Daniele Silvestro

• Two major ecological shifts shaped 60 million years of ungulate faunal evolution

  Fernando Blanco, Ignacio A. Lazagabaster, Oscar Sanisidro, Faysal Bibi, Nicola S. Heckeberg, Maria Rios, Bastien Mennecart, Maria Teresa Alberdi, Jose Luis Prado, Juha Saarinen, Daniele Silvestro, Johannes Mueller, Joaquin Calatayud, Juan L. Cantalapiedra
  NATURE COMMUNICATIONS - 2025
• The stepwise rise of angiosperm-dominated terrestrial ecosystems

  Wenna Ding, Daniele Silvestro, Renske E. Onstein, Mengxiao Wu, Zhekun Zhou, Yaowu Xing
  BIOLOGICAL REVIEWS - 2025
• Eco-Evolutionary Dynamics of Plant-Soil Feedbacks Explain the Spread Potential of a Plant Invader Under Climate Warming and Biocontrol Herbivory

  Yan Sun, Daniele Silvestro, Gregor H. Mathes, Marcel G. A. van Der Heijden, Heinz Muller-Scharer
  GLOBAL CHANGE BIOLOGY - 2025
• Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation

  Daniele Silvestro, Thibault Latrille, Nicolas Salamin
  SYSTEMATIC BIOLOGY - 2024
• DeepDive: estimating global biodiversity patterns through time using deep learning

  Rebecca B. Cooper, Joseph T. Flannery-Sutherland, Daniele Silvestro
  Nature Communications - 2024
• Benchmarking imputation methods for categorical biological data

  Matthieu Gendre, Torsten Hauffe, Catalina Pimiento, Daniele Silvestro
  METHODS IN ECOLOGY AND EVOLUTION - 2024
• Plant diversity darkspots for global collection priorities

  Ian Ondo, Kiran L. Dhanjal-Adams, Samuel Pironon, Daniele Silvestro, Matheus Colli-Silva, Victor Deklerck, Olwen M. Grace, Alexandre K. Monro, Nicky Nicolson, Barnaby Walker, Alexandre Antonelli
  NEW PHYTOLOGIST - 2024
• Reliable biogeography requires fossils: insights from a new species-level phylogeny of extinct and living carnivores

  Sören Faurby, Daniele Silvestro, Lars Werdelin, Alexandre Antonelli
  PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES - 2024
• Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks

  Torsten Hauffe, Juan L. Cantalapiedra, Daniele Silvestro
  SCIENCE ADVANCES - 2024
• Challenges in estimating species' age from phylogenetic trees

  Carlos Calderon del Cid, Torsten Hauffe, Juan D. Carrillo, Michael R. May, Rachel C. M. Warnock, Daniele Silvestro
  GLOBAL ECOLOGY AND BIOGEOGRAPHY - 2024
• The Clade Replacement Theory: a framework to study age-dependent extinction

  Carlos Calderon del Cid, Fabricio Villalobos, Ricardo Dobrovolski, Juan D. Carrillo, Daniele Silvestro, Bruno Vilela
  JOURNAL OF EVOLUTIONARY BIOLOGY - 2024
• Heterogeneous selectivity and morphological evolution of marine clades during the Permian-Triassic mass extinction

  Xiaokang Liu, Haijun Song, Daoliang Chu, Xu Dai, Fengyu Wang, Daniele Silvestro
  NATURE ECOLOGY & EVOLUTION - 2024
• Two Major Extinction Events in the Evolutionary History of Turtles: One Caused by an Asteroid, the Other by Hominins

  Anieli G. Pereira, Alexandre Antonelli, Daniele Silvestro, Sören Faurby
  AMERICAN NATURALIST - 2024
• The evolutionary history of the Central Asian steppe-desert taxon Nitraria (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data

  A. Woutersen, P. E. Jardine, Daniele Silvestro, R. G. Bogota-Angel, H. X. Zhang, N. Meijer, J. Bouchal, N. Barbolini, G. Dupont-Nivet, A. Koutsodendris, Alexandre Antonelli, C. Hoorn
  Botanical Journal of the Linnean Society - 2023
• Functional diversity of sharks and rays is highly vulnerable and supported by unique species and locations worldwide

  Catalina Pimiento, Camille Albouy, Daniele Silvestro, Theophile L. Mouton, Laure Velez, David Mouillot, Aaron B. Judah, John N. Griffin, Fabien Leprieur
  NATURE COMMUNICATIONS - 2023
• Light, rather than circadian rhythm, regulates gas exchange in ferns and lycophytes

  D. Aros-Mualin, C. R. Guadagno, Daniele Silvestro, M. Kessler
  Plant Physiology - 2023
• Patterns and drivers of heat production in the plant genus Amorphophallus

  C. Claudel, O. Loiseau, Daniele Silvestro, S. Lev-Yadun, Alexandre Antonelli
  Plant Journal - 2023
• Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae)

  F. Belluardo, A. J. Munoz-Pajares, A. Miralles, Daniele Silvestro, W. Cocca, F. M. Ratsoavina, A. Villa, S. H. Roberts, M. Mezzasalma, A. Zizka, Alexandre Antonelli, A. Crottini
  Molecular Phylogenetics and Evolution - 2023
• GDGT distribution in tropical soils and its potential as a terrestrial paleothermometer revealed by Bayesian deep-learning models

  C. Häggi, B. D. A. Naafs, Daniele Silvestro, Jr. Bertassoli, T. K. Akabane, V. R. Mendes, A. O. Sawakuchi, C. M. Chiessi, C. A. Jaramillo, S. J. Feakins
  Geochimica Et Cosmochimica Acta - 2023
• A timescale for placental mammal diversification based on Bayesian modeling of the fossil record

  E. Carlisle, C. M. Janis, D. Pisani, P. C. J. Donoghue, Daniele Silvestro
  Current Biology - 2023
• Conceptual and empirical bridges between micro- and macroevolution

  J. Rolland, L. F. Henao-Diaz, M. Doebeli, R. Germain, L. J. Harmon, L. L. Knowles, L. H. Liow, J. E. Mank, A. Machac, S. P. Otto, M. Pennell, N. Salamin, Daniele Silvestro, M. Sugawara, J. Uyeda, C. E. Wagner, D. Schluter
  Nature Ecology and Evolution - 2023
• Dollo meets Bergmann: morphological evolution in secondary aquatic mammals

  B. M. Farina, Sören Faurby, Daniele Silvestro
  Proceedings of the Royal Society B-Biological Sciences - 2023
• Machine learning enhances prediction of plants as potential sources of antimalarials

  A. Richard-Bollans, C. Aitken, Alexandre Antonelli, C. Bitencourt, D. Goyder, E. Lucas, I. Ondo, O. A. Perez-Escobar, S. Pironon, J. E. Richardson, D. Russell, Daniele Silvestro, C. W. Wright, M. J. R. Howes
  Frontiers in Plant Science - 2023
• Stratigraphy of a middle Miocene neotropical Lagerstatte (La Venta Site, Colombia)

  L. Mora-Rojas, A. Cardenas, C. Jaramillo, Daniele Silvestro, G. Bayona, S. Zapata, F. Moreno, C. Silva, J. W. Moreno-Bernal, J. S. Jaramillo, V. Valencia, M. Ibanez
  Geodiversitas - 2023
• Dwarfism and gigantism drive human-mediated extinctions on islands

  R. Rozzi, M. V. Lomolino, A. A. E. van der Geer, Daniele Silvestro, S. K. Lyons, P. Bover, J. A. Alcover, A. Benitez-Lopez, C. H. Tsai, M. Fujita, M. O. Kubo, J. Ochoa, M. E. Scarborough, S. T. Turvey, A. Zizka, J. M. Chase
  Science - 2023
• A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils

  T. Hauffe, M. M. Pires, T. B. Quental, T. Wilke, Daniele Silvestro
  Methods in Ecology and Evolution - 2022
• Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

  Alexandre Antonelli, R. J. Smith, Allison L. Perrigo, A. Crottini, J. Hackel, Weston L. Testo, Harith Farooq, Maria Fernanda Torres Jimenez, N. Andela, Tobias Andermann, A. M. Andriamanohera, S. Andriambololonera, S. P. Bachman, Christine D. Bacon, W. J. Baker, F. Belluardo, C. Birkinshaw, J. S. Borrell, S. Cable, N. A. Canales, J. D. Carrillo, R. Clegg, C. Clubbe, Robert S. Cooke, Gabriel Damasco, S. Dhanda, Daniel Edler, Sören Faurby, Paola De Lima Ferreira, B. L. Fisher, F. Forest, L. M. Gardiner, S. M. Goodman, O. M. Grace, T. B. Guedes, M. C. Henniges, R. Hill, C. E. R. Lehmann, II Lowry, L. Marline, P. Matos-Maraví, J. Moat, B. Neves, M. G. C. Nogueira, R. E. Onstein, A. S. T. Papadopulos, O. A. Perez-Escobar, L. N. Phelps, P. B. Phillipson, S. Pironon, N. A. S. Przelomska, M. Rabarimanarivo, D. Rabehevitra, J. Raharimampionona, M. T. Rajaonah, F. Rajaonary, L. R. Rajaovelona, M. Rakotoarinivo, A. A. Rakotoarisoa, S. E. Rakotoarisoa, H. N. Rakotomalala, F. Rakotonasolo, B. A. Ralaiveloarisoa, M. Ramirez-Herranz, J. E. N. Randriamamonjy, T. Randriamboavonjy, V. Randrianasolo, A. Rasolohery, A. N. Ratsifandrihamanana, N. Ravololomanana, V. Razafiniary, H. Razanajatovo, E. Razanatsoa, M. Rivers, F. Sayol, Daniele Silvestro, M. S. Vorontsova, K. Walker, B. E. Walker, P. Wilkin, J. Williams, T. Ziegler, A. Zizka, H. Ralimanana
  Science - 2022
• Madagascar’s extraordinary biodiversity: Threats and opportunities

  H. Ralimanana, Allison L. Perrigo, R. J. Smith, J. S. Borrell, Sören Faurby, M. T. Rajaonah, T. Randriamboavonjy, M. S. Vorontsova, Robert S. Cooke, L. N. Phelps, F. Sayol, N. Andela, Tobias Andermann, A. M. Andriamanohera, S. Andriambololonera, S. P. Bachman, Christine D. Bacon, W. J. Baker, F. Belluardo, C. Birkinshaw, S. Cable, N. A. Canales, J. D. Carrillo, R. Clegg, C. Clubbe, A. Crottini, Gabriel Damasco, S. Dhanda, Daniel Edler, Harith Farooq, Paola De Lima Ferreira, B. L. Fisher, F. Forest, L. M. Gardiner, S. M. Goodman, O. M. Grace, T. B. Guedes, J. Hackel, M. C. Henniges, R. Hill, C. E. R. Lehmann, II Lowry, L. Marline, P. Matos-Maraví, J. Moat, B. Neves, M. G. C. Nogueira, R. E. Onstein, A. S. T. Papadopulos, O. A. Perez-Escobar, P. B. Phillipson, S. Pironon, N. A. S. Przelomska, M. Rabarimanarivo, D. Rabehevitra, J. Raharimampionona, F. Rajaonary, L. R. Rajaovelona, M. Rakotoarinivo, A. A. Rakotoarisoa, S. E. Rakotoarisoa, H. N. Rakotomalala, F. Rakotonasolo, B. A. Ralaiveloarisoa, M. Ramirez-Herranz, J. E. N. Randriamamonjy, V. Randrianasolo, A. Rasolohery, A. N. Ratsifandrihamanana, N. Ravololomanana, V. Razafiniary, H. Razanajatovo, E. Razanatsoa, M. Rivers, Daniele Silvestro, Weston L. Testo, Maria Fernanda Torres Jimenez, K. Walker, B. E. Walker, P. Wilkin, J. Williams, T. Ziegler, A. Zizka, Alexandre Antonelli
  Science - 2022
• The origin and evolution of open habitats in North America inferred by Bayesian deep learning models

  Tobias Andermann, C. A. E. Strömberg, Alexandre Antonelli, Daniele Silvestro
  Nature Communications - 2022
• Climate warming can reduce biocontrol efficacy and promote plant invasion due to both genetic and transient metabolomic changes

  Yan Sun, Tobias Züst, Daniele Silvestro, Matthias Erb, Oliver Bossdorf, Pierre Mateo, Christelle Robert, Heinz Müller-Schärer
  Ecology Letters - 2022
• Regional landscape change triggered by Andean uplift: The extinction of Sparassodonta (Mammalia, Metatheria) in South America

  K. Pino, P. Vallejos-Garrido, N. Espinoza-Aravena, R. B. Cooper, Daniele Silvestro, C. E. Hernández, E. Rodríguez-Serrano
  Global and Planetary Change - 2022
• Drivers of diversification in freshwater gastropods vary over deep time

  Thomas A. Neubauer, Torsten Hauffe, Daniele Silvestro, Christopher R. Scotese, Björn Stelbrink, Christian Albrecht, Diana Delicado, Mathias Harzhauser, Thomas Wilke
  Proceedings of the Royal Society B: Biological Sciences - 2022
• Diversification dynamics of cheilostome bryozoans based on a Bayesian analysis of the fossil record

  Farideh Moharrek, Paul D. Taylor, Daniele Silvestro, Helen L. Jenkins, Dennis P. Gordon, Andrea Waeschenbach
  Palaeontology - 2022
• The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

  Christine D. Bacon, Daniele Silvestro, C. Hoorn, G. Bogota-Angel, Alexandre Antonelli, Nicolas Chazot
  Biology Letters - 2022
• Integrating machine learning, remote sensing and citizen science to create an early warning system for biodiversity

  Alexandre Antonelli, K. L. Dhanjal-Adams, Daniele Silvestro
  Plants People Planet - 2022
• Global diversity dynamics in the fossil record are regionally heterogeneous

  J. T. Flannery-Sutherland, Daniele Silvestro, M. J. Benton
  Nature Communications - 2022
• Spatio-temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions

  Maria Fernanda Calió, V. A. Thode, Christine D. Bacon, Daniele Silvestro, Alexandre Antonelli, L. G. Lohmann
  Journal of Biogeography - 2022
• Improving biodiversity protection through artificial intelligence

  Daniele Silvestro, Stefano Goria, Thomas Sterner, Alexandre Antonelli
  Nature Sustainibility - 2022
• Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time

  T. A. Neubauer, M. Harzhauser, J. H. Hartman, Daniele Silvestro, C. R. Scotese, A. Czaja, G. J. Vermeij, T. Wilke
  Scientific Reports - 2022
• Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence

  S. V. Silva, Tobias Andermann, A. Zizka, G. Kozlowski, Daniele Silvestro
  Frontiers in Plant Science - 2022
• Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning

  Tobias Andermann, Alexandre Antonelli, R. L. Barrett, Daniele Silvestro
  Frontiers in Plant Science - 2022
• Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests

  M. R. Carvalho, C. Jaramillo, F. de la Parra, D. Caballero-Rodriguez, F. Herrera, S. Wing, B. L. Turner, C. D'Apolito, M. Romero-Baez, P. Narvaez, C. Martinez, M. Gutierrez, C. Labandeira, G. Bayona, M. Rueda, M. Paez-Reyes, D. Cardenas, A. Duque, J. L. Crowley, C. Santos, Daniele Silvestro
  Science - 2021
• Long-term topographic growth and decay constrained by 3D thermo-kinematic modeling: Tectonic evolution of the Antioquia Altiplano, Northern Andes

  S. Zapata, M. Zapata-Henao, A. Cardona, C. Jaramillo, Daniele Silvestro, F. Oboh-Ikuenobe
  Global and Planetary Change - 2021
• raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML

  D. Edler, J. Klein, Alexandre Antonelli, Daniele Silvestro
  Methods in Ecology and Evolution - 2021
• sampbias, a method for quantifying geographic sampling biases in species distribution data

  A. Zizka, Alexandre Antonelli, Daniele Silvestro
  Ecography - 2021
• Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space

  A. Zizka, Oskar Rydén, Daniel Edler, Johannes Klein, Allison L. Perrigo, Daniele Silvestro, Sverker C. Jagers, Staffan I. Lindberg, Alexandre Antonelli
  Journal of Biogeography - 2021
• Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction

  T. A. Neubauer, T. Hauffe, Daniele Silvestro, J. Schauer, D. Kadolsky, F. P. Wesselingh, M. Harzhauser, T. Wilke
  Communications Earth & Environment - 2021
• Fossil data support a pre-Cretaceous origin of flowering plants

  Daniele Silvestro, Christine D. Bacon, W. N. Ding, Q. Y. Zhang, P. C. J. Donoghue, Alexandre Antonelli, Y. W. Xing
  Nature Ecology & Evolution - 2021
• iucn_sim: a new program to simulate future extinctions based on IUCN threat status

  Tobias Andermann, Sören Faurby, Robert S. Cooke, Daniele Silvestro, Alexandre Antonelli
  Ecography - 2021
• Automated conservation assessment of the orchid family with deep learning

  A. Zizka, Daniele Silvestro, P. Vitt, T. M. Knight
  Conservation Biology - 2021

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