ArticleG3 (Bethesda, Md.)2025
Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.
Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Inferring the Demographic History of Coppery Titi Monkeys (Plecturocebus cupreus) From High-Quality, Whole-Genome, Population-Level Data.American journal of primatology · 2026Article
- Inferring Patterns of Purifying, Positive, and Balancing Selection in the Coppery Titi Monkey (Plecturocebus cupreus) Utilizing a Well-Fit Evolutionary Baseline Model.Genome biology and evolution · 2026Article
- Genome-wide SNP data reveal hidden hierarchical population structure and demographic history of endangered black-and-white snub-nosed monkeys (Rhinopithecus bieti).Molecular biology and evolution · 2026Article
- Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River.bioRxiv : the preprint server for biology · 2026Article
- Interpreting Patterns of X Chromosomal Relative to Autosomal Diversity in Aye-Ayes (Daubentonia madagascariensis).American journal of primatology · 2025Article
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Article
- 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
- The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Estimating the Distribution of Fitness Effects in Aye-Ayes (Daubentonia madagascariensis), Accounting for Population History as Well as Mutation and Recombination Rate Heterogeneity.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
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
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Abstract
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.
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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.