Inferring the mammal tree

Explore thenew mammal tree of life!

Hosted here on OneZoom is the consensus tree of 5,911 species of mammals, reconstructed using probabilistic inference of molecular and fossil data for the first time (see full comparison to previous methods here ).

Movies of the credible sets of Mammalia trees (sample of 100 trees each of 10,000 total)

Shown is the evolutionary uncertainty propagated into each credible set of trees, consisting of both age and topological variation. The gray bars on the right show the location of the 1813 imputed species (i.e., those missing DNA sequences, of 5911 species total).

Citation: Upham, N. S., J. A. Esselstyn, and W. Jetz. 2019. Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology. https://doi.org/10.1371/journal.pbio.3000494

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 ~6000 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: (i) backbone relationships and ages among major lineages, using fossil node- or tip-dating; and (ii) species-level ‘patch’ phylogenies with non-overlapping 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 (i) node ages are broadly concordant among studies, and (ii) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous ‘supertree’ approaches where 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.

Supplementary files:

• Dryad of full data: https://doi.org/10.5061/dryad.tb03d03

• Taxonomic subsetting and download of mammal trees: http://verlife.org/phylosubsets

• All code for running analyses and plotting figures: https://github.com/n8upham/MamPhy_v1

• MCC consensus trees of the DNA-only distributions:

  – Node-dated exponential, 4098 species, backbone estimated with 17 node calibrations:pdf file (150 inches long); Nexus file

  – Fossilized birth-death, 4098 species + 76 fossil tips, backbone topology as in Zhou et al. (2013):pdf file (150 inches long); Nexus file

• FOR DISPLAY ONLY: MCC consensus trees of the completed trees. Note that completed trees are inappropriate for consensus analysis , since they contain DNA-missing species that randomly vary in topological position within taxonomic constraints (genus or family) across the credible set of trees. Thus, any single tree is not a meaningful representation of the unknown phylogenetic placement of these imputed species. Fig 1 in our paper is an example of plotting the MCC completed tree for display purposes. See the “Recommended uses” section of our PLOS Biology article for more discussion of this topic.

  – Node-dated exponential, 5911 species, backbone estimated with 17 node calibrations: Nexus file

  – Fossilized birth-death, 5911 species + 76 fossil tips, backbone topology as in Zhou et al. (2013): Nexus file