The<scp>r</scp>package divDyn for quantifying diversity dynamics using fossil sampling data

Kocsis, Ádám T.; Reddin, Carl J.; Alroy, John; Kiessling, Wolfgang

doi:10.1111/2041-210x.13161

Cited by 104 publications

(106 citation statements)

References 32 publications

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“…Our final fossil dataset consisted of 5880 fossil occurrences of 170 families and 1278 genera ( Supplementary Data 2). We reconstructed the fossil records from present-day coordinates back to their palaeo-position based on the mean age of the fossil in a temporal range using the 'reconstruct' function in the 'chronosphere' package 74 .…”

Section: Methodsmentioning

confidence: 99%

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

Lin

et al. 2020

Commun Biol

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The Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.

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Section: Methodsmentioning

confidence: 99%

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

Lin

et al. 2020

Commun Biol

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“…We used the “divDyn” function implemented in divDyn ( 72 ) to obtain the sample in bin diversity for each time bin in the 100 replicates. Then, we calculated the mean diversity of the 100 replicates for each time bin.…”

Section: Methodsmentioning

confidence: 99%

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

Carrillo

Faurby

Silvestro

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain this asymmetry: 1) Higher dispersal rate of North American mammals toward the south, 2) higher origination of North American immigrants in South America, 3) higher extinction of mammals with South American origin, and 4) similar dispersal rate but a larger pool of native taxa in North versus South America. We test among these mechanisms by analyzing ∼20,000 fossil occurrences with Bayesian methods to infer dispersal and diversification rates and taxonomic selectivity of immigrants. We find no differences in the dispersal and origination rates of immigrants. In contrast, native South American mammals show higher extinction. We also find that two clades with North American origin (Carnivora and Artiodactyla) had significantly more immigrants in South America than other clades. Altogether, the asymmetry of the interchange was not due to higher origination of immigrants in South America as previously suggested, but resulted from higher extinction of native taxa in southern South America. These results from one of the greatest biological invasions highlight how biogeographic processes and biotic interactions can shape continental diversity.

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“…We analyzed the marine mammal data set under the boundary-crossing and three-timer methods, for comparison. The ages of fossil occurrences were randomized 100 times based on the respective stratigraphic intervals, and the rates were estimated across equal time bins of 2 Myr, using the R package 'divDyn' (Kocsis et al 2019).…”

Section: Empirical Case Studymentioning

confidence: 99%

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

et al. 2019

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The estimation of origination and extinction rates and their temporal variation is central to understanding diversity patterns and the evolutionary history of clades. The fossil record provides the only direct evidence of extinction and biodiversity changes through time and has long been used to infer the dynamics of diversity changes in deep time. The software PyRate implements a Bayesian framework to analyze fossil occurrence data to estimate the rates of preservation, origination, and extinction while incorporating several sources of uncertainty. Building upon this framework, we present a suite of methodological advances including more complex and realistic models of preservation and the first likelihood-based test to compare the fit across different models. Further, we develop a new reversible jump Markov chain Monte Carlo algorithm to estimate origination and extinction rates and their temporal variation, which provides more reliable results and includes an explicit estimation of the number and temporal placement of statistically significant rate changes. Finally, we implement a new C++ library that speeds up the analyses by orders of magnitude, therefore facilitating the application of the PyRate methods to large data sets. We demonstrate the new functionalities through extensive simulations and with the analysis of a large data set of Cenozoic marine mammals. We compare our analytical framework against two widely used alternative methods to infer origination and extinction rates, revealing that PyRate decisively outperforms them across a range of simulated data sets. Our analyses indicate that explicit statistical model testing, which is often neglected in fossil-based macroevolutionary analyses, is crucial to obtain accurate and robust results.

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Therpackage divDyn for quantifying diversity dynamics using fossil sampling data

Cited by 104 publications

References 32 publications

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau

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

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

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