Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.

Details

Ressource 1Download: BIB_B79937CF9331.P001.pdf (1792.67 [Ko])
State: Public
Version: author
Serval ID
serval:BIB_B79937CF9331
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.
Journal
Systematic Biology
Author(s)
Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N.
ISSN
1076-836X (Electronic)
ISSN-L
1063-5157
Publication state
Published
Issued date
2014
Volume
63
Number
3
Pages
349-367
Language
english
Abstract
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
Keywords
BDMCMC, biodiversity trends, Birth-death process, incomplete fossil sampling, macroevolution, species rise and fall
Pubmed
Web of science
Open Access
Yes
Create date
23/05/2014 8:46
Last modification date
20/08/2019 15:25
Usage data