Silvestro lab publications

Recent peer-reviewed articles by members of the group (names in bold font). 




Neubauer T A, Harzhauser M, Hartman J H, Silvestro D, Scotese C R, Czaja A, Vermeij G J, Wilke T. Short-term paleogeographic reorganizations and climate events shaped diversification of North American freshwater gastropods over deep time. Scientific Reports, doi: 0.1038/s41598-022-19759-4.


Andermann T, Strömberg C A E, Antonelli A, Silvestro D. The origin and evolution of open habitats in North America inferred by deep learning models.  Nature Communications, doi: 10.1038/s41467-022-32300-5.


Sutherland J, Silvestro D, Benton M Global diversity dynamics in the fossil record are regionally heterogeneousNature Communications, doi: 10.1038/s41467-022-30507-0.


Andermann T, Antonelli A, Barrett R L, Silvestro D. Estimating alpha, beta, and gamma diversity through deep learningFrontiers in Plant Science, doi: 10.3389/fpls.2022.839407.


Calió M F, Thode V A, Bacon C D, Silvestro D, Antonelli A, Lohmann L G. Spatiotemporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions. Journal of Biogeography, doi: 10.1111/jbi.14368.


Silva S V, Andermann T, Zizka A, Kozlowski G, Silvestro D. Global estimation and mapping of the conservation status of tree species using artificial intelligence. Frontiers in Plant Science, doi: 10.3389/fpls.2022.839792 .


Hauffe T, Quental T B, Pires M M, Silvestro D. A quantitative framework to infer the ef- fect of traits, diversity and environment on dispersal and extinction rates from fossils. Methods in Ecology Evolution, doi: 10.1111/2041-210X.13845.


Sun Y, Züst T, Silvestro D, Erb M, Bossdorf O, Mateo P, Robert C, Muller-Scharer H. Climate warming can reduce biocontrol efficacy and promote plant invasion due to both genetic and transient metabolomic changes. Ecology Letters, doi: 10.1111/ele.14000.


Hoorn C, Palazzesi L, Silvestro D. Exploring the impact of Andean uplift and cli- mate on life evolution and landscape modification: From Amazonia to Patagonia. Global Planetary Change, doi: 10.1016/j.gloplacha.2022.103759.


Silvestro D, Goria S, Sterner T, Antonelli A. Improving biodiversity protection through artificial intelligence. Nature Sustainability, doi: 10.1038/s41893-022-00851-6.


Pino K, Vallejos-Garrido P, Espinoza-Aravena N, Cooper R B, Silvestro D, Hernán- dez C E, Rodríguez-Serrano E. Regional landscape change triggered by Andean up- lift: the extinction of Sparassodonta (Mammalia, Metatheria) in South AmericaGlobal Planetary Change, doi: 10.1016/j.gloplacha.2022.103758.


Neubauer T A, Hauffe T, Silvestro D, Scotese C R, Stelbrink B, Albrecht C, Delicado D, Harzhauser M, Wilke. Drivers of diversification in freshwater gastropods vary over deep timeProceedings Royal Society B, doi: 10.1098/rspb.2021.2057.






Zizka A, Andermann T, Silvestro D. IUCNN - deep learningapproaches to approximate species extinction risk. Diversity and Distributions doi : 10.1111/ddi.1345 


Moharrek F, Taylor P D, Silvestro D, Jenkins H L, Gordon D P and Waeschenbach A. Diversification dynamics of cheilostome Bryozoa based on a Bayesian analysis of the fossil record. Palaeontology, doi: 10.1111/pala.12586.


Zizka A, Ryden O, Edler D, Klein J, Aronsson H, Perrigo A, Silvestro D, Jagers S C, Lindberg S I, Antonelli A. Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and spaceJournal of Biogeography, doi: 10.1111/jbi.14256.



Zizka A, Ryden O, Edler D, Klein J, Aronsson H, Perrigo A, Silvestro D, Jagers S C, Lindberg S I, Antonelli A. Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space. Journal of Biogeography, doi: 10.1111/jbi.14256.


Zapata S, Zapata-Henao M, Cardona A, Jaramillo C, Silvestro D, Oboh-Ikuenobe F. Long-term topographic growth and decay constrained by 3D thermo-kinematic modeling: Tectonic evolution of the Antioquia Altiplano, Northern Andes. Global Planetary Change, doi: 10.1016/j.gloplacha.2021.103553.


Zhang Q, R H Ree, Salamin N, Xing Y, Silvestro D. Fossil-informed models reveal a Boreotropical origin and divergent evolutionary trajectories in the walnut family (Juglandaceae). Systematic Biology, doi: 10.1093/sysbio/syab030. 


Neubauer T, Hauffe T, Silvestro D, Schauer J, Kadolsky D, Wesselingh F, Harzhauser M, and Wilke T. Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinctionCommunications Earth & Environment, doi: 10.1038/s43247-021-00167-x


Carvalho M, Jaramillo C, de la Parra F, Caballero-Rodríguez D, Herrera F, Wing S, Turner B L, D'Apolito C, Romero-Báez M, Narváez P, Martínez C, Gutierrez M, Labandeira C, Bayona G, Rueda M, Paez-Reyes M, Cárdenas D, Duque A, Crowley J L, Santos C, Silvestro D. Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests. Science, doi: 10.1126/science.abf1969.


Silvestro D, Bacon C D, Ding W, Zhang Q, Donoghue P C J, Antonelli A, Xing Y. Fossil data support a pre-Cretaceous origin of flowering plants; Nature Ecology & Evolution, doi: 10.1038/s41559-020-01387-8. Press release


Andermann T, Faurby S, Cooke R, Silvestro D, Antonelli A. iucn_sim: a new program to simulate future extinctions based on IUCN threat status; Ecography, doi: 10.1111/ecog.05110.






Carrillo, J. D., Faurby, S., Silvestro, D, Zizka A, Jaramillo C, Bacon, C D, Antonelli, A. Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic InterchangeProceedings of the National Academy of Sciences USA, doi: 10.1073/pnas.2009397117. Press coverageNew York Times


 Zizka A, Silvestro D, Vitt P, Knight T M. Automated conservation assessment of the orchid family with deep learning; Conservation Biology, doi:10.1111/cobi.13616.


Andermann T,  Faurby S, Turvey S T, Antonelli A, Silvestro D. The past and future human impact on mammalian diversityScience Advances, doi: 10.1126/sciadv.abb2313. Press coverageBBC RTS (in French)


Edler D., Klein J., Antonelli A., Silvestro D. raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML; Methods in Ecology and Evolution, doi: 10.1111/2041-210X.13512.


Duchen P, Alfaro M L, Rolland J, Salamin N, Silvestro D. On the effect of asymmetrical trait inheritance on models of trait evolution; Systematic Biology, doi: 10.1093/sysbio/syaa055.


Bennett D J, Hettling H, Silvestro D, Vos R, Antonelli A. outsider: Install and run programs, outside of R, inside of R; The Journal of Open Source Software, doi: 10.21105/joss.02038.


Pimiento C, Leprieur F, Silvestro D, Lefcheck J, Albouy C, Rasher D B , Davis M, Svenning J-C, Gr ifn J N. Functional diversity and the fate of marine megafauna in the Anthropocene. Science Advances, doi: 10.1126/sciadv.aay7650.


Faurby S, Silvestro D, Werdelin L, Antonelli A. Brain expansion in early hominins predicts carnivore extinctions in East Africa. Ecology Letters, doi: 10.1111/ele.13451.


Gjesfjeld E, Silvestro D, Chang J, Koch B, Foster J G, Alfaro M E. A quantitative wor kow for modeling diversication in material culture. PLOS One, doi: 10.1371/journal.pone.0227579






Silvestro D, Castiglione, S; Mondanaro A, Serio C, Melchionna M, Piras P, Di Febbraro M, Carotenuto F, Rook L, Raia P (2019). A 450 million years long latitudinal gradient in age-dependent extinction; Ecology Letters, doi: 10.1111/ele.13441.


Harmon L J, Andreazzi C S, Debarre F, Drury J, Goldberg E E, Martins A B, Melian C J, Narwani A, Nuismer S L, Pennell M W, Rudman S M, Seehausen O, Silvestro D, Weber M, Matthews B. Detecting the Macroevolutionary Signal of Species Interactions. Journal of Evolutionary Biology, doi: 10.1111/jeb.13477

Meyer X, Dib L, Silvestro D, Salamin N. Simultaneous Bayesian inference of phylogeny and molecular coevolution. PNAS, doi: 10.1073/pnas.1813836116.


Silvestro D, Antonelli A, Salamin S, Meyer X (2019). Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework; Paleobiology, doi: 10.1017/pab.2019.23.


Zizka A, Silvestro D, Andermann T, Azevedo J, Ritter C D, Farooq H, Herdean A, Ariza M, Scharn R, Svateson S, Wenström N, Zizka V, Antonelli A. Coordinate- Cleaner: standardized cleaning of geographic occurrence records from biological collection databases. Methods in Ecology and Evolution, doi: 10.1111/2041-210X.13152.




Silvestro D, Warnock R C M, Gavryushkina A, Stadler T (2018). Closing the gap between palaeontological and neontological speciation and extinction rate estimates; Nature Communications, doi: 10.1038/s41467-018-07622-y