title: Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data.
abstract: Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal-extinction-sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland silvestro.daniele@gmail.com.
authors.forename: Daniele
authors.identifier: http://orcid.org/0000-0003-0100-0961
authors.initials: D
authors.lastname: Silvestro
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden.
authors.forename: Alexander
authors.initials: A
authors.lastname: Zizka
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden.
authors.forename: Christine D
authors.initials: CD
authors.lastname: Bacon
authors.affiliation: Department of Geology, University of Liege, 4000 Sart Tilman, Liege, Belgium.
authors.forename: Borja
authors.initials: B
authors.lastname: Cascales-Miñana
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
authors.affiliation: Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, Gothenburg 413 19, Sweden.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Antonelli
mesh_terms: D063147:Animal Distribution; D000818:Animals; D053476:Extinction, Biological; D005580:Fossils; D008954:Models, Biological; D058974:Phylogeography; D013997:Time Factors
keywords: biogeographic trends; dispersal; extinction; incomplete fossil sampling; macroevolution