Archaic adaptive introgression in TBX15/WARS2
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Abstract
A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.
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Some archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations.
“For instance, substantial evidence suggests that some archaic alleles and haplotypes are adaptive and persist at high frequencies in human populations [10, 13–19].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [18]
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- Authors
- Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., Albrechtsen, A., Carmel, L., Huerta-Sánchez, E., & Nielsen, R.
- Affiliations
- University of California, Berkeley (US)
- Hebrew University of Jerusalem (IL)
- University College London (GB)
- University of Copenhagen (DK)
- Corresponding author
- Racimo, Fernando
- Nielsen, Rasmus
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-12-21
- Volume
- 34
- Issue
- 3
- Pages
- msw283
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC5430617
- OpenAlex
- W2951292100
- Cited by
- 101
- References
- 17
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 9 · 2023: 11 · 2022: 6 · 2021: 14 · 2020: 10 · 2019: 12 · 2018: 18 · 2017: 15 · 2016: 1
- FWCI
- 12.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by-nc-nd)
- Spiral (Imperial College London) (submittedVersion, cc-by-nc)
- Funders
- National Science Foundation (1557151)
- Lundbeckfonden (R215‐2015‐4174)
- Israel Science Foundation (ISF 1430/13)
- National Institutes of Health
- University of California Merced
- National Human Genome Research Institute (R01HG003229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- archaic introgression, positive selection, TBX15, Inuit, Denisovans, haplotype divergence, body fat distribution, adipose tissue, adrenal gland, DNA methylation, gene expression
- MeSH terms
- DNA, Ancient, Adaptation, Biological, Adipose Tissue, Alleles, Animals, Inuit, Greenland, Haplotypes, Humans, Models, Genetic, Selection, Genetic, Sequence Analysis, DNA, DNA Methylation, Polymorphism, Single Nucleotide, T-Box Domain Proteins, Neanderthals
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