ArticlePLoS genetics2022
Denisovan introgression has shaped the immune system of present-day Papuans.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 42 citations in OpenAlex.
- Recovering the precolonial population structure of Khoe-San descendant populations.Science advances · 2026Article
- ARGformer: learning on ancestral recombination graphs with transformers.Bioinformatics (Oxford, England) · 2026Article
- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania.Science (New York, N.Y.) · 2026Article
- A Rarefaction Approach to Identify Local Introgression in a Three Population Tree.bioRxiv : the preprint server for biology · 2026Article
- Mapping the gene regulatory landscape of archaic hominin introgression in modern Papuans.PLoS genetics · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- enhancer3D: 3D chromatin structures and enhancer-promoter distance profiles for archaic and modern human genomes.Nucleic acids research · 2026Article
- Association of Chromosome 3p21.32 Haplotype Blocks Introgressed from Neanderthals with Critical COVID-19 in a Spanish Cohort.Life (Basel, Switzerland) · 2025Article
- Recovering the pre-colonial population structure of Khoe-San descendant populations.bioRxiv : the preprint server for biology · 2025Article
- Archaic adaptive introgression in modern human reproductive genes.Communications biology · 2025Article
- Lineage-specific regulatory evolution: insights from massively parallel reporter assays.Current opinion in genetics & development · 2025Review
- Archaic hominin admixture and its consequences for modern humans.Current opinion in genetics & development · 2025Review
- Adaptive introgression in modern human circadian rhythm genes.Npj biological timing and sleep · 2025Article
- COQ6 defies immune and metabolic expectations.Nature immunology · 2024Article
- A history of multiple Denisovan introgression events in modern humans.Nature genetics · 2024Review
- Novel coenzyme Q6 genetic variant increases susceptibility to pneumococcal disease.Nature immunology · 2024Article
- Article
- AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software.Bioinformatics (Oxford, England) · 2024Article
- Massively parallel approaches for characterizing noncoding functional variation in human evolution.Current opinion in genetics & development · 2024Review
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Authors and funding
9 authors at 5 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.
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