Journal ArticleDOI
Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
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TLDR
It is suggested that pronounced substitution rate changes around the angiosperm crown node may represent a challenge for relaxed clocks to model adequately and whole-genome rate accelerations or decelerations may underlie the similar ages and correlated absolute rates estimated with different genes.Abstract:
UNLABELLED PREMISE OF THE STUDY Land plants play an essential role in the evolution of terrestrial life. Their time of origin and diversification is fundamental to understanding the evolution of life on land. We investigated the timing and the rate of molecular evolution of land plants, evaluating the effects of different types of molecular data, including temporal information from fossils, and using different molecular clock methods. • METHODS Ages and absolute rates were estimated independently with two substitutionally different data sets: a highly conserved 4-gene data set and matK, a fast-evolving gene. The vascular plant backbone and the crown nodes of all major lineages were calibrated with fossil-derived ages. Dates and absolute rates were estimated while including or excluding the calibrations and using two relaxed clocks that differ in their implementation of temporal autocorrelation. • KEY RESULTS Land plants diverged from streptophyte alga 912 (870-962) million years ago (Mya) but diversified into living lineages 475 (471-480) Mya. Ages estimated for all major land-plant lineages agree with their fossil record, except for angiosperms. Different genes estimated very similar ages and correlated absolute rates across the tree. Excluding calibrations resulted in the greatest age differences. Different relaxed clocks provided similar ages, but different and uncorrelated absolute rates. • CONCLUSIONS Whole-genome rate accelerations or decelerations may underlie the similar ages and correlated absolute rates estimated with different genes. We suggest that pronounced substitution rate changes around the angiosperm crown node may represent a challenge for relaxed clocks to model adequately.read more
Citations
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Journal ArticleDOI
A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity
TL;DR: This time-frame documents an early phylogenetic proliferation that led to the establishment of major angiosperm lineages, and the origin of over half of extant families, in the Cretaceous.
Journal ArticleDOI
The Amborella Genome and the Evolution of Flowering Plants
TL;DR: Genome structure and phylogenomic analyses indicate that the ancestral Angiosperm was a polyploid with a large constellation of both novel and ancient genes that survived to play key roles in angiosperm biology.
Journal Article
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
TL;DR: A variety of local and relaxed clock methods have been proposed and implemented for phylogenetic divergence dating as discussed by the authors, which allows different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution.
Journal ArticleDOI
The timescale of early land plant evolution
Jennifer L. Morris,Mark N. Puttick,James W. Clark,Dianne Edwards,Paul Kenrick,Silvia Pressel,Charles H. Wellman,Ziheng Yang,Ziheng Yang,Harald Schneider,Philip C. J. Donoghue +10 more
TL;DR: A timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation is established.
Journal ArticleDOI
Origin of angiosperms and the puzzle of the Jurassic gap
Hong-Tao Li,Ting-Shuang Yi,Lian-Ming Gao,Peng-Fei Ma,Ting Zhang,Jun-Bo Yang,Matthew A. Gitzendanner,Matthew A. Gitzendanner,Peter W. Fritsch,Jie Cai,Yang Luo,Hong Wang,Michelle van der Bank,Shu-Dong Zhang,Qing-Feng Wang,Jian Wang,Zhirong Zhang,Chao-Nan Fu,Jing Yang,Peter M. Hollingsworth,Mark W. Chase,Mark W. Chase,Douglas E. Soltis,Pamela S. Soltis,Pamela S. Soltis,De-Zhu Li +25 more
TL;DR: A study reconstructed angiosperm phylogeny on the basis of plastome data representing 2,351 angiosperm and 187 gymnosperm species, and dated the origin of crown angiosperms to be significantly earlier than the estimates based on fossil data.
References
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Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Journal ArticleDOI
Relaxed Phylogenetics and Dating with Confidence
TL;DR: In this paper, the authors introduce a new approach to perform relaxed phylogenetic analysis, which can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.
Journal ArticleDOI
Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
David Posada,Thomas R. Buckley +1 more
TL;DR: It is argued that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages.
Journal ArticleDOI
Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL.
TL;DR: Two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups indicate that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling.
Journal ArticleDOI
Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
TL;DR: A semiparametric smoothing method is developed using penalized likelihood, a saturated model in which every lineage has a separate rate combined with a roughness penalty that discourages rates from varying too much across a phylogeny.
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