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Journal article
Living jewels: iterative evolution of iridescent blue leaves from helicoidal cell walls.
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Journal article
Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae).
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Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata).
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae.
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species... -
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Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar.
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Cytotype diversity in the Sorbus complex (Rosaceae) in Britain: sorting out the puzzle.
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Characterising subgenome recombination and chromosomal imbalances in banana varietal lineages.
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Species as a Heuristic: Reconciling Theory and Practice.
Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the “species problem” stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and...Wells, Tom ; Carruthers, Tom ; Muñoz-Rodríguez, Pablo ; Sumadijaya, Alex ; Wood, John R I …
Heuristic, Species problem, Cohesion, Homeostasis, and Lineage
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Journal article
Complementing model species with model clades.
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here... -
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Strategies of diaspore dispersal investment in Compositae: the case of the Andean highlands.
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Phylogeny and infrageneric classification of Clerodendrum (Lamiaceae).
The infrageneric classification of the genus Clerodendrum (Lamiaceae) has been highly problematic due to different concepts and subdivisions being applied to the treatment of Asian, Australian, and African species. Earlier molecular phylogenetic studies based on Sanger sequencing and limited sampling have indicated that previous morphology-based infrageneric classifications are not congruent... -
Journal article
Monnina (Polygalaceae), a New World monophyletic genus full of contrasts.
Endemic to the Neotropics, Monnina is the second largest genus of Polygalaceae, yet little is known about its phylogenetic history, biogeography, and morphological character evolution. To address these knowledge gaps, we conducted Bayesian and maximum likelihood (ML) analyses of nuclear ITS and plastid trnL–F regions to test the monophyly of...Freire-Fierro, Alina ; Forest, Felix ; Devey, Dion S. ; Barea Pastore, José Floriano ; Horn, James W. …
Ancylotropis, Pteromonnina, Evolution, Biogeography, Monnina, Polygalaceae, and Neotropics
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Journal article
Evolutionary history, traits, and weediness in Digitaria (Poaceae: Panicoideae).
Digitaria is a large pantropical genus, which includes a number of economically problematic agricultural weeds. Difficulties in species identification and the circumscription of the genus have previously hindered progress in understanding its evolution and developing a stable classification. We investigate the evolutionary history of Digitaria by combining two approaches: (i)... -
Journal article
Molecular phylogenetics shed light on polyploid speciation in gorses ( <i>Ulex</i> , Fabaceae: Genisteae) and on the origin of the invasive <i>Ulex europaeus</i>
Hybridization and polyploidy are key evolutionary forces in plant diversification, and their co-occurrence in the context of allopolyploid speciation is often associated with increased ability to colonize new environments and invasiveness. In the genus Ulex (Fabaceae), the European gorse (Ulex europaeus subsp. europaeus) is the only invasive and the only... -
Journal article
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics.
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that...Truszkowski, Jakub ; Perrigo, Allison ; Broman, David ; Ronquist, Fredrik ; Antonelli, Alexandre
Phylogeny, MCMC, Bayesian inference, and Sequential Monte Carlo
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Journal article
Tiptoe through the tulips - cultural history, molecular phylogenetics and classification of Tulipa (Liliaceae).
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Journal article
Repeated evolution of pollination syndromes in a highly diverse bromeliad lineage is correlated with shifts in life form and habitat.
Mutualistic plant-pollinator interactions play a critical role in the diversification of flowering plants. The spatiotemporal correlates of such interactions can be understood in a phylogenetic context. Here, we generate ddRAD-seq data for the highly diverse Vriesea-Stigmatodon lineage to test for correlated trait evolution among pollination syndromes and life form, habitat... -
Journal article
Harnessing the potential of symbiotic associations of plants in phosphate-deficient soil for sustainable agriculture.
Many plants associate with arbuscular mycorrhizal (AM) fungi for nutrient acquisition, while most legumes also associate with nitrogen-fixing rhizobial bacteria for nitrogen acquisition. The association of plants with AM fungi and rhizobia depends on the perception of lipo-chitooligosaccharides (LCOs) produced by these micro-symbionts. Recent studies reveal that cereals can perceive... -
Journal article
Digest: Multiple factors influence mountain orchid diversity and distribution.
How have orchid species diversified in the campos rupestres, Brazil? Fiorini et al. (2023) use genomic data sets and multidisciplinary approaches, including phylogenetics and population genomics, to investigate the diversity of Bulbophyllum. They demonstrate that geographic isolation alone does not explain diversification patterns in Bulbophyllum species throughout the sky forests....Phillips, Charlotte ; Pérez-Escobar, Oscar Alejandro ; Dodsworth, Steven
Geographical distribution, Diversity, Orchidaceae, Campos rupestres, Brazil, Bulbophyllum, and Orchids
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Journal article
SmartWoodID—an image collection of large end-grain surfaces to support wood identification systems.
Wood identification is a key step in the enforcement of laws and regulations aimed at combatting illegal timber trade. Robust wood identification tools, capable of distinguishing a large number of timbers, depend on a solid database of reference material. Reference material for wood identification is typically curated in botanical collections... -
Journal article
First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).
Lichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly opting for metagenomic sequencing followed by symbiont genome separation using bioinformatic pipelines. However, without knowing the true genome size of the...Llewellyn, Theo ; Mian, Sahr ; Hill, Rowena ; Leitch, Ilia J ; Gaya, Ester
Lichen, Genome size, Ramalina farinacea, Symbiosis, Ramalinaceae, Long-read sequencing, and Metagenomics
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Journal article
Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation.
Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study we demonstrate how the use of two...Wootton, Lara M. ; Forest, Félix ; Verboom, G. Anthony
Species delimitation, Ehrharta (Poaceae), Genotyping-by-sequencing, Integrative taxonomy, Population structure, and Cryptic species
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Journal article
A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis.
The root systems of most plant species are aided by the soil foraging capacities of symbiotic Arbuscular Mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just... -
Journal article
The Implications of Incongruence between Gene Tree and Species Tree Topologies for Divergence Time Estimation.
Phylogenetic analyses are increasingly being performed with data sets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences...Carruthers, Tom ; Sun, Miao ; Baker, William J. ; Smith, Stephen A. ; de Vos, Jurriaan M. …
Divergence time estimation, Species tree, Gene trees, and Topological incongruence
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Journal article
Rtapas: An R package to assess cophylogenetic signal between two evolutionary histories.
Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal... -
Journal article
Estimation of species divergence times in presence of cross-species gene flow.
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies...Tiley, George P ; Flouri, Tomás ; Jiao, Xiyun ; Poelstra, Jelmer W. ; Xu, Bo …
Gene flow, Divergence time, Introgression, MSci model, Hybridization, and Multispecies coalescent
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Journal article
Distimake vitifolius (Convolvulaceae): reclassification of a widespread species in view of phylogenetics and convergent pollen evolution.
Distimake vitifolius comb. nov. (Convolvulaceae), currently treated as Camonea vitifolia, is a common and widespread species in South-East Asia. A recent study on the re-delimitation of the genus Merremia classified its species into six genera. The results of molecular phylogenetic analyses and the presence of hexazonocolpate pollen informed the transfer... -
Journal article
Forty years of research into Crassulacean Acid Metabolism in the genus Clusia : anatomy, ecophysiology and evolution.
Clusia is the only genus containing dicotyledonous trees with a capacity to perform Crassulacean acid metabolism (CAM). Since the discovery of CAM in Clusia, 40 years ago, several studies have highlighted the extraordinary plasticity and diversity of life forms, morphology, and photosynthetic physiology of this genus. In this review we...Luján, Manuel ; Leverett, Alistair ; Winter, Klaus
Neotropics, Clusia, Trees, CAM photosynthesis, Plasticity, Ecophysiology, Plant anatomy, Carbon, and Evolution
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Journal article
The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data.
The transition from a greenhouse to an icehouse world at the Eocene-Oligocene Transition (EOT) coincided with a large decrease of pollen from the steppe-adapted genus Nitraria. This genus, now common along the Mediterranean coast, Asia and Australia, has a proposed coastal origin and a geographically widespread fossil record. Here we... -
Journal article
Tapping culture collections for fungal endophytes: first genome assemblies for three genera and five species in the Ascomycota.
The Ascomycota form the largest phylum in the fungal kingdom and show a wide diversity of lifestyles, some involving associations with plants. Genomic data is available for many ascomycetes that are pathogenic to plants, but endophytes, which are asymptomatic inhabitants of plants, are relatively understudied. Here, using short- and long-read...Hill, Rowena ; Levicky, Quentin ; Pitsillides, Frances ; Junnonen, Amy ; Arrigoni, Elena …
Cytometric completeness, Ascomycota, Culture collections, and Fungal endophytes
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Journal article
Let’s pluck the daisy: dissection as a tool to explore the diversity of Asteraceae capitula.
Asteraceae, the daisy family, are one of the most diverse families of angiosperms and are predominant in many ecosystems, including grasslands, deserts, savannas and high-elevation mountains. They are characterized by a peculiar inflorescence, the capitulum, which mimics a flower, but is actually made up of many tightly grouped florets. The...Fu, Lin ; Palazzesi, Luis ; Pellicer, Jaume ; Balant, Manica ; Christenhusz, Maarten J M …
Compositae, Asteraceae, Pseudanthium, Inflorescence, Dissection, Synflorescences, and Capitulum
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A morphological analysis of Syzygium, with a focus on fibre bundles and description of a new subgenus.
Syzygium is a large genus (1200–1500 species) of Old World tropical trees, currently divided into five subgenera containing widely different numbers of species. Syzygium subgenus Perikion was defined by the presence of fibre bundles in the hypanthium wall, although until now this feature has not been investigated or images published....Hatt, Sebastian ; Low, Yee Wen ; Burslem, David F R P ; Middleton, David J. ; Biffin, E. D. …
Perikion, Oborapi, New subgenus, Syzygium, Myrtaceae, Plant taxonomy, and Plant morphology
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Journal article
Molecular phylogenetics of Maranta (Marantaceae: Zingiberales): non-monophyly and support for a wider circumscription.
Neotropical Maranta has repeatedly emerged as non-monophyletic in molecular phylogenetic studies, but no taxonomic changes have been proposed due to previous weak support for the main clades and overall sparse taxonomic sampling. Our study includes a phylogenetic hypothesis strictly based on molecular evidence, using nuclear ribosomal (nrITS) and plastid (rps16,... -
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Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae).
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Metagenomics Shines Light on the Evolution of ‘Sunscreen’ Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota).
Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterising the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenised fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen... -
Journal article
The International Oryza Map Alignment Project (IOMAP): The Americas - Past achievements and future directions.
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary and functional characterization of the wild relatives of rice, facilitating... -
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Four o'clock pollination biology: nectaries, nectar and flower visitors in Nyctaginaceae from southern South America.
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Ultrastructure of stomatal development in early-divergent angiosperms reveals contrasting patterning and pre-patterning.
Rudall, Paula J. ; Knowles, Emma V. W.
Epidermal pre-patterning, ANITA, Early-divergent angiosperms, Perigenous stomata, Stomatal development, Mesogenous stomata, and Meristemoids
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Phylogenetic study of Plectranthus, Coleus and allies (Lamiaceae): taxonomy, distribution and medicinal use.
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Utilizing a phylogenetic plant classification for systematic arrangements in botanic gardens and herbaria.
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