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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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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
A phylogenomic analysis of Nepenthes (Nepenthaceae)
Nepenthaceae is one of the largest carnivorous plant families and features ecological and morphological adaptations indicating an impressive adaptive radiation. However, investigation of evolutionary and taxonomic questions is hindered by poor phylogenetic understanding, with previous molecular studies based on limited loci and taxa. We use high-throughput sequencing with a target-capture...Murphy, Bruce ; Forest, Félix ; Barraclough, Timothy ; Rosindell, James ; Bellot, Sidonie …
Genetics, Molecular Biology, and Ecology, Evolution, Behavior and Systematics
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Journal article
Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms
The world’s herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented... -
Journal article
The Use of Phylogenetic Diversity in Conservation Biology and Community Ecology: A Common Base but Different Approaches
The use of phylogenetic tools and studies has strongly increased in the last two decades especially in conservation biology and community ecology. Phylogenetic trees are essential to understand the processes of community or network assembly, to identify centers of diversification, and to help protect Earth?s evolutionary heritage. Despite two decades...Véron, Simon ; Saito, Victor ; Padilla-García, Nélida ; Forest, Félix ; Bertheau, Yves
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Journal article
The Callerya Group redefined and Tribe Wisterieae (Fabaceae) emended based on morphology and data from nuclear and chloroplast DNA sequences
The Tribe Wisterieae (Zhu 1994), founded on the single genus Wisteria, is emended and recircumscribed based on morphology and data from nuclear ITS and ndhJ-trnF, matK and rbcL chloroplast DNA sequences. This newly enlarged tribe comprises 36 species and 9 infraspecific taxa within 13 described genera. Six genera are new,...Compton, James ; Schrire, Brian ; Könyves, Kálmán ; Forest, Félix ; Malakasi, Panagiota …
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Journal article
Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes
Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the...Ojeda, Dario ; Koenen, Erik ; Cervantes, Sandra ; de la Estrella, Manuel ; Banguera-Hinestroza, Eulalia …