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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Posted ContentDOI
Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)
Jin Yu,Linzhou Li,Sibo Wang,Shan-Shan Dong,Ziqiang Chen,Nikisha Patel,Bernard Goffinet,Huan Liu,Yang Liu +8 more
TL;DR: The draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere, is reported, the third genome of mosses and the second genome for a seedless aquatic plant.
Journal ArticleDOI
Phylogenetic signal in the topographic niche of trees: Current and historical significance of habitat structure on the species arrangement pattern within East Asian rugged forests
Journal ArticleDOI
The genome of the king protea, <i>Protea cynaroides</i>
TL;DR: The genome of Protea cynaroides (Protea) is the first representative of the fynbos biome as discussed by the authors , and it has been used to reveal an ancestral whole-genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family.
Title: Best Practices for Justifying Fossil Calibrations
James F. Parham,Christopher J. Bell,Tyler Calway,Jason J. Head,Patricia A. Holroyd,Jun G. Inoue,Randall B. Irmis,Walter G. Joyce,Daniel T. Ksepka,Nathan D. Smith,James E. Tarver,Ziheng Yang,Kenneth D. Angielczyk,Jenny M. Greenwood,A Christy,Jessica M. Theodor,Michael J. Benton +16 more
Posted ContentDOI
Origin of photosynthetic water oxidation at the dawn of life
Tom H. Oliver,Patricia Sánchez-Baracaldo,Anthony W. D. Larkum,A. William Rutherford,Tanai Cardona +4 more
TL;DR: This work uses relaxed molecular clocks, ancestral sequence reconstruction, and comparative structural biology to demonstrate that photosystem II exhibits patterns of evolution through geological time that are indistinguishable from those of ATP synthase, RNA polymerase, or the ribosome, some of the oldest known enzymes.
References
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Journal ArticleDOI
PAML 4: Phylogenetic Analysis by Maximum Likelihood
TL;DR: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML), which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses.
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.
BookDOI
A Geologic Time Scale 2004
TL;DR: Gradstein et al. as discussed by the authors proposed a chronostratigraphy approach for linking time and rock in the context of geologic time scales, including the geomagnetic polarity time scale and stable isotope geochronology.
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