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Journal ArticleDOI

Establishing a time-scale for plant evolution

01 Oct 2011-New Phytologist (Wiley/Blackwell (10.1111))-Vol. 192, Iss: 1, pp 266-301
TL;DR: 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.
Citations
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Journal ArticleDOI
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.
Abstract: The establishment of modern terrestrial life is indissociable from angiosperm evolution. While available molecular clock estimates of angiosperm age range from the Paleozoic to the Late Cretaceous, the fossil record is consistent with angiosperm diversification in the Early Cretaceous. The time-frame of angiosperm evolution is here estimated using a sample representing 87% of families and sequences of five plastid and nuclear markers, implementing penalized likelihood and Bayesian relaxed clocks. A literature-based review of the palaeontological record yielded calibrations for 137 phylogenetic nodes. The angiosperm crown age was bound within a confidence interval calculated with a method that considers the fossil record of the group. An Early Cretaceous crown angiosperm age was estimated with high confidence. Magnoliidae, Monocotyledoneae and Eudicotyledoneae diversified synchronously 135-130 million yr ago (Ma); Pentapetalae is 126-121 Ma; and Rosidae (123-115 Ma) preceded Asteridae (119-110 Ma). Family stem ages are continuously distributed between c. 140 and 20 Ma. 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. While substantial amounts of angiosperm morphological and functional diversity have deep evolutionary roots, extant species richness was probably acquired later.

792 citations


Cites background from "Establishing a time-scale for plant..."

  • ...…with many recent estimates lying New Phytologist (2015) 207: 437–453 2015 The Authors New Phytologist 2015 New Phytologist Trustwww.newphytologist.com Research New Phytologist438 between c. 190 and 150Ma (e.g. Magall on, 2010; Smith et al., 2010; Clarke et al., 2011; Magall on et al., 2013; Fig....

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Journal Article
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.
Abstract: The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit 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 (Rambaut and Bromham 1998; Yoder and Yang 2000).

707 citations

Journal ArticleDOI
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.
Abstract: At this time, no abstract is available. SciVerse Scopus has content delivery agreements in place with each publisher and currently contains 30 million records with an abstract. An abstract may not be present due to incomplete data, as supplied by the publisher, or is still in the process of being indexed.

589 citations

Journal ArticleDOI
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.
Abstract: Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish 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. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

573 citations


Cites background from "Establishing a time-scale for plant..."

  • ...[62], while Cooksonia can be placed in the total group Tracheophyta with confidence, with additional synapomorphies such as stomata [68] and sporophyte branching [52, 69], other characters, such as the sterome [68], are not considered to be a synapomorphies of the crown group Tracheophyta....

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  • ...[62], the soft maximum age constraint is based on the first appearance of trilete spores, in the Qusaiba-1 core from the Qasim Formation, northern Saudi Arabia [139]....

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  • ...[62], Zosterophyllum is considered to be a member of the Lycopodiophyta total group, based on the lateral insertion of reniform sporangia along stems, which dehisce along their distal margins into two valves [69]....

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  • ...[62] proposed trilete spores as the minimum age providing fossils for the Embryophyta node, the oldest record known from Late Ordovician strata of Saudi Arabia (see node 112 for discussion on trilete spores)....

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  • ...[62], Rellimia thomsonii is considered to be the oldest unequivocal aneurophytalean progymnosperm fossil [163], thus the oldest record of crown Euphyllophyta....

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Journal ArticleDOI
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.
Abstract: Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages. However, the practical application of these methods is challenging because of the exorbitant calculation times required by current methods for contemporary data sizes, the difficulty in correctly modeling the rate heterogeneity in highly diverse taxonomic groups, and the lack of reliable clock calibrations and their uncertainty distributions for most groups of species. Here, we present 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. The method (RelTime) performed better than existing methods when applied to very large computer simulated datasets where evolutionary rates were varied extensively among lineages by following autocorrelated and uncorrelated models. On average, RelTime completed calculations 1,000 times faster than the fastest Bayesian method, with even greater speed difference for larger number of sequences. This speed and accuracy will enable molecular dating analysis of very large datasets. Relative time estimates will be useful for determining the relative ordering and spacing of speciation events, identifying lineages with significantly slower or faster evolutionary rates, diagnosing the effect of selected calibrations on absolute divergence times, and estimating absolute times of divergence when highly reliable calibration points are available.

502 citations

References
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Journal ArticleDOI
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.
Abstract: PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

10,773 citations


"Establishing a time-scale for plant..." refers methods in this paper

  • ...Molecular clock analysis was performed using MCMCTREE (Yang & Rannala, 2006; Rannala & Yang, 2007; Inoue et al., 2010), part of the PAML 4 package (Yang, 2007), with branch lengths estimated in BASEML....

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Journal ArticleDOI
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.
Abstract: In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

5,812 citations

Book
01 Jan 1982

4,055 citations

BookDOI
01 Jan 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.
Abstract: Part I. Introduction: 1. Introduction F. M. Gradstein 2. Chronostratigraphy - linking time and rock F. M. Gradstein, J. G. Ogg and A. G. Smith Part II. Concepts and Methods: 3. Biostratigraphy F. M. Gradstein, R. A. Cooper and P. M. Sadler 4. Earth's orbital parameters and cycle stratigraphy L. A. Hinnov 5. The geomagnetic polarity time scale J. G. Ogg and A. G. Smith 6. Radiogenic isotope geochronology M. Villeneuve 7. Stable isotopes J. M. McArthur and R. J. Howarth 8. Geomathematics F. P. Agterberg Part III. Geologic Periods: 9. The Precambrian: the Archaen and Proterozoic eons L. J. Robb, A. H. Knoll, K. A. Plumb, G. A. Shields, H. Strauss and J. Veizer 10. Toward a 'natural' Precambrian time scale W. Bleeker 11. The Cambrian period J. H. Shergold and R. A. Cooper 12. The Ordovician period R. A. Cooper and P. M. Sadler 13. The Silurian period M. J. Melchin, R. A. Cooper and P. M. Sadler 14. The Devonian period M. R. House and F. M. Gradstein 15. The Carboniferous period V. Davydov, B. R. Wardlaw and F. M. Gradstein 16. The Permian period B. R. Wardlaw, V. Davydov and F. M. Gradstein 17. The Triassic period J. G. Ogg 18. The Jurassic period J. G. Ogg 19. The Cretaceous Period J. G. Ogg, F. P. Agterberg and F. M. Gradstein 20. The Paleogene period H. P. Luterbacher, J. R. Ali, H. Brinkhuis, F. M. Gradstein, J. J. Hooker, S. Monechi, J. G. Ogg, J. Powell, U. Rohl, A. Sanfilippo, and B. Schmitz 21. The Neogene period L. Lourens, F. Hilgen, N. J. Shackleton, J. Laskar and D. Wilson 22. The Pleistocene and Holocene epochs P. Gibbard and T. van Kolfschoten Part IV. Summary: 23. Construction and summary of the geologic time scale F. M.. Gradstein, J. G. Ogg and A. G. Smith Appendices Bibliography Stratigraphic index General index.

2,890 citations