ArticleNature ecology & evolution2019
Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.
Article in Nature ecology & evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 61 citations in OpenAlex.
- Integrative Genomics Identifies Candidate Genes Underlying Trypanotolerance in Hybrid African Cattle.Evolutionary applications · 2026Article
- Comparing Neanderthal Introgression Maps Reveals Core Agreement But Substantial Heterogeneity.Molecular biology and evolution · 2026Article
- Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity.bioRxiv : the preprint server for biology · 2025Article
- Candidate Denisovan fossils identified through gene regulatory phenotyping.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.bioRxiv : the preprint server for biology · 2025Article
- Computational reconstruction of evolutionary selection in human brain networks.Frontiers in neuroinformatics · 2025Article
- Inferring DNA methylation in non-skeletal tissues of ancient specimens.Nature ecology & evolution · 2025Article
- Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations.Heredity · 2025Article
- Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale.PLoS biology · 2024Article
- Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry.Nature neuroscience · 2024Article
- More than a decade of genetic research on the Denisovans.Nature reviews. Genetics · 2024Review
- Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges.Current protocols · 2024Article
- A molecular signature for IL-10-producing Th1 cells in protozoan parasitic diseases.JCI insight · 2023Article
- Archaic Introgression Shaped Human Circadian Traits.Genome biology and evolution · 2023Article
- Genetic and environmental contributions to ancestry differences in gene expression in the human brain.bioRxiv : the preprint server for biology · 2023Article
- Resurrecting the alternative splicing landscape of archaic hominins using machine learning.Nature ecology & evolution · 2023Article
- Archaic hominin traits through the splicing lens.Nature ecology & evolution · 2023Article
- Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- The contribution of Neanderthal introgression to modern human traits.Current biology : CB · 2022Review
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.
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