Bold new 2014 DNA study proposes when and where the three major populations of Africa, Europe and East Asians diverged and suggests why the Ainu look like Europeans

The traditional view that humans fall into three major populations, Africans, East Asians, and Europeans, with the latter two diverging from the African ancestors ∼55,000 years ago, has been re-examined by a group of researchers, who have come to a bold and different conclusion — and who have put forward a new view that East Asians diverged from Africans first, and that only later did the Europeans diverge from the East Asian grouping.

The study also proposes a new theory of origins of the Ainu. The long-debated and mystifying European appearance of the Ainu people is explained, as congruent with the idea that the Ainu people emerged at the point of time when Europeans were beginning to diverge from East Asians.

The results of the research has just been published in the Genome Biology and Evolution Journal, entitled “Divergence of East Asians and Europeans Estimated Using Male- and Female-Specific Genetic Markers” by Yoshio TATENO et al. Genome Biol Evol (2014) 6 (3): 466-473. doi: 10.1093/gbe/evu027

Excerpted from the paper:

“We sequenced Y-STR makers in Y chromosome and collected complete mtDNAs for many East Asian and European individuals to reexamine that view” … “focused on the divergence of three major populations — Africans, Europeans, and East Asians—and East Asians and Europeans in particular, because they lived together for a while after coming out of Africa and likely interbred, perhaps similar to the hybridizations reported between Neanderthals and modern humans (Noonan 2006). After the divergence between Mongoloid (East Asian) and Caucasoid (European) people ~55,000 years ago (Nei and Roychoudhury 1993), they might have still interbred while en route to settlement in their present localities…”

“For the male lineages, we used the Y-STR markers for 453 individuals covering Japanese, Korean, Mongolian (Khalkh), American, and European people. We determined the evolutionary distances (RST) among them, and constructed a phylogenetic tree using the NJ method (Saitou and Nei 1987), as shown in figure 1. The Y-STR tree revealed that the male ancestral lineage contained two clades (Yap-A and Yap-B). While Yap-A clade includes the East Asian individuals only, Yap-B clade contains the East Asian and European individuals together. Surprisingly, the European males never formed an independent clade. Instead, they formed separate clades within Yap-B.”

Fig. 1

Fig. 1

” We then constructed a phylogenetic tree (Mt tree) for the 72 complete mtDNAs including the four ethnic groups, as shown in figure 2. We used Kimura’s two parameter method (Kimura 1980) for computing evolutionary distances among them and the NJ method for the tree construction. The Mt tree revealed two female descendant clades (Mt A and Mt B). Mt B consisted of the East Asian females only, while Mt A contained the East Asian and European females together. As in the case of males, the European females did not form an independent clade, but comprised several groups within the Mt A tree. As the Mt A cluster includes roughly as many European individuals as East Asian individuals, it is not clear which of them is ancestral to the other. The node marked with the blue circle in figure 2 suggests that the East Asians are ancestral to the Europeans. The bootstrap value of the node is 99%. Therefore, both male and female lineages suggest that Europeans diverged from within East Asian ancestors or that they interbred with East Asian individuals up to a certain divergence time.

Fig. 2

Fig. 2

Our next question was thus to estimate the divergence time of the European clade within the East Asian lineage, for males and females separately. To address that question, we computed the evolutionary distance (RST) between every pair of the male individuals to construct the Y-STR tree in figure 1. The researchers’ conclusion was that “the divergence time of the European males is ∼40,100 years ago” while they “estimated the divergence time of the European females, as ∼41,500 years ago.”

Our results suggest that the European people settled down in their territories ∼41,000 year ago, and have developed their own cultures and languages since then.

On the other hand, the East Asians were classified into two clusters; one is Type 1 East Asians denoted as Yap-A [this is the grouping that carries C,D hgs and YAP+ genes, i.e. the Jomon and Ainu ancestral line] and Mt B clusters in the male and female trees, respectively, and the other is Type 2 East Asians denoted as Yap-B and Mt A clusters in the male and female trees, respectively.

While Type 1 includes East Asian individuals only, Type 2 contains East Asians and European individuals together.

FIG. 4.— The general view of the East Asian and European divergences is summarized in figure 4.

Fig. 4

Fig. 4

Fig. 4 Phlyogenetic tree of the major human populations Africans, Type 1 East Asians, Europeans and Type 2 East Asians

Both the Y-STR and mtDNA trees consistently show that Europeans diverged from East Asian ancestors ∼41,000 years ago.”

Dealing with the question of differences in facial morphology and phenotypes, the paper proposed:

“Population genetic theory indicates that 41,000 years, or about 2,000 generations, are long enough to accumulate SNPs in the same loci in each lineage (Kimura 1983; Nei 1987) to account for the present genetic and phenotypic differences between the East Asians and Europeans, but too short to acquire independent loci between them. Recently, Liu (2012) reported on five genes responsible for the facial morphology of European people. The East Asian people must have the counterparts that differ at the SNP level from those in the European people. As our phylogenetic trees demonstrate, the European alleles at the five loci have diverged from the ancestral East Asian alleles.

Our result contrasts with the traditional view that Europeans and East Asians simultaneously diverged from African ancestors 55,000 years ago. It is noteworthy, however, that Shinoda (2007) investigated into the haplogroups of mtDNA, and revealed a number of evolutionary haplotype lineages. The lineages include L3 (African), N (East Asian), W (European), and L3 to N to R (East Asian) and then HV (European) among others. Though they did not explain their results, their haplotype lineages can now be understood by our finding that the Europeans diverged from the East Asians. Therefore, the discrepancy between the traditional view and ours lies mainly in that the traditional view was based on autosomal genes that evolved much slower than Y-STR or mtDNA, and could not distinguish the evolutionary lineages at the individual level. Note that, as estimated earlier, the evolutionary rate of mtDNA is 2.4 × 10−8 per site per year, while that of nuclear neutral sequences is 2.0 × 10−9 per site per year (Fukami Kobayashi 2005). The discrepancy also is due to the fact that while we dealt with many male and female individuals in our study, the other studies did not.

Our result contrasts with the traditional view that Europeans and East Asians simultaneously diverged from African ancestors 55,000 years ago. It is noteworthy, however, that Shinoda (2007) investigated into the haplogroups of mtDNA, and revealed a number of evolutionary haplotype lineages. The lineages include L3 (African), N (East Asian), W (European), and L3 to N to R (East Asian) and then HV (European) among others. Though they did not explain their results, their haplotype lineages can now be understood by our finding that the Europeans diverged from the East Asians. Therefore, the discrepancy between the traditional view and ours lies mainly in that the traditional view was based on autosomal genes that evolved much slower than Y-STR or mtDNA, and could not distinguish the evolutionary lineages at the individual level.

… according to the classification agreed at the Y Chromosome Consortium (2002) and elsewhere (Karafet et al. 2008), we found that all individuals in the Yap-B1 in figure 1 belonged to either haplogroup C or D, while the majority in the Yap- B2 belonged to haplogroup O. Since Yap-B1 includes mainly Japanese and Korean males, in which 91% individuals share haplotype O2b, the Korean and Japanese males are definitely closest to one another within East Asian humans. We also found a high frequency of the O2b haplotype in Manchu (Northern China) and Korean-Chinese samples (Katoh et al. 2005b; Kim et al. 2011).
The origin of the Ainu people is still an unresolved issue (Tajima et al. 2004). On the basis of our results, we propose a possible scenario for the origin of the Ainu people, who now live in the north-most island of the Japanese archipelago, Hokkaido. The Ainu people have European phenotypic characters, but they are genetically closer to East Asians than to Europeans (Watanabe 1975). These contradictory features of the Ainu people are puzzling. As shown in figure 4, Europeans may have diverged from East Asians ∼41,000 years ago, it is possible that hybrid individuals were born before the divergence, and some of them looked more like the Europeans while possessing a generally East Asian genotype. We suggest that the ancestor of the Ainu people was such a group of the hybrid individuals. We note that the present Ainu people share the mtDNA haplotype not with the Japanese but with the European living in Siberia, Russia (Adachi et al. 2009). Thus, we furthermore suggest that the ancestor of the Ainu originated in northern Eurasia and took a route through Siberia and north China before settling in northern regions of Japan and nearby places. There is a report that other people than the Ainu also lived in the northern regions but disappeared (Adachi et al. 2009). As the people in Okinawa islands are closest to the Ainu people in the East Asians (Jinam et al. 2012), they might also be descendants from of mixing of East Asian and European lineages.

Conclusion:
Phylogenetic trees of Y-STR makers and Mt genes suggest that the Europeans interbred with East Asians until ∼41,000 years ago. On the other hand, East Asians diverged from their African ancestors ∼55,000 years ago. Therefore, we suggest that the European and East Asian lineages diverged ∼41,000 years ago.

***

What are the implications for Japanese settlement and migrational history theory:

To recap, this is what we can glean from this study with respect to the populating of Japan.

– East Asians diverged from their African ancestors ∼55,000 years ago –>

Earliest East Asian grouping

YAP-A   which is made up of C, D and YAP+ hgs. This group comprises mainly of Khalkh Mongolians and predominantly Japanese (all arching Japanese grouping, note: ancestral lineages Jomon, Ainu showed highest frequencies of YAP+, but a significant component of the lineages of the modern Japanese population today still carry a strong signal of the ancient YAP+ gene. YAP+ is an ancient Out-of-Africa marker – borne only by group), Koreans and Europeans in somewhat more miniscule numbers. (This is presumably is the oldest Out-of-Africa grouping, because it includes YAP+ genes.)

The study proposes that Ainu arose out of hybrid individuals were born before the divergence of Europeans from East Asians ∼41,000 years ago, and some of whom looked more like the Europeans while possessing a generally East Asian genotype may have diverged. The ancestor of the Ainu originated in northern Eurasia and took a route through Siberia and north China before settling in northern regions of Japan and nearby places.

The study also proposes that the people in Okinawa islands being closest to the Ainu people in the East Asians (Jinam et al. 2012),were likely descendants from of mixing of East Asian and European lineages.

According to the study, the Y-STR tree (focusing on male lineages comprising Japanese, Korean, Mongolian (Khalkh), American, and European people only), revealed that the male ancestral lineage contained two clades (Yap-A and Yap-B). While Yap-A clade includes the East Asian individuals only, Yap-B clade contains the East Asian and European individuals together.

– East Asian and European groups diverge at around 41,000 ya

in the East Asian-only group – Yap-B1 in figure 1 belonged to either haplogroup C or D [Other studies have proposed that C and D lineages are the earliest or among the earliest groups to settle East Asia.  Hg C is thought to have come from a southerly possibly coastal origin, while D from a either a southerly or southwesterly direction]  However, since Yap-B1 includes mainly Japanese and Korean males, in which 91% individuals share haplotype O2b, the Korean and Japanese males are definitely closest to one another within East Asian humans (a high frequency of the O2b haplotype also found in Manchu (Northern China) and Korean-Chinese samples).

– The branching of NO – and the branching of Y-DNA O into subclades on the continent is a highly complex picture and the roots of the tree only beginning to be understood.  According to the study the majority of Yap- B2 belonged to haplogroup O.  The European males never formed an independent clade. Instead, they formed separate clades within Yap-B.

A few points I wish to make here:

Given that the study’s groupings of Yap A and YAP B1 and B2 groups involve the haplogroups C, D and O, it is surprising that the paper does not cite or try to reconcile the results of important studies that have proposed the origins and migrational paths for these groups.  For example,

Abstract: “…our detailed analysis of hg N suggests that its high frequency in east Europe is due to its more recent expansion westward on a counter-clock northern route from inner Asia/southern Siberia, approximately 12–14 ky ago. The widespread presence of hg N in Siberia, together with its absence in Native Americans, implies its spread happened after the founder event for the Americas. The most frequent subclade N3, arose probably in the region of present day China, and subsequently experienced serial bottlenecks in Siberia and secondary expansions in eastern Europe. Another branch, N2, forms two distinctive subclusters of STR haplotypes, Asian (N2-A) and European (N2-E), the latter now mostly distributed in Finno-Ugric and related populations. These phylogeographic patterns provide evidence consistent with male-mediated counter-clockwise late Pleistocene–Holocene migratory trajectories toward Northwestern Europe from an ancestral East Asian source of Paleolithic heritage.”

Excerpts from the body of the paper:

” … the spatial distributions for ancestral paragroup NO-M214*, paragroup N-M231* and the prevalent hg O-M175 (Figure 2a, c, d) are generally congruent and highlight Southeast Asia as the most parsimonious source region of these clades. The spread pattern of paragroup NO*approximates the same regions of Southeast Asia as paragroup N*, although being present at an even lower frequency compared with N*18, 19 (data from Kayser et al19 updated in present study). More notable, however, is the fact that the spatial dynamics of the whole N and O haplogroups greatly differ from each other. The split between N* and O is dated to 34.6plusminus4.7 thousand years (ky). The age of STR variation of hg O in Southeast Asia probably exceeds 26 ky,10 and its numerous subclades currently predominate in southern and southeastern Asia extending into northern China, Manchuria and some Siberian populations,7, 9, 11,20, 21 as well as westward to the eastern sector of the Indian subcontinent10 and eastward to Oceania.

The phylogeography of the NO* and N* lineages (Figure 2a, d) and the presence of N* chromosomes in southern East Asia (South China and Cambodia, see Supplementary Table 1) suggests that this region could be the source of the initial spread of hg N. In this scenario, the Altay/Sayan/southern Siberia region might have been a place of transition of hg N westward as all major subclades of hg N are still to be found there. …

In summary, Y chromosome haplogroup N presents a case of gene flow to eastern Europe that has its likely ultimate source in east Asia.”

See also the other paper by SHi H, et al, “Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N” and also  Austro-Asiatic Tribes of Northeast India Provide Hitherto Missing Genetic Link between South and Southeast Asia Mohan Reddy et al., PLoS ONE. 2007; 2(11): e1141. 2007 (alternative theory for the origin of O-M95 in the Austro-Asiatic tribes of N-E India.

***

The 2014 paper in ignoring the aforementioned research papers leaves hanging other fundamental questions: Before East Asia, what was the route taken out of Africa of all these founding haplogroups – a southern one or northern one, single migration route or multiple (See Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes, Vincent Macaulay et al.,  Science 13 May 2005: Vol. 308 no. 5724 pp. 10341036DOI:10.1126/science.1109792; ; Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Zhong H, et al. Mol Biol Evol. 2011 Jan;28(1):717-27.

Finally, the Japanese samples are classified broadly as Japanese samples (but Ainu and Okinawan and ancient Jomon DNA, are usually differentiated from modern Honshu Japanese samples, here it is all lumped here into one great grouping). Would the study’s results have showed a vastly different picture had they tested against specific samples of Ainu, ancient Jomon (different locations in Japan), as well as against against different continental populations of Altai-Buryat Mongols, Tibetans, Tungusic-Amur or Nikhs peoples, Yakuts, Evenkhs, Kazakhs???

See also:

DNA analyses and inferred genetic origins of the Ainu

Making sense of DNA data and the origins of the Japanese

YAP-positive element in the Y-chromosomes of the Ainu people

Resources on Ainu DNA

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27 responses to “Bold new 2014 DNA study proposes when and where the three major populations of Africa, Europe and East Asians diverged and suggests why the Ainu look like Europeans

  1. There is an error in your opening paragraph:

    “The traditional view that humans fall into three major populations, Africans, East Asians, and Europeans, with the latter two diverging from the African ancestors ∼55,000 years ago, has been re-examined by a group of researchers, who have come to a bold and different conclusion — and who have put forward a new view that East Asians diverged from Africans first, and that only later did the Europeans diverge from the East European grouping.”

    The authors of this study have claimed that the ancestors of East Asians diverged from the ancestors of (Sub-Saharan) Africans approximately 55,000 years ago, and that the ancestors of Europeans (actually, Western Eurasians or “Caucasoids” in general) subsequently diverged from the ancestors of East Asians 41,000 years ago. In other words, they have claimed that East Asians derive from Africans and that Caucasoids derive from East Asians. The first part of this claim (that East Asians derive from Africans) has been generally accepted for some time already; the second part of this claim (that Caucasoids derive from East Asians) is what is new and interesting.

    I suspect that you may have mistakenly written “East European” when you should have written “East Asian” or “East(ern) Eurasian.”

    Furthermore, the claim about the Ainu people is entirely unsupported by any data. In fact, the only published samples of Ainu Y-DNA and mtDNA show that they belong overwhelmingly to what the authors of this study have labeled as “Type 1 East Asians” (characterized by Y-DNA haplogroups C and D and mtDNA haplogroup M), i.e. the type of East Asians who are lineally less closely related to Western Eurasians. The Ainu also do not have any mtDNA that is found in “the European living in Siberia, Russia.” The Ainu do exhibit a couple mtDNA types (G1, a subgroup of M, and Y1a, a subgroup of N(xR)) that are also frequently found among other *indigenous* populations in eastern Siberia (especially those around the Sea of Okhotsk, such as Nivkhs, Negidals, Ulchis, Itelmens, etc.), but those peoples are not in any way “European,” and those mtDNA haplogroups are not found among any real Europeans or Western Eurasians.

  2. There is no error in what I wrote. The traditional view I stated is quoted verbatim from and as defined in the text of the paper. I also wrote East Asians and Europeans because those are the exact terms used in the paper, see Fig 4 and those are the broad categories, the researchers chose to focus on in determining the timing of the divergence of the defined groups.
    That aside, I understand what you are saying and agree with your terminology which is more commonly used in other genetics research papers, and in my final comments I allude to it as I question the usefulness of those results when it does not take into account other population groups present in Eurasia or East Asia however you wish to define the geosphere under consideration.
    From my reading of the paper, the authors do not say that the Ainu are European, what they do say is that the Ainu are genetically East Asian, but morphologically have hybrid looks that can go either way, look European or Asian, and then they explain why that is so…i.e. They emerged from the group that had not yet diverged into European or East Asian groupings.

  3. As regards DNA evidence supporting their theory of the origins of a Siberian origined Ainu there is in fact, supportable DNA data to put the Ainu’s ancestral lines in S. Siberia, although the paper does not really cite it (which I point out and try to plug their gaps) nor does it explain their outlined branching of their categories very well.
    The main tenet of their theory Ainu origins I think must lie with their idea of the shared origin of the YAP+ Hg allele carried by Ainu(at 100 pct frequency) and by Europeans, YAP+ Is ancestral to hgs D and E which branch off from YAP+ (this is not disputed by any of the YAP+ papers). The YAP+ marker, outside of Africa, as far as I can tell, it is also not in dispute that it is carried mostly by Europeans carrying the E-YAP+ Hg and E. Asians carrying the D-YAP+. That is not hard to follow if you’ve read all the YAP+ related literature and can draw a map in your head of the YAP+ and hg D trail in your head or on paper. Thus, what the authors must be saying is that the connection between Europeans and E. Asians must lie somewhere where two have once interacted/originated but then diverged later one stream Eastwards and one stream Westwards. D/YAP are not the only genetic markers in support of this view. The latest research puts the origin of N in North China, going westwards, and N subclades are most plentiful in North Eurasia, both on the Western side as well as on the Eastern side of the Ural or Altai divide. The NO split has been one of the greatest puzzles to be solved, but find the origin of N, you also find the origin of where O – the birthplace of E. Asia is. North China or S. Siberia, surely it’s merely quibbling over semantics as to where the possible interaction sphere or origin of the E. Asian-European cradle lies. N1c-Tat is one of the key markers of the early Japanese, Jomon specifically, and of the Ainu, though it has been watered down by intermarriage with E. Siberians and Amur-ians, which you have noted. There are at least two papers that have placed the Ainu’s closest affinity with remains in the Eygiin Gol graves, so it is not true that there is no support for Siberian DNA in the Ainu. Finally, D4 mtDNA (this time, distinguishable from D Y-DNA) are through and through Siberian as well as Mongol, and the Ainu also shares the Siberian-Native American mtdNA genes as well. It is also entirely possible, likely even, in view of the above, that the authors chose European over Caucasoid deliberately to underline the fact of the Eastern origins of Europeans because they are considering that both Y-DNA YAP+ and N linesges are traditionally considered to be part of the W. European and Scandinavian genetic package.

  4. I repeat: you have written, ““The traditional view that humans fall into three major populations, Africans, East Asians, and Europeans, with the latter two diverging from the African ancestors ∼55,000 years ago, has been re-examined by a group of researchers, who have come to a bold and different conclusion — and who have put forward a new view that East Asians diverged from Africans first, and that only later did the Europeans diverge from the East Europeaan grouping.”

    The authors of this paper have nowhere stated that Europeans “diverge from the East European grouping.” The entire purpose of this paper is to present the authors’ claim that the ancestors of modern Europeans/Western Eurasians are actually a subset of (i.e. have derived from) the ancestors of East Asians/Eastern Eurasians, and to provide evidence in support of their claim. Your “East European grouping” is an obvious error, and I do not understand why you refuse to acknowledge this fact.

    As for the Ainu, they do not belong 100% to haplogroup D-M174. Even in the meager sample (some 16 individuals) for which Y-DNA results have been published, some of the individuals belong to haplogroup C2-M217. C2-M217 is found very frequently in Mongols, Kazakhs, many indigenous Siberian ethnic groups (Buryats, Evenks, Evens, Nivkhs, Koryaks, etc.), and in some indigenous North American populations (Tanana, Cheyenne, Apache, etc.). It is also found throughout East Asia, Central Asia, and much of Southeast Asia at various frequencies (e.g. approximately 15% of Koreans and approximately 10% of Han Chinese and Vietnamese). C2-M217 is generally rare in Japan, but it is relatively common in the aforementioned sample of Ainus from Hokkaido and in another published sample of Japanese from Kyushu.

    The remainder of the published Ainu Y-DNA sample belongs to haplogroup D1b-M55. This haplogroup occurs with high frequency throughout the Japanese Archipelago, including the Ryukyu Islands, though there are some fluctuations in frequency of the various subclades. Some of these subclades also have been found in Korea with low frequency (approx. 2% of the total Korean male population), and they also have popped up sporadically in samples from China, Micronesia, and West Timor (Indonesia).

    Both Ainu Y-DNA haplogroups, D1b-M55 and C2-M217, are more closely related to Y-DNA haplogroups found among modern East Asians (D1a-M15 among Tibetans, Yi, Hmong, Mien, Thais, etc., D1c-P99 among Tibetans, Naxi, Pumi, etc., D2-L1366 among Filipinos, various other types of C2-M217 found throughout Eastern Eurasia as well as C1a1-M8 among Japanese and Ryukyuans and C*-M130 among Mien, Hmong, Han Chinese, Tibetans, Nanais, etc.) than to haplogroups that are commonly found (or found at all) among Western Eurasians.

    Ainu mtDNA haplogroups are also entirely Eastern, with Y1a (circum-Okhotsk) being related to Y1b (Chinese, etc.) and Y2 (Taiwan aborigines, Filipinos, Indonesians, etc.), D4 and D5 being squarely East Asian (D4 is the most common haplogroup among Japanese, Ryukyuans, Koreans, etc. and D5 is very common among Chinese), G1 being related to G2 (pan-East Asian), G3 (Koreans, Tibetans, Hmongs, etc.), and G4 (Japanese), and M7 being East-Southeast Asian (high frequencies among Japanese, Chinese, Vietnamese, Laotians, etc.). Actually, it may be pointed out that the Ainu have just about the least genetic connection to Native Americans of any modern East Asian population. The Ainus lack mtDNA haplogroup C (which is very common among Siberians and Native Americans) and its relative, haplogroup Z (found among Siberians, some East Asians, and some Northeastern Europeans e.g. Saami). The Ainus have very low frequencies of haplogroups A and B, much lower than the frequencies of these haplogroups among Japanese, Ryukyuans, Koreans, Chinese, etc., and the few representatives of these haplogroups that are found in the published Ainu sample (two A and one B) are more closely related to East Asian types than to Native American types. The only indicators of any possible genetic connection that the Ainus might have with Native Americans and their hypothetical Palaeolithic Siberian ancestors are mtDNA haplogroup D (and D4 in particular; Ainus also have some D5, but D5 is not found in the Americas) and Y-DNA haplogroup C2-M217 (but nearly all Native Americans in this haplogroup belong to a particular subclade that is related to a subclade found especially among Tungusic peoples and Kazakhs, whereas the Ainus in C2-M217 belong neither to the American C2b1-P39 nor to the Tungusic, Kazakh, etc. C2b2-M48).

    At least in regard to their genetics, the (modern) Ainus appear to be exactly what one might expect from geography: a mix of Japanese people and circum-Okhotsk indigenous Siberians (Nivkhs, Oroks, Itelmens, etc.). In terms of haplotype sharing, the Ainus tend to share mtDNA haplotypes with other circum-Okhotsk indigenous peoples, while their Y-DNA (mostly D1b-M55) is closer to other Japanese people. Neither Japanese nor indigenous Okhotsk people are European/Western Eurasian/Caucasoid at all.

    • The paper says they diverged from the East Asian grouping. I did not intend to mention E. european at all, it is a typo error. It should read East Asian, I only saw it now. I apologize for the confusion.
      As for 100 pct frequency, you misunderstand, when the group is tested and a hg appears in 100 pct or other frequency, it does not mean they are only 100 pct carriers of the gene, and carry nothing else. What it means is that everyone sample tested in the particular study showed up with the gene in question. Therefore, when the Ainu samples return with 100 pct frequency of the D/YAP+ Gene, it does not mean they can’t also carry N or some other haplogroup in combination. This is a common mistake made. Think of frequency as a kind of hit rate, in a certain population tested. And NOT how much percent of the genetic makeup package of the persons tested.

    • 100 pct frequency of a D-Yap+ gene found in the Ainu population does not mean they don’t bear other genes, this is a common mistake made by lay readers. It just means out of the samples tested from that population, it had a hit rate of 100 pct, i.e. every Ainu person test sample returned showing they had were YAP+, but it doesnt mean they aren’t carriers of the C hg or other hg. If you’ve read the other pages of this website you’ll know I’ve also written about the Nivkh, Okohtsk and Amur origins of the Ainu as well, and of the Buryats, etc. Buryat Mongols are by the way also considered Siberians and have mostly been in the Baikal area. Nivkhs, Okohtsk and Amur are also all considered to be northeast Siberians or a northerly peoples. Shinoda pointed out hg Y and most of the other southerly genes arrived in the Ainu population only after the 5th c. onwards. Why is this important? So that they can isolate the predominant hgs of the Palaeolithic and Jomon and determine the origin of those genes. Hg C is undoubtedly originally of a southern direction, but like mtDNA D4, its subclades have been in the north for a very long time, and the E.Asian specific subclades have northern Siberian distribution or radiation pattern. Don’t take it from me though. See the material. MtDNA Analysis of Hokkaido Jomon skeletons:. http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21561/abstract aplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period.

      Shinoda’s “Genetic structure of the Japanese and the formation of the Ainu population” on p. 19 gives a clear comparison of Hokkaido Jomon-EpiJomon or Satsumon Jomon and then Ainu MtDNA comparisons, and establishes beyond those mentioned in the above paper, hg Y only entered from the north from the 5th c. onwards, and many other haplogroups from the 9th c. Onwards
      See Shinoda on Jomon through Ainu mtDNA
      http://jspsusa.org/FORUM2012/presentation/3-2_Shinoda.pdf

      The Peopling of Japan http://genome.cshlp.org/content/14/10a/1832.long
      To further know the relative affinities of the Japanese between themselves and with the different Asian groups formed, the data obtained from the global approaches based on haplogroup frequency distances and on sequence match identities are presented in Table 4. Both values are moderately correlated in the comparisons involving the mainland Japanese (r = -0.479; two-tail probability 0.012) but not at all in those involving aborigine Ryukyuans (r = -0.310; two-tail probability 0.115) and Ainu (r = 0.087; two-tail probability 0.667). This result can be explained by assuming that these aboriginal people have suffered important genetic drift effects with substantial changes in haplogroup frequencies and lineage losses or, less probably, that these populations have been isolated long enough to have accumulated new variation. Results based on haplogroup frequencies by far relate mainland Japanese to Koreans followed by northern Chinese. Ryukyuans present the smallest distances to Buryats from South Siberia, followed in short by southern Chinese. In turn, the Ainu have their closest affinities with mainland Japanese, Koreans, and northern Chinese. As regards sequence matches, mainland Japanese also joins first to Koreans and second to Buryats. Aborigine Ryukyuans are closest to Buryats and then to Koreans. Finally, Ainu show comparatively less shared sequences, their greater affinities being toward Chukchi and Koryaks of Kamchatka. This global picture is congruent with an important influence on mainland Japanese from northern Asian populations through Korea, that the Ryukyuans had a dual northern and southern Asian background previous to the new northern influences acquired by admixture with mainland Japanese, and that the Ainu represent the most isolated group in Japan in spite of the genetic input received from Kamchatka. Also noticeable is the great distance and low identity values obtained for the Ainu-Ryukyuan pair compared with those obtained in their respective comparison to mainland Japanese, which is another hint of its notable maternal isolation.

      ….
      The distance and identity statistics used above are based on frequencies of haplogroups and haplotypes, respectively; however, frequencies are more affected by genetic drift than the number of different haplotypes present in a population. To measure the relative affinities of Japanese populations between them and to Continental Asia in a frequency-independent way, we chose a haplotype-sharing approach calculating the relative contribution of lineages shared with other areas to the number of different haplotypes present in each Japanese population. In these comparisons all other Asians were merged. Table 5 shows the results of this analysis. Note that despite the difference in sample size the haplotype frequency in mainland Japanese and Ainu is ∼50%, whereas in Ryukyuans it is 84%; which means that, if there was not a bias in the sampling process, in spite of its small size, the Ainu sample seems to be representative of that population. However, it would be desirable to enlarge that of the Ryukyuans (Helgason et al. 2000). Haplotypes present only in a given population account for 13% in Ainu but ∼50% in mainland Japanese (60%) and Ryukyuans (45%). This finding once more points to the existence of important drift effects in Ainu. Mainland Japanese exclusively share with Ryukyuans and Ainu only 3% and 2%, respectively, of its lineages, which could reach 6% and 3% if those also shared with Continental Asian populations are added. In comparison they shared 21% of its lineages with other Asians. On the contrary, Ryukyuans and Ainu share about 50% of their lineages with mainland Japanese and only 10% and 21%, respectively, with Continental populations, which may reflect other independent Asian influences on Japan. With respect to those lineages exclusively shared by Japanese and Continental Asian populations, it is worth mentioning that, again, Korea is the main contributor, participating in ∼50% of the haplotype sharing with mainland Japanese (55%), as much as with Ryukyuans (50%) and Ainu (50%). However, differences exist in the provenance of the rest of the shared lineages. Whereas in Ainu (northern China and Siberia) and in Ryukyuans (northern China and central Asia) they are from northern areas, the second region contributing to mainland Japanese is southern China (17.5%), followed, at the same level (12.5%), by northern China and central Asia. In addition, there exists a minor percentage of exclusive sharing with Indonesia (2.5%). On the other hand, all the matches with Siberia and Tibet are also shared with other populations. From these results, it can be deduced that the ancient Japanese inhabitants came from northern Asia and that southern areas affected the Japanese by later immigration

    • Finally, I’ll only address your point about Ydna D hg being found among the Thais, Hmongs, etc which makes us all think that E.Asian genes come from SEA, and have a southerly origin. That was the OLD view, which I myself held and some of my pages on a southerly origin are in need of revision. Lately, much of the research hold that the Dai-Thai, for example, migrated south from more northerly locations, possibly South China, Hainan Island. That is speaking of the O lineages. The origin of the O hg is suggested to be in Qiangic who are considered the ancestral Sino-tibetan population, see 2014 new study which states that they are a predominantly northern and Altaic-connected population with a southern pole in its O lineages http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121179/#!po=26.3889. MOn-Khmer, Tai-Kadai and Hmong are all downstream of the Qiang.
      Thus when speaking of the D lineages (Ydna), this suggests, their origins were from a more northerly origin (a westerly origin has not ruled out), before the populations began to migrate south or East. What is not disputed is that Yap+ and DE* which are upstream of the D ohylogenetic tree, are found much further north and nowhere in the south. Finally, it is also nowhere disputed that the radiation of the O hg occurs after all the key northern genes under discussion. (A northern origin of the discussed lineages does not rule out the admixture with other lineages of southerly origins, such as the Australiasian hg C or ISEA Melanesian aboriginal ones)

  5. It is good that you finally have recognized your typographical error, but you have mistakenly edited my previous comment instead of your error in the original blog post.

    There is no published sample of Ainu Y-DNA in which 100% of the individuals in the sample have carried haplogroup D-M174. They contain a mix of D-M174 (more specifically, D1b-M55) and C2-M217.

    • Sorry, I’ll put it back in your comment. Honestly dont know where the E European came from, never crossed my mind, probably a cut-and-paste error. But thank you btw, for pointing it out. I might never have realized it on my own without your insistence.

    • There is too, and it showed the percentage of D-Yap+ comparing the different populations all over Japan, I just can’t recall which study it is at the moment.

  6. “100 pct frequency of a D-Yap+ gene found in the Ainu population does not mean they don’t bear other genes, this is a common mistake made by lay readers. It just means out of the samples tested from that population, it had a hit rate of 100 pct, i.e. every Ainu person test sample returned showing they had were YAP+, but it doesnt mean they aren’t carriers of the C hg or other hg.”

    “This is a common mistake made by lay readers”? How presumptuous and rude! 貴女は思い込みの激しい方なのでしょうか?

    Having a 100% frequency of DE-YAP would *entail* by definition that that sample (not necessarily the entire ethnic population, of course, which is, from the perspective of population genetics, an unknown target population whose characteristics must be inferred through statistical analysis of samples) contained only DE-YAP Y-chromosomes. Because C-M130 is YAP negative (despite Mr. Tateno’s misleading use of terminology in his recently published paper), a 100% frequency of DE-YAP would preclude the presence of any C-M130 (or any other YAP negative haplogroup) in the sample. YAP positive (YAP+, i.e. DE-YAP) and YAP negative (YAP-, e.g. F-M89, C-M130, B-M60) are mutually exclusive categories.

    In any case, even the published data regarding the Y-DNA of modern Ainus does not suggest that every one of them possesses DE-YAP Y-DNA; C2-M217, which is YAP-, also has been found among them. Thus, they absolutely do *not* have 100% DE-YAP Y-DNA.

    Of course, there is a statistical phenomenon known as “sampling error.” It is possible that the actual Ainu population may contain some other Y-DNA haplogroup besides D1b-M55 and C2-M217 (e.g. N-M231, O-M175, Q-M242), and that the sampling simply has missed that other haplogroup (or those other haplogroups), but that is a hypothetical scenario and cannot be proved without additional sampling of Ainu males (and cannot be disproved without sampling and testing the Y-DNA of every single Ainu male in existence). In any case, without further testing revealing the presence of some other haplogroup in the Ainu gene pool, your idea of connecting them with Y-DNA haplogroup N1c1-Tat is pure speculation. N1c1-Tat has never been found in any Ainu individual in any published study, and it is not particularly common among any of their neighbors, so the motive for your speculation is quite a mystery.

    • I cant find the study I mentioned, but there’s close enough Yap+ data, it shows strongest in the Ainu at 87pct frequencies (but also strong all throughout Japan, weaker among the Korean-descended Populations of Japan) Follow the links at this page http://wp.me/P48G6-183 there are many studies but it is clear they consider the Yap+ frequency to be highest among the Asians, Yap negativity i.e. the loss of the Yap signal among Thai, Hmong, SEA tribes is particularly noted by the experts. Yap is noted to be 100 pct among some of the African, European populations, and the proposed Yap trail is drawn in a map in one of the studies.

      • E-M96, the other major subclade of DE-YAP besides East Asian D-M174, is found primarily in Africa, and it has been present in 100% of some samples of some populations on that continent. However, many other Y-DNA haplogroups, including the basal and very divergent A haplogroups and haplogroup B-M60, also have been found in many samples of modern Africans. DE*-YAP(xE-M96, D-M174), i.e. the potentially paraphyletic category of YAP+ Y-chromosomes that belong to neither of the major subclades (neither E-M96 nor D-M174), has been found in a few individuals in Africa and in East Asia (Tibet).

        DE-YAP is generally very rare outside of Africa and East Asia. The main exceptions are certain subclades of E1b1b1-M35 (which is itself a subclade of the typically African E-M96) that are found with notable frequency in some populations around the eastern end of the Mediterranean Sea (e.g. Albanians, Arabs, Greeks, Jews). Nearly all representatives of DE-YAP in western Eurasia belong to the African E-M96 clade rather than the East Asian D-M174 clade. However, in no population of western Eurasia does DE-YAP come even close to reaching 100% frequency (although it does come close in some populations of East Africa and North Africa that are partially or even mostly Caucasoid in regard to their overall autosomal genetics). In addition, some indigenous peoples of the Andaman Islands have been reported to possess D-M174 Y-DNA with high frequency, though those islands might be included under some broad definitions of East Asia (they are currently under Indian control, but are geographically considered by most people to be part of Southeast Asia, which is sometimes merged into a broad concept of “East Asia” or “Eastern Eurasia”).

        D-M174 is generally rare everywhere except Japan, Tibet, and the aforementioned Andaman Islands. There is no reason to single out Southeast Asians in particular; actually, D-M174 is even rarer among Siberians (found only among Southern Altayans, who only marginally may be considered as “Siberians” anyway) and Native Americans (completely absent). Actually, D2-L1366 is a basal branch of D-M174, and, as of today (August 17, 2014), its presence has been confirmed only in a few Filipinos, who certainly must be counted among “Southeast Asians.” All the D-M174 representatives among northern East Asians (mainly people in Japan and Tibet) belong to a different subclade, D1-CTS11577. The typically Tibetan subclades of D, D1a-M15 and D1c-P99, also appear to belong to a single clade opposed to the typically Japanese D1b-M55. In other words, there is first a split between Filipino D vs. Japanese+Tibetan D, and then there is a subsequent split between Japanese D and Tibetan D.

  7. I have been reading, discussing and writing on human population genetics for almost a decade (actually more but less intensely in the beginning) and the methodology of this paper strikes me as terribly tendentious and obsolete. Would I read this kind of thing in 2004, it would make sense, but today?!

    In this sense it strikes me that the study mostly references previous papers from the 20th century, what in such a quickly developing field as this one is a serious symptom. They do mention a few more modern studies but they seem to have very limited weight in their thinking.

    It is 100% true that European (and generally West Eurasian) “non-YAP” Y-DNA is a subset of the Asian one: it is almost exclusively within the macro-haplogroup F, the largest one out of Africa, which most likely first coalesced in South Asia (although an important share of Western lineages probably underwent migration to SE Asia and back, via India again, to the West before the Upper Paleolithic). These Western lineages (P→R) are related to the main East Asian lineage NO→O, as well as others from the Malay Archipelago and Australasia.

    Actually all this makes Europeans somewhat closer to mainline Japanese than to Ainu, at least via Y-DNA (but mtDNA also holds no surprises in the opposite direction) but, in any case, refers to events before the “racial” differentiation (as we know it today) took place in Eurasia.

    Critically: is European (and West Asian) “YAP+” related to Ainu (and mainline Japanese) haplogroup D? Nope. It is all of “recent” African derivation and belongs to haplogroup E1b, which mostly arrived in the Neolithic. The disdain for African lineages in this study, as well as for anything Asian except a few pet localities, messes everything up. Because neither Europeans nor Japanese live in any sort of bubble but are related to mainland Asia and, particularly in the European case, to Africa as well to some extent.

    The “YAP+” haplogroup D of Ainu (and lots of non-Ainu Japanese) is also dominant in Tibet, whose phenotype is typically East Asian, and in the Andaman Islands, whose phenotype is usually considered “Negrito” (although these are actually a varied bunch genetically speaking and the term must be considered a catch-all category with no phylogenetic value). Haplogroup D is totally absent in South Asia or West Eurasia. There’s hardly a more purely East Asian Y-DNA lineage than D. It’s not even present in Australasia either, nor in America.

    Its closest relative however is African E, some of whose offshoots had an impact in Europe much much later than the arrival of D to East Asia (which IMO dates to the same 100 Ka old wave that brought the other, more successful, CF lineages). When you obviate Africa, it may seem that European E is somehow related to East Asian D, but this is only true via Africa, the ultimate origin of all Humankind.

    The actual reason why Ainu sometimes look vaguely European-like is probably because the East Asian “Mongoloid” phenotype is (1) less well defined than many think and (2) became prominent only gradually. I won’t say this is the only possible truth but a plausible reconstruction suggests that the first wave of settlers of East Asia, beginning as early as 100 Ka ago according to the last archaeological data from Southern China, did not yet have a well defined phenotype, certainly not one resembling modern East Asians in many cases. A clear example is Upper Cave 101, whose phenotype reminds a bit to Ainu or a generic poorly differentiated pan-Eurasian type that would be now said “Australoid” by some (although really not too similar to Australian Aborigines either, again a catch-all term being used quite happily). Most other ancient East Asian Paleolithic remains are also pretty much out of the “Mongoloid” standards.

    Later on, maybe after the Toba episode or even later, an still poorly defined “proto-Mongoloid” phenotype became more common but not universal (different populations would sport different looks). This explains why Native Americans often look more like SE Asians than like NE Asians, even if genetically they are closer to the latter. Far NE Asians (Mongols, Siberians) also appear to be rather different in metrics from mainline East Asians (whose phenotype I’d term “Sinoid”, as Mongols seem out). This “Sinoid” type may well have spread at least partly as late as the Neolithic, at least judging from ancient Chinese Y-DNA, which shows that Northern China was still dominated by lineages other than O (N, C, surely also Q) in the Neolithic period. This implies a rather late demographic expansion from South China northwards, which probably also relates to what happened in Korea and Japan.

    I am also quite perplex about the claim of haplogroup C belonging to YAP+. It is the first time I hear that claim and it is a claim that, if correct, would radically alter the patrilineal phylogeny of Humankind. It would mean, if I’m correct, that C is actually part of a larger haplogroup with E and D, while until today, C is believed to be “brother” of F instead. Right now YSOGG (the online reference for Y-DNA nomenclature and phylogeny) retains the old DE/CF division and considers YAP (alias M1) as one of several markers defining DE (and excluding therefore C). Considering the other sloppiness of this study you mention, I strongly suspect that this will remain unchanged and that it is a mere conceptual error by the authors, who never bothered testing for SNPs (all their Y-DNA work is done on STRs, which are not “rocket-science” but a mere approximative tool).

    • “It is all of “recent” African derivation and belongs to haplogroup E1b, which mostly arrived in the Neolithic.”

      There is really no evidence about what you stated here. In Eurasia, there are several ancestral clades with no presence at all in Africa. Real E-M215* has only been found in Khorasan (Northeastern Iran) but no real (that is, post-2011) case has been reported in Africa. E-P2* has been found in a couple of individuals from Vladivostok (of probable Russian descent), but not in Africa. The super-rare E-P75 has been found in West Bank (Palestine), England and Canary Islands (the last individual is of probable Spanish origin). I really doubt that these are Neolithic. Moreover, the highest frequency of E-M96* is in Saudi Arabia, with probable cases in the Levant and one case of E-M96(xM2,M35) (and I also add xM33,xM75 looking at the STR haplotype) in Bulgaria. Neolithic then? Cruciani suggested that E-V13 entered Europe in the Neolithic, but this has been shown to be false by Battaglia et al., who assigned a Mesolithic age to E-V13 in Europe, and when its parent L618* was discovered, it only appeared in Northern and Central Europeans, with a single Southern European case (you can see that in the E-M35 Phylogenetic Project). In the future, geneticists will aknowledge all these facts and won’t write absurd things anymore.

      • Are you referring to the back-migration (of YAP and E) theory?

      • “Are you referring to the back-migration (of YAP and E) theory?”

        No, I personally do not believe in it (because of reasons hard to explain here but largely related to the mtDNA structure). I’m referring to the fact of E being an African lineage (the main one by numbers in fact) and only having very limited and always highly-derived presence outside Africa (all of it in West Eurasia). Whether it is Neo- or Meso- or even Paleolithic (as may well be the case with E1b-M81 in Atlantic Europe), all of it must necessarily have come to West Eurasia directly from Africa.

      • There is of course a lot of evidence and anyone familiar with human population genetics knows it. There is no (Y-DNA) D in Europe and instead there is quite a bit of E1b, all of which has African origins ultimately, be them via NW Africa-Iberia (E1b-M81) or, more commonly, via West Asia-Balcans (E1b-V13 mostly, which peaks in Kosovo but is also important in Greece, Albania and found at lower frequencies in most of Europe). E1b-V13 has been detected among Catalan Cardium Pottery first farmers. A so-called “Basal Eurasian” element (African tendency, as opposed to mainline Eurasianness) has been detected among early european farmers by Lazaridis 2013-14 and estimated to be Dinka-like by Skoglund 2014 (supp. materials). All converges to the point of a minor but notorious African element in European Neolithic (via West Asia). Additionally there is some other African genetics in Western Europeans, with West Iberia as core of it, which may be older (Paleolithic, as La Braña 1 seems to have a minor but quite apparent African affinity). This last African influence also seem to include some very old but rare L(xM,N) mtDNA lineages, as well as the NW African U6 mtDNA haplogroup.

        “Cruciani suggested that E-V13 entered Europe in the Neolithic, but this has been shown to be false by Battaglia et al., who assigned a Mesolithic age to E-V13 in Europe”…

        Age estimates are a continuous battlefield with no or very low probatory weight. Some argued very strongly for a Bronze Age origin of E-V13 but ancient DNA evidence from Catalonia (mentioned above) defeated their position.

        Regardless of whether the exact origins of E1b-V13 in Europe are Neo- or Mesolithic, the overall pattern of spread is the same: Nile → West Asia → SW Balcans → rest of Europe, having nothing to do with East Asian D, since the times of the Out of Africa migration.

        “… when its parent L618* was discovered”…

        That’s interesting indeed. I’m not knowledgeable on this detail. Whatever the case Scandinavia seems to act as retirement home of rare European lineages also in other cases, what does not mean that it is at the origin of all Europeans (not likely at all no matter how you look at it).

        One major problem with private commercial DNA “research” is that they heavily rely on their customers data, and these are invariably from very specific regions of the world, in Europe from NW Europe, which has both more interest on these matters but also greater purchasing power. This results in commercial DNA databases being pretty much useless to determine the origins of any haplogroup, because 90% of them are from those affluent regions, representing only a small fraction of the overall population even in Europe, never mind through the World. So it often happens that lineages look in them much more “Nordic” than they actually are when using academic samples (equivalent for all the regions surveyed). For example R1a may look “European” in a private DNA database but when such a prestigious researcher as Underhill researched it earlier this year, it became “Iranian”.

        I am not privy of the details in this case but your “single Southern European case” (in, I presume, FTDNA database) probably represents much more people than all the Northern European samples together. It is anyhow interesting and I hope they research it more with academic sampling quality, what will probably not result the way you expect (it has happened before).

        In any case, overall E1b, as all E, originates in Africa and only some very specific branches have spread to Europe. None of this has any relation with East Asia (unlike for example Y-DNA N1 in NE Europe).

  8. “E1b-V13 has been detected among Catalan Cardium Pottery first farmers. A so-called “Basal Eurasian” element (African tendency, as opposed to mainline Eurasianness) has been detected among early european farmers by Lazaridis 2013-14 and estimated to be Dinka-like by Skoglund 2014 (supp. materials).”

    aDNA shows us that until post-Neolithic times, Nubia was devoid of either YAP or F-M89-derived haplogroups (http://etd2.uofk.edu/documents/4312/uofk_etd-ID4312.en.pdf), so if that component is “Dinka-like”, it has nothing to do with Y-DNA E-V13 (which was absent in Neolithic Levant but very likely present and well in Mesolithic Europe). It probably has to do with (limited) admixture of G2a-carrying populations and individuals with Y-DNA A-M13, which has been found in a continuum from the Levant to the Aegean region (IMO Natufians, a mixed group, were carriers of A-M13, among others [like E-Z830]) and mtDNA L, the maternal counterpart of A-M13 found in PPNB individuals (sub-clades L2a1 and L3). mtDNA L has not been found in Neolithic Europe, therefore the A-M13/mtDNA L combo did not influence too much Neolithic farmers migrating towards Europe.

    “In any case, overall E1b, as all E, originates in Africa and only some very specific branches have spread to Europe.”

    You have ignored all of what I wrote above. There are many ancestral clades only found in Eurasia, plus the highest frequency of underived E-M96* is found in Saudi Arabia, not in Ethiopia or any other African region.

    • Thank you for the link to your work. I confess I have not read it nor seen references to it till now, there was no intention to ignore your work. It certainly complicates some of the scenarios for the haplotype tree as well as Y-DNA trees drawn by Underhill, Hammer, Karafet for the origins of DE and YAP polymorphism.

      Please help us make sense of and understand the implications of what you are saying in terms of timing and geolocation, and to understand which precedes which – in terms of antiquity, viz. the current theories on the origins of DE-YAP+, D and E hgs. Also as to where your E origin stands in relation to DE, E and the YAP polymorphism in the Phylogenetic Tree.

      Claudio Bravi et al. wrote “Monophyletic origin of haplo- and subhaplogroups – The possibility of recurrence for Alu markers is almost null. Therefore, all YAP1 chromosomes are known to derive from a single individual in whom the insertion took place for the first time (Hammer, 1995).” Bravi also wrote that the highest frequencies occur in African and Japanese populations at extreme ends of the world.” Bravi was ambivalent on whether YAP originated in Africa or Asia.

      Weale et al. reported “a new, very rare deep-rooting haplogroup within the YAP clade”

      I have, however, noted for a long time, the trail of sporadic DE-YAP+ in the Middle East as well as to North India, Kamla Raj‘s “study of YAP in nine populations of UP, North India, Agrawal et al. (2005) also did not find YAP insertion in any of the population groups, except for the Shia Muslims. Interestingly they did not find it in Sunni Muslims … The other population where the YAP insertion is found in very high frequency of 40% is the Siddis, a population of known East African ancestry found in Southern Andhra Pradesh (Ramana et al. 2001).”

      If YAP did not appear in Nubia till Nubian till post-Neolithic times (which is when? ca5,000BC?), and ydna E is still regarded as ancestral and originated in Africa, then are you in fact disagreeing with the current phylogenetic tree of Underhill, Hammer that locates YAP+at the root and as ancestral to both D and E? Are you in fact saying that D and E originated and diverged independently in Africa, but that YAP+ was the result of introgression the mixing of the two D and E?

      When and where would this have happened? The earliest Neolithic of Sub-Sahara is very much later than the early arrival of D-YAP+ in Asia. Palaeolithic Sudan-ancient Nubia is around 60,000 BC, so DE or D/E-YAP+ would have to have left Africa very early, sometime between 60,000-40,ooo BC in order to arrive in CAS during early Palaeolithic times?

      Can we contemplate a scenario where the Alu YAP+ polymorphism arose further to the south (of Sudan) independently of an YAP-E (what about D) since a Niger origin of D has been proposed, it would have left Africa in the south and proceeded along a southern coastal route (Vincent Macaulay’s paper) with YAP+ back-migrating to the European and sub-Saharan region, not from Caucasoid Eurasia but perhaps from the Middle East or Western Asia, given your mention of Neolithic and Basal Eurasian element? Qamar and Hammer: “YAP+ haplotype 5 may have entered Pakistan from the Arabian Peninsula by means of migrations across the Gulf of Oman, whereas males possessing YAP+ haplotype 4 may have traveled over land from the Middle East.”

      If your assertion is that YAP+ did occur in Africa, only not in early Nubia … YAP+ did arise early in Africa, it would have been south or elsewhere other than sub-Saharan Africa.

      This would be a very different picture as that presented by Alteide and Hammer, who presented and argued against an African ancestral state of YAP+ through the rather persuasive haplotype tree and branching scenario that they constructed. They presented several scenarios for the five G-A haplotypes, but came to the conclusion since the all the Western and Central African YAP haplotypes were all derived and 4 and 5 haplotypes were derived from 3, that – there was a clear-cut geographic trend in the distribution of the YAP+, that the haplotype 3G deemed ancestral occurred only in Asian populations and the derived haplotype 3A occurred only in African populations. (They did also allow for the scenario of an African origin in that 3G may have originated on an African Y chromosome, migrated to Asia, gave rise to the African 3A haplotype while 3G was subsequently lost in African populations)
      While your work discusses the E haplogroup, the YAP polymorphism appears so closely wrapped up with the origin and divergence of hgs D and E, how are we to reconcile Altheide and Hammer’s finding of an ancestral YAP+ in Asia??? Haplotype 3 is found at ~50% frequency in Tibet.

      Their discussion also observed the existence of both YAP+ and YAP- lineages exclusively in the Mongolian and Altai populations. Previously, Shi Hong et al‘s paper reported that “Mongolia was only found to have YAP+. Every ethnic group was found to have YAP+ in northwest China”. Among the Han, “only those populations living along the Yangtze River were found to have YAP+. …Primi have bery high YAP+ frequency, probably from founder effect …The ancestors of Uygur lived in adjacent places with ancient Diqiang populations … All these data implu that the YAP+ gene came from ancient Diqiang people.” Since the discussion in those papers, both YAP+ and YAP- lineages have also been observed in the different aboriginal groups in Sichuan, where the only all-YAP+ population was that of the Naxi, all of the others were mixtures, and the YAP+ polymorphism was found to be due to gene flows from the north, i.e. from the nomadic populations of Mongolia, which is not too far off from Altheide and Hammer’s P99 branch/twig.

      The P99 discovery is significant, because it now opens up the possibility that D2 traveled to Japan via the Altai Mongolian route (besides the DiQiang Yangtze river West to East route) which may support the Northern route position taken by He Yunggang in “Paleolithic Contingent in Modern Japanese“. Bing Su notes the very close relationship between the Sino-Tibetan and the Altaic populations.

      Van Driem in his very impressive overarching view of things in his 55 page “East Asian Ethnolinguistic Phylogeography” paper, takes a Trans-Himalayan origin for D-YAP+, he writes at p. 18~ “The set of ancestral Y chromosomal haplogroups CT (M168) encompasses a myriad of modern paternal lineages which first emerged from Africa in Palaeolithic times, first branching into the paternal lineages DE (YAP) and CF(P143). The paternal lineage DE (YAP) split into haplogroups D and E. The paternal lineage D may have originated inthe Himalayan region, where this haplogroup is still represented in the highest diversity, particularly in Nepal and Tibet. This paternal lineage migrated southward to the Andamans and eastward from the eastern Himalayans across the Tibetan plateau through what today is osuthern China, giving rise to the offspring clades D1 (M15), D2 (M55) and D3(M47), and ultimately reaching the Japanese archipealgo, where this paternal lineage is represented y the D2(M55) subclade (Xue et al. 2006, Shi, et al. 2008). The mtDNA clades M31 and M32, specific to the Andaman Islands, also suggest a rapid Pleistocene dispersal along the Indian littoral with maritime expansion to the Andamans (Tharanj et al 2005 etc…). By contrast, the fraternal clade E remained principally in Africa, though this lineage also occurs at a very low frequency in western Eurasia as far as east as India and Central Asia.”

      At present, I find Van Driem’s scenario to be the most attractive one, and likely route – perhaps there was a northern D2 migration via northern route into Hokkaido to form the ancestral component of the Ainu population today, and another D-YAP+ eastwards via the Yangtze River and into Southern Japan, since the latter region sees a great deal of O3 subclades, while the north sees none, but is adjacent to the later O2b arrivals. But what are we to make of your African ancestral origined E and its relationship to D and YAP+ in this scheme of things??? I do hope you will enlighten us.

      Can a Pakistan-N.-NE Indian origin for the emergence of the Asian YAP+ absolutely ruled out? See Chandrasekar A et al., YAP insertion signature in South Asia. Ann Hum Biol. 2007 Sep-Oct;34(5):582-6 AND YAP, signature of an African-Middle Eastern migration into India CURRENT SCIENCE, VOL. 88, NO. 12, 25 JUNE 2005 by Suraksha Agrawal et al.“The present study has been envisaged to ascertain the presence of the YAP insertion in various North Indian groups of Brahmins, Bhargavas, Chaturvedis, Kayastha, Rastogis, Vaish, Mathurs, Sunni and Shiya Muslims. YAP+ve lineage has been further analysed for M-145 and M-203 markers, which are equivalent to YAP insertion and M-174 and SRY-4064 markers, to delineate the two different lineages specific to African/Middle East Asian and East Asian/Japanese populations respectively.” A NE Indian YAP origin is not unsupported: See also Thangarai K. et al, Reconstructing the origin of Andaman Islanders as well as the comment which revealed “mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecessor of haplogroup M31 originated on the Indian subcontinent.” and see also Wang HW et al, Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics. 2011 Mar 20;38(3):117-22. Epub 2011 Mar 29

      This has implications for the construction of the Y-chromosome phylogenetic tree. Underhill and Kivilsid’s 2008 phylogenetic tree differed from their 2002 one. The Y-DNA tree was re-arranged (among other reasons) because: “The newly discovered P99 polymorphism that defines the D3 branch occurs in Mainland Asia, specifically in Tibet, the Altai, and Mongolia“. The Japanese D2 according to the tree, would have separated right off the DE parabranch, at the same time of the branching of the Sino-Tibetan Naxi-Di-Qiangic groups (Naxi being the only group without any YAP-lineages) in agreement with Karafet’s tree.

      This could still mean YAP+ arose somewhere very close to between Pakistan and Tibet, Altai and Mongolia??? A West Asian Trans Himalayan DE-YAP+? And one strand doubled back to sub Saharan Africa via Europe? The other continuing on to populate E. Asia?

      The Underhill and Karafet paper is very interesting because at the bottom of its Y-DNA tree, you can see that DE now appears ancestral to YAP and the DE-YAP line falls under Sub-Saharan Africa, while just next to it, the Tibetan D2. There is a discussion with various scenarios in Fig. 8 on the geographic location of CF DE haplogroups and the proposal that they occur inside Africa but migrate to colonize Asia within a very short period of time.

      Would your finding mean that your position would fit best with Underhill-Karafet’s option in Fig. 8c except that M168 should read CDEF instead of CDF?

      Qamar et al., African and Levantine origins of Pakistani YAP+ Y chromosomes

      Bravi, Claudio Origin of the YAP+ lineages of the Y-Chromosome

      Evidence for a Possible Asian Origin of YAP+ Y Chromosomes

      Seo Y, et al., Y chromosome DNA polymorphisms and their haplotypes in a Japanese population

      Karafet and Underhill et al., New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

      Underhill and Kivilsid, Use of Y Chromosome and Mitochondrial DNA
      Population Structure in Tracing Human Migrations

      Shi Hong et al The geographic polyorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan China.

      George Van Driem “East Asian Ethnolinguistic Phylogeography

      Vincent Macaulay et al., “Single, Rapid Coastal Settlement of Asia Revealed by Analysis of Complete Mitochondrial Genomes

      Hisham Yousif Hassan Mohamed Genetic patterns of Y chromosome and mtDNA variation with implications for the Peopling of Sudan

    • What a horrible PDF design: it’s very hard to read. Thanks that it’s short.

      The communication (too little data to call it a “paper”) does not say that E1b was absent in Neolithic Nubia but that A was more common:

      “Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post-Meroitic…”

      It’s a matter of frequency, not of absolute presence. It looks interesting anyhow and I look forward to learn more when a proper study is published.

      The Dinka affinity probably acts as mere proxy, indicating some sort of introgression from the Nile region into early European farmers (which was probably mediated by the Levant).

      “There are many ancestral clades only found in Eurasia, plus the highest frequency of underived E-M96* is found in Saudi Arabia, not in Ethiopia or any other African region”.

      E-M96* is not “underived”: it is a basal paragroup, i.e. a paraphyletic clade “brother” or “brothers” of other parallel haplogroups (E1 and E2 in this case), assuming it has been tested negative for these alternate options (something I do not know, but maybe you do). Same for the other paragroups you mention. It is still interesting and I would like to know more (any good link?) but I do not feel able to accept your claims upfront without one or two proper studies which actually bother sampling Africa properly (commercial DNA companies are not into that, you know).

      In the best case for your claims, it would mean that haplogroup E backmigrated to Africa soon after the preliminary out-of-Africa-to-Arabia migration and somehow managed to become hegemonic in the continent. Some of this no doubt happened (E is way too common compared with mtDNA diversity) but the alleged Near Asian origin is yet to be satisfactorily demonstrated.

      Let’s not forget that, other than two Tibetan individuals (probably pre-D remnants), all DE* we know of is found in Africa (West Africa). This alone weights for an African origin of DE and therefore of E.

  9. Maju wrote,

    “There is no (Y-DNA) D in Europe…”

    This is not exactly correct. Of course, an overwhelming majority of European (and Western Eurasian in general) YAP+ bearers do belong to a few subclades of E1b1b1-M35 (namely E1b1b1a1-M78, E1b1b1b2a-M123, or E1b1b1b1a-M81), but there have been a few cases of D-M174 (mainly in the D1c-P99 clade as far as I can tell) in Europe, mainly in regions influenced by historical migrations of Turkic peoples (e.g. Romania, Crimea). You are certainly correct that no subclade of D-M174 is a primary component of any Western Eurasian population, though.

    There is also an Australian person of mostly European ancestry who has posted on several online forums that he belongs to a highly derived subclade of the typically Japanese D1b-M55. His patrilineage is probably not from Europe, but it does show that D-M174 may appear in some individuals of primarily European ancestry as a result of recent intercontinental migration of individuals or families.

    • Conceded, Junjun. I was no doubt oversimplifying for the sake of clarity. “Recent” arrival of Turkic-vectored D does not change anything of what I said above.

      Actually the most striking Europe-Japan patrilineal link is via former C1/C6, now renamed as C1a (C1a1 and C1a2 respectively), which was sequenced in an Iberian Epipalelithic hunter-gatherer (La Braña 1). C1a is most rare in Europe and rather uncommon in Japan anyhow, making it somehow anecdotal, but at least it has been demonstrated to be of Paleolithic origins in Europe. Its ultimate origins must be from East Asia in any case, where overall C and C1 coalesced almost without any doubt.

  10. “Please help us make sense of and understand the implications of what you are saying in terms of timing and geolocation, and to understand which precedes which – in terms of antiquity, viz. the current theories on the origins of DE-YAP+, D and E hgs. Also as to where your E origin stands in relation to DE, E and the YAP polymorphism in the Phylogenetic Tree.”

    IMO haplogroup DE originated in or around Afghanistan. A part of its carriers migrated eastward and arrived in Tibet, where D originated 50-60 kya. D1 also originated around Tibet (as well as D1a and D1c), but one group of people carried D1 to the Japonese archipelago (where D1b originated 30-40 kya) through Korea. D2, the newly found sub-clade in the Philippines, originated in SE Asia 45-50 kya (IMO the reported Andamanese and SE Asian D* cases are in fact D2). I may not tell if D2 migrated to Australia too, but Hammer et al. 1994 reported a single YAP+ case in an Australian Aboriginal group, so possibly it reached Australia. Another part of the carriers of DE migrated westward and arrived in Syria, where haplogroup E arose 50-55 kya. Haplogroup E migrated both in East Africa (through the Arabian Peninsula) and in Europe together with its sub-clades E1, E1b and pre-E2 (E2 originated in Central-South Africa IMO and was possibly carried by Hofmeyr). Other migrations occurred later and involved E1b2, which migrated in Europe and E1b1, which migrated in East Africa (also through the Arabian Peninsula) where E1b1a (V38) arose. E1b1a2 (M329) originated in northern Tanzania, E1b1a1 (M2)  originated in West Africa. The last major migrations involved E1b1b, E1b1b1 and E1b1b2 (M281). The first originated around modern-day Iraq (one E1b1b* individual was found in Khorasan, but I believe it migrated from westerly areas), and its carriers separated into two groups, one migrating to East Africa, the other back to the Levant. E-M281 originated in Yemen and spread to Ethiopia (present only among Amhara people) and Saudi Arabia recently. The evidence for this is the fact that all E-M281 haplotypes in Ethiopia (Plaster 2011) and Saudi Arabia (E-M35 Phylogenetic Project) are identical, but a Yemeni haplotype differs from them (which form the modal haplotype), therefore it is older. E1b1b1 originated in the Levant 25-30 kya and its carriers migrated to East Africa (where they brought the “Ethio-Somali” autosomal component). E1b1b1-derived sub-clades from this point may or may not in majority have originated in East Africa, North Africa or in the Levant, I do not want to address this complicated issue in this comment.

    • D originated in Tibet? That’s not what the data of Hong Shi 2008 suggests. It is true that Tibetans (ethnic Tibetans, not just from Tibet) hold a strong diversity in D3 and to some extent also in D1 and D*, but the haplotype trees rather suggest Daic / Hmong-Mien cores for these two clades. D2 is of course 100% Japanese/Ainu.

      Overall I would think of a near-Tibet but surely not strictly Tibetan origin of D, rather from what is now South China or maybe even Indochina – awaiting especially for proper sampling of Myanmar, which has shown to hold a dearth of mtDNA diversity in recent studies among refugees, suggesting that they may also hold important Y-DNA clues – all of which makes perfect sense considering the pivotal location of the country. In the particular case of Y-DNA D, Myanmar is surrounded by D-carrying populations, not just to the North and NE but also to the South (Andamanese).

      As for what you say of E, I remain extremely cautious and would like to see a detail of the data that could support those claims.

  11. though again Japanese anthropologists wanna artificially separate Ainu from their Jomon roots; D2 originated from South but not from North it has no traces in North-East Asia; all genetic data should correlate with data of arcaheology, cultural anthropology and linguistics

  12. Heritage of Japan, I have Y Hg O-CTS5492 / O2-M133 (M134?) and mtDNA Hg B4c2. All of my Uniparental Haplogroups were from Southern Central Asia, Y Hg K2-M526 / MNOPS and mtDNA Hg N – R. So my DNA appear to be considered Type 2 East Asians. Majority of Southeast Asian like Western Indonesians / Thai / Vietnamese / (Probably) Burmese and a Southern Chinese, more refered to Fujian, Han Taiwanese, Guangdong, Guangxi, Hongkong, Sichuan”?” and some Provinces in Southeastern China like Zhejiang, etc. Their DNA both their Uniparental Haplogroups and an Autosomal World Regional and their physical appearance “Phenotype” were considered a Type 2 East Asians. At least if they have an ancient ancestors of Y Hg F*-M89 – GHIJK*-M576 – K*-M9 – k2-M526 and mtDNA Hg N and R and it’s subclades.

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