Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny

As the oldest extant lineages of land plants, bryophytes provide a living laboratory in which to evaluate morphological adaptations associated with early land existence. In this paper we examine reproductive and structural innovations in the gametophyte and sporophyte generations of hornworts, liverworts, mosses and basal pteridophytes. Reproductive features relating to spermatogenesis and the architecture of motile male gametes are overviewed and evaluated from an evolutionary perspective. Phylogenetic analyses of a data set derived from spermatogenesis and one derived from comprehensive morphogenetic data are compared with a molecular analysis of nuclear and mitochondrial small subunit rDNA sequences. Although relatively small because of a reliance on water for sexual reproduction, gametophytes of bryophytes are the most elaborate of those produced by any land plant. Phenotypic variability in gametophytic habit ranges from leafy to thalloid forms with the greatest diversity exhibited by hepatics. Appendages, including leaves, slime papillae and hairs, predominate in liverworts and mosses, while hornwort gametophytes are strictly thalloid with no organized external structures. Internalization of reproductive and vegetative structures within mucilage–filled spaces is an adaptive strategy exhibited by hornworts. The formative stages of gametangial development are similar in the three bryophyte groups, with the exception that in mosses apical growth is intercalated into early organogenesis, a feature echoed in moss sporophyte ontogeny. A monosporangiate, unbranched sporophyte typifies bryophytes, but developmental and structural innovations suggest the three bryophyte groups diverged prior to elaboration of this generation. Sporophyte morphogenesis in hornworts involves non–synchronized sporogenesis and the continued elongation of the single sporangium, features unique among archegoniates. In hepatics, elongation of the sporophyte seta and archegoniophore is rapid and requires instantaneous wall expandability and hydrostatic support. Unicellular, spiralled elaters and capsule dehiscence through the formation of four regular valves are autapomorphies of liverworts. Sporophytic sophistications in the moss clade include conducting tissue, stomata, an assimilative layer and an elaborate peristome for extended spore dispersal. Characters such as stomata and conducting cells that are shared among sporophytes of mosses, hornworts and pteridophytes are interpreted as parallelisms and not homologies. Our phylogenetic analysis of three different data sets is the most comprehensive to date and points to a single phylogenetic solution for the evolution of basal embryophytes. Hornworts are supported as the earliest divergent embryophyte clade with a moss/liverwort clade sister to tracheophytes. Among pteridophytes, lycophytes are monophyletic and an assemblage containing ferns, Equisetum and psilophytes is sister to seed plants. Congruence between morphological and molecular hypotheses indicates that these data sets are tracking the same phylogenetic signal and reinforces our phylogenetic conclusions. It appears that total evidence approaches are valuable in resolving ancient radiations such as those characterizing the evolution of early embryophytes. More information on land plant phylogeny can be found at: http://www.science.siu.edu/landplants/index.html.

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Laurussian land-plant diversity during the Silurian and Devonian: mass extinction, sampling bias, or both?

Paleobiology ◽

10.1017/s0094837300013087 ◽

1995 ◽

Vol 21 (1) ◽

pp. 74-91 ◽

Cited By ~ 53

Author(s):

Anne Raymond ◽

Cheryl Metz

Keyword(s):

Plant Diversity ◽

Mass Extinction ◽

Sampling Bias ◽

Land Plant ◽

Land Plants ◽

Data Sets ◽

Data Set ◽

Extinction Event ◽

Genus Richness ◽

Total Diversity

In phytogeographic data sets, the number of assemblages or floras from each interval may provide a test of the influence of sampling intensity on land-plant diversity. Using a data set of Silurian and Devonian compression-impression plant genera from Laurussia and the Acadian terrain, regression of five measures of land-plant diversity (total diversity, mean genus richness of floras, median assemblage diversity, most diverse assemblage, and standing diversity at interval boundaries) against the number assemblages or floras from thirteen intervals suggests that sampling bias influences all of the diversity measures to some extent, including within-habitat measures. The standing diversity of land plants at interval boundaries, the measure least influenced by sampling (r = 0.65, p = 0.05), increased steadily from the Middle Silurian to the late Givetian/early–middle Frasnian boundary, fell sharply in the early–middle Frasnian and remained low throughout the late Frasnian–middle Famennian. Standing diversity rose dramatically in the late Famennian and Strunian (latest Devonian): the Frasnian–Famennian extinction event may have affected land plants. The standing diversity of Silurian and Devonian microspore genera at interval boundaries mirrors that of compression-impression genera: neither record supports a land-plant diversity equilibrium during the Devonian.

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A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data

Systematic Biology ◽

10.1093/sysbio/syaa069 ◽

2020 ◽

Cited By ~ 1

Author(s):

Nicolás Mongiardino Koch ◽

Jeffrey R Thompson

Keyword(s):

Large Scale ◽

Sea Urchins ◽

Phylogenetic Signal ◽

Total Evidence ◽

Morphological Data ◽

Data Sets ◽

Crown Group ◽

Data Set ◽

Paleontological Data ◽

Time Calibration

Abstract Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.]

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

PeerJ ◽

10.7717/peerj.8995 ◽

2020 ◽

Vol 8 ◽

pp. e8995 ◽

Cited By ~ 2

Author(s):

Filipe Sousa ◽

Peter Civáň ◽

João Brazão ◽

Peter G. Foster ◽

Cymon J. Cox

Keyword(s):

Chloroplast Genome ◽

Molecular Phylogenetics ◽

Land Plant ◽

Land Plants ◽

Data Set ◽

Genome Data ◽

Plant Phylogeny ◽

Plant Group ◽

Strong Indicator ◽

Land Plant Phylogeny

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.

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Age of the Cedarberg Formation, South Africa and early land plant evolution

Geological Magazine ◽

10.1017/s0016756800033537 ◽

1986 ◽

Vol 123 (4) ◽

pp. 445-454 ◽

Cited By ~ 26

Author(s):

J. Gray ◽

J. N. Theron ◽

A. J. Boucot

Keyword(s):

South Africa ◽

Land Plant ◽

Plant Evolution ◽

Marine Phytoplankton ◽

Land Plants ◽

Table Mountain ◽

Plant Remains ◽

First Occurrence ◽

Land Plant Evolution ◽

Early Land

AbstractThe first occurrence of Early Paleozoic land plants is reported from South Africa. The plant remains are small, compact tetrahedral spore tetrads. They occur abundantly in the Soom Shale Member of the Cedarberg Formation, Table Mountain Group. Marine? phytoplankton (sphaeromorphs or leiospheres) occur with the spore tetrads in all samples. Rare chitinozoans are found in half the samples. Together with similar spore tetrads from the Paraná Basin (Gray et al. 1985) these are the first well-documented records of Ashgill and/or earlier Llandovery land plants from the Malvinokaffric Realm, and from the African continent south of Libya. These spore tetrads have botanical, evolutionary, and biogeographic significance. Their size in comparison with spore tetrads from stratigraphic sections throughout eastern North America, suggests that an earliest Llandovery age is more probable for the Soom Shale Member, although a latest Ordovician age cannot be discounted. The age of the brachiopods in the overlying Disa Siltstone Member has been in contention for over a decade. Both Ashgillian and Early Llandovery ages have been proposed. The age of the underlying Soom Shale Member based on plant spores and trilobites (earliest Llandovery or latest Ashgillian) suggests that the Disa Siltstone Member is also likely to be of Early Llandovery age, although the distance between the Soom Shale Member spore-bearing locality and rocks to the south yielding abundant invertebrate body fossils at one locality is great enough to permit diachroneity.

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The timescale of early land plant evolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1719588115 ◽

2018 ◽

Vol 115 (10) ◽

pp. E2274-E2283 ◽

Cited By ~ 244

Author(s):

Jennifer L. Morris ◽

Mark N. Puttick ◽

James W. Clark ◽

Dianne Edwards ◽

Paul Kenrick ◽

...

Keyword(s):

Molecular Clock ◽

Fossil Record ◽

Land Plant ◽

Plant Evolution ◽

Land Plants ◽

Early Land Plant ◽

Land Plant Evolution ◽

The Impact ◽

Earth’S System ◽

Early Land

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.

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Telomerase RNAs in land plants

Nucleic Acids Research ◽

10.1093/nar/gkz695 ◽

2019 ◽

Vol 47 (18) ◽

pp. 9842-9856 ◽

Cited By ~ 10

Author(s):

Petr Fajkus ◽

Vratislav Peška ◽

Michal Závodník ◽

Miloslava Fojtová ◽

Jana Fulnečková ◽

...

Keyword(s):

Repeat Unit ◽

Land Plant ◽

Land Plants ◽

Telomerase Rna ◽

Telomere Repeat ◽

Plant Phylogeny ◽

Representative Species ◽

Evolutionary Changes ◽

Related Plant ◽

Telomere Biology

Abstract To elucidate the molecular nature of evolutionary changes of telomeres in the plant order Asparagales, we aimed to characterize telomerase RNA subunits (TRs) in these plants. The unusually long telomere repeat unit in Allium plants (12 nt) allowed us to identify TRs in transcriptomic data of representative species of the Allium genus. Orthologous TRs were then identified in Asparagales plants harbouring telomere DNA composed of TTAGGG (human type) or TTTAGGG (Arabidopsis-type) repeats. Further, we identified TRs across the land plant phylogeny, including common model plants, crop plants, and plants with unusual telomeres. Several lines of functional testing demonstrate the templating telomerase function of the identified TRs and disprove a functionality of the only previously reported plant telomerase RNA in Arabidopsis thaliana. Importantly, our results change the existing paradigm in plant telomere biology which has been based on the existence of a relatively conserved telomerase reverse transcriptase subunit (TERT) associating with highly divergent TRs even between closely related plant taxa. The finding of a monophyletic origin of genuine TRs across land plants opens the possibility to identify TRs directly in transcriptomic or genomic data and/or predict telomere sequences synthesized according to the respective TR template region.

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The microfossil record of early land plants

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2000.0612 ◽

2000 ◽

Vol 355 (1398) ◽

pp. 717-732 ◽

Cited By ~ 136

Author(s):

Charles H. Wellman ◽

Jane Gray

Keyword(s):

Fossil Record ◽

Vascular Plants ◽

Major Change ◽

Land Plant ◽

Land Plants ◽

Early Land Plant ◽

Early Late ◽

Early Land ◽

Lines Of Evidence ◽

Plant Microfossil

Dispersed microfossils (spores and phytodebris) provide the earliest evidence for land plants. They are first reported from the Llanvirn (Mid–Ordovician). More or less identical assemblages occur from the Llanvirn (Mid–Ordovician) to the late Llandovery (Early Silurian), suggesting a period of relative stasis some 40 Myr in duration. Various lines of evidence suggest that these early dispersed microfossils derive from parent plants that were bryophyte–like if not in fact bryophytes. In the late Llandovery (late Early Silurian) there was a major change in the nature of dispersed spore assemblages as the separated products of dyads (hilate monads) and tetrads (trilete spores) became relatively abundant. The inception of trilete spores probably represents the appearance of vascular plants or their immediate progenitors. A little later in time, in the Wenlock (early Late Silurian), the earliest unequivocal land plant megafossils occur. They are represented by rhyniophytoids. It is only from the Late Silurian onwards that the microfossil / megafossil record can be integrated and utilized in interpretation of the flora. Dispersed microfossils are preserved in vast numbers, in a variety of environments, and have a reasonable spatial and temporal fossil record. The fossil record of plant megafossils by comparison is poor and biased, with only a dozen or so known pre–Devonian assemblages. In this paper, the early land plant microfossil record, and its interpretation, are reviewed. New discoveries, novel techniques and fresh lines of inquiry are outlined and discussed.

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Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

BMC Ecology and Evolution ◽

10.1186/s12862-021-01944-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dario Karmeinski ◽

Karen Meusemann ◽

Jessica A. Goodheart ◽

Michael Schroedl ◽

Alexander Martynov ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary History ◽

Phylogenetic Signal ◽

Set Covering ◽

Phylogenetic Position ◽

Data Sets ◽

Transcriptome Data ◽

Data Set ◽

Sea Slugs ◽

History Of

Abstract Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

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Morphometric analysis of Rhynia and Asteroxylon: testing functional aspects of early land plant evolution

Paleobiology ◽

10.1666/0094-8373(2000)026<0405:maoraa>2.0.co;2 ◽

2000 ◽

Vol 26 (3) ◽

pp. 405-418 ◽

Cited By ~ 18

Author(s):

A. Roth-Nebelsick ◽

G. Grimm ◽

V. Mosbrugger ◽

H. Hass ◽

H. Kerp

Keyword(s):

Water Transport ◽

Land Plant ◽

Plant Evolution ◽

Cross Sectional Area ◽

Land Plants ◽

Limiting Factor ◽

Vascular Bundles ◽

Sectional Area ◽

Cross Sectional ◽

Early Land

New morphometric data gathered from cross-sections of two Lower Devonian land plants (Rhynia gwynne-vaughanii and Asteroxylon mackiei) are interpreted in terms of the evolution of the function of vascular bundles in early land plants. The following conclusions can be drawn from these new data: (1) The ratio of the cross-sectional area of the xylem (representing the conducting volume supplying the axis with water) to the xylem perimeter (representing the “contact area” between xylem and parenchyma through which water leaves the xylem and enters the parenchyma) is not constant for Rhynia axes, almost constant for Asteroxylon axes, and different between Rhynia and Asteroxylon. Thus, Bowers hypothesis that the ratio of cross-sectional area of the xylem to xylem perimeter is constant during ontogenetic development is true for Asteroxylon. That this ratio is constant during phylogeny, however, is not supported by our data. (2) The ratio between cross-sectional area of xylem to parenchyma is higher in Asteroxylon than in Rhynia. (3) As predicted by previous computer simulations, the ratio of the xylem perimeter to the axis perimeter plays a major role in determining water transport performance of the transpiring axis. This ratio is constant within ontogeny but is different in Asteroxylon and Rhynia. In Asteroxylon axes, this ratio is about twice as large as in Rhynia axes. (4) Contrary to the expectations, the distance between the outermost layer of the xylem and the transpiring surface, which represents the low-conductivity pathway through the parenchyma, appears not to be a limiting factor for the water transport in axes of Rhynia and Asteroxylon. (5) From the analysis of the geometric parameters, it is evident that Rhynia and Asteroxylon with their distinct stelar geometries represent two different constructional types for which no transitional stages are known.

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Computer simulations of early land plant branching morphologies: canalization of patterns during evolution?

Paleobiology ◽

10.1017/s009483730000693x ◽

1982 ◽

Vol 8 (3) ◽

pp. 196-210 ◽

Cited By ~ 26

Author(s):

Karl J. Niklas

Keyword(s):

Computer Simulations ◽

Mechanical Design ◽

Vegetative Reproduction ◽

Land Plant ◽

Land Plants ◽

Fossil Plants ◽

Early Land Plant ◽

Plant Groups ◽

Branching Patterns ◽

Early Land

Using computer simulations and a quantitative method for describing bifurcating structures, the morphology of branching patterns seen in early land plants is analyzed. Four types or models of random branching (regular, geometric, binomial, and poisson) are shown to adequately describe the range of observed branching in most early land plants. Approximately 57% of all randomly generated computer patterns show reiterative branching events (=three successive identical modes of branching). Artificial canalization of reiterative events results in branching patterns structurally analogous with that of ancient fossil plants. Simulated phylogenetic changes among early land plant lineages, based on parsimonious transitions in branching patterns, indicate that most observed trends can be related directly to those seen in randomly generating branching patterns in which “size” is increased. The trimerophyte to progymnosperm trend in changing branching patterns is an exception, since the binomial model describing the progymnosperms has not been simulated by random processes.While the apparent phylogenetic changes among early land plant groups do not require deterministic explanations, the transition from regular to geometric branching and the “canalization” of reiterative branching patterns may represent a grade level response to selective pressures related to mechanical design and vegetative reproduction.

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