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Journal article
Phylogeny and re‐circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species.
Subfamily Cercidoideae is an early‐diverging lineage of Leguminosae, within which the number and classification of genera have been controversial. is a recently described genus in the Cercidoideae which requires revision and testing of its monophyly and circumscription. Here we infer the phylogenetic position and infrageneric relationships of as well as...Gu, Shi‐Ran ; Zeng, Qiu‐Biao ; Clark, Ruth ; Jiang, Kai‐Wen ; Pérez‐Escobar, Oscar Alejandro …
Bauhinia, Phylogeny, Re-circumscription, Southeast Asia, Phanera, Fabaceae, China, Cheniella, and Legume
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Journal article
Expert‐based range maps cannot be replicated using data‐driven methods but macroecological conclusions arising from them can.
Aronsson, Heléne ; Zizka, Alexander ; Antonelli, Alexandre ; Faurby, Søren
Range maps, Macroecology, IUCN ranges, Global biodiversity patterns, Biogeography, Bird distribution, and eBird global
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Journal article
A framework for tracing timber following the Ukraine invasion.
Scientific testing including stable isotope ratio analysis (SIRA) and trace element analysis (TEA) is critical for establishing plant origin, tackling deforestation and enforcing economic sanctions. Yet methods combining SIRA and TEA into robust models for origin verification and determination are lacking. Here we report a (1) large Eastern European timber... -
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Journal article
The origin of excavator nesting behavior and its impact on the evolution of Neotropical parrots.
How the origin of novel behaviors can shape the evolutionary trajectory of organisms in response to environmental change remains poorly understood. Birds, especially those with big brains like parrots, are benchmarks for their behavioral innovation capacity in novel environments. Here, we assess whether and how the emergence of open areas... -
Journal article
Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves.
Birds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the... -
Journal article
Connecting the multiple dimensions of global soil fungal diversity.
How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic... -
Journal article
Spiny but photogenic: Amateur sightings complement herbarium specimens to reveal the bioregions of cacti.
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Journal article
Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi.
Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2–3 million fungal species...Niskanen, Tuula ; Lücking, Robert ; Dahlberg, Anders ; Gaya, Ester ; Suz, Laura M. …
Fungi, Geographical distribution, Diversity, and Conservation
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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
Towards a co-crediting system for carbon and biodiversity.
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Journal article
Rediscovery of the lost skink Proscelotes aenea and implications for conservation.
Biodiversity loss is recognized as a grand challenge of the twenty-first century but ascertaining when a species is “lost” can be incredibly difficult—since the absence of evidence is not evidence of absence. This may be a relatively easy task for large and conspicuous animals, but extremely difficult for those living...Puruleia, Ali ; Nanvonamuquitxo, Cristóvão ; Ernesto, Milagre ; Jamal, Abdurabe ; Amade, Iassine …
Skinks, Proscelotes aenea, Lumbo (Mozambique), Mozambique, and Threatened species
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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
Machine learning enhances prediction of plants as potential sources of antimalarials.
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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
A call for improving the Key Biodiversity Areas framework.
Eight percent of all land surface has been designated as “Key Biodiversity Areas” (KBAs). Since these areas were established based on two percent of all terrestrial species estimated to exist, we ask what would happen if we used all species on Earth to identify additional KBAs. We explore this question... -
Book chapter
Foreword.
Antonelli, Alexandre
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Journal article
Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna.
Landscape dynamics are widely thought to govern the tempo and mode of continental radiations, yet the effects of river network rearrangements on dispersal and lineage diversification remain poorly understood. We integrated an unprecedented occurrence dataset of 4,967 species with a newly compiled, time-calibrated phylogeny of South American freshwater fishes—the most... -
Journal article
Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation.
Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus , whose species are strongly associated with seasonally flooded forests, watercourses and flooded... -
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
Integrating deep-time palaeontology in conservation prioritisation.
Halting biodiversity loss under growing anthropogenic pressure is arguably the greatest environmental challenge we face. Given that not all species are equally threatened and that resources are always limited, establishing robust prioritisation schemes is critical for implementing effective conservation actions. To this end, the International Union for Conservation of Nature...Pimiento, Catalina ; Antonelli, Alexandre
Fossil record, Extinction, Palaeontology, Biodiversity, and Conservation prioritisation
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Magazine article
Turn your garden into a biodiversity haven.
Antonelli, Alexandre
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Journal article
The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard.
While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae... -
Journal article
Diversification dynamics in the Neotropics through time, clades, and biogeographic regions.
The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150... -
Journal article
Integrating machine learning, remote sensing and citizen science to create an early warning system for biodiversity.
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Journal article
Global patterns in endemicity and vulnerability of soil fungi.
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Journal article
The origin and evolution of open habitats in North America inferred by Bayesian deep learning models.
Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth’s history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present...Andermann, Tobias ; Strömberg, Caroline A. E. ; Antonelli, Alexandre ; Silvestro, Daniele
North America, Grassland ecology, Palaeontology, Evolutionary ecology, and Bayesian models
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Journal article
Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation.
Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus (Nymphaeaceae). The systematics... -
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
The counteracting effects of anthropogenic speciation and extinction on mammal species richness and phylogenetic diversity.
Faurby, Søren ; Pedersen, Rasmus Østergaard ; Svenning, Jens‐Christian ; Antonelli, Alexandre
Extinction, Speciation, Mammals, Phylogenetic diversity, Anthropogenic, and Species diversity
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Journal article
Limited decadal growth of mountain birch saplings has minor impact on surrounding tundra vegetation.
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Journal article
Spatio‐temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions.
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Journal article
Improving biodiversity protection through artificial intelligence.
Over a million species face extinction, highlighting the urgent need for conservation policies that maximize the protection of biodiversity to sustain its manifold contributions to people’s lives. Here we present a novel framework for spatial conservation prioritization based on reinforcement learning that consistently outperforms available state-of-the-art software using simulated and... -
Journal article
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
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Journal article
Good news for habitat restoration projects: Eucalyptus does not inhibit the germination of Polylepis.
Meneses, Lidia ; Martinez, Yvonne Y. ; Antonelli, Alexandre ; Gareca, Edgar E.
Eucalyptus, Habitat restoration, Kewiña, Allelopathy, Reforestation, Polylepis, Exotic species, and Conservation
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Journal article
Certification of açaí agroforestry increases the conservation potential of the Amazonian tree flora.
The harvesting of açaí berries (palm fruits from the genus ) in Amazonia has increased over the last 20 years due to a high local and global market demand and triggered by their widely acclaimed health benefits as a ‘superfood’. Although such increase represents a financial boom for local communities,...Damasco, Gabriel ; Anhalt, Mandy ; Perdiz, Ricardo O. ; Wittmann, Florian ; de Assis, Rafael L. …
Açaí management, Amazonia, Biodiversity conservation, Euterpe, and Flooded forests
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Journal article
A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland.
The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and...Henniges, Marie C. ; Powell, Robyn F. ; Mian, Sahr ; Stace, Clive A. ; Walker, Kevin J. …
Taxonomy, Ireland, Great Britain, Plant ecology, Genetics, Biodiversity, Ecology, and Literature mining
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Journal article
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil.
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Journal article
Widespread homogenization of plant communities in the Anthropocene.
Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment... -
Journal article
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil.
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Journal article
The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin.
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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
Touch me carefully: a step towards understanding morphological diversity in the South American spiny sunflowers Compositae, Barnadesioideae).
de Lima Ferreira, Paola ; Antonelli, Alexandre ; Groppo, Milton
Distribution, Neotropical flora, Eudicots, Morphology, Asteraceae, Taxonomy, and South America
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Journal article
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.
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Journal article
Loss of functional diversity through anthropogenic extinctions of island birds is not offset by biotic invasions.
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Journal article
Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space.
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Journal article
The rise and fall of Neotropical biodiversity.
Antonelli, Alexandre
Conservation, Evolution, and Extinction
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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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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
Contrasting patterns of phylogenetic turnover in amphibians and reptiles are driven by environment and geography in Neotropical savannahs.
Azevedo, Josué A. R. ; Nogueira, Cristiano de C. ; Antonelli, Alexandre ; Faurby, Søren
Beta diversity, Cerrado, Generalized dissimilarity modelling, Regionalization, Connectivity, and Herptofauna
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Journal article
Genomic and niche divergence in an Amazonian palm complex.
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Journal article
Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding.
Duarte Ritter, Camila ; Forster, Dominik ; Azevedo, Josué A. R. ; Antonelli, Alexandre ; Nilsson, R. Henrik …
Fungi, Bacterias, Biodiversity, Protists, Metabarcoding, and Tropics
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Journal article
Taxonomic revision of the genus Xenopholis Peters, 1869 (Serpentes: Dipsadidae): Integrating morphology with ecological niche.
Gomes, Daniel Faustino ; Azevedo, Josué ; Murta-Fonseca, Roberta ; Faurby, Søren ; Antonelli, Alexandre …
Ecological niches, Spine , Skull , Dentition, Forests , Teeth , Taxonomy, and Brazil
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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
Fossil data support a pre-Cretaceous origin of flowering plants
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils....Silvestro, Daniele ; Bacon, Christine D. ; Ding, Wenna ; Zhang, Qiuyue ; Donoghue, Philip C. J. …
Evolution, Computational biology and bioinformatics , and Plant sciences
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Journal article
Ten golden rules for reforestation to optimize carbon sequestration, biodiversity recovery and livelihood benefits
Urgent solutions to global climate change are needed. Ambitious tree‐planting initiatives, many already underway, aim to sequester enormous quantities of carbon to partly compensate for anthropogenic CO2 emissions, which are a major cause of rising global temperatures. However, tree planting that is poorly planned and executed could actually increase CO2... -
Journal article
Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange.
The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually... -
Journal article
sampbias, a method for quantifying geographic sampling biases in species distribution data
Geo‐referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility...Zizka, Alexander ; Antonelli, Alexandre ; Silvestro, Daniele
collection effort, Global Biodiversity Information Facility (GBIF), roadside bias, presence only data, and sampling intensity
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Journal article
iucn_sim: a new program to simulate future extinctions based on IUCN threat status
The ongoing environmental crisis poses an urgent need to forecast the who, where and when of future species extinctions, as such information is crucial for targeting conservation efforts. Commonly, such forecasts are made based on conservation status assessments produced by the International Union for Conservation of Nature (IUCN). However, when...Andermann, Tobias ; Faurby, Søren ; Cooke, Robert ; Silvestro, Daniele ; Antonelli, Alexandre
generation length, extinction, MCMC, Bayesian , Aves , and IUCN