Let me start a new thread on han chinese genetics as I think the old ones seem to be much of combinations of the radom posting of the unordered materials.

What is really matter in question is the human population genetics.

We do have roughly three types of the approaches when examining the human population:

(1) Microsatellite/RFLP in loci other than Y-chromosome/mtDNA. An extension of Mendelian genetics. A rather too broad, and generally not useful.

(2) Y-chromosome/mtDNA: Currently most credited study due to larger sample sizes. Non-recombining nature allows the easy analysis, and thus accessible to many genetics novices.

*QTL are usually used. (1) is more prone to Linkage disequilibrium.

(3) Complete genome approaches: Still premature at this stage. Number of population were never more than 300 in each group, thus difficult to make inferences.

Other approaches which are in general more experimental nature, and has low credit from academia include HLA, Loci-homogeniety, random mating (HWP), simulation-based, etc.

In conclusion, (2) is currently most useful. (3) would replace (2) when technological advance allows, but the results of (2) would still be viable.

That is a good point. I think it's hard to disprove you on this one, as you did not touch biologically more important aspects.

mtDNA is arguably non-recombinant. Schwartz and Vissing 2002 showed that this would not be the case, and there are even recombinations between female and male mtDNA. However, this seemingly important finding was easily proven to unaffect the existing population studies.

(1) The slight recombination factor we see is just too small to make impact to existing studies.
(2) clonal assumption does not hold for the human population genetics and methodology

But the male/female ancestry detection by means of mtDNA should be really biological non-sense, because of the possible recombination leakage from female to male, and vice versa.

Y chromosome has a characteristic of passing from father to orphan. It has 78 genes, coding for only 23 distinct proteins. mtDNA codes for 37 genes overall. Genetic studies make use of the non-recombining portion of the Y-chromosome.

I come back to your point that mtDNA is not as reliable as Y. This is correct, as the mutation rate in mtDNA can even be 0.1% in one generation (as a result of shorter nucleotides), which means that in thousand years, we might get the huge biases, which we can usually not tolerate. Y is however only pointing male ancestral relationship, thus we need the mtDNA to find the support for the conclusion from Y.

This is however questioned by the recombination events in mtDNA between male and female. However, the existing mtDNA results should be still a sound indicator comparing to the HLA, loci-homogeneity, RFLP/microsatellites, since the mutation rates in these loci are much higher, and thus even less credible.

If you want, I can post up some materials, which I found on other sites, and I believe that these are documented by some good academic people on the existing literature.

So, on this thread, I should like to post some materials based on Y-chromosomes, and mtDNA.

As a reference, I cite the nomencature system for Y-haplogroup.


Genome Research, Vol. 12, Issue 2, 339-348, February 2002

A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
The Y Chromosome Consortium1


Figure 1 The single most parsimonious tree of 153 haplogroups (left) showing correspondences with prior nomenclatures (right). The root of the tree is denoted with an arrow. Haplogroup names and Y Chromosome Consortium (YCC) sample numbers are given at the tips of the tree, and major clades are labeled with large capital letters and shaded in color (the entire cladogram is designated haplogroup Y). The "*" symbol indicates an internal node on the tree or paragroup (see text). For space reasons, subclade labels are entered to the left of the corresponding links. Mutation names are given along the branches; major clades are labeled with a larger font than are their subclades. The length of each branch is not proportional to the number of mutations or the age of the mutation; each subclade is given a unit of depth in the tree. Some of the branches were elongated artificially to make room for a number of phylogenetically equivalent markers on a single branch. The order of phylogenetically equivalent markers shown on each branch is arbitrary. Prior nomenclatures are named according to author and are taken from the following publications: () Jobling and Tyler-Smith (2000) and Kaladjieva et al. (2001); () Underhill et al. (2000); () Hammer et al. (2001); () Karafet et al. (2001); () Semino et al. (2000); () Su et al. (1999); and () Capelli et al. (2001). Noncontiguous naming systems in prior nomenclatures result either from the use of non-PCR markers that have not been typed on the YCC panel or unpublished lineage definitions. Prior haplogroup names shown in red are found in more than one position in the phylogeny. Cross-hatching within the "Semino" nomenclature indicates lineages that cannot be named according to their system. Mutations M104 and P22 on lineage M2 are independent discoveries of the same polymorphic marker.

Y chromosomal DNA variation in east Asian populations and its potential for inferring the peopling of Korea.

Kim W, Shin DJ, Harihara S, Kim YJ.

Department of Biology, Dankook University, Cheonan, Choong-Nam, Republic of Korea. wookkim@ansco.dankook.ac.kr

We have examined variations of five polymorphic loci (DYS287, DXYS5Y, SRY465, DYS19, and DXYS156Y) on the Y chromosome in samples from a total of 1260 males in eight ethnic groups of East Asia. We found four unique haplotypes constructed from three biallelic markers in these samples of East Asians. The Japanese population was characterized by a relatively high frequency of either the haplotype I-2b (-/Y2/T) or II-1 (+/Y1/C). These dual patterns of the distribution of Y chromosomes (I-2b/II-1) were also found in Korea, although they were present at relatively low frequencies. The haplotype II-1 was present in Northeast Asian populations (Chinese, Japanese, Koreans, and Mongolians) only, except for one male from the Thai population among the Southeast Asian populations (Indonesians, Philippines, Thais, and Vietnamese). The Japanese were revealed to have the highest frequency of this haplotype (27.5%), followed by Koreans (2.9%), Mongolians (2.6%), and mainland Chinese (2.2%). In contrast, the frequency of the haplotype I-2b was found to be 17.1% in the Japanese, 9.5% in Indonesian, 6.3% in Korean, 3.8% in Vietnamese, and 2.7% in Thai samples. These findings suggested that the chromosomes of haplotype I-2b were likely derived from certain areas of Northeast Asia, the region closest to Southeast Asia. Phylogenetic analysis using the neighbor-joining tree also reflected a general distinction between Southeast and Northeast Asian populations. The phylogeny revealed a closer genetic relationship between Japanese and Koreans than to the other surveyed Asian populations. Based on the result of the dual patterns of the haplotype distribution, it is more likely that the population structure of Koreans may not have evolved from a single ancient population derived from Northeast Asians, but through dual infusions of Y chromosomes entering Korea from two different waves of East Asians.

PMID: 10721667 [PubMed - indexed for MEDLINE]


Fig. 2 Distribution of Y haplogroups in east Asia. Circle area is proportional to sample size, and the nine haplogroups are represented by different colors

The distribution of Y-chromosomal variation surveyed here reveals significant genetic differences among east Asian populations. Haplogroup DE-YAP (the YAP+ allele) was present at high frequency only in the Japanese and was rare in other parts of east Asia (Table 2, Fig. 2). This result is consistent with previous findings of YAP+ chromosomes only in populations from Japan and Tibet in east Asia (Hammer and Horai 1995; Hammer et al. 1997; Kim et al. 2000; Tajima at al. 2002). However, haplogroup DE-YAP is also found at low frequencies in all the other northeast Asian populations sampled here (2.4% overall, excluding the Japanese; 9.6%, including the Japanese), but only in two of the southern populations (0.8% overall), suggesting that the Korean YAP+ chromosomes are unlikely to have been derived from a southeast Asian source. The prevalence of the YAP+ allele in central Asian populations suggests a genetic contribution to the east Asian populations from the northwest, probably from central Asia (Altheide and Hammer 1997; Jin and Su 2000; Karafet et al. 2001).

Haplogroups C-RPS4Y711 and K-M9 were widely but not evenly distributed in the east Asian populations. Haplogroup C-RPS4Y711 appears to be the predominant northeast Asian haplogroup, with high frequencies in Mongolians (Buryats, 37.3%; Khalkhs, 42.9%) and Manchurians (22.7%; Table 2, Fig. 2). The moderate frequency of haplogroup C-RPS4Y711 Y-chromosomes in Korea (15.0%) implies a genetic influence from northern populations of east Asia, starting possibly in east Siberia. Su and Jin (2001) suggest that the RPS4Y711-T chromosome originated in east Asia, probably in the southeast, and then expanded to the north (Siberia), based on the genetic diversity of Y-STR markers. However, the observed low Y-STR diversity of haplogroup C-RPS4Y711 chromosomes in their surveys of Siberian and central Asian populations compared with east Asian populations could also be explained by a more northern (Mongolian and/or Siberian) origin followed by genetic drift resulting from small effective population sizes (Pakendorf et al. 2002). Recently, Cavalli-Sforza and Feldman (2003) have suggested that haplogroup C-RPS4Y711 expanded both through a southern route from Africa (e.g., India) to Oceania, and a northern one to Mongolia, Siberia, and eventually to northwest America. Further genetic surveys are required to test these hypotheses, with additional markers and more samples from diverse regions of Asia.
In contrast, M9-G Y-chromosomes show an opposing distribution to those carrying RPS4Y711-T in east Asia: they are more frequent in southern populations than in northern ones, showing a clinal variation from about 90% to 60% (Table 1). The haplogroups carrying the M9-G mutation and additional sublineages of M9-G in Korea appear to be at an intermediate frequency (81.9%) between southeast and northeast Asian populations. This result implies that the Korean population may be influenced by both the northeast and southeast Asian populations. Even within haplogroup O, the most frequent Korean STR haplotype (23-10-13 with the markers DYS390-DYS391-DYS393, 19% of haplogroup O; Table 3) is the most frequent in the Philippines (27%), whereas the second most frequent Korean haplotype (24-10-12, 16%) is the most frequent in Manchuria (45%). Thus, the distribution of haplogroups K-M9 and C-RPS4Y711 may reflect dispersals from both north and south. The settlement of each region at different times needs to be considered in order to understand the peopling of east Asia. Recently, Karafet et al. (2001) have noted that realistic explanations for the peopling of east Asia have to accommodate more complex multidirectional biological and cultural influences than earlier models have allowed.


Fig. 3 Principal components (PC) analysis of haplogroup frequencies in 11 east Asian populations (circle Koreans, open diamonds southeast populations, closed diamonds northeast populations)


In this study, the Koreans appear to be most closely related overall to the Manchurians among east Asian ethnic groups (Fig. 2), although a principal components analysis of haplogroup frequencies reveals that they also cluster with populations from Yunnan and Vietnam (Fig. 3). The genetic relationship with Manchuria is consistent with the historical evidence that the Ancient Chosun, the first state-level society, was established in the region of southern Manchuria and later moved into the Pyongyang area of the northwestern Korean Peninsula. Based on archeological and anthropological data, the early Korean population possibly had a common origin in the northern regions of the Altai Mountains and Lake Baikal of southeastern Siberia (Han 1995; Choi and Rhee 2001). Recent studies of mtDNA (Kivisild et al. 2002) and the Y-chromosome (Karafet et al. 2001) have also indicated that Koreans possess lineages from both the southern and the northern haplogroup complex. In conclusion, the peopling of Korea can be seen as a complex process with an initial northern Asian settlement followed by several migrations, mostly from southern-to-northern China.

The Emerging Limbs and Twigs of the East Asian mtDNA Tree
Toomas Kivisild*, Helle-Viivi Tolk*, Jüri Parik*, Yiming Wang, Surinder S. Papiha, Hans-Jürgen Bandelt and Richard Villems*

*Department of Evolutionary Biology, Tartu University and Estonian Biocentre, Estonia;
Department of Medical Genetics, Sun Yat-Sen University of Medical Sciences, People's Republic of China;
Department of Human Genetics, University of Newcastle-upon-Tyne;
Department of Mathematics, University of Hamburg, Germany

We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control region sequencing or restriction fragment length polymorphism (RFLP) typing. Our results confirm that the East Asian mtDNA pool is locally region-specific and completely covered by the two superhaplogroups M and N. The phylogenetic partitioning based on complete mtDNA sequences corroborates existing RFLP-based classification of Asian mtDNA types and supports the distinction between northern and southern populations. We describe new haplogroups M7, M8, M9, N9, and R9 and demonstrate by way of example that hierarchically subdividing the major branches of the mtDNA tree aids in recognizing the settlement processes of any particular region in appropriate time scale. This is illustrated by the characteristically southern distribution of haplogroup M7 in East Asia, whereas its daughter-groups, M7a and M7b2, specific for Japanese and Korean populations, testify to a presumably (pre-)Jomon contribution to the modern mtDNA pool of Japan.



Fig. 3.—Phylogenetic reconstruction and geographic distribution of haplogroup M7. a, A network of HVS-I haplotypes, which comprises the superposition of the most parsimonious trees for the three postulated sets of M7a, M7b, and M7c sequences. The mutations along the bold links were only analyzed for a few Japanese sequences (Ozawa et al. 1991 ; Ozawa 1995 ; Nishino et al. 1996 ) and—toward the root of M—for some Chinese sequences (this study): the corresponding individuals with (partial) coding region information are boxed. Numbers along links indicate transitions; recurrent HVS-I mutations are underlined. The age of mtDNA clades is calculated (along the tree indicated by unbroken lines) according to Forster et al. (1996) , with standard errors estimated as in Saillard et al. (2000) . Sample codes (and sources): AI—Ainu (Horai et al. 1996 ); CH—Chinese (Betty et al. 1996 ; Nishimaki et al. 1999 ; Qian et al. 2001 ; Yao et al. 2002 ; this study); IN—Indonesian (Redd and Stoneking 1999 ); JP—Japanese (Ozawa et al. 1991 ; Ozawa 1995 ; Horai et al. 1996 ; Nishino et al. 1996 ; Seo et al. 1998 ; Nishimaki et al. 1999 ); KN—Koreans (Horai et al. 1996 ; Lee et al. 1997 ; Pfeiffer et al. 1998 ); MA—Mansi (Derbeneva et al. 2002 ); MJ—Majuro (Sykes et al. 1995 ); MO—Mongolians (Kolman, Sambuughin, and Bermingham 1996 ); PH—Philippines (Sykes et al. 1995 ; Maca-Meyer 2001 ); RY—Ryukyuans (Horai et al. 1996 ); SB—Sabah (Sykes et al. 1995 ); TW—Taiwanese Han (Horai et al. 1996 ) and aboriginals (Melton et al. 1998 ); UI—Uighur (Comas et al. 1998 ; Yao et al. 2000 ); YA—Yakuts (Derenko and Shields 1997 ). b, Frequencies of the subgroups of M7 in Asian populations are inferred from the preceding HVS-I as well as partial HVS-I and RFLP data (VN—Vietnamese: Ballinger et al. 1992 ; Lum et al. 1998 ). Mainland Han Chinese are denoted as follows: GD—Guangdong, LN—Liaoning, QD—Qingdao, WH—Wuhan, XJ—Xinjiang, YU—Yunnan (Yao et al. 2002 ), SH—Shanghai (Nishimaki et al. 1999 ). The number of M7 sequences in relation to the sample size is indicated under each pie slice proportional to the M7 frequency



Fig. 2. Frequency distributions of the eight Y-chromosome haplotypes for the 14 global populations, with their approximate geographic locations. The frequencies of the eight haplotypes are shown as colored pie charts (for color codes, see upper left insert). JP Japanese

Only four Japanese populations exhibited ht1 (defined only by YAP+) at various frequencies (also see Table 1). The highest frequency (87.5%) was found in JP-Ainu, followed by JP-Okinawa (55.6%) living in the southwestern islands of Japan, JP-Honshu (36.6%), and JP-Kyushu (27.9%). The ht2 haplotype (defined by YAP+/M15+) was found in only two males, one each from Thais and Thai-Khmers; ht3 (defined by YAP+/SRY4064-A) was completely absent in the Asian populations examined, whereas Jewish in the Uzbekistan and African populations had this haplotype with a frequency of 28.3% and 100%, respectively. Thus, the YAP+ lineage was found in restricted populations among Asian populations, consistent with previous reports (Hammer and Horai 1995; Hammer et al. 1997; Shinka et al. 1999).

The ht4 haplotype (defined only by M9-G) was widely distributed among north, east, and southeast Asian populations, except for the Ainu. This haplotype was frequent (60.5%) in overall Asian populations (Table 1). Among them, the Han Chinese and southeast Asian populations were characterized by high frequencies ranging from 81.0% to 96.0%. In contrast to ht4, ht5 (defined by M9-G/DYS257108-A) and ht6 (defined by M9-G/DYS257108-A/SRY10831-A) were small contributors to Asian populations. The highest frequency of ht5 was observed in Nivkhi (19.0%) and that of the ht6 in Thai-Khmers (10.8%). The ht5 haplotype is widely distributed among European, Asian, and Native American populations and is proposed to be one of the candidates for founder haplotypes in the Americas (Karafet et al. 1999). Furthermore, high frequencies of ht6 were observed in north Europe, central Asia, and India (Karafet et al. 1999). Thus, the presence of ht5 in Nivkhi may account for the founder effect of peopling of the Americas.

The ht7 haplotype (defined by RPS4Y-T) was also widely distributed throughout Asia with the exceptions of Malaysia and the Philippines, whereas this was absent in two non-Asian populations. The highest frequency of ht7 was found in Buryats (83.6%), followed by Nivkhi (38.1%). Thus, the geographic distribution of ht7 in Asia appears to contrast with that of ht4.

Only eight individuals (1.4%) in Asia belonged to ht8, which was the major haplotype in Jewish population (Table 1). The ht8 haplotype may not be useful for inferring population relatedness among Asian populations because it is defined by no mutations. Additional Y-polymorphic markers such as M89 and M168 (Underhill et al. 2000; Ke et al. 2001) will be needed to investigate details of the formation of modern Asian populations.

Frankly,I am so sick of reading posts on so-called " genetics " crap for East Asian or SE Asian peoples,as it's mainly about COMPLEX ISSUE of some internet junkies with psychological problem.

In real life,very few individuals talk crap about this at all.

How does that response contribute to the topic at hand?

Understanding genetics is difficult for the layman (i.e. me), and it is understandable that people don't ask each other, "why is the YAP+ allele present in Tibetans and Japanese, but not in the Chinese?" while standing in line at the grocery store.

But, though ignorant, I find these mitochondrial DNA comparisons between ethnic populations interesting. They give me an idea of how humans may have migrated, settled, and intermingled with indigineous populations.

And such studies make me wonder, where did those Ainu come from? The ht1 YAP+ allele is isolated to the islands around Japan.

color red, thanks for sharing and keep it up.

I think Ainu was the first settlements around 10000 years in japan before the ancestor of today japan chase them to the hokaiido island and sakhalin island , i think they are not closely related to mongoloid people .

According to the forum I found the above materials, there is a chart showing the distribution of the ainu people.

Courtesy of National Science Museum at Ueno/Shinjuku



Mainstream hypothesis of migrations into the Japanese islands from Sibelia and Korea. Red=Jomon/Ainu (native islanders), Yellow=Yayoi (korean/chinese)



Predicted distribution of Ainu/Jomon Japanese. The red stands for the Ainu ethnicity in modern japanese in molecular levels, and the yellow indicates the yayoi japanese.

Two Y-chromosome-specific polymorphisms 12f2 and
DFFRY in the Japanese population and their relations
to other Y-polymorphisms, Ashraf A Ewis, Juwon Lee, et al



Table 2. Frequency distribution of the polymorphisms of 12f2 and DFFRY gene among males from different populations
considering their Y chromosome compound haplotypes using three (YAP, 47z/StuI, and SRY) biallelic markers.

Michael F. Hammer ﾃ・Tatiana M. Karafet, Hwayong Park et al
Dual origins of the Japanese: common ground for hunter-gatherer
and farmer Y chromosomes



Fig. 2 Maximum-parsimonytree of 44 Y chromosomehaplogroups together with their frequencies in Japan and five Asian regions. Samples sizes for each region: Japan 259; northeast Asia (NEA) 441; Southeast Asia (SEA) 683; central Asia (CAS) 419; south Asia (SAS) 496; Oceania (OCE) 209. Major clades (i.e., C窶迭) are labeled with upper case letters to the left of each clade. Mutation names are given along the branches. The length of each branch is not proportional to the number of mutations or the age of the mutation. Dotted lines indicate internal nodes not defined by downstream markers (i.e., paragroups). The names of the 41 haplogroups observed in the present study are shown to the right of the branches. Haplogroup frequencies are shown on the far right, and frequencies of selected Japanese clades are shown within black boxes.

Y-haplogroup results are clearly most reliable results, so in this thread, I
will mainly post the results on Y-chromosome. Any other studies will enrich
the variability of population, but they will never replace the primary positions
of Y-chromosome based studies. Most charts I found seem to agree well,
and thus, there seems to be scientific consensus on the genetic composition
of east asian people.

I thought mtDNA is preserved from mother to daughters only. If mtDNA do recombine to some extent, what does this tell us? Is there a passage of mtDNA ( nonrecombined ) from father to daugthers as well?

You said Y-chromosome passage has to be confirmed by mtDNA, how do this work? Is there any nonrecombined genes passed from mother to sons?

In Fig 3.

the cluster of Manchurian, Yunnan, Korean, Vietnamese is there because of M175
the Japanese are not in cluster because of DE-YAP
the Buryats and Khalkhs are not in the cluster because of C-RPS4Y

why do you think, O-47z ( red ) is in Korea/Japan/Manchuria and Vietnam/Thai but not in Beijing(Han),Yunnan, Buryats/Khalkhs?

I alway thought Jomon people were Islander ( austroasiatic ) type from southeast asia, ancient migration.

And Ainu was mixture of Jomon and Yayoi.

If they originated from central-asia, they must be related to turks or aryans.. Where does YAP haplogroup originate from?

I can refer to my original sources.

http://content.nejm.org/cgi/content/extract/347/8/576
Paternal Inheritance of Mitochondrial DNA
Marianne Schwartz, Ph.D., and John Vissing, M.D., Ph.D.

http://www.nature.com/hdy/journal/v92/n4/abs/6800413a.html
A reanalysis of the indirect evidence for recombination in human mitochondrial DNA
Piganeau1 and A Eyre-Walker1



Although the strong maternal assumption of mtDNA is doubtful, you can still say that mtDNA can still pass maternal lineage. According to the recent findings which I posted above, recombination might take place, but the observations on the maternal lineages roughly follow the standard non-recombination analysis for the reasons I posted before.

I am taking issues with the low credibility of using mtDNA as an independent source of evidences. My suggestion was that our primary source should be Y-chromosome-based Finding the pathway from mother to son would be interesting, but I doubt the feasibility of doing such analysis. I would say, first find the Y results, and then carefully consider the mtDNA as a secondary result.

You are asking my opinions. If you allow me to take more deductive views, I'd say that there used to be people in greater east asia probably around 10-20kya. Series of migrations in the great flat plains of northern china displaced some of these people carrying O-47z to the north and south, which explains the distribution in the chart.

O-47z is O-haplogroup which suggest the possible mutation events, but I would think highly unlikely as the biggest asian population, han chinese, do not possess despite higher chances of such mutation incidences.

This article looks quiet popular, as it explains great deal about the two hypotheses concerning japanese origin.

http://www.pitt.edu/~annj/courses/notes/jomon_genes.html



Actually, there were some YAP+ carrying populations in south east asia, but as they are early migrant to the east, it does not seem enough to reject the northern hypothesis.

Is O-47z common marker used in pop. gen. analysis for east asia region? or only for this particular study?

based on what you said, we should test Hmong people for this marker, if they are the indeed displaced people.

The links you posted only mentioned about the possiblilities of mtDNA recombining and not being a full prof gen. marker for pop. gen. study purpose. mtDNA can reveal some surprising results.. As one of the article you posted said, some modern japanese carry mtDNA of pre-Jomon period? Before Jomon was pigmy people inhabited vast pacific rims. ( eg. menehuni's of hawaii ).

" testify to a presumably (pre-)Jomon contribution to the modern mtDNA pool of Japan. "

According to the report, the YAP+ marker was newly found to support their hypothesis that Jomon came from else where than southeast asia.

" an addition to the chromosome, the Y Alu polymorphic element, or YAP."

I find this whole report rather politically motivated , as usual Japanese always claim their origins away from Korea/China. If YAP+ marker was not used, Japanese will be in the same cluster as Korea/Vietnam/Yunnan etc in the Fig. 3.

And you failed to answer my question as to where did the YAP+ originated from.. ( nothing originates from central asia, it has to go back to africa )


As I said earlier, genetic study must support archaeology, not the other way around.

"any genetic data must also be reconciled with traditional archaeological evidence "

Haha, of course, because of Yayoi contribution, but if you exclude the YAP+ markers, the studies aren't interesting at all. I doubt about the political motivations, as I can see that the Travis isn't really pro-japanese, or ever intend to become one.



I did not think I got the exact question on the origin of YAP+. But these will obviously trace back to Africa, and then to central asia. YAP+ is fairly prevalent in the west asian population, and in some central asians.



Haha, actually, that's your inner political take, isn't it? anyway, it's a good view, but I beg to differ, in that my interest is not reconstructing the forgotten history, but the contemporary connections between east asian populations, and how we can reverse engineer the evolutionary events.

I thought "circle bracket" means "unsure" rather than the sure conclusion. At least, that's how I and my colleagues read the article. You also need to understand that Kivisid is really good, and has a good tracking record.

Jomon is a population we generally associate with the people living in the islands 10kya, but before that we can only say that pre-Jomon. It's only a definition, nothng special or surprising as you think.

I've seen this guy posting on Japan forums. He actually posted T.V Soong to represent the "typical Chinese face".

Do you have information about a global distribution of this gen. marker?

Yes. I do have a few, but can only give you one reference now.



Origin of YAP+ lineages of the human Y-chromosome
Am J Phys Anthropol. 2000 Jun;112(2):149-58. Related Articles, Links Click here to read Origin of YAP+ lineages of the human Y-chromosome. Bravi CM, Bailliet G, Martinez-Marignac VL, Bianchi NO. Multidisciplinary Institute of Cell Biology (IMBICE), 1900 La Plata, Argentina.

We screened a total of 841 Y-chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested 5 biallelic and 8 polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chronological structuring of ancestral and derived YAP+ lineages, giving rise to 4 haplogroups, 14 subhaplogroups and 60 haplotypes. Moreover, we propose a monophyletic origin for each one of the YAP+ lineages. Out-of-Africa and out-of-Asia models have been suggested to explain the origin
-------------------------------
In this article, only three asian group (japanese, tibetan, jew), african, and a few European have a genetic marker YAP+ on the non-recombining portion of Y-chromosomes. Tibetan (Central Asian): 1 out of 1 sample Japanese: 4 out of 13 samples Chinese: 0 out of 23 samples Laotian: 0 of 7 samples Cambodian: 0 out of 3 samples South East Asians: 0 out of 16 samples South Asians: 0 out of 152 samples West Asians: Jews: 4 out of 18 samples Lebanese: 0 out of 2 samples Syrian: 0 out of 6 samples Melanesian: 0 out of 2 samples African: 37 out of 72 samples European: 3 out of 68 samples

I am amused by the very small size of the samples, and the choice of the groupings which were made... One Tibetan, 2 melanesians, 3 Cambodians, 7 Laotians, 13 Japanese, you can't expect any statistical reliability from such tiny groups... In fact, if you consider that the sampling is random (a hypothesis which could be disputed), the only significant result in this data is the african one.

In my opinion it shows that such studies, interesting as they might be, are still in infancy, using them as proof of the origin of such or such population might be a bit rash.

Francois

This is a predictable choice. This study is about testing the african origin of YAP+ hypothesis against all asian including indian, chinese, south east asian, japanese central asian, so the east asian samples were negligible from the design. The study was also inflexible to reject taking the results of the other studies where thousands of the samples were already tested on YAP+. In a sense, they give a higher priority to eliminate the between-study biases. That sort of decision is often political. In order to secure the funding, you must say that you are going to do different things on even a minor detail, and moreover it's much easier to publish with independent results.



It is really naive to conclude about the whole genetic study from one study particularly when you don't even understand the nature and objective of the study. And that was clear from the title and abstract.

One thing you should know is that the researchers aren't perfect, but they are not stupid either. Please reread at least abstract, and pay a due respect to what was stated in the study rather than making your own assumptions.

Well, you are the one who quoted this story in a thread called "han chinese and east asian genetics". And your quote included this : "In this article, only three asian group (japanese, tibetan, jew), african, and a few European have a genetic marker YAP+ on the non-recombining portion of Y-chromosomes."

I merely commented that from a statistical standpoint, little could be inferred from such small samples, and I believe the people who published these results are quite aware of it. Basically, this is hardly proof. Some might see it as suggestive, but I must say that I tend to trust numbers more than suggestions.

I don't conclude about the whole genetic study, which is probably a promising subject, but then, for what I know, the mechanisms underlying it are still not perfectly known (eg the probabilities of mutations, etc. are still educated guesses). What I am saying is that it is probably a bit early to jump to conclusions and consider these proofs. Also, when I read such stories, I can't help thinking about previous scientific theories about racial differenciations, like the shapes of skulls (remember that one?), which all resulted in publications in respectable journals, but were nonetheless proven inadequate in the long run.

Again, I am not saying scientists are stupid, just that some care is needed when dealing with "new science".

Francois

But what number of samples you are talking about? Drug acceptance test requires about 10000, but each of people are subcategorized into age, sex, smoking habits, choresterol level, previous medical records, races, and so on, then each of the respectable population is about 1000, where the number is not any different from the tests conducted for the other studies of YAP+. We are talking about the consistent drug study where the sufficient statistical power is ensured. We even have placebo, and drug level study, then the number on the tested individuals could go below 500. Do you think that drug assessment is just merely suggesting and medical treatment by drugs are still premature?

Not at all, even though there is a vast body of litterature explaining why some statistical protocols related to drug acceptance tests are inadequate (eg overreliance on parametric tests, like Student or similar statistics, which discard the possibility of "large outliers" in the underlying distribution), these drug test protocols are relatively reliable. First because, as you mentioned, the samples are larger and random. Splitting them into subgroups via a controlled experience plan is part of the statistical theory, it actually improves, not decrease, the reliability of the results. In a nutshell, it incorporates external knowledge, eg placebos, or factors which are known to have influence, like smoking habit, into the test protocol. Note that this is possible because testing a drug is a controlled experiment, whereas detecting some genetic origin is by nature an uncontrolled measurement. Besides, the aim of medical treatment by drugs is to save lives, so there probably is some kind of risk-benefit trade-off at work here. Finally, it often happens that drugs which were thought (proven?) to be efficient, are later found less promising than once thought, or even harmful, once they get "tested in real".

But there is a very big difference between a controlled experience plan of 10 000 persons, and an uncontrolled surveys on a few hundred samples, split into groups of 10 or 50. The problem is twofold. First, the sampling is probably not random, nor controlled, which means that statistical laws hold less well. Second, the samples are below the minimal limits for basic theorems of probability to hold (ie the various forms of the law of large number, convergence of empirical means to expectations, uniform convergence of frequencies to distributions, or convergence of the underlying residuals to a normal law). The sample you presented is not very small in itself, but its splitting into very small groups (of less than 100 persons, and sometimes less than 10), sort of prevent any proper statistics to be done. In general, most statisticians tend to consider that samples of a few hundreds are unsatisfactory, and samples below 50 are hopeless...

My impression is that such isolated cases are good for inducing general hypotheses, which is what the papers you quote probably do. But in order for them to become proof, or evidence, larger samples, and statistical tests are needed.

In all fairness, there are a few theories on induction from small samples (you could search for Vapnik as a starter), but samples are often much larger than a few units (most of these samples are large samples, but with a large number of controlled parametres, a frequent case in medical research), and they are quite complex to design and use (this branch of statistics is in infancy too)

Francois

Outliers are for the quantitative measurements, not a simple measure like allells, or microsattelites. Allowances for the correspondence are usually too broad for any biological random events. Nature of these studies also require the presence or absence of some patterns. Anyway, ask me any questions if you don't understand these, I can explain each in details.

Regarding drug test, you are not surely increasing power by splitting them, as you can clearly see by increasing the degree of freedoms. (I can show you how it works, but please post another thread to discuss)



Weak convergence is sufficient, and as I told you, normality assumption does not need to hold because of the discrete nature of nucleotides. Do you think we need an almost sure sense of random variable? no, we don't even need an estimate of the powers.

Random sampling is not that considered important, as it means less in genome studies. Human genome won't mutate in the same generation, and mutation rate is extremely low for Y-chromosomes. That's why we can even "infer" that human is out of africa, because of the constant behaviours across the samples within the same group.

Not necessarily. You assumption is at the moment on the laws of random variables which you can model. Bootstrapping is just enough in most cases.



You are making assumptions again. You seem to assume that I understand little about the theory which might be true, as has been a while I studied last time, but in reality, all these college stuffs are useless, and mostly statisitcs remains arts rather than a complete beautiful mathematics.

That's why scientist call "scientific evidences". But these are usually good enough estimates, that you might not be aware of.

Hi Color Red,

I changed the order of your paragraphs so as to adress them in a more logical fashion. Sorry about that...



Actually, I think we would agree on this. What I was trying to say is that experience plans are a way to "make the best" out of a certain sample size. Of course, a larger sample is always better than a smaller one, but given a fixed sample size, experience plans provide better test power.


My impression is that random sampling and convergence serve two purposes. First, they even out the possible variance in the data measured. This seems not to be the problem here. But they also act as a guarantee against possible sampling errors. For instance, the above survey tested one tibetan, and a score of japanese. But how do we know they are "typical" tibetan and japanese, once we want to trace back their lineage over tens or hundreds of generations? It seems to me that the only way out of this question is the sample size.

These sampling outliers will have an even larger effect, I think, it the data you observe is stable over time (and you tell me it is). Also, I have the impression that these studies do much more than just testing one hypothesis : they build whole phylogenetic maps, a very complex modelling process, do you think that such sampling errors (even a small number of them) would have no effect?

To me, the out of africa theory is different, because it is supported by a number of studies on large samples.


Well, bootstrapping works because the data is random, else it would reproduce the original biases in the sample... Besides, you can't really bootstrap a very small sample (well, you always can, I suppose, but I don't think it can provide any meaningful result).

I must say I disagree with your point about statistics being an art. It is often used informally, because the underlying theorems which make it work are deep and not well understood, but this informal approach only works when the samples are large enough for the "nice theorems" to set in (and in fact, these theorems do explain why statistics can be seen as an art, ie why informal methods often work, this is the gist of the strong law of large numbers). Which boils down to my original point, sample sizes... can you really infer something on groups of 10 or 50 persons, which are taken as representative of a whole population?

Francois

That's not a problem. Your response has been quiet fast, and I couldn't honestly keep up with your speed, since I have some other things to do. The structure of my reply could be broken down as you wish.



It is of course possible to estimate the power of sample, but experimentalists aren't supposed to increase the power more than they needed it. Surely, there must be a well-planned experimental plan, but that's not as much need as in the case of high variability population. As I will explain below, there will be tiny within population-variability, and even negligible experimental biases in Y-chromosome results, which aren't the case with other studies.



Well, let me take a more didatic approach in giving you the clear problem statement. Until you clearly understands the problem, our discourse never meets on the same grounds. Take the above article for example. We have about 68 for European, 243 for Asian, and 72 for African for each. The sampling number is comparative low where the total sample number usually varies around 1000.

Natural biological assumption is:

(1) Genes within groups will be homogeneous (e.g., Y-chromosome is not disease linked, age independent, only male population allowed)
(2) Mutation rate is extremely low and negligible (Y does not recombine)
(3) Each of our sample has 58 million base pairs (sample points) or less.

For each sample, we have extensive univariate systems. A(1) will rule out the concerns of "typical tibetans". A(2) will eliminate the concerns for the generations.



See Assumption (2) above.

Phylogeny is an independent science, and more of computational mathematics than statistics. It shares the underlying framework with statistics, but the procedures are much different. Modelling schemes are remarkably simple for all the articles I cited in this thread. (Complex modelling are used for the ab initio experiments where you try to fit the models based on limited information and assumptions).



A(3) mentions that we have say the replication of at least 1 million bases. Experimental biases are usually very low when we tests the correspondence of the low mutation rate sequences. Bootstrapping tests are used for the quality checks and to ensure that samples are selected radomly. For your information, some experimentalists use Bayesian arguements for variance reduction by using the simulation scheme, but in my opinion, it's only for the ab initio studies, where you know little about the true responses.



Most usual genetic studies have the total population size of 1000, and these studies devote more shares of the pie to, say, japanese, korean, mongolian, indian, lebanese, etc. Your point of 10-50 persons are least happening in genetic experiments.

LLN is useful for the mathematical modelling, but I see little applications, and i don't think you've discussed enough how that applies to the sampling issues.

Do you have any nice graphs or drawing that explains it? ( pictures are worth thousand words.)

Most interesting aspect of the sample space is that 37 out of 72 africans had this marker. Could you break down further as to what part of Africa the samples came from?

Because, most pop.gen. think that only small part of africans actually made outof africa to populate the globe. I want to make sure that the sample in question came from the same set of africans.

Thanks for your patience, here is what I understand (trying to summarise in case other neophytes, like me, are interested in the subject).

We are looking at the sequence of genes, which are present on the Y chromosome of men. The idea is that one’s version of this chromosome is inherited from one’s father, from which it is a “perfect copy”, because these genes are copied at birth, and very rarely change over time. As such, all male descendents of the same ancestors should have the same Y chromosome, unless a mutation of the gene has occurred, which is very unlikely over short periods of time.

As such, when looking at the genetic patrimony of two individual we can, by focusing on the differences between their Y chromosomes, get an idea of the closeness between them (how far back is their common ancestor).

Better still, and I think this is what you call phylogeny, by looking at a specific differences (ie past mutations), you can draw some kind of “family tree” of groups of people, by classifying them according to the presence in their patrimony of certain specific differences (mutations). I believe this is what is called a “marker”. The idea behind phylogeny is that mutations are so rare, and we have so many genes, that the possibility of the same “marker” happening twice in an unrelated manner is extremely low.

The only aspect which is more difficult is to be able to date these mutations, as it implies the estimation of a very low probability, and slight changes in the estimate can produce big changes in the derived chronology.

So, what is being done in this survey is to test 841 males, of various regions for a specific marker, and see where the marker is more or less prevalent. Right? And the results are as follows.

“In this article, only three asian group (japanese, tibetan, jew), african, and a few European have a genetic marker YAP+ on the non-recombining portion of Y-chromosomes. Tibetan (Central Asian): 1 out of 1 sample Japanese: 4 out of 13 samples Chinese: 0 out of 23 samples Laotian: 0 of 7 samples Cambodian: 0 out of 3 samples South East Asians: 0 out of 16 samples South Asians: 0 out of 152 samples West Asians: Jews: 4 out of 18 samples Lebanese: 0 out of 2 samples Syrian: 0 out of 6 samples Melanesian: 0 out of 2 samples African: 37 out of 72 samples European: 3 out of 68 samples”

A short observation is passing, the results you quote here correspond to a total sample of 383 persons… What happened to the 458 others? (more than half of the sample)

Now, the first thing I’d like to observe is that if the populations were as homogeneous as you seem to say, then the marker would either be present or absent in all a population (except probably in the “original source”) the fact that you can measure something like 4 out of 13 on the Japanese, or 3 out of 68 for Europeans, shows that inside each of these populations, there is some diversity, ie people with and people without the marker.

This creates my first problem: the conclusion says that only three asian groups have the marker
1 tibetan out of 1
4 japanese out of 13
4 Western Asian Jews out of 18

But note that these proportions are very low, on such samples it is impossible to estimate precisely the proportion of this marker (is it really 100% of the Tibetans? Probably not, or just 30% of the Japanese? We don’t know, but it seems unlikely, we just don’t have enough data).

Now is it so certain that the gene is absent from Laotian (0 out of 7), or Cambodians (0 out of 3), it could be because the marker is absent, or because we were unlucky, and just didn't measure the "right person"

Now look at the Europeans, we see 3 out of 68 having the marker, this is an even lower probability, but the result is "the marker is present".

Now note that we have 23 chinese in the sample, none of which have the marker. What if was had asked 68?I think there could quite be a low prevalence of this marker among chinese, in a proportion equivalent to Europeans, or maybe even larger, but that, as the sample is small, it failed to appear. Yet the conclusion will be, the marker is absent in China.

This is where the law of large numbers sets in, it gives probabilities that this is likely or unlikely to happen, but it needs larger samples.

Just as an example, if I aggregate a bit more the information:
Suppose I try to “recut” the sample into Africans, Europeans, Northern Asians and Southern Asians, I get
Africans 37/72
Europeans 3/68
Northern and western Asians (Chinese, Japanese, Tibetans, West Asians) 9/65
South+SouthEast Asians 0/178

I get observations which are slightly less probant. Note though that I didn’t doctor the data, I tried to find groups which are geographically close.

This, in my opinion, is one reason why sampling is important, especially when dealing with relatively rare events (such as the prevalence of this marker), and this is where the law of large number (weak, strong, or uniform) applies.


My second concern is linked to the methodology itself. If I were to take the test, I'd count as French, so far up in my family tree I look, we are all French, and besides, I look very French. The problem is that one of my ancient male ancestors could well not be French, in which case I could have the "wrong" Y marker. But the test would detect this, you might say. Or would it? Suppose only four French were tested, the test might also conclude that this marker is present to some proportion in the French population. My problem is that you cannot use the measured quantity as a way to detect errors in the data. This is strictly equivalent to the outliers one can observe in empirical datasets, which can result from measurement errors, or improbable events. Again, the only solution is to dilute them by increasing sample size.

Finally, a problem can happen if the original sample is biased (ie if the 13 japanese, or the 23 chinese, had some particular characteristic which made the result wrong, like them being less, or more, related (family wise) than they should in a pure random setting. The problem here is with the constitution of the sample. Ask any pollster about it, he'll probably tell you that achieving purely random samples is a daunting tasks, because biases tend to creep in many unexpected fashions, especially when the sample is small. Again, the only solution to this problem is having larger samples.

Now, don't get me wrong, I am not saying that this is not serious, or the researchers don't know what they do. I would even agree that 841 persons is not a bad sample (I've seen worse, believe me!). But I think my original problem remains. The results given here are calculated over 350 persons only, and cut into too many small parts (ie samples of 10, 20, 30…) to make a precise analysis possible.

Francois

Some population has high level of homogenity. eg. tibetan ( testing 1 or 100 gets the same result ).

Also, there pop.gen. field personnel will find the most indigenous people to use as sample, goto small isolated villages and so forth.

We should let color red explain, and present his case .. before questioning the credibilities..

Tibetans are not homogenous, they have a huge variety of looks.

I would like to first comment that there is one thing that you keep repetitively bringing up the same point, which I already eliminated. In this reply, I will highlight my points with bold font so that you can perhaps see what I was trying to say.

(*) This study has a roughly three major groups: Asian, African, European. Rest of the sample population has American, Oceanian, etc. All the minor breakdowns are noted for peer review which has nothing to do with what paper is trying to test.
(*) Other studies I cited are more detail focused. Say only on japanese, and chinese. therefore, do not suffer the similar problems



Well, I appreciate that you recognize the importance of explaining words in simple words.



ok.



I don't know how you get this "marker" idea. But, low variability idea seems ok. You should still discard using phylogeny as it's not used in the study. I'm confused because later, you seem to be using the correct notion of marker.



Not following you. What estimate are you talking about? Again, you are going even farther to say that mere assumptions must be an integral part of phylogeny. But we already ruled out the possibility of using phylogeny, didn't we?



A seemingly correct observation of facts. But if you are interested in diversity research, this should not be a study you focus on. Take korean Y study I posted, if you like to discuss farther.



Again. you are following the wrong assumption on the study, although the division is probably more appropriate than the original study.



I can see how you make use of LLN. Interesting as it may be, you made several wrong description. Phenotype (eg, looks) and genotype (e.g., genes) are two different things. In Y-chromosome study, there is only a genotype. But I honestly think that this is a trivial use of LLN, as, in most studies, we do have sufficient number of samples, and idea of outliers sounds rather artificial.



Study objective is not to conclude about the absence of YAP+ in chinese, that part of work on individual population is reserved for another research which I cited in the first page of this thread.

In summary, this article is not my liking at all. That's why I cited only in response to herousabi's request. I justified the study's perspective, and general philosophy of the researches, but there seems to be better ways to do it. I pointed out that their methods are sufficient for their study and objective, as you rather carelessly criticizes the study.

I don't have a picture for this article. This article is copyrighted, so I can use only author's peer review comments, where the figure comes from. I don't think they divided african into pieces. Their research methods are lumping all asian together, and likewise on other populations.

Anyway, I thought this is just enough to illustrate the general view of the global distributions of YAP+.

With the amount of information provided, I am not convinced. I will hold my original opinion.

End of discussion.

Not quiet sure what you mean though. I posted the article just for an extra reference requested by you.

As long as I have read repository of your previous posts, I do not see much disagreements though. I guess you are seeking korean genome's uniqueness, and that point can be granted with the existing references.

Korean Y-haplogroup is least studied amongst east asian populations. It is quiet easy to note the general distribution of the japanese and chinese, because of the huge sample sizes, but that luxury was not given so far to korean.

Last chance, If you would provide sources for that copy righted article, I will look it up.

either by web link or name the journal.

Well, I thought you ended the conversation. anyway, here is a link to an article, which I already gave when I first cited for your little request. I still don't understand why you asked me this link though.

For your information, if you want to search journal, you only need to go to NCBI web site, and just search the relevant information. This is a common sense to any geneticists, so you better be familiar now.

Origin of YAP+ lineages of the human Y-chromosome
Am J Phys Anthropol. 2000 Jun;112(2):149-58. Related Articles, Links Click here to read Origin of YAP+ lineages of the human Y-chromosome. Bravi CM, Bailliet G, Martinez-Marignac VL, Bianchi NO. Multidisciplinary Institute of Cell Biology (IMBICE), 1900 La Plata, Argentina.

http://www3.interscience.wiley.com/cgi-bin...=1&SRETRY=0

thanks, give me a few days to digest the materials, and I will be back for some questions.

Well, I did some looking into Haplogroup D,E. And D is the east asian marker with YAP. All the resources I read said D is the part of M130 coastal linage. Although D is fragmented and showing up in various places, It was part of the coastal migration when the sea level was much lower and most of the southeast asia including the Philipines, Taiwan were connected to the mainland, and possibly Yellow sea drained. You can see how most of the ancient clues of the D are submerged in water today and showing up in only in a few places.



http://en.wikipedia.org/wiki/Haplogroup_D_%28Y-DNA%29

" The Ainu of Japan and the Jarawa and Onge of the Andaman Islands are notable for possessing almost exclusively Haplogroup D chromosomes "



Haplogroup E with YAP is exclusive to Middle east, and trace to sub-saharan Aftrica origin and delineate from D.

Sketch of Jomon ( Left ) and Yayoi ( Right ) period Japanese

Click to view attachment

Click to view attachment Click to view attachment

Ainu of Japan

It seems that those islanders including japanese must share the most recent common ancestor, and thus studying about them seems worthwhile. I haven't still had a look but I found the article on that. Just please don't expect that I read the article at all.

J Hum Genet. 2006;51(9):800-4. Epub 2006 Aug 19.

Unique origin of Andaman Islanders: insight from autosomal loci.Thangaraj K, Chaubey G, Reddy AG, Singh VK, Singh L.
Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.

Our mtDNA and Y chromosome studies lead to the conclusion that the Andamanese "Negrito" mtDNA lineages have survived in the Andaman Islands in complete genetic isolation from other South and Southeast Asian populations since the initial settlement of the region by the out-of-Africa migration. In order to obtain a robust reconstruction of the evolutionary history of the Andamanese, we carried out a study on the three aboriginal populations, namely, the Great Andamanese, Onge and Nicobarese, using autosomal microsatellite markers. The range of alleles (7-31.2) observed in the studied population and heterozygosity values (0.392-0.857) indicate that the selected STR markers are highly polymorphic in all the three populations, and genetic variability within the populations is significantly high, with a mean gene diversity of 77%. The Andaman "Negrito" populations do not show particular affinities either with the African populations or with the Indian populations, confirming their unique origin. In contrast, Nicobarese show close affinities with the Southeast Asian populations, suggesting their recent entry in the Islands.

I Want to ask ,are Nivki in Sakhalin have any link with japanese or han chinese ,thank you .

it seems to me that the question is whether Yap+ was carried with M130...do the M130 carrying populations also include YAP+?
can these early migrants (carrying Yap+) be traced to those who first migrated north along the East asia coastline... the other question is whether Yap+ in Japan can be traced to Yap+ in Central Asia, which would almost prove northern hypothesis...


Actually, there were some YAP+ carrying populations in south east asia, but as they are early migrant to the east, it does not seem enough to reject the northern hypothesis.
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