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Search Results
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Journal article
Global conservation status of the jawed vertebrate Tree of Life.
Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86–150 billion years (11–19%) of jawed vertebrate evolutionary...Gumbs, Rikki ; Scott, Oenone ; Bates, Ryan ; Böhm, Monika ; Forest, Félix …
Tree of Life, Conservation status, Jawed vertebrates, and Vertebrates
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Journal article
Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems.
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Journal article
Author Correction: Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems.
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Journal article
Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae).
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Journal article
Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae).
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Journal article
The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action
The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there... -
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
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... -
Journal article
The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.
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Journal article
Evolutionary diversity of the endemic genera of the vascular flora of Chile and its implications for conservation.
As a direct consequence of global change, both natural and human-induced, a high percentage of biodiversity is now under threat worldwide. This has urged conservation planners to formulate and/or improve existing strategies to preserve species and their ecosystems. In this context, the present study focuses on two strategies using phylogeny-based... -
Journal article
Indicators to monitor the status of the tree of life.
Following the failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversity's Kunming–Montreal Global Biodiversity Framework (GBF) presents the opportunity to preserve nature's contributions to people (NCPs) for current and future generations by conserving biodiversity and... -
Journal article
Strategies of diaspore dispersal investment in Compositae: the case of the Andean highlands.
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Journal article
Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats.
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Journal article
A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus phylogeny.
Duncan, Graham D. ; Schlichting, Carl D. ; Forest, Félix ; Ellis, Allan G. ; Lemmon, Alan R. …
Molecular systematics, Classification, Southern Africa, Lachenalia, and High-throughput sequencing
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Journal article
The rise of grasslands is linked to atmospheric CO2 decline in the late Palaeogene.
Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO and temperature fluctuations and the...Palazzesi, Luis ; Hidalgo, Oriane ; Barreda, Viviana D. ; Forest, Félix ; Höhna, Sebastian
Palaeogene, Grasslands, Evolution, Environmental sciences, and Phylogeny
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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
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
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
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
A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus phylogeny.
(Asparagaceae; Scilloideae; Hyacintheae) is a large and morphologically diverse genus of more than 140 bulbous species endemic to southern Africa. Previous attempts to infer a well‐resolved and robustly supported phylogeny of using Sanger sequencing of candidate loci and/or morphological characters have been largely unsuccessful. Consequently, the current infrageneric classification is...Duncan, Graham D. ; Schlichting, Carl D. ; Forest, Félix ; Ellis, Allan G. ; Lemmon, Alan R. …
High-throughput sequencing, Molecular systematics, Southern Africa, and Lachenalia
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Journal article
Harnessing large-scale biodiversity data to infer the current distribution of Vanilla planifolia (Orchidaceae).
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Journal article
Phylogenetic and Biogeographic Analysis in Myrcia Sect. Myrcia (Myrcia s.l., Myrtaceae) with Focus on Highly Polyphyletic Myrcia splendens.
Lima dos Santos, Leidiana ; Forest, Félix ; Fernandes Lima, Duane ; Sales, Margareth F. ; Vasconcelos, Thais Nogales …
Cerrado, Atlantic Forest, Molecular dating, Myrcia, Amazon, and Myrteae
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Journal article
A New and Expanded Phylogenetic Analysis of Hyptidinae (Ocimeae-Lamiaceae).
Hyptidinae, ca. 400 species, is an important component of Neotropical vegetation formations. Members of the subtribe possess flowers arranged in variously modified bracteolate cymes and nutlets with an expanded areole and all share a unique explosive mechanism of pollen release, except for . In a recent phylogenetic study, the group... -
Journal article
Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines
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Journal article
A revised infrageneric classification of Bellevalia Lapeyr. (Asparagaceae: Scilloideae) based on molecular analysis.
Jafari , Azarnoosh ; Vaezi , Jamil ; Forghanifard , Mohammad Mahdi ; Forest, Félix ; Manning, John C.
Molecular phylogenetics, Systematics, Iran, Bellevalia, Hyacintheae, and Asparagaceae
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Journal article
Settling a family feud: A high-level phylogenomic framework for the gentianales based on 353 nuclear genes and partial plastomes.
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Journal article
The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.
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Journal article
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
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Journal article
An updated infra-familial classification of sapindaceae based on targeted enrichment data.
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Journal article
Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits
Shah, Toral ; Schneider, Julio V. ; Zizka, Georg ; Maurin, Olivier ; Baker, William …
Coalescence, Custom , Universal, Probe kit , Maximum likelihood, Phylogenetic informativeness , and Missing data
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Journal article
Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments.
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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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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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Conference paper (published)
Conservando A História Evolutiva De Radiações Rápidas E Recentes: Um Estudo Com Um Clado Endêmico Em Campos Rupestres.
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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
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
Extinction risk and threats to plants and fungi
Societal Impact Statement There is increasing awareness that plants and fungi, as natural solutions, can play an important role in tackling ongoing global environmental challenges. We illustrate how understanding current and projected threats to plants and fungi is necessary to manage and mitigate risks, while building awareness of gaps and... -
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
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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
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
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
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
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
From the frying pan: an unusual dwarf shrub from Namibia turns out to be a new brassicalean family
Tiganophyton karasense, an evergreen dwarf shrub, is described as a new species. A new genus and family are also proposed for it in the order Brassicales. Phylogenetic analysis of DNA sequence data indicate that Tiganophyton is sister to Bataceae/Salvadoraceae, and all three sister to Koeberliniaceae. First realized to be undescribed... -
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
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
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
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
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
Phylogenetic analysis in Myrcia section Aulomyrcia and inferences on plant diversity in the Atlantic rainforest.
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Journal article
Pollinator shifts as triggers of speciation in painted petal irises (Lapeirousia: Iridaceae).
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