Journal ArticleDOI
Establishing a time-scale for plant evolution
TLDR
A post-Jurassic origin of angiosperms and a post-Cambrian origin of land plants are rejected, and it is suggested that the establishment of the major embryophyte lineages occurred at a much slower tempo than suggested in most previous studies.Abstract:
• Plants have utterly transformed the planet, but testing hypotheses of causality requires a reliable time-scale for plant evolution. While clock methods have been extensively developed, less attention has been paid to the correct interpretation and appropriate implementation of fossil data. • We constructed 17 calibrations, consisting of minimum constraints and soft maximum constraints, for divergences between model representatives of the major land plant lineages. Using a data set of seven plastid genes, we performed a cross-validation analysis to determine the consistency of the calibrations. Six molecular clock analyses were then conducted, one with the original calibrations, and others exploring the impact on divergence estimates of changing maxima at basal nodes, and prior probability densities within calibrations. • Cross-validation highlighted Tracheophyta and Euphyllophyta calibrations as inconsistent, either because their soft maxima were overly conservative or because of undetected rate variation. Molecular clock analyses yielded estimates ranging from 568-815 million yr before present (Ma) for crown embryophytes and from 175-240 Ma for crown angiosperms. • We reject both a post-Jurassic origin of angiosperms and a post-Cambrian origin of land plants. Our analyses also suggest that the establishment of the major embryophyte lineages occurred at a much slower tempo than suggested in most previous studies. These conclusions are entirely compatible with current palaeobotanical data, although not necessarily with their interpretation by palaeobotanists.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 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
Best practices for justifying fossil calibrations
James F. Parham,James F. Parham,James F. Parham,Philip C. J. Donoghue,Christopher J. Bell,Tyler Calway,Jason J. Head,Patricia A. Holroyd,Jun G. Inoue,Randall B. Irmis,Walter G. Joyce,Daniel T. Ksepka,Daniel T. Ksepka,José S. L. Patané,Nathan D. Smith,Nathan D. Smith,James E. Tarver,James E. Tarver,Marcel van Tuinen,Ziheng Yang,Kenneth D. Angielczyk,Jenny M. Greenwood,Christy A. Hipsley,Christy A. Hipsley,Louis L. Jacobs,Peter J. Makovicky,Johannes Müller,Krister T. Smith,Jessica M. Theodor,Rachel C. M. Warnock,Michael J. Benton +30 more
TL;DR: A specimen-based protocol for selecting and documenting relevant fossils is presented and future directions for evaluating and utilizing phylogenetic and temporal data from the fossil record are discussed, to establish the best practices for justifying fossils used for the temporal calibration of molecular phylogenies.
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
Estimating divergence times in large molecular phylogenies
Koichiro Tamura,Fabia U. Battistuzzi,Fabia U. Battistuzzi,Paul Billing-Ross,Oscar Murillo,Alan Filipski,Sudhir Kumar +6 more
TL;DR: RelTime is presented, a method that estimates relative times of divergences for all branching points (nodes) in very large phylogenetic trees without assuming a specific model for lineage rate variation or specifying any clock calibrations.
References
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Book ChapterDOI
Evolutionary Divergence and Convergence in Proteins
Emile Zuckerkandl,Linus Pauling +1 more
TL;DR: The evaluation of the amount of differences between two organisms as derived from sequences in structural genes or in their polypeptide translation is likely to lead to quantities different from those obtained on the basis of observations made at any other, higher level of biological integration.
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Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL.
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On The Geologic Time Scale
TL;DR: GTS2012 as mentioned in this paper summarizes the international divisions and ages in the Geologic Time Scale, published in 2012, since 2004, when GTS2004 was detailed, major developments have taken place that directly bear and have considerable impact on the intricate science of geologic time scaling.
Journal ArticleDOI
Bayesian Phylogenetic Analysis of Combined Data
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Journal ArticleDOI
Evolution of the angiosperms: calibrating the family tree.
TL;DR: Angiosperm divergence times are estimated using non–parametric rate smoothing and a three–gene dataset covering ca.
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