ArticleScience advances2021
An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.
Article in Science advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 111 citations in OpenAlex.
- Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations.bioRxiv : the preprint server for biology · 2026Article
- Article
- Comparing Neanderthal Introgression Maps Reveals Core Agreement But Substantial Heterogeneity.Molecular biology and evolution · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- Moonshine.jl: a Julia package for genome-scale model-based ancestral recombination graph inference.Frontiers in genetics · 2026Article
- Human ancestries simulation and inference: a review of ancestral recombination graph-based approaches.Frontiers in bioinformatics · 2026Review
- The promise and challenge of spatial inference with the full ancestral recombination graph under Brownian motion.G3 (Bethesda, Md.) · 2025Article
- Comparing Neanderthal introgression maps reveals core agreement but substantial heterogeneity.bioRxiv : the preprint server for biology · 2025Article
- Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.bioRxiv : the preprint server for biology · 2025Article
- The emergence of genetic variants linked to brain and cognitive traits in human evolution.Cerebral cortex (New York, N.Y. : 1991) · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events.Nature ecology & evolution · 2025Article
- Constructing ancestral recombination graphs through reinforcement learning.Frontiers in genetics · 2025Article
- Inference and applications of ancestral recombination graphs.Nature reviews. Genetics · 2025Review
- Article
- Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings.Molecular psychiatry · 2024Article
- Article
- A general and efficient representation of ancestral recombination graphs.bioRxiv : the preprint server for biology · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.