(1) Show that Loschbour has two components and one of the two ("the green ancestry") is a better source population than the Loscbour ancestry (via log likelihood comparisons).
(3) Show the previous structure plots and remember that it was hard to visually distinguish between additional real source populations versus non-identifiable source populations. We showed that indeed, the modern data has extra clusters that doesn't get picked up by pooling the data.
(4) We pooled in additional data including Asian populations along with European populations to see how the new patterns show up.
We present the Structure plot from general admixture model fit on pooled ancient and modern data.
Now we data 692 populations, with 620 modern and the rest being ancient populations.
(1) Show that Loschbour has two components and one of the two ("the green ancestry") is a better source population than the Loscbour ancestry (via log likelihood comparisons).
Loglikelihoods: https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/loglik_values
Structure Plots:
The analysis was done on Moderns+Ancient pooled data but we plotted separately
Source: Yamnaya, LBK-EN, Loschbour
Moderns plot :
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/modern_yam_lbk_losch/clus_3/struct_clus_3_.png?raw=true
Ancient plot:
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/ancient_yam_lbk_losch/clus_3/struct_clus_3_.png?raw=true
Source: Yamnaya, LBK-EN, Green cluster
What is the green cluster here? Check first figure:
http://htmlpreview.github.io/?https://github.com/halasadi/ancient-structure/blob/master/exploratory/plot_exploratory.html
Moderns plot :
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/modern_yam_lbk_green/clus_3/struct_clus_3_.png?raw=true
Ancient plot:
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/ancient_yam_lbk_green/clus_3/struct_clus_3_.png?raw=true
Source: Yamnaya, LBK-EN, One unknown cluster
Moderns plot :
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/modern_yam_lbk_unknown/clus_3/struct_clus_3_.png?raw=true
Ancient plot:
https://github.com/halasadi/ancient-structure/blob/master/issues/issue21/Admixture/ancient_yam_lbk_unknown/clus_3/struct_clus_3_.png?raw=true
(2). Show the scree plots and that: (i) there doesn't seem to be three dominant eigenvalues and (ii) the ancients have large variability
Check scree plot for both moderns and ancients
https://github.com/halasadi/ancient-structure/blob/master/exploratory/PCA/scree_pooled_and_moderns.png
Check scree plot for moderns only
https://github.com/halasadi/ancient-structure/blob/master/exploratory/PCA/scree_moderns_only.png
(3) Show the previous structure plots and remember that it was hard to visually distinguish between additional real source populations versus non-identifiable source populations. We showed that indeed, the modern data has extra clusters that doesn't get picked up by pooling the data.
For previous Structure plots, check:
http://htmlpreview.github.io/?https://github.com/halasadi/ancient-structure/blob/master/exploratory/plot_exploratory.html
Loglikelihood values of the comparison
https://github.com/halasadi/ancient-structure/blob/master/issues/issue23/loglik_values
(4) We pooled in additional data including Asian populations along with European populations to see how the new patterns show up.
We present the Structure plot from general admixture model fit on pooled ancient and modern data. Now we data 692 populations, with 620 modern and the rest being ancient populations.
K=7
Ancients: https://github.com/halasadi/ancient-structure/blob/master/issues/issue26/Admixture/ancient/clus_7/struct_clus_7_.png?raw=true
Moderns: https://github.com/halasadi/ancient-structure/blob/master/issues/issue26/Admixture/modern/clus_7/struct_clus_7_.png?raw=true
K=10
Ancients: https://github.com/halasadi/ancient-structure/blob/master/issues/issue26/Admixture/ancient/clus_10/struct_clus_10_.png?raw=true
Moderns: https://github.com/halasadi/ancient-structure/blob/master/issues/issue26/Admixture/modern/clus_10/struct_clus_10_.png?raw=true