Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

/pdf/phylotranscriptomic-analysis-of-the-origin-and-early-4cs38v80rr.pdf

Phylotranscriptomic analysis of the origin and early diversification of land plants

http://www.noahwhiteman.org/uploads/7/1/3/1/7131048/trplsc952.pdf

Evolution of jasmonate and salicylate signal crosstalk.

Although macroscopic plants, animals, and fungi are the most familiar eukaryotes, the bulk of eukaryotic diversity is microbial. Elucidating the timing of diversification among the more than 70 lineages is key to understanding the evolution of eukaryotes. Here, we use taxon-rich multigene data combined with diverse fossils and a relaxed molecular clock framework to estimate the timing of the last common ancestor of extant eukaryotes and the divergence of major clades. Overall, these analyses suggest that the last common ancestor lived between 1866 and 1679 Ma, consistent with the earliest microfossils interpreted with confidence as eukaryotic. During this interval, the Earth's surface differed markedly from today; for example, the oceans were incompletely ventilated, with ferruginous and, after about 1800 Ma, sulfidic water masses commonly lying beneath moderately oxygenated surface waters. Our time estimates also indicate that the major clades of eukaryotes diverged before 1000 Ma, with most or all probably diverging before 1200 Ma. Fossils, however, suggest that diversity within major extant clades expanded later, beginning about 800 Ma, when the oceans began their transition to a more modern chemical state. In combination, paleontological and molecular approaches indicate that long stems preceded diversification in the major eukaryotic lineages.

/pdf/estimating-the-timing-of-early-eukaryotic-diversification-10j7axrrzp.pdf

Estimating the timing of early eukaryotic diversification with multigene molecular clocks

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.

/pdf/the-timescale-of-early-land-plant-evolution-2e9rvqrjsv.pdf

The timescale of early land plant evolution

http://earthdynamics.org/papers-ED/in-press/2013-Torsvik-Cocks-GondwanaResearch-AM.pdf

Gondwana from top to base in space and time

Summary
•The advent of embryophytes (land plants) is among the most important evolutionary breakthroughs in Earth history. It irreversibly changed climates and biogeochemical processes on a global scale; it allowed all eukaryotic terrestrial life to evolve and to invade nearly all continental environments. Before this work, the earliest unequivocal embryophyte traces were late Darriwilian (late Middle Ordovician; c. 463–461 million yr ago (Ma)) cryptospores from Saudi Arabia and from the Czech Republic (western Gondwana).
•Here, we processed Dapingian (early Middle Ordovician, c. 473–471 Ma) palynological samples from Argentina (eastern Gondwana).
•We discovered a diverse cryptospore assemblage, including naked and envelope-enclosed monads and tetrads, representing five genera.
•Our discovery reinforces the earlier suggestion that embryophytes first evolved in Gondwana. It indicates that the terrestrialization of plants might have begun in the eastern part of Gondwana. The diversity of the Dapingian assemblage implies an earlier, Early Ordovician or even Cambrian, origin of embryophytes. Dapingian to Aeronian (Early Silurian) cryptospore assemblages are similar, suggesting that the rate of embryophyte evolution was extremely slow during the first c. 35–45 million yr of their diversification. The Argentinean cryptospores predate other cryptospore occurrences by c. 8–12 million yr, and are currently the earliest evidence of plants on land.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2010.03433.x

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytol

Palynomorph assemblages have been recovered from deposits believed to straddle the Ordovician/Silurian boundary, from the upper member of the Salar del Rincon Formation, in the Puna region of north-west Argentina. The palynomorph assemblages are dominated by terrestrial cryptospores, but also contain marine elements (acritarchs, prasinophycean algae and chitinozoans). The cryptospore assemblages are similar in composition to those described from coeval deposits worldwide, suggesting that the producers were cosmopolitan and tolerated a wide range of climatic conditions. They are correlated with the Imperfectotriletes spp. Interval Biozone (sub-biozone α) of the Imperfectotriletes spp.-Laevolancis divellomedia Assemblage Biozone, indicating a Hirnantian (latest Ordovician) age. Acritarchs include late Ordovician species such as Eupoikilosusa striata and Villosacapsula cf. setosapellicula, that coexist with the Llandovery species Dactylofusa estillis. Based on lithological and palynological evidence, an early Llandovery, or a late Hirnantian (post-glacial) age is proposed for the basal part of the upper member of the Salar del Rincon Formation.

Cryptospore Assemblages from the Ordovician/silurian Boundary in the Puna Region, North‐west Argentina

Veryhachium Deunff 1954, originally described from the Ordovician of western France, in one of the most frequently recorded acritarch genera. Over 250 species and subspecies, from the Cambrian to the Neogene, have been attributed to the genus. This genus has a simple morphology; it displays a triangular, rectangular, or polygonal central vesicle, with a few, simple processes drawn out from the angles of the vesicle in a single plane, ad sometimes with supplementary or auxillary processes arising from the vesicle body. Veryhachium has been emended and reised numerous times. The number of valid species is excessive: most are probably synonyms. To facilitate effective classification, only a few morphological categories should be retained. For the Lower Paleozoic, the use of two informal groups is proposed. These are the Veryhachium trispinosum group for triangular specimens, and the Veryhachium lairdii group for rectangular forms. Although generally abundant and widespread throughout the Phanerozoic, Veryhachium is of limited biostratigraphic, paleoecologic, or paleogeographic value. However, its First Appearance Datum (FAD) is of great importance for Ordovician stratigraphy; the first Veryhachium morphotypes appear in the Tremadocian Stage, making the genus and important biostratigraphic marker.

Claudia V. Rubinstein

Papers

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). New Phytol

Cryptospore Assemblages from the Ordovician/silurian Boundary in the Puna Region, North‐west Argentina

The acritarch genus veryhachium deunff 1954: taxonomic evaluation and first appearance

Lochkovian (earliest Devonian) miospores from the Solimões Basin, northwestern Brazil