The Genetic Genealogist

AncestryByDNA is a popular genetic test developed by DNAPrint Genomics, Inc. The company offers a variety of genetic testing, including Y-chromosome and mtDNA ancestry. They are most well-known, however, for their two admixture tests. Admixture tests examine SNPs, or single nucleotide polymorphisms, in the 22 autosomal chromosomes in each of our cells. Although every human’s DNA is 99.9% identical, the 0.1% differences make each one of us unique. Researchers have noticed that people in a particular region often have a mutation in common, one that people in most or all other regions of the world do not have. These usually harmless mutations, called SNPs, are believed to have bio-geographic properties – people endogenous to certain regions of the world have different versions of the SNPs. A person who submits his DNA for analysis could have SNPs which reveal genetic contributions from a wide variety of regions.

Admixture tests have many caveats. For instance, inheritance of autosomal DNA is completely random and no test can accurately predict your entire heritage. With every generation an ancestor’s DNA contribution can be passed down in its entirety, in part, or not at all. As well, many scientists are still debating whether or not SNPs have the bio-geographic properties that make admixture tests possible. What if the SNP that is supposedly unique to Native Americans has also developed in a large but undetected European population? The test would misconstrue that SNP as being Native American rather than European.

Despite a number of concerns, admixture tests are becoming increasingly popular and huge resources are being poured into admixture research by a number of different companies. The tests will undoubtedly only increase in popularity and thus become even more accurate and informative. With low-cost genome sequencing just around the corner, this field will explode in the next 5 to 15 years. You can expect to hear much more about admixture tests and genealogy.

The AncestryByDNA 2.5 test examines 175 SNPs (Version 2.0 only offered 71 markers). The test reveals percentages for the following four regions – Native American (North, South, and Central America); European (European, Middle Eastern, and the Indian subcontinent); East Asian (Japanese, Chinese, Korean, Pacific Islander); and African (Sub-Saharan African as well as Nigeria and Congo regions). The results of the test are given as percentages for each group.

AncestryByDNA also offers the EuroDNA 1.0 test. This test, only available to people that have taken the company’s other test and revealed at least 50% European ancestry, uses 145 additional SNPs to delineate European ancestry into four groups – Northern European, Southeastern European, Middle Eastern, and South Asian.

DNAPrint Genomics recently completed a project with five middle school classes at the Laboratory School of Finance and Technology in the Bronx. The project involved analysis of DNA from 11 students and one teacher.

How many founding Asian groups braved their way across the Bering land bridge during those frigid Pleistocene ice ages? Was it a single wave of people who later developed into the three distinct linguistic and cultural groups that populated the Americas, or were there multiple waves of people each with their own language and culture? Or was it some mix of the two? The issue has been and continues to be a topic of debate.

Linguistic studies of the Na-dene, Aleut-Eskimo, and Amerind language groups suggested that there were three waves across the land bridge, one for each language group. Recent genetic research, however, has suggested that there was only a single wave of founding groups into the Americas. (Read a free online review here).

Let’s assume, for the moment, that there was only a single wave of migration into the Americas over the Bering land bridge. The next obvious question might be, who was in that group? Like the previous question, this one can also be addressed with recent advances in genetic research, particularly the use of mitochondrial DNA. The current dogma (which in your opinion may or may not be struck down by today’s article) is that there were 5 founding haplogroups – A, B, C, D, and X. Indeed, the vast majority of Native Americans tested in modern times as well as ALL previous ancient remains have belonged to one of those five haplogroups.

A new study from a group of American and Canadian anthropologists has revealed the existence of sixth founding haplogroup in prehistoric Native Americans. DNA was extracted from the remains of two individuals found together in central British Columbia dated at 4950 +/- 170 years old and the haplogroup was analyzed through sequencing. Both individuals belonged to haplogroup M with the mutations 16093, 16213, and 16223. This is the first time that haplogroup M has been detected in Native American samples, either modern or prehistoric. Importantly, haplogroup M is found in Siberia, the source of the Native American’s ancestors.

What impact does this have on Native American studies? Together this study and another, discussed recently here on this blog, suggest that more than five haplogroups settled the Americas, and within each haplogroup there may have been more than a single haplotype. This could significantly reduce many of the estimates for the timing of the peopling of the Americas.

With the arrival of Black History Month and following on the heels of PBS’s popular series ‘African American Lives’, increasing numbers of African Americans are deciding to explore the world of DNA testing and genetic genealogy. As a result many newspapers and magazines are taking the opportunity to introduce their readers to this increasingly popular avenue of genealogical research.

The Rocky Mountain News in Denver, Colorado is currently three articles into a six-part series examining the role and effect of genetic genealogy in African American research [Thanks to Genealogy Reviews Online]:

Saturday, 17 February 2007 (Two articles, here and here).
Monday, 19 February 2007
Tuesday, 20 February 2007
Wednesday, 21 February 2007
Thursday, 22 February 2007
Friday, 23 February 2007

Fortune Magazine published an article, ‘Tracing African Roots Through DNA’, on February 16^th in which the author uses the DNA testing firm African Ancestry to analyze his mtDNA and Y chromosome. The article also describes the (positive) psychological effects the results have on himself and his family.

Another magazine, Diverse: Issues in Higher Education has an older article, ‘Regaining a Lost Heritage‘. The author of this article also tests her mtDNA through African Ancestry. Interestingly, the author cites Dr. Bruce A. Jackson, Co-director of the African-American DNA Roots Project at the University of Massachusetts Lowell. Dr. Jackson explains his skepticism of African Ancestry’s ability to pinpoint a person’s mtDNA or Y chromosome ancestry to a single ethnic or geographic group because the databases are still so small. African Ancestry, however, contends that their DNA database is 5 times larger than any other comparable databases.

Genealogists interested in researching their Scottish roots will soon have a new resource thanks to a new genealogy center created by the Glasgow Caledonian University in Scotland.  The center will join together traditional genealogical research with recent advances in genetic genealogy to help individuals verify their Scottish roots with DNA testing.  According to the Scottish Tourist Board at VisitScotland.com, more than 50 million people throughout the world can claim Scottish ancestry.

This testing will be done by mouth swab and will be conducted in a new forensics lab built at the University.  The center will use both Y-chromosome and mtDNA results to build their database.  Researchers at the University hope that the center will eventually be able to build a genetic map of the clans of Scotland by looking for markers that are specific for each particular clan.  The test should cost around GBP60 ($120USD), and a number of people have already expressed an interest in the test.

The center will also involve the genealogy company Scottish Roots Ltd. and the 1745 Trading Company, a sales and marketing firm.

[Thanks to UK Family Search]

African Ancestry has had a very good year.  The popular PBS series ‘African American Lives’, which analyzed the African roots of nine famous figures (such as Oprah, Quincy Jones, Whoopi Goldberg, Chris Tucker, and Dr. Sara Lawrence-Lightfoot), used the African Lineage Database developed by the Scientific Director of African Ancestry, Dr. Rick Kittles.  This publicity has resulted in African Ancestry being featured in a wide array of newspaper and magazine articles around the world.

African Ancestry offers two types of DNA analysis, the Matriclan test and the Patriclan test.  The Matriclan test sequences a portion of an individual’s mtDNA to determine whether the ancestry of that lineage is African, European, or other ethnic group.  If the ancestry is African the company will compare the sequence to the African Linage Database.  This exclusive database is African Ancestry’s strongest selling point.  It contains lineages sampled from over 30 countries and 160 ethnic groups in Africa.  The maternal lineage database, for example, contains almost 14,000 samples.

The Patriclan test analyzes nine markers of a male’s Y chromosome (DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS394, and the YAP) and compares the results to the African Lineage Database.  The Database contains almost 12,000 paternal lineages.  African Ancestry is careful to note that 30% of Black paternal lineages tested are of European descent.  If this is the case the company has the resources to compare the results to a worldwide database.

African Ancestry’s African Lineage Database is a fantastic tool to accompany traditional research done by African Americans who typically run into genealogical brick walls due to a paucity of 19^th-century records.  It should be noted that the Matriclan and Patriclan tests are being offered for a special reduced rate as of 17 February 2007.

Researchers have analyzed the (abstract here) HVR1 (hypervariable region 1) of the mtDNA control region belonging to an ancient female skeleton.  The skeleton, approximately 3,600 years old, was discovered in 1980 in a frozen Neolithic grave in northeastern Siberia.

Sequencing of a 377-base pair fragment (16015-16391) revealed three mutations; C16223T, T16298C, and C16327T.  These mutations are characteristic of haplogroup C in Siberian and Asian populations.

A recent study by has characterized an allele that is present in all Native American populations tested. The allele, 9RA (9 repeat-allele) is a 9 tetranucleotide repeat allele composed of 275 bp at autosomal (meaning non-sex chromosome) microsatellite locus D9S1120 (on chromosome 9). Microsatellites are small DNA repeats that are typically neutral and are often used as molecular markers for population studies. According to the report, 9RA was found at an average percentage of roughly 30% among all the populations.

Although 9RA was found among Chukchi and the Koryaks of Western Beringia (on the eastern edge of Siberia), the allele was not identified in the large number of Asian populations tested (perhaps because this is a mutation that arose in populations as they approached the land bridge or because the sample size was not big enough to detect it).

The study has larger implications for migration theory. One of the prevailing migration theories is the three-wave hypothesis which proposes that the Na-Dene, Aleut-Eskimo, and Amerind groups migrated into the Americas in three separate waves. This theory, from Joseph Greenberg, is based on linguistic studies of the three language groups. The ubiquitous presence of the 9RA allele among all three groups suggests that a single founding population contributed a large percentage of ancestry to all Native American populations. That single population was most likely located in the eastern portion of Siberia just before the crossing over the Bering land bridge.

For more information.

Sciona, Inc., a Boulder, Colorado company that sells personalized genetic tests for lifestyle counseling based on an individual’s diet, exercise, lifestyle, and genetic screening, has recently launched the website MyCellf to explore the growing field of nutritional genomics. Nutrigenomics is the study of the interaction between genes and diet.

According to a recent press release, MyCellf is designed to:

“provide a balance between information, customer interaction and commerce for interested consumers and healthcare professionals. The company offers a unique non-medical, lifestyle counseling based on an individual’s diet, exercise and lifestyle history and a confidential genetic screening. By supplying this information direct to consumers through a detailed Action Plan, Sciona is able to guarantee complete privacy and confidentiality to the customer and total individual control of genetic information. The Sciona programs focus on lifestyle and nutritional adjustments to enhance health and longevity.”

Participants order a MyCellf kit by mail and return a DNA swab along with a diet and lifestyle questionnaire. MyCellf uses the swab to test 19 genes that affect diet and lifestyle and then couples that information with the questionnaire to create a confidential and personalized MyCellf Action Plan. According to the website, you can use the MyCellf Action Plan to “make your most important health decisions based not on fad or fashion, but on a personalized scientific roadmap that avoids the one-size-fits-all guide to health”. It is unknown which 19 genes MyCellf tests, but Sciona’s partner Genelex also tests 19 genes, which can be found here.

 

I recently highlighted an article published in the American Journal of Physical Anthropology entitled “Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the America”.

I thought it might be interesting to ask one of the authors, Dr. Brian M. Kemp, his thoughts on the relationship between genetic genealogy and anthropological research, the future of Native American anthropology, and how he entered the field. Dr. Kemp, who is currently doing a post-doc at Vanderbilt University, was kind enough to share some of his valuable time.

Will genetic testing of the public through companies such as Family Tree DNA and Oxford Ancestors have any impact on the study of anthropology?

“Well, it certainly places anthropologists in an important position of helping the general public contextualize the results of such testing. Some of the major issues that have surfaced, and will continue to do so, from the recent fascination of genetic ancestry are those of race, evolution, and identity. These are topics of long-standing interest to anthropologists. It is my hope that the proliferation of genetic ancestry tests will cause the general public to become more interested in anthropology and human evolution in general.”

Is ancient DNA the best source of data for determining the spread of Native American populations into and throughout the Americas? What other sources of information might shed light on the topic?

“No. It is only one piece of a much larger puzzle. Reconstructing prehistory is best done when genetic, linguistic, cultural, and archaeological evidence is all taken into account. However, I think archaeological data will be the most informative in addressing more precisely when humans first entered the Americas. The oldest well-dated human remains in the Americas will place a minimum on the time of entry.”

Do the results of your study suggest that additional founder Native American haplogroups or subhaplogroups might be identified in the future?

“Absolutely. In fact, my colleagues and I have already identified an additional mitochondrial DNA lineage in prehistoric North America in two ~5,000 year old human remains. The report will be published in the Journal of Archaeological Science and is currently available on-line in an advanced electronic form. The early Americans are going to continue to reveal surprises.

Malhi, R. S., B. M. Kemp, J. A. Eshleman, J. Cybulski, D. G. Smith, S. Cousins and H. Harry. In Press. Haplogroup M Discovered in Prehistoric North America.  Journal of Archaeological Science.  Available on-line May 2nd, 2006.”

How did you get interested in the study of Native American mtDNA?

“As an undergraduate at the University of Michigan I took a class in molecular anthropology from Dr. Andrew Merriwether and quickly became fascinated by the fact that really cool genetic methods could be used to study the evolution and prehistory of our species. I was sold. At that point, to the dismay of my parents perhaps, I decided to not become a medical doctor, but rather to pursue the study of anthropology. At that time Dr. Merriwether had an active research program studying mtDNA of South American Indians and I volunteered to help in his lab. There I received my initial training in molecular techniques and one thing led to another and I entered graduate school to continue to study about Native American prehistory and using genetic evidence to reconstruct the past.”

23andMe is a startup company in California that describes themselves as “an early startup developing tools and producing content to help people make sense of their genetic information. Our goal is to take advantage of new genotyping technologies and help consumers explore their genetics, informed by cutting edge science.”

What are the goals of 23andMe? The website claims that a person’s personal genetic information “will provide personal insight into ancestry, genealogy and health. For society, the collection of genotypic and phenotypic information on a large scale will provide scientists with novel avenues for research.” It should also be noted that 23andMe has ‘strong financial backers” and is looking for “talented, motivated individuals in many areas who have a passion for health and technology.”

A database that allows users to store, explore, or share their own genetic code could potentially be extremely useful for both society and the individual. The ability to visually identify and label genes, to compare DNA to identify relationships among people, and to volunteer in genetic research initiatives (if these turn out to be aims of 23andMe) seems both exciting and lucrative. Many predict that within the next 5 to 10 years genome sequencing will be rapid and inexpensive, suggesting that these sort of databases will be needed to help people understand the results of sequencing.

The biggest concern, of course, is security. Keeping a database of genetic information safe would be paramount. Another concern might be the psychological effects of sequencing. What happens if thousands of people sequence their DNA and discover (on their own, without the benefit of a doctor or genetic counselor) that they have an untreatable genetic disorder, or a 50% chance of breast cancer? It will be interesting to see how 23andMe and other companies deal with these possible concerns.

On the website you can sign up to stay updated with new development as the company grows.