Author:
Costa Fernanda P.,Schrago Carlos G.,Mello Beatriz
Abstract
AbstractAdvances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
Publisher
Springer Science and Business Media LLC
Reference93 articles.
1. Doolittle RF, Blomback B. Amino-acid sequence investigations of Fibrinopeptides from various mammals: evolutionary implications. Nature. 1964;202:147.
2. Margoliash E. Primary structure and evolution of cytochrome C. Proc Natl Acad Sci U S A. 1963;50:672–9.
3. Zuckerkandl E, Pauling L. Molecular disease, evolution, and genic heterogeneity. In: Kasha M, Pullman B, editors. Horizons in biochemistry. New York, USA: Academic Press; 1962. p. 189–225.
4. Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. In: Evolving Genes and Proteins: Elsevier; 1965. p. 97–166. https://www.elsevier.com/books/evolving-genes-andproteins/bryson/978-1-4832-2734-4.
5. Blair C, Bryson RW, Linkem CW, Lazcano D, Klicka J, McCormack JE. Cryptic diversity in the Mexican highlands: thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus ). Mol Ecol Resour. 2019;19:349–65.
Cited by
5 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献