La Braña 1 closest to Basque, Sardinians and Lithuanians in geneology

This is the second look at the recently released La Braña 1 diploid genome. The previous analysis was done using Plink MDS tool and gave a limited overview. This time I am using first the Chromopainter-Finestructure unlinked model and second the Chromopainter-Finestructure linked model.

Unlinked model

The unlinked model appear to show a result consistent with the previous analysis with the La Braña 1 in the same heatmap box as Finns and Saamis especially what appear to be East-Finns and North-Saami. However also notice that the La Braña 1 in the heatmap show affiliation to Basque, Lithuanians and a mixed group of Scandinavians and Finns. This affiliation  is interesting as particular Saami and Finns do not show much sharing to Lithuanians and Basque. It may be that La Braña 1 is "ancestral" to these modern populations but through the generation or 7000 years the populations may have drifted and/or mixed with other populations..

ChunkCount 54k unlinked aggregated

The PCA plot generated from Finestructure shows a slightly different plotting in the previous analysis Plink MDS plotting (may be due to pruning). In dimension 3 (horizontal) the La Braña 1 still cluster with Finns and Saamis but in dimension two (vertical) the La Braña 1 is at the same height as the Basque.

 ChunkCount 54k unlinked PCA 

Linked model

As I understand from the authors the unlinked and linked model may give different time depths in the analysis with the unlinked model showing the most ancient time depth and the linked analysis more recent ancestry. This analysis may confirm this statement. The difference between the linked and unlinked model may be the "masking" effect of recombination that may hide ancient relationships seen in the unlinked model. This is to my knowledge the first haplotype based analysis of the La Braña 1 as the La Brãna 1 was phased.

As we can see the linked analysis shows a very different clustering of the La Braña 1. He is in the same heatmapbox as with Western Europeans and in particular with Basque and Sardinians. The La Braña 1 also show strong "heat" to the Lithuanians but the strong affiliation to Finns and Saami we so earlier is in the linked model much weaker but still quite easy to see.. 

 ChunkCount 54k aggregated linked

We can also see in the heatmap that there is strong divergence between haplotypes painted vs haplotypes donated for the La Braña 1. The La Braña 1 find related haplotypes among the modern populations but the modern populations find closer related haplotypes among themself. This suggest La Braña 1 have haplotype variation that no longer exists in the modern populations and also due to recombination the modern populations would make the La Braña 1 haploblocks very small.

The PCA for the unlinked model shows a different clustering from the unlinked model. This time at the center of the plot between the Scandinavians and Vologda Russians.

 ChunkCount 54k linked PCA

Conclusion

As we can see the different models appear to give different results and its due to that in geneology the La Braña 1 closest to Basque, Sardinians and Western Europeans but in ancient ancestry closest to Finns and Saamis. The clustering in geneology with Basque, Sardinians and Western Europeans in the linked model make sense as the La Braña 1 individual was found in today northern Spain. This means that the La Braña 1 like haplotypes is still much present among Western Europeans of today suggesting continuity in the autosomes.


As a sidenote to this also notice the change of clustering for the Saamis, Mordovians and Vologda Russians between the unlinked and linked model. In the linked model Saamis and Finns cluster together and the Vologda Russians and Mordovians cluster with Easern Europeans, but in the unlinked model Finns are seperatae from the Saamis, while the Saamis cluster with Mordovians and Vologda Russians. Also in the unlinked mode the Mordovians and Vologad Russians is part of a greater cluster also including Saamis and Finns.