ArticleBioinformatics (Oxford, England)2014
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- RRmorph-a new R package to map phenotypic evolutionary rates and patterns on 3D meshes.Communications biology · 2024Article
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- Bayesian Analyses of Comparative Data with the Ornstein-Uhlenbeck Model: Potential Pitfalls.Systematic biology · 2022Article
- Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota.Nature communications · 2022Article
- Where Do We Stand in Regularization for Life Science Studies?Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Terrestrial reproduction and parental care drive rapid evolution in the trade-off between offspring size and number across amphibians.PLoS biology · 2022Article
- Vertical clinging and leaping induced evolutionary rate shifts in postcranial evolution of tamarins and marmosets (Primates, Callitrichidae).BMC ecology and evolution · 2021Article
- Butterfly dichromatism primarily evolved via Darwin's, not Wallace's, model.Evolution letters · 2020Article
- Driven progressive evolution of genome sequence complexity in Cyanobacteria.Scientific reports · 2020Article
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- Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
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2 authors.
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Abstract
motivationAncestral character state reconstruction describes a set of techniques for estimating phenotypic or genetic features of species or related individuals that are the predecessors of those present today. Such reconstructions can reach into the distant past and can provide insights into the history of a population or a set of species when fossil data are not available, or they can be used to test evolutionary hypotheses, e.g. on the co-evolution of traits. Typical methods for ancestral character state reconstruction of continuous characters consider the phylogeny of the underlying data and estimate the ancestral process along the branches of the tree. They usually assume a Brownian motion model of character evolution or extensions thereof, requiring specific assumptions on the rate of phenotypic evolution.
resultsWe suggest using ridge regression to infer rates for each branch of the tree and the ancestral values at each inner node. We performed extensive simulations to evaluate the performance of this method and have shown that the accuracy of its reconstructed ancestral values is competitive to reconstructions using other state-of-the-art software. Using a hierarchical clustering of gene mutation profiles from an ovarian cancer dataset, we demonstrate the use of the method as a feature selection tool. AVAILABILITY AND IMPLEMENTATION: The algorithm described here is implemented in C++ as a stand-alone program, and the source code is freely available at http://algbio.cs.uni-duesseldorf.de/software/RidgeRace.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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