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. 2020 Apr 28:8:e8995.
doi: 10.7717/peerj.8995. eCollection 2020.

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

Filipe Sousa  1 , Peter Civáň  1   2 , João Brazão  1 , Peter G Foster  3 , Cymon J Cox  1
Affiliations

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

Filipe Sousa et al. PeerJ. .

Abstract

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.

Keywords: Bryophytes; Compositional heterogeneity; Land plants; Phylogenomics; Substitutional saturation.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. A schematic representation of the topologies obtained from tree-homogeneous and tree-heterogeneous analyses of nucleotide, codon-degenerate nucleotide, and amino acid translation data.
Analyses of nucleotide data place mosses as the earliest-branching lineage of the embryophytes (A, B). Analyses of codon-degenerate and amino acid data under tree-homogeneous models place liverworts as the sister-group to the remaining embryophytes (C, E), whereas analyses under tree-heterogeneous models show support for the clade Setaphyta (D, F).
Figure 2
Figure 2. Majority-rule consensus tree inferred from the 36 gene, 26 taxon concatenated amino acid data.
Bayesian MCMC with a tree-heterogeneous composition model NDCH2, marginal likelihood -L_h = 142829.112. Additional analysis statistics can be found in the legend of Fig. S7. All branches fully supported (PP = 1.0). Taxa indicated as follows: outgroups, grey; hornworts, olive green; liverworts, cyan blue; mosses, orange; vascular plants, violet.
See this image and copyright information in PMC

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Grants and funding

This study received Portuguese national funds from FCT - Foundation for Science and Technology through project UIDB/04326/2020, and from the operational programmes CRESC Algarve 2020 and COMPETE 2020 through projects EMBRC.PT ALG-01-0145-FEDER-022121 and BIODATA.PT ALG-01-0145-FEDER-022231. This work was also supported through FCT project grant PTDC/BIA-EVF/1499/2014 to Cymon J. Cox. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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