Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants – Nature.com

Berry, J. A., Beerling, D. J. & Franks, P. J. Stomata: key players in the Earth system, past and present. Curr. Opin. Plant Biol. https://doi.org/10.1016/j.pbi.2010.04.013 (2010).

Pires, N. D. & Dolan, L. Morphological evolution in land plants: new designs with old genes. Phil. Trans. R. Soc. B https://doi.org/10.1098/rstb.2011.0252 (2012).

Wellman, C. H. & Strother, P. K. The terrestrial biota prior to the origin of land plants (embryophytes): a review of the evidence. Palaeontology 58, 601627 (2015).

Article Google Scholar

Christenhusz, M. J. M. & Byng, J. W. The number of known plants species in the world and its annual increase. Phytotaxa https://doi.org/10.11646/phytotaxa.261.3.1 (2016).

de Vries, J. & Archibald, J. M. Plant evolution: landmarks on the path to terrestrial life. N. Phytol. https://doi.org/10.1111/nph.14975 (2018).

Raven, J. A. Selection pressures on stomatal evolution. N. Phytol. https://doi.org/10.1046/j.0028-646X.2001.00334.x (2002).

Harrison, C. J. & Morris, J. L. The origin and early evolution of vascular plant shoots and leaves. Phil. Trans. R. Soc. B https://doi.org/10.1098/rstb.2016.0496 (2018).

Donoghue, P., Harrison, C., Paps Montserrat, J. & Schneider, H. The evolutionary emergence of land plants. Curr. Biol. 31, R1281R1298 (2021).

CAS PubMed Article Google Scholar

Wilhelmsson, P. K. I., Mhlich, C., Ullrich, K. K. & Rensing, S. A. Comprehensive genome-wide classification reveals that many plant-specific transcription factors evolved in streptophyte algae. Genome Biol. Evol. 9, 33843397 (2017).

CAS PubMed PubMed Central Article Google Scholar

Bowles, A. M. C., Bechtold, U. & Paps, J. The origin of land plants is rooted in two bursts of genomic novelty. Curr. Biol. 30, 530536 (2020).

CAS PubMed Article Google Scholar

Floyd, S. K. & Bowman, J. L. The ancestral developmental tool kit of land plants. Int. J. Plant Sci. 168, 135 (2007).

CAS Article Google Scholar

Wang, B. et al. Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants. N. Phytol. 186, 514525 (2010).

Article Google Scholar

Bowman, J. L. et al. Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell 171, 287304.e15 (2017).

CAS PubMed Article Google Scholar

Gao, B., Wang, L., Oliver, M., Chen, M. & Zhang, J. Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants. Plant Methods 16, 70 (2020).

CAS PubMed PubMed Central Article Google Scholar

Harris, B. J., Harrison, C. J., Hetherington, A. M. & Williams, T. A. Phylogenomic evidence for the monophyly of bryophytes and the reductive evolution of stomata. Curr. Biol. https://doi.org/10.1016/j.cub.2020.03.048 (2020).

Radhakrishnan, G. V. et al. An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages. Nat. Plants 6, 280289 (2020).

PubMed Article Google Scholar

Szvnyi, P., Gunadi, A. & Li, F.-W. Charting the genomic landscape of seed-free plants. Nat. Plants 7, 554565 (2021).

PubMed Article Google Scholar

Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature https://doi.org/10.1038/s41586-019-1693-2 (2019).

Cox, C. J., Li, B., Foster, P. G., Embley, T. M. & Civ, P. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Syst. Biol. 63, 272279 (2014).

PubMed PubMed Central Article Google Scholar

Puttick, M. N. et al. The interrelationships of land plants and the nature of the ancestral embryophyte. Curr. Biol. https://doi.org/10.1016/j.cub.2018.01.063 (2018).

Rensing, S. A. Plant evolution: phylogenetic relationships between the earliest land plants. Curr. Biol. 28, R210R213 (2018).

CAS PubMed Article Google Scholar

Sousa, F., Foster, P. G., Donoghue, P. C. J., Schneider, H. & Cox, C. J. Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.). N. Phytol. https://doi.org/10.1111/nph.15587 (2019).

Su, D. et al. Large-scale phylogenomic analyses reveal the monophyly of bryophytes and Neoproterozoic origin of land plants. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msab106 (2021).

Tomescu, A. M. F., Bomfleur, B., Bippus, A. C. & Savoretti, A. Why are bryophytes so rare in the fossil record? A spotlight on taphonomy and fossil preservation. Transform. Paleobot. 375416 (2018).

Feldberg, K. et al. Checklist of fossil liverworts suitable for calibrating phylogenetic reconstructions. Bryophyte Divers. Evol. 43 (1):14-71 (2021).

Flores, J. R., Bippus, A. C., Surez, G. M. & Hyvnen, J. Defying death: incorporating fossils into the phylogeny of the complex thalloid liverworts (Marchantiidae, Marchantiophyta) confirms high order clades but reveals discrepancies in family-level relationships. Cladistics 37, 231247 (2021).

CAS PubMed Article Google Scholar

Szllsi, G. J. et al. Relative time constraints improve molecular dating. Syst. Biol. 71, 797809 (2022).

PubMed Article Google Scholar

Sousa, F., Civ, P., Foster, P. G. & Cox, C. J. The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models. Front. Plant Sci. 11, 1062 (2020).

PubMed PubMed Central Article Google Scholar

Bergsten, J. A review of long-branch attraction. Cladistics 21, 163193 (2005).

PubMed Article Google Scholar

Philippe, H. et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9, 1000602 (2011).

Article CAS Google Scholar

Williams, T. A. et al. Inferring the deep past from molecular data. Genome Biol. Evol. 13, evab067 (2021).

PubMed PubMed Central Article CAS Google Scholar

Bell, D. et al. Organellomic datasets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. Am. J. Bot. 107, 91115 (2020).

CAS PubMed Article Google Scholar

Wickett, N. J. et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.1323926111 (2014).

Szllosi, G. J., Tannier, E., Lartillot, N. & Daubin, V. Lateral gene transfer from the dead. Syst. Biol. 62, 386397 (2013).

PubMed PubMed Central Article Google Scholar

Emms, D. M. & Kelly, S. STRIDE: species tree root inference from gene duplication events. Mol. Biol. Evol. 34, 32673278 (2017).

CAS PubMed PubMed Central Article Google Scholar

Coleman, G. A. et al. A rooted phylogeny resolves early bacterial evolution. Science 372, eabe0511 (2021).

CAS PubMed Article Google Scholar

Li, F. W. et al. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc. Natl Acad. Sci. USA 111, 66726677 (2014).

CAS PubMed PubMed Central Article Google Scholar

Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl Acad. Sci. USA 115, E2274E2283 (2018).

CAS PubMed PubMed Central Google Scholar

Hedges, S. B., Tao, Q., Walker, M. & Kumar, S. Accurate timetrees require accurate calibrations. Proc. Natl Acad. Sci. USA 115, E9510E9511 (2018).

CAS PubMed PubMed Central Google Scholar

Zhang, Z. et al. Origin and evolution of green plants in the light of key evolutionary events. J. Integr. Plant Biol. 64, 516535 (2022).

PubMed Google Scholar

Morris, J. L. et al. Accurate timetrees do indeed require accurate calibrations. Proc. Natl Acad. Sci. USA 115, E9512E9513 (2018).

CAS PubMed PubMed Central Google Scholar

Villarreal, J. C. & Renner, S. S. A review of molecular-clock calibrations and substitution rates in liverworts, mosses, and hornworts, and a timeframe for a taxonomically cleaned-up genus Nothoceros. Mol. Phylogenet. Evol. 78, 2535 (2014).

PubMed Article Google Scholar

Raposo, G. & Stoorvogel, W. Extracellular vesicles: exosomes, microvesicles, and friends. J. Cell Biol. 200, 373383 (2013).

CAS PubMed PubMed Central Article Google Scholar

Chen, J. & Wang, N. Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments. Acta Mech. Sin. Xuebao 35, 270274 (2019).

CAS Article Google Scholar

Popper, Z. A. et al. Evolution and diversity of plant cell walls: from algae to flowering plants. Annu. Rev. Plant Biol. 62, 567590 (2011).

CAS PubMed Article Google Scholar

Bauer, H. et al. The stomatal response to reduced relative humidity requires guard cell-autonomous ABA synthesis. Curr. Biol. https://doi.org/10.1016/j.cub.2012.11.022 (2013).

Cannell, N. et al. Multiple metabolic innovations and losses are associated with major transitions in land plant evolution. Curr. Biol. 30, 17831800.e11 (2020).

CAS PubMed Article Google Scholar

Clark, J. W. et al. The origin and evolution of stomata. Curr. Biol. 32, R539R553 (2022).

CAS PubMed Article Google Scholar

Wellman, C. H., Steemans, P. & Vecoli, M. Palaeophytogeography of OrdovicianSilurian land plants. Geol. Soc. Lond. Mem. 38, 461476 (2013).

Article Google Scholar

Chanderbali, A. S., Berger, B. A., Howarth, D. G., Soltis, D. E. & Soltis, P. S. Evolution of floral diversity: genomics, genes and gamma. Phil. Trans. R. Soc. Lond. B 372, 20150509 (2017).

Article Google Scholar

Clark, J. W. & Donoghue, P. C. J. Whole-genome duplication and plant macroevolution. Trends Plant Sci. 23, 933945 (2018).

CAS PubMed Article Google Scholar

Walden, N. et al. Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nat. Commun. 11, 3795 (2020).

CAS PubMed PubMed Central Article Google Scholar

Stull, G. W. et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nat. Plants 7, 10151025 (2021).

PubMed Article Google Scholar

Albalat, R. & Caestro, C. Evolution by gene loss. Nat. Rev. Genet. 17, 379391 (2016).

CAS PubMed Article Google Scholar

OMalley, M. A., Wideman, J. G. & Ruiz-Trillo, I. Losing complexity: the role of simplification in macroevolution. Trends Ecol. Evol. 31, 608621 (2016).

PubMed Article Google Scholar

Guijarro-Clarke, C., Holland, P. W. H. & Paps, J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat. Ecol. Evol. 4, 519523 (2020).

PubMed Article Google Scholar

Sharma, V. et al. A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat. Commun. 9, 1215 (2018).

PubMed PubMed Central Article CAS Google Scholar

Helsen, J. et al. Gene loss predictably drives evolutionary adaptation. Mol. Biol. Evol. 37, 29893002 (2020).

More:
Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants - Nature.com