Constraining the timing of whole genome duplication in plant evolutionary history

@article{Clark2017ConstrainingTT,
  title={Constraining the timing of whole genome duplication in plant evolutionary history},
  author={James W. Clark and Philip C. J. Donoghue},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  year={2017},
  volume={284}
}
Whole genome duplication (WGD) has occurred in many lineages within the tree of life and is invariably invoked as causal to evolutionary innovation, increased diversity, and extinction resistance. Testing such hypotheses is problematic, not least since the timing of WGD events has proven hard to constrain. Here we show that WGD events can be dated through molecular clock analysis of concatenated gene families, calibrated using fossil evidence for the ages of species divergences that bracket WGD… 
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References

SHOWING 1-10 OF 167 REFERENCES

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

It is suggested that polyploid establishment is promoted during times of environmental stress, and considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time ofpolyploidization could mitigate the stark contrast in the proposed evolutionary fates.

Ancient WGD events as drivers of key innovations in angiosperms.

Reconstructing the genome of the most recent common ancestor of flowering plants

We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of…

Early genome duplications in conifers and other seed plants

Analysis of transcriptomes from 24 gymnosperms and 3 outgroups indicates that polyploidy has contributed to the evolution of conifers and other gymnos perms, contrary to previous genomic research that reported an absence of polyploidsy in the ancestry of contemporary gymnOSperms.

Plants with double genomes might have had a better chance to survive the Cretaceous–Tertiary extinction event

It is proposed that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the KT extinction event and might have been better able to adapt to the drastically changed environment 65 million years ago.

Two evolutionarily distinct classes of paleopolyploidy.

A new class of ancient WGD is proposed, with Musa (alpha), poplar, and soybean as members, where genes are both deleted and expressed to an equal extent (unbiased fractionation and genome equivalence).

A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

  • D. MacqueenI. Johnston
  • Biology, Environmental Science
    Proceedings of the Royal Society B: Biological Sciences
  • 2014
An extensive set of gene paralogues retained from the salmonid WGD are characterized, showing that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

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.

Allopolyploidy, diversification, and the Miocene grassland expansion

It is found that genome duplication has occurred at a remarkable rate, accounting for at least a third of all speciation events in a group of about 1,200 species, focusing here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids.

Has the connection between polyploidy and diversification actually been tested?

  • E. Kellogg
  • Biology
    Current opinion in plant biology
  • 2016
...