Université de Fribourg

The rise of angiosperms pushed conifers to decline during global cooling

Condamine, Fabien L. ; Silvestro, Daniele ; Koppelhus, Eva B. ; Antonelli, Alexandre

In: Proceedings of the National Academy of Sciences, 2020, vol. 117, no. 46, p. 28867–28875

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 in the Cretaceous. It is...

Université de Fribourg

RaxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML

Edler, Daniel ; Klein, Johannes ; Antonelli, Alexandre ; Silvestro, Daniele

In: Methods in Ecology and Evolution, 2020, vol. -, no. -, p. -

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 setup and run phylogenetic analyses.Our program offers automated...

Université de Fribourg

Automated conservation assessment of the orchid family with deep learning

Zizka, Alexander ; Silvestro, Daniele ; Vitt, Pati ; Knight, Tiffany M.

In: Conservation Biology, 2020, p. cobi.13616

International Union for Conservation of Nature (IUCN) Red List assessments are essential for prioritizing conservation needs but are resource intensive and therefore available only 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...

Université de Fribourg

Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange

Carrillo, Juan D. ; Faurby, Søren ; Silvestro, Daniele ; Zizka, Alexander ; Jaramillo, Carlos ; Bacon, Christine D. ; Antonelli, and Alexandre

In: Proceedings of the National Academy of Sciences, 2020, vol. 117, no. 42, p. 26281–26287

The biological interchange between North and South America associated with the formation of the Isthmus of Panama is key to defining current gradients of species diversity. A major gap in our understanding of the interchange is its asymmetry, where mammals of North American origin attained higher diversity in South America than vice versa. The prevailing view is that this asymmetry resulted...

Université de Fribourg

Sampbias, a method for quantifying geographic sampling biases in species distribution data

Zizka, Alexander ; Antonelli, Alexandre ; Silvestro, Daniele

In: Ecography, 2020/n/a/n/a/-

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 are...

Université de Fribourg

The past and future human impact on mammalian diversity

Andermann, Tobias ; Faurby, Søren ; Turvey, Samuel T. ; Antonelli, Alexandre ; Silvestro, Daniele

In: Science Advances, 2020, vol. 6, no. 36, p. eabb2313

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 over the past 126,000 years, inferring...

Université de Fribourg

Cenozoic evolution of the steppe-desert biome in Central Asia

Barbolini, N. ; Woutersen, A. ; Dupont-Nivet, G. ; Silvestro, Daniele ; Tardif, D. ; Coster, P. M. C. ; Meijer, N. ; Chang, C. ; Zhang, H.-X. ; Licht, A. ; Rydin, C. ; Koutsodendris, A. ; Han, F. ; Rohrmann, A. ; Liu, X.-J. ; Zhang, Y. ; Donnadieu, Y. ; Fluteau, F. ; Ladant, J.-B. ; Le Hir, G. ; Hoorn, C.

In: Science Advances, 2020, vol. 6, no. 41, p. eabb8227

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. Our synthesis shows that the Central Asian...

Université de Fribourg

A multi-platform package for the analysis of intra- and interspecific trait evolution

Gaboriau, Théo ; Mendes, Fábio K. ; Joly, Simon ; Silvestro, Daniele ; Salamin, Nicolas

In: Methods in Ecology and Evolution, 2020, p. -

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 continuous trait evolution at both inter‐...