ArticleMolecular biology and evolution2018
Effects of Demographic History on the Detection of Recombination Hotspots from Linkage Disequilibrium.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus).Heredity · 2026Article
- Comparing the genomic inbreeding of an isolated rhesus macaque study population to wild populations.bioRxiv : the preprint server for biology · 2026Article
- Natural selection and recombination interact to structure genome-wide variation in pines.The Plant journal : for cell and molecular biology · 2026Article
- Mixed Outcomes in Recombination Rates After Domestication: Revisiting Theory and Data.Molecular ecology · 2025Review
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Convergent Evolution and the Epigenome.Epigenomes · 2025Review
- Inferring Fine-Scale Mutation and Recombination Rate Maps in Aye-Ayes (Ecology and evolution · 2025Article
- Re-Evaluating the Demographic History of, and Inferring the Fine-Scale Recombination Landscape For, Wild Chinese Rhesus Macaques (Macaca mulatta).American journal of primatology · 2025Article
- Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets (Callithrix jacchus) from High-Quality, Whole-Genome, Population-Level Data.Molecular biology and evolution · 2025Article
- Article
- Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes.Molecular biology and evolution · 2024Article
- Understanding the Genetic Basis of Variation in Meiotic Recombination: Past, Present, and Future.Molecular biology and evolution · 2024Review
- The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects.Genome biology and evolution · 2024Article
- The role of recombination dynamics in shaping signatures of direct and indirect selection across theProceedings. Biological sciences · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
- Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds.Genome biology and evolution · 2024Article
- Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.Genome biology and evolution · 2024Article
- Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques (Macaca mulatta).Genome biology and evolution · 2024Article
- Recombination map tailored to Native Hawaiians may improve robustness of genomic scans for positive selection.Human genetics · 2024Article
- Review
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2 authors.
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Abstract
In some species, meiotic recombination is concentrated in small genomic regions. These "recombination hotspots" leave signatures in fine-scale patterns of linkage disequilibrium, raising the prospect that the genomic landscape of hotspots can be characterized from sequence variation. This approach has led to the inference that hotspots evolve rapidly in some species, but are conserved in others. Historic demographic events, such as population bottlenecks, are known to affect patterns of linkage disequilibrium across the genome, violating population genetic assumptions of this approach. Although such events are prevalent, demographic history is generally ignored when making inferences about the evolution of recombination hotspots. To determine the effect of demography on the detection of recombination hotspots, we use the coalescent to simulate haplotypes with a known recombination landscape. We measure the ability of popular linkage disequilibrium-based programs to detect hotspots across a range of demographic histories, including population bottlenecks, hidden population structure, population expansions, and population contractions. We find that demographic events have the potential to greatly reduce the power and increase the false positive rate of hotspot discovery. Neither the power nor the false positive rate of hotspot detection can be predicted without also knowing the demographic history of the sample. Our results suggest that ignoring demographic history likely overestimates the power to detect hotspots and therefore underestimates the degree of hotspot sharing between species. We suggest strategies for incorporating demographic history into population genetic inferences about recombination hotspots.
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