89 replies to this topic

[color red]

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.

[color red]

QUOTE(heosuabi @ Oct 20 2006, 10:56 AM)

Also, mtDNA has gene sequence 1,000 times shorter than Y-chromosome. I question its validity of usage especially if it is from an ancient source. ( may be, someone more knowledgable can disprove me and say no.. mtDNA is as good as Y-chromosome ).

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.

Edited by color red, 05 November 2006 - 12:22 PM.

[color red]

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.

Edited by color red, 20 October 2006 - 01:32 PM.

[color red]

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.

Edited by color red, 20 October 2006 - 01:33 PM.

[Publius]

Frankly,I am so sick of reading posts on so-called " genetics " c**p 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 c**p 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.

[galvatron prime]

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 .

[color red]

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.

[color red]

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.

Edited by color red, 20 October 2006 - 10:29 PM.

[color red]

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.

[color red]

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?

I can refer to my original sources.

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

http://www.nature.co...s/6800413a.html
A reanalysis of the indirect evidence for recombination in human mitochondrial DNA
Piganeau1 and A Eyre-Walker1

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?

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.

[color red]

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?

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.

Edited by color red, 21 October 2006 - 07:49 AM.