Major Plant Clades Research Articles

Compositional shifts associated with major evolutionary transitions in plants.

Heterogeneity in gene trees, morphological characters, and composition has been associated with several major plant clades. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both nucleotide and amino acids across a recent large-scale transcriptomic dataset for plants. We find shifts in composition across both nucleotide and amino acid datasets, with more shifts detected in nucleotides. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes.

How similar are the venation and cuticular characters of Glossopteris, Sagenopteris and Anthrophyopsis?

Venation architectures and cuticular micromorphology of leaf fossils play important roles in higher-level taxonomic segregation, as these characters are broadly fixed within major plant clades. Three common fossil plant taxa are characterized by similar-shaped leaves or leaflets and anastomosing venation to such an extent that examples have commonly been assigned to the wrong taxon in past studies where fragmentary or ill-preserved material is available. We use standardized descriptions of vein cross-connection types and stomatal features to compare and contrast the venation patterns and stomatal architectures of these genera. Our reanalysis of the macro- and micromorphology of Glossopteris, Sagenopteris and Anthrophyopsis leaves reveals important differences that help segregate these taxa even on the basis of incomplete specimens. Anthrophyopsis has distinctive alignments of vein cross-connections in the outer lamina and paracytic stomata consistent with those of Bennettitales. Glossopteris has perigenous and monocyclic—normally stephanocytic to actinocytic—stomata commonly protected in pits or by overarching papillae. Sagenopteris has more consistently evanescent midribs and surficial anomocytic or stephanocytic stomata with weakly modified subsidiary cells. Considering the putatively close relationship of glossopterids (Glossopteris), Caytoniales (Sagenopteris) and Bennettitales (here encompassing Anthrophyopsis) resolved as members of the ‘glossophyte’ clade in some past phylogenetic studies, cuticular features suggest that these groups are not closely related. In addition, anastomosing venation, superficially similar to that of Glossopteris, Sagenopteris and Anthrophyopsis appears to have arisen independently in numerous other plant groups suggesting that this character has ecological or physiological benefits and is strongly prone to homoplasy.

Independent recruitment of FRUITFULL-like transcription factors in the convergent origins of vernalization-responsive grass flowering

Flowering in response to low temperatures (vernalization) has evolved multiple times independently across angiosperms as an adaptation to match reproductive development with the short growing season of temperate habitats. Despite the context of a generally conserved flowering time network, evidence suggests that the genes underlying vernalization responsiveness are distinct across major plant clades. Whether different or similar mechanisms underlie vernalization-induced flowering at narrower (e.g., family-level) phylogenetic scales is not well understood. To test the hypothesis that vernalization responsiveness has evolved convergently in temperate species of the grass family (Poaceae), we carried out flowering time experiments with and without vernalization in several representative species from different subfamilies. We then determined the likelihood that vernalization responsiveness evolved through parallel mechanisms by quantifying the response of Pooideae vernalization pathway FRUITFULL (FUL)-like genes to extended periods of cold. Our results demonstrate that vernalization-induced flowering has evolved multiple times independently in at least five grass subfamilies, and that different combinations of FUL-like genes have been recruited to this pathway on several occasions.

Susana Magallón.

Susana Magallón.

Vacuolar Protein Sorting 26C encodes an evolutionarily conserved large retromer subunit in eukaryotes that is important for root hair growth in Arabidopsis thaliana.

The large retromer complex participates in diverse endosomal trafficking pathways and is essential for plant developmental programs, including cell polarity, programmed cell death and shoot gravitropism in Arabidopsis. Here we demonstrate that an evolutionarily conserved VPS26 protein (VPS26C; At1G48550) functions in a complex with VPS35A and VPS29 necessary for root hair growth in Arabidopsis. Bimolecular fluorescence complementation showed that VPS26C forms a complex with VPS35A in the presence of VPS29, and this is supported by genetic studies showing that vps29 and vps35a mutants exhibit altered root hair growth. Genetic analysis also demonstrated an interaction between a VPS26C trafficking pathway and one involving the SNARE VTI13. Phylogenetic analysis indicates that VPS26C, with the notable exception of grasses, has been maintained in the genomes of most major plant clades since its evolution at the base of eukaryotes. To test the model that VPS26C orthologs in animal and plant species share a conserved function, we generated transgenic lines expressing GFP fused with the VPS26C human ortholog (HsDSCR3) in a vps26c background. These studies illustrate that GFP-HsDSCR3 is able to complement the vps26c root hair phenotype in Arabidopsis, indicating a deep conservation of cellular function for this large retromer subunit across plant and animal kingdoms.

The Cerrado (Brazil) plant cytogenetics database.

Cerrado is a biodiversity hotspot that has lost ca. 50% of its original vegetation cover and hosts ca. 11,000 species belonging to 1,423 genera of phanerogams. For a fraction of those species some cytogenetic characteristics like chromosome numbers and C-value were available in databases, while other valuable information such as karyotype formula and banding patterns are missing. In order to integrate and share all cytogenetic information published for Cerrado species, including frequency of cytogenetic attributes and scientometrics aspects, Cerrado plant species were searched in bibliographic sources, including the 50 richest genera (with more than 45 taxa) and 273 genera with only one species in Cerrado. Determination of frequencies and the database website (http://cyto.shinyapps.io/cerrado) were developed in R. Studies were pooled by employed technique and decade, showing a rise in non-conventional cytogenetics since 2000. However, C-value estimation, heterochromatin staining and molecular cytogenetics are still not common for any family. For the richest and best sampled families, the following modal 2n counts were observed: Oxalidaceae 2n = 12, Lythraceae 2n = 30, Sapindaceae 2n = 24, Solanaceae 2n = 24, Cyperaceae 2n = 10, Poaceae 2n = 20, Asteraceae 2n = 18 and Fabaceae 2n = 26. Chromosome number information is available for only 16.1% of species, while there are genome size data for only 1.25%, being lower than the global percentages. In general, genome sizes were small, ranging from 2C = ca. 1.5 to ca. 3.5 pg. Intra-specific 2n number variation and higher 2n counts were mainly related to polyploidy, which relates to the prevalence of even haploid numbers above the mode of 2n in most major plant clades. Several orphan genera with almost no cytogenetic studies for Cerrado were identified. This effort represents a complete diagnosis for cytogenetic attributes of plants of Cerrado.

The Cerrado (Brazil) plant cytogenetics database

Cerrado is a biodiversity hotspot that has lost ca. 50% of its original vegetation cover and hosts ca. 11,000 species belonging to 1,423 genera of phanerogams. For a fraction of those species some cytogenetic characteristics like chromosome numbers and C-value were available in databases, while other valuable information such as karyotype formula and banding patterns are missing. In order to integrate and share all cytogenetic information published for Cerrado species, including frequency of cytogenetic attributes and scientometrics aspects, Cerrado plant species were searched in bibliographic sources, including the 50 richest genera (with more than 45 taxa) and 273 genera with only one species in Cerrado. Determination of frequencies and the database website (http://cyto.shinyapps.io/cerrado) were developed in R. Studies were pooled by employed technique and decade, showing a rise in non-conventional cytogenetics since 2000. However, C-value estimation, heterochromatin staining and molecular cytogenetics are still not common for any family. For the richest and best sampled families, the following modal 2n counts were observed: Oxalidaceae 2n = 12, Lythraceae 2n = 30, Sapindaceae 2n = 24, Solanaceae 2n = 24, Cyperaceae 2n = 10, Poaceae 2n = 20, Asteraceae 2n = 18 and Fabaceae 2n = 26. Chromosome number information is available for only 16.1% of species, while there are genome size data for only 1.25%, being lower than the global percentages. In general, genome sizes were small, ranging from 2C = ca. 1.5 to ca. 3.5 pg. Intra-specific 2n number variation and higher 2n counts were mainly related to polyploidy, which relates to the prevalence of even haploid numbers above the mode of 2n in most major plant clades. Several orphan genera with almost no cytogenetic studies for Cerrado were identified. This effort represents a complete diagnosis for cytogenetic attributes of plants of Cerrado.

Dynamics of dental evolution in ornithopod dinosaurs.

Ornithopods were key herbivorous dinosaurs in Mesozoic terrestrial ecosystems, with a variety of tooth morphologies. Several clades, especially the ‘duck-billed’ hadrosaurids, became hugely diverse and abundant almost worldwide. Yet their evolutionary dynamics have been disputed, particularly whether they diversified in response to events in plant evolution. Here we focus on their remarkable dietary adaptations, using tooth and jaw characters to examine changes in dental disparity and evolutionary rate. Ornithopods explored different areas of dental morphospace throughout their evolution, showing a long-term expansion. There were four major evolutionary rate increases, the first among basal iguanodontians in the Middle-Late Jurassic, and the three others among the Hadrosauridae, above and below the split of their two major clades, in the middle of the Late Cretaceous. These evolutionary bursts do not correspond to times of plant diversification, including the radiation of the flowering plants, and suggest that dental innovation rather than coevolution with major plant clades was a major driver in ornithopod evolution.

Why should we investigate the morphological disparity of plant clades?

Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses. Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications. Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades. Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and ecological features of plants make them ideally suited to investigating intrinsic and extrinsic constraints on disparity.

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record.

Summary Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination–extinction balance have contributed to shaping the current flora.We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the ‘Big Five’ mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms.Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process.Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous–Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore‐bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance.

The origins of multicellular organisms

Multicellularity has evolved in several eukaryotic lineages leading to plants, fungi, and animals. Theoretically, in each case, this involved (1) cell-to-cell adhesion with an alignment-of-fitness among cells, (2) cell-to-cell communication, cooperation, and specialization with an export-of-fitness to a multicellular organism, and (3) in some cases, a transition from "simple" to "complex" multicellularity. When mapped onto a matrix of morphologies based on developmental and physical rules for plants, these three phases help to identify a "unicellular ⇒ colonial ⇒ filamentous (unbranched ⇒ branched) ⇒ pseudoparenchymatous ⇒ parenchymatous" morphological transformation series that is consistent with trends observed within each of the three major plant clades. In contrast, a more direct "unicellular ⇒ colonial or siphonous ⇒ parenchymatous" series is observed in fungal and animal lineages. In these contexts, we discuss the roles played by the cooptation, expansion, and subsequent diversification of ancestral genomic toolkits and patterning modules during the evolution of multicellularity. We conclude that the extent to which multicellularity is achieved using the same toolkits and modules (and thus the extent to which multicellularity is homologous among different organisms) differs among clades and even among some closely related lineages.

Fingerprinting the Asterid Species Using Subtracted Diversity Array Reveals Novel Species-Specific Sequences

BackgroundAsterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.Methodology/Principal FindingsPooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5%) subtraction efficiency. Twenty-five Asterid species (mostly medicinal) representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants.Conclusions/SignificanceSubtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting) plant species. In addition, this method allowed detection of several new loci that can be explored to solve existing discrepancies in phylogenetics and fingerprinting of plants.

Plant Developmental Biology in the Post-Genomic Era

Plant Developmental Biology in the Post-Genomic Era

Genomic tools development for Aquilegia: construction of a BAC-based physical map

BackgroundThe genus Aquilegia, consisting of approximately 70 taxa, is a member of the basal eudicot lineage, Ranuculales, which is evolutionarily intermediate between monocots and core eudicots, and represents a relatively unstudied clade in the angiosperm phylogenetic tree that bridges the gap between these two major plant groups. Aquilegia species are closely related and their distribution covers highly diverse habitats. These provide rich resources to better understand the genetic basis of adaptation to different pollinators and habitats that in turn leads to rapid speciation. To gain insights into the genome structure and facilitate gene identification, comparative genomics and whole-genome shotgun sequencing assembly, BAC-based genomics resources are of crucial importance.ResultsBAC-based genomic resources, including two BAC libraries, a physical map with anchored markers and BAC end sequences, were established from A. formosa. The physical map was composed of a total of 50,155 BAC clones in 832 contigs and 3939 singletons, covering 21X genome equivalents. These contigs spanned a physical length of 689.8 Mb (~2.3X of the genome) suggesting the complex heterozygosity of the genome. A set of 197 markers was developed from ESTs induced by drought-stress, or involved in anthocyanin biosynthesis or floral development, and was integrated into the physical map. Among these were 87 genetically mapped markers that anchored 54 contigs, spanning 76.4 Mb (25.5%) across the genome. Analysis of a selection of 12,086 BAC end sequences (BESs) from the minimal tiling path (MTP) allowed a preview of the Aquilegia genome organization, including identification of transposable elements, simple sequence repeats and gene content. Common repetitive elements previously reported in both monocots and core eudicots were identified in Aquilegia suggesting the value of this genome in connecting the two major plant clades. Comparison with sequenced plant genomes indicated a higher similarity to grapevine (Vitis vinifera) than to rice and Arabidopsis in the transcriptomes.ConclusionsThe A. formosa BAC-based genomic resources provide valuable tools to study Aquilegia genome. Further integration of other existing genomics resources, such as ESTs, into the physical map should enable better understanding of the molecular mechanisms underlying adaptive radiation and elaboration of floral morphology.

Do food-plant preferences of modern families of phytophagous insects and mites reflect past evolution with plants?

The evolutionary history of phytophagous insects and mites and of their food-plants is traced in the conservative preferences of modern-day insects for plants. Based on UK data in the Phytophagous Insects Data Bank, a correspondence analysis displays 182 insect families and 117 plant families in a bi-variate plot. The overall pattern suggests the expansion of diversity of insects and host plants from Gymnosperms to Dicots. Plots for phytophagous insect orders and major plant clades are described, with families provisionally ranked as evolutionarily basal, intermediate or advanced. There are blurred patterns of evolutionary advancement from basal insect families with more species on conifers and on ferns and Eurosid I trees. Intermediate families are commoner on Malpighiales and Fabales, and advanced insects more frequent on later evolved euasterids II (Asterales and Lamiales), Caryophyllales and Gramineae. Basal Hymenoptera have associations with conifers, basal Lepidoptera to Eurosid I trees, and Diptera are mainly advanced families on commelinids (grasses) and Asteraceae. Blurred traces of similar phylogenetic sequences are described for subfamilies within eight example insect families. Basal families and clades tend to have fewer species than derived advanced clades. Insect communities on plants should be seen in the light of this linked past evolutionary background. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 78, 51–83.

The Scaling of Plant Height: A Comparison Among Major Plant Clades and Anatomical Grades

The scaling plant height h (m) with respect to stem diameter d (m) was determined for a total 610 species (mosses, n = 40; pteridophytes, n = 16; dicotyledonous herbs, n = 117; palms, n = 17; gymnosperms, n = 105; dicotyledonous trees, n = 315); axial length or mass vs. d was determined for the pteridophyte Psilotum nudum ; and the scaling of critical buckling height hcrit of gymnosperm and dicotyledonous trees was calculated based on the record trunk d and average Young's modulus E and density p of 33 wood species. The scaling exponents (based on least squares and reduced major axis regressions; αLS and αRMA, respectively) of these relations were compared to expected values for three scaling models: elastic similarity, α = 0·666; stress similarity, α = 0·500; and geometric similarity, α = 1·00. Least squares regression of the data from all species yielded h = 22 d0·91 (r2 = 0·955, n = 610; αRMA = 0·93). The scaling exponent of this formula complied best with the geometric similarity model (α ≈ 1·00). However, α differed among plant clades and anatomical grades: mosses, αLS = 1·10 (r2 = 0·974; αRMA = 1·12); pteridophytes, αLS = 1·69 (r2 = 0·847; αRMA = 1·83; herbaceous dicotyledons, αLS = 1·26 (r2 = 0·742; αRMA = 1·46); palms, αLS = 1·76 (r2 = 0·940; αRMA = 1·82); gymnosperm trees, αLS = 0·430 (r2 = 0·247; αRMA = 0·87); dicotyledonous trees, αLS = 0·488 (r2 = 0·515; αRMA = 0·69); woody species (gymnosperm and dicotyledonous trees, αLS = 0·538 (r2 = 0·541; αRMA = 0·73); and non-woody species, αLS = 1·29 (r2 = 0·949; αRMA = 1·32). Based on αRMA, the interspecific scaling of woody species complied neither with the stress or elastic similarity model. Regression of hcrit yielded the formula hcrit = 97·7 d0·689 (r2 = 0·969; αRMA = 0·70), which was interpreted to support the assumption that E/p ≈ a constant among gymnosperm and dicotyledonous woods. Intra- and interspecific variations in αRMA caution against using any of the three scaling models to predict h based on d across a broad taxonomic spectrum of species, although, on the average, αRMA < 1·0 and αRMA > 1·0 for woody and non-woody species, respectively.