Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates.

@article{Magalln2013LandPE,
  title={Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates.},
  author={Susana Magall{\'o}n and Khidir W Hilu and Dietmar Quandt},
  journal={American journal of botany},
  year={2013},
  volume={100 3},
  pages={
          556-73
        }
}
UNLABELLED PREMISE OF THE STUDY Land plants play an essential role in the evolution of terrestrial life. Their time of origin and diversification is fundamental to understanding the evolution of life on land. We investigated the timing and the rate of molecular evolution of land plants, evaluating the effects of different types of molecular data, including temporal information from fossils, and using different molecular clock methods. • METHODS Ages and absolute rates were estimated… 
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References

SHOWING 1-10 OF 74 REFERENCES
Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms.
TLDR
This study explores the effect of the long branch subtending angiosperm stem branch in molecular dating and how different relaxed clocks react to it, and suggests a more adequate molecular dating approach might combine moderate background rate heterogeneity with large changes in rate at particular points in the tree.
ANGIOSPERM DIVERGENCE TIMES: THE EFFECT OF GENES, CODON POSITIONS, AND TIME CONSTRAINTS
TLDR
Although absolute age estimates of angiosperms and angiosperm clades are older than their earliest fossils, the estimated pace of phylogenetic diversification largely agrees with the rapid appearance ofAngiosperm lineages in stratigraphic sequences.
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.
An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
We present molecular dating analyses for land plants that incorporate 33 fossil calibrations, permit rates of molecular evolution to be uncorrelated across the tree, and take into account…
Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils
TLDR
This study minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes.
Accommodating heterogenous rates of evolution in molecular divergence dating methods: an example using intercontinental dispersal of Plestiodon (Eumeces) lizards.
TLDR
It is found that extreme saturation has obscured the underlying rate of evolution in the mitochondrial DNA, resulting in severe underestimation of the rate in this locus, indicating an inadequacy of current models to capture the complex nature of mtDNA evolution in over large time scales.
Dating the Time of Origin of Major Clades: Molecular Clocks and the Fossil Record
▪ Abstract Molecular and paleontological data provide independent means of estimating when groups of organisms evolved in the geological past, but neither approach can be considered straightforward.…
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
TLDR
Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times.
Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary.
TLDR
Tertiary macrofossils of the flowering plant family Leguminosae were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies, pointing to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic.
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
TLDR
The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life.
...
1
2
3
4
5
...