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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.

The question of ancestry has been of human concern in virtually all cultures and over all times of which we have any knowledge. Whether it be a story about the origin of a particular tribe or nation and its subsequent mixture with other groups, or curiosity about a family history, there is always the implication that we understand ourselves better if we know our ancestors and that we, within ourselves, reflect properties that have come to us by an unbroken line from past generations. As treasurer of the Marlboro Historical Society in Vermont, I am the recipient of requests for printed copies of the Reverend Ephraim Newton’s mid-eighteenth-century history of our town, 70 percent of whose pages consist of “Genealogical and Biographical Notes” and a “Catalog of Literary Men.” Over and over our correspondents write of the “pride” they have in descending from these early settlers.

Surely pride or shame are appropriate sentiments for actions for which we ourselves are in some way responsible. Why, then, do we feel pride (or shame) for the actions of others over whom we can have had no influence? Do we, in this way, achieve a false modesty or relieve ourselves of the burdens of our own behavior? As a descendant of late-nineteenth-century Eastern European immigrants I cannot depend on Reverend Newton’s pages to explain my frequent contributions to The New York Review, but neither have the extensive “begats” in Genesis 10 or Matthew 1 been more enlightening.  Read More...

Behind the Numbers:  Elizabeth Hirschman

  (Part Two of a Series)

We interviewed Rutgers marketing professor Elizabeth Caldwell Hirschman, author of several books and articles incorporating DNA in her research, to hear her personal story in our continuing series about the people behind the scenes in the field of DNA testing.

Elizabeth Hirschman with MBA students at Rutgers in December 2009.

When did you first get interested in DNA?

ECH: I got interested in DNA testing around 2000 when I discovered I was Melungeon after reading Brent Kennedy's 1994 book. Brent suggested several different ancestries that possibly contributed to the Melungeon population and I wanted to find out which of these were correct and which ones I had. I already suspected Jewish ancestry because of the naming patterns in my family over the past 300 years, as well as some of their habits --e.g., not eating pork, getting married in a home instead of a church, cleaning house on Friday afternoon, no eggs with blood spots, washing all meat, etc. We also had some genetic anomalies -- shovel teeth (sinodonty), palatal tori and large rear cranial extensions, as well as polydactylism.

Tell us more.

ECH:  Over the course of the past decade I have been found to have Native American, Spanish, Ashkenazi Jewish, African, Mediterranean and Gypsy/Northwestern India ancestry. My Dad turned out to have substantial Gypsy and African ancestry. He and I share a large cranial rear extension that I believe likely comes from the African ancestry -- the photos I have seen of the !Kung Bushmen look just like our head shapes. My Mom has Native American and/or Sino-Siberian ancestry. She also possessed the Asian teeth and palatal tori found in this group.

You've written several books and articles with Donald Yates; how did that come about?

ECH:  We shared ancestry from the Coopers, a prominent pioneer family in Daniel Boone’s time. In 2000, I wrote him out of the blue when he was a professor in Georgia and introduced myself and asked if possibly the Coopers were Jewish. We began to correspond by email. I told him I was sure one of the reasons I was working so hard to figure out the Melungeon story was because I had to figure out who I am. “Up until last year,”  I remember telling him, “I thought I was Scotch-Irish, English , white and Presbyterian.” It was a big transition to Sephardic, brown and Jewish. It turned out that we were distant cousins and had numerous links in our Melungeon ancestry.

What was a typical publication?

ECH: One article was called “Suddenly Melungeon! Reconstructing Consumer Identity Across the Color Line.” This was published by Routledge in 2007 in a handbook on consumer culture theory edited by Russell Belk.  

How did the Jewish findings play out?

ECH:  On a personal level, both Don and I, as well as his wife Teresa, returned to Judaism, he and Teresa in Savannah and I in New Jersey. On a professional level, we started the Melungeon Surname DNA Project, which focused on Scottish clan and Melungeon surnames (i.e., male or Y chromosome lines), and later included Native American mitochondrial DNA.  Initially, many people in the genetic genealogy community were frustrated that the incoming Jewish DNA results were not originating in the Middle East, as they had strongly believed and hoped, but were showing a lot of Khazar, Central Asian, Eastern European and Western European/Spanish/French input.

Can you elaborate?

ECH:  Critics were not happy that DNA was proving a wider and more inclusive picture of the Jewish people. Where Don and I have performed a service, I believe, is by just following the DNA trail and accepting new findings (e.g., the Gypsy/Roma) when they come in, instead of clinging to an a priori theory/belief/wish, for instance, the claim of a Middle Eastern origin for the majority of Jews.

What tests have you ordered from DNA Consultants?

ECH: I ordered every test as they became available over the years, first the Y chromosome and mitochondrial or male-line and female-line tests and later the autosomal or DNA fingerprint tests that analyze your total ancestry.  I helped organize the first autosomal Melungeon study by contributing samples from my mother and brother and obtaining samples from well-known Melungeons like Brent Kennedy and his brother Richard. Increasingly, our testing took on the aspect of a family group study. For instance, I was able by comparing multiple results from relatives to reconstruct my father’s ancestry quite satisfactorily, even though he died many years ago. I took the Rare Genes from History for all available family members. There is a streak of the Thuya Gene and First Peoples Gene in all of us, as well as the Sinti Gene (which is Gypsy), while my brother Dick got our father’s Khoisan Gene, which is African. Incidentally, it has the same source as the !Kung people and head shape I mentioned before.

If you had H. G. Wells' time machine where would you go?

ECH: I would love to be able to visit my ancestors and see what they looked like, where they lived, how they lived and learn how they got to Appalachia from such disparate parts of the world. I wish I could talk with them. My project now is to visit all the places they are known to have come from and see what the architecture, climate, food, and people are like. That is about as close to "meeting" them as I will be able to get. So far, I’ve traveled to Scotland, Ireland, Wales, England, Spain, Tunisia and Morocco on the trail of my Sephardic Jewish ancestors. I am trying to get to the Silk Road to see Central Asia, Turkey and Northwest India in the near future.

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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

 

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. 

We previously reviewed Jon Entine's masterful book on Jewish DNA:  Rounding Up the Usual Suspects. But Arlene Belzer has now sent us a new video on the subject with an interview of the author from Israel. The Israeli video is perhaps the latest word on this controversial subject, and everyone with an interest in the genetic character of the Jewish people should watch it.








http://youtu.be/rTJFziTzOeg

Short answer: pre-Roman times.

As is well known, Haplogroup E1b1b1 accounts for approximately 18% to 20% of Ashkenazi and 8.6% to 30% of Sephardic Y-chromosomes. This North African type appears to be one of the major founding lineages of the Jewish population.[i]

In Britain, this quintessential Jewish type (together with J, another telltale sign of Middle Eastern roots) is absent or negligible in many towns and regions but reported in elevated frequencies in Wales (Llanidloes 7%, Llangefni 5%), the Midlands (Southwell, Nottinghamshire 12%, Uttoxeter 8%), Faversham in Kent (9%), Dorchester in the West Country with historic harbors (7%), Midhurst in West Sussex commanding ancient sea-ports (5%)  and the Channel Islands, always an important crossroads of influences (5%).[ii] Bryan Sykes’ survey of paternal clans in England and Wales confirms significant traces of the E haplogroup which he dubs Eshu in southern England (4.9%) and Wales (3.1%).[iii] It reaches its highest point in Britain in Abergele, Wales (nearly 40%), an anomaly that has been attributed to Roman soldiers of Balkan origin but may have alternative and more complex explanations.

See our blog post "Right Church, Wrong Pew," arguing that the footprint of E in Britain is attributable to North African influence, not the descendants of Roman legionnaires from the Balkans.

In 2011, Llangefni  and Wrexham in North Wales became the focus of a call for local men to provide samples of their unusual DNA. A team of scientists lead by Andy Grierson and Robert Johnston from the University of Sheffield hoped to link the migration of men from the Mediterranean to the copper mined at Parys Mountain on Anglesey and on the Great Orme promontory nearby. A preliminary analysis of 500 participants showed 30% of the men carried E1b1b, compared to 1% of men elsewhere in the United Kingdom.[iv]

Significantly, Welsh tradition associates the Iron Age hilltop town on Conwy Mountain known as Castell Caer Seion with a settlement of ancient Jews. This site overlooks Conwy Bay on the north coast of Wales and lies on the ancient road between Prestatyn in Denbighshire and Bangor in Gwynedd opposite Angelsey.  In the Black Book of Caermarthen, the Welsh national bard Taliesin casually remarks in the persona of the battling hero,

When I return from Caer Seon,

From contending with Jews,

I will come to the city of Lleu and Gwidion.[v]

Every year in the United States about half a million paternity cases are performed proving or disproving whether an alleged father is the true parent of a child. Sometimes there is a court order to do this; at other times, it is sheerly for personal information. The determination of parentage is made based on a simple comparison of a small rock-hard number of genetic markers in the DNA fingerprint of the child and alleged father. Samples are extracted from a 30-second cheek swab and processed at any of an estimated 2,000 forensic labs across the country. The standard in place since about 1997 has been a set of 30-32 biallelic or double values each person carries on loci spread across their chromosomes, making for a virtually unique identification signature that reflects the equal DNA input of mother and father (and in fact all grandparents and all ancestors).

Often termed CODIS markers (standing for Combined DNA Identification System), these alleles or variations are the magic numbers underlying the popularity of paternity tests as well as the national passion for jailing or exonerating crime suspects. If a value is found in the DNA profile of the child and is not present in the two observed values of the alleged father on the same locus, this constitutes what is known in the paternity business as an exclusion:  the alleged father is almost certainly not the true father. Conversely, if all the alleged father’s values can be detected in the child’s on each location, one after another, that male is judged to be the child’s biological father to a 99.999% certainty. Paternity tests are simple math.

A famous paternity test involved proving who was the true father of the baby born to Anna Nicole Smith in 2006. After her death in early 2007, several men came forward claiming to be in father, including a European prince, Anna Nicole’s bodyguard and a convict who had been a former boyfriend. Larry Birkhead pressed his case. When the results came in, he was declared by Bahamian court to be the baby’s biological father. The child’s original birth certificate was amended to show this.

Can paternity testing be used in a reverse process to establish the identity of a father, given only the child’s DNA profile? No, but with enough DNA profiles available for comparison the missing member of a family group can be reconstructed by comparing alleles they must share, called obligate.  Doing so is a matter of logic and statistics, mostly just either-or, deductive logic.

I became interested in reconstructing a parent’s profile after many of DNA Consultants’ customers inquired if such a calculation or estimate was even possible. Some were adopted persons who had no recourse to testing their parents, some knew one parent but not the other, and some had no access to parents. They were either uninterested or unavailable. In a special category were females who were only-children with both parents deceased who wanted to know something about their father, but who could not take a Y-chromosome haplotyping test, as they did not carry a copy of their father’s male DNA. In this respect, autosomal DNA testing is the great equalizer.

My father, Lawden Henry Yates, died in 1978. My mother, Bessie Cooper Yates, lived to the advent of DNA tests, but I failed to obtain any sample from her before her death in 2006. I had siblings and half-siblings still living, however, so in 2010, I constructed a family group autosomal DNA study with the help of Crystal Wagner at Chromosomal Laboratories/Bode Technology. The results were very satisfying. This paper and blog post will serve as a report to those who are interested.

Step One
I was fortunate to have the participation of three half-sisters by my father, along with his second wife, their mother. Comparing mother and daughters I was able to verify the obligate alleles each daughter must have received from the mother.

Autosomal alleles are fixed in our genealogy, have little or no mutations (unlike YSTRs, which mutate from generation to generation, as do mitochondrial nucleotide positions, though more gradually over time)[*] and derive from both parents equally by recombination at the moment of conception. They are copied and preserved without change in every cell of our bodies. The mother is responsible for half of the equation.  By a process of elimination the other number on each row of the lab report must represent the father’s contributions.  This method is completely logical and unequivocal. There can be no other answer to the problem. No studies suggest these pieces of our double helix DNA change significantly in transmission from one generation to the next or mutate over time in genealogies. Their values and patterns are strictly attributable to heredity.

Step Two
The father’s alleles are confirmed by a comparison with three children by his first wife, my mother.  

Step Three
By the same watertight process we can now proceed to the mother’s reconstructed DNA profile. In it, we can expect to visualize the final piece of the puzzle, proceeding from the known to the unknown according to the immutable laws of autosomal DNA and genetic inheritance.

We have arrived at my mother Bessie Yates’ DNA profile by a multi-step process of extrapolating it using three of her children and three children by her husband’s second marriage, along with the test results of my half-sisters’ mother. Seven tested profiles yielded two reconstructed ones. In the process we have also recovered my deceased father’s DNA profile.

Separating Mother and Father’s Contributions to Ancestry
Having overcome these hurtles, I was most interested in the utility of the results. I felt confidant about the method. But what excited me most was to see how my own autosomal ancestry results might be respectively apportioned in my parents. For this, I ran a DNA Fingerprint Plus on them both. The findings were very satisfying to me personally, helping solve many questions I had always had about what ancestry I got from my father, what from my mother and what from both.

Let’s start with American Indian admixture. My own DNA Fingerprint Test, as well as percentage tests through another company, suggested a relatively large amount, perhaps one-quarter all told by various measures, but family tradition had placed Native American heritage solely on my mother’s side. To be sure, my mother gave me a Native American mitochondrial haplotype, indicating a female line going back to a Cherokee woman in Georgia, traced as far back in records as 1790. Extensive genealogy research showed, however, that my father’s great-grandmother was also a Cherokee with the surname Thomas from North Carolina. What did the new autosomal DNA profiles say?

On a rough measure, I have received a “double dose” of Native American II, a marker co-relating with 80% of 24 tested American Indian populations in the atDNA 4.0 database. (Two siblings and one half-sibling received only single doses.) This seemed to indicate that I had some degree Native American (not possible to say how much) from both parents. True enough apparently, judging from the top world matches for my mother and father. I give here the top ten for comparison.

These results confirmed that my father did have some Native American, although evidently not as much. They also suggested that although both bore about the same mixture of European and Native American ancestry (including high matches to Melungeon), my mother had a more pronounced Native American cast, her highest match being to North Asian, one of the supposed Asiatic feeder populations of Native Americans, whereas my father’s top match was European American. Based on profile frequencies, my father was five times more likely to be European American than American Indian if subjected to forensic profiling, whereas my mother was 18 times more likely to come out as a Siberian Native than Northern European. Sometimes, it seems, exotic ancestry rises to the top. My overall conclusion was that my mother probably had 3/8 and my father 1/8 Native American heritage, which corresponds to their proved genealogies.

In my own profile, combining those of my parents, here are my megapopulation results:

Self (Donald N. Yates)

According to these frequencies, my mother and father’s Native American ancestry reinforced each other in me to make my top four matches Native American (or Siberian-Mongol-Turkic), so that I am about twice as likely to be graded into the Native American category by population statistics than the European. Similar conclusions emerged from my siblings’ tests, and a diminished presence of Native American indicators was confirmed in my half-siblings, although their mother seemed to evince some Native American as well as my father, the shared parent. All participants in this study had grandparents born in North Alabama.

Further observations are possible. For instance, I was surprised to see a large indication of Jewish ancestry in my father’s profile. Genealogy confirms as much, as the family surname is Hebrew (an anagram of Ger Tzedek similar to Katz, Kohen Tzedek). The emigrant Yates figure was reportedly an English Jew in seventeenth-century Virginia. My mother also showed Jewish ancestry. Both parents matched Melungeons, an Appalachian ethnic type suspected to have Sephardic Jewish forebears. My father’s family included uncles named Josephus, Manaen, Irbin, Azariah, Lazarus and Sherith—apparently his Middle Eastern matches were truthful to a partial Muslim background. My mother’s mother was named Palestine, and the names Isaac and Jacob were ubiquitous in her family tree. But neither side of the family claimed any Jewish heritage. It was left to autosomal DNA to reveal that hidden inheritance.

Although never performed before to my knowledge, this method of reconstructing autosomal profiles can be useful to others seeking to recover unavailable relatives’ genetic fingerprints and to separate parents’ contributions to their children’s ethnic and ancestral stories. Since it is based on immutable markers in DNA it rests on more solid ground than Y chromosome alleles or mitochondrial mutations. The challenge in exploiting the method is to have enough subjects in your family group study. In my case, I was fortunate to have a prolific father with six living children. I would like to conclude by thanking all my siblings, half-sisters and my father’s widow. Their participation made it possible to present a true first in DNA genealogy.

Read the working paper
A Method of Reconstructing Parentage and Ancestry by Autosomal DNA Profiles

Go to Learn about DNA

Ruling Applies to All Their Ancestors and Descendants

Majorcan Jews belong to the Sephardic (Spanish) division of world Jews. The name of the island is Majorca in Spanish, Mallorca in Catalan (in whose orbit historically it fell). In 2011, a Rabbinical court recognized the Majorcan Chuetas and all their genealogically related families as Jews. It is possible that the Franciscan Majorcan Junipero Serra who founded California's Spanish mission system was Jewish (Converso), as was probably the family of Christopher Columbus.

DNA Consultants is fortunate to have population data on Majorcan Jews. Here is a description, along with some links on Majorca's history and people. The Majorcan – Chueta (also spelled Mallorcan and Xueta, respectively) population data represent DNA samples from 102 unrelated Chuetan (Jewish) individuals on Majorca (http://en.wikipedia.org/wiki/Majorca) -- one of the Balearic Islands (http://en.wikipedia.org/wiki/Balearic_Islands) in the Mediterranean Sea, which mark the easternmost part of the Kingdom of Spain, the nation’s official title (http://www.state.gov/r/pa/ei/bgn/2878.htm and http://en.wikipedia.org/wiki/Spain). Samples were obtained by the Genetics Laboratory of the Biology Dept. at the University of the Balearic Islands.

For more details on the Chuetas, also called Majorcan Jews, see http://www.majorca.com/v/history/; http://en.wikipedia.org/wiki/Chueta;
http://www.espana-spain.com/sephardic-route-palma-de-majorca.html http://www.myetymology.com/encyclopedia/Chueta.html; http://www.jewishideas.org/min-hamuvhar/welcoming-chueta-back-his-jewishness; http://www.skyscrapercity.com/showthread.php?t=234668 http://www.northsouthguides.com/history_of_mallorca.html
http://www.northsouthguides.com/mallorca_history.html

Source publication:  Genetic Variability at Nine STR Loci in the Chueta (Majorcan Jews) and the Balearic Populations Investigated by a Single Multiplex Reaction, IJLM, 2000, p263-267.