Discrodance between the Global Ancestry estimates using FLARE and ADMIXTURE and large estimate of Admixture time

Hi, ABM_Flare_g70.out.log ABM_Flare.out.log

I started implementing FLARE in Admixed Indian Subpopulations. Indian Populations are a result of complex admixture history of four ancestral populations Indo-European(IE), AustroAsiatic(AA), Dravidian(DR), Tibet-Berman(TB) speakers. The time since last admixture is around 70 generations as populations started endogamy.

By taking representative population for each of the four ancestral populations(having global ancestry~1) based on ADMIXTURE results and taking the Admixed populations data I am running FLARE.

Chromosome 21 has been taken to perform the analysis.

################## FLARE output ##################################### Model 1: Default Parameters

list of ancestries IE DR AA TB

list of reference panels IE DR AA TB

T: number of generations since admixture 1163.9318

mu[i]: proportion of target genotypes with ancestry i 1.0 0.0 0.0 0.0

p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i 0.52692056 0.16545793 0.16131613 0.14630541 0.1464599 0.6767872 0.10465198 0.07210092 0.14689372 0.11054649 0.64248073 0.10007905 0.21040414 0.12552024 0.1592307 0.5048449

theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4

rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i 1257.5281 795.9301 783.3869 1147.2806

Model 2: gen=70, list of ancestries IE DR AA TB

list of reference panels IE DR AA TB

T: number of generations since admixture 910.75415

mu[i]: proportion of target genotypes with ancestry i 1.0 0.0 0.0 0.0

rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i 1257.5281 795.9301 783.3869 1147.2806

############## ADMIXTURE Global Ancestry for Admixed population taken under study

Ancestral_pop IE DR TB AA Global Ancestry 0.26 0.3 0.18 0.26

I have also attached log files for your reference.

Please help me in understanding what is getting wrong here.

Thanks, Devashish Tripathi

Dear Devanish, Please send analysis related questions to Sharon @.***). Sharon does not monitor this GitHub page.

Please include the log file and output .model file from your analysis as e-mail attachments.

Thanks,

Brian Browning

On Fri, Aug 26, 2022 at 4:08 PM Devashish Tripathi @.***> wrote:

Hi, ABM_Flare_g70.out.log https://github.com/browning-lab/flare/files/9436745/ABM_Flare_g70.out.log ABM_Flare.out.log https://github.com/browning-lab/flare/files/9436746/ABM_Flare.out.log

I started implementing FLARE in Admixed Indian Subpopulations. Indian Populations are a result of complex admixture history of four ancestral populations Indo-European(IE), AustroAsiatic(AA), Dravidian(DR), Tibet-Berman(TB) speakers. The time since last admixture is around 70 generations as populations started endogamy.

By taking representative population for each of the four ancestral populations(having global ancestry~1) based on ADMIXTURE results and taking the Admixed populations data I am running FLARE.

Chromosome 21 has been taken to perform the analysis.

################## FLARE output ##################################### Model 1: Default Parameters list of ancestries

IE DR AA TB list of reference panels

IE DR AA TB T: number of generations since admixture

1163.9318 mu[i]: proportion of target genotypes with ancestry i

1.0 0.0 0.0 0.0 p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i

0.52692056 0.16545793 0.16131613 0.14630541 0.1464599 0.6767872 0.10465198 0.07210092 0.14689372 0.11054649 0.64248073 0.10007905 0.21040414 0.12552024 0.1592307 0.5048449 theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i

9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i

1257.5281 795.9301 783.3869 1147.2806

Model 2: gen=70, list of ancestries

IE DR AA TB list of reference panels

IE DR AA TB T: number of generations since admixture

910.75415 mu[i]: proportion of target genotypes with ancestry i

1.0 0.0 0.0 0.0 p[i][j]: probability that a model state haplotype is in reference panel j when the model state ancestry is i

0.52692056 0.16545793 0.16131613 0.14630541 0.1464599 0.6767872 0.10465198 0.07210092 0.14689372 0.11054649 0.64248073 0.10007905 0.21040414 0.12552024 0.1592307 0.5048449 theta[i][j]: probability that a model state haplotype and the target haplotype carry different alleles when the model state haplotype is in reference panel j and the model state ancestry is i

9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 9.54659E-4 rho[i]: rate of the exponential IBD segment cM-length distribution when the most recent common ancestor precedes admixture and has ancestry i

1257.5281 795.9301 783.3869 1147.2806

############## ADMIXTURE Global Ancestry for Admixed population taken under study

Ancestral_pop IE DR TB AA Global Ancestry 0.26 0.3 0.18 0.26

I have also attached log files for your reference.

Please help me in understanding what is getting wrong here.

Thanks, Devashish Tripathi

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browning-lab / flare

Discrodance between the Global Ancestry estimates using FLARE and ADMIXTURE and large estimate of Admixture time #4