Workpapers Links

Click on workpapers Links (three bars) top right corner, to toggle links.

Autosomal Test Reveals Ancestry

A Work In Progress by Herbert Holeman, PhD.

Draft Workpaper Posted.

For discussion purposes, my DNA tests and findings are used as examples.

In summary, the work paper findings thus far rely on three types of DNA tests readily available to the public: Autosomal (atDNA), Mitochondrial (mtDNA), and Y-DNA.

Figure 35
DNA Test Types

image from Living Dna


Autosomal atDNA analysis infers your genetic ancestry sorted by geographical origins. It enables the study of biogeographical ancestry in a search for lineage inherited from all your maternal and paternal ancestors. My DNA test providers included the 23andMe Company, the Ancestry Company, the FamilyTreeDNA Company, and the MyHeritage Company, which are among the most popular. Additionally, I included Next Generation Sequencing (NGS), which in this case is Whole Genome Sequencing (WGS). In contrast to Y and mitochondrial DNA tests, whole genome is an autosomal test of chromosomes 1-22 to provide in-depth comprehensive genomic coverage. I tested with the Nebula Genomics Company

Mitochondrial (mtDNA) analysis traces my biogeographical mother-line ancestry to follow the migration path of my Matrilineal ancestors. I tested with the FamilyTree Company.

Y-Chromosome (Y-DNA) analysis provides an in-depth view of paternal ancestry. Its Y-DNA lens views intact copies of Y-DNA that each generation of fathers pass on intact to their sons. I took the full panel O-175 test at YSEQ DNA Company and the NGS Big-Y test at the FamilyTree Company.

My DNA tests and findings are used as examples for purpose of discussion.

• Autosomal testing reveals my ancestry is mostly Asian, following in order by European and Latin American.

• Estimates of my ancestry at the continental level are relatively consistent among DNA companies.

• There are no established guidelines among DNA service providers for the representation of ancestry.

• Deep ancestry reference populations are needed as current sampling is essentially based on present-day populations.

Discussion.

Research to depict my ancestry began with the autosomal (atDNA) test. Findings among companies reached a general consensus of my ancestral admixture at the continental level. However, marked differences exist in their assigning ethnicity to regions within continents. This is not surpising as explained in this video of the limitations in determining anyone person's national ancestry.

Notable difference among DNA test providers, particularly in in assigning ethnicity to surveyed populations, selecting the survey timeframe, and in disproportionate sampling.

As for the accuracy of their ancestry estimates, I concur with genealogist Amy Johnson Crow, "the estimate is good on the continental level. Getting down to the country or region is much more problematic." Anthropological geneticist, Dr. Deborah Bolnick. adds to this view. "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." For example, my autosomal test results:

Figure 36
Ancestry Estimate

Ancestry

As Table 1 reveals, in arriving at my results, the DNA companies were in general consensus in their estimates.

Ancestry

Population Selection

The geographic population boundries selected to survey differ by company. To that point, companies differ in delineating the geographical, political boundaries to calculate the population admixture percentages they assign to test-takers. Arguably, this accounts for much of the variance among the companies. Table 2 is one example of such differences. For Iberia, the 23andMe Company combines the population count of Spain and Portugal, while the Ancestry Company lists the population count individually for Spain, Basque, and Portugal.

Ancestry

Ethnicity Assignment

Ethnic description of surveyed populations differs among companies. Genetic genealogist, Kitty Cooper points out, sometimes East Asian Ancestry is, in reality, American Indian, and South Asian might be Gypsy or Indian from India. Scandinavian might be British or North German, and British and Irish might be Scandinavian.

Note the labels in Table 2 referring to my Iberian ancestry. Speaking of what is meant by the ethnic category Iberia, Bronz says "people who live in Portugal, Spain, France, Morocco, Italy, and Algeria can, and usually do, show strong genetic links to the Iberian Peninsula. People who are native to the Iberian Peninsula DNA region are generally very admixed as well, showing only about 51% Iberian DNA, on average. A person from this region is likely to have DNA from Europe South, Great, Britain, Ireland, North Africa and Europe West, along with others."

Also, in Table 3, note the lavel to report native american ancestry estimate from all four companies. The term Native American, used by 23andMe.com, is the most inclusive. But, for localizing ancestry, it is less definitive both ancestrally and geographically because it encompasses North, Central, and South American ancestry. Most definitive are the labels used by Ancestry.com.

Ancestry

Survey Timeframe

The timeframes when populations are surveyed differ among companies. Companies come at ancestry timeframes from different perspectives. For the most part, the companies 23andme and Ancestry are oriented on recent genealogy, around 500 years ago. In contrast, the XCode Company and FamilyTreeDNA Company strive to give ancestral information deeper than 500 years. Yet, to learn such deep ancestry, geneticist, Razib Khan points out Europeans as we understand them today, genetically did not exist 10,000 years ago. Descriptively, the same applies to South Asia (Afghanistan, India, Pakistan, Bangladesh, Sri Lanka, Nepal, Bhutan, and the Maldives).

A consensus of scientists share khan's view. In his article, Ker Than writes, "such tests 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." Moreover, "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," adds noted geneticist Dr. Adam Rutherford.

Yet, my research interest conversely calls for sampling deep ancestry. It requires a type-population in a given geographical region with a good DNA profile of ancient people. Such a population is one without admixture, a sampling population composed of pure-bloods from the tested region. This is a difficult, if not somewhat unlikely. To build their reference populations, companies must settle on selecting modern people they hop are representative of a place or region

Disproportionate Sampling

In essence, the accuracy of ancestry estimations depends much on the test-taker's admixture. It is a question of how well one's mix of ancestry matches up with the mix of the company's reference population. Company reference populations are not selected in proportion to the global population. People of European Ancestry make up less than 25% of people worldwide. Yet, they represent most of the participants in the genetic research of companies. The makeup of Ancestry.com test-takers is an example as it leans heavily toward British/Australian test takers.

Mark Thomas, professor of evolutionary genetics at University College London adds "The databases are skewed towards different parts of the world, too. The 23andMe Company has more American customers, and AncestryDNA Company has more British and Australian."

These companies have an extensive Eurocentric database but relatively small and limited Asian reference populations for estimating ancestry. Even so, as Figure 38 shows, these companies continue to refine their estimations of ancestry by expanding their reference population databases for global coverage, including Asian populations.

Figure 38
Measuring company databases.
ancestry

Fortunately, there are three companies currently serve the people of Asia, which accounts for ~60% of the world's population. One such company is XCode. It is based in India and claims to cover 23% of the world's population of South Asia heritage. This area includes the 1.75 billion people of Afghanistan, Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka.

Two other companies, WeGene and Zuyan, based in China serve the 1.6 billion people who live in East Asia and make up 38% of the world's population. These are China, Mongolia, North Korea, South Korea, Japan, Hong Kong, Taiwan, and Macau.

These two companies also cover 9% of the world's population who live in Southeast Asia. It includes Brunei, Cambodia, Southern China, Indonesia, Laos, Malaysia, Myanmar, Philippines, Singapore, Thailand, Timor Leste, Vietnam, Christmas Island, Cocos Islands. The WeGene company boasts an extensive Asian reference population database and specializes in the genetic exploration of Asian heritage. WeGene's analytical algorithm uses machine learning based on the Admixture ancestor analysis tool developed by the University of California (UCLA), Los Angeles.

In any case, ancestry estimates will likely differ among companies because their sampling reference differ. Each company relies on its proprietary database for DNA reference sampling. There are no established guidelines for the representation of ancestry.

NEXT
BACK
HOME
Copyright © 2018 Herbert P. Holeman, Ph.D. All Rights Reserved.