ArticleAlgorithms for molecular biology : AMB2019
A branching process for homology distribution-based inference of polyploidy, speciation and loss.
Article in Algorithms for molecular biology : AMB, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed.
- GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events.Plant physiology · 2022Article
- Integrated synteny- and similarity-based inference on the polyploidization-fractionation cycle.Interface focus · 2021Article
- Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment.BMC bioinformatics · 2019Article
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Authors and funding
3 authors.
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Abstract
backgroundThe statistical distribution of the similarity or difference between pairs of paralogous genes, created by whole genome doubling, or between pairs of orthologous genes in two related species is an important source of information about genomic evolution, especially in plants.
methodsWe derive the mixture of distributions of sequence similarity for duplicate gene pairs generated by repeated episodes of whole gene doubling. This involves integrating sequence divergence and gene pair loss through fractionation, using a branching process and a mutational model. We account not only for the timing of these events in terms of local modes, but also the amplitude and variance of the component distributions. This model is then extended to orthologous gene pairs.
resultsWe apply the model and inference procedures to the evolution of the Solanaceae, focusing on the genomes of economically important crops. We assess how consistent or variable fractionation rates are from species to species and over time.
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