This work was supported by the Gordon and Betty Moore Foundation through grant no. 4). The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models. Genome Biol. 24, 15861591 (2007). eCollection 2023. Article Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. USA 111, 66726677 (2014). Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. Pires, N. D. & Dolan, L. Morphological evolution in land plants: new designs with old genes. We inferred a new gene tree for NEO using the expanded sampling of lineages now available, which confirmed the donor and recipient lineages originally reported84 (Extended Data Fig. Taking our analyses together with other recent work15,20,22,23,28 suggests that a root between monophyletic tracheophytes and bryophytes is the best-supported hypothesis of land plant phylogeny. Individual maximum likelihood gene trees were inferred for each of the 160 single-copy gene families in IQ-TREE69, using the best-fitting model, selected individually for each gene using the Bayesian information criterion. 1a) and used an approximately unbiased (AU) test (Fig. https://doi.org/10.1186/1471-2148-10-210 (2010). and A.M.H. Epub 2023 Jun 7. 10.1093/molbev/msl091 Solved: Which of the following structures is not found in - Chegg Data access for the 1,000 Plants (1KP) project. Wang, H. C., Minh, B. Q. government site. Brief. & Li, F.-W. Charting the genomic landscape of seed-free plants. Before However, topological uncertainty in the NEOCHROME gene tree allows the possibility that the transfer could have occurred into a more ancient lineage (A). https://doi.org/10.1111/nph.14975 (2018). T.A.W., J.W.C. The inference that the common ancestor of embryophytes lived during the Cambrian is robust to the choice of maximum age constraints (Supplementary Methods). In liverworts the sporangium remains close to the gametophore until it is mature; thus, a conducting system is not formed in the seta. Sci. The summed copy number of each gene family (under each branch) was determined using custom Python code (branchwise_number_of_events.py). Biol. 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. 58). Philippe, H. et al. Extant bryophytes remain highly diverse, and it is possible that bryophytes represent another example of specialization and evolutionary success via gene loss. Epub 2018 Dec 7. Criscuolo, A. & Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. Instead, the best model organism(s) for investigating the nature of early plants will depend on the trait being investigated, alongside a careful appraisal of the phylogenetic diversity, including algal outgroups. SOG1, a plant-specific master regulator of DNA damage responses, originated from nonvascular land plants. Coleman, G. A. et al. The Chloroplast Land Plant Phylogeny: Analyses Employing - PubMed Unrooted maximum likelihood tree inferred from an alignment of 11 species and single copy orthogroups under the LG+C60+G4+F model. Mol. These suggested that, while the number of inferred gene losses on the bryophyte stem varies, it remains an event of major gene loss under all conditions tested. Inferring the deep past from molecular data. These authors contributed equally: Brogan J. Harris, James W. Clark. The site is secure. They carry out the same function as in higher plants. Evol. -, Abascal F., Zardoya R., Telford M. J. Biol. Neither lineage occupies an ancestral position, with lineage-specific gene gain and loss events driving high disparity in both bryophytes and tracheophytes, reinforcing the view that there are no extant embryophytes that uniquely preserve the ancestral state20,21,60. However, rooting phylogenies with an outgroup can influence the ingroup topology due to long-branch attraction (LBA)29,30,31, where distantly related or fast-evolving taxa artifactually branch with the outgroup. The size of the circles in both a and b are proportional to sample size of the lineage they represent. Geyer, C. J. Markov chain Monte Carlo maximum likelihood. Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. 17, 379391 (2016). Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Correspondence to The analysis of ancestral gene content highlighted considerable gene gain along the ancestral embryophyte branch (Fig. B 282, 20141013 (2015). TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Insights from the development of non-seed plants. 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. Phil. The rationale for this analysis is that the evolution of these families may be poorly described by the model, and so they may contribute misleading signals36. Plots of p-values for Bowker's, Stuart's, and Ababneh's matched-pairs tests of model homogeneity, Bayesian MCMC tree-heterogeneous composition analyses, Bayesian MCMC tree-heterogeneous composition analyses of the amino acid data (gcpREV+ 4 +F, A summary of bryophyte relationships obtained from nucleotide, codon-degenerate, and amino acid translation, MeSH The NEOCHROME horizontal gene transfer is predicted to have occurred from hornworts into the ancestor of polypod ferns. HHS Vulnerability Disclosure, Help We used the genome dataset from the ALE rooting analysis with the addition of five algal genomes, to better place the origin of families that predate the origin of embryophytes (Supplementary Fig. Nature https://doi.org/10.1038/s41586-019-1693-2 (2019). PubMed Biol. OMalley, M. A., Wideman, J. G. & Ruiz-Trillo, I. Within bryophytes, the divergence between Setaphyta (mosses+liverworts) and hornworts occurred by 479450Ma (Ordovician), with the radiation of crown mosses by 420364Ma (latest Silurian to Late Devonian) and crown liverworts 440412Ma (early Silurian to Early Devonian). Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. and transmitted securely. Plant Kingdom - Classification and Characteristics - BYJU'S The likelihood of each gene family under each root was calculated; the credible roots were determined using an AU test89,90. Hornworts developed stomata and possess a single chloroplast per cell. Relative time constraints improve molecular dating. Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL. official website and that any information you provide is encrypted Furthermore, an exponential hyperprior with mean 1.0 was used for the birth and death rates, as well as for the mean and variance of the gamma prior of the branch rates. Mol. We reconciled 18,560 gene families under the 12 rooted and dated embryophyte trees (Fig. Nat. Molecular clock methods represent one of the only credible means of obtaining an evolutionary timescale, integrating molecular and palaeontological evidence bearing on the phylogenetic and temporal relationships of living clades. We repeated the analysis with alternative placements for the relative time constraint, with the age of crown hornworts becoming increasingly ancient when the transfer was placed into the ancestor of more inclusive clades, Cyatheales+Polypodiales (258419Ma) or before the divergence of Gleicheniales from the Cyatheales+Polypodiales clade (331445Ma), respectively (these scenarios are illustrated in Extended Data Fig. Third, like mosses, they have stomata (little gas-exchanging pores) on their spore-capsules. https://doi.org/10.1093/sysbio/syt022 (2013). 2023 Jun 1;39(6):btad332. However, recent phylogenetic evidence has suggested that bryophytes are monophyletic, and thus that the first split among land plants gave rise to the lineages that today we recognize as the bryophytes and tracheophytes. Bergsten, J. Plant Biol. The sizes of the circles are proportional to the summed number of events (the scale is indicated by the grey circle). Spores of bryophytes are generally small, 5-20 micrometres on the average, and usually unicellular, although some spores are multicellular and considerably larger. The sequence data were obtained from published transcriptomes18,63 or whole-genome sequences from the NCBI repository64. 714774. Some recent studies of the timing of land plant evolution have argued that fossil calibrations should not exert undue influence over divergence time estimates23,40. Careers. Genome Biol. Gene family clusters for the genomic dataset were inferred using the same methods as described above, but the dataset was expanded to contain the genomes of five algal outgroups to allow inference of gene content evolution prior to the embryophyte root (Supplementary Figs. Lett. Ecol. Sin. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. 5.3: Mosses - Biology LibreTexts Get the most important science stories of the day, free in your inbox. We first infer a rooted phylogeny of land plants using outgroup-free rooting methods and both concatenation and coalescent approaches. To evaluate the nature of the root signal for these three branches, we performed a family-filtering analysis in which families with high DTL rates were sequentially removed and the likelihood re-evaluated. Xuebao 35, 270274 (2019). Evol. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Consequently, inferred HGT events can be used as relative node order constraints between divergent scions27; this is especially useful when fossil calibrations are not uniformly distributed across a tree. One thousand plant transcriptomes and the phylogenomics of green plants. Gene family clusters were inferred by an all-versus-all DIAMOND BLAST86 with an e-value threshold of 105, in combination with Markov clustering with an inflation parameter of 2.0 (ref. Cannell, N. et al. Harris BJ, Clark JW, Schrempf D, Szllsi GJ, Donoghue PCJ, Hetherington AM, Williams TA. The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. They include mosses, liverworts and hornworts. Federhen, S. The NCBI Taxonomy database. Katoh, K. & Toh, H. Recent developments in the MAFFT multiple sequence alignment program. It is attached to the substratum by rhizoids, which are unicellular or multicellular. Microbial symbioses facilitated plant colonization of land by enhancing nutrient uptake leading to improved plant growth and fitness. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. https://doi.org/10.1093/molbev/msab106 (2021). Biol. Mol. ISSN 2397-334X (online). Accurate timetrees do indeed require accurate calibrations. On this basis, we defined our maxima following the principles defined in Parham et al.80, and fossil calibrations were defined as minimum and maximum age constraints, in each case modelled as uniform distributions between minima and maxima, with a 1% probability of either bound being exceeded (Supplementary Methods). National Library of Medicine 1997 Jun;7(3):377-93. doi: 10.1006/mpev.1996.0395. PubMed 3). 3 and 4). 5 Non-vascular Plants and Plants Without Seeds FOIA N. Phytol. 3). Reductive evolution in bryophytes has been demonstrated previously, where the loss of several genes has resulted in the lack of stomata15,48. The Chloroplast Endoplasmic Reticulum: Structure, Function, and Would you like email updates of new search results? Nat. Gao, B., Wang, L., Oliver, M., Chen, M. & Zhang, J. Phylogenomic synteny network analyses reveal ancestral transpositions of auxin response factor genes in plants. Google Scholar. Plant Sci. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. A maximum likelihood tree was inferred from an alignment of 30 species of plants and algae, comprising 185 single-copy orthologues and 71,855 sites, under the LG+C60+G4+F model in IQ-TREE69, and rooted in accordance with our previous phylogenetic analysis. This approach yielded 160 single-copy gene families from 114,016 orthogroups. Philos Trans R Soc Lond B Biol Sci. Definition of the category tree fern bluebells Vascular plants ( tracheophytes) differ from the nonvascular bryophytes in that they possess specialized supporting and water-conducting tissue, called xylem, and food-conducting tissue, called phloem. https://github.com/ak-andromeda/ALE_methods/, https://doi.org/10.6084/m9.figshare.c.5682706.v1, https://doi.org/10.1016/j.pbi.2010.04.013, https://doi.org/10.11646/phytotaxa.261.3.1, https://doi.org/10.1046/j.0028-646X.2001.00334.x, https://doi.org/10.1016/j.cub.2020.03.048, https://doi.org/10.1038/s41586-019-1693-2, https://doi.org/10.1016/j.cub.2018.01.063, https://doi.org/10.1016/j.cub.2012.11.022, https://doi.org/10.1093/bioinformatics/btv351, https://doi.org/10.1186/s13059-019-1832-y, https://doi.org/10.1093/bioinformatics/17.12.1246, https://doi.org/10.1080/10635150290069913. PDF Chapter 22 Bryophytes - UC Davis & Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. 15). Science 372, eabe0511 (2021). We placed the relative node calibration such that hornworts must be more ancient than (i) Polypodiales (ii) Cyatheales + Polypodiales and (iii) Gleicheniales+Cyatheales+Polypodiales. 3b). ER cisternae that are, at times, associated with the plastids of bryophytes and vascular plants are very different from chloroplast ER in algae. This suggests that some duplication and loss, or perhaps within-fern transfer, may have occurred in this family. R. Soc. 13 and 14 and Supplementary Table 13). (2010). N. Phytol. One feature of any molecular clock analysis is that, in the absence of admixture or gene transfer, the divergence of gene lineages must logically occur prior to the divergence of the organismal lineages that contain them76. Biol. Liverworts Homepage | UNB The presence or absence of each gene family was determined from the ALE analysis for each tip and internal node in the phylogeny. While the balance of evidence favours bryophyte monophyly, it is interesting to note that the inference of high levels of gene loss in bryophytes is not contingent on this hypothesis: extensive within-bryophyte gene loss was inferred under all three of the roots within the credible region identified in the ALE analysis (Supplementary Table 11). P.C.J.D. 375416 (2018). R. Soc. The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). The loss of these orthologous gene families strengthens the hypothesis that ancestral embryophytes had a more complex vasculature system than that of extant bryophytes8. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. 3c). The likelihood of the four embryophyte roots was assessed with an approximate unbiased (AU) test. Syst Biol. The fluctuation between these diploid and haploid stages that occurs in plants is called the alternation of generations. A tailored set of random-walk proposals executed in random order per iteration, and the Metropolis-coupled Markov chain Monte Carlo algorithm85 with four parallel chains, resulted in near independence of consecutive samples.

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