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Archaic Adaptive Introgression in TBX15/WARS2.

Fernando Racimo1, David Gokhman2, Matteo Fumagalli3

  • 1Department of Integrative Biology, University of California Berkeley, Berkeley, CA.

Molecular Biology and Evolution
|December 24, 2016
PubMed
Summary

Ancient Denisovan DNA introgressed into Inuit populations, influencing fat distribution and gene expression. This adaptive genetic selection spans beyond Greenland, impacting WARS2 and TBX15 gene activity.

Keywords:
DenisovaNative Americansadaptive introgressionadmixture.methylationpositive selection

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Area of Science:

  • Human evolutionary genetics
  • Population genomics
  • Archaic admixture

Background:

  • The Inuit population in Greenland exhibits unique genetic adaptations.
  • Genome-wide scans are crucial for identifying signatures of natural selection.
  • Archaic hominin introgression has contributed to human adaptive evolution.

Purpose of the Study:

  • To investigate a strong signal of positive selection in Greenlandic Inuit.
  • To identify the genetic origin and functional impact of an introgressed haplotype.
  • To determine the geographical extent and phenotypic consequences of this adaptive introgression.

Main Methods:

  • Genome-wide scan for selection using single nucleotide polymorphism (SNP) chip data.
  • Phylogenetic analysis to determine haplotype relatedness to archaic hominins (Denisovans).
  • Gene expression and DNA methylation analyses in relevant human tissues.

Main Results:

  • A haplotype closely related to Denisovan sequences showed strong positive selection in Greenlandic Inuit.
  • This introgressed haplotype is geographically widespread beyond Greenland.
  • The selected allele is associated with altered expression of WARS2 and TBX15 genes in adipose tissue and the adrenal gland.
  • Regional DNA methylation changes in TBX15 were also observed.

Conclusions:

  • Archaic introgression from Denisovans contributed to adaptive selection in Inuit populations.
  • This genetic adaptation influences human adipose tissue differentiation and body fat distribution.
  • The identified adaptive haplotype has broader geographical distribution and functional consequences than previously known.