DNA Haplogroup E as a clearly African rooted distribution.

Y-DNA haplogroup E is the predominant Y-DNA haplogroup in most of Africa. Y-DNA haplogroup E is common in three of the four major linguistic groups of Africa (Afro-Asiatic, Nilo-Saharan, Niger-Congo) and is present in all of them, unlike back migrating Y-DNA haplogroups T and R1b-V88, and back migrating mtDNA haplogroups M1 and U6, all of which are principally found in Afro-Asiatic language speakers. Auotosomal genetic components from West Eurasia in Africa likewise are predominantly found in Afro-Asiatic speakers, while they are nearly absent in West African Niger-Congo speakers.

Furthermore, Neanderthal DNA, which is found at about the same percentage frequency in all Eurasians, is absent from most African populations who are overwhelming Y-DNA haplogroup E bearers. Thus, back migrating early Y-DNA haplogroup DE* or haplogroup E bearers, if they existed, would have had to do so prior to Neanderthal admixture which appears to have happened before or at around the same time as West Eurasian and East Eurasian populations became distinct (and certainly prior to 45,000 years ago, as Australian Aborigines and Papuans have the same levels of Neanderthal admixture as other Eurasians). Indeed, even if the YAP mutation that defined Y-DNA macrohaplogroup DE actually did take place in Eurasia, the circumstantial evidence would suggest that this would have had to have taken place before these people developed most of the genetic features that make Eurasians genetically distinct from Africans - call them "pre-Eurasians" in Eurasia, perhaps.

Y-DNA haplogroup E subhaplogroups that do not appear to have a source in Bantu introgression are found in African pygmies, whose population genetic split from other Africans is one of the most basal dating to perhaps 70,000 years ago, and who were believed to have been linquistically distinct prior to Bantu introgression. This points to its African antiquity.

Africa also has basal branches of Y-DNA hg E not found anywhere else (e.g. E2). The most basal lineages, paragroup E*, have been found in a single Bantu-speaking male from South Africa, amongst pygmies and Bantus from the Cameroon/Gabon region, and in two individuals from Saudi Arabia. The distribution of Y-DNA haplogroup E overall in Africa is continuous throughout Northern and Subsaharan Africa, and is terrestrial.

All of the basal branches of Y-DNA haplogroup E are found in Africa, including Y-DNA subhaplogroup E2, some major lineages within subhaplogroup E1, and parahaplogroup E* that are found only in Africa. In contrast, all of the subhaplogroups of Y-DNA haplogroup E which are found in West Eurasia are from phylogenies rooted in Africa. Moreover, the SW European and SE European Y-DNA haplogroup E subhaplogroups don't have a common European source - their phylogeny reveals separate West Asian and Northwest African origins for Y-DNA haplogroup E in Europe with European specific lineages within these African rooted clades that are comparatively recent.

Inconsistently with a back migrating Y-DNA haplogroup, Y-DNA haplogroup E is less common in East Africa, where Y-DNA haplogrups A and B (found only in Africa and basal to both Y-DNA macrohaplogroups DE and CF) are more common, than Y-DNA haplogroup E is in most of the rest of Africa. All other back migrating uniparental markers and automomal genetic clines display the opposite trend in their distributions.

Y-DNA Haplogroup D has a sporadic East Eurasian distribution.

Y-DNA D is a rare haplogroup that has a sporadic Asian distribution with a deep rooted divide between D2 a Japanese subhaplogroup, and D*, D1 and D3 found in a network centered on the Andaman Islands and Tibet, with low frequencies in Eastern India and Southeast Asia, and seeps out from Tibet at low frequencies into Central Asia. Y-DNA haplogroup D is absent from Africa (including Madagascar), Oceania (which was colonized first by Austronesians), Europe, other parts of West Eurasia, the Americans, Melanesia and Australia.

It appears from the mtDNA make up of populations where Y-DNA haplogroup D is found that the earliest Y-DNA haplogroup D populations in East Eurasia probably had female counterparts who were part of mtDNA M (excluding later separately named mtDNA haplogroups) which is found only in East Eurasia, with no counterparts who were from mtDNA haplogroup N and its decendants that are found in both West and East Eurasia.

The geography of D is consistent with long range maritime migration to successive uninhabited islands or unoccupied areas in the wake of migrations occupying most territory by CF clade members. It may represent a secondary Out of Africa migration.

Modern humans did not arrive in Japan until about 30,000 years ago, the likely root of the Y-DNA D2 subhaplogroup which is restricted almost entirely to Japan or in much lower frequencies adjacent areas traceable to Japanese migration, so Y-DNA haplogroup D in East Eurasia can be no younger. The Andaman islands may not have had modern human occupants until about 20,000 years ago. Tibet had modern human occupants prior to 20,000 years ago, but possibly not much before 30,000 years ago.

Despite the fact that modern humans were in South Asia at the time of the Tobu erruption, 74,000 years ago, Y-DNA D is not distributed widely throughout South Asia. It is instead geographically limited to areas with high levels of Ancestral South Indian (ASI) admixture (which has its closest extant match in the Andaman islanders), but the distribution of Y-DNA D in India is more localized than the ASI autosomal genetic component in India and Y-DNA haplogroup D is uncommon even in mainland India.

Modern humans arrived in Europe around 40,000 years ago and it lacks Y-DNA haplogroup D. Australia and New Guinea were first occupied by modern humans around 45,000 years ago and lack Y-DNA haplogroup D. Denisovian autosomal DNA does not overlap with the populations where Y-DNA haplogroup D is found (basically Melanesians, Aborginal Australians and to a lesser extent Philippino Negritos), suggesting that Y-DNA haplogroup D populations probably didn't co-exist with the archaic hominin Denisovians for any prolonged period of time, if at all. Thus, there is strongly suggestive circumstantial evidence to suggest that Y-DNA haplogroup D dispersed after 40,000 years ago, but before 30,000 years ago, long after the initial Out of Africa migration, and close in time to when the Neanderthals began the downward spiral into extinction in West Eurasia.

The Americas, which lack Y-DNA haplogroup D, were mostly first occupied by modern humans starting around 14,000 years ago via the Bering Strait from Siberia (in mainland East Eurasia), although that founding population could have arrived in Beringia as soon as about 22,000 years ago. The Beringian first Native American founding population, among other things, supported itself by hunting mammoths. And, the earliest modern human migrants to the Americas from Beringia probably didn't have boating capabilities on a part with Y-DNA haplogroup D dominanted peoples who first settled the Andaman Islands and Japan, since if they did, the North American glaciers of the last glacial maximum would not have presented a serious barrier to their migration into the rest of the Americas. Later circumpolar populations in the Americas who did have solid maritime abilities arrived in the Americas many thousands of years later than 14,000 years ago.

Of course, the population bottleneck associated with the founding population of the Americas, which may have numbered in the hundreds on a census basis, could easily have excluded many Y-DNA lineages present on the East Eurasian mainland and could even have omitted many Y-DNA lineages that were present at low frequences in the founding population of Berginia before it expanded into the rest of the Americas as these lineages could have been lost due to genetic drift. Still, it is safe to say that the founding population of the Americas was probably not derived from a population in which Y-DNA haplogroup D was predominant, and Native American population genetics show more affinity to Siberia than Japan or Tibet, where Y-DNA haplogroup D is common.

The confined distribution of Y-DNA haplogroup D bearers to places that were probably either completely or nearly completely unpopulated by modern humans when they arrived, whille they are absent from places were Y-DNA clade CF bearers were already present in any great numbers, also disfavors the notion that an offshoot of their particular culture took Africa by storm in a way that made Y-DNA haplogroup E the predominant patriline genetic source for all of Africa, displacing all of its predecessors and being found in all of Africa's major language family populations.

The split of Y-DNA D and E took place long before the other back migrations to Africa sometime after men with Y-DNA in pre-split haplogroup DE left Africa.

There are just eight known cases of individuals from paragroup DE*, two in Tibet, and six from West Africa, although they may be some in the Andaman Islands. This implies that the dispersal of bearers of pre-split y-DNA haplogroup DE split between Asian and African populations, wherever it happened, took place at some point shortly before, rather than after the DE split.

The YAP mutation that defines DE and associated hinted at research from the 1000 Genomes project suggest that DE's divide is vary ancient, dating to roughly the Out of Africa era, or at the latest, early Upper Paloelithic. Mutation rate evidence that Y-DNA haplogroup D is older than Y-DNA haplogroup E has been contradicted by later research by some of the same investigators.

While mutation dating is problematic, it isn't so irrelevant and inaccurate that one cannot say that the DE divide is much more ancient than the mtDNA M1/mtDNA U6/Y-DNA T/Y-DNA R1b-V88 backmigrations or events giving rise to Ethiosemitic languages.

The timing of the Y-DNA DE split is at an age roughly contemporaneous with the split of the Khoisan and Pygmy populations from other Africans, the most basal population split in African population genetics.

The timing of the haplogroup D expansion suggested by the geographic distribution of Y-DNA haplogroup D is much younger than the date suggested by mutatioon rates which indicate that Y-DNA haplogroup D is only a bit younger than the root of Y-DNA macrohaplogroup CF, which is the dominant non-African Y-DNA clade and the only one found at any great distance from Africa in East Eurasia other than much more rare Y-DNA haplogroup D. The date implied by the mutation rates is on the order of twenty thousand to thirty thousand years more recent than the best estimate of the date at which Y-DNA macrohaplogroup DE split into Y-DNA haplogroups D and E.

A back migration of people with Y-DNA haplogroup E to Africa, in addition to preceding Neanderthal admixture with non-Africans, would also have to have been made up exclusively of men and of women with mtDNA haplogroup L3, the only African mtDNA lineage that is a source for non-African mtDNA lineages, because mtDNA haplogroup M1, the only potentially East Eurasian origin mtDNA lineage in Africa, arrived in Africa scores of millennia later. But, there are no indigeneous populations of East Eurasia who had mtDNA haplogroup L3 prior historic or almost historic era migrations (i.e. prior to 6,000-7,000 years ago).

A more plausible possibility that could explain this gap is that a small group of pre-split haplogroup DE bearing men from Africa either migrated to a refugium (perhaps in somewhere Arabia that subsequently became too arid to leave a remnant population in Arabia, or perhaps in South India) where they were part of a small endogameous community until their maritime expansion into East Eurasia that wasn't swept up in the initial Southern route expansion out of Africa, much later.

Alternately, this small endogamous community of pre-split haplogroup DE men could have existed for tens of thousands of years somewhere in Africa, only to be totally replaced within Africa during the more successful expansion of haplogroup E within Africa sometimes between then and the Bantu expansion, leaving only a handful of of descendents who ultimately ended up in West Africa behind, and leaving no surviving members who had been part of a D lineage that emerged in Africa.

Conclusion

After considering all of the evidence, it becomes clear that a scenario in which Y-DNA haplogroup E back migrates from Eurasia to Africa is grossly implausible, even though it is possible to imagine highly contrived and unprecedented set of events. It might not be proof beyond a reasonable doubt, but there is surely clear and convicing evidence that Y-DNA haplogroup E has its origins entirely in Africa.

Also, even if Y-DNA haplogroup E did back migrate from Eurasia to Africa, this would have had to have happened so early on in the Out of Africa migration process that its place of emergence would not different in practical observable implications in any meaningful way from an African origin, because it would have had to have predated the point at which the Out of Africa population had become very distinct genetically from Eurasians.

None of this is highly controversial. All of the facts, although not quite all of the connecting of the dots made in this post, is derived from peer reviewed published scholarly journal articles, either directly, or as citation support for my sources. I haven't taken the time to annotate this post (although I aspire to at some point), but have read almost all of those articles and blogged many of them.

The last published paper to argue seriously for a non-African origin of Y-DNA haplogroup E in Africa was published in 2007, and many of the sources I am relying upon in this post (including all of the Neaderthal DNA work and a lot of the detailed subtyping of Y-DNA haplogroup D and Y-DNA haplogroup E in Europe and Ethiopian DNA and much of the automsomal work, in general) has been published since then. The Asian origin for Y-DNA haplogroup E was a distinctly minority view in 2007, was disavowed by one of its original proponents based upon new evidence in 2008, and has almost surely lost informed supporters based upon the increasing weight of the evidence against this theory since then. I wouldn't yet call the theory pseudo-science, but it is starting to approach that threshold as our picture of humanity's genetic prehistory grows clearer.

We also know from recent research on Y-DNA haplogroup E in Europe, which I've previously blogged, that most of the Y-DNA haplogroup E in Europe has African sources in the Holocene era and in many cases much more recent African origins.

One important consequence of an African origin for Y-DNA haplogroup E (or at least a very early back migration that left no traces behind in Eurasia), is that it allows us, as we try to glean humanity's prehistory with archaeogenetics, to focus our attention entirely on Africa, with significant back migration from Europe taking place only fairly late in the game and probably in at most just a few main waves (Epipaleolithic, Neolithic, Ethiosemitic, and some historic era migration).

To the extent that particular Y-DNA haplogroup E lineages are associated with particular linguistic families or subfamilies in Africa, the populations that expanded and spread those languages expanded and spread those languages from a population that was mostly African in origin, even if there may have been outside thin superstate influences in the initial population from which it expanded.

While not nearly so decisive, this conclusion is also an important clue that tends to favor an African continental, rather than a Levatine origin of the Afro-Asiatic languages, because Semitic language speakers in the Levant have much more frequently bear Y-DNA haplogroup E than other West Eurasian populations. So does the fact that we can historically date the time period when Semitic languages first started to be spoken in the Eastern part of the Fertile Crescent (after about 2000 BCE), and their absence from Anatolia apart from small Akkadian trading colonies and influences from Arabic speakers in the last thirteen hundred years (after about 700 CE).

This conclusion isn't decisive, because it departs from the usual trend in which the first farmers exert cultural dominance over the people they encounter as they expand. But, an emerging picture of the North African Neolithic in which much of the demic influence of West Eurasia on North Africa precedes the Neolithic by a few thousand years as the area is repopulated during a "wet Sahara" climate phase, and North Africans become herders long before becoming farmers in a process that allows for a transition that has a stronger cultural component and a weaker demic component than parallel developments in Europe, weaken the strength of a first farmers paradigm for the linguistics of the Afro-Asiatic language family.

Instead, a scenario in which Afro-Asiatic languages are spread by indigenous hunting and gathering populations who adopted Fertile Crescent herding practices with animals domesticated there, while avoiding a profound introgression of peoples from the Fertile Crescent at that point, seems more plausible. The expansion was probably driven by food production technologies, and individual subfamilies within the Afro-Asiatic language family do show strong signs of demic expansion. But, some of the different linguistic families, at least, probably arose from language shift rather than population replacement, because the Afro-Asiatic language family, while made up of populations that have a number of genetic features distinct for Africa, are not geneticallly homogeneous and can't be linked in any simple phylogenetic tree at a population genetic level.

9 comments:

terryt said...

"The geography of D is consistent with long range maritime migration to successive uninhabited islands or unoccupied areas in the wake of migrations occupying most territory by CF clade members".

I think it is very difficult to make a convincing case for that. Any Y-DNA D presence in South Asia is from the northeast and even though D is found on the Andamans it most likely moved there from the nearby mainland. Have a look again at your own assessment of D's distribution:

"a deep rooted divide between D2 a Japanese subhaplogroup, and D*, D1 and D3 found in a network centered on the Andaman Islands and Tibet, with low frequencies in Eastern India and Southeast Asia, and seeps out from Tibet at low frequencies into Central Asia. Y-DNA haplogroup D is absent from Africa (including Madagascar), Oceania (which was colonized first by Austronesians), Europe, other parts of West Eurasia, the Americans, Melanesia and Australia".

Surely if D's original distribution had been coastal we would find it in many of the regions you list as 'absent', especially Australia and Melanesia.

"Thus, there is strongly suggestive circumstantial evidence to suggest that Y-DNA haplogroup D dispersed after 40,000 years ago, but before 30,000 years ago, long after the initial Out of Africa migration"

But that dispersal looks very unlikely to have been from Africa. It must have been from somewhere within Eurasia, although I agree there appears to be no Denisova component.

"Native American population genetics show more affinity to Siberia than Japan or Tibet, where Y-DNA haplogroup D is common".

Which would place D's origin somewhere between Japan and Tibet. Perhaps the hill country of Western China.

"There are just eight known cases of individuals from paragroup DE*, two in Tibet, and six from West Africa"

Which suggests that DE* was the migrator, as you suggest:

"This implies that the dispersal of bearers of pre-split y-DNA haplogroup DE split between Asian and African populations, wherever it happened, took place at some point shortly before, rather than after the DE split".

Perhaps DE has been replaced by CF through the region between haplogroups D and E. In which case DE's expansion would have been earlier than that of CF, or that of F-derived haplogroups such as R.

"It might not be proof beyond a reasonable doubt, but there is surely clear and convicing evidence that Y-DNA haplogroup E has its origins entirely in Africa".

I agree that E must be African. However I am not convinced that DE is. But just a small population containing DE having entered africa is the most likely scenario.

"The vast majority of Africans with significant back migrating uniparental and autosomal genetic traces (apart from the people of Madagascar who have quite recent Asian genetic origins in addition to their African roots and cases of recent European admixture such as colored South Africans), speak an Afro-Asiatic language, and most of the rest speak a Nilo-Saharan language. Prehistoric Eurasian admixture is almost completely absent in Paleo-African populations (Khoisan, Pygmies, San, etc.), and populations that speak Niger-Congo languages, apart from some small communities near the outer boundaries of the Niger-Congo linguistic region like the Fulani of Northern Cameroon".

However haplogroups, especially Y-DNA can travel far beyond autosomal DNA. When a man has children with a local woman his sons have his Y-DNA but only half his n-DNA. If these sons have sons with local women their sons will also have the same Y-DNA but only one quarter of the original incoming n-DNA, ans so on. Men can be very mobile and so it is easy to see howY-DNA can travel ahead of n-DNA or mt-DNA, sometimes independently of them.

andrew said...

"Surely if D's original distribution had been coastal we would find it in many of the regions you list as 'absent', especially Australia and Melanesia."

The boat trip to Australia and Melanesia is much more demanding than the boat trip to the Andamans or Japan at ca. 20kya to 40kya. The Andaman migration could have been secondary to a coastal Southeast Indian location. But, you can't get to Japan or the Andaman's without boats - neither has been connected to the mainland of Europe by a land bridge in the last 120,000 years or so (the Out of Africa era), and certainly not in the last 30,000-40,000 years when modern humans have been in Japan.

If D's origins are in the Hill Country of Western China, then you need to put somebody with DE there (given the Tibetan root, not impossible), but how do you get from Y-DNA B in Africa to DE in Western China? There is zero Y-DNA B between Africa and China except by slight migration to adjacent areas in the Middle East (certainly there is no ancient Y-DNA B in Siberia or Central Asia or East Asia or Tibet), while there is lots of Y-DNA B in the area where Y-DNA E appears to center. And, if you are going to pick a place for a Y-DNA B descendants to branch out, doesn't someplace relatively close to Africa (like E India) make more sense than someplace in inland China?

I'm agnostic about the path of D2 to Japan (maritime v. overland via Tibet), but the fact that D2 is not a branch of D1/D3 which is found from the Andaman's to Siberia via East India and Tibet, and the lack of Y-DNA D haplogroup diversity in Japan, and the pretty old documented age of Japanese modern human occupation, as well as the need for boats to get to Japan all make me favor a maritime root for the Japanese over a non-maritime route.

The reason for Y-DNA D to be absent from so many places despite a possible maritime dispersal is that muscling into an already occupied area without superior technology doesn't seem to happen. This wave would have had to make due with scraps. To go overland, you have to go through a lot of territory that someone already has dips on for thousands of miles without leaving traces.

You could propose that they were widespread in Siberia pre-LGM (spreading via some sort of Northern route and then back down to India out of Siberia), wiped out in the LGM except a handful of refugia, and not present in the post-LGM repopulation, which keeps them away from Australia and Melanesia. But, then, why is Y-DNA D still pretty rare in Paleosiberians? Still, it could happen. Still, at dates that ancient, and given the antiquity of E in Africa and the antiquity of the DE split, it is still pretty hard to make this work.

terryt said...

"The Andaman migration could have been secondary to a coastal Southeast Indian location".

I'm sure humans reached the Andamans from the nearby coast, but that doesn't mean at all that they had moved all the way from Africa via the coast. In fact the arrival at the Andamans looks to have been long after any OoA. In fact it is almost certainly some time after humans had reached Japan.

"neither has been connected to the mainland of Europe by a land bridge in the last 120,000 years or so (the Out of Africa era), and certainly not in the last 30,000-40,000 years when modern humans have been in Japan".

I'm fairly sure that, in spite of what you say, Japan was periodically connected to the mainland at times of low sea level. Especially in the north but also possibly from Korea. As a result the Sea of Japan was virtually land-locked at times.

"If D's origins are in the Hill Country of Western China, then you need to put somebody with DE there (given the Tibetan root, not impossible)"

Quite likely in fact.

"but how do you get from Y-DNA B in Africa to DE in Western China?"

But that same problem arises for Y-DNA C and mt-DNA N. I have my own theory, but Maju flies into a blind rage whenever I bring it up. I'll return to the subject soon.

"there is lots of Y-DNA B in the area where Y-DNA E appears to center".

But a complete absence of C, D or F anywhere near any B. So the same problem arises with those haplogroups.

"And, if you are going to pick a place for a Y-DNA B descendants to branch out, doesn't someplace relatively close to Africa (like E India) make more sense than someplace in inland China?"

I certainly wouldn't place any basal Y-DNA haplogroup in inland China. I'd place the origin of all basal Y-DNA halogroups (and basal mt-DNA haplogroups) quite close to Africa.

"I'm agnostic about the path of D2 to Japan (maritime v. overland via Tibet), but the fact that D2 is not a branch of D1/D3 which is found from the Andaman's to Siberia via East India and Tibet, and the lack of Y-DNA D haplogroup diversity in Japan, and the pretty old documented age of Japanese modern human occupation, as well as the need for boats to get to Japan all make me favor a maritime root for the Japanese over a non-maritime route".

I very much doubt a maritime route to Japan. And D1, D2 and D3 are three separate D haplogroups. ISOGG has this to say:

"The high frequency of haplogroup D in Tibet (about 50%) and in Japan (about 35%) implies some early migratory connection between these areas".

That basically rules out a maritime connection. ISOGG also has this to say:

"Y-DNA haplogroup D is seen primarily in Central Asia, Southeast Asia, and in Japan and was established approximately 50,000 years ago. Sub-group D1 (D-M15) is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the sub-groups D* (D-M174) and D3 (D-P47) are seen in Central Asia. The sub-group D2 (D-M55) is seen almost exclusively in Japan. ... Examination of the genetic diversity seen in sub-group D2 in Japan implies that this group has been isolated in Japan for between 12,000-20,000 years. The highest frequencies of D2 in Japan are seen among the Ainu and the Ryukyuans".

So between them D1, D2 and D3 are spread through Japan, Mongolia to Tibet, with basically a single haplogroup in each region. D1 is the most widespread reaching SE Asia and Central Asia, but those two geographically extreme regions are most likely later additions to its original range.

terryt said...

"The reason for Y-DNA D to be absent from so many places despite a possible maritime dispersal is that muscling into an already occupied area without superior technology doesn't seem to happen".

On that subject ISOGG has this to say:

"An isolated incidence of haplogroup D has also been seen in the Andaman Islands in the Indian Ocean. This implies that the group may once have had a much greater range, but has subsequently been displaced by more recent population events".

So they argue replacement, not isolated establishment.

"To go overland, you have to go through a lot of territory that someone already has dips on for thousands of miles without leaving traces".

Only if its expansion was later than everybody else's, which I think unlikely.

"You could propose that they were widespread in Siberia pre-LGM (spreading via some sort of Northern route and then back down to India out of Siberia), wiped out in the LGM except a handful of refugia, and not present in the post-LGM repopulation, which keeps them away from Australia and Melanesia. But, then, why is Y-DNA D still pretty rare in Paleosiberians?"

D's original spread probably did not include Siberia. More likely to have been through the Mongolia/Tibet region. The small amount found today in Central Asia is a product of what you describe as 'you have to go through a lot of territory that someone already has dips on'.

"Still, at dates that ancient, and given the antiquity of E in Africa and the antiquity of the DE split, it is still pretty hard to make this work".

I disagree. If a single B-derived Y-DNA haplogroup emerged from Africa along with two L3-derived mt-DNAs everything falls into place easily. The single Y and two mts occupied some region within Iran/Anatolia for some time before they expanded and diversified. DE expanded both northeast and southwest, C northeast and F southeast. The mt-DNA haplogroups N and M also fit an expansion from that region, rather than from South Asia, although M certainly diversified greatly in South Asia, especially in the border region between India and China.

terryt said...

I found this link from 2006 that you will almost certainly find interesting. Comments by JCA (who I think is Ebizur with a different name here):

http://s6.zetaboards.com/man/topic/8659569/1/

As you will guess I tend to agree with most of what JCA has written. His belief at the time seems to be that D originated somewhere in the region of Mongolia, Xinjiang, and Tibet, similar to what I suggested above. I have no idea if JCA still accepts that region as the most likely region of origin.

TheIsraelite Mosque said...

Since D never entered Africa, the point when D and E divided from DE they both had to be outside of Africa. This means E had to migrate into Africa: I will post a more detailed explanation.

TheIsraelite Mosque said...

WHO IS THE ASIATIC BLACKMAN? (ASIATIC AMURRU-MOORS)


The "Asiatic Blacks" were the Hamitic and Semitic tribesmen that were settled in Mesopotamia under the authority of Nimrod the Cushite. Those who moved westward settling in the lands of Syria, Lebanon, Palestine and throughout the African Continent became known as the Amurru or Moors. The Amurru migration also included what became known as the Bantu expansion. Linguistic evidence has now connected the Bantu tribes to ancient Sumeria. However it is DNA evidence that now conclusively proves that the Bantu tribes who make up the majority of present day Africans did not originate in Africa but were counted among the aboriginal inhabitants of Sumeria.


The only indigenous and aboriginal inhabitants of what is now known as the African Continent are those tribes that have a dominant representation of Y-Chromosome Haplogroups A and B. All other Y-Chromosome Haplogroups emerged or mutated outside of Africa. The Dinka of East Africa are by vast majority representative of Haplogroup A while the Pygmy and San tribes of Southern Africa are of Haplogroup B. Haplogroup A is the original or Adamic Haplogroup from which all others emerged. Haplogroup A mutated into B and it was segments of the B Haplogroup that migrated to areas outside of Africa and in particular Eurasia(Colchias) or Mesopotamia.


At this point members from within the migrating B Haplogroup mutated into a cluster group known as CDEF. From this point CDEF mutated into two groupings which were those known as CF and those which were DE. CF further divided into C and F while DE divided into D and E. Since it is known that members of Y-Chromosome Haplogroup D such as the Ainu of Japan never appeared in Africa it can then be concluded that at the point that Haplogroup DE divided into D and E they were both outside of Africa. This means that the Bantu and other Amurru who are members of Haplogroup E which has further divided into E1b1a(Bantu) and E1b1b(Cushitic) migrated into Africa from Sumeria or Mesopotamia from whence the term Asiatic Blackman(Asiatic Moor) has emerged.


Haplogroup F mutated into several clusters which ultimately produced J. As is the case with Y-Chromosome Haplogroup E members of J(J1) also migrated into Africa from Sumeria and therefore they were likewise counted among the Amurru. J1 is the dominant Haplogroup of the Solomonic Amhara in Ethiopia, the Black Arabs and Nubians of Sudan and the Beja. It is also found in extremely high percentages among the ancient and isolated Omotic tribes of Ethiopia. In fact to this day there is an Omotic tribe that still retains the name Amurru. J1 is also the dominant Y-Chromosome Haplogroup found among the Buba Kohen Priests of the Lemba in Southern Africa. Therefore all members of E and J that migrated to Africa from Sumeria are Asiatic Amurru or Asiatic Moors. The Westward Amurru migration from Sumeria or Mesopotamia included the family of Abraham and Lot.


THE ANCIENT AND ISOLATED AMURU OF ETHIOPIA WERE PART OF THE ORIGINAL AMURU MIGRATION FROM MESOPOTAMIA INTO AFRICA.

http://www.peoplegroups.org/Explore/GroupDetails.aspx?peid=11541

andrew said...

DE* has been found in both West Africa and Tibet.

The Bantu and the Moors have nothing to do with each other.

SE Europe has a subset of E consistent with migration of some E clades from Africa via the Levant, and SW Europe has a subset of E consistent with migration of some E clades via the Strait of Gibraltar. But, only Africa has a full set of E clades, and there are intermediate E clades connecting the set in SE Europe that are found in Africa and not Europe; and there are intermediate E clades connection in SE Europe that are found in Africa and not Europe. Of course, there are a great many broad subsets of E that are private to Africa, while only the very least basal sub-haplogroups of E are private to Europe. Moreover, E is not at all common in SW Asia (especially in non-Semitic peoples), and is essentially absent from West Asia.

None of this is consistent with a Eurasian origin of Y-DNA E.

The most plausible Y-DNA migrants to Africa from Mesopotamia are back migrations of Y-DNA T and J (especially J1), all Holocene.

TheIsraelite Mosque said...

DE was never found in West Africa. DE no longer exists and was the original haplogroup from which D and E split. There is no record of D appearing in Africa at anytime. This clearly indicates at the point D and E became independent haplogroups it was outside of Africa.