New Paper: An incomplete sweep of a metabolizing gene

A whole gene deletion sounds awful! You lose one entire gene and hence the protein that this gene is coding.  However, there exist several gene deletions which have been maintained polymorphically among human populations. In our previous work, we found that a cellular detoxification gene, the GSTM1, to remain polymorphically deleted in both humans and chimpanzees.

This time, we asked whether the GSTM1 deletion polymorphism in humans is adaptive. Our efforts are now online at G3 – and highlighted on the front page carousel.

We spent, by we, I mean our great postdoctoral fellow Marie Saito, spent countless hours to consolidate the discouraging variation observed in this locus – both structral and single nucleotide.  After that, we managed to test whether neutral forces alone can explain the variation observed in this locus in humans.  We found a haplogroup, which shows linkage disequilibrium with the GSTM1 deletion in East Asia and recently rose in frequency in Asia to approximately 70%. We further showed using both simulation and empirical methods that this haplogroup has likely undergone a sweep in East Asian human populations.

Since the complicated recombination history of this region made its evolutionary background hard to resolve, we named this haplogroup Tanuki after Japanese folktales in which Tanuki is a master of disguise. True to its name, we still do not know what exactly the functional impact of this haplogroup, even though we found that it is associated with gene expression changes of multiple members of GSTM family. We hope that future studies further delineate the functional impact of the variation in this locus and the methods we developed here may be useful to investigate neutrality in other complex regions.

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