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  1. ; ; ; ; ; ( , Frontiers in Plant Science)
    null (Ed.)
    Coevolution between plants and insects is thought to be responsible for generating biodiversity. Extensive research has focused largely on antagonistic herbivorous relationships, but mutualistic pollination systems also likely contribute to diversification. Here we describe an example of chemically-mediated mutualistic species interactions affecting trait evolution and lineage diversification. We show that volatile compounds produced by closely related species of Zamia cycads are more strikingly different from each other than are other phenotypic characters, and that two distantly related pollinating weevil species have specialized responses only to volatiles from their specific host Zamia species. Plant transcriptomes show that approximately a fifth of genes related to volatile production are evolving under positive selection, but we find no differences in the relative proportion of genes under positive selection in different categories. The importance of phenotypic divergence coupled with chemical communication for the maintenance of this obligate mutualism highlights chemical signaling as a key mechanism of coevolution between cycads and their weevil pollinators. 
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  2. ; ( , PLANTS, PEOPLE, PLANET)
  3. ; ; ; ; ; ; ; ; ; ; et al ( , Nature Plants)
    Abstract The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii . The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology. 
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  4. ; ; ; ; ; ; ( , Functional Ecology)
    Abstract

    Photosynthetic traits suggest that shade tolerance may explain the contrasting success of two conifer taxa, Podocarpaceae and Pinaceae, in tropical forests. Needle‐leaved species fromPinus(Pinaceae) are generally absent from tropical forests, whereasPinus krempfii, a flat‐leaved pine, and numerous flat‐leaved Podocarpaceae are abundant. Respiration (R) traits may provide additional insight into the drivers of the contrasting success of needle‐ and flat‐leaved conifers in tropical forests.

    We measured the short‐term respiratory temperature (RT) response between 10 and 50°C and foliar morphological traits of three needle‐ and seven flat‐leaved conifer species coexisting in a tropical montane forest in the Central Highlands of Vietnam containing notable conifer diversity. We fit a lognormal polynomial model to each RT curve and extracted the following three parameters:a(basalR), andbandc(together describing the shape of the response).

    Needle‐leaved species (Pinus kesiya,Pinus dalatensisandDacrydium elatum) had higher rates of area‐basedRat 25°C (R25‐area) as well as higher area‐based modelled basal respiration (a) than flat‐leaved species (P. krempfii,Podocarpus neriifolius,Dacrycarpus imbricatus,Nageia nana,Taxus wallichiana,Keteeleria evelynianaandFokienia hodginsii). No significant differences were found between needle‐ and flat‐leaved species in mass‐basedR25(R25‐mass) or in the shape of the RT response (bandc); however, interspecific differences inR25‐mass,Rat nighttime temperature extremes (R4.1andR20.6) and leaf traits were apparent.

    Differences inR25‐areaandasuggest that needle‐leaved foliage may be more energetically costly to maintain than flat‐leaved foliage, providing new insight and additional support for the hypothesis that shade tolerance is an important driver of Podocarpaceae success and Pinaceae absence in the majority of tropical forests.

    Interspecific differences inR25‐massand leaf traits highlight that varying ecological strategies are employed by conifers to coexist and survive in the Central Highlands of Vietnam. Ultimately, these data further our understanding of current conifer biogeographical distributions and underscore the need for additional studies to elucidate the effects of extreme temperature events on the continued survival of conifers in this unique forest.

    A freePlain Language Summarycan be found within the Supporting Information of this article.

     
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  5. ; ; ; ; ; ; ; ; ; ; et al ( , Proceedings of the National Academy of Sciences)
  6. ; ; ; ; ; ; ; ; ; ; et al ( , American Journal of Botany)
  7. ; ; ; ; ; ; ; ; ; ; et al ( , Nature)
    Green plants (Viridiplantae) include around 450,000–500,000 species of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life. 
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  8. ; ; ; ; ; ; ; ; ; ; et al ( , American Journal of Botany)
    Premise

    Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution.

     Methods

    We employed diverse likelihood‐based analyses to infer large‐scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements.

     Results

    Overall land‐plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four‐taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion ofRNAedit sites restores cases of unexpected non‐monophyly to monophyly forTakakiaand two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophicAneurabut notBuxbaumia. Plastid genome structure is nearly invariant across bryophytes, but thetufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.

     Conclusions

    A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavilyRNA‐edited taxa. TheBuxbaumiaplastome lacks hallmarks of relaxed selection found in mycoheterotrophicAneura. Autotrophic bryophyte plastomes, includingBuxbaumia, hardly vary in overall structure.

     
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