Montag, 25. Juli 2011

Mei jrine Kusine 2: A genetic Tsunami?

Again I’m looking for an illustrative explanation concerning the simple fact, that people with an Ashkenazim background have about ten times more genetic cousins than me. The two main reasons, cited in countless forum postings are heading both historical developments and a higher inbreeding ratio. This always sounds logical, but is nevertheless hard to understand. So here it goes with a personal visual approach!
In Cologne we have just started to explore a new excavation site in the old Jewish quarter, built in the 12th century, when the town expanded toward a muddy Rhine arm. They already found fine jewellery, burnt remains of the Bartholomew night and even a big Jewish romance of chivalry, containing a lot of erotic adventures. At that time the members of the Jewish community along the Rhine valley named them self  Ashkenazim.  There are thought to be about 25000 in the cities of Speyer, Worms, Mainz and Köln. Beside their ritual language Hebrew they spoke a German medieval dialect as everyday language.  In the dynamics of the beginning crusades with all its hate propaganda they were pushed by west-European Christian anti-Semitism to leave their homes and move more and more eastwards, enriching their language with Czechish, Polish and Russian idioms, thus developing Yiddish.
There are almost 2000 years of Jewish presence in Europe. In 321 Caesar Diocletian confirmed a declaration from Cologne, demanding, that members of the Jewish community now should have the right to join the city government, what exactly means, that there must have been a considerable amount of Jewish citizens with enough cultural and financial power to compete in a city of about 30.000 people. The soldier camps along the roman LIMES ( including Mainz, Speyer, Worms and other) are exactly the same as mentioned to be Jewish centers later, what makes me believe, they had been here since roman times. Romans lived in the Rhine valley for about 500 years - enough time for Jewish merchants and families to find a way up north.
While the Ashkenazim were forced to emigrate eastward, parts of their Sephardic distant cousins joined them, leaving Spain and Portugal. Later on others became the first to cross the ocean for the Americas. They reached New Amsterdam via Brazil in 1654. This first immigration wave was followed by a German one after 1840, before the main wave started around 1880,  bringing until 1924 more than 2500000 eastern Jews into the US. This seems to be the wave, whose genetic echo we encounter nowadays.
But this alone cannot explain the amount of matches, so I wanted to have a closer look on what is called the “inbreeding ratio”. Traditional genealogy already gave definitions, explaining the simple fact, that our binary ancestor tree (doubling in each generation) would produce an absurd situation, outnumbering the world population after enough generations. The solution for this paradox is called implex or pedigree collapse or Ahnenschwund. It means that further back in time some ancestors must appear in several positions, that there must have been more and more cases of cousin or uncle-niece marriages. I do not want to focus on the different reasons for this phenomenon, but head for its principal genetic implications, which are to illustrate. The usual pedigree tree gives us eight great-grandparents, thus shrinking the genetic partition of each to about 12,5 % of a great-grandson or daughter after three generations.
This is what it looks like in the light of a cousin or uncle-niece marriage. As one can easily see, a cousin marriage reduces the number of great-grandparents to six and produces two generations of same percentage, while marrying an uncle only needs four great-grandparents.

Freitag, 8. Juli 2011

Mei jrine Kusine 1

The main goal of the regband-project was a visual one from the very beginning. How does it look, when multiple matches cluster together, are we able to detect visual pattern, that allow additional interpretation to usual algorythms. Three forms of clusters are quickly distinguishable and seem to be related to different time-frames. Independent from centiMorgan values a cluster, spreading his matches in a wider field, a looser composition ( soft edge ) looks definitely very much younger than those, who have already developed one sharp start- or ending point (hard edge ). Smaller clusters of only three to five MB length with sharp start AND endpoints can perhaps be contributed a considerable age. They are probably real ancestry bands, shared by people of very distant and different countries.
We all have still to learn about the nature of our IBD segments and it would be helpful to clearly distinguish between individual familiar matches, very old ancestry matches, shared by most Europeans and regionally composed stretches, which should have been enriched by specific motives, shaped through natural geographic, ethnic or religious borders up to the complete isolation of a small gene pool.
Ten Ancestry Finder screenshots of Ashkenazim, merged in one.
This is true of the Ashkenazim and knowing, that they show up with about ten times more relatives than a common European, I have to admit – I was much afraid of looking at the first inevitable CSV-files from Ancestry Finder for the regband project. I should have known! At the end of 2010 there were around 300 matches in my own AF-file, the usual range for a continental European. In files of colonial or Finnish descent this number could double, but encountering more than 3000 matches really caused more than one problem. Until then the checking of those usual files took one hour to a whole evening, but now I was busy for more than a week. The threshold problem, the team of 23andme faced in the beginning, showed up as well as a logistic one – namely the difficulty of a clear definition for soft or hard edge clusters. Scrolling up and down an excel-file cannot reveal the true shaping of different clusters, this can only the visual detour of a handmade collection in a chromosome style sheet. Since I don’t work with a computer program, it was impossible and too time consuming to head for all chromosomes, so I simply show the given problems exemplary in the picture of the smaller chromosome 15. On the left side we see a collection of single matches, as explored in two AF-files of full Ashkenazim descent, on the right side the compilation of all the other files.