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))
Parameters:
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
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))
Parameters:
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].
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:
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:
