ArticleGenetics2016
Efficient Strategies for Calculating Blockwise Likelihoods Under the Coalescent.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Chromosome Fissions and Fusions Act as Barriers to Gene Flow between Brenthis Fritillary Butterflies.Molecular biology and evolution · 2023Article
- On the origin and structure of haplotype blocks.Molecular ecology · 2023Article
- Inversions maintain differences between migratory phenotypes of a songbird.Nature communications · 2023Article
- Graph-based algorithms for Laplace transformed coalescence time distributions.PLoS computational biology · 2022Article
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- Variational inference using approximate likelihood under the coalescent with recombination.Genome research · 2021Article
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- Estimating divergence times from DNA sequences.Genetics · 2021Article
- Signatures of Introgression across the Allele Frequency Spectrum.Molecular biology and evolution · 2021Article
- Maintenance of Species Differences in Closely Related Tetraploid ParasiticPlant communications · 2020Article
- The impact of global selection on local adaptation and reproductive isolation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Divergence of chemosensing during the early stages of speciation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes.Genetics · 2020Article
- A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis.Molecular biology and evolution · 2020Article
- Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.PLoS biology · 2020Article
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Authors and funding
4 authors.
Funding
Abstract
The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno.
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