Establishing a time‐scale for plant evolution

Abstract

Summary• 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.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

“…A starting tree with branch lengths satisfying all fossil prior constraints was created according to the consensus APGIII phylogeny 71 . Fossil calibrations were implemented using log-normal calibration priors on the following nodes: the node uniting the Malvidae based on the fossil Dressiantha bicarpellata 72 The offsets of these calibrations represent hard minimum boundaries, while their means represent locations for their respective peak mass probabilities in accordance with some of the most recent and taxonomically complete dating studies available for these specific clades 14,80 . A run without data was performed to ensure proper placement of the marginal calibration prior distributions 81 .…”

Integrating Early Cretaceous Fossils into the Phylogeny of Living Angiosperms: ANITA Lines and Relatives of Chloranthaceae

“…Such analyses address the age of the angiosperm crown group, i.e., the most recent common ancestor of all living angiosperms; diagnostic synapomorphies such as the flower, the carpel, or columellar exine structure could be significantly older. Most molecular dating analyses indicate that the angiosperm crown group extended back into the Jurassic ( Smith et al 2010;Clarke et al 2011). If these results are accepted, they raise the question of why convincing angiosperms have not been recognized in the fossil record until the Cretaceous.…”

“…By contrast, Amborella and Austrobaileyales are restricted to wet, shaded forest understory sites. Feild et al (2004Feild et al ( , 2009) reconstructed such habitats as ancestral for angiosperms and argued that the rarity of such environments in the Triassic and Jurassic could explain why angiosperms escaped detection if they existed at that time, as indicated by many molecular dating analyses (Magalló n 2010; Smith et al 2010;Clarke et al 2011;see Doyle 2012). If Appomattoxia is near the base of the tree, it could challenge this view of ecology of the first angiosperms or else indicate that members of the basal grade were able to break out of the ancestral niche and adapt to dry climates more easily than might be expected.…”

Distribution of living Cupressaceae reflects the breakup of Pangea

“…Using ancient fossils to calibrate genetic distances in molecular phylogenies can be problematic, because the older a fossil is, the more likely it is to represent an extinct lineage that diverged somewhere along the line leading to the extant taxon with which it is being compared (37). However, probability distributions on fossil calibration ages allow some manipulation of this uncertainty (38), and judicious use of multiple fossils also may help circumvent calibration pitfalls (39).…”