A species-level timeline of mammal evolution integrating phylogenomic data

Sandra Álvarez-Carretero, Asif U. Tamuri, Matteo Battini, Fabrícia F. Nascimento, Emily Carlisle, Robert J. Asher, Ziheng Yang, Philip C. J. Donoghue () and Mario Reis ()
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Sandra Álvarez-Carretero: Queen Mary University of London
Asif U. Tamuri: University College London
Matteo Battini: University of Bristol
Fabrícia F. Nascimento: Imperial College London
Emily Carlisle: University of Bristol
Robert J. Asher: University of Cambridge
Ziheng Yang: University College London
Philip C. J. Donoghue: University of Bristol
Mario Reis: Queen Mary University of London

Nature, 2022, vol. 602, issue 7896, 263-267

Abstract: Abstract High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1–3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the growing number of available genomes4. In the case of mammals, molecular-clock analyses of limited datasets have produced conflicting estimates of clade ages with large uncertainties5,6, and thus the timescale of placental mammal evolution remains contentious7–10. Here we develop a Bayesian molecular-clock dating approach to estimate a timetree of 4,705 mammal species integrating information from 72 mammal genomes. We show that increasingly larger phylogenomic datasets produce diversification time estimates with progressively smaller uncertainties, facilitating precise tests of macroevolutionary hypotheses. For example, we confidently reject an explosive model of placental mammal origination in the Palaeogene8 and show that crown Placentalia originated in the Late Cretaceous with unambiguous ordinal diversification in the Palaeocene/Eocene. Our Bayesian methodology facilitates analysis of complete genomes and thousands of species within an integrated framework, making it possible to address hitherto intractable research questions on species diversifications. This approach can be used to address other contentious cases of animal and plant diversifications that require analysis of species-level phylogenomic datasets.

Date: 2022
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DOI: 10.1038/s41586-021-04341-1

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