Daniele Silvestro

Daniele Silvestro
Université de Fribourg · Department Biology

PhD

About

180
Publications
79,041
Reads
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6,953
Citations
Additional affiliations
January 2016 - present
University of Gothenburg
Position
  • Research Associate
August 2013 - December 2015
University of Gothenburg
Position
  • PostDoc Position
August 2012 - December 2012
University of Lausanne
Position
  • PostDoc Position
Education
November 2008 - February 2012
Senckenberg Research Institute
Field of study
  • Evolutionary Biology
September 2006 - July 2008
Università degli Studi di Torino
Field of study
  • Natural Sciences

Publications

Publications (180)
Article
Full-text available
1. raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. 2. 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 graph-ical front-end to setup and run p...
Article
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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. To resolve t...
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The end-Cretaceous event was catastrophic for terrestrial communities worldwide, yet its long-lasting effect on tropical forests remains largely unknown. We quantified plant extinction and ecological change in tropical forests resulting from the end-Cretaceous event using fossil pollen (>50,000 occurrences) and leaves (>6000 specimens) from localit...
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Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temper...
Article
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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-o...
Preprint
Full-text available
We live in a time of highly accelerated extinction, which has the potential to mirror past mass extinction events. However, the rarity of these events and the restructuring of diversity that they cause complicate direct comparisons between the current extinction crisis and earlier mass extinctions. Among animals, turtles (Testudinata) are one of fe...
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Climate change may affect plant–herbivore interactions and their associated ecosystem functions. In an experimental evolution approach, we subjected replicated populations of the invasive Ambrosia artemisiifolia to a combination of simulated warming and herbivory by a potential biocontrol beetle. We tracked genomic and metabolomic changes across ge...
Article
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Global diversity patterns in the fossil record comprise a mosaic of regional trends, underpinned by spatially non-random drivers and distorted by variation in sampling intensity through time and across space. Sampling-corrected diversity estimates from spatially-standardised fossil datasets retain their regional biogeographic nuances and avoid thes...
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Trees are fundamental for Earth's biodiversity as primary producers and ecosystem engineers and are responsible for many of nature's contributions to people. Yet, many tree species at present are threatened with extinction by human activities. Accurate identification of threatened tree species is necessary to quantify the current biodiversity crisi...
Article
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The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value and threat considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species...
Article
The biotic assembly of one of the most species‐rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity...
Article
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1. Speciation, dispersal and extinction govern the spatial and temporal dynamics of biodiversity. The fossil record offers the opportunity to directly estimate range expansion and contraction via dispersal and extinction, respectively. However, due to the incomplete occurrence record, determining the dynamics of these processes and the biotic and a...
Article
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Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. How...
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Aim The Red List (RL) from the International Union for the Conservation of Nature is the most comprehensive global quantification of extinction risk, and widely used in applied conservation as well as in biogeographic and ecological research. Yet, due to the time-consuming assessment process, the RL is biased taxonomically and geographically, which...
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The aim of this Special Issue is to improve understanding of the uplift of the Andes and its far-reaching impact on climate and biodiversity in South America from the late Mesozoic onwards. The Andes form the backbone of the South American continent and are the world's most biodiverse mountain system (Pérez-Escobar et al., in press). This biodivers...
Article
Sparassodonta, a Metatherian monophyletic group, was the main mammalian carnivore predator clade in South America from the Paleogene to the Early Pliocene (c. 66–3.5 Ma). However, there is still no consensus on the causes of their demise. Here, we use the fossil record and Bayesian diversification models to infer the origination and extinction rate...
Preprint
Full-text available
The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsample...
Article
Cheilostomata is the most diverse and ecologically dominant order of bryozoans living today. We apply a Bayesian framework to estimate macroevolutionary rates of cheilostomes since the Late Jurassic across four datasets: (I) manually curated genus ranges; (II) published text-mined genus ranges; (III) non-revised Paleobiology Database (PBDB) records...
Preprint
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Open vegetation today constitutes one of the most extensive biomes on earth, including temperate grasslands and tropical savannas. Yet these biomes originated relatively recently in earth history, likely replacing forested habitats as recently as the second half of the Cenozoic, although the timing of their origination and the dynamics of their exp...
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Aim Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (www.bio-dem.surge.sh), an open-source software to explore the relationsh...
Preprint
Full-text available
Aim: The global Red List (RL) from the International Union for the Conservation of Nature is the most comprehensive global quantification of extinction risk, and widely used in applied conservation as well as in biogeographic and ecological research. Yet, due to the time-consuming assessment process, the RL is biased taxonomically and geographicall...
Article
The construction and destruction of mountain belts exert a first-order control in ecosystems by creating bridges and barriers for populations, modifying river-drainage networks and local and regional climate patterns. Several questions including How climate and tectonics control topographic growth and decay and what is the thermal and geological re...
Article
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The Cretaceous–Paleogene mass extinction event 66 million years ago eradicated three quarters of marine and terrestrial species globally. However, previous studies based on vertebrates suggest that freshwater biota were much less affected. Here we assemble a time series of European freshwater gastropod species occurrences and inferred extinction ra...
Preprint
Full-text available
Over a million species face extinction, carrying with them untold options for food, medicine, fibre, shelter, ecological resilience, aesthetic and cultural values. There is therefore an urgent need to design conservation policies that maximise the protection of biodiversity and its contributions to people, within the constraints of limited budgets....
Preprint
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In a recent paper we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. App...
Article
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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 domina...
Article
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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 re...
Article
Full-text available
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 exclusive mechanisms may explain t...
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The origins and development of the arid and highly seasonal steppe-desert biome in Central Asia, the largest of its kind in the world, remain largely unconstrained by existing records. It is unclear how Cenozoic climatic, geological, and biological forces, acting at diverse spatial and temporal scales, shaped Central Asian ecosystems through time....
Article
Full-text available
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...
Article
Full-text available
The scarcity of high-resolution empirical data directly tracking diversity over time limits our understanding of speciation and extinction dynamics and the drivers of rate changes. Here, we analyze a continuous species-level fossil record of endemic diatoms from ancient Lake Ohrid, along with environmental and climate indicator time series since la...
Article
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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 have changed...
Article
Full-text available
IUCN Red List assessments are essential for prioritizing conservation needs but are resource‐intensive and therefore only available for a fraction of global species richness. Automated conservation assessments based on digitally available geographic occurrence records can be a rapid alternative, but it is unclear how reliable these assessments are....
Article
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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, or functional...
Article
Full-text available
Current phylogenetic comparative methods modelling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after...
Article
1. Evolutionary forces affect the distribution of phenotypes both within and among species. Yet, at the macro‐evolutionary scale, the evolution of intraspecific variance is rarely considered. Here, we present an R and a BEAST 2 implementation that extends the JIVE (Joint inter‐ and Intraspecific Variance Evolution) model aimed at the analysis of co...
Preprint
When, how, and why does culture change over time? Sociological theory and mechanisms to explain cultural change are underdeveloped. This study links contemporary sociological theories of culture to a burgeoning cultural evolution literature emerging across other social sciences. By shifting our analytical focus from social actors to cultural repres...
Preprint
Full-text available
IUCN Red List assessments are essential for prioritizing conservation needs but are resource-intensive and therefore only available for a fraction of global species richness. Tropical plant species are particularly under-represented on the IUCN Red List. Automated conservation assessments based on digitally available geographic occurrence records c...
Preprint
Full-text available
Deep Bayesian neural networks (BNNs) are a powerful tool, though computationally demanding, to perform parameter estimation while jointly estimating uncertainty around predictions. BNNs are typically implemented using arbitrary normal-distributed prior distributions on the model parameters. Here, we explore the effects of different prior distributi...
Preprint
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Identifying species with disproportionate contributions to biodiversity can lead to effective conservation prioritisation. Despite well-established methods for identifying endangered species adding inordinately to evolutionary diversity, in this context functional diversity has been overlooked. Here, we compare different metrics designed to identif...
Article
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Marine megafauna, the largest animals in the oceans, serve key roles in ecosystem functioning. Yet, one-third of these animals are at risk of extinction. To better understand the potential consequences of megafaunal loss, here we quantify their current functional diversity, predict future changes under different extinction scenarios, and introduce...
Article
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Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly...
Article
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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 carnivores over the last four m...
Preprint
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Background: Understanding why species go extinct has become a major goal of evolutionary biology. Recent studies have suggested that both species traits and rates of evolution might predict extinction probability in a changing world. Here, we tested whether species conservation status correlates with recent rates of niche evolution within their lin...
Preprint
Full-text available
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 socio-economic v...
Article
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Questions about the evolution of material culture are widespread in the humanities and social sciences. Statistical modeling of long-term changes in material culture is less common due to a lack of appropriate frameworks. Our goal is to close this gap and provide robust statistical methods for examining changes in the diversity of material culture....
Article
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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 one’s researc...
Preprint
Full-text available
Georeferenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a limiting factor that could severely affect usefulness of such data for understanding species diversity and distributions. In particular, differences in sampling intensity ac...
Preprint
Full-text available
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...
Preprint
Full-text available
RaxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0-beta, a complete rewrite of the GUI, which replaces raxmlGUI and seamlessly integrates RAxML binaries for all major operating systems providing an intuitive graphical fro...
Article
Full-text available
Background and aims: The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogene...
Preprint
Full-text available
Current phylogenetic comparative methods modeling quantitative trait evolution generally assume that, during speciation, phenotypes are inherited identically between the two daughter species. This, however, neglects the fact that species consist of a set of individuals, each bearing its own trait value. Indeed, because descendent populations after...
Article
Full-text available
The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the only direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time....
Article
Full-text available
The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta', which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the...
Article
Species interactions lie at the heart of many theories of macroevolution, from adaptive radiation to the Red Queen. Although some theories describe the imprint that interactions will have over long time scales, we are still missing a comprehensive understanding of the effects of interactions on macroevolution. Current research shows strong evidence...
Article
Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Co...