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Our work on archaic introgression in enhancers is out in @NatureEcoEvo! We find enhancers to be depleted of young archaic variants introgressed from both Neandertals and Denisovans, esp. enhancers with high pleiotropy and activity in certain tissues:
https://www.nature.com/articles/s41559-020-01284-0.epdf?sharing_token=S0tHwX3q8vurEOZGxPOei9RgN0jAjWel9jnR3ZoTv0NYrNvqmdTq_kmEDNx_VC_Ux3VdzSXc-hFrHICH52agT_uxWfX2AGqBk0tqtp190LhMtUPBZk0thakpwtUz2Uuyw5kgwL29KOw_thRdOIAnc2skx5M4riTzzuvJO3jxclc%3D
https://www.nature.com/articles/s41559-020-01284-0.epdf?sharing_token=S0tHwX3q8vurEOZGxPOei9RgN0jAjWel9jnR3ZoTv0NYrNvqmdTq_kmEDNx_VC_Ux3VdzSXc-hFrHICH52agT_uxWfX2AGqBk0tqtp190LhMtUPBZk0thakpwtUz2Uuyw5kgwL29KOw_thRdOIAnc2skx5M4riTzzuvJO3jxclc%3D
We tested whether introgressed variants identified by Sankararaman, et al. occur less often in enhancers than control variants matched for allele frequency and B statistic. The answer turns out to depend on allele age at the time of introgression…
Introgressed haplotypes that are significantly closer to the Neandertal reference than the Denisovan reference (or vice versa) are depleted from enhancers, but haplotypes with similar affinity to both archaic reference genomes is not.
This makes sense given that older shared variation is less likely to be deleterious than younger variation, and implies that focusing on younger variants may give us more detailed insight into how selection shapes hybrid genomes.
Across enhancers active in different tissues, the strength of recent purifying selection is correlated with the depletion of young archaic alleles, but there are neat hints of tissue-specific regulatory divergence between humans and archaic hominins...
When @NatalieTelis and I started this work as a fun side project as trainees in the @jkpritch lab, we never thought we’d get to see it blossom into the first published research to come out of my independent lab at @uwgenome!
Big thanks to @seesmallthings for contributing to the project during a Harris Lab rotation and creating an exquisite enhancer-themed art piece in the style of ancient human and Neandertal cave paintings, which headlines this thread!
