Freitag, 25. Februar 2011

Triangulation 2 ( reflections )

My Chinese cousin

Comparing even two identical mitochondrial Full Genome Sequences cannot proof a possible familiar relationship, since the last mutation may have occurred 2 – 5 thousand years ago. Y-chromosomes are mutating faster and can scratch on the timeframe of genealogical interest, but are also not easy to handle possible relationships. Only autosomal comparing can reveal stretches, pointing to a common ancestor. Beside the mere information about the genetic distance, start and endpoints of the predominant smaller HIR’s, “Ancestry Finder” lists all the countries, our grandparent generation comes from plus a possible Ashkenazi heritage.
At first glance almost everybody will have been surprised to find countries listed, no one would have expected as part of his own ancestry. How is it possible with my pure German descent to have a distant cousin with some grandparents from China?
This is a point worth to be focused – and illustrated.
There has been a famous son of my town Cologne in the 17th century – Johann Adam Schall von Bell, whom I would like to abuse as an example in an experiment of thoughts. He was a Jesuit missionary and succeeded in becoming a mandarin of the first class at the Chinese emperors court, named Tang Ruowang. The fundament for this career have been his skills in mathematics, astronomy and his knowledge in the cannonball construction. As a highly gifted young man of sixteen he decided in 1608 to leave Cologne and head for Rome to join the Collegium Germanicum, although the age of entrance was eighteen, but he could successfully convince them.
There are no spouses or love affairs reported, but let us pretend for our experiment, that he had at least two of them. We could imagine, that he left a young German girl pregnant behind in Cologne and later in China had an affair with a noble Chinese woman.
As a possible common ancestor we should have a look, what could become of his genome in two different geographical contexts.
Due to recombination his original genome will be reduced by halves in each generation, but we cannot know, which segments will completely vanish or rest conserved as tiny bits and pieces. In our Chinese simulation we can expect this reduction in the given ratio, as his German contribution functions like a drop in the ocean. After 12/13 generations it will be hard to trace German parts in his Chinese offsprings.
 If we draw the triangle comparing the genomes of Schall von Bells offsprings, we can perceive two phenomenons: at about the same ratio of proportions there should be a slightly different outcome, because recombination not occurs at the same breaking points. The second difference is the important one for me: in the Chinese genepool original segments will vanish regularly and rapidly, but in a regional German genepool there are repeated chances in the course of generations, that segments could accumulate and recombine over and over, thus creating segments, whose real age is unclear, but who should be considered as specific for geographical regions. But this has to be proved!

Montag, 14. Februar 2011

Triangulation 1 ( Reflections )

My tyrolean cousin 

Each comparison generates its own visual form. Genetic ones don't need a spatial background like a measure scale, but something inevitable - time! And this form seems shaped to me like a ladder or a triangle. The most simple way of comparing works with mitochondria, since they are small, stable and mutate very slowly. One foot of that ladder now is defined by the revised full genome raw file of the Cambridge Reference Sequence, the rCRS. Before there has been a Yoruba sequence and others, since Anderson extracted the first sequence in 1981.
The third part of that triangle is the MRCA, the most recent common ancestor and depending on the amount of mutations he has to be placed further back in time.
Here is a first triangle, combining the rCRS with cousin clade - H11a2. The listed mutations correspond to the usual phylogenetic tree ( ). The faces belong to a series of drawings, tying various women of all parts of the world together in a vertical social network ( ) .

For a better understanding I laid the ladder aside, so the MRCA is now left hand instead of the top. But still each mutation – or better haplogroup – functions like a rung of a ladder.

I started to mistrust the former age estimations. H11 has been considered to be older than 40000 years, probably due to the fact, that each mutation on the Hyper Variable Region 1 was handled with a rate of 10000 years. In this clade you usually find four mutations, while most of the other about 40 subclades of haplogroup H can only be defined by a Coding Region mutation - ergo! The appearance of H11 in Siberia supported this time estimation.

The more mutations you find, the further back in time your last common ancestor must be considered. In the case of H11 you only have to go back until H, then turn aside on the branch of H11. To reach my own haplogroup K1b2a or that of my distant tyrolean cousin, the iceman from the Ötztal, we have to pass H and go back until R, about 60000 years, before we come to K via U and U8b.

Freitag, 11. Februar 2011


List of anonymised contributors

Set of chromosome stylesheets

First online version of a flagged european landscape

Project description

Each new match in „Relative Finder“ opens up a line of possible connections towards a common recent ancestor somewhere back in 4, 7, 10 generations. RF was released by 23andme in autumn 2009, binding a small community of about 30000 genetoholics together in a facebook-like social network. Very few of them ended up to actually proof such a genetic connection in a traditional genealogical way, most are still full of hope. RF only encompasses half-identical regions (HIR’s) with a genetic distance value of greater than 7 centiMorgan and more than 700 single nucleotid polymorphisms (SNP’s).
Half a year later the users of 23andme could welcome an additional new tool – „Ancestry Finder“, listing also smaller matches between 5 and 7 centiMorgan and all the emigration-, coemigration and immigration countries, our grandfather generation comes from. The computer generated graphic design of AF is rather poor – the tiny chromosomes can only show one match on one spot, all additional clustering matches must stay hidden. And there is no scale!
I wanted to have a visual representation of a chromosome set, giving them an individual face with enough room for hundreds of matches. I therefore created a handle of stylesheet with columns for names, haplogroups and the number of SNP’s (URL).
Collecting ones matches in those stylesheets soon reveals, that most are not spread randomly along all chromosomes, but cluster together or are at least considerably overlapping, while a few others stay relatively isolated. Some of these clusters, especially those of lower cM values tend to start or end exactly at the same positions. Probably they are of a high age due to inversion or yet unknown geneprotecting reasons. Between single matches of perhaps individual interest and such of old pan-european background there are I expect clustering chromosome segments, recombined over and over, thus accumulating region specific pattern and shaping a possible european genetic landscape. This is actually not proven and may turn out to be just a phantom, but anyway a collection of clustering HIR’s should give a valuable background to judge ones matches. All postings around the Regional Ancestry Bands will be displayed in the form of Settings, Reflections and Results.