ArticleSystematic biology2022
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Macroevolutionary dynamics and predictors of tropical rain forest plant diversity.Science advances · 2026Article
- Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid-Proterozoic.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits.bioRxiv : the preprint server for biology · 2026Article
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- Exploring the impact of Cenozoic climate change on diversification of the Australian endemic Eurepini crickets (Orthoptera: Gryllidae: Eneopterinae).Communications biology · 2026Article
- Multiple bursts of speciation in Madagascar's endangered lemurs.Nature communications · 2025Article
- Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy.Science advances · 2025Article
- Diversification and extinction of Hemiptera in deep time.Communications biology · 2025Article
- Reading tree leaves: inferring speciation anfd extinction processes using phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Broad geographic dispersal is not a diversification driver for Emberizoidea.Proceedings. Biological sciences · 2025Article
- Comparative diversification analyses of Hydrangeaceae and Loasaceae reveal complex evolutionary history as species disperse out of Mesoamerica.American journal of botany · 2025Article
- Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies.Evolution letters · 2024Article
- Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner.Proceedings. Biological sciences · 2023Article
- Angiosperm phylogenetic diversity is lower in Africa than South America.Science advances · 2023Article
- The diversification of Caribbean Buxus in time and space: elevated speciation rates in lineages that accumulate nickel and spreading to other islands from Cuba in non-obligate ultramafic species.Annals of botany · 2023Article
- Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes.Ecology and evolution · 2023Article
- Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa.Ecology and evolution · 2023Article
- Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Diversification dynamics in Caribbean rain frogs (Proceedings. Biological sciences · 2023Article
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11 authors.
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Abstract
Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth-death models; extinction; phylogenetics; speciation.].
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