ArticleGenetics2015
Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks.
Article in Genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.Molecular biology and evolution · 2026Article
- Coalescent theory of the ψ directionality index.G3 (Bethesda, Md.) · 2025Article
- Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies.Molecular ecology · 2024Article
- Graph-based algorithms for Laplace transformed coalescence time distributions.PLoS computational biology · 2022Article
- Genomic consequences of domestication of the Siamese fighting fish.Science advances · 2022Article
- Efficient ancestry and mutation simulation with msprime 1.0.Genetics · 2022Article
- Population dynamics of caribou shaped by glacial cycles before the last glacial maximum.Molecular ecology · 2021Article
- Article
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- The impact of purifying and background selection on the inference of population history: problems and prospects.bioRxiv : the preprint server for biology · 2021Article
- The determinants of genetic diversity in butterflies.Nature communications · 2019Article
- Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.GigaScience · 2019Article
- ABLE: blockwise site frequency spectra for inferring complex population histories and recombination.Genome biology · 2018Article
- Whole-genome data reveal the complex history of a diverse ecological community.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.G3 (Bethesda, Md.) · 2017Article
- Article
- Inferring Demographic History Using Two-Locus Statistics.Genetics · 2017Article
- Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.PLoS genetics · 2016Article
- Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks--extreme population size changes of short duration--not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin's pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations.
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