USING AUTOSOMAL TESTING FOR ANCESTRY
Chromosomes, Haplogroups, and Markers


In autosomal testing, each company relies on its proprietary database of reference populations on which to base its findings of ancestry so my raw DNA data file from a given test provider is not a record of my entire genome. It lacks certain genetic markers and only covers those relevant for the company's algorithms. Moreover, my biogeographical admixture is not 100% accurate because of the test provider's use of imputation to estimate missing genotype information. Imputation is a process by which gaps in one's genome which weren't sequenced can be inferred. As a result, some of my ancestry calculations could be skewed and vary from company to company.

To compensate for this, the pie chart in Figure 1 reflects Next Generation Sequencing (NGS) technology to read out my entire human genome. This process is referred to as Whole Genome Sequencing. The table reports the autosomal test results from Nebula Lab's whole genome sequencing, which covers ~ 1.3 billion sequenced bases out of ~ 3 billion base pairs in the human genome and is 99% accurate and results in one thousand times more data than tests that use microarray-based genotyping. The Nebula test enables imputation (prediction) of unsequenced positions with an accuracy that is sufficiently high for most use cases. "In comparison, such labs as 23andMe and AncestryDNA, which use microarray-based genotyping that reads the human genome at only ~500,000 positions" in comparison to the 0.4x coverage (~ 1.3 billion positions) by Nebula Genomics. Additionally, unlike DNA microarrays, low-coverage WGS can discover novel genetic variants and it produces more accurate results for those with no or little European ancestry.

Figure 2
My Ethic Genetic Ancestry
Nebula Whole Genome Sequencing

Ancestry

Figure 2 depicts my genetic ancestry at the continental level, which is generally considered to be reliable. Beyond that, there are limitations. According to genetic genealogist Blaine Bettinger, "the ethnicity estimate is good on the continent level; getting down to the country or region is much more problematic." And, writing in Live Science, Ker Than adds, "Such tests also cannot account for recent migrations of peoples from their ancient homelands. "Present-day patterns of residence are rarely identical to what existed in the past, and social groups have changed over time, in name and composition." Noted geneticist, Adam Rutherford, recently wrote in the prestigious magazine, Scientific American, "For deeper family roots, these tests do not really tell you where your ancestors came from. They say where DNA like yours can be found on Earth today. By inference, we are to assume that significant proportions of our deep family came from those places. But to say that you are 20 percent Irish, 4 percent Native American or 12 percent Scandinavian is fun, trivial and has very little scientific meaning."

As for genealogical ethnicity, Roberta Estes: adds, "I've said this before, and I want to say it again. Ethnicity is the least precise and the least accurate of DNA tools for genetic genealogy. Ethnicity estimates are the most accurate at a continental level. Within continents, like Europe, Asia and Africa, there has been a lot of population movement and intermixing over time making the term “ethnicity” almost meaningless."

In his article inScience on popular DNA testing, Ker Than asserts "Such tests also cannot account for recent migrations of peoples from their ancient homelands."Present-day patterns of residence are rarely identical to what existed in the past, and social groups have changedover time, in name and composition," However, "If a test-taker is just interested in finding out where there are some people in the world that share the same DNA as them, then these tests can certainly tell them that," says noted Anthropology professor, Deborah Bolnick.

So, with these words in mind, I acknowledge my genetic ancestral findings as broadly accurate at the continental level. Yet, to find out where there are some people in the world with whom I share the same DNA, Table 1 presents these findings.

Table 1
My Biogeographic Ancestry
Nebula Whole Genome Sequencing

Ancestry

Given Asian DNA represents the largest percent of my admixture, I pursued autosomal findings from different test providers to yield a more definitive consensus of my Asian ancestry.

Figure 3
My Asian DNA



Figure 3 and Table 2 below show my Asian Ancestry as the result of DNA tests conducted by 23andMe, Ancestry, DNA.Land, DNA Tribes, Family Tree DNA, Gencove, My Heritage, WeGene, and Xcode.Life. Also included is the finding of the Zuyuan DNA Lab, which captures 60% more DNA markers than do such labs as 23andMe and AncestryDNA for ethnic Chinese.

Table 1
My Autosomal DNA Tests Results for Asian Ancestry

23andMe
49%
Ancestry.Com
49%
DNA Land
48%
DNA Tribes
54%
Ethnogene
50%
FTDNA
48%
GENCOVE
50%
My Heritage
49%
Nebula
53%
WeGene
47%
Xcode
51%
AVG
49%

Chromosome Painting

Chromosome painting is one means by which autosomal testing provides a way of looking at ancestry. The Chromosomes Painting in Figure 1 is a view of my ancestry composition. Its 46 chromosomes are passed between generations in the form of 23 pairs. My interest is with the first 22 because they represent ancestries I match. They are called autosomes and come in pairs of two, each represented by one of the colored horizontal lines.

Figure 4
My Chromosomes Shown in Color by Ancestry

Chromosome Painting

The horizontal lines are colored to reflect the geographical origin of my ancestry at the continental level with a reportedly probability level of confidence of 90 percent. My Chromosome painting is multi-colored, revealing an admixture of genetic mixing of different populations. The horizontal line shown in yellow is primarily Asian (Chinese & Southeast Asian 45.6%) and the blue is European (23%), both of which colors make up the greater bulk my ancestral heritage. This gives rise to the question whether my ancestors admixture started recently or generations ago.

The long, unbroken stretches of color are evidence of recent ancestry, while the short segments suggest those of many generations ago. Recent sources of ancestry will have segments of that ancestry on more chromosomes. Moreover, those segments will be longer than of my ancestors of many generations ago. Of course, a major limitation is that test providers, such as 23andMe, base test their results on different databases and, as a result, may not be consistent from one provider to another.

My genetic markers identified through autosomal testing also uncover my ethnic ancestry by haplogroup. A haplogroup makes it possible to group populations with the same marker by geographical point of origin and "Admixture analysis. more properly known as biogeographical ancestry analysis). It is a method of inferring someone's geographical origins based on an analysis of their combined maternal and paternal genetic ancestry."

Roberta Estes is a good resource for how the DNAPainter can be used for various purposes.

Haplogroups

Haplogroups categorize ancestral heritage. A given haplogroup is a genetic population group of people who share a common ancestor. Thus, its conceptual structure is based on the assertion, "All people alive today belong to distinct haplogroups of people belonging to the same haplogroup and can trace their descent to a common ancestor and even a specific place where that ancestor may have lived."

In my case, DNA autosomal tests place my genetic ancestry maternally in Haplogroup B and paternally in Haplogroup O, both which originated in what is present day China.

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