X_Chromosome_NA_Haploblock

Genome scans involving approximately 1 Mb (1 million) SNP (single nucleotide polymorphism) markers by decodeme (http://www.decodeme.com) and 550 Kb SNP markers by 23andme (http://www.23andme.com) have provided the opportunity to deploy this data to search for ancestral sequences written on the X chromosome. Since a male only has one X chromosome, and it came from his mother (the father gave the counterpart Y), it will be easier at this time to search its 154 Mb extent to locate ancestrally significant haploblocks of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). In essence a male is little more than a holding vessel (no recombination occurs, only the occasional mutation) until it is passed on to his daughters who then recombine that X with the one from their mother to give what is a changed entity (thanks to the mixing processes of cross-over / recombination), where the original chromosome is changed (sometimes very little, sometimes dramatically) with each meiosis to then pass along the new X (with a largely unpredictable number of sequences from what she was given from her mother and father) to her children.

With a female, with some haploblocks may be shared by both the mother and father and she will be homzygous (e.g., CC GG TT rather than CG etc.) along that sequence of bases. These haploblocks can be located by visual inspection or via the use of Excel formula. Otherwise there is no way to know which allele (e.g., the C or G) came from which parent without very sophisticated programs such as PLINK which can do "phasing" of the sequences to place the correct allele on the correct chromosome with a very high degree of accuracy (using mother - son pairs as a way to validate the approach).

As research into Euopean ancestry accelerates it will soon be possible to answer some of these questions about where in Europe certain haploblocks originated. For the moment it will be easier to search for blocks involving "minority" ancestry (non - European). They may stand out quite dramatically from the rest by only matching East Asians and Native Americans.

The only documented non-European ancestry for the author is found via mother's side of the family. A potential problem is that this ancestor, Catharine (Brant-Hill) Young (both of whose parents were Six Nations Mohawk), is found 8 generations back and only contributed (on paper) 1/256 to the genome. Perhaps the probability of finding this ancestry inscribed on the DNA will be increased by turning to the only chromosome which does not follow "standard rules" of inheritance - the X chromosome.

It would be difficult to impossible to "find" the contribution of one ancestor from 8 generations back without a great deal of luck tossed into the mix. A hint at what might be found can be seen below in the decodeme "Ancestral Origins" snapshot of all chromsomes, showing European (blue), African (green), and East Asian (brown). It should be noted that an unknown part of the ancestry assessment will be "noise" or "false positives". However there is a rather large brown swath which appears to extend across the entire X chromosome suggesting a likely location where Asian sequences may be found. Since there is no Native American category, Asian is a stand in since the literature has confirmed that there are similarities between the two groups which are likely a function of the relatively recent link between the parent stock (East Asia) and an "off shoot" which separated about 15,000 years ago. It is expected that the coalescence time between some Native American groups (e.g., in South America) and other Native American groups (e.g., from the Great Lakes) may differ little from that between the latter group and the descendants of their Asian ancestors. Hence finding East Asian ancestors with a known genetic link to Native Americans, or Native Americans from perhaps South America will essentially be saying the same thing - that the region of the X can be attributed to documented ancestors from Eastern North America.

The genealogical work of the author has shown that most of the true blocks of nucleotide bases attributable to specfic ancestry should be European, with only a small component of Native American. Since neither decodeme nor 23andme are able at this point to differentiate Native American from East Asian, only the latter category is used - hence there will be some degree of underestimation of true Native American ancestry due to failure to "recognize" some sequences from this source. This is particuarly problematic since the Native American reference samples are from the Mexican border (e.g., Pima) into South America (e.g., Surui). There are no reference samples for Native Americans of Eastern North America and so inferences must be made as to whether they are more likely to resemble other Native Americans, or the descendants of the original East Asian and Siberian parent stock. At this point the answer is unknown, except that in virtually all studies using various technologies and approaches, the Yakut of southern Siberia are the closest people genetically to Native Americans.

The inheritance pattern of the X chromosome is like none other. Of 128 potential ancestors to the 7th generation in a male, only 21 will be represented on the X at all. Each potential ancestor made a statistical contribution which may or may not hold true in fact (the range can in theory be from zero to 100%). The question here is whether Catharine (Brant-Hill) Young, my Mohawk ancestor, could be among those 21 ancestors, and based on probability, what percentage she would have contributed. This can be visualized in the fan chart below (thanks to Blaine Bettinger) with myself located in the central blue circle.

In plotting out the various ancestors who fit into the blue (male) and pink (female) spaces, Abraham Young, who would have possessed one of his mother Catharine (Hill) Young's X chromosomes intact is seen in the 9th coloured area down, and his contribution is 1/16 (the percentages range from 1/8 in the first pink space at the top to 1/64 - the bottom most pink area). This means that statistically my Mohawk ancestor made a 6.25% contribution to my X chromosome (a 12.5% contribution to my mother's three brothers where Catharine (Brant-Hill) Young is at the top of the fan chart). Now, bearing this in mind and noticing the large patch of brown (Asian) in the decodeme display, it appears that this region holds the most promise for being the DNA segment given to me by Catharine. It will now be necessary to examine this area in much greater detail.

Method 1 a: In this pursuit I was fortunate to be able to enlist the assistance of Anders Palsen who had perfected the use of various programmes to identify the individuals among the 1045 worldwide from 52 populations who most closely match my marker profile on the X. It turns out that the second largest block (European or otherwise) that matches anyone in this database (HGDP-CEPH panel) is precisely where the brown patch is above, and which is shown in the decodeme browser as being "East Asian". There are various ways to bracket this region for in depth study, but Anders used a programme called PLINK to add my data to the above panel, and to the output.

The analysis for FAUX resulted in 8 exact matches as follows:

1) Palestinian - 6,983 Kb - 101,722,468 to 108,705,215
2) Xibo (China) HGDP01247 - 6,136 Kb - position 80,509,534 to 86,645,097
3) Druze - 5,874 Kb - 103,667,502 to 109,541,859
4) Orcadian - 5,158 Kb - 101,825,740 to 106,984,092
5) French - 5,151 Kb - 103,990,078 to 109,141,445
6) Palestinian - 4,840 Kb - 33,447,147 to 38,287,149
7) Sardinian - 2,933 Kb - 110,630,851 to 113,563,909
8) Russian - 2,624 Kb - 146,802,608 to 149,426,932

The Palestinians and Druze tend to match all Europeans as well as those immediately to the east.

Hence the only "out of place" match for a European would be the Xibo match originating within one of the candidate regions thought to be a point of origin of American native peoples. This Xibo had 9 blocks identified (the bar set at a minimum of 1 Mb and 100 SNPs), and the one he shared with the author was his 4th largest. As noted this is just one of a number of analyses which have all generated the same output with the Xibo as having the largest match. His only other matches are to other East Asian tribes from the same vicinity.

The analysis for XIBO resulted in 9 exact matches as follows:

1) Han - 14,233 Kb - 52,026,252 to 66,264,421
2) Burusho - 9,416 Kb - 75,066,117 to 84,482,293
3) Lahu - 6,670 Kb - 47,780,010 to 54,449,653
4) Faux - 6,136 Kb - 80,509,534 to 86,645,097
5) Miaozu - 4,694 Kb - 102,205,014 to 106,898,943
6) Mongolia - 3,962 Kb - 110,441,491 to 114,403,828
7) Tu - 3,947 Kb - 93,877,273 to 97,823,973
8) Han - 3,796 Kb - 109,768,396 to 113,563,909
9) Daur - 3,230 Kb - 136,195,927 to 139,425,732

Before seeing if there are other matches to East Asians (or anyone) in the same position on the X it will be important to validate the finding with an analysis of how this observation fits into the entire dataset.

Each region on the X may have its own history, and certainly has its own individality in terms for example of likelihood of a recombination event occurring in this area. At 0.60769 cM/Mb this region has a very low probability of experiencing a recombination event that would split it and so is an area that is highly conserved.

Another feature to look at is who else has start and stop positions identical to the Xibo match. While no one in the database shared the end location of the block, a number had the same start or first SNP in the chain of matching markers. Specifically:

Han - Xibo (2) - East Asian
Maya - Karitiana (2) - Native American
Maya - Pima (4) - Native American
Karitiana - Pima (3) - Native American
Pima - Karitiana (2) - Native American
Maya - Maya (3) - Native American
Sururi - Maya - Native American
San - San - African

This would seem to be rather dramatic evidence that any blocks beginning at the above position are vastly more likely to be Native American, but is also found in East Asians (but not Europeans).

Another approach is to create a network diagram of this position (shown as a pink dot below) of the data to others in various populations. The yellow are East Asians and the red is Native Americans - the rest (Africans, Europeans and so on). The first image is a general overview; and the second focuses in on the specific area around the pink dot to show a closer context to see the nearest neighbors.

Some Conclusions: Verification of the East Asian - Native American origin of the "Xibo Block" will come when more aboriginal peoples of the Great Lakes Region are tested using the large number of ancestrally informative SNPs and genome scans available in a cost effective way through chip technology. At this point in time the data appear to be consistent with the hypothesis that the "Xibo Block" represents the DNA contribution of my Mohawk ancestor to my X chromosome. At the theoretical level she "should" have contributed about 6.5% of the chromsome. However considering the evidence that the Mohawks in general and the Green family in particular were already admixed, then perhaps 4% would be a more likely estimate. Curiously the "Xibo Block" at 6.5 Mb of 154 Mb represents 4% of the total. However another way of approaching the analysis is to add the number of nucleotide bases in all 8 blocks and divide the "Xibo Block" by that number to get a percentage of the total. Using this approach the East Asian / Native American block is .1545 or 15% of the total.

A detailed examination of the entire match profile of the complete X chromosome seen here, shows that there is a likely block beginning at the start position of the Xibo Block circa 80 Mb and ending about 102 Mb. If this is correct, then the block may be about 20.2 Mb. There are 4 meioses between the author and the NA ancestor, and since mother - son studies suggest that on average (p and q arms) there are 2 cross - over (recombination events) per meiosis, one might expect blocks in the order of 19.3 Mb. It appears that a block of about 20 Mb is well within the expected range. In addition it is perhaps important to note that this region has a very low probability of recombination in relation to other regions on the X. On study particularly flagged this area (e.g., positions 80 to 90 Mb) as the least likely to experience a recombination event anywhere on this chromosome. Specifically a distance of about 16.8 MB with a 2.7 cM/Mb probability of experiencing a recombination anywhere along this large stretch (0.16 cM/Mb) average at various datapoints (very low).

To test out whether any match even fragmentary could be coaxed into appearing in this area, Anders dropped the match requirement to a mere 500 Kb and 25 SNPs and absolutely nothing appeared in any form. A close inspection of the output of this analysis showed that the only group to show large block structures in the void but at the flanking region of the "Xibo Block" were the Pima. While this may be coincidence it may be suggesting that there is a Native American group that is not represented within the very restricted samples in the HGDP-CEPH database, and perhaps that either the sampling is too restricted among the Xibo to see the few East Asian matches that may be out there. In addition, since there are no reference samples from the Great Lakes Region it may be wondered if the "mystery block" could be found among some of the tribes in this region (a very long way from the nearest HDGP-CEPH sample, the Pima from the Mexican - Arizona border). This may suggest some founder effect. There is a very good precedence for this hypothesis when exploring mtDNA. While most Native Americans are found among "the big four", haplogrops A, B, C or D there is on other group X2a. This has not been found in Asia (although a related branch X2e has), but clusters in the northern Plains States (e.g., North and South Dakota) and the Northern Great Lakes of Canada. There are scattered examples elsewhere but this haplogroup is not found below the middle of the United States (not in South America at all). This situation would seem to offer a close parallel as to what may be the distribution of the author's haploblock extending from about 86 to 102 Mb total.

If the above holds true, this would represent 13% of the X. There does not appear to be any other region which could be expected to yield a significant Native American block. Likely the entire rest of the chromsome includes sequences from the British Isles and Germany (the only other geographical regions represented on the X of the author).

Hence the tentative conclusion is that the haploblock from the Native American ancestor who is 4 recombination events removed from the author is 13% of the total sequences on the X.

Since the author's uncle is one recombination event closer to the Mohawk ancestor (3 recombinations), the 12.5% predicted figure from the fan chart could be more or less than his nephew - chance operating to an unknown degree . However both received the same chromosome from their great grandfather and grandfather respectively. The unknown part relates only to the meioses that would result in a different configuration given to a brother (author's uncle) and sister (author's mother). In theory and fact the uncle may have received an entirely different block than his sister and so not having any Native American on the X; or possibly a different version of the block if it was subject to recombination involving only part of its length; or possibly a much larger block with a considerably higher percentage of Native American. Until testing is accomplished nothing more than speculation is possible. Testing is now in progress.

Certainly, as expected, the percentage of apparent Mohawk DNA heritage written on the X chromosome is considerably higher than that seen on the autosomes. It also appears that the decodeme browser is better able to flag "Asian" areas on the X relative to the autosomes. However it is possible that this is because the match was to a Xibo more closely linked to other East Asians than the Yakut when using their phasing program and the HapMap Japanese and Chinese reference samples.

Future research: We could continue pursing the above findings to see if the profile is found on the X chromosome and autosomes in other family members. Other efforts could include extending the research to the Mohawk communities of Canada to ascertain what haploblocks are common among members of this group. A problem is that extensive admixture has affected the DNA profile in unknown ways. Comparisons could also be made with members of the other Six Nations groups, and other Native American tribes or nations (e.g., Ojibwa) residing in the central and eastern parts of North America.

It is apparent from many academic studies that the autosomes and the X can have their own demographic history and in a sense each tell its own story. The limited evidence seen here suggests the possibility that the X may have had its origin among the tribal groups who resided along the Amur River of Northeast China (Manchuria), and the autosomes may have strong links to the peoples of the Lake Baikal area of Southern Siberia. In other words the genome of the author may reflect at least two migrational events from Eastern Asia to North America. This observation may in turn reflect the fact that by the 1600s the "true" Mohawk were but few in number (thanks to warfare and smallpox epidemics), and that a majority in the tribe had origins within the area frequented by the Mohawks on their raiding expeditions. They were extracting tribute from tribes from the mouth of the St. Lawrence River in the northeast, to the Virginia tidelands in the south to the Great Lakes in the west. There is ample documentation indicating that the Mohawks replaced their losses by adopting individuals from all of these areas. It is very unlikely that there will be a homogeneous set of "Mohawk haploblocks". Instead what can be expected is a tapestry of the genomic structure of the Northeast of North America. It would be very interesting and instructive if perchance the author's data is pointing toward a more multi-dimensional understanding of the genetic heritage of this poorly researched area of the Americas.

Additionally, at the more "micro level" it would be interesting to know the Y chromosome of the kinfolk of Catharine (Brant-Hill) Young. The Brant descendants or relatives of her father, who can be documented, largely seem to have daughtered out (e.g., Young Brant Canadagaia), with the possible exception of the Brants who joined the Wyandots and Senecas in Ohio then Oklahoma; and possibly the Brant family of Delawares from Ft. Hunter and the Bay of Quinte who may be descendants in the male line. Her mother's Hill and Green connections are still to be found at both Grand River and Tyendinaga, Ontario where most with these surnames in the latter location would be direct descendants. The surnames are common at Six Nations but their affiliation to the family of Catharine is less well known due to the wide representation of these surnames among all bands (tribes). It is unfortunate that the mtDNA (mitochondrial, direct maternal line, DNA) lineage of Catharine's daughter died out in the 1800s. Catharine's sister Margaret (Brant-Hill) Cotter, who joined the Wyandots of Anderdon Township Ontario in 1817, had two sons but no known daughters. To complicate matters, at some point in the mid 1800s the entire package of Astawenserontha Bear Clan family names was "loaned" to the Dehennakarineh Bear Clan family and it is unknown at present if they were returned and hence which lineage would connect with those who were Astawenserontha family members in the early 1800s.

The largest "East Asian" block seen again in brown in the diagram below is easily visualized on the X below the centromere separating the chromosome into a p arm (top) and a q arm (bottom). It is on the q arm and can be seen clearly as a yellow colored (East Asian) block on the decodeme browser and bracketed closely to the area approximately between position 79 Mb and 86 Mb, along cytobands Xq21.1 and Xq21.31 seen in the diagram below. This region is situated between well known markers DXS986 and DXS1196.

Only preliminary work has been done to date. Neither of the two companies who do the testing provide in depth analysis to be able to compare a customer's genome to specific individuals in the worldwide HGDP-CEPH panel of 52 populations. It is unclear at this point what specific methodology is used by decodeme, but 23andme only compares an individual to three reference groups - a Utah population (representing northwest Europe), the Yoruba (representing Africa), and a sample of Japanese (representing Asia and North America). Clearly this analysis is going to result in a questionable output, and the blue (European), green (African), and orange (Asian) in their "Ancestry Painting" feature needs to be assessed with caution. At this point they have not yet "painted" the X. In the decodeme browser the Asian ancestry is denoted by yellow blocks, waves or spikes which can be examined "microscopically" to see specifically where the block is located, how large it is, and which SNPs are associated with this region. There is no Native American and one must at this point assume that to find this category one must search for East Asian regions. Excel formula will in essence do the same thing, but with more "surgical precision" as will be seen later.

Anders Palsen assisted the present author in performing two separate analyses of the data from decodeme:

1) Taking the raw data and subjecting it to an analysis by PLINK, a powerful program which allows the use of both males and females from the HDGP-CEPH panel by separating the SNP pairs of females to their respective chromosomes (although it cannot determine whether each is from the father or mother - for this other family members need to be tested). It uses 657 Kb of SNPs (hence only a decodeme scan will provide sufficient data for comparison with this panel). The "bar" is set defining a match between two individuals in the dataset of 1049 persons (with the addition of my data into the mix) as a minimum of 1 Mb and 100 SNPs that are identical (shared). The search was restricted to only East Asian (any population, there are 15 groups designated as East Asian) and Native American (there are 5 groups) exact matches. However all were recorded to ensure that a match is valid. Many groups have some degree of admixture, and it is imperative to focus only on relevant matches. If there are matches to, for example, a Melanesian from the Pacific, or a Cambodian, although both tend to cluster with East Asians, and in the case of the latter are East Asian, the specific match is not a good "fit". In this case the match must include certain key features or it could be considered spurious. Hence it must either be Native American, or an East Asian group that research has shown is among those most closely related to Native Americans.

2) A second analysis was completed using Excel and a formula to locate haploblocks in each reference sample from the HGDP-CEPH panel and those of the person being analyzed. The same parameters as noted above were also used for this inspection of the data. It is a more direct approach.

Before the results of the analyses are described, some background relating to the X chromosome will be needed.

X-CHROMOSOME: Search for Ancestry Via SNP Testing

The first chart above is a STRUCTURE run. The above chart from Wang et al. (2007) shows the genetic proximity of the Yakut to various tribes of the Americas with the closest genetic relationship being between this East Asian (Siberian) group and the Natives of the Canadian central and eastern regions such as the Chipewayan, Cree and Ojibwa - and to a lesser extent to the tribes of Central and South America.

The chart below (Kidd, 2000), using an entirely different methodological approach shows that the same conclusion is reached in relation to the close genetic relationship between the Yakut and tribes such as the Cheyenne (originally from the Great Lakes region), a closeness comparable to that between the Yakut and other East Asian groups.

THE GENETIC RELATIONSHIP BETWEEN THE YAKUT OF SIBERIA (EAST ASIA) AND NATIVE AMERICANS

Method 1 b: In order to ensure that this is not an anomaly, it would make sense that others, likely East Asian, should be exact or almost exact matches to the Xibo. One way to accomplish this is to move the bar a little bit and see who appears. Anders did this with 1,000 Kb and 50 SNPs are the criteria (bar). The result brought into view others who, based on other criteria (see Excel analysis below) "should" be present and accounted for. With this approach the findings of the decodeme browser emerged, for example the 100% African block around the centromere circa 55 to 65 Mb. While an almost identical block appeared for me in Europeans and Middle Easterners, there was one African match of the same size. Thus the validity of this approach seems secure. Hence, in relation to the "Xibo Block", two Yakut with almost identical matches, plus a Hazara (Central Asian) and a Palestinian with "chopped" versions of the block (in different locations) made an appearance. Here are the specific results:

1) Xibo (China) HDGP01247 - 135 SNP markers - 6,136 Mb - position 80,509,534 to 86,645,097
2) Yakut (Siberia) HDGP00957 - 66 SNPs - 4,419 Mb - position 80,063,759 - 84,482,293
3) Yakut (Siberia) HDGP00968 - 72 SNPs - 4,304 MB - position 80,509,534 to 84,813,544
4) Hazara (Central / Southern Asian) HGDP00121 - 66 SNPs - 4,496 Mb - position 79,513,028 to 84,009,392
5) Palestinian HGDP00726 - 94 SNPs - 3,111 Mb - position 83,401,106 to 86,511,650

What is interesting about the latter two matches is that if they are added together they comprise almost the whole "Xibo Block" with some extra on the front flanking region. Anders opined that this may reflect the merging of an original late "Out of Africa" block in Central Asia to form the Xibo Block in both the Xibo and Yakut, progenitor groups to Native Americans. Hence only the latter block moved out of Asia and into the Americas.

It is imperative to demonstrate that the Yakut who approximate the complete Xibo Block have East Asian and, although less likely considering the limited sampling involving mostly South America, Native American matches. Yakut HGDP00968 is described below in relation to the Excel analysis, so here is the information on the matches from the PLINK analysis (1 Mb, 100 SNPs):

The analysis for the Yakut resulted in 73 exact matches as follows:

Yakut = 29
Japanese = 10
Han = 10
Tu = 5
Lahu = 4
Hezhen = 3
Daur = 2
Xibo = 2
Yizu = 2
Mongola = 1
Melanesian = 1
Pima (Native American) = 1
Maya (Native American) = 1

It is evident that all of the numerous matches were to East Asian, primarily Yakut and those from northeastern China. There was one Melanesian (who cluster with East Asians), plus one Pima and one Maya. The latter two Native American matches are to the same two groups which the author matches in the autosomal analysis, and are the only two from north of South America.

Additionally, Anders took the entire output in relation to my X chromosome to display on one page all of my matches by region, by position on the X, and by length. The patterning is extremely instructive and the information has the power to "tell a story" of each position on the X. To view this "whole X" display, click here. Click on the small box that appears in the lower right corner to increase the size and clarity. What is apparent is that at almost the precise point that the Xibo block begins, there is a European match that encompasses a long stretch from that beginning point further down the chromosome. This suggests that perhaps the block received from the Native American ancestor began about position 80 Mb. However in exploring up the chromosome to about position 102 Mb, there is a complete gap. Not even a fragmentary match to any region. Perhaps that is because, due to a founder effect and sampling issues, that there is no one in the database who can fill the gap between these two numbers - but that if Native Americans around the Great Lakes were tested, that perhaps the "gap would be filled". If this is correct then the actual size of the intact block received from Catharine (Brant-Hill) Young was closer to 20.2 Mb.

Method 2: Anders Palsen examined the HDGP-CEPH panel using an Excel formula to identify those matches closest to me in relation to the 672 males. This approximates direct visual inspection. Here follow the results of the highest matches on the author's X chromosome:

1) Xibo (China) HGDP01247 - 364 SNP markers - 6,136 Kb (6.1 Mb) - position 80,509,534 to 86,645,097
2) Yakut (Siberia) HGDP00968 - 307 SNP markers - 4,501 Kb (4.5 Mb) - position 80,509,534 to 85,010,435

Based on this analysis, the match with the Xibo was the largest block on the author's entire X chromosome, and the Yakut match represented the second largest block among the 672 males worldwide in the HGDP-CEPH panel. Comparing all three in terms of the region where there was an exact match for all: Xibo - Yakut - Faux - 4,501 Kb - 80,509,534 to 85,010,435.

It might be asked whether there is a biasing factor related to the relative lack of samples from northwest Europe. Sean MacGorman Powell used the database created by Ben Moscia from complete X data submitted from customers of 23andme and compared himself to others. Although some individuals may have had some level of mixed ancestry, the vast majority of all individuals had ancestry from northwest Europe, particularly the British Isles and Ireland which are not represented in the HDGP-CEPH panel and compared himself to the 22 other males in the dataset. The results of this analysis follow. He set the bar via direct visual inspection as any match of 2 Mb or greater::

1) 2 Mb - 11 matches
2) 3 Mb - 5 matches
3) 4 Mb - 3 matches
4) 5 Mb - 2 matches
5) 6 Mb - 1 match
6) 7 Mb - 0 matches

Hence it would appear that the author's 6 Mb match to the Xibo is in the vanishingly rare category. It should also be noted that the author did not find any European matches in the HDGP-CEPH database greater than 5 Mb.

It is interesting to note the differences obtained via the two methodologies - Excel and PLINK. With Excel the comparisons are direct, and do not involve a "phasing" program to address the problem when both sexes are represented in a database. Females have two X chromosomes and so the phasing procedure must allot each nucleotide base to one or the other chromosome. Although PLINK has an excellent ability to do this, some degree of error will be introduced. It is also interesting that the above Yakut did not show up in the PLINK analysis. However, to ensure that the Yakut did not have European matches, which would have called into question the validity of the finding in relation to the author linking his match to a clear East Asian one, the following findings from PLINK, with the author's PLINK findings from Excel (generally smaller than the PLINK findings), are reported here. Due to the way missing data is handled, the Faux - Yakut match was not seen in the PLINK analysis::

The analysis for the Yakut resulted in 14 exact matches as follows:

1) Yakut - 20,127 Kb - 68,143,456 to 88,280,663
2) Yakut - 14,373 Kb - 96,994,230 to 111,367,654
3) Yakut - 13,642 Kb - 114,939,821 to 128,581,275
4) Yakut - 12,788 Kb - 55,336,563 to 68,124,714
5) Yakut - 4,759 Kb - 33,129,635 to 37,888,713
6) Faux - 4,501 Kb - 80,509,534 to 85,010,435
7) Karitiana (Native American) - 4,333 Kb - 95,270,318 - 99,608,685
8) Yakut - 3,888 Kb - 114,580,118 - 118,468,548
9) Yakut - 3,836 Kb - 107,992,736 to 111,828,710
10) Yakut - 3,630 Kb - 12,717,652 to 16,347,761
11) Yakut - 3,518 Kb - 114,580,118 to 118,098,109
12) Han - 3,332 Kb - 108,429,039 to 111,761,278
13) Yakut - 3,120 Kb - 123,323,504 to 126,443,595
14) Oroquen - 2,641 Kb - 37,994,512 to 40,643,808

The majority of matches for this individual are to other Yakuts, plus two other East Asian groups, one Native American group, and myself. After five large Yakut - Yakut matches, this man then matched myself and the Native American, then four more Yakut - Yakut matches. There are no "out of place" matches whatsoever. East Asian and Native American only. The results are the same as for the analysis for the Xibo noted earlier.

Considering the above findings, they represent the two areas which are believed to have generated the ancestral populations of the Americas:

a) Amur River in northeast China (Manchuria) where the Xibo originate
b) Lake Baikal in southern Siberia where the Yakut originate

As noted above, numerous studies have shown that genetically, the Yakut are the most closely related group in Asia to the aboriginal peoples of the Americas. A close second are the tribes of Northeast China.

The above map on the left illustrates where the archaeological, historical, lingusistic and genetic evidence indicate that the Yakut resided until the Middle Ages, when they migrated from their home on the northwestern shore of Lake Baikal to the northeast (shown in the map to the right, and another immediately below). The Xibo, until a few centuries ago, resided immediately to the east of Lake Baikal in the white area (northern Manchuria, China) which makes a large loop following the River Amur and the border in northeastern China.

The diagram below shows the possible migration routes of the peoples from the Lake Baikal area (ancestors of the Yakut) and Northeast China (ancestors of the Xibo) into the New World via the coastal route and via the inland route which in the earliest Paleolithic days would have involved a passage through the corridor between the Laurentide Glacier to the east and the Cordilleran Glacier to the west. With a futher retreat of both glaciers multiple routes from the north were possible.

Research design and statistical analysis by Anders Palsen. Click here to download full X chromosome analysis.

Ancestral make up of chromosomes according to Decodeme genome scan. Blue = European; Green = African; Brown = Asian

UNIQUE FEATURES OF THE INHERITANCE PATTERN OF THE X CHROMOSOME

SOME HINTS AS TO NON - EUROPEAN ANCESTRY

CHROMOSOME X ANALYSIS

CONCLUDING REMARKS

Below is a map showing there the Xibo resided until recently (the golden-yellow square north of Korea). A study by Powell et al., 2007 confirmed their genetic similarity to those in their ancestral home of Northeast China of a few hundred years ago, and essentially nothing to indicate interbreeding with those in the geographical vicinity where they now reside further west in China. The study by Tian et al., 2008 below shows the a principle component analysis in "A". Here the Xibo (small yellow-golden squares along the PC1 line left of PC2) resemble more closely (cluster with) their former neighbors such as the Oroquen and Daur rather than the Yakut who are shown in the far lower left hand corner reflecting the Central Asian heritage of the Yakut (note proximity to the Mongols (brown triangles); and northern East Asian heritage of the Xibo.

AUTOSOMAL ANALYSIS

As a compliment to the X chromosome analysis, the author has included an exploration of what information is inscribed on the 22 autosomes. Documentary evidence of Native American ancestry, an analysis using the DNAPrint test, and another with decodeme using SNP chip technology can be seen by followng the link below.

The chart below from Wang et al., 2007 illustrates very clearly the significantly stronger genetic relationship of the Native American peoples of North America to the tribes of Northeast Asia (Siberia), relative to those of South America. The northern most group the Chipewayans, from the Canadian Northwest, show about 3/4 genetic similarity to the Siberians. There is a strong north to south gradient with a tapering off of the Siberian relationship as a function of geographical distance from ancient Beringia. Hence the groups from the more southern regions of Canada (Cree, Ojibway) maintain a genetic link that is close to 1/2 sharing with Siberians (but with significant admixture with Europeans hence in the pre - contact era probably above 1/2). The genetic affinity to Siberians has dropped to about 1/3 in the Pima who reside in the Arizona - Mexican border region. The South American groups show zero Siberian linkage. Thus it would be expected that South Americans are perhaps a less adequate proxy for Native Americans of say the Great Lakes region, and that a better group would be the Siberians (which includes the Yakut, Ket, Selkup and tribes that extend into Northeast China).