ArticleSystematic biology2014
Bayesian estimation of speciation and extinction from incomplete fossil occurrence data.
Article in Systematic biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 216 citations in OpenAlex.
- Global patterns are key to understanding macroevolution.Communications biology · 2026Article
- Evolutionary Footprint: A Systemic Indicator in Evolution, Ecology and Conservation.Evolutionary applications · 2026Article
- The fate of South America's endemic mammalian fauna in response to the most dramatic Cenozoic climate disruption.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Diversification and extinction of Hemiptera in deep time.Communications biology · 2025Article
- Speciation completion rates have limited impact on macroevolutionary diversification.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Reading Yule in light of the history and present of macroevolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.Systematic biology · 2024Article
- Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks.Science advances · 2024Article
- Late Cretaceous ammonoids show that drivers of diversification are regionally heterogeneous.Nature communications · 2024Article
- The Angiosperm Terrestrial Revolution buffered ants against extinction.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The angiosperm radiation played a dual role in the diversification of insects and insect pollinators.Nature communications · 2024Article
- The extinct marine megafauna of the Phanerozoic.Cambridge prisms. Extinction · 2024Review
- A quantitative test of the "Ecomorphotype Hypothesis" for fossil true seals (Family Phocidae).PeerJ · 2024Article
- Drivers of the artiodactyl turnover in insular western Europe at the Eocene-Oligocene Transition.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models.bioRxiv : the preprint server for biology · 2023Article
- Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity.The New phytologist · 2023Article
- Fluctuation in the diversity of mayflies (Insecta, Ephemerida) as documented in the fossil record.Scientific reports · 2023Article
- Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction.Nature communications · 2023Article
- Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change.Scientific reports · 2022Article
- Global diversity dynamics in the fossil record are regionally heterogeneous.Nature communications · 2022Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.