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. 2021 Jul 29;38(8):3332-3344.
doi: 10.1093/molbev/msab106.

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

Danyan Su  1 , Lingxiao Yang  1 , Xuan Shi  1 , Xiaoya Ma  1 , Xiaofan Zhou  2 , S Blair Hedges  3 , Bojian Zhong  1
Affiliations

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

Danyan Su et al. Mol Biol Evol. .

Abstract

The relationships among the four major embryophyte lineages (mosses, liverworts, hornworts, vascular plants) and the timing of the origin of land plants are enigmatic problems in plant evolution. Here, we resolve the monophyly of bryophytes by improving taxon sampling of hornworts and eliminating the effect of synonymous substitutions. We then estimate the divergence time of crown embryophytes based on three fossil calibration strategies, and reveal that maximum calibration constraints have a major effect on estimating the time of origin of land plants. Moreover, comparison of priors and posteriors provides a guide for evaluating the optimal calibration strategy. By considering the reliability of fossil calibrations and the influences of molecular data, we estimate that land plants originated in the Precambrian (980-682 Ma), much older than widely recognized. Our study highlights the important contribution of molecular data when faced with contentious fossil evidence, and that fossil calibrations used in estimating the timescale of plant evolution require critical scrutiny.

Keywords: bryophytes; land plants; maximum bounds; phylogeny; timescale.

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Figures

Fig. 1.
Fig. 1.
The concatenation species tree of land plants and their algal relatives. The cladogram is reconstructed using an amino acid supermatrix of 1,440 genes by IQ-TREE. Nodal support values are estimated by SH-aLRT test (SH) and ultrafast bootstrap (UFBS) in IQ-TREE, and Bayesian posterior probabilities (BPP) in ExaBayes. The first three are SH, UFBS, and BPP values based on codon-degenerate nucleotide data, and the last three are SH, UFBS, and BPP values based on amino acid data. The nodes without values indicate full support.
Fig. 2.
Fig. 2.
The coalescent species tree of land plants and their algal relatives. The cladogram is reconstructed using 1,440 genes by ASTRAL. Nodal support values are estimated by local posterior probability and multilocus bootstrapping (gene+site resampling) (PP/MLBS), and the nodes without values indicate full support.
Fig. 3.
Fig. 3.
Comparison of results from three different strategies. (a) Comparison of divergence time estimates from three fossil strategies. Node ages are plotted at the posterior means, with horizontal bars representing 95% credibility intervals. (b) Comparison of the age distributions on the crown node of land plants for the specified priors (black line), effective priors (purple), and posteriors (orange red).
Fig. 4.
Fig. 4.
Timetree of Streptophyta inferred from Strategy 2. Node ages are plotted at the posterior means and horizontal bars represent 95% credibility intervals. A total of 22 fossil calibration nodes are marked by red dots.
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