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Journal article
A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number...Viruel, Juan ; Conejero, María ; Hidalgo, Oriane ; Pokorny, Lisa ; Powell, Robyn …
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Journal article
A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)
Premise We developed a target enrichment panel for phylogenomic studies of Dioscorea, an economically important genus with incompletely resolved relationships. Methods Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in Dioscorea, assessed here using a preliminary taxon sampling that includes both distantly and closely related...Soto Gomez, Marybel ; Pokorny, Lisa ; Kantar, Michael ; Forest, Félix ; Leitch, Ilia …
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Journal article
Incorporating evolutionary history into conservation assessments of a highly threatened group of species, South African Dioscorea (Dioscoreaceae)
In an era of increasing threat most species of plant still lack an assessment of extinction risk or an understanding of priority for conservation. Evolutionary distinctiveness (ED) has been used in conjunction with extinction risk to prioritise species for conservation. We apply this approach to an economically important group of...Hills, R ; Bachman, S ; Forest, Félix ; Moat, Justin ; Wilkin, Paul
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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 …
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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
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
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
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
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
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
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
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
Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA
Leguminosae, Polygalaceae, Quillajaceae and Surianaceae together comprise the order Fabales. Phylogenetic relationships within Fabales remain an unsolved problem even though interfamilial relationships have been examined in a number of studies using different sampling approaches and both molecular and morphological data. In this study, we gather information from the nuclear 26S...Aygoren Uluer, Deniz ; Hawkins, Julie A. ; Forest, Félix
Sqd1, MatK, 26S, Polygalaceae, Quillajaceae, RbcL, Leguminosae, Surianaceae , and Fabales
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Journal article
Conserving orthodox seeds of globally threatened plants ex situ in the Millennium Seed Bank, Royal Botanic Gardens, Kew, UK: the status of seed collections
We reviewed the status of orthodox seed collections of globally threatened plants conserved in − 20 °C long-term storage at the Millennium Seed Bank, Royal Botanic Gardens, Kew, UK in terms of their geographic and bioclimatic representativeness, taxonomic and genetic diversity, quality and physiological status. The comprehensive dataset used spans... -
Journal article
Plant richness, turnover, and evolutionary diversity track gradients of stability and ecological opportunity in a megadiversity center
Research on global patterns of diversity has been dominated by studies seeking explanations for the equator-to-poles decline in richness of most groups of organisms, namely the latitudinal diversity gradient. A problem with this gradient is that it conflates two key explanations, namely biome stability (age and area) and productivity (ecological...Colville, Jonathan F. ; Beale, Colin M. ; Forest, Félix ; Altwegg, Res ; Huntley, Brian …
spatial models, phylogenetic diversity, beta diversity, Cape Floristic Region, and longitudinal gradient
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Journal article
Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity
Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity... -
Journal article
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity
Hybridisation has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing inter‐specific gene flow. However, hybridisation in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its... -
Journal article
Crop wild phylorelatives (CWPs): phylogenetic distance, cytogenetic compatibility and breeding system data enable estimation of crop wild relative gene pool classification
Enabling food security requires access to a broad range of genetic resources to facilitate crop breeding. This need is increased in a climate change scenario, which will require the production of novel crops adapted to new conditions. However, many major crops have reduced genetic diversity due to the genetic bottlenecks...Viruel, Juan ; Kantar, Michael B ; Gargiulo, Roberta ; Hesketh-Prichard, Peri ; Leong, Nathan …
reproductive biology, Asparagus, plant breeding, and chromosome