DNA Consultants Home of the DNA Fingerprint

Maybe If It's First Generation Sex-Linked Testing, Not Autosomal 

Dust off the crystal ball. Scientists consider DNA ancestry services “genetic astrology,” according to a recent BBC article by Pallab Ghosh. In “Some DNA Ancestry Services Akin to ‘Genetic Astrology’,” Ghosh quotes Professor David Balding as maintaining that ‘“such histories are either so general as to be personally meaningless or they are just speculation from thin evidence.’” One article, “Don’t Believe the Guy Who Claims He’s Descended From Vikings,” quotes evolutionary geneticist Mark Thomas, as saying “these tests have so little rigor that they are better thought of as genetic astrology.”  That may be right about some tests. But the key word is “some.”

Not all DNA ancestry tests or companies are created equal.  It is as much an oversimplification to suggest they are as it would be to claim that all lab tests are the same or all pharmaceutical drugs are the same. Do you get a shot for epilepsy when you have diabetes? Hardly. There are DNA tests and there are DNA tests. Customers are generally careful to get  the right medicine from a reputable doctor. A customer needs to be just as careful choosing a DNA test and a DNA ancestry company. Not all DNA ancestry companies, even some of the larger companies, have an ISO certified lab, for instance. This not only guarantees the reliability of results, it is also the highest standard in the genomics industry. A few have this laboratory benchmark, but it is, unfortunately, not required, in direct- to-the-consumer DNA testing. Would you want to entrust your genetic identity with anything less? The buyer needs to be aware that with non-certified labs there is a stronger possibility of contamination or lost or swapped samples. I know someone who was the unknown victim of a sample swapped. He thought he was someone else for two years.

Secondly, there are a variety of tests to choose from. There are sex-linked tests (Y chromosome, X chromosome- mitochondrial) and non-sex linked tests called autosomal. The sex-linked tests are haplotype tests based on genetic markers handed down by the male (Y chromosome, received only by other males) or female (mitochondrial). The industry started out with sex-linked testing, but its limitations dictated a move increasingly to autosomal or non-sex linked testing. There are weaknesses with sex-linked tests.

The mitochondrial genome is small compared with the nuclear genome according to the article “Mitochondrial Genome Analysis with Haplotyping” which means there cannot be that much variation with mitochondrial DNA analysis. For instance, some have expressed doubts that the recently found Leicester skeleton could be Richard III because of the mitochondrial DNA analysis that was done. Live Science writer, Stephanie Pappas, quoted Maria Avila, a computational biologist at the Center for GeoGenetics at the [British] Natural History Museum as saying “people could share mitochondrial DNA even if they don’t share a family tree” (Pappas).  

How is this possible? Mitochondrial DNA is ancient DNA and mutates slowly.  In the article, “Doubts Remain that the Leicester Body is Richard III,” a Mark Thomas at University College London is quoted as saying that “people can have matching mitochondrial DNA by chance and not be related.” So, it might not be Richard III after all. Male line haplotype testing has different limitations. “The Male Y- linked tests have very rapid mutation rates and are very fragile, so you can get a lot of errors with that type of testing,” according to Dr. Donald N.Yates, head of Research and Development for DNA Spectrum.

According to a recent New Scientist article by Colin Baras, “The Father of All Men Is 340,000 Years Old,” the Y chromosome seems more ancient than previously thought. If so, it is also less stable than we thought. Brian Sykes, Professor of Genetics at Oxford University and the author of The Seven Daughters of Eve, makes a strong argument that the Y chromosome is weakening and in trouble in his book, Adam’s Curse. He says it is “doomed to a slow and humiliating decline” (279) because of its instability and rapid genetic mutation and is thus headed toward extinction. Before the 1990’s paternity testing was based on Y chromosome comparisons and limited to fathers and sons. Sometimes, an uncle would be mistaken as the father. Today, it relies on autosomal DNA comparisons, can be applied to females, and is 99.99% accurate.

But then there are non-sex-linked Autosomal DNA tests which are based on a different science altogether. Anyone can take this traditional type of Autosomal DNA test because it does not rely on X or Y chromosomes (women are unable to take the Male Y- linked test and must entice a male in her line, if one is available, to take this test). This test is not testing ancient DNA but  goes back only some four or five generations, so it does not have these limitations. And it provides a complete analysis of all ancestral lines. Not just one line at a time as in haplotype testing. This is next generation ancestry DNA testing and the wave of the future. Moreover, this type of testing is more stable and has more scientific validity as it uses the same science that is used in the legal court system, by the government, and on CSI comparing loci markers to population databases. And two research teams independently reached the same groundbreaking results that the DNA mutation rate is slower than previously thought:  James X Sun et al., in the article, "A Direct Characterization of Human Mutation Based on Microsatellites," in Nature Genetics 44/10 (October 2012):1161-65, and A. Kong et al., in the article "Rate of de novoMutations and the importance of Father's Age to Disease Risk," in Nature 488 (2012):471-75. All done by the magic of math and laws of large numbers.

What does this mean concerning autosomal DNA ancestry tests? They have even more scientific validity. This second-generation type of DNA ancestry testing is based on these same genetic markers, and that is confirmation that the alleles on your DNA that are examined using a statistical basis have been relatively 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. These are markers that everyone has (and why anyone can take an autosomal ancestry test).  These genetic markers change at a much slower rate than the Y chromosome which seems to be highly changeable, depending on the father’s age (Kong 201). (The Y chromosome is a marker only males have. It is used for other types of tests: male, haplotype, sex-linked DNA tests. Only males can take these tests, and it only provides information about that one male line).

Of course, anything can be over-interpreted. DNA testing is not magic. Maybe you should put that crystal ball up after all.

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 Gypsies, or Roma, or Romani (so called because of their concentration in Romania) are a far-flung distinctive population with a lot of diversity. In our database, we have samples of four Gypsy populations, plus samples for Romania, Macedonia and Hungary which you can match if you have even a small degree of Gypsy/Romani.

Gypsy DNA can sometimes be conflated or confused with Jewish DNA because both populations originated in the Middle East and often lived in the same Central European areas in modern times, but true Gypsy matches usually come with Indian, especially north Indian matches, because that's where the Gypsies lived around the 900s before they backtracked into Iran and Turkey and eventually crossed the Bosporus into Europe.

The Gypsy language, Romani, shows a strong Romanian influence but its basic vocabulary and grammar point to a north Indian origin.

The Gypsy religion, on the other hand, is not Indian or Hindu but closest to Jewish, Persian and Zoroastrian forms of monotheism.

"It is not known when or why the Gypsies left India but they were living in Iran by the tenth century AD. The Iranian poet Firdausi (c. 930-1020) wrote of the Gypsies in his epic history of the Iranians, the Shah Nama (Book of Kings), that they were originally a tribe of musicians who had been sent to the ruler of Iran by an Indian king. Once they had eaten the ruler out of house and home, the Gypsies took to the roads. By the 11th century Gypsies were living in the Byzantine empire and soon afterwards were spreading through the Balkans. When the Ottoman Turks began to overrun the Balkans in the 14th century, groups of Gypsies dispersed across western Europe, reaching Bohemia in 1399, Bavaria in 1418, Paris in 1421, Rome in 1423 and Spain in 1425. In the early 16th century Gypsies spread to Britain, Scandinavia, Poland and Russia, but the Balkans remained the main Gypsy centre." John Haywood, The Great Migrations from the Earliest Humans to the Age of Globalization (London:  Quercus), p. 142.


Gypsy Migrations according to Haywood.

Phyllis Starnes drew many threads of Melungeon research together when she delivered her presentation on autosomal DNA validation studies at the Fifteenth Melungeon Union, held atWarren Wilson College, Swannanoa, NC July 15-16, 2011. Sponsored by the Melungeon Heritage Association of Kingsport, Tenn., the conference was appropriately titled, "Carolina Connections: Roots and Branches of Mixed Ancestry."

Starnes, who is administrator of DNA Consultants' Melungeon DNA Studies as well as an assistant investigator responsible for authoring reports, began her presentation by telling her own story. In 2002, she read an article about the occurrence of Familial Mediterranean Fever in Appalachia, where she grew up. "This article was the catalyst for me to address my own health and ancestry," she told participants.

She had met N. Brent Kennedy, author of the touchstone book The Melungeons:  The Resurrection of a Proud People, and soon became acquainted with both Elizabeth Hirschman (Melungeons:  The Last Lost Tribe in America) and Donald Panther-Yates, both speakers at Melungeon Fourth Union in Kingsport. The resources she needed for understanding her peculiar heritage were coming together.

Starnes summarized the Hirschman-Yates study of Melungeon DNA results published last December in Appalachian Journal and went on to reveal the results of a validation study of the Melungeon data in which the DNA profiles of the 40 participants were fed back into the database atDNA, expanded to reflect the world's only autosomal DNA Melungeon sample.

Astoundingly, many Melungeon DNA project participants had Melungeon as their No. 1 match, including Starnes.

In 1990, physical anthropologist and chemist James Guthrie analyzed blood sampled from 177 Southern Appalachian people identifying as Melungeon tested by Pollitzer and Brown in 1969. Guthrie's analysis was consistent to a remarkable degree with the Hirschman-Yates study.

All studies to date have verified and confirmed repeatedly that Melungeon descendants carry an unusual mix of Jewish, Mediterranean, Turkish, Iberian, Native American and African DNA. They also inherit genetic predispositions toward developing Familial Mediterranean Fever and other disorders.

This overarching thesis explaining what makes Melungeons different was advanced over twenty years ago by Brent Kennedy. It has now been re-examined, probed, tested and validated by unimpeachable followup studies, but little has turned up to change Kennedy's original thinking. It would be wrong to say that Melungeon origins today are controversial or mysterious. There is much we do not know about them, but their genetic and medical profiles are clear.

Starnes is enrolling people in Phase II of the Melungeon DNA Study. She has also inaugurated a password-secured blog where participants can freely share their experiences.

More information about Melungeons
Toward a Genetic Profile of Melungeons in Southern Appalachia
Melungeon Studies
Melungeon Match

This posting will review some of the material we have previously made available about the science behind our three Jewish markers in the autosomal 18 Marker Ethnic Panel. First, it may be worthwhile to recount the chronology of our testing innovations in this area.

2006 - DNA Consultants introduces the DNA Fingerprint Test, one of the first simple autosomal ancestry tests based on population databases

2009 -Donald N. Yates, Ph.D., principal investigator, makes the discoveries in July that lay the foundation for the DNA Fingerprint Plus, rolled out in early September. The enhanced product includes simple autosomal markers for Native American, European, Jewish, Asian and African ancestry, based upon their frequencies of occurrence in these ethnicities.

2010 - Several important studies on Jewish genetics appear; DNA Consultants introduces Jewish DNA Test

2011 - DNA Consultants releases version 2.0 of its autosomal population database atDNA, marking the addition of the population Melungeon (n=40).

In the Fall of 2010, our project administrator tabulated results for more than 450 people who had ordered a Jewish Ancestry Test through our partner Jewish Voice. It was found that 99.97% showed at least one Jewish marker, that is, had some Jewish ancestry.  Some had all three markers while others had a combination of the three in some way.  The informal study indicated 74% of Jewish Ancestry Test takers had Jewish I, 30% had Jewish II and 82% Jewish III.

Surely Not "Ancestry Painting and Global Similarity"

We were surprised to see what DNA testing companies are calling their autosomal products these days. Ours is the DNA Fingerprint family of products, but 23&me calls their entry "Ancestry Painting and Global Similarity" and "Personal Genome Service." Others offer "Genetic Ancestry Analysis," "Family Finders," and "Ancestral Origins."

Before the introduction of DNA fingerprinting for ancestry purposes, DNA testing was limited to the father’s male line or mother’s mitochondrial lineage. Newer autosomal tests can be taken by a male or female. They analyze all your lines at once, not just the two traditional ones of genetic genealogy. Autosomal DNA is the great equalizer, but it's not being marketed very adroitly.

A beginner’s class titled "Ancestry Tracing with an Autosomal DNA Test:  Conceptions and Misconceptions" will be presented by DNA Consultants principal investigator Donald N. Yates, Ph.D., at the upcoming Arizona Family History Expos. It will provide an overview of autosomal DNA tests that are capable of yielding a more complete picture of your family tree and its roots. Covered are the science and history of DNA fingerprinting, what markers are delineated, the databases used for finding matches, and methods and strategies for interpreting your results, including follow-up websites, social networking and readings.

The event takes place at the Arizona Family History Expo 2011, Lecture 73, Conference Theater, 11:00 a.m., Saturday, Jan. 22, 2011, Mesa Convention Center, 263 North Center Street, Mesa, Arizona 85201. For information on attending, visit Family History Expos or contact Holly T. Hansen at info@fhexpos.com.

Early experiments with our new Melungeon Match product show that members of the original research study score extremely high for a match to the population Melungeon (n=40) recently added to the database atDNA (Beta Version).

A sample of forty self-identifying Melungeons was assembled for a study by Donald N. Yates and Elizabeth C. Hirschman that should appear in the fall issue of Appalachian Journal. Their autosomal profiles formed the first population to be added to our new computer program atDNA, which contains the database used for the DNA Fingerprint Test. 

As an example, one of the participants, with known Melungeon ancestry including Ramey descent through her father, elicited the following top five matches in the new database, with Melungeon as her No. 3 match:

In the participant's father's results (Floyd Milton Grimwood, deceased), Melungeon was higher, occupying the No. 1 spot:

Such results tend to confirm the representativeness of the original sample, which contained closely and distantly related people of declared Melungeon ancestry, and validate its conclusions.

Melungeon DNA Project Administrator, Phyllis Starnes, who is also a moderator for the Melungeon Forum on DNA Communities, is coordinating the check for Melungeon ranking for the 40 participants. She will have a summary statement ready soon.

Statistically, the results are nothing short of astounding. They show Melungeon autosomal DNA reflects a well-defined population isolate with multiple interrelatedness. Melungeon is a valid historical and scientific label, not an arbitrary or adventitious designation or construct.

Pictured above:  four generations of the Tennessee Melungeon Ramey family.

More information about Melungeons
Toward a Genetic Profile of Melungeons in Southern Appalachia
Melungeon Studies
Melungeon Match