Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms

After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylog...

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Published in:	Proceedings of the Royal Society. B, Biological sciences Biological sciences, 2018-06, Vol.285 (1881), p.20181012-20181012
Main Authors:	Ran, Jin-Hua, Shen, Ting-Ting, Wang, Ming-Ming, Wang, Xiao-Quan
Format:	Article
Language:	eng
Subjects:	Angiosperms Coalescence Coalescing Convergence Cycadopsida - classification Cycadopsida - genetics Evolution Evolution, Molecular Ferns Genes, Plant Genome, Plant Gnetales Gymnosperms Homoplasy Magnoliopsida - classification Magnoliopsida - genetics Molecular chains Molecular evolution Phylogenetics Phylogeny Seeds
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Summary:	After decades of molecular phylogenetic studies, the deep phylogeny of gymnosperms has not been resolved, and the phylogenetic placement of Gnetales remains one of the most controversial issues in seed plant evolution. To resolve the deep phylogeny of seed plants and to address the sources of phylogenetic conflict, we conducted a phylotranscriptomic study with a sampling of all 13 families of gymnosperms and main lineages of angiosperms. Multiple datasets containing up to 1 296 042 sites across 1308 loci were analysed, using concatenation and coalescence approaches. Our study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis. Cycads plus is sister to the remaining gymnosperms. We also found that Gnetales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms. This implies that Gnetales and angiosperms might have experienced similar selective pressures in evolutionary histories. Convergent molecular evolution or homoplasy is partially responsible for the phylogenetic conflicts in seed plants. Our study provides a robustly reconstructed backbone phylogeny that is important for future molecular and morphological studies of seed plants, in particular gymnosperms, in the light of evolution.
ISSN:	0962-8452 1471-2954