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Japanese/Jomon Y-chromosones
Topic Started: Jan 4 2006, 03:08:02 AM (1,250 Views)
Ibra
Global Mod
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Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes

Michael F. Hammer1, 2, Tatiana M. Karafet1, Hwayong Park3, Keiichi Omoto4, Shinji Harihara5, Mark Stoneking6 and Satoshi Horai

Abstract: Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning ~2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan ~20,000 and ~12,000 years ago, respectively, while haplogroup O-47z began its expansion only ~4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.
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Ibra
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Quote:
 
Given that we have identified putative Y chromosome markers of Jomon (or pre-Jomon) and Yayoi migrations, can we trace the origins of these lineages before they entered Japan? We infer that the Japanese have at least two lineages (D-P37.1 and C-M8) that descend from Paleolithic founders. Evidence from SNPs and STRs (Table 2) suggests that both lineages have great genealogical depth. In the case of haplogroup D, a striking number of point mutations have accumulated on this Japanese lineage (Fig. 2). The divergence of the Japanese D lineage implies a very early period of dispersal into the Japanese archipelago followed by a long period of isolation from populations on the mainland. There is only one other lineage that exhibits more mutations along an internal branch on the Y chromosome haplogroup tree (YCC 2002; Jobling and Tyler-Smith 2003). This branch, A2, is found among the Khoisan of Namibia, a population that also may have been isolated for a very long period of time (Hammer et al. 2001; Wilder et al. 2004).


Japanese have two Paleolithic lineages (D-P37.1 and C-M8), a sure indicator of Paleolithic ancestry in Ainu and Japanese, while O is linked to the Yayoi; nothing new here.

Ainu SNP D

Quote:
 
The highest frequency of continental D lineages is found in central Asia (Fig. 2), especially in Tibet (50.4%). Evidence for shared ancestry between Tibetans and Japanese is seen in the MDS plot (Fig. 3). We hypothesize that the area between Tibet and the Altai Mountains in northwestern China is the primary candidate region for the geographic source of Paleolithic Japanese founding Y chromosomes. Although Tibetans and people from the Altai have D lineages that are differentiated from those in Japan, there are still  ancestral  chromosomes that are not marked by any known mutations on the D lineage in Tibet and the Altai (Fig. 2). Historical records suggest that Tibetan populations were derived from ancient tribes of northwestern China that subsequently moved to the south and admixed with southern natives in the last 3,000 years (Ruofu and Yip 1993; Cavalli-Sforza et al. 1994; Wen et al. 2004). The survival of ancient lineages within haplogroup D in Tibetans and Japanese may well reflect long periods of isolation for both groups. Interestingly, a Y-SNP survey of Andaman Islanders found a very high frequency of haplogroup D-M174* chromosomes in this isolated population that likely descends from Paleolithic Asian ancestors (Thangaraj et al. 2003). Recent expansions and population replacements in Asia, perhaps associated with the spread of agriculture, may have led to the near extinction of haplogroup D in other Asian populations.


NO* and C8

Quote:
 
The other postulated Japanese Paleolithic founding haplogroup, C-M8, is associated with Y-STR haplotypes that are related to Indian and central Asian C chromosomes (Fig. 4d). The presence of NO* chromosomes in Japan also may be an indication of a remnant Tibetan ancestry (Deng et al. 2004). A recent mtDNA study revealed direct connections of Japanese haplotypes with Tibet, parallel to those found for the Y chromosome (Tanaka et al. 2004). Haplogroup M12 is the mitochondrial counterpart of Y chromosome D lineage. This rare haplogroup was detected only in mainland Japanese, Koreans, and Tibetans, with the highest frequency and diversity in Tibet (Tanaka et al. 2004).


South East Asian origin for O (?):
Quote:
 
Our data also support the hypothesis that other Y haplogroups, such as lineages within haplogroup O-M122 (i.e., O-M134 and O-LINE), as well as the O-M95 lineage within O-P31, entered Japan with the Yayoi expansion (Fig. 5). High frequencies of these lineages in southwestern Japan, Korea, and Southeast Asian populations likely explain the affinity of these populations in the MDS plot (Fig. 3). The entire O haplogroup has been proposed to have a Southeast Asian origin (Su et al. 1999; Kayser et al. 2000; Capelli et al. 2001; Karafet et al. 2001). In fact, nearly all lineages within the O-M175 clade in Fig. 2, except O-SRY465 and O-47z, are present at their highest frequencies (e.g., O-M95, O-P31*, M122*, O-LINE, O-M119) in southeastern Asia/Oceania (Fig. 2), and have been proposed to have southern Chinese origins (Santos et al. 2000; Su et al. 2000; Karafet et al. 2005). Their expansion into surrounding regions likely accompanied the proliferation of Neolithic culture and rice cultivation. We hypothesize that the dispersals of Neolithic farmers from Southeast Asia also brought haplogroup O lineages to Korea and eventually to Japan.


Conclusion:
Quote:
 
In summary, our data suggest that Paleolithic male lineages entered Japan at least (12,000–20,000 years ago from central Asia, and were isolated for thousands of years once land bridges between Japan and continental Asia disappeared at the end of the last glacial maximum (~12,000 years ago). More recently, Y chromosomes that originated in Southeast Asia expanded to Korea and Japan with the spread of wet rice agriculture. The ages and spatial patterns of haplogroups D and O in Japan are concordant with the hypothesis that Y chromosomes spread via a process of demic diffusion during the Yayoi period (Sokal and Thomson 1998). Each of the populations carrying these differentiated lineages made separate contributions to modern Japanese, both genetically and culturally. In contrast to previous models, we propose that the Yayoi Y chromosomes descend from prehistoric farmers that had their origins in southeastern Asia, perhaps going back to the origin of agriculture in this region. This places the Yayoi in the context of other population expansions stimulated by the acquisition of agriculture, whereby farming societies gained advantages over hunter-gatherer societies (Diamond and Bellwood 2003). In this case, however, the Jomon hunter-gatherers may have held off the onslaught of farmers for thousands of years as a result of their highly successful brand of subsistence. The dramatic Yayoi transition finally may have been triggered in 400 B.C. by a combination of developments, such as rice field irrigation, cold-resistant rice strains, an increasing Korean population, and the invention of iron tools for producing farming
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ren
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You beat me to it. I was gonna post this but forgot.

Quote:
 
Evidence from SNPs and STRs (Table 2) suggests that both lineages have great genealogical depth. In the case of haplogroup D, a striking number of point mutations have accumulated on this Japanese lineage (Fig. 2). The divergence of the Japanese D lineage implies a very early period of dispersal into the Japanese archipelago followed by a long period of isolation from populations on the mainland. There is only one other lineage that exhibits more mutations along an internal branch on the Y chromosome haplogroup tree (YCC 2002; Jobling and Tyler-Smith 2003). This branch, A2, is found among the Khoisan of Namibia, a population that also may have been isolated for a very long period of time (Hammer et al. 2001; Wilder et al. 2004).

This is very interesting. This would suggest D in Japan could be as old as 30,000 years old, the start of archaeological evidence of modern man there.

Quote:
 
The highest frequency of continental D lineages is found in central Asia (Fig. 2), especially in Tibet (50.4%). Evidence for shared ancestry between Tibetans and Japanese is seen in the MDS plot (Fig. 3).The highest frequency of continental D lineages is found in central Asia (Fig. 2), especially in Tibet (50.4%). Evidence for shared ancestry between Tibetans and Japanese is seen in the MDS plot (Fig. 3). We hypothesize that the area between Tibet and the Altai Mountains in northwestern China is the primary candidate region for the geographic source of Paleolithic Japanese founding Y chromosomes. Although Tibetans and people from the Altai have D lineages that are differentiated from those in Japan, there are still  ancestral  chromosomes that are not marked by any known mutations on the D lineage in Tibet and the Altai (Fig. 2). Historical records suggest that Tibetan populations were derived from ancient tribes of northwestern China that subsequently moved to the south and admixed with southern natives in the last 3,000 years (Ruofu and Yip 1993; Cavalli-Sforza et al. 1994; Wen et al. 2004). The survival of ancient lineages within haplogroup D in Tibetans and Japanese may well reflect long periods of isolation for both groups. Interestingly, a Y-SNP survey of Andaman Islanders found a very high frequency of haplogroup D-M174* chromosomes in this isolated population that likely descends from Paleolithic Asian ancestors (Thangaraj et al. 2003). Recent expansions and population replacements in Asia, perhaps associated with the spread of agriculture, may have led to the near extinction of haplogroup D in other Asian populations.

I find this logic backwards. If the greatest % of D-M174* (in fact they only have M-174* and nothing else AFAIK) is found among the Andamanese, then that's the logical source, as already concluded in other studies, not the other way around. This association of D with a NW origin is also puzzling, since D is not found further west.

Quote:
 
The other postulated Japanese Paleolithic founding haplogroup, C-M8, is associated with Y-STR haplotypes that are related to Indian and central Asian C chromosomes (Fig. 4d).

Hehe.. C-M8, AFAIK, is mainly located in E. Asia, since when was it in India? If they just mean that it's related to C3 in Altaics and C* in India, then it's misleading, since C3 reaches its greatest concentration and diversity in coastal Siberia above Japan, Manchuria, and Korea. And it's generally agreed that C3 was carried westwards in recent times by the Altaic expansions. And why not mention the C* in Australia and other C types in SE Asia but only mention India and "central Asia"?

I find this rather biased and baseless.. basically forcing the issue of a Central Asian origin of Jomon: "The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence."

Uh no.. besides being "contra" to "previous models based on morphological and genetic evidence".

Quote:
 
The presence of NO* chromosomes in Japan also may be an indication of a remnant Tibetan ancestry (Deng et al. 2004).

Wow, they found NO* in the Japanese.

Quote:
 
A recent mtDNA study revealed direct connections of Japanese haplotypes with Tibet, parallel to those found for the Y chromosome (Tanaka et al. 2004). Haplogroup M12 is the mitochondrial counterpart of Y chromosome D lineage. This rare haplogroup was detected only in mainland Japanese, Koreans, and Tibetans, with the highest frequency and diversity in Tibet (Tanaka et al. 2004).

Yeah, this was covered in the Tanaka paper, likely a stratum before neolithic expansion.

Quote:
 
Our data also support the hypothesis that other Y haplogroups, such as lineages within haplogroup O-M122 (i.e., O-M134 and O-LINE), as well as the O-M95 lineage within O-P31, entered Japan with the Yayoi expansion (Fig. 5). High frequencies of these lineages in southwestern Japan, Korea, and Southeast Asian populations likely explain the affinity of these populations in the MDS plot (Fig. 3). The entire O haplogroup has been proposed to have a Southeast Asian origin (Su et al. 1999; Kayser et al. 2000; Capelli et al. 2001; Karafet et al. 2001).  In fact, nearly all lineages within the O-M175 clade in Fig. 2, except O-SRY465 and O-47z, are present at their highest frequencies (e.g., O-M95, O-P31*, M122*, O-LINE, O-M119) in southeastern Asia/Oceania (Fig. 2), and have been proposed to have southern Chinese origins (Santos et al. 2000; Su et al. 2000; Karafet et al. 2005).
Covered here I guess:
http://journeyofman.info/index.php?showtopic=427
Things I'd add,
-SE Asia or southern China are not the same. O's presence in India and Oceania seems to be recent, so it's unlikely from SE Asia.
-O*/M-175, AFAIK, is highest % in Korea
-highest % doesn't necessarily tell anything, though % STR and haplotype diversity would tell more

Quote:
 
Their expansion into surrounding regions likely accompanied the proliferation of Neolithic culture and rice cultivation. We hypothesize that the dispersals of Neolithic farmers from Southeast Asia also brought haplogroup O lineages to Korea and eventually to Japan.

The problem is that in archaeology, the neolithic expansion went from north to south but this keeps getting ignored. The earliest rice cultivation is in Korea, followed by central China (southern half). That's not SE Asia.

Quote:
 
In contrast to previous models, we propose that the Yayoi Y chromosomes descend from prehistoric farmers that had their origins in southeastern Asia, perhaps going back to the origin of agriculture in this region.

The Koreans and Japanese, to any Asian familiar with Asian faces, have a decidedly Siberian look. Archaeology and mtDNA also points to Korea, not SE Asia.

And again, the origin of agriculture is in northern Asia. Besides rice, other crops show up earliest in the arcaheology of Inner Mongolia.

Quote:
 
This places the Yayoi in the context of other population expansions stimulated by the acquisition of agriculture, whereby farming societies gained advantages over hunter-gatherer societies (Diamond and Bellwood 2003). In this case, however, the Jomon hunter-gatherers may have held off the onslaught of farmers for thousands of years as a result of their highly successful brand of subsistence.

Talked about this in hypothesizing about spread of rice from Korea 15,000: http://journeyofman.info/index.php?showtop...dpost&p=2080811
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black man
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Ibra
Jan 4 2006, 03:13 AM
Japanese have two Paleolithic lineages (D-P37.1 and C-M8), a sure indicator of Paleolithic ancestry in Ainu and Japanese, while O is linked to the Yayoi; nothing new here.

C1-M8 is a very special case. Tajima reported:
http://www.ncbi.nlm.nih.gov/entrez/query.f...3&dopt=Citation
Quote:
 
the Ainu exhibited no other Y-haplogroups (C-M8, O-M175*, and O-M122*) common in mainland Japanese and Okinawans.


Ibra, if you have the frequency/diversity/age estimate data for C-M8 and the other hgs in Ryukyuans, mainland Japanese etc, please post them.

In Hammer's table there is no hint for undifferentiated C or even the Australian-specific type of it in Japanese. Yet, e.g. Ainus sometimes have a pseudo-Australian appearance. Generalising, I'd say C1 could have been brought by people with a relationship to the aborigines of "Sahul"/Australia to the Japanese archipelago.
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Ibra
Global Mod
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Quote:
 
Ibra, if you have the frequency/diversity/age estimate data for C-M8 and the other hgs in Ryukyuans, mainland Japanese etc, please post them.


Here are the frequencies of various haplogroups across

Japan
North East Asia (NEA)
South East Asia (SEA)
Central Asia (CAS)
South Asia (SAS)
Oceania (OCA)

img438.imageshack.us/my.php?image=japan9zr.gif


Median-joining microsatellite networks

Posted Image

They add,

"Fig. 4 Median-joining microsatellite networks for lineages O-47z [a], O-SRY465* , O-M95* [c], and C* [d] (the position of the M8 mutation is denoted by a black line and the open circle represents a single central Asian haplotype). Microsatellite haplotypes are represented by circles with area proportional to the number of individuals with that haplotype. Branch lengths are proportional to the number of one-repeat mutations separating the two haplotypes. Haplotypes are color-coded by geographic region (see key), with haplotype sharing indicated by pie chart divisions"

Age Estimates
Quote:
 
Absolute dating estimates based on our Y-STR data provide further support for an earlier wave(s) of migration of haplogroups D and C into Japan and a more recent Yayoi expansion of haplogroup O, in concordance with the hybridization model. Coalescence times for the D and C-M8 lineages are ~20,000 years ago, assuming a constant population size. However, populations have clearly grown dramatically during the Jomon (ca. 21,000 B.P. to 400 B.C.) and Yayoi (ca. 400 B.C. to 300 A.D.) periods (Koyama 1992), so this model may be unrealistic. Pure exponential growth is also unlikely to provide a good model for human population size throughout the Jomon and Yayoi periods because recent high growth rates would imply a vanishingly small population size just a few thousand years ago. Koyama (1992) estimated the number of Paleolithic inhabitants to be ~3,000 individuals based on archaeological, ecological, and ethnographic data. Taking into account marked population growth throughout the Jomon period from ~10,000 until about 4,500 B.P., and more explosive growth during the Yayoi and Kofun (ca. 300–600 A.D.) periods (Koyama 1992), a model of exponential growth from a constant-size ancestral population should yield the most realistic dates. Under this model, the D lineage has a coalescence time of ~19,400 years, with an expansion that started ~12,600 years ago (Table 2). The coalescent time of haplogroup C-M8 is estimated to be ~14,500 years ago, with evidence for population expansion starting ~10,820 years ago. We assume that both systems are detecting the same expansion process given the large confidence intervals on our estimates. Therefore, it is quite possible that these two lineages represent a major and a minor component in a single polymorphic Paleolithic founding population.
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ren
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I don't see any logic here in there conclusions.. in placing Japanese D and C1-M8 together, when C1-M8 isn't found in the Jomon, who have C3-M217 AFAIK, which is percentage and diversity-wise concentrated in Siberia and the Pacific Northwest.

C1-M8 is mainly East Asian in distribution and since it's found in Japanese but not Ainu, it would make sense that it came in with NO lineages.

Quote:
 
In Hammer's table there is no hint for undifferentiated C or even the Australian-specific type of it in Japanese. Yet, e.g. Ainus sometimes have a pseudo-Australian appearance. Generalising, I'd say C1 could have been brought by people with a relationship to the aborigines of "Sahul"/Australia to the Japanese archipelago.

Since "C*" is also present in India, that is another likely source for C1. Both places had plesiomorphic native populations not long ago. One wave going south and one going north as they ventured east into SE Asia from India.
This likely happened long ago, and such people could've led, in part or whole, through isolation mechanisms, selection, random change to what is referred to as "Mongoloids".
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black man
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ren
Jan 5 2006, 08:46 PM
I don't see any logic here in there conclusions.. in placing Japanese D and C1-M8 together, when C1-M8 isn't found in the Jomon, who have C3-M217 AFAIK, which is percentage-wise concentrated in Siberia and the Pacific Northwest.

I don't think that C3 can be associated with the stereotypical (pre-)Jomon. In contrast to D2, it's very rare in mainland Japanese (see Hammer's table). So mainstream Japanese C3 probably arrived together with O from Korea.

The Ainu, however, are a different case because they mixed with Nivkhs, whose genetic presence in Ainu is also supported by mtDNA hg Y. The collected genetic material (Tajima 2004) apparently refutes the thesis that Ainu have a mainstream Japanese admixture. Instead, it is more likely that the Nivkhs contributed the modern mainstream East Asian phenotypes as well as y hg C3 to the Ainus. Anyway, I don't know the age estimates of C3 (on Hokkaido and in Siberia).

Quote:
 
C1-M8 is mainly East Asian in distribution and since it's found in Japanese but not Ainu, it would make sense that it came in with NO lineages.


Yes, that's why the data of Ryukyuans are necessary for a comparison. (Btw, there could be other South Japanese islands in the Pacific with a larger percentage of pre-Yayoi phenotypes than e.g. Okinawa. They should be tested, too.)
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ren
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Something funny I've noticed. O* in this study:
.7 in NE Asia
.1 in SE Asia,
.5 in Central Asia

There conclusions (O from SE Asia, C and D from Central Asia) seems to be very arbitrary. I could use their same argument, only switch C/D with O. It just seems to me it's about forcing a "Caucasoid" origin for Jomon/Ainu.

black man
Jan 6 2006, 04:21 AM
ren
Jan 5 2006, 08:46 PM
I don't see any logic here in there conclusions.. in placing Japanese D and C1-M8 together, when C-M8 isn't found in the Jomon, who have C3-M217 AFAIK, which is percentage-wise concentrated in Siberia and the Pacific Northwest.

I don't think that C3 can be associated with the stereotypical (pre-)Jomon. In contrast to D2, it's very rare in mainland Japanese (see Hammer's table). So mainstream Japanese C3 probably arrived together with O from Korea.

The Ainu, however, are a different case because they mixed with Nivkhs, whose genetic presence in Ainu is also supported by mtDNA hg Y. The collected genetic material (Tajima 2004) apparently refutes the thesis that Ainu have a mainstream Japanese admixture. Instead, it is more likely that the Nivkhs contributed the modern mainstream East Asian phenotypes as well as y hg C3 to the Ainus. Anyway, I don't know the age estimates of C3 (on Hokkaido and in Siberia).

Quote:
 
C1-M8 is mainly East Asian in distribution and since it's found in Japanese but not Ainu, it would make sense that it came in with NO lineages.


Yes, that's why the data of Ryukyuans are necessary for a comparison. (Btw, there could be other South Japanese islands in the Pacific with a larger percentage of pre-Yayoi phenotypes than e.g. Okinawa. They should be tested, too.)


Opps, might've made a mistake.
On this map I see that C3-M8 isn't found anywhere but Japan (I thought it was in China and the rest of East Asia).
If it's only found in Japan, then it's likely Paleothic and indigenous prior to Yayoi.

However, its lack in Ainu is puzzling.

Yes, it seems that C-M217 is very rare in Japan, so the high % of C-M217 in Ainu does seem like a recent admixture with Siberian groups. I'll have to change some topics regarding Ainu when I have time.

-----------------------------------------------------------------------------------------------

Ibra's upload of the study: http://rapidshare.de/files/12916849/japan.ainu.pdf.html
http://rapidshare.de/files/12916849/japan.ainu.pdf.html
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black man
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ren
Jan 9 2006, 10:57 PM
Opps, might've made a mistake.
On this map I see that C3-M8 isn't found anywhere but Japan (I thought it was in China and the rest of East Asia).
If it's only found in Japan, then it's likely Paleothic and indigenous prior to Yayoi.

However, its lack in Ainu is puzzling.

According to the data, C1-M8 can be traced back to a bottleneck event in Jomon age. I'd say, that's why it doesn't correlate with Australian-like morphology: at some point of local history the C1-M8 population was severely reduced, maybe due to new diseases brought from somewhere else. The remaining carriers were mixed by origin and assimilated by a mainstream population.

In Hammer's table there are only 20 Ainus tested. Concerning the non-Ainus, when we ignore those who carry Y(xD), C1-M8 is carried by every sixth Aomorian and every tenth or so Okinawan. But also those samples (including Y[xD] ) are quite small (26 and 45), especially when you want to estimate the percentages of rare substrata.

Quote:
 
I find this logic backwards. If the greatest % of D-M174* (in fact they only have M-174* and nothing else AFAIK) is found among the Andamanese, then that's the logical source, as already concluded in other studies, not the other way around. This association of D with a NW origin is also puzzling, since D is not found further west.


Paragroup D* was found in Altaians. However, that is only a paragroup. The root of D could equally be found in Thailand, from where they reported DE* without any results regarding high resolution.
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Ebizur
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I don't know for sure what ren's problem with the results of Hammer et al's study is, but I have a feeling it has something to do with certain antagonistic feelings toward the Japanese. ;)

The reason these researchers came to the conclusion that Y-chromosomes belonging to Haplogroup C1-M8 represent a minor component of the male ancestry of a polymorphic Jomon Era population of the Japanese Archipelago is quite evident: first, Haplogroup C1-M8 has not been detected in any population outside of the Japanese Archipelago; second, the STR profiles associated with the Y-chromosomes that belong to Haplogroup C1-M8 most closely resemble those of certain Haplogroup C* Y-chromosomes that have been sampled from populations of South and Central Asia; third, the STR diversity of Haplogroup C1-M8 Y-chromosomes is astounding and rivals that of the closely associated Y-chromosome Haplogroup D2, despite the overall rare occurrence of the C1-M8 lineage in modern human populations, even in Japan, the only country where it has been found so far. These three facts taken together suggest that the M8 mutation that defines Haplogroup C1 occurred on a Haplogroup C* Y-chromosome of ultimately South Asian or Central Asian origin at a very early date after the bearer of this ancestral Haplogroup C* Y-chromosome had migrated to (what would become) the Japanese Archipelago from South or Central Asia (or, less parsimoniously, from some hypothetical source region from which the populations of South Asia, Central Asia, and Jomon Era Japan ultimately sprang), and since that early founding event, the C1-M8 Y-chromosomes have diversified within the Japanese Archipelago along with the evolution of the Paleolithic-Mesolithic human inhabitants (i.e., the Jomon race) of that region. The slightly lower diversity of the C1-M8 lineage when compared to the D2 lineage, whose distribution is also limited to the Japanese Archipelago, can be explained as a side effect of the lower frequency of the C1-M8 lineage compared to the D2 lineage among an already polymorphic Jomon population that possessed a major D2 component and a minor C1 component, or else it can be explained as the trace of a hypothetical population bottleneck that might have occurred when some Paleolithic population in which Haplogroup C1 had become fixed as the sole male lineage became merged with a numerically dominant population that carried Haplogroup D2 Y-chromosomes. Personally, I find the first hypothesis, which is also that of the researchers who published the article in question, i.e. that haplogroups D2 and C1 represent a major and a minor component of the male ancestry of a single polymorphic Paleolithic population that occupied the land that is now the Japanese Archipelago, to be more parsimonious and therefore more likely to be the true explanation.

The fact that Haplogroup C1-M8 has not yet been detected in the modern Ainu population could be the result of a severe population bottleneck associated with the foundation of the group ancestral to the modern Ainu population, probably coincident with the separation of the Jomonic ancestors of the modern Japanese from the Jomonic ancestors of the modern Ainu (perhaps identical with the event related in the ancient Japanese chronicles, Nihon Shoki and Kojiki, as the separation of the niki-emishi, or "Soft/Gentle Ainu," who submitted to the authority of the Yamato Emperor, from the ara-emishi, or "Rough/Violent Ainu," who stubbornly maintained their independence). This would make some sense, since it is likely that a greater number of the Jomonic people(s) have become ancestors of the modern Japanese as opposed to ancestors of the modern Ainu; i.e., the fact that the modern Japanese show evidence of such major Jomonic ancestry, coupled with the fact that the Japanese population is spread over a much larger geographical area and is numerically much greater than the Ainu population, suggest that the majority of the Jomonic people(s) have been merged into the ancestral pool of the modern Japanese population, and that the ancestral pool of the modern Ainu was just a small subset of the greater Jomonic population of ancient times. However, there is also a strong possibility that C1-M8 Y-chromosomes will eventually be found in a sample from the modern Ainu population, considering that (as far as I know) this population has not been thoroughly surveyed for Y-chromosome haplogroup data.

On a side note, I am sorry to burst your bubble, but numerous studies of autosomal DNA have shown that the Ainu, and to a somewhat lesser extent the Japanese population in general, are genetically much more similar to European populations than Chinese or Southeast Asian populations are to European populations. This data on autosomal DNA by itself would be enough to support a hypothesis that the ancestors of the Jomon Era aborigines of the Japanese Archipelago originated from a source population that was relatively genetically similar, and therefore probably located geographically more closely, to (at least one of) the source population(s) from which the modern European populations have derived. On the basis of various lines of genetic, archeological, and anthropological evidence, a very ancient South Central Asian (Pamir Mountain region, or some place close to what is now Tajikistan or Afghanistan) origin of the Paleolithic ancestors of the (pre-)Jomonic people(s), followed by a migration through the Altai Mountain region and the Mongolian Plateau to the Korean Peninsula and thence to the land that would become the Japanese Archipelago, seems most likely.
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ren
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JCA
Aug 12 2006, 06:37 AM
 

Quote:
 
I don't know for sure what ren's problem with the results of Hammer et al's study is, but I have a feeling it has something to do with certain antagonistic feelings toward the Japanese.  ;)

I stated some of my problems with the study to anyone who can read.

Quote:
 
a polymorphic Jomon Era population of the Japanese Archipelago

How does the word "polymorphic" play into this and what implies it?

Quote:
 
the STR profiles associated with the Y-chromosomes that belong to Haplogroup C1-M8 most closely resemble those of certain Haplogroup C* Y-chromosomes that have been sampled from populations of South and Central Asia

I'm not sure what this means; comparing STR is usually within a single lineage; to compare Japanese STR C-M8 to Indian C types that are not C-M8 would be meaningless; and furthermore, can you quote from something?

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These three facts taken together suggest that the M8 mutation that defines Haplogroup C1 occurred on a Haplogroup C* Y-chromosome of ultimately South Asian or Central Asian origin at a very early date after the bearer of this ancestral Haplogroup C* Y-chromosome had migrated to (what would become) the Japanese Archipelago from South or Central Asia (or, less parsimoniously, from some hypothetical source region from which the populations of South Asia, Central Asia, and Jomon Era Japan ultimately sprang),

This is a pretty meaningless statement.
1. The C types of SE Asia and Oceania as well as E and NE Asia also presumably came from India/South Asia.
2. "central Asia" here refers to Mongolia, Tibet, and Uygurs, and following the convention of other studies the C of these places followed a east-west migration pattern with dispersal of "Altaic" peoples.

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and since that early founding event, the C1-M8 Y-chromosomes have diversified within the Japanese Archipelago along with the evolution of the Paleolithic-Mesolithic human inhabitants (i.e., the Jomon race) of that region.

I haven't said otherwise, but I don't understand how you arrived at C from A. What logic are you using?

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On a side note, I am sorry to burst your bubble, but numerous studies of autosomal DNA have shown that the Ainu, and to a somewhat lesser extent the Japanese population in general, are genetically much more similar to European populations than Chinese or Southeast Asian populations are to European populations.

Yes, everyone in NE Asia are, according to many studies, closer to West Eurasian populations than to SE Asian populations (I think most of the genes have to do with immune system responses so it's a matter of environmental selection) but the importance of that depends on your assumptions. IN FACT, the Ainu in Cavalli-Sforza's studies are the most un-Western of the bunch.

Does it make sense a SE Asian "Mongoloid" population, mixing with a "proto-Caucasoid" population, became closer to Europeans in NE Asia? If so, wouldn't the average Korean look less "Mongoloid" than the average southern Chinese, half of whom can pass for Hispanics if you've ever been worldly enough to step outside your house?

I dunno.

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This data on autosomal DNA by itself would be enough to support a hypothesis that the ancestors of the Jomon Era aborigines of the Japanese Archipelago originated from a source population that was relatively genetically similar, and therefore probably located geographically more closely, to (at least one of) the source population(s) from which the modern European populations have derived.

I trust that you are intelligent, and thus can see the faultiness of this "logic", given my above response.

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On the basis of various lines of genetic, archeological, and anthropological evidence, a very ancient South Central Asian (Pamir Mountain region, or some place close to what is now Tajikistan or Afghanistan) origin of the Paleolithic ancestors of the (pre-)Jomonic people(s), followed by a migration through the Altai Mountain region and the Mongolian Plateau to the Korean Peninsula and thence to the land that would become the Japanese Archipelago, seems most likely.

What basis? You just cited some random facts and non-facts that doesn't automatically imply, even, anything. It only makes sense in your mind because, when twisted, it supports your assumptions. This is a case where seeing something golden does not mean it is "gold". :rolleyes: If you already smell "gold", then seeing something golden may further entrench your faith in what you smell, but it may be something else golden and shiny besides gold. I trust you know what I mean. :D

And cite sources. What you've posted above are incomplete or inaccurate or non-factual or uncontexted "points" which, when pasted together, contradicts itself.

Any lineage of C is derived from C in South Asia; this doesn't mean it came from "Central Asia" and certainly doesn't mean it is related to Europeans. C is not indigenous to Europe. In fact, European lineages are either phylogenetically closer to E in Africa or O in SE Asia than to C.

"central Asia" in the paper refers to Mongolians, Tibetans, and Uygurs. A historically documented movement of east-west nomads is most likely responsible for this, not prehistoric west-to-east migrations of proto-Europeans.

As for genetic affinity, as I said, the Ainu do not stand out from the rest of NE Asians, some of whom are the benchmark of "Mongoloid" physiological, osteology, and anthropometric definitions in legit anthropology. There is no earlier "Asian" morphology in SE Asia and it's modern presence is most likely a spread from north to south, NOT south-to-north. If indeed there were "proto-Caucasoids" that mixed with "SE Asians" in prehistoric times, then both groups developed into "Mongoloids". It's not that hard a concept to understand. An Australian aboriginal doesn't look like a Japanese sumo wrestler.
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ren
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By the way, I think your criticisms of Hammer et alia's paper are totally unfounded. I would be willing to rethink my position on this issue if black_man would give me a link to the results of that study that claimed to have found a branch of Haplogroup DE* in Thailand, but otherwise, I think it is obvious that the Jomon (and hence, the Ainu) are simply a relic of a very early migration from South Asia to Japan via Central Asia and Mongolia at some time prior to the acquisition of typical Mongoloid characteristics by their cousins who they left behind on the mainland. Unless I get some clearer information on the presence or absence of DE* or D* in SE Asia, I see absolutely no possibility of the Jomon being related directly to SE Asians, which is basically what Hammer et al. were trying to point out in their article. I agree with you that most or all Haplogroup O lineages in SE Asia are probably derived ultimately from the same route (South Asia > Central Asia > NE Asia > SE Asia), but the modern populations of SE Asia (including South China and Polynesia) show some odd genetic characteristics, such as extremely high frequency or near fixation of Gm immunoglobulin haplotype afb1b3, which to me suggests that the ancestral gene pool of SE Asians has gone through a population bottleneck or has been somehow isolated from the other populations of Eurasia. There is no evidence that afb1b3 has been positively selected within these populations, is there? What is your preferred explanation for the origin of modern SE Asians, then? Would you propose that a recent Neolithic expansion of a relatively small ancestral population carrying a concentration of Gm haplotype afb1b3 and Y-chromosomes belonging to certain branches of Haplogroup O and possessing derived Mongoloid characteristics has spread southward from (central) China and assimilated most of the descendants of the Paleolithic inhabitants of the SE Asian region? At any rate, I don't see that you have offered any explanation preferable to that proposed by Hammer et al. on the origin of the Jomon.


Here's a bigger picture of the C network Ibra had posted earlier,
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