January 26, 2013

Indonesian mega-study (Tumonggor et al. 2013)

A new comprehensive survey of Y chromosome/mtDNA variation in Indonesia has just appeared online. From the paper:
The first stage of Indonesian prehistory represents the archipelago’s initial settlement as part of the African dispersal ~50 kya. The geography of the region was then markedly different from today. Sea levels were much lower, most modern islands had merged into larger landmasses, and the westernmost parts of Indonesia were physically contiguous with mainland Asia. This first stage is recorded by deep mtDNA lineages (M17a, M73, M47, N21, N22, R21, R22 and R23), which trace back to the main branching of macrohaplogroups M and N, and have a spotty distribution across both mainland and island southeast Asia today.
and:
The second stage reflects recurrent colonization events from mainland Asia throughout the later Paleolithic. Many haplogroups (B4a, B4b, B4c, B4c1b3, B5a, B5b, B5b1, D and E) show origin dates of 10-40 kya (Supplementary Table 6) 25, 63 and are distributed across a wide range of mainland and island southeast Asian populations. 
and:
The third stage represents Neolithic movements into and around island southeast Asia. Some of these may involve population dispersals from (and perhaps to) Taiwan, while others reflect movements between Indonesian island groups. Representative haplogroups include M7b3, E1a1a, M7c3c and Y2. Autosomal data strongly supports large demic movements of Asian populations into eastern Indonesia from around 4 kya 67.
and, finally:
The fourth stage reflects historic movements into Indonesia, largely involving trade and the associated spread of major religions from India, Arabia and China 71. Although found at relatively low frequency today, Y chromosome lineages representing these movements occur across Indonesia 20, notably in the west, such as the Hindu dominated island of Bali
It would be useful to study Indonesian haplogroups as a means of testing the hypothesis of Indian settlement in Australia, since it is difficult to see any such settlement that would not have passed through the Indonesian archipelago.

Of the lineages found in Indonesia, the deepest ancestry appears to be associated with mtDNA haplogroups P (54+/-16ky) and Q (38+/-9ky), both of which appear to have clear "Australo-Melanesian" associations. Of the B subclades that are lately of interest due to the publication of Tianyuan ancient DNA, the oldest one appears to be B4a (33+/-13ky).

One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N in the eastern portion of Eurasia vs. the dominance of N in the western part thereof. The peninsulas of Arabia and India probably hold a key to this riddle, although in both cases the situation is obscured by subsequent events: in Arabia, there has probably been substantial population turnover during its "desert" phases, while in India there has been recent admixture between the aboriginal population and West Eurasian-derived inhabitants.

Journal of Human Genetics , (24 January 2013) | doi:10.1038/jhg.2012.154

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific 

Meryanne K Tumonggor et al.

Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date—2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region’s complex history of immigration, transitory migrants and populations that have endured in situ since the region’s first settlement.

Link

20 comments:

bmdriver said...

''While in India there has been recent admixture between the aboriginal population and West Eurasian-derived inhabitants.''
...Where are these studies? Or is just assumed. lol

genetiker said...

Where are these studies?

Try this.

For a shorter, more accurate genetic history of India, read this.

genetiker said...

The first stage of Indonesian prehistory represents the archipelago’s initial settlement as part of the African dispersal ~50 kya.

Negritoids.

The second stage reflects recurrent colonization events from mainland Asia throughout the later Paleolithic.

Ainoids.

The third stage represents Neolithic movements into and around island southeast Asia.

Mongoloids.

Some of these may involve population dispersals from (and perhaps to) Taiwan

Austronesian-speaking Mongoloids.

The fourth stage reflects historic movements into Indonesia, largely involving trade and the associated spread of major religions from India

Veddoids, Caucasoids.

Arabia

Caucasoids.

and China

More Mongoloids.

since it is difficult to see any such settlement that would not have passed through the Indonesian archipelago.

It did. See this. There are, or were, Veddoid populations along the route I describe.

Of the lineages found in Indonesia, the deepest ancestry appears to be associated with mtDNA haplogroups P (54+/-16ky) and Q (38+/-9ky)

P was brought in by the Ainoids. Q originated in Sahul from the M brought in by the Negritoids.

Of the B subclades that are lately of interest due to the publication of Tianyuan ancient DNA, the oldest one appears to be B4a (33+/-13ky).

Brought in by Ainoids.

One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N in the eastern portion of Eurasia vs. the dominance of N in the western part thereof.

N originated ~60 ka in Veddoids or proto-Veddoids in North or Central India. M originated ~50 ka in Negritoids in Southeast India or Bangladesh. The Veddoids/proto-Veddoids leaving India for the West tended to leave earlier, and encountered no M as they did so. The Veddoids/proto-Veddoids leaving India for the East tended to leave later, and as they did they encountered and absorbed M mtDNA.

G Horvat said...

"One of the major puzzles in prehistory is the co-occurrence of mtDNA macro-haplogroups M and N ..."

I agree. There are clines, though. Siberia is mainly 'M' and Australia mainly 'N'. Between these two regions the frequencies of M and N are about 50-50.

Ed said...

Close what Razib gathered from the "Antipode of Asia" post.

Nirjhar007 said...

Actually as you know there are west asian specific components found in Indians but its not about the proportion but the age of the components in certain populations with the help of trustable aDNA of a period.

Nirjhar007 said...

As you know there are west asian similar components in Indians but its about the age of a component rather than the proportion with the help of trustable aDNA data.

sidoroffs said...

Dienekes, You don't have access to the Y-DNA part or You're not interested anymore?

Anyone else?

genetiker said...

"The Veddoids/proto-Veddoids leaving India for the West tended to leave earlier, and encountered no M as they did so. The Veddoids/proto-Veddoids leaving India for the East tended to leave later, and as they did they encountered and absorbed M mtDNA."

That's incorrect. There's no reason to think that there was any difference in when they left. The geography alone explains it. It should simply be

"The Veddoids/proto-Veddoids leaving India for the West didn't encounter any M. The Veddoids/proto-Veddoids leaving India for the East after 50 ka encountered and absorbed M mtDNA."

bmdriver said...


Try this.


No its the age of the population, like i said, its not a migration from West asia to India, but a migration from India to west asia. Many studies have proven this. Its your clan of Abrahamic centric Noahs theory that hold to the view it was Migration from West Asia to India. Studies have proven migration from India to West Asia. There is NOT ONE SET OF DATA that demonstrats a migration from west asian to India. NOT ONE.

bmdriver said...

Study of human DNAs finally rule out any Aryan arrival from the Central Asia into India. Rather the suggested Aryan gene R1a (M17) evolved and migrated out from India about 16,000 to 14,000 years back crossing through Central Asia ultimately reaching Pontic-Caspian area and Russia (Sahoo, 2006; Sengupta, 2006; Trivedi, 2008; Underhill, 2009). Study of West Asian genes also suggests that that there was a human migration from India to West Asia, indicated by presence of Indian genes in the West Asian population (Y-DNA HGs: F*, L1, H (M-69), K2, C5, C*, R1a (M-17). On the other hand West Asian genes (Y-DNA: J1, G, I and R1b3) are not found in India, ruling out migration from West Asia to India. L1, which was earlier suggested to be a marker of migration of Dravidian speakers from Elam region of West Asia, has now been confirmed to be of Indian origin from where it migrated to Iran and West Asia (Sengupta, 2006; Sahoo, 2006).

bmdriver said...

As you know there are west asian similar components in Indians but its about the age of a component rather than the proportion with the help of trustable aDNA data.''

This is real heart of the matter, its no if west asian genome is present in India, or vice versa, its which is older and more diverse, ie which came earlier. South Asian genome is more diverse than west asian, therefore older than west asian, therefore migration from India to West asia.

The Aryan theory or Noahs theory is very hard to kill off, when scholars laced with predujice voice their opinions.


'There has been no foriegn migration into the Indian mainstream in the last 60,000years'

Genographic project IBM. 2011.

genetiker said...

"The Veddoids/proto-Veddoids leaving India for the West didn't encounter any M. The Veddoids/proto-Veddoids leaving India for the East after 50 ka encountered and absorbed M mtDNA."

In fact, this should be further simplified to just

"The Veddoids leaving India for the West didn't encounter any M. The Veddoids leaving India for the East after 50 ka encountered and absorbed M mtDNA."

In my timeline I said that proto-Veddoids left India, during Veddoid evolution 70-55 ka. But the times of origin of the Veddoid C and F Hgs indicate that Veddoids probably did not leave until their evolution was complete. And that means that heidelbergensis hybridization probably took place in the narrow window of 55-47 ka, or at first contact and only for a few ky thereafter.

Nirjhar007 said...

bmdriver told-
''This is real heart of the matter, its no if west asian genome is present in India, or vice versa, its which is older and more diverse, ie which came earlier. South Asian genome is more diverse than west asian, therefore older than west asian, therefore migration from India to West asia.

The Aryan theory or Noahs theory is very hard to kill off, when scholars laced with predujice voice their opinions.


'There has been no foriegn migration into the Indian mainstream in the last 60,000years''
No actually there are archaeological data for intrusion to south asia in 6000bc,4500bc and the last one in ~600bc,mention of that you can find in this vast and beautiful analysis-
http://www.archaeologyonline.net/artifacts/19th-century-paradigms.html
and some recent genetic researches also have said of the presence of archaic intrusions like the Metspalu et al-
http://www.sciencedirect.com/science/article/pii/S0002929711004885
and there is another one p. moorjani et al-
http://www.ichg2011.org/cgi-bin/showdetail.pl?absno=20758
on that presentation they found the ANI-ASI mix to be 1,200-3,500 years old that they found indicating the aryan migration but in a later revision they discarded the connection and found-
''ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown. Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within the last four thousand years, a cultural shift led to widespread endogamy, decreasing the rate of additional mixture.''
http://www.harappadna.org/2012/06/ani-asi-admixture-dating/
So again the evidence for the Indo-European Migration went absent.
So,the aDNA of farmana will indeed just not solve the riddle but will also give the Indo-European studies a true direction.
Good times.

apostateimpressions said...

The Rig Veda appears to recount the Indo-Aryan conquest.


RIG VEDA

Dasyus = Dark Skinned Peoples

Panis = Semites, Phoenicians

Source: Rig Veda

"The mighty Thunderer with his fair-complexioned friends won the land, the sunlight, and the waters." (Rig Veda I.100.18)

"Indra in battles helps his Aryan worshipper, he who hath hundred helps at hand in every fray, in frays that win the light of heaven. Plaguing the lawless he gave up to Manu's seed the dusky skin; Blazing, 'twere, he burns each covetous man away, he burns the tyrannous away." (Rig Veda I.130.8)

"Thou, Hero, winner of the spoil, urgest to speed the car of man. Burn, like a vessel with the flame, the lawless Dasyu, Conqueror!" (Rig Veda I.175.3)

"Stirrer to action of the poor and lowly, of priest, of suppliant who sings his praises; Who, fair-faced, favors him who presses Soma with stones made ready, He, O men, is Indra." (Rig Veda II 12.6)

"He verily, the God, the glorious Indra, hath raised him up for man, best Wonder-Worker. He, self-reliant, mighty and triumphant, brought low the dear head of the wicked Dasya." (Rig Veda II.20.6)

"Indra the Vrittra-slayer, Fort-destroyer, scattered the Dasya hosts who dwelt in darkness. For men hath he created earth and waters, and ever helped the prayer of him who worships." (Rig Veda II.20.7)

"He gained possession of the Sun and Horses, Indra obtained the Cow who feedeth many. Treasure of gold he won; he smote the Dasyus, and gave protection to the Aryan color." (Rig Veda III.34.9)

"For thou art he, O Indra, who stormeth all castles of the foe, Slayer of Dasyus, man's Supporter, Lord of Heaven." (Rig Veda VIII.87.6)

"Blowing away with supernatural might from earth and from the heavens the swarthy skin which Indra hates." (Rig Veda IX.73.5)

More quotes here:

http://www.worldfuturefund.org/wffmaster/Reading/Germany/Caste%20Quotes.htm

shenandoah said...

It's possible (and I believe true) that the Aryans did originate in India, **yet were not technically the aboriginal, indigenous people** of India. They are a mixed race, after all. Yes, I realize they have long claimed to be a "pure" (and ancient) race -- but DNA evidence proves that they are not either. So I believe that only a few ~components of their genome is aboriginal to India (perhaps some mtDNA portions, some of their maternal lineages etc., that's my theory).

If I am correct, then there is a little bit of truth in both of the popular mainstream theories (Invasion vs Aboriginal). Ie, India was 'invaded' from ~within their own society, via their mating habits.

I believe the ancient Hindus created the Aryan race through their particular mating habits, then because they liked the Aryans' appearance (ie "white", "shining", colorful, etc.) made them into objects of worship and highest caste.

After the Aryans were definitely established in India, they eventually and naturally formed many subtribes and then gradually migrated to many other places.

Aryans are not the oldest Human race; Caucasoids are, in my humble opinion. Aryans are not precisely Caucasoids, because Aryans are a mixed race. Of course, I realize that at this late date in Human History, there are no 'pure' race(s) left anyway. It's just my own theory that Caucasoids were the original Homo Sapiens, Cro-Magnons, and that Aryans certainly were not that ancient.

In fact, it is quite likely that nothing at all closely resembling the original Human species exists anymore.

apostateimpressions said...

shenandoah, What you say sounds feasible, that the Indo-Aryans evolved through socially directed selective breeding though I dont know how realistic that would be in India. We know that fair traits naturally concentrate northward, which is consistent with a conquest from the north. FAIK the autosomal diversity of ancient specimens might indicate whether the Indo-Aryans may have evolved through an artificial bottle neck or invaded en masse but we would need data for that.

The early Indian nationalist Bal Gangadhar Tilak presented an interesting theory. He argued in his book _The Arctic Home in the Vedas_ that astronomical descriptions in the Vedas indicate that the Indo-Aryans originated near the north pole before the last ice age. That would not exclude a West Asian home of the Indo-Aryans during the Bronze Age. Indeed, we would need to know where (those) West Asians dwelt before the ice age, whether they long ago evacuated down south. One may also ask whether the accounts of the early Vedas originated with the ancestors of the Indo-Aryans or whether they acquired the traditions.


Quotes:

In 1903, he wrote the book The Arctic Home in the Vedas. In it he argued that the Vedas could only have been composed in the Arctics, and the Aryan bards brought them south after the onset of the last ice age. He proposed the radically new way to determine the exact time of the Vedas.[8] He tried to calculate the time of Vedas by using the position of different Nakshatras. Positions of Nakshtras were described in different Vedas.

http://en.wikipedia.org/wiki/B%C3%A2l_Gang%C3%A2dhar_Tilak


- At the North Pole, one sees the heavenly dome above seems to revolve around one like a potter's wheel. The stars will not rise and set but move round and round in horizontal planes during the long night of six months. The Sun, when it is above the horizon for six months, would also appear to revolve in the same way but with some difference. The Northern celestial hemisphere will alone be visible spinning round and round and the Southern half remain invisible. The Sun going into the Northern hemisphere in his annual course will appear as coming up from the South. Living in the temperate and tropical zones, however, one sees all heavenly objects rise in the East and set in the West, some passing over the head, others traveling obliquely.
- The long dawn of two months is a special and important characteristic of the North Pole. As we descend southward, the splendor and the duration of the dawn will be witnessed on a less and less magnificent scale. But the dawn occurring at the end of the long night of two, three or more months will still be unusually long, often of several days duration.
- All these characteristics of an Arctic home are clearly recorded in several Vedic hymns and Avestic passages and they come to us sometimes as the description of the prevailing conditions or the day-to-day experience or stories told by the earlier generation and sometimes as myths.

http://en.wikipedia.org/wiki/The_Arctic_Home_in_the_Vedas

Book:

http://archive.org/details/TheArcticHomeInTheVedas

shenandoah said...

Thanks for the link, apostateimpressions; lots of food for thought there! Here's one for you, a book by Yogi Ramacharaka c1930-ish. He mostly explains the Religions and Philosophies of India, but does touch upon the History of the Aryans both at the beginning of the book and starting on around page 34. I have a complete copy of this book at home; unfortunately it seems a few pages are missing here and there on this online copy.

Anyway, Ramacharaka indicates his belief that according to the Hindu texts the Aryans came to India from a land called Lemuria which he says included Australia and Islands of the Pacific still in existence; although much of their ancient homeland became flooded and submerged, causing their mass upheaval.

He then goes on to explain that after conquering the indigenous people(s) of India, they (Aryans now mixed somewhat with the indigenous genes) immigrated from India to Europe and other regions.

The Arctic angle is also quite interesting, in light of the many drastic changes in climate (and maybe even in the axis) of our planet. I'm aware that for example, the remains of fossilized hippopotami have been found in England alongside the remains of ancient Humans. I wouldn't lightly dismiss either man's reasoning, before more thorough investigation, because I can understand how there could be elements of truth in all of the above (and maybe yet fit my own theory well enough, too).

However, I do think that in view of the Hindu idealization of Aryanism with their position at the top of their caste system, that they might be a little bit "Aryan-centric" in the same manner that some other cultures tend to be "Euro-centric", etc. In that respect, I think it's quite possible that their ancient priests, scribes probably tweaked their legends a bit, in order to maintain their position of social and political power. They certainly would not be the only tribe to engage in that sort of propaganda, lol.

...I guess where I differ the most from any of those theories, is that I just don't accept the idea that contemporary Aryans in all their variety of forms are very much ~directly descended from the original Human species. (Neither do I believe, as some do, that the legendary 'Giants' were the ~original Human species; although I suppose I could someday be proven wrong on all counts, to some degree anyway. And I don't consider the Neanderthal, Denisovan and other Hominids to have been anything other than some kinds of Human-Hybrids; although that is a problem which obviously still hasn't been completely solved by geneticists).

http://archive.org/stream/TheArcticHomeInTheVedas/TilakLokamanya-TheArcticHomeInTheVedas1903470P.#page/n463/mode/2up

shenandoah said...

http://archive.org/details/ThePhilosophiesAndReligionsOfIndia

And here is the correct link for Ramacharaka's book, sorry.

alpha-eagle said...

great blog wanna asked
was proto Malay and deutro Malay geneticly related ???,
I means proto Malay like mentawai,batak,Malay like Palembang,dayak,toraja physicly closer to Chinese,Japanese,Korea, Thai, Vietnam they has small eyes, Single Eyelid, small nose, black straigh hairs, and white yellowish skin.
while deutro Malay like acehnese,sundanese,javanese,maduranese,balinese has wide eyes, double Eyelid, sharp nose, wavy to light curly black reddish hair, brown redish skin.