ArticlePLoS genetics2019
Inference of recombination maps from a single pair of genomes and its application to ancient samples.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Introgression and Divergence in a Young Species Group.Molecular ecology · 2026Article
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Genomic perspectives on the inference of evolutionary changes in ecological life-history traits.Quantitative plant biology · 2026Review
- The interplay of recombination landscape and a transposable element in European populations of Chironomus riparius.BMC genomics · 2025Article
- How Did Evolution Halve Genome Size During an Oceanic Island Colonization?Molecular biology and evolution · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Article
- Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.Nature communications · 2024Article
- On the estimation of genome-average recombination rates.Genetics · 2024Article
- Article
- Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations.The American naturalist · 2023Review
- RecView: an interactive R application for locating recombination positions using pedigree data.BMC genomics · 2023Article
- Fast inference of genetic recombination rates in biobank scale data.Genome research · 2023Article
- Article
- FastRecomb: Fast inference of genetic recombination rates in biobank scale data.bioRxiv : the preprint server for biology · 2023Article
- Rapid and predictable genome evolution across three hybrid ant populations.PLoS biology · 2022Article
- Article
- Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley.BMC genomics · 2022Article
- The distribution of waiting distances in ancestral recombination graphs.Theoretical population biology · 2021Article
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3 authors.
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Abstract
Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.
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