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Austronesian y hg profiles in short
Topic Started: Sep 19 2009, 02:00:48 PM (322 Views)
black man
The Right Hand
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C*: in one network there is a cluster of "SE Asian" samples in between three clusters of Australian aboriginal samples (D, fig. 3)
C3: to be checked later on
D: to be checked later on
F(xK): to be checked later on
K(xNO, P): probably pre-Austronesian and related to Papuan and Melanesian hgs (see different threads)
NO(x O): to be checked later on
O1-M119: most Filipino samples are close to Taiwanese aboriginal samples but relatively many Indonesian samples are more distant from the latter and possibly closer to continental SE Asian samples (D, fig. 3, note that they call Taiwanese aborigines "East Asian", too; LH, fig. 3; M, supplemental file "mmc3"; LJH, supplementary file 3)
O2a-M95 (apparently PK4 negative according to supplementary file 3 of Loo et al.): very common in Malaysia, Borneo, Sumatra, Java, Bali (S, table S3; C, table 1; H, fig. 1; K, table S2); interestingly, there seem to be many hts TKs and ANs have in common as well as many hts MKs and TKs have in common but the MK/AN combination is by far less common; plus, there doesn't seem to be any separate AN branch (CXY, fig. 2); so hts restricted to TKs can be tentatively counted as relics of extinct mainland AN populations
O2a-M95, M88, PK4: probably came to the Philippines from the east, i.e., maybe via Borneo but not via Taiwan (LJH, supplementary file 3)
O3-M7: common in Borneo (K, table S2); Sumatran Batak (SB, table 1) and very typical to southern MK populations (CXY, table 1); this seems to indicate that O2a and O3-M7 in Austronesians is from meanwhile extinct MK or other non-AN people who started to speak AN before their AN descendants went to Borneo and Sumatra

Sources:
C: Capelli et al. 2001, A Predominantly Indigenous Paternal Heritage for the AustronesianSpeaking Peoples of Insular Southeast Asia and Oceania
CXY: Cai Xiaoyun 2011, Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes
D: Delfin et al. 2010, The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups
H: Hurles et al. 2005, The Dual Origin of the Malagasy in Island Southeast Asia and East Africa: Evidence from Maternal and Paternal Lineages
K: Karafet et al. 2010, Major East-West Division Underlies Y Chromosome Stratification Across Indonesia
LH: Li Hui et al. 2008, Paternal genetic affinity between western Austronesians and Daic populations
LJH: Loo Junhun et al. 2011, Genetic affinities between the Yami tribe people of Orchid Island and the Philippine Islanders of the Batanes archipelago
M: Mirabal et al. 2011, Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga
S: Simonson et al. 2011, Ancestry of the Iban Is Predominantly Southeast Asian: Genetic Evidence from Autosomal, Mitochondrial, and Y Chromosomes
SB: Su Bing et al. 2000, Polynesian origins: Insights from the Y chromosome
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Ebizur
Advanced Member
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black man, do you have access to the full text of Nicolas Brucato, Veronica Fernandes, Stéphane Mazières, et al., "The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor"?

Apparently, the authors have found one individual who belongs to Y-DNA haplogroup "C" in a sample of 43 male individuals in Lamu, Kenya and one individual who belongs to Y-DNA haplogroup "O2a" in a sample of 60 male individuals in Kilifi, Kenya. They also have found one individual who belongs to mtDNA haplogroup F3b1b in a sample of people on Grande Comore, Comoros and one individual who belongs to mtDNA haplogroup "M" (but apparently none of the tested subclades of haplogroup M1) in a sample of Swahili people in Mombasa, Kenya. Individuals whose mtDNA belongs to one of several subclades of haplogroup M1a were found in the samples of Swahili people in Lamu and Kilifi.

I suppose the "O2a" individual in Kilifi probably belongs to O-M95, which has been found previously among Malagasy in Madagascar, but it would be nice to have this confirmed. The Y-DNA haplogroup "C" in Lamu and mtDNA haplogroup "M" in Mombasa are also a bit intriguing.






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black man
The Right Hand
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The authors themselves uploaded their paper at their own website. See tables S1 and S2. But I don't know where they go into details like Y SNP markers.
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Ebizur
Advanced Member
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black man
Jan 13 2018, 10:22:23 PM
The authors themselves uploaded their paper at their own website. See tables S1 and S2. But I don't know where they go into details like Y SNP markers.
Thank you, black man.

On the second page of the PDF (or page 59 of The American Journal of Human Genetics 102, 58–68, January 4, 2018), the authors have written the following in regard to their analysis of Y-DNA and mtDNA:

"Paternal lineages of the Swahili groups were characterized via a method described previously[23] (n = 109). DNA quantity for the Comorian samples prevented us from performing analyses on the non-recombining region of the Y chromosome (NRY). In brief, 96 binary markers on the NRY were analyzed with a nanofluidic dynamic array and the BioMark HD system (Fluidigm, USA). Haplogroups were assigned on the basis of the updated ISOGG Y-DNA haplogroup tree[24] and the Y-Phylotree[25] (Table S1). The full list of markers is described by Kusuma and colleagues.[23] We characterized maternal lineages for all samples by sequencing the complete mtDNA (n = 276). In brief, double bar-coded libraries were prepared and enriched for mtDNA as described previously.[26,27] Base calling, quality filtering, and further steps aimed at obtaining consensus sequences were carried out as described previously.[28] Sequences (see Accession Numbers) were then analyzed and aligned against the revised Cambridge Reference Sequence (rCRS)[29] with MAFFT aligner v7.[30] Mitochondrial haplogroups were determined with the HaploGrep program based on Phylotree build 17[31] (Table S2)."

According to ISOGG 2014 v. 9.70, "haplogroup O2a" means O2a-PK4. According to Kusuma et al. 2015, "haplogroup O2a1" means O-M95*, and "O2a1a" means O-M88. The cited Y-Phylotree has "haplogroup O2" defined with the SNPs M268 and P31. Therefore, it is clear that the authors have intended to indicate that that individual in their sample of Swahili people in Kilifi belongs to O-PK4 or O-M95.

Judging from Table 1 and Table S1 of Kusuma et al. 2015, the haplogroup C individual in the sample of Swahili people in Lamu probably belongs to C-M130(xM38, M217).

If Brucato et al. 2018 have precisely followed the nomenclature of Phylotree build 17, then the "haplogroup M" mtDNA that they have reported finding in a Swahili individual in Mombasa should not belong to any well-known subclade of haplogroup M.

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Ebizur
Advanced Member
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Filipino Y-DNA

Philippines total (Trejaut et al. 2014)
2/146 = 1.37% F-M89(xG-M201, H1a-M69, J-P209, K-M9) [1/31 Visayas, 1/8 Mindanao]
1/146 = 0.68% G-M201 [1/55 South Luzon]
1/146 = 0.68% H1a-M69(xH1a1-M52) [1/55 South Luzon]
1/146 = 0.68% J-P209 [1/31 Visayas]
1/146 = 0.68% L-M20 [1/31 Visayas]
10/146 = 6.85% K-M9(xL-M20, NO-M214, P1-M45) [0/24 Ivatan, 0/6 North Luzon, 6/55 South Luzon, 2/31 Visayas, 0/8 Mindanao, 2/22 unknown Philippines]

8/146 = 5.48% NO-M214(xO-M175, N1a2a-M128, N1a1a-M178) [4/31 Visayas, 2/55 South Luzon, 2/22 unknown Philippines] (Among these, only one of the Visayans tested positive for the LLY22g SNP.)

1/146 = 0.68% O-M175(xO1a-M119, O1b-P31, O2-M122) [1/55 South Luzon]

25/146 = 17.12% O1a-M119(xO1a1a-P203, O1a2-M50) [10/24 Ivatan, 2/6 North Luzon, 2/55 South Luzon, 3/31 Visayas, 2/8 Mindanao, 6/22 unknown Philippines]
20/146 = 13.70% O1a1a-P203 [1/24 Ivatan, 2/6 North Luzon, 9/55 South Luzon, 4/31 Visayas, 0/8 Mindanao, 4/22 unknown Philippines]
17/146 = 11.64% O1a2-M50 [4/24 Ivatan, 0/6 North Luzon, 10/55 South Luzon, 1/31 Visayas, 1/8 Mindanao, 1/22 unknown Philippines]

3/146 = 2.05% O1b-P31(xO1b1a1-PK4, O1b2-SRY465) [3/55 South Luzon]
5/146 = 3.42% O1b1a1a1a1a-M88 [1/55 South Luzon, 2/31 Visayas, 2/22 unknown Philippines]

1/146 = 0.68% O2a-M324(xO2a1-KL1, O2a2-P201) [1/55 South Luzon]
7/146 = 4.79% O2a1c-JST002611 [6/24 Ivatan, 1/31 Visayas]
2/146 = 1.37% O2a2-P201(xO2a2a1a1a-M159, O2a2a1a2-M7, O2a2b-P164) [1/24 Ivatan, 1/55 South Luzon]
1/146 = 0.68% O2a2a1a1a-M159 [1/55 South Luzon]
3/146 = 2.05% O2a2a1a2-M7(xO2a2a1a2a1a1-M113) [1/6 North Luzon, 1/55 South Luzon, 1/31 Visayas]
26/146 = 17.81% O2a2b-P164(xO2a2b1-M134) [2/24 Ivatan, 1/6 North Luzon, 10/55 South Luzon, 7/31 Visayas, 4/8 Mindanao, 2/22 unknown Philippines]
2/146 = 1.37% O2a2b1-M134(xO2a2b1a1a-M133) [1/31 Visayas, 1/22 unknown Philippines]
3/146 = 2.05% O2a2b1a1a-M133(xM162) [2/31 Visayas, 1/22 unknown Philippines]

1/146 = 0.68% R1-M173(xR1a1-SRY10831.2, R1a1a-M17, R1b-M343) [1/22 unknown Philippines]
1/146 = 0.68% R1a1-SRY10831.2(xR1a1a-M17) [1/55 South Luzon]
3/146 = 2.05% R1a1a-M17 [3/55 South Luzon]
1/146 = 0.68% R1b-M343 [1/55 South Luzon]

Haplogroups found in more than 5% of this set of Filipino samples, which have been tested to a fairly high resolution:

26/146 = 17.81% O2a2b-P164(xO2a2b1-M134) [2/24 Ivatan, 1/6 North Luzon, 10/55 South Luzon, 7/31 Visayas, 4/8 Mindanao, 2/22 unknown Philippines] (These individuals almost certainly belong to haplogroup O2a2b2a2b-B451, which is distributed in the Malay Archipelago and Oceania, and whose closest extant outgroups have been found in people from Hunan, coastal China, and Korea. It looks like this haplogroup might have lost out demographically to members of O1a-M119 in northern parts of the Philippines as among the indigenous peoples of Taiwan.)

25/146 = 17.12% O1a-M119(xO1a1a-P203, O1a2-M50) [10/24 Ivatan, 2/6 North Luzon, 2/55 South Luzon, 3/31 Visayas, 2/8 Mindanao, 6/22 unknown Philippines]
20/146 = 13.70% O1a1a-P203 [1/24 Ivatan, 2/6 North Luzon, 9/55 South Luzon, 4/31 Visayas, 0/8 Mindanao, 4/22 unknown Philippines]
17/146 = 11.64% O1a2-M50 [4/24 Ivatan, 0/6 North Luzon, 10/55 South Luzon, 1/31 Visayas, 1/8 Mindanao, 1/22 unknown Philippines] (Most mainland members of O1a-M119 belong to O1a1a-P203. The same holds true for Taiwan Aborigines and the people of Nias and Flores according to Karafet et al. 2010. The Philippines appears to have an idiosyncratic mix of subclades of O1a-M119; perhaps its closest parallel may be found in the people of Sumba, although the people of the latter island also exhibit C-M38* with a high frequency.)

10/146 = 6.85% K-M9(xL-M20, NO-M214, P1-M45) [0/24 Ivatan, 0/6 North Luzon, 6/55 South Luzon, 2/31 Visayas, 0/8 Mindanao, 2/22 unknown Philippines] (Probably direct patrilineal descendants of assimilated "Negritos," although perhaps one of the ten might be a member of T-M70 from the erstwhile Empire of Spain.)

8/146 = 5.48% NO-M214(xO-M175, N1a2a-M128, N1a1a-M178) [4/31 Visayas, 2/55 South Luzon, 2/22 unknown Philippines] (Among these, only one of the Visayans tested positive for the LLY22g SNP. Most likely belong to some subclade of the predominantly Chinese N1b-F2905; I think the same is likely true for similar cases of NO-M214(xO-M175, LLY22g) in samples from Japan.)

62/146 = 42.5% of Trejaut's samples from the Philippines belong to haplogroup O1a-M119, and another 26/146 = 17.8% belong to haplogroup O2a2b-P164(xO2a2b1-M134). On these grounds, one may estimate that approximately 88/146 = 60.3% of modern Filipino males may be descended in the direct paternal line from Proto-Austronesian ancestors. The Y-DNA of Filipinos appears to be very different from that of Vietnamese on the continental shore of the South China Sea, who tend to belong to O1b1a1a1a1a-M88/M111, O1b1a1a1b-M1283, O2a2a1a2-M7, or any of a number of "Han-like" clades (e.g. O2a1c-JST002611, O2a2b1a2-F444, O2a2b1a1a-M133, Q1a1a1a1a-Y529).
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