Characterising private and shared signatures of positive selection in 37 Asian populations

A new paper by Liu et al¹ examines patterns of genetic diversity and positive natural selection, and finds that populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions.

Here is their abstract:

“The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly locatedin South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.”

It seems that most of the 37 populations studied are heavily East Eurasian admixed, with the exception of Kurds, Tajiks, Tamil, Sinhalese, GIH, and INS, which they categorize with the South Asian clade in the Phylogenetic tree.

To investigate whether local adaptation may have driven the genetic diversity between Asian populations, they selected 33 populations. They observed that 693 selection signals were located in 140 distinct genomic regions, where the majority of the signals were present in multiple populations but located in the same genomic regions. They further investigate the pattern of sharing of the 140 selected regions among the 33 populations by calculating a similarity matrix for the 33 populations, where each entry indicates the number of regions out of 140 that are positively selected in the respective population pair. A PCA was done on the similarity matrix, the first 2 principal components indicate that population groups that are geographically closer are more likely to share the same selection signals than populations more distant. They observe that populations in South and Central Asia can be grouped separately by the extent of sharing of selection signals, whereas there was considerable overlaps between the populations in East and Southeast Asia.

The following is the K=2 thru K=12 admixture analysis using ADMIXTURE.

References:

1-Characterising private and shared signatures of positive selection in 37 Asian populations, Xuanyao Liu, Dongsheng Lu, Woei-Yuh Saw, Philip J Shaw, Pongsakorn Wangkumhang et al. , European Journal of Human Genetics, Nature Publishing Group, 12/16

https://www.researchgate.net/publication/312521886_Characterising_private_and_shared_signatures_of_positive_selection_in_37_Asian_populations