Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies

  title={Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies},
  author={Cymon J. Cox},
  journal={Critical Reviews in Plant Sciences},
  pages={113 - 127}
  • C. Cox
  • Published 4 May 2018
  • Biology
  • Critical Reviews in Plant Sciences
Abstract Land plants evolved from freshwater charophyte algal ancestors during a single transition to the terrestrial environment. The six major lineages of land plants are divided into two groups: the bryophytes (liverworts, mosses, and hornworts) and the tracheophytes (lycophytes, ferns, and seed plants); while the tracheophytes are thought to be monophyletic, the bryophytes have typically been considered as the direct ancestors of tracheophytes and therefore an artificial, nonmonophyletic… 

The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models

Analyses of non-synonymous site nucleotide data and amino acid translation data result in congruent phylogenetic trees showing the monophyly of bryophytes, with the Zygnematophyceae as the charophyte group most closely related to land plants.

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.).

A large published dataset of nuclear data was reanalysed and modelled these processes using degenerate-codon recoding and tree-heterogeneous composition substitution models and resolved bryophytes as a monophyletic group and showed that the nonnonmonophyly of the clade that is supported by the analysis of nuclear nucleotide data is due solely to fast-evolving synonymous substitutions.

The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models

Recon reconstructing the mitochondrial land plant phylogeny from a newly compiled data set demonstrates partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provides further incentive for revision of how plants arose on land.

Phylogenomic Evidence for the Monophyly of Bryophytes and the Reductive Evolution of Stomata

Chloroplast phylogenomics of liverworts: a reappraisal of the backbone phylogeny of liverworts with emphasis on Ptilidiales

This study provides empirical evidence to support the significance of plastid genome sequencing to reconstruct the phylogeny of this important plant lineage, and suggests that the GC content has played a critical role in the evolutionary dynamics ofplastid genomes in land plants.

Large-Scale Phylogenomic Analyses Reveal the Monophyly of Bryophytes and Neoproterozoic Origin of Land Plants

The monophyly of bryophytes is resolved by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions, and it is estimated that land plants originated in the Precambrian (980–682 Ma), much older than widely recognized.

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.

A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornwort, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups.

Morphology supports ­the setaphyte hypothesis: mosses plus liverworts form a natural group

It is pointed out that although bryophytes may or may not be monophyletic, mosses plus liverworts form a natural group, and this inference is neither new nor surprising as it has been the fundamental conclusion of morphological analyses for over 25 years.



Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants.

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate

Evidence for the most basal split in land plants dividing bryophyte and tracheophyte lineages

Analysis of concatenated datasets of nucleotide and amino-acid sequences of 57 protein-coding genes common to 17 chloroplast genomes of land plants and a charophyte alga Chaetosphaeridium globosum recovers an alternative, strongly supported topology wherein both bryophytes and tracheophytes are monophyletic.

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

The phylogeny of land plants: A cladistic analysis based on male gametogenesis

Longer treelengths are required to produce tree topologies in which either lycophytes are monophyletic or to reconstruct the paraphyletic bryophyte phylogeny of recent authors, and provides new insight into land plant evolution.

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

A well-supported, 160-nuclear-gene phylogenomic analysis supporting the Zygnematales as the closest living relative to land plants and providing a solid phylogenetic tree for future green-lineage research, whether it be related to plants or green algae.

The deepest divergences in land plants inferred from phylogenomic evidence

It is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.

Bryophyte phylogeny: Advancing the molecular and morphological frontiers

This review of bryophyte evolution includes a re-valuation of the evolution of sperm cells, sporogenesis, stomata, symbioses, conducting cells and chloroplast ultrastructure in hornworts and explores the prospects for future discoveries and advances.

Origin of land plants: Do conjugating green algae hold the key?

A large data set of nuclear-encoded genes from 40 green plant taxa including 21 embryophytes and six streptophyte algae is used to investigate the phylogenetic relationships of streptophical algal lineages, and phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zyghmatales and the Coleochaetales are the sister group to embryophyts.


It is concluded that cladistic analysis of molecular data can provide an independent data set for the study of bryophyte phylogeny, but the differences between the molecular and morphological results are a topic for further investigation.

Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta.

This study supports the placement of Mesostigma in the Streptophyta (as an early diverging lineage) and provides evidence that systematic biases have played a role in generating some of the previous conflicting results.