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.

Behind the Numbers:  Jim Bentley

Jim Bentley, DNA Frontiersman

(Part Three of a Series)

We interviewed  one of Chromosomal Labs Bode Technology’s senior staff members, Director of Sales and Marketing Jim Bentley, to get his perspective on industry changes over the past thirty-five-plus years.

Jim Bentley.

When did you first get interested in DNA?

JB: I’ll have to preface my answer with a few remarks on “the early days.” When I graduated from Arizona State University in the 1970s, DNA testing as we know it, was not really a field that was in existence. There was not a lot going on. The little work I did with chromosomes was using electron microscopy. I worked in the biochemistry department, however and performed hundreds of assays using poly-acrylamide gel electrophoresis, mainly for separation of proteins. This technique, although improved and streamlined remains in use today for DNA-STR separation. The field we’re in today where we can determine a person’s profile and compare it with others for forensics  for relationships, ancestry, missing persons, adoptions and the like, that technology hadn’t been developed yet. It wasn’t quite as easy as it is today.

Tell us more about the evolution of DNA testing.

JB: It basically began with blood groups and types. The first paternity test was done in a court case with Charlie Chaplin in the 1940s. He was excluded as the father, but the court said he could go ahead and pay child support anyway—probably, because he could afford it. Since that time, scientists started moving past groups and types into some other techniques. Human Leukocyte Testing (HLA), DQ-Alpha, and Restriction Enzyme STR testing (RFLP) are examples of the evolution of DNA testing.

The big breakthrough came when Dr. Alec Jeffreys at the University of Leicester discovered STR testing in England the late 1980s. He used STR profiling on the Colin Pitchfork case. Colin Pitchfork became the first criminal convicted on the basis of DNA evidence and as a result of a mass DNA screening operation. He was charged with raping and murdering two teenage girls. Since that time the forensic community has really refined the techniques to perform STR testing. They’ve made it simpler and more accurate. It’s really moved exponentially in the last twenty years. Today competent biologists and chemists can produce excellent results, every time.  Dr. Jeffreys has been knighted for his contributions.

So what got you involved?

JB:  I came out of college as a chemist, one interested in the medical field. I started out working in clinical chemistry and toxicology. The work we did with DNA was extremely limited and very costly. But I did stick with a career in clinical chemistry. Within four years after graduating from school I was managing a clinical laboratory in Houston, Texas called National Health Laboratories. It was a laboratory of about one hundred scientists and support staff. After mergers, acquisitions and such, that company remains as Lab Corp. (It performs more than 1 million tests on more than 370,000 specimens each day.)

What opportunities for professional growth did you have over the years?

JB: Through taking a lot of continuing education coursework, I became proficient and qualified as a general supervisor in clinical chemistry, toxicology, hematology, parasitology, microbiology, serology—everything except for tissue work like histology and cytology, which was done by certified medical experts in those specialties. My interests kept me in touch with the staff pathologists, however, as well as all the rest of the laboratory. Though my present-day field did not exist at the time I graduated, by staying current I was able to benefit from the changes and be part of an emerging valuable service provided not only to the medical community but also to the forensic one, and the general population at large.

What are some famous cases you’ve been involved with . . . that you can talk about?

JB:  Actually, that’s my problem. We’ve been involved in a number of high-profile cases, but we’re not allowed to talk about any of them. Most have been on the forensic side, serial killer trials in Arizona, also in California, some that made the news in Florida . . Texas . . .Georgia.

Were you involved in catching the Grim Sleeper?

JB:  Actually, that’s an ongoing case in Los Angeles we are familiar with, but we didn’t do the work on it, so we can talk about that one. The importance of the Grim Sleeper case has to do with familial testing and autosomal DNA. It was termed the Grim Sleeper case because there were a number of homicides that took place beginning in the mid-1980s, all with the same basic MO [modus operandi], and then the murderer went underground for fourteen years. The victims were typically prostitutes shot with a firearm. In 2010, a suspect, Lonnie David Franklin Jr., 57, was arrested and charged with multiple counts of murder. He has not yet been convicted, nor the evidence against him tested in court.

How was DNA used to catch him?

JB: So here were a number of cold cases, but they were being tracked, and the law enforcement authorities in Los Angeles continued to monitor progress. The sole survivor of one of the Grim Sleeper’s attacks furnished a description of him as a black man in his 30s, along with other details. According to her story in the press, he lured her into an orange Ford Pinto, shot her in the chest with a pistol, took Polaroid’s and raped her, leaving her for dead. In 2008, the body count was thirteen, and a $500,000 reward was put out for “America’s Most Wanted.”

It became the first use in California, and one of the first three cases in the United States, of the use of familial DNA searching, that is, using the FBI’s CODIS database to match one family member’s profile with a suspect’s profile. The LA police were able to provide a close partial match to  Franklin’s crime scene profile with that of his son, whose CODIS markers were on file for a minor crime. They then set up a kind of mini-sting operation at a pizza parlor in Buena Park, where they knew the family liked to eat. Undercover detectives masqueraded as waiters and busboys. When the family left, they whisked away an unfinished pizza slice. The crust yielded DNA which police linked on a more solid basis to Lonnie Franklin. It was the first high-profile case in which a family member’s DNA had been used to catch a criminal. The ACLU and others had been critical of familial searching on grounds of privacy, and there is still a lot of debate over familiar searching because it might open up the search and include those who hadn’t committed any crime.

Did this help produce new commercial products like the “cousin finders”?

Only a few states are doing familial searching, and they are pretty guarded about it. It’s hard for me to make a connection. Certainly, these developments have been concentrated in the past three or four years, but the use of this technique is spreading.

Are people legitimately suspicious about DNA databases?

JB: Fears surface from time to time. There have been claims that keep popping up that someone’s going to take everything that’s in the database and use it to determine genetic deficiencies that could lead to medical issues down the road. Once it was speculated that if such  information was released, insurance companies would begin denying people coverage based on their profiles.

This is the mother of conspiracy theories, isn’t it?

JB:  It really is. For the most part—not for everyone—the vast majority of the markers we are using are in the “junk DNA” area. That is, they don’t by themselves “do” anything or give you genetic information on the face of things. There may be one or two markers that possibly could be construed as yielding some medical information—such as a trisomy at vWA or TPOX [a CODIS locus]. But by and large, you are not going to be able to do any medical diagnostics with the markers we run. Usually trisomies such as Down’s syndrome would be physically expressed and not hidden. It’s a little different with SNP panels [single nucleotide polymorphisms] such as those run by 23&me. With a high number of those, it’s entirely possible to predict medical predisposition. That’s what they base their business on.

Let’s talk some more about the CODIS database.

JB:  It’s important to realize that even law enforcement doesn’t provide much access to the CODIS [Combined DNA Identification System] databank. That’s something I have to give the FBI credit for. They have developed a system that is secure. It’s the DNA administrator at each facility who has undergone FBI training and uploads the data under very strict rules, and they are notified of any “hits” that involve them, but otherwise there is very little access, and the use of the database is very even across the country. There are not a large number of portals that can be used to access the CODIS database. There are several hundred law enforcement laboratories that are running profiles across the country, and the database is best thought about on three different levels:  LDIS, SDIS and NDIS, local, state and national versions. Between our labs in Phoenix and Virginia, we’ve tested over a million profiles for entry into CODIS. That’s about one-tenth of the entire number. I can tell you there is tight security. Hundreds of thousands of investigations have been aided by a DNA hit (we don’t like to say “match” so much, because statistically nothing is 100%) generating a lead.

How did you get bitten by the genealogy bug?

JB: I’ve always been fascinated with ancestry. I think it came about because my father took an interest in discovering our family’s roots and had to do so at the time by traveling to Salt Lake City, Utah, and poring over whatever records he could find there about our fathers, and great-grandfathers, and great-great-grandfathers, and so forth. He had tintypes of some of the relatives. We had various pieces of the puzzle. My father pretty much consolidated everything back to William Bentley, who settled in Rhode Island in the early 1700s and had come from Bedfordshire, England. He put together a book for family use. He glorified a few of them and left a few out that weren’t ready for glorification. For the sensitivity of some of the relatives, he left a few details out, but it was a pretty solid piece of work. For me, it kind of fostered this interest in ancestry and its importance. Certainly, when I started at Chromosomal Labs • Bode Technology, we started looking at the various tools that could be used. Our history, to be sure, is passed down from generation to generation. Initially, we were using mitochondrial DNA, Y-SNP’s and Y-STRs and then autosomal STRs to determine how we’re connected to general and specific individuals back to the Revolutionary War days and how you are linked with the world population, what your roots were. I have a particular Y haplogroup of G2a, which is not one of the more common ones.

Hmm . . . you and Joseph Stalin.

JB:  [Laughs]. Is that what his haplogroup was? Uh-oh! He was one of the worst. Well, I got interested in G2a and hooked up with about 50 other Bentleys and we identified our founder  patriarch haplotype. I get emails from them on a regular basis. The other thing we tried to find out was what in the world were all these G2a’s doing in England. I don’t know. But one of the things I find in the literature most often was that the Sarmatians were horsemen that gave the Romans a pretty rough time. Eventually, they were decimated. The Romans took their remaining cavalry and pressed them into service for 12 to 13 years or longer. Some were dispatched to Hadrian’s Wall. Now do I know for a hundred percent certainty that’s where I came from? No, but its fun to regard that as a hypothetical personal history.

You have a Scythian gene, don’t you?

JB:  Yes, I do according to the analysis DNA Consultants did for my autosomal ancestry. The work Dr. Yates has done on the rare alleles supports a lot of the stuff the family has been putting together for years and years.  I was very pleased to get my Rare Genes from History report back showing I had the Scythian gene. That seems to go along with the Sarmatian theory about the Bentleys.

How do you see the industry changing over the next few years?

JB:  I can speak best about changes I am seeing in the field. They’re getting closer to having rapid DNA testing on a chip. This gives flexibility to those who want to use DNA as “point of use” testing. The FBI this past year came out at the Promega conference and said that within the next two years they would like to see wide adoption of “point of use” testing. The IntegenX prototype allows you to put your swab into a cartridge, insert it into the instrument on the fly and get your STR results in a few hours. Previously, Rapid DNA testing was not only time-consuming and lab-bound but it was very expensive. It cost several hundred dollars in reagents alone. As the technology improves to allow 2 hour testing in our lab or on a chip, reagent and personnel time continue to drop,  Now, the FBI would like to see point of use testing in every booking station in the country. At the last show, I also saw an instrument from Illumina that would run Y-STRs, mtDNA and autosomal DNA profiles simultaneously on one sample. Another change that is coming is we will see an expanded profile becoming the standard, perhaps something similar to the GlobalFiler kit from Life Technologies with its 24 loci. With the new technology you can increase the speed for amplifying the specimen by five times and achieve nine times the discriminating power or resolution.

Any final remarks?

JB: The DNA testing field is on the threshold of even greater accolades of appreciation both from the scientific community and the public. If DNA wasn’t even in anyone’s mind twenty years ago, soon it will be part of everyone’s daily lives.

 
























Sir Alec Jeffreys, inventor of DNA fingerprinting, and Jim Bentley at forensics meeting.

We are our DNA. It was not a surprise to find that our entire DNA is Functional (“Junk DNA Isn’t Junk, and That Isn’t Really News”). The surprise is in the discovery of what we can do with what we once thought was junk. According to that recent NPR article, “It is a massive control panel that regulates the activity of our genes.” Our genes “would not work” without it. So instead of being junk- they are critical and “control how cells, organs, and other tissues behave.” But we can also now read the markers and mutations on this “panel” and discover much more information than knowing it is just working efficiently for our body. This knowledge is considered a “major medical and scientific breakthrough” (Ibid.). We just have to read it well.

But first, what is DNA exactly? John Wilwol, in his recent NPR article, “A ‘Thumb’ on the Pulse of What Makes Us Human,” quotes Sam Kean, author of the book, The Violinist’s Thumb And Other Lost Tales of Love, War, and Genius, As Written by Our Genetic Code, as saying that DNA is what makes us who we are. Wilwol further quotes Kean to help us understand what DNA is and how it differentiates from genes: “ ‘While DNA is a thing- a chemical that sticks to your fingers, he writes, genes are more conceptual in nature, …“‘like a story with DNA as the language the story is written in.”

So if DNA is a language how are we able to read it? All parts of our genetic code are now readable and meaningful. Marker locations (loci) are spread across one’s entire genome, not confined to one’s male (Y chromosome) or female (mitochondrial) DNA. (This is how sex-linked, haplotype tests that follow one line at a time are analyzed). Different mutations are handed down genetically – different according to the region where one’s ancestors lived.

Because of this new ability to read markers, consumers are now able to buy Autosomal DNA tests that provide a complete analysis of where all one’s ancestors’ ethno-geographic origins – reflecting the entire spectrum 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. Anyone can take an 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). The future is now in many ways.

What else can you learn from Autosomal DNA testing? Anne Tergesen, in a recent article in the Wall Street Journal,” quotes Megan Molenyak, author of, Hey America, Your Roots Are Showing, as saying that this relatively new test deciphers the amount of DNA shared between those whose common ancestors lived within the last half-dozen or so generations. Tergersen explains it like this, “Y-DNA and mitochondrial DNA can connect people whose common ancestors lived recently or hundreds of years ago. But to find out how closely you are related—and to locate relatives besides those on your direct maternal or paternal lines—you will need an autosomal DNA test.” (Of course, you would both need one to compare) and “in general, the more DNA two people share, the closer their connection”.

But there are even more things on the horizon with Autosomal DNA for the future. Personalized Medicine. According to a recent Smithsonian article, “Fetal Genome Sequenced Without Help From Daddy,” “A fetus’ entire genome can now be sequenced” from the mother alone with a “99.8% accuracy.” How is that possible? It was just “last month clinicians announced that they could sequence a fetus’ entire genome by taking samples from the pregnant mother’s blood and that of the father to be” (“Fetal Genome”). Now they have a “more difficult, but more complete method [that] uses DNA from the pregnant woman and the fetus to map out every last letter of the fetal genome…with the advantage that it can pick up mutations that a fetus has but its parents do not” (Ibid.).  Rob Stein quotes Dr. Alan Guttmacher, director of the National Institute for the Child Health and Human Development in a recent NPR article, “Genome Sequencing For Babies Brings Knowledge and Conflicts,” as saying, “Instead of screening for currently something like 30 conditions, it would allow you to screen for hundreds if not thousands, [of conditions] at birth.  He goes on to say that, “One could imagine a day where knowing someone’s entire genome sequence at birth, you could really begin to think about structuring health care, their dietary choices, their exercise choices…early in life, in a way that would have an impact on truly lifelong health.” Stein says that this gene sequencing could “spot babies that are prone to conditions such as obesity, diabetes, heart attacks or cancer” and that we may soon be “sequencing all babies when they’re born.”  It could be a wonderful tool. But we are not there yet.

According to Rob Stein in another recent NPR article, “Perfection is Skin Deep: Everyone has Flawed Genes,” Scientists have determined we are all more flawed than they thought. “Researchers discovered that normal, healthy people are walking around with a surprisingly large number of mutations in their genes.” Chris Tyler-Smith of the Wellcome Trust Sanger Institute in Cambridge, England and his colleagues analyzed the DNA of 179 people from several countries who volunteered their genetic information to the 1,000 Genomes Project.

In a published paper in the American Journal of Human Genetics, the researchers reported that though none of the people whose DNA was studied were sick, the average person has about 400 minor flaws and one or two that could contribute to disease. Tyler-Smith says, “It’s a bit surprising that people should be walking around apparently healthy yet we’re seeing known disease-causing mutations in their genomes,” he says. “But the answer was that these tended to be for mild and very often late-onset conditions. Things like heart disease, an increased risk of disease or developing cancer. On its website, the American Diabetes Association highlights the interaction of genetic and environmental factors: “You inherit a predisposition to the disease then something in your environment triggers it. Genes alone are not enough.”

So the problem is not so much with the analytical tool but rather the possibility of over- interpretation. Again, we just have to read it well, with the same critical eye for what is written in us as that which is written by us. And who knows what else we will soon be able to discover from reading our DNA?

Sorry, Jack, no cigar. Your Grandpa's Indians are not what you think. And it is not true "most free African American families that originated in colonial Virginia and Maryland descended from white servant women who had children by slaves or free Africans" (source). Negro males did not go around selectively "fathering" little man-children on "white servant women" in early America.

It is ironic that these fantasies should even emerge in the recently publicized report, "Melungeon DNA Study Reveals Ancestry, Upsets a 'Whole Lot of People.'" The authors of the report, Roberta J. Estes, Jack H. Goins, Penny Ferguson and Janet Lewis Crain, have spent the better part of ten years trying to prove they and others with Melungeon ancestry are just plain folks, that is, white folks.

Maybe they are just that, though. Among the conclusions of the report are that Melungeons aren't Portuguese, aren't Native American, aren't Jewish, aren't Romani/Gypsy, aren't . . . . On and on. They just have a teeny-tiny bit of Sub-Saharan African in some lines. Not to worry, though, it is just a little soupçon of non-white. And it goes back to a few heroic "negroes" (the report's language) who left a trace their Sub-Saharan African Y chromosomes in the fathers and sons and grandpas of three Melungeon families.

From an article published, lo! way back in 2002 in the Appalachian Quarterly, now sadly defunct,

Shalom and Hey, Y'all (243 KB)

comes the true story of these "negroes" (the report's language) fathering "multiethnic" babies on innocent white indentured servant women.

In discussing the will of Indian trader James Adair, the author of the study remarks on the fact that Adair did not apparently approve of his daughter Agnes marrying John Gibson (from the selfsame Melungeon Gibson family that is creating all the brouhaha today). (Agnes, by the way, was not an indentured servant; her father had a considerable fortune.)

           "Notice the harsh treatment Adair accords his daughter Agnes, leaving her and her husband John Gibson the nominal sum of only one shilling (if he had left her nothing, she could have protested to the probate court that he simply forgot her). John was one of the “mulatto” Gibsons of the Great Pee Dee river valley region. Gideon Gibson stands large on the pages of history for his role in the so-called Regulators Revolt. The Gideon Glass Antiques Store today pays testimony to the “richest man in South Carolina” of his time. When members of the Gibson family first moved to the state in 1731, representatives in the House of Assembly complained “several free colored men with their white wives had immigrated from Virginia.” Governor Robert Johnson summoned Gibson and his family and reported:

            I have had them before me in Council and upon Examination find that they are not Negroes nor Slaves but Free people, That the Father of them here is named Gideon Gibson and his Father was also free, I have been informed by a person who has lived in Virginia that this Gibson has lived there Several Years in good Repute and by his papers that he has produced before me that his transactions there have been very regular. That he has for several years paid Taxes for two tracts of Land and had several Negroes of his own, That he is a Carpenter by Trade and is come hither for the support of his Family [Box 2, bundle:  S.C. Minutes of House of Burgesses (1730-35), 9, Parish Transcripts, N.Y. Hist. Soc. By Jordan, White over Black, 172.]

"The Gibsons are discussed as Melungeons in Brent Kennedy and as true-to-form Sephardic Jews in Hirschman. Melungeon Gibsons derive their origins from the Chavis family, one of the oldest Portuguese-Jewish names in America. If they are Jewish, it is ironic—and probably funnier than any Fanny Brice skit—that historians trot them forth as shining examples of non-slave African American colonials owning land and marrying white women."

The moral of the story? Melungeons have often been hauled into court to prove they are not black. Now they are being dragged through the court of Internet opinion. The outcome is doubtful.

Now about those Indians . . . That will have to wait until another blog post.

Photo: Black Revolutionary soldier. Blackpast.org.

Article cited:  Donald N. Panther-Yates, “Shalom and Hey, Y’all:  Jewish-American Indian Chiefs in the Old South,” Appalachian Quarterly 7/2 (June 2002) 80-89.

More information about Melungeons
Toward a Genetic Profile of Melungeons in Southern Appalachia
Melungeon Studies
Melungeon Match
Melungeon DNA Fingerprint Plus
The War on Melungeons
Melungeons.com

Shalom and Hey, Y'all (243 KB)

Brent Kennedy's book on Melungeons
Elizabeth Hirschman's book on Melungeons
Lisa Alther's new novel on Melungeons

Dienekes' Anthropology Blog is the grand ole man of genetic blogs, well-praised in all quarters with archives going back to 2004. It is run by Dienekes Pontikos (blogger pseudonym), a Pontos Greek whose family is from Turkey, and who describes himself, far too modestly, as "an anthropology dilettante."

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A member of the International Society of Genetic Genealogy (ISOGG) wrote an article online five years ago. Now a substantial number of listers on the discussion board DNA-Genealogy-L believe their male lines may go back to a Balkan legionnaire in Roman Britain. This theory has been enshrined in popular belief, thanks to ISOGG members, who contribute most of the material on Y chromosome DNA to Wikipedia articles.

Read our review from an appendix on Jewish DNA hot spots in England and Wales in our book-in-progress, New Jerusalem:  The Story of Britain's Earliest Jews and Muslims.

Steven Bird in “Haplogroup E3b1a2 as a Possible Indicator of Settlement in Roman Britain by Soldiers of Balkan Origin,” is, as the title makes clear, most interested in proving a Roman Balkan origin for the haplotype he investigates, now known as Elblbla, the most common type of the haplogroup Elblb (formerly denominated E3b) in Europe. The structure and subclades of this very ancient North African Caucasian lineage have only recently been resolved and overhauled, and the ink is not yet quite dry. But the data used by Bird with the sometimes confused or outdated nomenclature of older reports can still provide valuable clues for our purposes, although one must proceed with caution in making too many differentiations in the tangled branches of the E tree. We must bear in mind that the target haplotype E1b1b1a2 (also called E-V13) represents 85% of the parent haplogroup E1b1b (also denoted as the E-M78 clade) and keep simple E before us without being distracted.

            Bird’s study appeared in one of the first publications of the Journal of Genetic Genealogy, an online journal of the International Society of Genetic Genealogy (ISOGG), founded in 2005 by DNA project administrators of the commercial DNA testing company Family Tree DNA based in Houston, Texas, “who share the common vision of the promotion and education of genetic genealogy.” It is an ambitious work with a very small goal. It uses arguments not only from genetics and statistics but also archeology, geography, history, anthropology and linguistics, often involving such fine points as the epigraphy of a Spanish soldier’s diploma from the British Museum issued in 103 CE and the detailed movements of Thracian cohors II and VII in the Roman army. Where angels fear to thread. Bird’s theory about the origins of Elblb have been enshrined in popular belief. We do not wish to appear ungrateful but there are problems.

            Bird’s first mistake occurs in his review of the literature. He misreads Stephen Oppenheimer and represents the author of The Origins of the British as having British E “originating from the Balkan peninsula (26).” If we open Oppenheimer’s book to the page cited (207) we see a map illustrating “Near Eastern [British English for American English ‘Middle Eastern’] Neolithic male migrations via the Mediterranean of E3b [i.e. E1b1b] and J.” The vector standing for the migration of these types launches forth from the Peloponnese in Greece at the cropped lower right corner, obviously intending to suggest origins from that general direction, not “the Balkan peninsula.”  There is no mention of Balkan DNA in Oppenheimer except as part of the bigger picture. The archeological sites Bird adduces as evidence for E settlements in the Bronze Age are not necessarily associated “directly” or solely or chiefly with “proto-Thracian culture,” whatever that term may mean. Nova Zagora in Bulgaria is a Stone Age multi-site. Ezero Culture occupied most of Bulgaria and extended far north into the Danube region of Romania. Yunatsite, Dubene-Sarovka and the other “proto-Thracian culture” examples Bird mentions date to before the Thracians or even the Greeks. They cannot tell us anything about haplogroup E. If anything, all these sites vindicate Oppenheimer’s theory of the demic spread of Middle Eastern (read Anatolian) agriculture, which Bird calls “flawed fundamentally” (27). The center for the diffusion of E in the Balkans is not in Bulgaria or Thrace but northwestern Greece, Albania and Kosovo. The Balkan Peninsula does not have to be the only place from which Bird can manage to derive E and get it to Britain in time to become part of the historical record. It is also strong throughout Greece, Cyprus, the Greek parts of southern Italy, North Africa and even parts of Spain. In fact, its presence in many of those locations is acknowledged to be “due to a founder effect, i.e. the migration of a small group of settlers carrying mostly this lineage (but also a small amount of other North-East African lineages, notably E-M123 and T.” (See http://www.eupedia.com/europe/Haplogroup_E1b1b_Y-DNA.shtml.)

            Despite these failings relating to statement of thesis and validity of arguments, Bird’s work is based on useful data. Three population surveys with frequencies for E in Britain were available to him, the data sets of Capelli, Weale and Sykes. Notwithstanding the nomenclature confusion, only the Sykes data set has true shortcomings, as the Oxford Genetic Atlas Project at the time contained only forty E haplotypes, too small for a valid sample. There are problems comparing them, as Bird realizes, but trends and general conclusions are certainly possible. Before attempting to analyze the haplogroup E variation in Britain, though, we must address the matter of time depth.

            We have no quarrel with geneticists’ and genetic genealogists’ methods of gauging coalescence times. Thus, Bird reiterates that the “time to most recent common ancestor” or TMRCA of Cruciani and others led to the “important finding . . . that E-V13 [read 85% of E] and J-M12 [read J] had essentially identical population coalescence times (27).” E and J are companion types that expanded from their Middle Eastern homelands together in the same fashion and probably reinforced each other in multiple phases of gene flow. But who is to say in any specific case of a haplotype that it arrived in Britain 4,000 years ago (TMRCA) or at any subsequent time, including the time when our grandfathers lived. The TMRCA sets a haplotype’s time of origin but not its place of origin, except by inference. We hypothesize that from a host of other factors, chiefly present-day clusters, genetic distance between types and high concentration of haplotype diversity.  Using TMRCA, Bird argues that a specific form of E “could not have arrived in Britain during the Neolithic era (6.5-5.5 kya) if it had not yet expanded from the southern Balkans (27).” We prefer to believe that it came to the British Isles at several critical times, first in Neolithic times but later with the Phoenicians, Jews, Egyptians, Iberians and related peoples.    

            Bird cherry-picks the data to support his Roman Balkan or what might be called Diocletian thesis, but data are data; these are amenable not only to bearing out the general storyline we present but also to supporting, within the same historical context, the existence of certain hot spots for Jewish and Middle Eastern DNA in England and Wales.  We agree somewhat with Bird the Welsh cluster for E is “underestimated by an arbitrary division by Sykes into two geographic regions (‘Wales’ and ‘Northern England’) . . . [creating] an impression of a large number of ‘Eshu’ haplotypes located throughout Northern England, when in fact the Northern English cluster is linked to Welsh cluster geographically (29).” Only, we would see in that Northern English cluster the remains of the historical Welsh Old North (chapters 1 and 7). We would not necessarily see in the Wales-to-Nottingham cluster the fading footprints of “the Ordovices, the Deceangi, the Cornovii, the Brigantes and the Coritani tribes (30),” about whom little is known in any event, but a belt of pre-existing Mediterranean culture reinforced by Roman occupation and somewhat resistant to Anglo-Saxon and Viking intrusions. Another shrinking pocket of the old British culture is shown in the elevated frequencies for both E and J in Strathclyde and Cumbria, part of the Welsh Old North.

            Bird has an informative map of Britain illustrating E1b1b distribution according to the Kringing method (34). In this we can trace all the major pockets of Mediterranean and Jewish DNA. Leaving aside Scotland, and aside from the Midlands pocket already mentioned, our eye is drawn to North Wales (along with a clear wall of high incidence surrounding it as though beating back the forces of history on all sides), Dorset, London and East Anglia. It cannot be coincidence that these are the very regions where we have diagnosed the presence of Jews and picked up their trail through the chapters of our book.

            As a final note, a 2005 paper by Robert Tarín provides phylogenetic analyses of E1b1b haplotypes that cast serious doubt on Bird’s assertions and confirm our reading of the evidence. Tarín used 290 individual Y chromosome results to characterize “a separate cluster of mostly Iberian haplotypes which seem to represent a North African entry into Iberia distinct from the E3b [E1b1b] in Europe that may have arisen from Neolithic or other migratory events.” He wrote that “it is unknown whether this finding reflects relatively recent gene flow from the Islamic rule of Spain or an older influx possibly from the Phoenicians”—the same quandary about time frame and coalescence we see above. Utilizing the Y Chromosome Haplotype Reference Database (YHRD), Tarín found levels of the Iberian E haplotype as high as 61% in one Tunisian population (Zriba, near ancient Carthage), while Andalusian Arabs and Tunisian Berbers both showed frequencies of about 7%. We believe this Iberian haplotype is a small, but important Jewish lineage that expanded from Tunisia to the Iberian Peninsula with the Berbers who aided Arab armies in conquering Spain. Interestingly, it accompanied Spanish Jews to Mexico and other places in the diaspora following the events of 1492.  Its distribution in Britain should reveal an implantation originally under the Phoenicians reinforced by periodic migrations of North African and Spanish or French Jews throughout the medieval and early modern periods of British history.

Geneticists seized the opportunity provided by an international Basque cultural event held in Idaho in 2010 to sample volunteers and study Basque DNA. The result was two studies, including "The Y-STR Genetic Diversity of an Idaho Basque population, published in Human Biology.

It was the first DNA study to document the spread of the Basque male chromosome overseas. The Basque people were renowned seafarers.

"The idea is to better understand health risks for Basque people, including an increased incidence of both Alzheimer's and Parkinson's diseases," said Josu Zubizarreta, a Boise State graduate who conducted research with the lead author, Greg Hampikian.

Mitochondrial DNA, which reflects a deeper history, was also studied.

Basques are credited with the invention of the rudder. They provided the crew and navigators for Magellan. Basque names are common on antique maps. The Bay of Biscayne is named for them, and many harbors, points and landfalls on the Atlantic Coast of North America are thought to come from the Basque language, which is known as an isolate and is unrelated to other European languages.

Sculpture of Basque sailor, Victorio Macho, Toledo. Travelpod.

Citation
Zubizarreta, Josu; Davis, Michael C.; and Hampikian, Greg (2011) "The Y-STR genetic diversity of an Idaho Basque population, with comparison to European Basques and US Caucasians," Human Biology: Vol. 83: Iss. 6, Article 2.
Available at: http://digitalcommons.wayne.edu/humbiol/vol83/iss6/2

San Diego State University professor D. Emily Hicks has traced some common ancestry with President Barack Obama. According to the professor of Chicana/o Studies, she and the President share Melungeon roots. Obama is a descendant of Mary Collins of Orange County, Virginia as well as of Nathaniel Bunch of Louisa County and John Bunch of New Kent--well known "feeder" counties for what became the Melungeon settlement described in Brent Kennedy's book, The Melungeons, The Resurrection of a Proud People.

Obama's Bunch line was found to carry E1b1a haplogroup, a sub-Saharan African male lineage. He is also supposed to have Cherokee ancestry in his mother's colonial genealogies.

Read the whole story at PRLOG.

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

The whole business of direct-to-the-consumer DNA tests was founded upon the revelation in 1997 that Jewish men with the last name Cohen ("priest" in Hebrew) or something similar often preserved the genetic signature of Old Testament priests in the Y chromosome type handed down from father to son. Last year at long last, the so-called Cohen Modal Haplotype was completely pinned down and defined to everyone's satisfaction ("Does He or Doesn't He?"). Now similar genetic traces are being sought, and found, for other religions from the Middle East.

In response to customers asking whether being a Jew was a matter of ancestry or culture, genes or religion, I used to say, "Genes don't have religion, genes are older than religions, your DNA doesn't know what religion you are." But the increasingly adept methods of populations genetics are changing that pat response. The key tool is a program that uses advanced statistics to estimate population differentiations, BATWING. Standing for Bayesian Analysis of Trees With Internal Node Generation, this software can calculate the effective population sizes and growth rates from microsatellite data, assuming there was a split into several populations in the past. It is a little over 10 years old. The following article is likely to become a classic in this regard:

Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon

Marc Haber et al.

European Journal of Human Genetics (2011) 19, 334–340; doi:10.1038/ejhg.2010.177; published online 1 December 2010

Abstract

Cultural expansions, including of religions, frequently leave genetic traces of differentiation and in-migration. These expansions may be driven by complex doctrinal differentiation, together with major population migrations and gene flow. The aim of this study was to explore the genetic signature of the establishment of religious communities in a region where some of the most influential religions originated, using the Y chromosome as an informative male-lineage marker. A total of 3139 samples were analyzed, including 647 Lebanese and Iranian samples newly genotyped for 28 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y chromosome. Genetic organization was identified by geography and religion across Lebanon in the context of surrounding populations important in the expansions of the major sects of Lebanon, including Italy, Turkey, the Balkans, Syria, and Iran by employing principal component analysis, multidimensional scaling, and AMOVA. Timing of population differentiations was estimated using BATWING, in comparison with dates of historical religious events to determine if these differentiations could be caused by religious conversion, or rather, whether religious conversion was facilitated within already differentiated populations. Our analysis shows that the great religions in Lebanon were adopted within already distinguishable communities. Once religious affiliations were established, subsequent genetic signatures of the older differentiations were reinforced. Post-establishment differentiations are most plausibly explained by migrations of peoples seeking refuge to avoid the turmoil of major historical events.

Meanwhile, in Autosomal DNA

A like expansion and intensification of research interests has also transformed the field of Finnish DNA. In the old days it was well appreciated, through the work of Finnila and others, that the people of Finland, Estonia, Sweden and neighboring regions in Russia had a peculiar genetic history. Strangely, at least on the basis of mitochondrial DNA, they were more closely related to the Berbers of North Africa than the neighboring Swedes, Poles, Lithuanians and Russians. Female haplogroups UK were associated with a risk of occipital stroke, migraine and other neuro-deficiencies. On another level, their unique genetic history was approached through the study of male haplogroup N, common among Laplanders and Saami.

The focus has now shifted from haplotyping and sex-linked genes to population genetics and autosomal DNA just as it has in consumer tests. After 10 years, an important autosomal study of the Saami has revolutionized the subject and shows promise of becoming the pilot to a new series of genome-wide disease association studies.

A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies

Jeroen R Huyghe et al. 

European Journal of Human Genetics (2011) 19, 347–352; doi:10.1038/ejhg.2010.179; published online 8 December 2010

Abstract

The understanding of patterns of genetic variation within and among human populations is a prerequisite for successful genetic association mapping studies of complex diseases and traits. Some populations are more favorable for association mapping studies than others. The Saami from northern Scandinavia and the Kola Peninsula represent a population isolate that, among European populations, has been less extensively sampled, despite some early interest for association mapping studies. In this paper, we report the results of a first genome-wide SNP-based study of genetic population structure in the Finnish Saami. Using data from the HapMap and the human genome diversity project (HGDP-CEPH) and recently developed statistical methods, we studied individual genetic ancestry. We quantified genetic differentiation between the Saami population and the HGDP-CEPH populations by calculating pair-wise FST statistics and by characterizing identity-by-state sharing for pair-wise population comparisons. This study affirms an east Asian contribution to the predominantly European-derived Saami gene pool. Using model-based individual ancestry analysis, the median estimated percentage of the genome with east Asian ancestry was 6% (first and third quartiles: 5 and 8%, respectively). We found that genetic similarity between population pairs roughly correlated with geographic distance. Among the European HGDP-CEPH populations, FST was smallest for the comparison with the Russians (FST=0.0098), and estimates for the other population comparisons ranged from 0.0129 to 0.0263. Our analysis also revealed fine-scale substructure within the Finnish Saami and warns against the confounding effects of both hidden population structure and undocumented relatedness in genetic association studies of isolated populations.

The key to emerging triumphs of research here is the international HapMap project.

On two fronts--religious history and rare diseases--genetics has brought more advances in the past decade than in the previous century before that. That consumers can take part in these exciting developments by ordering an affordable autosomal analysis of their entire ancestry or confirming the paternity of their child with a simple test purchased at their local drugstore is a tribute to the present golden age of American science and industry. 

Only His Geneticist Knows for Sure 

A visit to the temple by a Canadian doctor and one-page letter to the journal Nature in 1997 started it all, a frenzied hunt for the multi-study, double-blind, placebo-controlled proof that Jewish men of the surname Cohen carried the same genes as the biblical patriarch Aaron, the mystical Cohen Modal Haplotype (Skorecki et al., 1997).  Early testing showed that nearly half of men named Cohen—Cohanim in the Hebrew plural—had the same values at six locations on their Y chromosome. For the record, here are the magic numbers that first defined the “Y chromosome of Old Testament Priests”:

DYS19 - 14

DYS388 - 16

DYS390 - 23

DYS391 - 10

DYS392 - 11

DYS393 – 12

But having those scores did not make you a member of the club. As the authors of an article on the “extended CMH” finally appearing last year write, the original research by Thomas et al. (1998) “produced a ‘low resolution’ CHM that was shared among many non-Jewish populations” (M. F. Hammer et al., “Extended Y Chromosome Haplotypes Resolve Multiple and Unique Lineages of the Jewish Priesthood,” Human Genetics 126:707-17). 

That would never do. Moreover, such sketchy data “did not provide the phylogenetic resolution needed to infer the geographic origin of the CHM lineage.”

So Hammer at the University of Arizona, partnering with the National Laboratory for the Genetics of Israeli Populations, spent ten years and millions of dollars narrowing down the definition of the CMH and pinpointing its origin in history. Glossing over the statistics, subjects and methods—are you ready—the extended CMH is not much different from the original CMH, only it has no living matches.

Yes, you read that right. Whereas Skorecki’s minimal 6-locus haplotype might be proudly shared by thousands who eagerly sent in their DNA samples to genetic testing companies over the years, the new and improved CMH of Hammer et al. with twice the definition or 12 loci when “compared with the YHRD [Y-STR Haplotype Reference Database in Berlin]. . . yielded zero out of 10,243 possible haplotypes in 66 populations” (711).

Way to go, I hear from Marketing.

From a dybbuk the CMH has gone to being a dynosaur. It was once doubted whether it existed. It is now proven to be extinct.

No further research is needed on this subject, not as far as I'm concerned.