Inferring Branch-Specific Rates of Lineage Diversification Under the Birth-Death-Shift Process.

Sebastian Höhna, William A Freyman, Zachary Nolen, John P Huelsenbeck, Michael R May, Bruce Rannala, Brian R Moore

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Article in Systematic biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Habitat-specific temporal variation in the pace of fish diversification.Proceedings of the National Academy of Sciences of the United States of America · 2026
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5 · Who and what money

Authors and funding

7 authors.

Sebastian HöhnaDepartment of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.ORCID 0000-0001-6519-6292

William A FreymanDepartment of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.

Zachary NolenDepartment of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden.ORCID 0000-0001-8146-8016

John P HuelsenbeckDepartment of Integrative Biology, University of California, Berkeley, 3060 VLSB #3140, Berkeley, CA 94720-3140, USA.

Michael R MayDepartment of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA.

Bruce RannalaDepartment of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA.

Brian R MooreDepartment of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA.

Funding

Deutsche Forschungsgemeinschaft 6201/1-1European Union 101043187National Science Foundation DBI-1356737National Science Foundation DBI-1759909National Science Foundation DEB-0842181National Science Foundation DEB-0919529National Science Foundation DEB-1457835National Science Foundation DEB-1655478

6 · The paper itself

Abstract

Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here, we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification rates may vary across both extant and extinct and unsampled lineages. We estimate the parameters of this model in a Bayesian statistical framework from phylogenies of exclusively extant lineages. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical primates data set, which reveal that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a statistically coherent model.

Indexed as

ClassificationGenetic SpeciationModels, BiologicalPhylogenyAnimalsBayes TheoremComputer SimulationPrimatesBirth–death processlineage-diversification ratesphylogenyRevBayes

Identifiers

PMID41578966

DOI10.1093/sysbio/syag003

PMCPMC13445636

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