ArticleGenetics2018
Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography.
Article in Genetics, 2018. 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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Who cites it
27 citing papers in PubMed.
- Article
- Inference of Multiple Mergers while Dating a Pathogen Phylogeny.Systematic biology · 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 demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Multiple merger coalescent inference of effective population size.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.bioRxiv : the preprint server for biology · 2024Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Interpreting the pervasive observation of U-shaped Site Frequency Spectra.PLoS genetics · 2023Article
- Article
- Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa.Molecular biology and evolution · 2023Article
- Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution.PLoS genetics · 2022Review
- How Can We Resolve Lewontin's Paradox?Genome biology and evolution · 2022Article
- The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis.G3 (Bethesda, Md.) · 2022Article
- Recommendations for improving statistical inference in population genomics.PLoS biology · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies.Heredity · 2022Article
- Effects of Selection at Linked Sites on Patterns of Genetic Variability.Annual review of ecology, evolution, and systematics · 2021Article
- Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale-analogous to the Kingman coalescent-we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
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