DNA Consultants Home of the DNA Fingerprint

We received an interesting email from Bailey Edsall-Parr, an anthropology student, customer and genealogy enthusiast from Michigan. We present it here as a guest blog post.

I am currently researching the inter-relatedness of most, if not all, humans alive today. Anyways, I have a personal interest in genetics, mathematics, statistics and probability theory and have incorporated it into my studies. Any information if my theory is in any way "valid" is what I am seeking.  Before I elaborate my theory, here is some background information: According to the Law of Truly Large Numbers... "that with a sample size large enough, any outrageous thing is likely to happen. In a sample of 1000 independent trials, the probability that the event does not happen in any of them is 
or 36.8%. The probability that the event happens at least once in 1000 trials is then 1 − 0.368 = 0.632 or 63.2%. The probability that it happens at least once in 10,000 trials is .

If there were random intermixing, then we would each have ~1 million ancestors living in 1500 AD, out of a world population of ~500 million. So the fractional overlap between two people would be about 1/500th.

But the probability that two people share at least one common ancestor would be essentially 100%.   Basically, you are choosing a random number between 1 and 500 a million times and you're asking whether you ever choose number 500.  In a million trials, we expect this to happen 2000 times.  So that it happens at least once is guaranteed.

If we get rid of the random intermixing, the fractional overlap will drop to much less than 1/500th.  But I suspect that the probability of at least one overlap will remain very high.

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Phyllis Starnes:  Designer Genes

We interviewed Phyllis E. Starnes, assistant investigator, to find out what fascinates her about the field of DNA testing. Her story is the first in a series titled "Behind the Numbers" about the workers behind the scenes in our industry, from lab technicians to statisticians.

Interviewer:  How did you first get interested in DNA?

PES:  I went to the Melungeon Union in Kingsport [Tennessee, in 2002]. Beth Hirschman had her “stalk,” a diagram of her Melungeon family tree with all the names in her genealogy, many of which were also my surnames. I heard Dr. Yates speak at that meeting. They had their lines all pinpointed, thanks to DNA studies.

Interviewer:  What was your next step after that?

PES:  I came home and did a lot of genealogy research on the computer.

Interviewer: And then?

PES:  The first year DNA Consultants opened for business, which was 10 years ago, I ordered a Y chromosome test for my husband Billy. Other companies were offering the same product, but DNA Consultants was the only one to give you a full analysis and customized explanation of things. Then I ordered my own mitochondrial DNA test.

Interviewer:  Any surprises?

PES:  Billy’s top matches for his male line, the Starnes surname line, were Macedonia and Albania. My mitochondrial mutations matched Native Americans. I became the first of the “Anomalous Cherokees” whose female lineages didn’t fit in the traditional scheme of “Indians out of Asia.” In fact, my Hypervariable Region 2 mutations matched only one other sample in the world, and that was Dr. Yates, who is Cherokee in his direct female line.

Interviewer:  What did your husband and the rest of your family think?

PES:  Some were excited, as I was, but most were just not interested. My kids thought the strong Native American matches were very interesting.

Interviewer:  What other family members did you test?

PES:  As soon as autosomal testing arrived, with the DNA Fingerprint Test, I did Billy and myself, of course, Julia, Kiely and Holli (our three daughters), our granddaughter Keely, my Dad’s sister and Mother’s sister, an uncle and his wife, a niece and a cousin.

Interviewer:  What did you find out?

PES:  Within the immediate family, it was obvious who got which ancestry and trait from whom, and how they all resonated. One of the big surprises was my father’s side, which proved to have quite a bit of Native American and Iberian. The “First Peoples” gene came from his side and passed on down through our girls. On my mother’s side, 11 out of 20 matches was India.

Interviewer:   India!?

PES:  Yes, it appears we were finally seeing the extensive Romani/Gypsy heritage in her family. People had always told me I was like a Gypsy, from my clothes and jewelry to my attitude and outlook. When Billy was in the Navy, I told him one day, ‘I’m tired of being a Gypsy.’ I said I wanted to settle down in one place.

Interviewer:  Did you settle down?

PES:  Yes, we’ve lived in a small town in East Tennessee for almost 40 years. We moved here in 1973.

Interviewer:  Any other surprises in your DNA?

PES:  If you were to chart our geographical matches, both in terms of autosomal DNA as well as the female and male lines, it would surround the Mediterranean. That’s where Familial Mediterranean Fever comes in.

Interviewer:  Who has FMF in your family?

PES:  Billy, myself, Julia, Holli and a cousin. I’m sure others have it but it has not been diagnosed and they may call it instead fibromyalgia. Brent Kennedy [author of a book on Melungeons and their genetics] is a cousin many times over.

Interviewer:  What do you enjoy about your job?

PES:  It’s like a holiday every day. With customers coming out of North Carolina or East Tennessee, I see a lot of the same matches and genealogy I have personally encountered in my own experience with DNA testing. I recognize a lot of genetic cousins.

Interviewer:  When did you first hear the word “Melungeon”?

PES:  I grew up in Southwest Virginia in the little town where the Stony Creek Church is located. The church minutes contain the first written instance of the word. The register is all of mine and Billy’s ancestors, and part of Beth’s [Elizabeth Hirschman, author of books on Melungeons].

Interviewer:  What do you see in the future of DNA testing?

PES:  I think we’ve only glimpsed the tip of the iceberg so far, even though it’s been 10 years. We’ll continue to have new knowledge, new products. I highly recommend our customized approach.

Interviewer:  Any parting shots?

PES:  I’ve worked in sales all my life—jewelry management and design, my own interior decorating shop, running my own hair salon—but I have found something to be truly excited about in DNA. Funny I couldn’t get this excited about selling diamonds! If you think about it, your genes are the ultimate design for living.



Donald Yates and Elizabeth Hirschman speaking at Fourth Melungeon Union, Kingsport, Tenn., in June 2002. Hirschman, a professor at Rutgers University, went on to publish Melungeons: The Last Lost Tribe in America. Yates, a professor at Georgia Southern University at the time, founded a service for evaluating DNA reports that became DNA Consultants. The two authors have collaborated on a number of books and articles, including Jews and Muslims in British Colonial America. 

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As often happens in the annals of science, two research teams independently reached the same groundbreaking results, and publication to the scientific world occurred simultaneously. The breakthrough in the present case concerned the mutation rate of DNA and has profound implications for human evolution as well as for DNA Consultants' new offerings in autosomal DNA ancestry analysis, specifically our Rare Genes from History Panel.

The following two studies are already much cited by geneticists, though they have garnered little attention in the press. They appeared in online versions on the same day, August 23.

James X Sun et al., "A Direct Characterization of Human Mutation Based on Microsatellites," Nature Genetics 44/10 (October 2012): 1161-65.

A. Kong et al., "Rate of de novo Mutations and the importance of Father's Age to Disease Risk," Nature 488 (2012):471-75.  

DNA Mutation Rates

 
From this it can be seen that mutation rates vary from a low with SNPs to the high rate of Y chromsome STRs (as much as 0.4 % per generation). DNA keeps surprising us by proving to be more stable than we would tend to expect, dutifully transcribing its original values from generation to generation without many mistakes or changes. Only Y chromosome seems to be highly changeable, depending on the father's age (Kong 2012). Autosomal STRs mutate at a rate between SNPs and the Y chromosome, between every 19,000 or 25,000 and 250,000 years. 

For our new autosomal ancestry markers, that is confirmation that the alleles we are examining on a statistical basis are pretty much unchanged for the past 20,000 years. That's about twice the length of what we call world history, hence a meaningful enough time frame for valid inferences about population patterns and ancestry of individuals.

See also:  Rare Genes from History:  DNA Consultants’ Next-Generation Ancestry Markers

Rare Genes from History Panel Now Available for $289

Prelaunch of New Autosomal Products

Emerging Prehistory of Ethnic Groups

Technical Literature on Genotyping, including autosomal DNA and Forensic Literature

 

DEFINITION:  mutation   A change in a DNA sequence, either spontaneous within a generation or inherited, sometimes from a very distant ancestor. Mutations usually do not affect our health or cause any differences in our appearance. In other words, they are not genes proper and do not “code” for new proteins. Even though they are non-coding genes, though, they are useful in tracing lineages.             From A Glossary of Common DNA Terms

 

Authentic sequences from the ancient human past are a rarity in the world of DNA testing. But when a team of archeologists put the mummies of King Tut and his immediate family on the operating table in 2010, they were successful in deriving almost complete DNA profiles for the boy king and others in the Amarna dynasty that ruled Egypt more than three thousand years ago. Now three of the DNA signatures of Egyptian pharoahs from that famous forensic study by Zahi Hawass and the Supreme Council of Antiquities in Cairo--plus others newly discovered--are available as part of a commercial direct-to-the-consumer autosomal DNA testing panel.

In October 2012, DNA Consultants launched its Rare Genes from History Report. Based on a customer's DNA fingerprint or autosomal profile, the additional analysis sells for $289. It compares your laboratory results with 26 rare alleles or ancestry markers whose trail has been traced through world history and evolving population changes by the company's statisticians. 

Take the Thuya Gene, for instance. Like most of the other Rare Genes from History, it has an African origin in deep time. But it experienced its greatest expansion in ancient Egypt, where it was carried by the queens of Upper and Lower Egypt and High Priestesses of the temples. It was reported in the profile of Queen Thuya's mummy, and we can see that she passed it to her children, grandchildren and descendants. King Tut was a great-grandson and has it, according to the new forensic evidence.

Today, as many as one-fourth of all people on earth would test positive for the Thuya Gene. It is twice as common in Somalia as outside Africa and is found in 40% of Muslim Egyptians.

That's not so rare after all, but unsurprising. Egyptian civilization lasted for three thousand years and sowed the seed of its peoples and ideas throughout the world. We can imagine that Autosomal Thuya started out in East Africa about 100,000 years ago, and that her descendants were prominent in the first out-of-Africa group as well as in the Middle Easterners who helped spread agriculture, animal husbandry, religion and settled town life to Europe. 

The spirit of Thuya lives on in 27% of Jews who have been tested in academic studies. Extrapolating to world population figures, that's nearly 400,000 people, about evenly divided between the United States and Israel.

See also "Prelaunch of New Autosomal Products" (August 26, 2012)
"Rare Genes from History" (webpage)
"Rare Genes from History Panel Now Available for $289.00"

The classic DNA study by the Supreme Council of Antiquities in Cairo, Egypt is: Hawass Z, Gad YZ, Ismail S, et al. Ancestry and Pathology in King Tutankhamun's Family. JAMA. 2010;303(7):638-647. The feat by scientists has also been featured on Discovery Channel. 

PRESS RELEASE
Rare Genes from History:  DNA Consultants’ Next-Generation Ancestry Markers

PHOENIX -- (Oct. 1, 2012) -- DNA typing has gone from successes in the criminal justice system and paternity testing to new heights in mapping genetic diseases and tracing human history. John Butler in the conclusion to his textbook Fundamentals of Forensic DNA Typing raised an important question about these trends. How might genetic genealogy information intersect with forensic DNA testing in the future?

"At DNA Consultants, that new chapter in DNA testing arrived several years ago," said Donald Yates, chief research officer and founder. "As we approach our tenth anniversary, examining human population diversity continues to be the whole thrust of our research, and it just gets more and more exciting."

The company's DNA database atDNA 4.0 captures and puts to use every single published academic study on forensic STR markers, the standard CoDIS markers used in DNA profiles for paternity and personal identification. In 2009, the company introduced the first broad-scale ethnicity markers and created the DNA Fingerprint Plus.

But its innovations didn’t stop there. In October 2012, the company announced the launch of its Rare Genes from History Panel.

Why CoDIS Markers?

“Theoretically,” noted Butler in 2009, “all of the alleles (variations) that exist today for a particular STR locus have resulted from only a few ‘founder’ individuals by slowly changing over tens of thousands of years.”

How true! Hospital studies have determined that the most stable loci (marker addresses on your chromosomes) have values that mutate at a rate of only 0.01%. That means the chance of the value at that location changing from parent to progeny is once every 10,000 generations.

So the autosomal clock of human history ticks at an even slower quantum rate than mitochondrial DNA. Like “mitochondrial Eve,” its patterns were set down in Africa over 100,000 years ago when anatomically modern humans first appeared on the stage of time.

Though the face value of the cards in the deck of human diversity never changed—and all alleles can be traced back to an African origin—as humans left Africa and eventually spread throughout the world, alleles were shuffled and reshuffled. Humanity went through bottlenecks and expansions that emphasized certain alleles over others. Genetic pooling, drift and selection of mates produced regional and country-specific contours much like a geographic map. 

By the twentieth century, when scientists began to assemble the first genetic snapshots of people, it was found that nearly all populations were mixed, some more than others. The geneticist Luigi-Luca Cavalli-Sforza at Stanford University proved that there is almost always more diversity within a population than between populations.

So if there is no such thing as a “pure” population—a control or standard—how are we to make sense of any single individual’s ancestral lines? Statistical analysis provides the answer. And rare genes are easier to trace in the genetic record than common ones. Their distinctive signature stands out.

Back Story:  It All Began with the Melungeons

About the same time as DNA Consultants' scientists were cracking the mystery of the Melungeons, a tri-racial isolate in the Appalachians, they became aware of certain very rare alleles carried by this unusual population in relatively large doses. The Starnes family, for instance, in Harriman, Tennessee, was observed to have a certain rare score repeated on one location in the profiles of members through three generations. The staff dubbed it “the Starnes gene.”

Soon, company research had characterized 26 rare autosomal ancestry markers—tiny, distinctive threads of inheritance that reflected an origin in Africa and expansion and travels through world history. Genes in this new generation of discoveries were named after some distinctive feature associated with the pattern they created in human genetic history--for instance, the Kilimanjaro Gene after its source in Central East Africa. The Thuya, Akhenaten and King Tut genes were named for the royal family of Egypt whose mummies were investigated by Zahi Hawass’ team in 2010.

The Starnes Gene” became the Helen Gene. Because of its apparent center in Troy in ancient Asia Minor and predilection for settling in island populations, it was named for "the face that launched a thousand ships," in the famous phrase by Christopher Marlowe.  

All 26 of DNA Consultants' new markers are rare. Not everyone is going to have one. But that’s what makes them interesting, according to Dr. Yates.

Coming from all sections of human diversity—African, Indian, Asian and Native American—they are like tiny gold filaments in a huge, outspread multi-colored tapestry, explains Phyllis Starnes, assistant principal investigator and wife of the namesake of the first discovery. But does that mean that her husband has a connection to Helen of Troy? The markers don’t work on such a literal level, but it does imply that Billy Starnes shares a part of his ancestral heritage with an ancient Greek/Turkish population prominent on the page of history.

Over the past two decades, geneticists have worked out the macro-history and chronology of human migrations in amazing detail and agreement. The Rare Genes from History Panel is another reminder--in the words of an American Indian ceremonial greeting--that “We Are All Related.”

These rare but robust signals of deep history can act as powerful ancestral probes into the tangled past of the human race as well as unique touchstones for the surprising stories of individuals.

For more information about the science of autosomal DNA ancestry testing, visit DNA Consultants or check out its Twitter or Facebook page. 

The dictionary defines "megapopulation" as a very large one, from the Greek suffix mega, the same element as in "megabyte." In statistics, a population is the whole field from which you choose a sample or representative segment. Thus, to test American Hispanic/Latinos you might draw a sample of 400 people from a predefined population of everyone with a Hispanic surname in a telephone book.

How reliable and valid your sample is depends on methodology. By combining populations you can study a metapopulation (all related populations, for instance North and South American Latin or Iberian populations) or megapopulation (all populations with Iberian ancestry in the world).

Going from the small to the large, we  have then:

Individual

Sample

Population

Metapopulation

Megapopulation

Universe

Arizona Hispanic study (n=104, that is 104 persons in the sample)

U.S. Hispanics

North American Hispanic

Iberian American

Iberian or Part-Iberians in the World

Megapopulation Names

and number of populations included

African 17

African American 28

American Indian 24

Australoid 3

Austronesian 6

Central Asian 39

Central European 13

East Asian 39

East European 8

European American 24

Iberian 32

Iberian American 61

Jewish 3

Mediterranean European 20

Melungeon 1

Middle Eastern 36

North Asian 3

Northern European 15

Romani 4

South Asian 35

Southeast Asian 12

Beyond Megapopulations (and percentage of total populations) These categories correspond roughly to what people used to think of as "race," a now-discredited notion. They are continent-specific, with African and Caucasian extended to North and South American African and European populations.

African   45     11%  

Amerind   24    6%

Austral 9    2%

Asian  67    17%

Caucasian  255    64%

Another Calculation We created these totals to see what kind of white versus non-white coverage the database has.

White  255  64%

Non-White  145   36%

30-Nov-2011
After a lot of hard work, DNA Consultants has introduced "bottom l... (more)

New Megapopulations: The Bottom Line
17-Nov-2011
Work by our head of statistics over the summer has made it possible to... (more)