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Thursday, November 15, 2012

New add-on tool to MDLP World-22 calculator

Alex_Axe from Molgen forum announced the release of a new tool Oracle_AdMix4.
Basically, you can think of this tool as an useful add-on that extends the Oracle two-population results into four-population format.

Currently the tool support only DOS/Windows platform, and its usage is quite straightforward. The current distribution of  Oracle_AdMix4 includes the required file (data.txt) with the frequencies of 22 components in each of reference populations. The second file - input.txt - is the one you need to modify in order to use the tool on your own World-22 calculator results:

30     {Quantity of output results}
1,5    {Threshold of components to ignore noise} 
0,5    {Threshold of method to ignore noise}
2      {Power parameter for weighted method or zero for least-squares method}   
0      Pygmy
15     West-Asian
0      North-European-Mesolithic
0      Indo-Tibetan
0      Mesoamerican
0      Arctic-Amerind
0      South-America_Amerind
5      Indian
0      North-Siberean
25     Atlantic_Mediterranean_Neolithic
5      Samoedic
0      Indo-Iranian
0      East-Siberean
40     North-East-European
0      South-African
0      North-Amerind
0      Sub-Saharian
0      East-South-Asian
10     Near_East
0      Melanesian
0      Paleo-Siberian
0      Austronesian

All you need to do is to change the default values of components with your own results of World-22 calculator.

The output should appear in the following format:

1 Mordovian+Russian_South+Swedish+Swedish @ 20,749639
2 Estonian+Mordovian+Swedish+Swedish @ 23,267935
3 Finnish-North+Mordovian+Polish+Swedish @ 23,656645
4 Finnish-North+Mordovian+Russian_South+Swedish @ 23,83736
5 Estonian+Finnish-South+Mordovian+Swedish @ 24,192354
6 Mordovian+Polish+Swedish+Swedish @ 24,846391
7 Estonian+German-North+Mordovian+Swedish @ 25,176036
8 Lithuanian+Mordovian+Swedish+Swedish @ 25,511204
9 Finnish-North+Lithuanian+Mordovian+Swedish @ 25,523722
10 Finnish-South+Lithuanian_V+Mordovian+Swedish @ 25,539837

Sunday, November 11, 2012

The levels and dating of admixture in Belorusians

Following Dienekes's suggestion on using Pathan and Lithuanian samples as references for ROLLOFF analysis, i decided to undertake a second attempt of formal analysis of admixture and dating of admixture events in Belorusian samples which are available to me: the reference dataset of Belorusians from Behar et al.2011., and Belorusian samples collected by our project.

Below  you can glean the results of experiment which i deem less noisy in contrast to my previous attempt. 

valid snps: 746877
group 0 Lithuanian
group 1 Pathan
number admixed: 13 number of references: 2
numsnps: 746877  numindivs: 55
starting main loop. numsnps: 158101

Summary of fit:

Formula: wcorr ~ (C + A * exp(-m * dist/100))

   Estimate Std. Error t value Pr(>|t|)  
C 2.332e-04  3.029e-04   0.770  0.44165  
A 3.306e-02  1.227e-02   2.695  0.00728 **
m 1.169e+02  3.851e+01   3.037  0.00252 **
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.006508 on 493 degrees of freedom

Number of iterations to convergence: 0
Achieved convergence tolerance: 9.103e-06

mean (generations):  116.9416
jackknife (generations)   105.086+-52.591 
The date of admixture event in Belarusian_V sample with Belarusian and Pathan being reference populations appears to be very close to the date which was estimated by Dienekes for Lithuanian [Lithuanian_D;Pathan].

Inference of Admixture Parameters in Belarusians using Weighted Linkage Disequilibrium

On 1 November 2012 Po-Ru Loh, Mark Lipson, Nick Patterson, Priya Moorjani, Joseph K Pickrell, David Reich, Bonnie Berger announced and published their new paper, in which they introduced a new approach that harnesses the exponential decay of admixture-induced linkage disequilibrium (LD) as a function of genetic distance. They proposed a new weighted LD statistic that can be used to infer mixture proportions as well as dates with fewer constraints on reference populations than previous methods.

I haven't had enough time to investigate this method in full extent, but i used a software package ALDer which implements the weighted LD statistic for a quick & dirty experiment of dating the admixture events in Belarusian sample: