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Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies.
Syst Biol. 2018 May 01; 67(3):458-474.SB

Abstract

The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.

Authors+Show Affiliations

Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland. Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland. Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden.Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden. Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden.Departamento de Ecologia, Universidade de São Paulo, 05508-900 São Paulo, Brazil.Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden. Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden. Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-413 19 Göteborg, Sweden.Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden. Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden. Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.

Pub Type(s)

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

Language

eng

PubMed ID

29069434

Citation

Hagen, Oskar, et al. "Estimating Age-Dependent Extinction: Contrasting Evidence From Fossils and Phylogenies." Systematic Biology, vol. 67, no. 3, 2018, pp. 458-474.
Hagen O, Andermann T, Quental TB, et al. Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Syst Biol. 2018;67(3):458-474.
Hagen, O., Andermann, T., Quental, T. B., Antonelli, A., & Silvestro, D. (2018). Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Systematic Biology, 67(3), 458-474. https://doi.org/10.1093/sysbio/syx082
Hagen O, et al. Estimating Age-Dependent Extinction: Contrasting Evidence From Fossils and Phylogenies. Syst Biol. 2018 May 1;67(3):458-474. PubMed PMID: 29069434.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. AU - Hagen,Oskar, AU - Andermann,Tobias, AU - Quental,Tiago B, AU - Antonelli,Alexandre, AU - Silvestro,Daniele, PY - 2016/12/19/received PY - 2017/10/15/accepted PY - 2017/10/27/pubmed PY - 2018/10/24/medline PY - 2017/10/26/entrez SP - 458 EP - 474 JF - Systematic biology JO - Syst Biol VL - 67 IS - 3 N2 - The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution. SN - 1076-836X UR - https://www.unboundmedicine.com/medline/citation/29069434/Estimating_Age_Dependent_Extinction:_Contrasting_Evidence_from_Fossils_and_Phylogenies_ L2 - https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syx082 DB - PRIME DP - Unbound Medicine ER -