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Where Do I Come From: Donald Yates

Monday, July 29, 2013

Where Do I Come From

Real People's DNA Stories 


Sizemore Indians and British Jews

By Donald N. Yates

As soon as EURO DNA was released last month I quickly studied my new list of European nationalities where I have significant ancestral lines according to DNA Consultants' new autosomal population analysis. I had come to know and accept, of course, the usual suspects, compiled from the 24 populations available from ENFSI (European Network of Forensic Science Institutes). But the new list represented 71 populations and far surpassed ENFSI or any other database in commercial use. It had, for instance, the first European comparisons for countries like Hungary, Lithuania, Malta and Iceland. So how would my familiar matches—Scotland, Ireland, England, Belgium and the rest—shake out in the new oracle?

Some of the top matches—above British Isles or Northern European ancestry—were Central European. Here were the top 20:

Rank European Population Matches
1 Slovakia – Saris (n=848)
2 Finland (n = 469)
3 Slovakia – Zemplin (n=558)
4 Netherlands  (n = 231)
5 Slovakia – Spis (n=296)
6 Romanian - Transylvanian - Szekler (n = 257)
7 Romanian - Transylvanian - Csango (n = 220)
8 Scotland/Dundee (n = 228)
9 Switzerland (n = 200)
10 England/Wales (n = 437)
11 Ireland (n = 300)
12 Italy (n =103)
13 Denmark  (n = 156)
14 Romanian (n=243)
15 Swedish (n = 311)
16 Serbian - Serbia / Vojvodina / Montenegro (n = 100)
17 Icelandic (n=151)
18 Estonia (n = 150)
19 Romanian - Transylvania/Banat (n = 219)
20 Norwegian (n=1000)

Slovakia? Romania? To be sure, I had always had a fascination with both countries. In my salad days I studied in Europe and traveled to Bratislava, where I fell in love at first sight with the chiseled blonde visage of a friend of my university classmate. And I had also been to Romania in the days of its Communist regime, when my long-haired travel companion and I were welcomed like long lost relatives or conquering pop heroes. 

Admittedly, the results of an autosomal ancestry test are cumulative and combinatory. While they do reflect all your ancestry, as no other test can, you are cautioned not to use the matches to try to pinpoint lines in your family genealogy. There is always a temptation to over-interpret. 

My European admixture results from AncestryByDNA had yielded a confirmatory result:  20% Southeast Europe. That struck me at the time as odd. Yet Hungarian was now one of my top metapopulation results, too. (Remember, Hungarian data did not figure into ENFSI because Hungary is not in the European Union.)

The Scottish (my grandmother was a McDonald) made sense, as did all the other matches from what I knew through years of paper genealogy research. But I was unaware of any strong Central European lines.

Sizemore Research:  Pitfalls of Genetic Genealogy
Then I recalled the Sizemores. My great-great-grandmother was a Sizemore, and they were multiply connected with my Coopers, my mother's maiden name. Could the Central European effect in my EURO result be from the Sizemores?

Much ink—or at least many keystrokes—has been expended on the Sizemore controversy. There are pitched battles on genealogy forums and edit wars in cyberspace. One armed camp has them down as Melungeons and admixed Cherokees with crypto-Jewish strains. Another holds it as an article of faith that the Sizemores were a lily-white old Virginia British family and the surname comes from something like Sigismund (think Goetterdaemmerung). Y chromosome DNA shows ambiguous conclusions:  you can visit the advertisement page sponsored by Family Tree DNA. 

Alan Lerwick, a Salt Lake City genealogist, upset the apple cart some years ago by linking America's Sizemores to Michael Sismore, buried in the Flemish cemetery of the Collegiate Church of St Katherine by the Tower in London in 1684. That was the same parish as my Coopers lived in. Then and now, it is the most Jewish section of London.

Sizemore is not a British surname before the sixteenth century. It was clear to me long ago that neither my Sizemores nor my Coopers were Mama Bear, Papa Bear families. Spurred by my EURO DNA test results, I dug into my subscription at Ancestry.com and learned that Michael Sismore was recorded as being born as Michael Seasmer in Ashwell, an important village in north Hertfordshire, November 1, 1620. His parents were Edward Seasmer and Betterissa (a form of Beatrice). New information! Alert the list moderators and surname project guardians!

Seasmer is undoubtedly the same as Zizmer, an old Central European Jewish surname adduced in multiple families in Israel, Romania, Czechoslovakia, Germany, Austria, Russia, Moldavia and the United States. Edward and Michael are favored first-names in the U.S. branches. The Hebrew letters, which can be viewed on numerous burials in Israel, are  (in reverse order, right to left) RMZZ. Cooper is a similar Jewish surname, common in Russia and Lithuania and Israel as well as the British Isles and the U.S. In fact, my father's surname, Yates, is a Hebrew anagram common in the same countries, meaning "Righteous Convert."

Hertfordshire was an important center for British Jewry, mentioned in the works of Hyamson, Jacobs and others (see map above). A good hypothesis to explain the transformation of Michael's name from Seasmer to Sismore and thence to Sizemore is this. His grandfather, a Zizmer, came to England in the time of Elizabeth, perhaps via the Low Lands, possibly as a soldier or cloth merchant. This could account for Michael Sizemore's burial in the Flemish cemetery of St Katharine's by the Tower, usually reserved for foreigners. It also explains the predilection in descendants for such names as Ephraim, Michael, Edward, William, John, Richard, James, George, Hiram, Isaac, Samuel, Solomon and Henry. And why girls were named Lillie, Lydia, Louisa, Naomi, Pharaba, Rebecca, Sarah and Vitula. The last name (also found in my wife's grandmother's name) was a Jewish amulet name. It meant "old woman" in Latin and was given to a child to augur a long life. 

Zismer took the form of Cismar, Cismarik, Zhesmer, Zizmor, Ziesmer, Zausmer, Cismaru and Tzismaro—all amply attested in the records of European Jewry, including Jewish Gen's Holocaust Database, with the records of over two million victims and survivors of the Nazi genocide of World War II. I am proud of my Jewish heritage through my great-grandmother and through my half-blood Cherokee Indian mother Bessie Cooper Yates. 

Thank you for indulging me in this genealogical excursion into a family mystery. Like the restaurateur, I would be to blame if I didn't eat in my own establishment. I can confidently say that DNA Consultants' new EURO DNA is a smorgasbord of genetic delights for those jaded by the old-fashioned sex-linked testing. I thank our R&D team, in particular Professor Wendell Paulson, our head statistics consultant, along with all those who helped vet its amazing power, and I encourage you to try it today!














Comments

Zoltan commented on 13-Sep-2013 03:48 PM

About Seizmore. If it really relates to Zizmer, Cismar etc. then it is a pure Hungarian surename: Csizmár, with the meaning of boot maker (Csizma=boot from the old turkish word of cizme)
Please note that the refferred areas of Slovakia and Transylvania are former Hungarian territories, so the connection is clear and matches with your DNA.

I do not know when you wrote the article but Hungary is in the EU since 2005.

I hope I could help.


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Where Do I Come From: Shawn

Monday, July 22, 2013

Where Do I Come from:  Shawn

Real People's DNA Stories

Ethnicity Beyond European Migration

By Shawn

My journey into DNA testing began with my desire to expand on my known heritage, while clarifying debated Jewish ancestry.  What I have found in return is that my ancestral paper trail only uncovers a small portion of the blood that runs through my veins.  My DNA Consultants results, for the most part were quite surprising.  My European matches were fairly consistent with my country origins on paper and surrounding areas.  The major surprise, however, was that my number one European match was Romani/Gypsy and my number 10 match was Czech Republic.... 

Things became much more interesting with my World Population Matches.  My scores (in order) were Romani/Gypsy, Middle Eastern, African, Iberian, Central European, African-American, Jewish, Mediterranean European, European American and Eastern European.  I also came up with Native American admixture to top it off.  These results are causing me to believe that there may be a line or more of family lineages that I have yet to tap into. 

Looking back on things now, I have received comments from others concerning my phenotype such as "I'm not sure what you are,” "You don't look Irish" and "You must have some Black ancestry."  Some have even just assumed I was Hispanic or Caucasian.  Interestingly enough, almost all acknowledge that they see my Italian/Spanish phenotype, while a few also see slight Native American.   

While my results provided insight into how diverse my blood really is, they also put an end to an age-old family debate as to our Jewish ethnicity.  One of my relatives from a few generations past would passionately defend her position that our family line was indeed Jewish, while another family member would vigorously put forth his position that we were not Jewish.  He would try to prove our non-Jewishness any time he could.  I also had another family member along that same family line say that he almost did not get hired for a job because the hirer thought he was Jewish.  I always believed these accounts, especially since as young as I can remember I have found this side of my family (Italian and German) to phenotypically look Italian and/or Jewish.  

So where does all this leave me now?  My results show my blood is much more than simply Italian, French, Irish and German.  They confirm family testimony of Spanish/Portuguese/Iberian and Jewish ancestry.  Perhaps more interestingly, my results leave me re-assessing my ethnicity or multi-ethnic heritage, end years of family verbal passages or debates and leave me with intriguing new ancestries that are waiting to be discovered. 

Comments

Maria OConnor commented on 23-Jul-2013 12:42 AM

Shawn: Countries frontiers are artificial. For example, there are people of celtic heritage in northern Spain, northern Portugal, all over Ireland, all over England, all over Scotland, all over Wales, Southern Germany, northern France, Northern Italy, etc. All of them, even considering the come from different places have the same celtic DNA. So, if you have an ancestor from Spain or Portugal, could be of celtic origen, or mediterranean origen.
If a person has jewish sefardi dna, it could be originated from Southern Spain, Southern Portugal, North Africa, Middle East, etc.
Also, in South America there are great numbers of people of European ancestry, including non hispanic non portugue ancestry, like Irish, German, Italians, etc.
Is quite complicated, due to ancient and new migrations.


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Khazarian Hypothesis of European Jewish Origins Vindicated

Friday, March 22, 2013

New Genetic Study Shows Rhineland Hypothesis False, 'Thirteenth Tribe' Theory Correct After All

In "Heretical History" and numerous other posts, we have argued that the contributions, genetic and cultural, of the Turkic-Iranic Khazars deserve much more attention than the cosseted theories of European Zionist Jews and the official views of the state of Israel on Jewish history. A new study by Eran Elhaik titled "The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypothesis," (Genome Biol. Evol. 5.1:61-74) bears out our thinking with hard evidence that seems likely to settle that rancorously-fought-over question once and for all. 

According to Science Daily (Jan. 16, 2013), "Despite being one of the most genetically analysed groups, the origin of European Jews has remained obscure . . . but the new study . . . sets to rest previous contradictory reports of Jewish ancestry." Elhaik's findings strongly support the Khazarian Hypothesis, as opposed to the Rhineland Hypothesis, of European Jewish origins. 

Ashkenazi ("Germanic") Jews embraced a Western European origin myth not only because it presented Jews as very white, at the top of the race pyramid, but because of the prestige it brought them of being a spin off of the Roman Empire. 

The Khazarian thesis acknowledges that the most important element is Middle Eastern among "brown" peoples, and that the period of efflorescence of Judaism in Europe began in the late Middle Ages under the influence of migrating Khazars. 

That's an entirely different version of history, one much closer to Arthur Koestler's "Thirteenth Tribe" account, a theory for which he was castigated by fellow Jews and especially Zionists. 

The new study was not possible until recently, when many of the gaps in Caucasian and Jewish genetics were filled for the first time, using autosomal approaches rather than sex-linked haplotype surveys. Elhaik's masterwork examines a comprehensive dataset of 1,287 unrelated individuals in 8 Jewish and 74 non-Jewish populations genotyped over a range of half a million single nucleotide polymorphisms (SNPs) or markers. These data were adapted from a study by Doron Behar and colleagues from three years ago.

The central role of Khazaria was also not wanted or wished for among Eurocentric scholars, who tended to denigrate Ostjuden or Eastern Jews. Few historians conceded even the fact that Khazaria was a Jewish state that lasted nearly a millennium, where Hebrew was spoken, preferring to think of it as a sort of travelers tale or land of religious fiction.  

Elhaik used seven measures of ancestry, relatedness, admixture, allele sharing distances, geographical origins and migration patterns to identify the Caucasus-Near Eastern and European ancestral signatures in European Jews' genome along with a smaller, but substantial Middle Eastern genome. "The results were consistent in depicting a Caucasus ancestry for all European Jews," according to Science Daily

Heresy in a Nutshell

Elhaik wrote:  "The most parsimonious explanation for our findings is that Eastern European Jews are of Judeo-Khazarian ancestry forged over many centuries in the Caucasus. Jewish presence in the Caucasus and later Khazaria [a Hebrew-speaking Central Asian empire] was recorded as early as the late centuries BCE and reinforced due to the increase in trade along the Silk Road, the decline of Judah (1st-7th centuries), and the rise of Christianity and Islam. Greco-Roman and Mesopotamian Jews gravitating toward Khazaria were also common in the early centuries and their migrations were intensified following the Khazars' conversion to Judaism… The religious conversion of the Khazars encompassed most of the Empire's citizens and subordinate tribes and lasted for the next 400 years until the invasion of the Mongols. At the final collapse of their empire in the 13th century, many of the Judeo-Khazars fled to Eastern Europe and later migrated to Central Europe and admixed with the neighbouring populations."

According to Science Daily, Elhaik's findings explain otherwise conflicting results describing high heterogeneity among Jewish communities and relatedness to Middle Eastern, Southern European, and Caucasus populations not accounted for under the Rhineland Hypothesis. Although the study links European Jews to the Khazars, there are still questions to be answered. How substantial is the Iranian ancestry in modern day Jews (Khazars were themselves mixed)? Since Eastern European Jews arrived from the Caucasus, where did Central and Western European Jews come from, those usually called Sephardic?

Finally, if there was no mass migration out of Palestine at the 7th century, what happened to the ancient Judeans? --Shlomo Sand, the author of The Invention of the Jewish People, has maintained that there never were any expulsions or exoduses out of Palestine, only wholesale conversions to Islam. Thus, the true heirs of Judah are the persistent inhabitants who still occupy Jerusalem and the Holy Land, that is, Palestinians. 

It is ironic, to say the least, that these ancient Judeans are dispossessed by a nationalist colonial power with roots no deeper than nineteenth century Europe which exercises a force majeur based on mistaken notions of genetics and history. 

Photo above:  Arthur Koestler, the arch-heretic and persona non grata in the eyes of Jewish authorities, was unorthodox politically, religiously and sexually. 


Comments

Lee commented on 06-Jun-2013 09:23 PM

Your comments re: Rhineland vs Khazar theories are confused and wrong. Rhineland theory asserts that Jews origin is found in Palestine, firmly in the Middle East, not Europe. In fact, this belief is the basis for Jews returning to Palestine to claim what they see as their true ancestral land. This, of course, was critical in touching off the ongoing conflict in Palestine. The Kharzar theory posits that Jews are mostly descended from Turkic peoples, those who occupied the Caucus Mountain range. These people would be much closer to what you refer to as the "top of the race pyramid" because they would be far whiter than the "brown people" of Palestine aka the Middle East. So, you have your theories arse-backwards, if you will.

Hezakiah Levinson commented on 21-Nov-2013 06:59 PM

Hogwash. Archaeology shows Jews in Europe over three hundred years before the Khazarian Monarchy even converted.The Köln Synagogue in Cologne, Germany has been excavated 2007/2012 and dates clearly pre Carolingian (bef. 780/90). There is at the moment some strong evidence that it dates back to the early 4th century when emperor Constantine in 321 issued a privilege for the Cologne Jews. This has been confirmed recently by the find of a rainwater mikveh of the 4th century inside the building complex). The oldest synagogue in Western Europe uncovered in an archaeological dig to date is the Ostia Synagogue in the ancient Roman port of Ostia, in Italy. The present building, of which partial walls and pillars set upright by archaeologists remain, dates from the 4th century. However, excavation revealed that it is on the site of an earlier synagogue dating from the middle of the 1st century CE, that is, from before the destruction of the Temple.The Main Synagogue of Barcelona, built in the 3rd or 4th century, has been described as the oldest synagogue in Europe.


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An Anthropology Student's Theory

Monday, March 18, 2013

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

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

.
This means that this 'unlikely event' has a probability of 63.2% of happening if 1000 chances are given, or over 99.9% for 10,000 chances. In other words, a highly unlikely event, given enough tries, is even more unlikely to not occur.

That was the Law of Truly Large Numbers. What I have below is from a computer scientist:   

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

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

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

Calculations and Premises
If the population in 1500 was 500 million, and it is 6 billion today (12x larger).

If the average generation length is 30 years, there are 17 generations in 500 years.

So the average number of surviving children per mother is exp((log 12)/17) = 1.157

Since a child has two parents, the average number of surviving children per person is 2 * 1.157 = 2.315

So this is the average growth rate per generation for the descendants of a person in 1500.
2.315^17 = 1.575 million. So an average person in 1500 has about 1.5 million offspring alive today.  Sampling from the whole world, the probability that a random person from 1500 is an ancestor of a random person in 2000 would be 1.5 million / 6 billion = 0.025%. If you were only considering people in a region like Europe, it would probably be something like 1.4 million / 700 million = 0.2%.

Here is my theory:

Let's say 500 years ago, due to this probabilistic law, almost everyone alive today had at least one ancestor from like say, China, Japan or other far-off places. This may not apply, of course, to isolated populations. 

Would this theory likely be true given enough time?

Thank you for your time and efforts. I have never been disappointed with your products and your postings are quite interesting for me,especially, being an anthropology student.

Bailey Edsall-Parr

Comment? Contact the author at baileyedsallparr (a) yahoo.com.


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Genetic Genealogy Like Astrology?

Monday, March 18, 2013

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 of DNA Consultants.

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.

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Some Indians Migrated to Australia 4,000 Years Ago

Tuesday, January 15, 2013

Genome-wide data substantiate Holocene gene flow from India to Australia

  1. Mark Stonekinga
  1. Edited by James O’Connell, University of Utah, Salt Lake City, UT, and approved November 27, 2012 (received for review July 21, 2012

    From PNAS Online:  http://www.pnas.org/content/early/2013/01/09/1211927110

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

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Junk DNA? We Don't Think So

Monday, January 14, 2013

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?

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Is There an Irony Gene?

Thursday, December 13, 2012
Richard Lewontin's Disappearing Act

The octogenarian bête noir of biological determinism reviews three new books about why we should be proud of our ancestry--or just be quiet about it. "There is a certain irony," he writes, "in claiming an undemonstrated biological superiority for a group, six million of whom were slaughtered for their claimed natural degeneracy." If your dynosaur feathers are not ruffled yet, read on. 

"Is There a Jewish Gene?"

by Richard Lewontin

December 6, 2012,

The New York Review of Books


Legacy:  A Genetic History of the Jewish People
by Harry Ostrer
Oxford University Press, 264 pp. $24.95


The Genealogical Science:  The Search for Jewish Origins and the Politics of Epistemology
by Nadia Abu El-Haj
University of Chicago Press, 311 pp., $35.00



Zionism and the Biology of the Jews (Zionut Vehabiologia Shel Hayehudim

by Raphael Falk
Resling, 2006 (not yet published in English)
Richard Lewontin.
Courtesy Istituto Veneto.

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...

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Behind the Numbers: Phyllis Starnes

Tuesday, November 20, 2012

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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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Evolution and Ancestry: DNA Mutation Rates

Tuesday, October 23, 2012
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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.  
 
A table summarizing their findings and older data is provided below for DNA testing customers' convenience.

 

DNA Mutation Rates

Study or Source

Type of DNA

Sample or Method

Rate per Generation

Time Depth in Years

Sun 2012

autosomal

microsatellites

2,477 mutations

in Icelanders

.001-

.0001

25,000 to

250,000

Kong 2012

single nucleotide

polymorphisms

4,933 mutations

in Icelandic trios

63.2 or

.000000012

Very great

 

Butler 2009

Core CoDIS STRs

(microsatellites)

compiled from

studies

.0028-.0001

9,000 to

25,000

Zhivotovsky 2004

Y chromosome

STRs

Y haplogroup

comparisons

.00069

36,000

Heyer 1997

Y chromosome

tetranucleotides

42 males in forensic database

.002

12,500

FamilyTreeDNA

2004

Y chromosome

STRs

Estimated from

customer base

.004

6,250

Brinkmann 1998

STRs (CoDIS

markers)

10,844 Father-son comparisons

0-.007

3,500 to

Very Great

Parsons  1997

mitochondrial

DNA

134 mtDNA

lineages

.000029

862,000

DNA Consultants

Rare Genes

from History

average estimate

across loci

.001325

19,000

 
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

 











 
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