ArticleMolecular biology and evolution2014
Prospects for building large timetrees using molecular data with incomplete gene coverage among species.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
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- On estimating evolutionary probabilities of population variants.BMC evolutionary biology · 2019Article
- A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies.Molecular biology and evolution · 2019Article
- Genomic and Proteomic Characterizations ofFrontiers in microbiology · 2019Article
- Genetic exchanges are more frequent in bacteria encoding capsules.PLoS genetics · 2018Article
- Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements.Molecular biology and evolution · 2018Article
- Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates.Molecular biology and evolution · 2018Article
- RelTime Relaxes the Strict Molecular Clock throughout the Phylogeny.Genome biology and evolution · 2018Article
- MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Molecular biology and evolution · 2016Article
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5 authors.
Funding
Abstract
Scientists are assembling sequence data sets from increasing numbers of species and genes to build comprehensive timetrees. However, data are often unavailable for some species and gene combinations, and the proportion of missing data is often large for data sets containing many genes and species. Surprisingly, there has not been a systematic analysis of the effect of the degree of sparseness of the species-gene matrix on the accuracy of divergence time estimates. Here, we present results from computer simulations and empirical data analyses to quantify the impact of missing gene data on divergence time estimation in large phylogenies. We found that estimates of divergence times were robust even when sequences from a majority of genes for most of the species were absent. From the analysis of such extremely sparse data sets, we found that the most egregious errors occurred for nodes in the tree that had no common genes for any pair of species in the immediate descendant clades of the node in question. These problematic nodes can be easily detected prior to computational analyses based only on the input sequence alignment and the tree topology. We conclude that it is best to use larger alignments, because adding both genes and species to the alignment augments the number of genes available for estimating divergence events deep in the tree and improves their time estimates.
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