| Majority of Indonesian Y-DNA are of Paleolithic origins | |
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| Tweet Topic Started: Mar 12 2010, 05:05:53 PM (3,218 Views) | |
| natsuya | Mar 12 2010, 05:05:53 PM Post #1 |
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Major East-West Division Underlies Y Chromosome Stratification Across Indonesia Tatiana M. Karafet et al. The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion. http://mbe.oxfordjournals.org/cgi/content/short/msq063v1 http://dienekes.blogspot.com/2010/03/major-east-west-divide-in-indonesian-y.html Download: http://www.brsbox.com/filebox/down/fc/e50b15af7b6cc60d385f76c9fa593b2d/rand/1894020356 Click on the green arrow, and you'll download the whole paper. Edited by natsuya, Mar 12 2010, 05:08:03 PM.
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| natsuya | Mar 12 2010, 05:43:28 PM Post #2 |
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In this Karafet's 2010 paper, K-M526*(MNOPS*) is found in 45.8% of Filipino samples(n=48). I wonder if these K-M526* are related to pre-Austronesian lineages, such as "Aeta" lineages. Spencer Wells has tested Y-DNA of Aeta people, but that's still unpublished data. "The earlier trip with Dr. Rand Allingham yielded data from more than 100 Aeta, and the genetic results we have obtained are fascinating. We're currently writing them up, and don't want to discuss them in too much detail until they have been published, but the Aeta certainly seem to be a mix of both Austronesian and earlier genetic lineages, and their Y-chromosomes appear to be almost completely pre-Austronesian." http://blogs.nationalgeographic.com/blogs/genographic/2008/12/meeting-the-ati-peoples-in-the.html Edited by natsuya, Mar 13 2010, 09:29:59 PM.
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| natsuya | Mar 13 2010, 09:34:11 PM Post #3 |
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I found that Taiwanese aboriginals look very different from Indonesians. This is exactly like what this Karafet's 2010 paper indicates, only <20% of Indonesian Y-DNA were derived from Austronesian neolithic farmers migrating from Taiwan ~5,000 years ago. What Austronesian neolithic farmers brought to Indonesia were mainly linguistic and cultural changes. The majority of Indonesian Y-DNA (such as O2a-M95) carriers are descendants of non-Austronesian speakers coming from paleolithic mainland Southeast Asia when ISEA was still "Sundaland" during the LGM. |
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| natsuya | Mar 13 2010, 09:39:04 PM Post #4 |
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These are some charts taken from the paper. (1) Hg O1 (2) Hg O2 (3) Hg O3 (4) Hg C (5) 4-phase colonization model Edited by natsuya, Mar 13 2010, 09:40:01 PM.
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| natsuya | Mar 13 2010, 10:43:33 PM Post #5 |
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I've put the paper and data on Zoho viewer. http://viewer.zoho.com/docs/odaScbj http://viewer.zoho.com/docs/kdaNd9 http://viewer.zoho.com/docs/ndaMDc |
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| ren | Mar 14 2010, 05:31:24 AM Post #6 |
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The origin of Western Austronesian Y-chromosomes have been discussed for a long time now o this forum. We figure they are sub-merged Austro-Asiatic lineages which are Neolithic. |
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| natsuya | Mar 14 2010, 01:47:46 PM Post #7 |
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The status of O2a-M95 is still controversial. But the lineage most likely came from paleolithic mainland SEA. From the paper: Accordingly, we suggest that lineages within haplogroup O represent a later contribution to the genetic strata of Indonesia. A careful examination of the distributions of particular O lineages does, indeed, support the hypothesis of an Austronesian connection; however, the presence of the most common O haplogroups in Indonesia may be better explained by earlier Paleolithic contributions. In western Indonesia, O-M175 derived lineages account for over 80% of Y chromosomes. Paragroup O-M95* is notable because it is common in western Indonesia, (e.g., achieving frequencies of >50% on Java and Bali), but is virtually absent east of Flores. This paragroup is widespread in south and southeast Asia (Karafet et al. 2005) and it is unclear when it initially entered western Indonesia. The ancient time to the most recent common ancestor (TMRCA) of this lineage and Asian distribution supports the hypothesis of a pre-Austronesian incursion of O-M95* into western Indonesia from southeast Asia (Kumar et al. 2007). It has also been suggested that O-M95* chromosomes appeared in Indonesia after the initial colonization of the Pacific by Austronesian farmers and that the high frequency of O-M95* in Bali and Java may reflect an even more recent influx of males from the Indian subcontinent (e.g., possibly concomitant with the spread of Hinduism and the establishment of Indian kingdoms in the first millennium) (Karafet et al. 2005). |
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| natsuya | Mar 15 2010, 06:45:00 PM Post #8 |
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Some comments in the blogs: http://dienekes.blogspot.com/2010/03/major-east-west-divide-in-indonesian-y.html http://leherensuge.blogspot.com/2010/03/indonesian-y-dna-is-mostly-paleolithic.html |
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| Ibra | Mar 16 2010, 01:02:33 AM Post #9 |
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I don't know Natsuya, as per usual the methods in this type of analysis seems questionable. If a researcher had no historical perspective of the Americas and planed to sample the Euro-American inhabitants using the same mutation rate and methods they could very well conclude that Canada for example was populated in the late paleolithic by Europeans. Also, BTW the variance of O2a is 2/3 that of R1b1b2 that was shown to be ~6.5kya in another paper, so it must be younger than that.
Edited by Ibra, Mar 16 2010, 01:03:17 AM.
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| ren | Mar 16 2010, 04:47:16 AM Post #10 |
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I don't see anything from the quote to suggest evidence for a Paleolithic age of O2a in SE Asia. The best correspondence between O2a and archaeological and ethnographical evidence is the Neolithic entry of Austro-Asiatic peoples into South and SE Asia from South China. I don't think Karafet et al. is aware of the Austro-Asiatic factor, even attributing O2a to possible migrations of Indians into Indonesia. Besides the Austro-Asiatic link with O2a, I'm aware of something about Hoabinhian Complex/Culture that might link Island SE Asia and Mainland SE Asia in the Paleolithic, and it even links perhaps with South China. But this possibility doesn't correspond as well, given the age of O2a and the directional flow, with O2*/O2a/O2b found north of the North China Plain, O2*/O2a found in Mainland East Asia (China), and only O2a found in SE Asia.
It probably is the pre-Austronesian Phillippines lineage(s). It probably represents an as yet undefined KMNOPS lineage. Edited by ren, Apr 5 2010, 04:04:10 PM.
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| natsuya | Mar 19 2010, 05:16:10 AM Post #11 |
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Many discussions going on here: http://dienekes.blogspot.com/2010/03/major-east-west-divide-in-indonesian-y.html http://leherensuge.blogspot.com/2010/03/indonesian-y-dna-is-mostly-paleolithic.html |
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| ren | Mar 19 2010, 06:07:14 AM Post #12 |
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I think yesterday China started even blocking viewing the comment section. BTW, check your forum inbox. The red (Austro-Asiatic) in Western Austronesians seems to support the Austro-Asiatic substratum hypothesis.
Edited by ren, Mar 19 2010, 07:27:29 AM.
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| natsuya | Mar 19 2010, 10:13:30 AM Post #13 |
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Asia-Pacific Y-DNA/mtDNA data (in 13 papers) collected by Mr. Argiedude: http://www.sendspace.com/file/hhdn5k |
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| natsuya | Mar 21 2010, 05:25:03 AM Post #14 |
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Yes, western Indonesians have notable "red" component which is related to Austro-Asiatic populations. It reminds me of the status of Austro-Asiatic-related O2a-M95 among western Indonesians in Karafet's study. I suppose that "bright green" would support the Austro-Tai macrofamily theory connecting Daic and Austronesian language families. And it also reminds me of O1a-M119 found in both of the populations. Edited by natsuya, Mar 21 2010, 05:36:58 AM.
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| ren | Mar 21 2010, 08:15:55 AM Post #15 |
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Austro-Tai was something Benedict came up with. It has serious flaws, although his evidence for common basic vocabulary was useful to the next level of theory. The new theory is that Tai-Kadai is a sub-group of Austronesian, so the correct name for the proposed language family would still be Austronesian (including Tai-Kadai) and the Austro-Tai name/hypothesis is at this point rather out-dated. I actually have to qualify what I said in a previous post. 1. Kumar estimated O2a to be 60,000 years. I don't even know if humans came out of Africa that early, do his estimate is definitely over-shagging it. 2. O2* and O2b have been found in significant numbers in SE Asia, but I'm not sure if the O2b was tested properly (no contamination) by the Korean team (Hong). They rather contrast sharply with anything the other studies have shown. The O2* in Thais could be brought by the SW Tai migration from South China. (I will delete the corrected comments on Kumar in a previous post now.) Edited by ren, Apr 5 2010, 04:02:45 PM.
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| natsuya | Jun 19 2010, 02:35:31 PM Post #16 |
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It was suggested there was a wave of Neolithic dispersal from Indochina into ISEA before the Austronesian expansion from Taiwan. This wave of people might have brought O2a-M95* to western Indonesia and Borneo. Crossing the Luzon Strait: Archaeological Chronology in the Batanes Islands, Philippines and the Regional Sequence of Neolithic Dispersal Atholl Anderson http://beta.nmp.gov.tw/main/07/7-3/3-3-2/2.025-045.pdf "In reviewing the chronological data in relation to linguistic and archaeological evidence, the existence of at least two neolithic dispersals can be proposed (Figure 5). Neolithic I, if it can be called that, may be represented by expansion from South China through Thailand and Vietnam then through Malaya to Borneo, if not more widely, of basket or cord-marked ceramics amongst other types (but amongst which red-slipped pottery is scarce or absent). This seems to have occurred relatively early and it has been associated, in part at least, with the expansion of Austroasiatic languages (Higham 2004). It is not necessarily a neolithic defined exclusively by agricultural expansion. At Gua Sireh, in Borneo there is rice at about 2500 BC but at Nong Nor, in coastal Thailand, and quite widely in coastal Vietnam, there are middle-Holocene sites containing polished stone tools and pottery, but no sign of food production (Higham 2004, Su 1997)." Edited by natsuya, Jun 19 2010, 03:57:39 PM.
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| ren | Jun 20 2010, 06:43:23 AM Post #17 |
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Actually many papers besides this one mention this phenomenon. That is why I told you that I thought O2a entered SE Asia in the Neolithic when we first discussed this issue. |
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| natsuya | Jun 20 2010, 06:41:04 PM Post #18 |
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Here's some more: THE NEOLITHIC AND AUSTRONESIAN EXPANSION WITHIN ISLAND SOUTHEAST ASIA AND INTO THE PACIFIC Matthew Spriggs http://arts.anu.edu.au/arcworld/resources/papers/Spriggs/2007/Spriggs_b2007.pdf Given that most of the diversity of Austronesian languages is in Taiwan, any model linking the spread of that language family and the spread of Neolithic cultures would require that the dates for the beginning of the Neolithic in Taiwan should be substantially earlier than those in related areas to the south. They are indeed earlier by somewhere around 1,000 to perhaps 2,000 years. In a sentence: the diversity and pattern of subgrouping of the Austronesian languages are exactly mirrored in the chronology and pattern of nearly all of the Island Southeast Asian and Western Pacifi c Neolithic early pottery-using cultures. The one tracks the pattern of the other. The only area investigated so far where this may not be the case is in the major part of Borneo, and there are both linguistic and archaeological clues (see below) which have been suggested in the past as showing some earlier involvement of this area in the spread of a second, independent Neolithic movement linked to the separate spread of the Austro-Asiatic languages down through the Malay Peninsula. Hence we may need to talk of Island Southeast Asian “Neolithics.” The early Neolithic cultural assemblages from Gua Sireh, Niah Cave and the Upper Birang River have in the past been suggested as having more in common with those of the Malay Peninsula and southern Thai Neolithic sites than the other sites in Island Southeast Asia discussed so far (Bellwood 1997: 236-241). In relation to this other Neolithic tradition Bellwood noted that the Malay Peninsula Neolithic was “a completely separate cultural entity from the islands” (Bellwood 1997: 219). The early Sarawak and Kalimantan sites contain cord or basketry-wrapped paddle impressed pottery, and the typically Island Southeast Asian red slip and/or incised wares are virtually absent. Later assemblages seem to fit much better the usual Island pattern, possibly suggesting a change in cultural and perhaps linguistic affiliation over time (cf. Chazine 2003: 49-50). Bellwood noted that there is a claimed Austroasiatic linguistic substratum in some Borneo languages and Austroasiatic influence is also suggested for Sumatra, but may be of much later date (Bellwood 1996: 483). These putative influences would of course provide a further link to Mainland Southeast Asia where languages of this family are found. More recently Bellwood has reconsidered his interpretation and now believes that the links of the earliest cord-marked pottery from Borneo are likely to be back to the Fine Corded Ware of Taiwan, a tradition that occurred in sites in Taiwan along with red-slipped pottery in its latest phases (Bellwood, pers. Comm. 2006). His research on this issue is ongoing. Edited by natsuya, Jun 20 2010, 06:43:16 PM.
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| ren | Jun 22 2010, 05:34:49 AM Post #19 |
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Thanx for the paper. I'll add it to my collection. |
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| natsuya | Jul 3 2010, 05:48:57 PM Post #20 |
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According to Karafet's email, here's Y-SNP data of four specific Han populations as "Han" in the paper. http://viewer.zoho.com/docs/fezif Taiwan Han (n=81): 6/81 = C3-M217 1/81 = D1-M15 3/81 = N1-LLY22g 2/81 = N1c1-M178 2/81 = O3-M122* 5/81 = O3a-P197* (O3a-M324*) 12/81 = O3a3-P201* 1/81 = O3a3b-M7 8/81 = O3a4-002611 20/81 = O3a3c-M134 1/81 = O1a-M119* 8/81 = O1a1-P203 6/81 = O2-P31* 5/81 = O2a-M95* 1/81 = O2a1-M111 Guangdong Han (n=40): 2/40 = C3-M217 1/40 = N-M231 6/40 = N1-LLY22g 1/40 = O3a-P197* (O3a-M324*) 1/40 = O3a3b-M7 2/40 = O3a4-002611 9/40 = O3a3c-M134 6/40 = O1a1-P203 4/40 = O2a-M95* 8/40 = O2a1-M111 Sanxi Han (n=42): 2/42 = C3-M217 1/42 = G2a-P15 1/42 = J2-M172 1/42 = N-M231 3/42 = N1-LLY22g 1/42 = N1a-M128 1/42 = O3a-P197* (O3a-M324*) 2/42 = O3a3-P201* 1/42 = O3a3b-M7 7/42 = O3a4-002611 18/42 = O3a3c-M134 2/42 = O2-P31* 1/42 = O2a-M95* 1/42 = Q1-P36* Guizhou Han (n=2): 1/2 = O3a4-002611 1/2 = O1a1-P203 Edited by natsuya, Jul 3 2010, 05:58:40 PM.
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| black man | Jul 3 2010, 05:58:11 PM Post #21 |
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Thanks for the information, natsuya. What kind of northern Han sample is this? In Karafet's paper Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes (Am. J. Hum. Genet. 69:615–628, 2001) Shaanxi is mentioned in the text but the dot on the map is placed in Shanxi. |
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| Ebizur | Jul 3 2010, 07:33:07 PM Post #22 |
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The development of this thread is giving me a terrible sense of d¨¦j¨¤ vu. We have discussed the question of whether we should trust the text or the map of Karafet et al. 2001 regarding the province of origin of their "Northern Han" sample at least one time several years ago. Natsuya, has Dr. Karafet clarified for you whether this sample is from Shaanxi Province (ÉÂÎ÷Ê¡) or from Shanxi Province (ɽÎ÷Ê¡)? |
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| ren | Jul 4 2010, 03:42:12 PM Post #23 |
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Thanx, natsuya. Has anyone analyzed the STR of M7 in Indonesia so far? Is it close to the Chinese samples? |
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| natsuya | Jul 15 2010, 07:15:38 PM Post #24 |
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You're welcome. No, I'm afraid that Karafet didn't clarify the "Sanxi" problem. |
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