ArticleGenetics2024
A general and efficient representation of ancestral recombination graphs.
Article in Genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66 citing papers in PubMed.
- Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.Genome biology and evolution · 2026Article
- Phylogenetically Diverse Introgression Drives Subtle Population Structure in Pacific Rockfishes.Molecular ecology · 2026Article
- ARGformer: learning on ancestral recombination graphs with transformers.Bioinformatics (Oxford, England) · 2026Article
- MixedUpParents: A New and Improved Method for Genetic Parentage Assignment in Admixed Populations.Molecular ecology resources · 2026Article
- Rapid expansion overcomes inbreeding in cross-hemisphere colonization of Barn Swallows.bioRxiv : the preprint server for biology · 2026Article
- ARGscape: a modular, interactive tool for manipulation of spatiotemporal ancestral recombination graphs.Bioinformatics (Oxford, England) · 2026Article
- Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome.Nature ecology & evolution · 2026Article
- Allelic association analyses: estimation recommendations.Genetics · 2026Article
- Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genetic prediction with ARG-powered linear algebra.Genetics · 2026Article
- Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity.Genome research · 2026Article
- Ubiquitous impact of natural selection on nucleotide diversity in 178 species of primates.Genome biology · 2026Article
- General, orders-of-magnitude faster whole-genome analysis with genotype representation graphs.bioRxiv : the preprint server for biology · 2026Article
- e3SIM: Epidemiological-ecological-evolutionary simulation framework for genomic epidemiology.Methods in ecology and evolution · 2026Article
- Recovering signatures of archaic introgression using ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Article
- On ARGs, pedigrees, and genetic relatedness matrices.Genetics · 2026Article
6 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
As a result of recombination, adjacent nucleotides can have different paths of genetic inheritance and therefore the genealogical trees for a sample of DNA sequences vary along the genome. The structure capturing the details of these intricately interwoven paths of inheritance is referred to as an ancestral recombination graph (ARG). Classical formalisms have focused on mapping coalescence and recombination events to the nodes in an ARG. However, this approach is out of step with some modern developments, which do not represent genetic inheritance in terms of these events or explicitly infer them. We present a simple formalism that defines an ARG in terms of specific genomes and their intervals of genetic inheritance, and show how it generalizes these classical treatments and encompasses the outputs of recent methods. We discuss nuances arising from this more general structure, and argue that it forms an appropriate basis for a software standard in this rapidly growing field.
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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.