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
Lifestyles in transition: evolution and natural history of the genus Lactobacillus.
Rebbeca M. Duar,Xiaoxi B. Lin,Jinshui Zheng,Maria Elena Martino,Théodore Grenier,Maria Elisa Perez-Muñoz,François Leulier,Michael G. Gänzle,Jens Walter +8 more
TL;DR: This model can provide a framework for the elucidation of the natural and evolutionary history of Lactobacillus species and valuable information to improve the use of this important genus in industrial and therapeutic applications.
Journal ArticleDOI
Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications
David C. Tank,Jonathan M. Eastman,Matthew W. Pennell,Pamela S. Soltis,Douglas E. Soltis,Douglas E. Soltis,Cody E. Hinchliff,Joseph W. Brown,Emily B. Sessa,Luke J. Harmon +9 more
TL;DR: Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time, and it is suggested that stochastically changing diversification rates across the phylogeny explain these patterns.
Journal ArticleDOI
Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates
TL;DR: 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.
Journal ArticleDOI
The Apostasia genome and the evolution of orchids
Guo-Qiang Zhang,Ke-Wei Liu,Zhen Li,Rolf Lohaus,Yu Yun Hsiao,Shan Ce Niu,Shan Ce Niu,Jie Yu Wang,Jie Yu Wang,Yao-Cheng Lin,Yao-Cheng Lin,Qing Xu,Li Jun Chen,Kouki Yoshida,Sumire Fujiwara,Zhi Wen Wang,Yong-Qiang Zhang,Nobutaka Mitsuda,Meina Wang,Guo Hui Liu,Lorenzo Pecoraro,Hui Xia Huang,Xin Ju Xiao,Min Lin,Xin Yi Wu,Wan Lin Wu,Wan Lin Wu,You Yi Chen,Song Bin Chang,Shingo Sakamoto,Masaru Ohme-Takagi,Masaru Ohme-Takagi,Masafumi Yagi,Si Jin Zeng,Si Jin Zeng,Ching Yu Shen,Chuan Ming Yeh,Yi-Bo Luo,Wen Chieh Tsai,Yves Van de Peer,Zhong Jian Liu +40 more
TL;DR: New light is shed on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
Journal ArticleDOI
Palaeozoic landscapes shaped by plant evolution
TL;DR: Fluvial landscapes diversified markedly over the 250 million years between the Cambrian and Pennsylvanian periods as discussed by the authors and the diversification occurred in tandem with the evolution of vascular plants and expanding vegetation cover.
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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