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Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.
Syst Biol. 2014 May; 63(3):349-67.SB

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.

Authors+Show Affiliations

Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland;No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24510972

Citation

Silvestro, Daniele, et al. "Bayesian Estimation of Speciation and Extinction From Incomplete Fossil Occurrence Data." Systematic Biology, vol. 63, no. 3, 2014, pp. 349-67.
Silvestro D, Schnitzler J, Liow LH, et al. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst Biol. 2014;63(3):349-67.
Silvestro, D., Schnitzler, J., Liow, L. H., Antonelli, A., & Salamin, N. (2014). Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology, 63(3), 349-67. https://doi.org/10.1093/sysbio/syu006
Silvestro D, et al. Bayesian Estimation of Speciation and Extinction From Incomplete Fossil Occurrence Data. Syst Biol. 2014;63(3):349-67. PubMed PMID: 24510972.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. AU - Silvestro,Daniele, AU - Schnitzler,Jan, AU - Liow,Lee Hsiang, AU - Antonelli,Alexandre, AU - Salamin,Nicolas, Y1 - 2014/02/08/ PY - 2014/2/11/entrez PY - 2014/2/11/pubmed PY - 2014/6/15/medline SP - 349 EP - 67 JF - Systematic biology JO - Syst Biol VL - 63 IS - 3 N2 - 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. SN - 1076-836X UR - https://www.unboundmedicine.com/medline/citation/24510972/Bayesian_estimation_of_speciation_and_extinction_from_incomplete_fossil_occurrence_data_ L2 - https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syu006 DB - PRIME DP - Unbound Medicine ER -