October 18, 2010

Joe Pickrell on his ancestry

Joe Pickrell has a nice post on his ancestry at Genomes Unzipped, prompted in part by my use of the EURO-DNA-CALC program on his data. He explores his data using PCA on a much larger set of markers than the 192 used by EURO-DNA-CALC (the overlap between the Price et al. paper on which it is based and the 23andMe set).

I did not report Joe's results in my re-analysis of the Genomes Unzipped data, as his confidence interval intersected 0. For the record, his sample, like that Vincent Plagnol, didn't show any of the "yellow" cluster that was shared by Arabs and Dan Vorhaus (an Ashkenazi Jew).

Joe's explanation that his anomalous results is due to similar allelic frequencies in some markers between Ashkenazi Jews and southern Europeans is quite interesting, and it is based on a dissection of the markers used by EURO-DNA-CALC.

As I stated in my reanalysis of Plagnol's data, his result might also be due to:
a European-origin component in the composite Ashkenazi Jewish gene pool that he happens to share.
Joe's discovery about similar allele frequencies in some markers between Ashkenazi Jews and Italians is quite interesting in terms of my theory about the origin of the European component in the Ashkenazi Jewish gene pool.

Some early studies on AJ, using Y-chromosomes (pdf) overestimated their Near Eastern component by considering them a mix between Levantine and north/central European populations. But, this made the assumption that Jewish ancestors took a Lufthansa flight to Germany rather than spend 1,000+ years in the territory of the Roman Empire and the Hellenistic world where there might also have been introgression of European elements into their gene pool.

Thus, it may very well be that Ashkenazi Jews are distinctive with respect to NW Europeans both in terms to an ancient Near Eastern ancestry (shared with Arabs and "discovered" in my re-analysis) and with respect to Southern European ancestry corresponding to particular populations they interacted with during their sojourn in the Roman Empire.

To conclude, the release of the Genomes Unzipped data on the web has been beneficial to all involved: a few bloggers like myself could run and test their tools on the data, and people like Joe could give feedback on these tools. This is a strong argument in favor of open source tools and public available data and against the use of proprietary databases/ancestry estimation methods/datasets barricaded behind various controls.

As I continue my various ADMIXTURE-experiments, I will be sure to revisit the Genomes Unzipped folk and all those who wish to join them.

UPDATE (Oct 23): A much more detailed analysis of Genomes Unzipped individuals.
UPDATE (Nov 1): Joe Pickrell discovers Jewish great-grandparent

25 comments:

Gioiello said...

This is what I wanted to hear from you and this is what I have said in starting my presence on the blogs. My two banishments were undeserved.

Marnie said...

to boldly go where no man has gone before

http://www.youtube.com/watch?v=hdjL8WXjlGI

Gioiello said...

The great Latin poet, probably from an Etruscan family from Campania, Titus Lucretius Caro, who wrote the poem “De rerum natura”, a follower of the greatest Greek Philosopher, Epicurus, didn’t think to explore the space like Star Trek, but from the earth, our house, desired only “noctes vigilare serenas”, searching for truth.

Marnie said...

Gioiello,

You can't say that you've really lived until you've had a few banishments. Good for you, and us, and I hope now 23andme will clean up their act.

pconroy said...

Of course, let's not forget that according to this site on History of Ancient Israel and Judah, and many other similar ones, that:


In 66 the Jews revolted against Rome. The rebellion was crushed and the Temple destroyed (70 CE); over 100,000 Jews died during the siege of Jerusalem, nearly 100,000 were taken to Rome as slaves , and many others fled to Mesopotamia and to other countries. In 132 a second revolt, Bar Kokhba's Revolt, began, led by Simon bar Kokhba, and an independent state in Israel was declared. By 135 this revolt also was suppressed, and the Romans reorganized Judaea as part of the province of Syria-Palestine.


So I think I've probably specifically located the origin of Judean (aka Jewish) admixture in Central Italians...

Jack said...

I knew Gioiello would comment. Ah, ah.
I think it's obvious that Jews absorbed a few South European genes, but it is also true that to a limited extent there was "pollution" of certain areas such as tuscany by Near eastern people, namlely etruscans.
Btween Etruscans and Greeks in Italy and a few other areas, Arabs in Spain and a few other areas, etc., there is going to some overlap between Jews and South Europeans even if the former hadn't stayed in SE.
Add that they absorbed some N. African stuff since large Jewish communities were in NAfrica.
Bottom line is that they "look" like ME populations and that tells the story.
Unless of course someone wants to prove that SEuros originated in Palestine or Saudi Arabia...

Cuah123 said...

Bravo Dienekes! I hope that 23andme et al go back and refocus their results...hope it doesn't open them up to law suits, especially if people changed their lifestyles...

This also points people of different cultural backgrounds creating offspring, either by love or force.

Marnie said...

De Rerum Natura

http://en.wikipedia.org/wiki/De_rerum_natura

Jack said...

The 100,000 jwish taken to italy is a possibility. Ironic. Tons of slaves were brought to Italy Mainly to Rome.
THis may explain some genetic southerness or wierdness in parts of Lazio (from what I remeber) around Rome besides the etruscan effect. There is an ancient jewish community in Rome, the oldest in Europe I think, and the most inbred. Some still have "arabic" names and have nothing to do with the rest of the population.
However, from what I have read slave survival rate and reproduction in Roman times is estimated close to zero in general.
Slavery was not the nice and easy going thing they had in the United States.

Ponto said...

The Etruscans probably proceeded the Latins and other I.E speakers into Italy. The I.E urheimat is somewhere in Siberia. So who is foreign and who native?

I wouldn't give any credence to Bible stories as real history, or accept what people write they did to their enemies. The Egyptians, Ramses for example, the great one, had a lot of BS written on many stonewalls about his achievements. The Romans were no different. The Arabian historians were very inventive. Sometime happened in the year 70 C.E but not what those Roman historians said happened. Just because it is written or said often does not make it fact.

onur said...

However, from what I have read slave survival rate and reproduction in Roman times is estimated close to zero in general.
Slavery was not the nice and easy going thing they had in the United States.


Ottoman slaves and Islamic slaves in general were in much better conditions than Ancient Hellenic/Roman slaves. They generally became Muslims and were set free after some time and even became part of the family they served. In the Turkish-speaking parts of the Ottoman Empire (we can also include here the Seljuk Sultanate and Anatolian beyliks) the overwhelming majority of slaves (there were many many slaves) were White slaves (taken from Christian populations of Asia Minor, the Balkans, Caucasus and other European domains) and Muslims living there were usually fond of having children from them (through marriage or concubinage). Black slaves, OTOH, were a very small minority in the Turkish-speaking parts of the Ottoman Empire (because that they were far away from Sub-Saharan Africa), and Muslims living there almost always even if not always shunned marriage and/or mixing with Black slaves and generally sterilized them by castration. Another thing of note, Muslims in the Turkish-speaking parts of the Ottoman Empire highly valued having fair skin, fair hair, colored eyes and fine features, as they still do.

alfio said...

"The 100,000 jwish taken to italy is a possibility. Ironic. Tons of slaves were brought to Italy Mainly to Rome."

The average age of death for slaves was 17,5 years.
Slaves were not from middle east only but from every part of Europe too.
So i can't see why jews should have left more traces than celts or thracians to make an example.

Major Tom said...

Jack is right, the presence of Jews in Italy and in Europe is linked more to businesses than to the slaves.
In Rome there were Jews already in the Republican era, but I believe that the Jewish presence is overrated and a more careful analysis can give very different answers about the origin of aaskenazis, but many Jewes of Rome, a small comunity of about 15.000 members, are sephardis from Spain, not askenazs.

alfio said...

"I knew Gioiello would comment. Ah, ah.
I think it's obvious that Jews absorbed a few South European genes, but it is also true that to a limited extent there was "pollution" of certain areas such as tuscany by Near eastern people, namlely etruscans."


Etruscans left almost no traces of them in modern day tuscans and we still don't know exactly if they were from middle east nor if they were only an elite from Anatolia in a sea of villanovian people.
Any study cluster Tuscany with middle east, save few lineages in the autosomal tests that to me only show an Adigey\caucasian legacy more than M.e
Beside this Tuscany haven't had any contact with middle eastern or north african populations.
So I can't see why after years of shouted paternity of many people in S.Europe some jews can't accept that is them who are similar to some S.europeans and not the other way around.

onur said...

BTW, Janissaries were allowed to marry and have children (not necessarily through marriage, having children through concubinage with female slaves was allowed for every male Muslim in Islam) after retirement (as is the case with soldiers in general, they retired early in life) by the Ottoman rulers, but many of them married and had children even before retirement so much so that the Ottoman rulers afterwards allowed them to marry and have children whenever they wished.

Also of note is the fact that marrying and having children from non-Muslim women is allowed for every male Muslim in Islam. So the non-Muslim wife of the Muslim husband can keep her non-Muslim faith all through her marriage and can die as a non-Muslim. But all of her children from the Muslim husband have to be raised as Muslims and cannot be non-Muslims according to Islam.

For female Muslims to marry and have children from a male non-Muslim, OTOH, the male non-Muslim has to convert to Islam first in order to marry with the female Muslim according to Islam.

Lastly and very importantly, once someone becomes a Muslim, there is no return according to Islam.

pconroy said...

Gioiello,

Did you read Joe Pickrell's recent comment??


According to that analysis as well, I have a bit of Ashkenazi ancestry (15-30%, or 3-6% if restricting to only 4 grandparents from the same place). I’d be slightly suspicious again, though, about what exactly this means. Certainly the results depend on the composition of the 23andMe database. My guess is that some groups are much more represented than others, and thus more likely to contribute IBD matches (ie., in this analysis I appear to have no Italian ancestry). It would be nice to see some PCA maps of the 23andMe database to figure this out.


Bolded by me...

Marnie said...

Mη χειρότερα.

Aaron said...

"According to that analysis as well, I have a bit of Ashkenazi ancestry (15-30%, or 3-6% if restricting to only 4 grandparents from the same place). I’d be slightly suspicious again, though, about what exactly this means. Certainly the results depend on the composition of the 23andMe database. My guess is that some groups are much more represented than others, and thus more likely to contribute IBD matches (ie., in this analysis I appear to have no Italian ancestry). It would be nice to see some PCA maps of the 23andMe database to figure this out."

--He states 3-6% have self declared Ashkenazi. I wonder what the self reported countries associated with this ancestry are?

Grendal said...

We should also remember that while Judea and Israel were part of the pre Alexandrian empires there were a number of occasions when large sections of their populations were transplanted to other parts of the empires. Thus "jewish" DNA would be scattered around the Middle East and beyond. Israel ended in this way. Also other populations were often settled in Judea/Israel in exactly the same way. What happened to their genes?

This is why I wonder whether discussions about "ashkenasi genes" or even "jewish genes" are
meaningful without very specific definitions and frames of reference.

Gioiello said...

To Pconroy:

GregRM says: “having more than 1000 Relative Finder cousins is a pretty solid indicator of recent Ashkenazi ancestry”.

I have explained this in another posting: I was speaking of an ancient introgression of Italian genes into Ashkenazim, not a recent one. They have more relatives because they have multiplied in these last centuries from about 25.000 who from Italy migrated to the Rhine Valley. The introgression happened then and it is that introgression which gives our “Ashkenazi ancestry”.

Ponto said...

NW Europeans and Colonials obsess too much about Jewish ancestry or Jewish genes.

23andMe have a simple method of working out you are Jewish, at least Ashkenazim. If on RF you have 1000 RF cousins ergo you are Ashkenazim Jewish. Even half AJ or quarter AJ have many RF relatives. On Leon Kulls HIR search site, it is easy to pick out the Jews. As for other "Middle Eastern" types for example Samaritans, there is one Samaritan on Leon's site and he scores well with the AJs, not as high as the AJs but higher than non Jews score with each other.

For my part, I have 35 RF cousins.

I think the statement that hidden "Southern European" ancestry, Italian specifically, can give mainly NW Europeans or Euro Americans, a higher Ashkenazim score on dienekes program, it correct.

Ponto said...

By the way, every ethnic group or antique nation had there slaves. Mostly the slaves were from their own country or from similar ethnic groups. There was no need to import slaves. The Spartans had their Helotes who were other Greeks from Laconia. They had no need for Middle Eastern or Egyptian or sub Saharan slaves. The ancient Romans and other Italici enslaved other inhabitants of the Italian peninsula. The Vikings had their slaves and those Vikings traded extensively with the Byzantine Greeks, various Arabs, and partook in the selling of slaves to the North Africans.

When it comes to slavery, no one has clean hands.

pconroy said...

Ponto, Gioiello,

I'm not denying that some Southern European ancestry - be it Anatolian, Greek or Itlalian - introgressed into the founder Ashkenazi genepool, but in addition to that, Jewish ancestry introgressed into Southern Europeans.

This was a two way process, but it would seem that the bulk of enslaved Jews became Christians eventually, with only a minority migrating to Ashkenaz (Germanic lands) and giving rise to Ashkenazi Jews.
Therefore your family could be Christian for 2,000 years, but you could still be of part Jewish ancestry, especially in Central Italy, that's all.

Aaron said...

"I think the statement that hidden "Southern European" ancestry, Italian specifically, can give mainly NW Europeans or Euro Americans, a higher Ashkenazim score on dienekes program, it correct.
"

I don't think this is correct. If they had South European ancestry, ie: Italian they would have fewer relatives. I haven't heard of Italians having more than 50-60 (rough ballpark) matches.

Cuah123 said...

"Certainly the results depend on the composition of the 23andMe database"

I've posted this before, (coming from the video game industry were we use database for a variety of data manipulation and metrics) the results depend on the population and balance of the database. Is the database "balanced" to represent world populations? If its skewed one way or another it then the results will be skewed as well.