ArticlePLoS genetics2020
Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Coalescence and translation: A language model for population genetics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Late Quaternary climate impact on the genome of the woodland strawberry (Fragaria vesca), a perennial herb.Communications biology · 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
- 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
- Going New Places: Successful Adaptation and Genomic Integrity of Grain Amaranth in India.Evolutionary applications · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High-recombining genomic regions affect demography inference based on ancestral recombination graphs.Genetics · 2025Article
- Patterns of presence-absence variation of NLRs across populations of Solanum chilense are clade-dependent and mainly shaped by past demographic history.The New phytologist · 2025Article
- Trans-Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior.Molecular ecology · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.bioRxiv : the preprint server for biology · 2025Article
- Article
- Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates.Genome biology and evolution · 2024Article
- Assessing the extinction risk of the spontaneous flora in urban tree bases.PLoS computational biology · 2024Article
- Article
- Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing.Genome biology and evolution · 2023Article
- Approximate Bayesian Computation Untangles Signatures of Contemporary and Historical Hybridization between Two Endangered Species.Molecular biology and evolution · 2022Article
- Principles of seed banks and the emergence of complexity from dormancy.Nature communications · 2021Review
- Correction: Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data.PLoS genetics · 2021Article
- Biased Gene Conversion Constrains Adaptation inGenetics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.
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