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View Full Version : 32.7% of DE (presumably D) in the Moluccas (Karafet 2005)



Passa
06-23-2015, 09:43 PM
http://www.researchgate.net/profile/John_Lansing/publication/7645574_Balinese_Y-chromosome_perspective_on_the_peopling_of_Indonesi a_genetic_contributions_from_pre-neolithic_hunter-gatherers_Austronesian_farmers_and_Indian_traders/links/0912f50fd88e5bdd6a000000.pdf

18 out of 55 Eastern Indonesians (Moluccans, judging by the map in the paper) belong to Y-DNA haplogroup DE. The authors typed the SNPs for D and E but didn't show them in the frequency table. I think it is made up of D only, though, and specifically of D-M226.2. This is really interesting and gives some evidence of a population replacement in Paleolithic Island Southeast Asia. I have always been saying that the first Y-DNA to settle in Sunda and Sahul was D. Now we have got a new sub-clade of D (D-M226.2, estimated 50.5 ky old) in Island Southeast Asia (Philippines) and plenty of D in an isolated Melanesian (Moluccan) population.

VOX
06-23-2015, 10:39 PM
That's interesting to know D still exist in South East Asia, however I never bought into replacement theories to explain the sparseness of the C and D lines and the success of the F line during paleolithic time frames. Rather I think it has more to do with the characteristics of the out of Africa founding population which likely had a higher diversity/ frequency of F types compared to C and D types. As a result the C and D lines were more likely to hit a zero frequency and drift our of existence. This is a conjecture that could be tested by repeatedly sampling aDNA at the 45KYA mark.

Passa
06-23-2015, 11:10 PM
That's interesting to know D still exist in South East Asia, however I never bought into replacement theories to explain the sparseness of the C and D lines and the success of the F line during paleolithic time frames. Rather I think it has more to do with the characteristics of the out of Africa founding population which likely had a higher diversity/ frequency of F types compared to C and D types. As a result the C and D lines were more likely to hit a zero frequency and drift our of existence. This is a conjecture that could be tested by repeatedly sampling aDNA at the 45KYA mark.

The distribution and frequency of D reflect the fact that an incoming population drove it into isolated and harsh locations (Tibet, Andaman Islands, Japan and now the Moluccas).

Ebizur
07-02-2015, 09:50 AM
Y-DNA haplogroup DE is extremely rare in the Moluccas/Wallacea/eastern Indonesia. I recall one case of Y-DNA D1b-M55 (typically Japanese) and one case of Y-DNA E1b1a1-PN1 (typically Niger-Congo/Bantu) in a set of samples from West Timor, Indonesia.

The number 18 in the DE-YAP column of Table 1 of the Bali paper by Karafet et al. (2005) is an obvious typographical error: look at the numbers in bold text at the top of each column. They represent the total of each haplogroup among all samples from a particular region. The total for "DE-YAP" among "Southeast Asians" (which includes the Eastern Indonesians in question) is 3/825 = 0.36%, contributed by 2/70 = 2.9% Vietnamese and 1/32 = 3.1% Malaysians. The 18/55 = 32.7% East Indonesians rather belong to haplogroup C-RPS4Y, whose high frequency in eastern Indonesia has been corroborated by other studies. (Note the datum of 35/825 = 4.24% C-RPS4Y in the pooled sample of "Southeast Asians" despite the listing of a total of only 17 cases of C-RPS4Y among the individual samples from Southeast Asia.)

A comparison of results from different studies suggests that Y-DNA haplogroup D is probably not even so common among Vietnamese and Malaysians. (The Karafet team's samples of those populations are the only ones that have contained any carriers of Y-DNA haplogroup D.) Furthermore, the Y-DNA haplogroup D in the Karafet team's samples of Vietnamese and Malaysians belongs to a typically Sino-Tibetan-Hmong-Mien subclade, D1a1-M15, and not to the Filipino D2-M226.2 clade.

As you may see, haplogroup D1a1-M15 is a very minor haplogroup in the Vietnamese and Malaysian populations, and may have been introduced by e.g. Chinese immigrants (possibly ethnic Han, or perhaps some other people from what is now China, such as Hmong). It is comparable in frequency to other haplogroups whose representation in Vietnam and Malaysia is sometimes ascribed to historical immigration (e.g. R1a1a, G, J, N, Q).

Viet-Muong total (Cai et al. 2011)
2/27 = 7.4% F-M89(xK-M9)
2/27 = 7.4% O-M175(xO1a-M119, O2a1-M95, O3-M122)
8/27 = 29.6% O3-M122(xM7, M134)
2/27 = 7.4% O3a2c1-M134(xM117)
2/27 = 7.4% O3a2c1a-M117
1/27 = 3.7% O1a-M119(xM110)
10/27 = 37.0% O2a1-M95(xM88)

Kinh from Hanoi, Vietnam (He et al. 2012)
9/76 = 11.8% C2-M217
1/76 = 1.3% K-P131(xN-M231, O-P191, Q1-P36, R-M207)
2/76 = 2.6% N-M231
5/76 = 6.6% O1a1-P203(xM101)
9/76 = 11.8% O2a1-M95(xM88)
23/76 = 30.3% O2a1a-M88
7/76 = 9.2% O3a-P200(xM121, M164, P201, JST002611)
2/76 = 2.6% O3a2-P201(xM7, M134)
8/76 = 10.5% O3a2b-M7
7/76 = 9.2% O3a2c1-M134
2/76 = 2.6% O3a1c-JST002611
1/76 = 1.3% R1a1a-M17

Vietnam (Karafet et al. 2010)
3/70 = 4.3% C2-M217
2/70 = 2.9% D1a1-M15
1/70 = 1.4% J-M304(xJ1-M267, J2-M172)
1/70 = 1.4% J2-M172(xJ2b-M12)
2/70 = 2.9% N-M231 [LLY22g+]
2/70 = 2.9% O3a-P197(xP201, JST002611)
10/70 = 14.3% O3a1c-JST002611
1/70 = 1.4% O3a2-P201(xM7, M134)
4/70 = 5.7% O3a2b-M7
11/70 = 15.7% O3a2c1-M134
4/70 = 5.7% O1a1-P203
1/70 = 1.4% O2-P31(xO2a1-M95, O2b-SRY465)
1/70 = 1.4% O2b-SRY465(x47z)
2/70 = 2.9% O2b1a-47z
5/70 = 7.1% O2a1-M95(xM111)
14/70 = 20.0% O2a1a-M111
5/70 = 7.1% Q1-P36(xM346)
1/70 = 1.4% R1a1a-M17

Kota Kinabalu, Borneo, Malaysia (Hurles et al. 2005)
10/65 = 15.4% C-M130
1/65 = 1.5% F(xJ-12f2, K-M9)
1/65 = 1.5% J-12f2
1/65 = 1.5% NO-M214(xO-M175) [LLY22g+]
12/65 = 18.5% O1a-M119(xM101, M50)
1/65 = 1.5% O1a1a-M101
6/65 = 9.2% O1a2-M50
14/65 = 21.5% O2a1-M95(xM88)
2/65 = 3.1% O2a1a-M88
11/65 = 16.9% O3-M122(xM134)
3/65 = 4.6% O3a2c1-M134
3/65 = 4.6% R1a1-SRY10831b

Malaysia (Karafet et al. 2010)
1/32 = 3.1% C-RPS4Y(xM38, M217)
1/32 = 3.1% D1a1-M15
1/32 = 3.1% G-M201(xP15)
1/32 = 3.1% G2a-P15
2/32 = 6.3% K2-M526(xK2c-P261, M-P256, NO-M214, P1-P27, S-M230)
1/32 = 3.1% M1a-P34
4/32 = 12.5% O3a2-P201(xM7, M134)
4/32 = 12.5% O3a2b-M7
3/32 = 9.4% O3a2c1-M134
1/32 = 3.1% O1a-M119(xP203, M110)
1/32 = 3.1% O1a1-P203
10/32 = 31.3% O2a1-M95(xM111)
1/32 = 3.1% O2a1a-M111
1/32 = 3.1% R1a1a-M17

Passa
07-04-2015, 06:30 PM
^I didn't notice that small yet important detail, thanks. Anyway, how do you explain the presence of such a very ancient clade as D2 among Filipinos? The first post of this thread is not completely eliminated, and there are still chances that D2 has been in Sunda since Upper Paleolithic times.

Ebizur
07-05-2015, 03:45 AM
No problem.

It is possible that D2 has been in the Philippines or their vicinity since Upper Palaeolithic times, but it is also possible that it has been introduced into the area more recently. As I recall, Y-DNA haplogroup D2 has been found only in a very few individuals, all or most of whom have roots in tiny Mactan Island, which is located next to the larger island of Cebu in the Visayas.

At present, a hypothesis of ancient origin in the Philippines is parsimonious, but the Philippines have hardly been isolated since the Upper Palaeolithic. There are linguistic connections with the indigenous peoples of Taiwan to the north and Indonesia to the south, and there has been historical contact with Chinese, Japanese, Spanish, Americans, etc. If D2 has not been in the Philippines since the Upper Palaeolithic, then I suppose Taiwan or Indonesia would be the second most likely location of origin, followed by China or Japan.