ArticlePLoS biology2019
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation.
Article in PLoS biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 483 papers, 4 of them syntheses that pooled it.
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Who cites it
483 citing papers in PubMed, 4 syntheses or guidelines pooled it.
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- Paramyxoviruses in Old World fruit bats (Pteropodidae): An open database and synthesis of sampling effort, viral positivity, and coevolution.PLoS neglected tropical diseases · 2025Pooled it
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- Host phylogeny and microbiome composition predict gut nematode community composition within a diverse assemblage of African herbivores.Biology letters · 2026Article
- Fossil record biases skew inferences of mammal trait evolution.Nature communications · 2026Article
- Diversification in small mammals is associated with climatic specialisation, whereas species accumulation reflects evolutionary time.Nature communications · 2026Article
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- Broadening the semiaquatic scene: Quantification of long bone microanatomy across pinnipeds.Anatomical record (Hoboken, N.J. : 2007) · 2026Article
- Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models.Molecular biology and evolution · 2026Article
423 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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