ArticleNature ecology & evolution2023
Resurrecting the alternative splicing landscape of archaic hominins using machine learning.
Article in Nature ecology & evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 13 citations in OpenAlex.
- Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population.Molecular biology and evolution · 2025Article
- Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence.bioRxiv : the preprint server for biology · 2025Article
- A history of multiple Denisovan introgression events in modern humans.Nature genetics · 2024Review
- Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.Genome biology and evolution · 2024Article
- More than a decade of genetic research on the Denisovans.Nature reviews. Genetics · 2024Review
- A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs.Cell genomics · 2024Article
- Archaic Introgression Shaped Human Circadian Traits.Genome biology and evolution · 2023Article
- Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2).Genes and immunity · 2023Review
- Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.bioRxiv : the preprint server for biology · 2023Article
- Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution.Nature reviews. Genetics · 2023Review
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.
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