ArticleProceedings of the National Academy of Sciences of the United States of America2023
Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Geology, climate, and competition as drivers of diversification in the neotropical palm genus Geonoma.The New phytologist · 2026Article
- Unidentifiability and false-positive inference in state-dependent diversification models.Nature communications · 2026Article
- Habitat-specific temporal variation in the pace of fish diversification.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Diversity patterns in terrestrial tetrapod clades are governed by equilibrium dynamics.PLoS biology · 2026Article
- Exploring the impact of Cenozoic climate change on diversification of the Australian endemic Eurepini crickets (Orthoptera: Gryllidae: Eneopterinae).Communications biology · 2026Article
- Detecting branching rate heterogeneity with tree balance statistics in lineage tracing trees.bioRxiv : the preprint server for biology · 2025Article
- The effects of cryptic diversity on diversification dynamics analyses in Crocodylia.Proceedings. Biological sciences · 2025Article
- Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- The Fossilized Birth-Death Model Is Identifiable.Systematic biology · 2025Article
- Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.Bioinformatics and biology insights · 2025Article
- A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics.Bulletin of mathematical biology · 2024Article
- Article
- Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies.Evolution letters · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
- No phylogenetic evidence for angiosperm mass extinction at the Cretaceous-Palaeogene (K-Pg) boundary.Biology letters · 2023Article
- Explanations for latitudinal diversity gradients must invoke rate variation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes.Ecology and evolution · 2023Article
- Alternate histories in macroevolution.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Abstract
The birth-death model is commonly used to infer speciation and extinction rates by fitting the model to phylogenetic trees with exclusively extant taxa. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth-death models that have the same likelihood is called a congruence class, and there is no statistical evidence to favor one model over the other. This issue has led researchers to question if and what patterns can reliably be inferred from phylogenies of only extant taxa and whether time-variable birth-death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios. For these empirical phylogenies, we assume that we inferred the true congruence class. Thus, our conclusions apply to any empirical phylogeny for which we robustly inferred the true congruence class. When we summarize shared patterns in the congruence class, we show that strong directional trends in speciation and extinction rates are shared among most models. Therefore, we conclude that the inference of strong directional trends is robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Interestingly, the space of valid speciation rates is narrower and more limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates.
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