Phylogeny and Evolution of Vascular Plants

Abstract

Vascular plants play a major role in global carbon cycling and are of fundamental importance to life on earth. Over the last half‐century, phylogenetic studies of morphological and molecular data have brought tremendous progress in our understanding of origin, phylogeny and evolution of these plants. It is clear that they evolved from a bryophytic ancestor, which likely resembles hornworts in the modern earth flora. Among all living vascular plants, lycophytes represent the first diverging lineage. Ferns and other free‐sporing vascular plants make up a clade called monilophytes, which are sister to seed plants. Extant gymnosperms form a monophyletic group in most molecular studies, but this result may need further investigation as morphological support is lacking. Among living angiosperms, Amborella , Nymphaeales and Austrobaileyales have been unequivocally demonstrated to represent the oldest lineages, a result that will facilitate solving Darwin's abominable mystery – the origin of angiosperms. Key Concepts Origin of vascular plants: Current phylogenetic and fossil evidence tends to support bryophytes as a paraphyletic group and thus vascular plants originated from a bryophytic ancestor. Phylogeny and evolution of life cycle in land plants: The bryophytic origin of vascular plants supports antithetic theory: The multicellular diploid sporophyte generation in land plants was an interpolation of a new structure derived from delay of meiosis in the life cycle, and continuously increased as plants evolved, eventually outweighing the haploid gametophyte generation. Relationships among early vascular plants: The long‐standing issue of how several relictual vascular plant lineages are related to each other have been finally resolved, with lycophytes representing the oldest living member of vascular plants and Equisetum being sister to a group composed of Psilotaceae and eusporangiate and leptosporangiate ferns. Monilophytes and origin of seed plants: Among extant free‐sporing vascular plants, Equisetum , Psilotaceae and ferns together make up a monophyletic group called monilophytes, which is sister to seed plants. The first angiosperms: Among all living angiosperms, Amborella , a shrub from New Caledonia, and Nymphaeales represent the basalmost lineages and they could offer some clues to what the first angiosperms looked like. Phylogenomics and phylogeny: The colossal amount of information that is being unearthed from genomes is enabling a new quantum leap in phylogenetics and evolutionary biology, but the data need to be carefully and rigorously analysed so that the results are not simply trees with high statistical support, and instead can withstand repeated falsification tests.

Phylogenomic Analysis Reconstructed the Order Matoniales from Paleopolyploidy Veil

“…Taxon sampling bias was considered as an important factor affecting the phylogenetic relationship [36]. According to PPG I, gleichenioid ferns include approximately 172 species in 10 genera in the three families Dipteridaceae, Matoniaceae, and Gleicheniaceae [20].…”

“…However, Matoniaceae, belonging to Matoniales [30] and considered as the sister lineage of Dipteridaceae [25,28], was not included in these two studies. Taxon sampling, which is considered as a common pitfall in phylogenetics [31,32], plays an important role in phylogenetic inference accuracy [5,[33][34][35], and thus it is expected that a degree of the sampling within a study can be compromised by systematic errors [36]. Here, in order to increase taxa coverage, we analyzed the transcriptome data of 31 ferns, including 21 newly sequenced species.…”