August 08, 2012

fastIBD analysis of several Jewish and non-Jewish groups

This is more of a "just the data" kind of post, inspired by the two recent papers on Jewish origins. A few quick points:
  • fastIBD was run with default parameters over a dataset of 512 individuals/264,539 SNPs
  • fastIBD identifies segments of relatively recent origin that are shared by individuals. These results should not be construed as measures of overall genetic similarity or origins. Rather, they suggest which populations have exchanged genes in the relative recent past, say, the last two thousand years or so.
  • I included all Ashkenazi_D and North_African_Jews_D samples; of the other Dodecad and reference populations, I took random samples of 10 each; running time of fastIBD increases with the square of the number of individuals, so doing this allowed me to run this in less than a day as opposed to about a week.
With that said, you can get:
  • Spreadsheet of numeric results, showing sharing (in centi-Morgans, cM)
  • Population-level graphical results, showing an ordering of other populations based on mean IBD sharing.
The following heat map allows for a quick appraisal of populations sharing an excess of IBD sharing (read row-by-row)



And, here are a couple of the visualizations for a few Jewish populations:

Note that all sources of data are listed on the bottom left of the Dodecad blog.

4 comments:

  1. Charles NydorfWednesday, August 08, 2012 10:44:00 pm

    Really interesting. There is a lot to mull over here.

    ReplyDelete
  2. Auditor George DanosThursday, August 09, 2012 12:34:00 am

    How is that Sephardic Jews share a larger IBD with Ashkenazic Jews than with each other?

    ReplyDelete
  3. DienekesThursday, August 09, 2012 1:03:00 am

    Sephardic Jews are very diverse compared to Ashkenazi Jews. A similar finding was reported in the recent Graham and Coop paper in which Germans shared more IBD with Poles on average than with each other.

    The best way to think about this is by drawing a trapezoid like this:

    http://en.wikipedia.org/wiki/File:Trapezoid.svg

    if AB is much longer than CD, and h is small, then random points in AB are usually further apart than they are to CD.

    So, populations with reduced genetic diversity (such as Balto-Slavs, a very recent population expansion, or AJ, a quite recent population isolate) tend to IBD share a lot.

    ReplyDelete
  4. raffi17Thursday, August 09, 2012 8:21:00 am

    Interesting to see that Morocco Jews How share a larger IBD with non-Jewish Moroccans than with some Ashkenazi, for example. It confirms what was found by the study:
    "Admixture occurred
    with North African non-Jewish populations. However, as
    demonstrated by the apparent unrelatedness of the Jewish and
    non-Jewish North Africans, these events were not recent."

    ReplyDelete

Stay on topic. Be polite. Use facts and arguments. Be Brief. Do not post back to back comments in the same thread, unless you absolutely have to. Don't quote excessively. Google before you ask.