A fast likelihood approach for estimation of large phylogenies from continuous trait data
| Autor: | Arindam RoyChoudhury, Haseena Rajeevan, Jing Peng, Laura Kubatko |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
0301 basic medicine Maximum likelihood Genomic data Bayesian probability Mathematical properties Inference Scale (descriptive set theory) Biology 010603 evolutionary biology 01 natural sciences 03 medical and health sciences Gene Frequency Genetics Quantitative Biology::Populations and Evolution Humans Continuous trait Molecular Biology Ecology Evolution Behavior and Systematics Phylogeny Estimation Likelihood Functions Reproducibility of Results Bayes Theorem Quantitative Biology::Genomics ComputingMethodologies_PATTERNRECOGNITION 030104 developmental biology Phenotype Research Design Algorithm |
| Zdroj: | Molecular phylogenetics and evolution. 161 |
| ISSN: | 1095-9513 |
| Popis: | Despite the recent availability of large-scale genomic data for many individuals, few methods for phylogenetic inference are both computationally efficient and highly accurate for trees with hundreds of taxa. Model-based methods such as those developed in the maximum likelihood and Bayesian frameworks are especially time-consuming, as they involve both computationally intensive calculations on fixed phylogenies and searches through the space of possible phylogenies, and they are known to scale poorly with the addition of taxa. Here, we propose a fast approximation to the maximum likelihood estimator that directly uses continuous trait data, such as allele frequency data. The approximation works by first computing the maximum likelihood estimates of some internal branch lengths, and then inferring the tree-topology using these estimates. Our approach is more computationally efficient than existing methods for such data while still achieving comparable accuracy. This method is innovative in its use of the mathematical properties of tree-topologies for inference, and thus serves as a useful addition to the collection of methods available for estimating phylogenies from continuous trait data. |
| Databáze: | OpenAIRE |
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