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2023
Journal article
Machine learning enhances prediction of plants as potential sources of antimalarials.
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2023
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... -
2022
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,... -
2022
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... -
2022
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... -
2022
Journal article
Integrating machine learning, remote sensing and citizen science to create an early warning system for biodiversity.
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2022
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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2022
Journal article
Spatio‐temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions.
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2022
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... -
2021
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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2020
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... -
2020
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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2020
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
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2020
Journal article
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front‐end to...Edler, Daniel ; Klein, Johannes ; Antonelli, Alexandre ; Silvestro, Daniele
phylogenetics, evolutionary biology, software, bioinformatics, and molecular biology
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2020
Journal article
The rise of angiosperms pushed conifers to decline during global cooling
Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms...Condamine, Fabien L. ; Silvestro, Daniele ; Koppelhus, Eva B. ; Antonelli, Alexandre
macroevolution, competition, paleoenvironment, and gymnosperms
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2020
Journal article
Selective extinction against redundant species buffers functional diversity
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role,...Pimiento, Catalina ; Bacon, Christine D. ; Silvestro, Daniele ; Hendy, Austin ; Jaramillo, Carlos …
global change, molluscs, competition, Caribbean, extinction, and invertebrates
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2020
Journal article
The past and future human impact on mammalian diversity
To understand the current biodiversity crisis, it is crucial to determine how humans have affected biodiversity in the past. However, the extent of human involvement in species extinctions from the Late Pleistocene onward remains contentious. Here, we apply Bayesian models to the fossil record to estimate how mammalian extinction rates...Andermann, Tobias ; Faurby, Søren ; Turvey, Samuel T. ; Antonelli, Alexandre ; Silvestro, Daniele
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2020
Research report
Exploring the Impact of Political Regimes on Biodiversity
National governments are the main actors responsible for mapping and protecting their biodiversity, but countries differ in their capacity, willingness, and effectiveness to do so. We quantify the global biodiversity managed by different regime types and developed a tool to explore the links between level of democracy and other key...Zizka, Alexander ; Rydén, Oskar ; Edler, Daniel ; Klein, Johannes ; Aronsson, Heléne …
Democracy, Regime type, Autocracy, Specimen collection, and Biodiversity
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2020
Journal article
outsider: Install and run programs, outside of R, inside of R
In many areas of research, product development and software engineering, analytical pipelines – workflows connecting output from multiple software – are key for processing and running tests on data. They can provide results in a consistent, modular and transparent manner. Pipelines also make it easier to demonstrate the reproducibility of...Bennett, Dominic ; Hettling, Hannes ; Silvestro, Daniele ; Vos, Rutger ; Antonelli, Alexandre
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2020
Journal article
Brain expansion in early hominins predicts carnivore extinctions in East Africa
While the anthropogenic impact on ecosystems today is evident, it remains unclear if the detrimental effect of hominins on co‐occurring biodiversity is a recent phenomenon or has also been the pattern for earlier hominin species. We test this using the East African carnivore fossil record. We analyse the diversity of...Faurby, Søren ; Silvestro, Daniele ; Werdelin, Lars ; Antonelli, Alexandre