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

Abstract

PREMISE: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. METHODS:We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements. RESULTS:Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. CONCLUSIONS:A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure. , et al. 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. APPENDIX S6. Circular plastome map of Buxbaumia aphylla. APPENDIX S7. Circular plastome map of Diphyscium foliosum. APPENDIX S8. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the unpartitioned plastid nucleotide analysis, with likelihood bootstrap support values indicated above branches. APPENDIX S9. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the gene-by-codon partitioned plastid nucleotide analysis, with likelihood bootstrap support values indicated above branches.APPENDIX S10. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the unpartitioned plastid amino-acid analysis, with likelihood bootstrap support values indicated above branches. APPENDIX S11. Cladogram of land-plant relationships relative to the algal outgroup, inferred from the gene-partitioned plastid amino-acid analysis, with likeli...

A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns

“…We used AliView and Mesquite v. 3.04 (Maddison and Maddison, 2015) to perform alignment adjustments on separate plastid and mitochondrial matrices, respectively, using criteria laid out in Graham et al (2000), Kelchner (2000), and Simmons and Ochoterena (2000). We staggered regions that were difficult to align globally, resulting in offset blocks of locally aligned sequences, which should minimize errors due to misalignment while retaining potentially informative variation (e.g., Steane et al, 1999; Graham et al, 2006; Bell et al, 2020). We verified open reading frames for all plastid protein‐coding genes.…”

From the Machete to the Microscope: Dennis Stevenson, Plant Morphologist

“…His early phylogenetic papers focused on morphological cladistics; rooted in empiricism and addressing large-scale analyses of several major clades, including monocots and seed plants (Loconte and Stevenson 1990;Nixon et al 1994;Stevenson and Loconte 1995). These groups continue to form the core of his more recent phylogenetic publications, which include molecular data ranging from few-gene phylogenies to phylogenomics and transcriptomics (e.g., Davis et al 2004;Givnish et al 2018;Meerow et al 2019;Bell et al 2020).…”

Cell Division Patterns in the Peristomial Layers of the Moss Genus Costesia: Two Hypotheses and a Third Solution

“…However, the expanded analyses of Liu et al (2019) found Tetraphidaceae in a more basal position than Polytrichaceae, albeit with low support. Bell et al (2020) showed that the Tetraphidaceae is sister to the Polytrichaceae plus all other peristomate mosses in the analysis of plastid data, whereas mitochondrial data places these two families in a clade sister to all other peristomate mosses. In summary, the interrelationships of nematodontous mosses and especially the transition to arthrodontous mosses remains insufficiently understood, being inconsistent in studies of different authors.…”