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Journal article
Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling.
Mountains are among the most biodiverse places on Earth, and plant lineages that inhabit them have some of the highest speciation rates ever recorded. Plant diversity within the alpine zone - the elevation above which trees cannot grow—contributes significantly to overall diversity within mountain systems, but the origins of alpine... -
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Distribution of leaflet traits across different habitats: a phylogenetically controlled test using Neotropical palms.
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Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats.
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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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Truongsonia (Arecaceae: Arecoideae: Truongsonieae)—a new palm genus and tribe from Vietnam.
A genus and species of palm from the Truong Son Range in Vietnam, Truongsonia lecongkietii, is described as new to science. Phylogenomic analysis strongly supports the placement of the new taxon in subfamily Arecoideae as sister to the African endemic tribe Podococceae, which comprises a single genus Podococcus. A new... -
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Strategies of diaspore dispersal investment in Compositae: the case of the Andean highlands.
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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
Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication.
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to... -
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The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.
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Journal article
Palaeo-precipitation is a major determinant of palm species richness patterns across Madagascar: a tropical biodiversity hotspot.
The distribution of rainforest in many regions across the Earth was strongly affected by Pleistocene ice ages. However, the extent to which these dynamics are still important for modern-day biodiversity patterns within tropical biodiversity hotspots has not been assessed. We employ a comprehensive dataset of Madagascan palms (Arecaceae) and climate...Rakotoarinivo, Mijoro ; Blach-Overgaard, Anne ; Baker, William J. ; Dransfield, John ; Moat, Justin …
Species richness, Palaeoclimate, Arecaceae, Palms, Last ice age, and Madagascar
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Journal article
Madagascar’s extraordinary biodiversity: Threats and opportunities.
Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats,... -
Journal article
Madagascar’s extraordinary biodiversity: Evolution, distribution, and use.
Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated... -
Journal article
A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding... -
Journal article
Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar.
Eiserhardt, Wolf L. ; Bellot, Sidonie ; Cowan, Robyn S. ; Dransfield, John ; Hansen, Lars Emil S.F. …
Target sequence capture, Madagascar, Hyb-Seq, Dypsis, Phylogeny, Chrysalidocarpus, and Palmae
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Journal article
A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data.
Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato ( L.), the ornamental morning glories ( L.), bindweeds ( L.), and dodders, the parasitic vines ( L.). Earlier phylogenetic studies, based predominantly...Simões, Ana Rita G. ; Eserman, Lauren A. ; Zuntini, Alexandre R. ; Chatrou, Lars W. ; Utteridge, Timothy M. A. …
Angiosperms353, Cuscuta, Classification, Phylogeny, Convolvulus, and Ipomoea
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Journal article
The ecology of palm genomes: repeat‐associated genome size expansion is constrained by aridity.
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Journal article
Global variation in diversification rate and species richness are unlinked in plants.
Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world’s most important engineers of terrestrial ecosystems, we investigated the role...Tietje, Melanie ; Antonelli, Alexandre ; Baker, William J. ; Govaerts, Rafaël ; Smith, Stephen A. …
Diversification, Biogeography, Biodiversity, Macroecology, and Plant diversity drivers
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Journal article
Standards recommendations for the Earth BioGenome Project.
A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample...Lawniczak, Mara K. N. ; Durbin, Richard ; Flicek, Paul ; Lindblad-Toh, Kerstin ; Wei, Xiaofeng …
Earth BioGenome Project, Ethics, Genomics, and Genome assembly
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Journal article
The Cenozoic history of palms: Global diversification, biogeography and the decline of megathermal forests.
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Journal article
Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella.
Torres Jiménez, Maria Fernanda ; Prata, Eduardo M. B. ; Zizka, Alexander ; Cohn-Haft, Mario ; de Oliveira, Ayslaner V. G. …
Amazonia, Phylogenomics, Palmae, Mauritiella, and Africa
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Journal article
On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae).
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The demographic history of Madagascan micro-endemics: have rare species always been rare?
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Journal article
Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections.
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Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family.
Siniscalchi, Carolina M. ; Hidalgo, Oriane ; Palazzesi, Luis ; Pellicer, Jaume ; Pokorny, Lisa …
Target capture, Paralogy , Asteraceae , Angiosperms, and Phylogenomics
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Journal article
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
Ufimov, Roman ; Zeisek, Vojtěch ; Píšová, Soňa ; Baker, William J. ; Fér, Tomáš …
Angiosperms353 , Customized probe set , Target enrichment , Malinae, and Universal probe set
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Journal article
A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae
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Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments.
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Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
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The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.
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An updated infra-familial classification of sapindaceae based on targeted enrichment data.
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Settling a family feud: A high-level phylogenomic framework for the gentianales based on 353 nuclear genes and partial plastomes.
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Combination of Sanger and target-enrichment markers supports revised generic delimitation in the problematic ‘Urera clade’ of the nettle family (Urticaceae)
Urera Gaudich, s.l. is a pantropical genus comprising c. 35 species of trees, shrubs, and vines. It has a long history of taxonomic uncertainty, and is repeatedly recovered as polyphyletic within a poorly resolved complex of genera in the Urticeae tribe of the nettle family (Urticaceae). To provide generic delimitations...Wells, Tom ; Maurin, Olivier ; Dodsworth, Steven ; Friis, Ib ; Cowan, Robyn …
Lianas, Secondary woodiness, Generic delimitation, and Angiosperms353
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Journal article
Botanical Monography in the Anthropocene
Botanical monographs have been the gold standard for communicating comprehensive systematic information about plants for over 300 years. Monographs catalyse species discovery, biodiversity documentation and conservation, and facilitate downstream research on wild and cultivated plant species. Increased availability of DNA sequence data and digitised resources now provide powerful resources for...Grace, Olwen M. ; Pérez-Escobar, Oscar A. ; Lucas, Eve J. ; Vorontsova, Maria S. ; Lewis, Gwilym P. …
conservation, Tree of Life, taxonomy , plants systematics , and biodiversity
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Journal article
Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.
Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus... -
Journal article
A robust phylogenomic framework for the calamoid palms
Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550...Kuhnhäuser, Benedikt G. ; Bellot, Sidonie ; Couvreur, Thomas L.P. ; Dransfield, John ; Henderson, Andrew …
Systematics, Calamoideae, Phylogenomics, Gene tree conflict, Rattan, and Arecaceae
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Journal article
Resolving generic limits in Cyperaceae tribe Abildgaardieae using targeted sequencing
Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothesis for Abildgaardieae using targeted...Larridon, Isabel ; Zuntini, Alexandre R. ; Barrett, Russell L. ; Wilson, Karen L. ; Bruhl, Jeremy J. …
Fimbristylis, C4 photosynthesis, generic circumscription, Bulbostylis, and Angiosperms353
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Journal article
New Guinea has the world’s richest island flora
New Guinea is the world’s largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet3 and to intact ecological gradients—from mangroves to tropical alpine grasslands—that are unmatched in the Asia-Pacific region4,5, it is a globally recognized centre of biological and cultural... -
Journal article
The global abundance of tree palms.
Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses... -
Journal article
A roadmap for global synthesis of the plant tree of life
Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience... -
Journal article
A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design.... -
Journal article
Earth BioGenome Project: Sequencing life for the future of life
Increasing our understanding of Earth’s biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet’s organisms. Herein, we present a perspective on the...Lewin, Harris A. ; Robinson, Gene E. ; Kress, W. John ; Baker, William J. ; Coddington, Jonathan …
genome sequencing, data science, biodiversity, genomics, and access and benefit sharing
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A taxonomic revision of the myrmecophilous species of the rattan genus Korthalsia (Arecaceae)
The rattan genus Korthalsia Blume (Arecaceae: Calamoideae: Calameae) is widespread in the Malesian region. Among the 28 accepted species are 10 species that form intimate associations with ants. The ants inhabit the conspicuous ocreas that are produced by these species, using them as domatia to care for their young and...Shahimi, Salwa ; Conejero, Maria ; Prychid, Christina J. ; Rudall, Paula J. ; Hawkins, Julie A. …
taxonomy, Calamoideae, myrmecophily, ocrea, morphology, ant-plant mutualism, Malesia, and domatia
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Journal article
Tackling Rapid Radiations With Targeted Sequencing
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a... -
Journal article
TRY plant trait database - enhanced coverage and open access
Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community...