Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

Silvestro, Daniele; Zizka, Alexander; Bacon, Christine D.; Cascales‐Miñana, Borja; Salamin, Nicolas; Antonelli, Alexandre

doi:10.1098/rstb.2015.0225

Cited by 53 publications

(63 citation statements)

References 69 publications

(155 reference statements)

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“…[32,33]). The past decade or so has also witnessed the merging of two fields to develop the new discipline of phylogenetic community ecology [34][35][36] along with the emergence of conservation palaeobiology [37], the rise of palaeobiogeography ( [38] and see [39]) and the recognition of the importance of biodiversity time series [9] and palaeo(macro)ecology. This issue builds upon these efforts, highlighting the importance of integrating the dynamic nature of environmental, biological and geological processes through time and thus necessitating the synthesis of many of these individual fields.…”

Section: Introductionmentioning

confidence: 99%

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

Price

Schmitz

2016

Phil. Trans. R. Soc. B

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One contribution of 11 to a theme issue 'The regulators of biodiversity in deep time'. Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart.

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Section: Introductionmentioning

confidence: 99%

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

Price

Schmitz

2016

Phil. Trans. R. Soc. B

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“…A major problem with most methods that use extant data only is the fact that ancestral geographical ranges inferred from phylogenies might be blind to local past extinction and temporal changes in the asymmetry of dispersal rates. Silvestro et al [97] applied their method to a genus-level empirical dataset of Cenozoic terrestrial plants. Their empirical results suggest a predominant dispersal from Eurasia to North America in the Eocene climatic cooling period, but a higher dispersal from North America to Eurasia during the more stable climatic period between 32 and 14 Ma.…”

Section: The Regulators and Their Signaturesmentioning

confidence: 99%

“…The preservational biases of the fossil record are exacerbated when variations through space and time require analytical attention. In this volume, Silvestro et al [97] develop flexible new dispersal-extinction approaches that use fossil data to infer macroevolutionary and biogeographic processes while taking into account the incompleteness (temporal and spatial) of the fossil record [98,99]. The impact of migration is not symmetric [97,100], implying a role for biotic interactions among already existing species and the new invaders in determining macroevolutionary fates.…”

Section: The Regulators and Their Signaturesmentioning

confidence: 99%

“…In this volume, Silvestro et al [97] develop flexible new dispersal-extinction approaches that use fossil data to infer macroevolutionary and biogeographic processes while taking into account the incompleteness (temporal and spatial) of the fossil record [98,99]. The impact of migration is not symmetric [97,100], implying a role for biotic interactions among already existing species and the new invaders in determining macroevolutionary fates. A major problem with most methods that use extant data only is the fact that ancestral geographical ranges inferred from phylogenies might be blind to local past extinction and temporal changes in the asymmetry of dispersal rates.…”

Section: The Regulators and Their Signaturesmentioning

confidence: 99%

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The challenges to inferring the regulators of biodiversity in deep time

Ezard

Quental

Benton

2016

Phil. Trans. R. Soc. B

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Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas.

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“…These numbers include not only living species but also fossil taxa, allowing for biogeographic analyses based on both sources of data (e.g., Antonelli et al 2015; Silvestro et al 2016). Species occurrence data are steadily increasing thanks to new agreements on data sharing, on-going digitalization programs, and tools that enable automated geo-referencing of older museum specimens (Guralnick et al 2006; Garcia-Milagros and Funk 2010).…”

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confidence: 99%

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution

et al. 2016

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Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years.

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Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

Cited by 53 publications

References 69 publications

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

The challenges to inferring the regulators of biodiversity in deep time

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution

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