Evolution of phenotypic disparity in the plant kingdom.

The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.

Leaves and sporangia developed in rare non-Fibonacci spirals in early leafy plants.

Lateral plant organs, including leaves and reproductive structures, are arranged on stems in distinct patterns termed phyllotaxis. Most extant plants exhibit phyllotactic patterns that are mathematically described by the Fibonacci series. However, it remains unclear what lateral organ arrangements were present in early leafy plants. To investigate this, we quantified phyllotaxis in fossils of the Early Devonian lycopod Asteroxylon mackiei. We report diverse phyllotaxis in leaves, including whorls and spirals. Spirals were all n:(n+1) non-Fibonacci types. We also show that leaves and reproductive structures occurred in the same phyllotactic series, indicating developmental similarities between the organs. Our findings shed light on the long-standing debate about leaf origins and demonstrate the antiquity of non-Fibonacci spirals in plants.

The origin and evolution of stomata.

The acquisition of stomata is one of the key innovations that led to the colonisation of the terrestrial environment by the earliest land plants. However, our understanding of the origin, evolution and the ancestral function of stomata is incomplete. Phylogenomic analyses indicate that, firstly, stomata are ancient structures, present in the common ancestor of land plants, prior to the divergence of bryophytes and tracheophytes and, secondly, there has been reductive stomatal evolution, especially in the bryophytes (with complete loss in the liverworts). From a review of the evidence, we conclude that the capacity of stomata to open and close in response to signals such as ABA, CO2 and light (hydroactive movement) is an ancestral state, is present in all lineages and likely predates the divergence of the bryophytes and tracheophytes. We reject the hypothesis that hydroactive movement was acquired with the emergence of the gymnosperms. We also conclude that the role of stomata in the earliest land plants was to optimise carbon gain per unit water loss. There remain many other unanswered questions concerning the evolution and especially the origin of stomata. To address these questions, it will be necessary to: find more fossils representing the earliest land plants, revisit the existing early land plant fossil record in the light of novel phylogenomic hypotheses and carry out more functional studies that include both tracheophytes and bryophytes.

Cost-effectiveness analysis of prosthesis provision for patients with transfemoral amputation in Tanzania.

BACKGROUND: Limb loss leads to significant disability. Prostheses may mitigate this disability but are not readily accessible in low- and middle-income countries (LMICs). Cost-effectiveness data related to prosthesis provision in resource-constrained environments such as Tanzania is greatly limited. OBJECTIVES: This study aimed to compare the cost-effectiveness of a prosthesis intervention compared with that of no prosthesis for persons with transfemoral amputations in an LMIC. STUDY DESIGN: This is a prospective cohort study. METHODS: Thirty-eight patients were prospectively followed up. Clinical improvement with prosthesis provision was measured using EuroQuol-5D, represented as quality-adjusted life years gained. Direct and indirect costs were measured. The primary outcome was incremental cost per quality-adjusted life year, measured at 1 year and projected over a lifetime using a Markov model. Reference case was set as a single prosthesis provided without replacement from a payer perspective. Additional scenarios included the societal perspective and replacement of the prosthesis. Uncertainty was measured with one-way probabilistic sensitivity analysis. RESULTS: From the payer perspective, the incremental cost-effectiveness ratio (ICER) was $242 for those without prosthetic replacement over a lifetime, and the ICER was $390 for those with prosthetic replacement over a lifeime. From the societal perspective, prosthesis provision was both less expensive and more effective. One-way sensitivity analysis demonstrated the ICER remained below the willingness to pay threshold up to prosthesis costs of $763. CONCLUSIONS: These findings suggest prosthesis provision in an LMIC may be cost-effective, but further studies with long-term follow up are needed to validate the results.

The Making of Plant Armor: The Periderm.

The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO2. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research.

Impact of prostheses on quality of life and functional status of transfemoral amputees in Tanzania.

BACKGROUND: The rise of diabetes and traumatic injury has increased limb loss-related morbidity in low- and middle-income countries (LMICs). Despite this, the majority of amputees in LMICs have no access to prosthetic devices, and the magnitude of prosthesis impact on quality of life (QOL ) and function has not been quantified. OBJECTIVES: Quantify the impact of prostheses on QOL and function in Tanzanian transfemoral amputees. METHOD: A prospective cohort study was conducted. Transfemoral amputees at Muhimbili Orthopaedic Institute were assessed twice before and three times after prosthetic fitting using EuroQol-5D-3L (EQ-5D-3L), Prosthetic Limb Users Survey of Mobility (PLUS-M), 2-minute walk test (2MWT) and Physiologic Cost Index (PCI). Data were analysed for change over time. Subgroup analysis was performed for amputation aetiology (vascular or non-vascular) and prosthesis use. RESULTS: Amongst 30 patients, EQ-5D, PLUS-M and 2MWT improved after prosthesis provision (p < 0.001). EuroQol-5D increased from 0.48 to 0.85 at 1 year (p < 0.001). EuroQol-5D and 2MWT were higher in non-vascular subgroup (p < 0.030). At 1-year, 84% of non-vascular and 44% of vascular subgroups reported using their prosthesis (p = 0.068). CONCLUSION: Prosthesis provision to transfemoral amputees in an LMIC improved QOL and function. This benefit was greater for non-vascular amputation aetiologies. Quality of life and function returned to pre-prosthesis levels with discontinued use of prosthesis.

An evidence-based 3D reconstruction of Asteroxylon mackiei, the most complex plant preserved from the Rhynie chert.

The Early Devonian Rhynie chert preserves the earliest terrestrial ecosystem and informs our understanding of early life on land. However, our knowledge of the 3D structure, and development of these plants is still rudimentary. Here we used digital 3D reconstruction techniques to produce the first well-evidenced reconstruction of the structure and development of the rooting system of the lycopsid Asteroxylon mackiei, the most complex plant in the Rhynie chert. The reconstruction reveals the organisation of the three distinct axis types - leafy shoot axes, root-bearing axes, and rooting axes - in the body plan. Combining this reconstruction with developmental data from fossilised meristems, we demonstrate that the A. mackiei rooting axis - a transitional lycophyte organ between the rootless ancestral state and true roots - developed from root-bearing axes by anisotomous dichotomy. Our discovery demonstrates how this unique organ developed and highlights the value of evidence-based reconstructions for understanding the development and evolution of the first complex vascular plants on Earth.

Cost Analyses of Prosthetic Devices: A Systematic Review.

OBJECTIVE: To synthesize extant literature on the cost-effectiveness of prosthetic interventions and explore applicability to low- and middle-income country (LMIC) settings. DATA SOURCES: A systematic literature review using subject headings including "prosthetics," "amputation," and "cost analysis" was performed with PubMed, Embase, and Web of Science search engines, yielding 1194 articles. An additional 22 articles were identified via backward citation searching for 1144 total after duplicate removal. The search was last run in May of 2019. STUDY SELECTION: Studies were included if they conducted an economic analysis of an upper or lower extremity prosthetic device. Studies were excluded if (1) full text was unavailable in English; (2) study was a systematic review or meta-analysis; or (3) study did not have a prosthetic comparison group. Using DistillerSR software, 2 authors independently conducted title and abstract screening. One author conducted full-text screening. The proportion of initially identified studies that met final inclusion criteria was 1% (12 of 1144). DATA EXTRACTION: Data were dually extracted by 2 authors and reviewed by 3 additional authors. DATA SYNTHESIS: All included studies (N=12) examined lower extremity amputations comparing advanced technology. No studies were conducted in LMICs. Comparable data between studies demonstrated (1) the cost-effectiveness of microprocessor- over nonmicroprocessor-controlled knees for transfemoral amputation in high-income settings; (2) equivocal findings regarding osseointegrated vs socket-suspended prostheses; and (3) increased cost for ICEX and modular socket systems over patellar tendon-bearing socket systems with no functional improvement. CONCLUSIONS: There are few prosthetic cost analyses in the literature. Additional analyses are needed to determine the direct and indirect costs associated with prosthetic acquisition, fitting, and maintenance; the costs of amputee rehabilitation; and long-term economic and quality-of-life benefits. Such studies may guide future prosthetic and rehabilitative care, especially in resource-austere settings where prosthetic needs are greatest.

Gene expression data support the hypothesis that Isoetes rootlets are true roots and not modified leaves.

Rhizomorphic lycopsids are the land plant group that includes the first giant trees to grow on Earth and extant species in the genus Isoetes. Two mutually exclusive hypotheses account for the evolution of terminal rooting axes called rootlets among the rhizomorphic lycopsids. One hypothesis states that rootlets are true roots, like roots in other lycopsids. The other states that rootlets are modified leaves. Here we test predictions of each hypothesis by investigating gene expression in the leaves and rootlets of Isoetes echinospora. We assembled the de novo transcriptome of axenically cultured I. echinospora. Gene expression signatures of I. echinospora rootlets and leaves were different. Furthermore, gene expression signatures of I. echinospora rootlets were similar to gene expression signatures of true roots of Selaginella moellendorffii and Arabidopsis thaliana. RSL genes which positively regulate cell differentiation in roots were either exclusively or preferentially expressed in the I. echinospora rootlets, S. moellendorffii roots and A. thaliana roots compared to the leaves of each respective species. Taken together, gene expression data from the de-novo transcriptome of I. echinospora are consistent with the hypothesis that Isoetes rootlets are true roots and not modified leaves.

Multiple origins of dichotomous and lateral branching during root evolution.

Roots of extant vascular plants proliferate through lateral branching (euphyllophytes) or dichotomy (lycophytes)1-4. The origin of these distinct modes of branching was key for plant evolution because they enabled the development of structurally and functionally different root systems that supported a diversity of shoot systems3-6. It has been unclear when lateral branching originated and how many times it evolved4,7,8. Here, we report that many euphyllophytes that were extant during the Devonian and Carboniferous periods developed dichotomous roots. Our data indicate that dichotomous root branching evolved in both lycophytes and euphyllophytes. Lateral roots then evolved at different times in three major lineages of extant euphyllophytes-the lignophytes, ferns and horsetails. The multiple origins of dichotomous and lateral root branching are extreme cases of convergent evolution that occurred during the Devonian and Carboniferous periods when the land-plant flora underwent a radiation in morphological diversity.

Aquatic stem group myriapods close a gap between molecular divergence dates and the terrestrial fossil record.

Identifying marine or freshwater fossils that belong to the stem groups of the major terrestrial arthropod radiations is a longstanding challenge. Molecular dating and fossils of their pancrustacean sister group predict that myriapods originated in the Cambrian, much earlier than their oldest known fossils, but uncertainty about stem group Myriapoda confounds efforts to resolve the timing of the group's terrestrialization. Among a small set of candidates for membership in the stem group of Myriapoda, the Cambrian to Triassic euthycarcinoids have repeatedly been singled out. The only known Devonian euthycarcinoid, Heterocrania rhyniensis from the Rhynie and Windyfield cherts hot spring complex in Scotland, reveals details of head structures that constrain the evolutionary position of euthycarcinoids. The head capsule houses an anterior cuticular tentorium, a feature uniquely shared by myriapods and hexapods. Confocal microscopy recovers myriapod-like characters of the preoral chamber, such as a prominent hypopharynx supported by tentorial bars and superlinguae between the mandibles and hypopharynx, reinforcing an alliance between euthycarcinoids and myriapods recovered in recent phylogenetic analysis. The Cambrian occurrence of the earliest euthycarcinoids supplies the oldest compelling evidence for an aquatic stem group for either Myriapoda or Hexapoda, previously a lacuna in the body fossil record of these otherwise terrestrial lineages until the Silurian and Devonian, respectively. The trace fossil record of euthycarcinoids in the Cambrian and Ordovician reveals amphibious locomotion in tidal environments and fills a gap between molecular estimates for myriapod origins in the Cambrian and a post-Ordovician crown group fossil record.

Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution.

Investigating the evolution of plant biochemistry is challenging because few metabolites are preserved in fossils and because metabolic networks are difficult to experimentally characterize in diverse extant organisms. We report a comparative computational approach based on whole-genome metabolic pathway databases of eight species representative of major plant lineages, combined with homologous relationships among genes of 72 species from streptophyte algae to angiosperms. We use this genomic approach to identify metabolic gains and losses during land plant evolution. We extended our findings with additional analysis of 305 non-angiosperm plant transcriptomes. Our results revealed that genes encoding the complete biosynthetic pathway for brassinosteroid phytohormones and enzymes for brassinosteroid inactivation are present only in spermatophytes. Genes encoding only part of the biosynthesis pathway are present in ferns and lycophytes, indicating a stepwise evolutionary acquisition of this pathway. Nevertheless, brassinosteroids are ubiquitous in land plants, suggesting that brassinosteroid biosynthetic pathways differ between earlier- and later-diverging lineages. Conversely, genes for gibberellin biosynthesis and inactivation using methyltransferases are found in all land plant lineages. This suggests that bioactive gibberellins might be present in bryophytes, although they have yet to be detected experimentally. We also found that cytochrome P450 oxidases involved in cutin and suberin production are absent in genomes of non-angiosperm plants that nevertheless do contain these biopolymers. Overall, we identified significant differences in crucial metabolic processes between angiosperms and earlier-diverging land plants and resolve details of the evolutionary history of several phytohormone and structural polymer biosynthetic pathways in land plants.

Reconstructing trait evolution in plant evo-devo studies.

Our planet is teeming with an astounding diversity of plants. In a mere single group of closely related species, tremendous diversity can be observed in their form and function - the colour of petals in flowering plants, the shape of the fronds in ferns, and the branching pattern of the gametophyte in mosses. Diversity can also be found in subtler traits, such as the resistance to pathogens or the ability to recruit symbiotic microbes from the environment. Plant traits can also be highly conserved - at the cellular and metabolic levels, entire biosynthetic pathways are present in all plant groups, and morphological characteristics such as vascular tissues have been conserved for hundreds of millions of years. The research community that seeks to understand these traits - both the diverse and the conserved - by taking an evolutionary point-of-view on plant biology is growing. Here, we summarize a subset of the different aspects of plant evolutionary biology, provide a guide for structuring comparative biology approaches and discuss the pitfalls that (plant) researchers should avoid when embarking on such studies.

Evolution: Diversification of Angiosperm Rooting Systems in the Early Cretaceous.

A monocot from the Early Cretaceous developed a cluster of anatomically similar roots from the base of a stocky stem. This discovery indicates that angiosperm rooting systems were more diverse than previously thought at this time.

Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase.

Although UVA radiation (315-400 nm) represents 95% of the UV radiation reaching the earth's surface, surprisingly little is known about its effects on plants [1]. We show that in Arabidopsis, short-term exposure to UVA inhibits the opening of stomata, and this requires a reduction in the cytosolic level of cGMP. This process is independent of UVR8, the UVB receptor. A cGMP-activated phosphodiesterase (AtCN-PDE1) was responsible for the UVA-induced decrease in cGMP in Arabidopsis. AtCN-PDE1-like proteins form a clade within the large HD-domain/PDEase-like protein superfamily, but no eukaryotic members of this subfamily have been functionally characterized. These genes have been lost from the genomes of metazoans but are otherwise conserved as single-copy genes across the tree of life. In longer-term experiments, UVA radiation increased growth and decreased water-use efficiency. These experiments revealed that PDE1 is also a negative regulator of growth. As the PDE1 gene is ancient and not represented in animal lineages, it is likely that at least one element of cGMP signaling in plants has evolved differently to the system present in metazoans.

Neofunctionalisation of basic helix-loop-helix proteins occurred when embryophytes colonised the land.

ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes control the development of structures from single cells at the surface of embryophytes (land plants) such as rhizoids and root hairs. RSL proteins constitute a subclass (VIIIc) of the basic helix-loop-helix (bHLH) class VIII transcription factor family. The Charophyceae form the only class of streptophyte algae with tissue-like structures and rhizoids. To determine if the function of RSL genes in the control of cell differentiation in embryophytes was inherited from a streptophyte algal ancestor, we identified the single class VIII bHLH gene from the charophyceaen alga Chara braunii (CbbHLHVIII). CbbHLHVIII is sister to the RSL proteins; they constitute a monophyletic group. Expression of CbbHLHVIII does not compensate for loss of RSL functions in Marchantia polymorpha or Arabidopsis thaliana. In C. braunii CbbHLHVIII is expressed at sites of morphogenesis but not in rhizoids. This finding indicates that C. braunii class VIII protein is functionally different from land plant RSL proteins. This result suggests that the function of RSL proteins in cell differentiation at the plant surface evolved by neofunctionalisation in the land plants lineage after its divergence from its last common ancestor with C. braunii, at or before the colonisation of the land by embryophytes.

Rhynie chert fossils demonstrate the independent origin and gradual evolution of lycophyte roots.

Mapping fossil traits onto the land plant phylogenetic framework indicates that there were at least two independent origins of roots among extant vascular plants - once in lycophytes and independently in euphyllophytes. At least two rooting structural types are found among extinct species preserved in the Rhynie chert. First, species that lacked roots and developed horizontal axes that developed rhizoids. Second, the rooting axes of Asteroxylon mackiei resembled the roots of extant lycopsids but lacked root hairs and root caps. These two rooting structures preceded the evolution of the roots of extant lycophytes comprising axes on which root hairs and root caps developed. These data demonstrate the defining root characters evolved gradually in the lycophyte lineage.

Stepwise and independent origins of roots among land plants.

Roots are one of the three fundamental organ systems of vascular plants1, and have roles in anchorage, symbiosis, and nutrient and water uptake2-4. However, the fragmentary nature of the fossil record obscures the origins of roots and makes it difficult to identify when the sole defining characteristic of extant roots-the presence of self-renewing structures called root meristems that are covered by a root cap at their apex1-9-evolved. Here we report the discovery of what are-to our knowledge-the oldest meristems of rooting axes, found in the earliest-preserved terrestrial ecosystem10 (the 407-million-year-old Rhynie chert). These meristems, which belonged to the lycopsid Asteroxylon mackiei11-14, lacked root caps and instead developed a continuous epidermis over the surface of the meristem. The rooting axes and meristems of A. mackiei are unique among vascular plants. These data support the hypothesis that roots, as defined in extant vascular plants by the presence of a root cap7, were a late innovation in the vascular lineage. Roots therefore acquired traits in a stepwise fashion. The relatively late origin in lycophytes of roots with caps is consistent with the hypothesis that roots evolved multiple times2 rather than having a single origin1, and the extensive similarities between lycophyte and euphyllophyte roots15-18 therefore represent examples of convergent evolution. The key phylogenetic position of A. mackiei-with its transitional rooting organ-between early diverging land plants that lacked roots and derived plants that developed roots demonstrates how roots were 'assembled' during the course of plant evolution.

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.

Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.