Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

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.

Feeding ecology has a stronger evolutionary influence on functional morphology than on body mass in mammals

“…The overall jaw size (i.e., the geometric mean of the linear measurements) tends to increase with greater herbivory, especially in nonrodents. Figure 3 displays frequency data for the mammalian sample and a phylogenetic tree (Upham et al 2019) with mammals classified into two dietary regimes (i.e., faunivory and herbivory). JAPr angles have a bimodal distribution that largely separates faunivores and herbivores (Fig.…”

“…To help account for the nonindependence of data due to varying levels of phylogenetic relatedness among species, I used phylogenetic comparative methods to examine the association between morphology and diet in mammals. Due to uncertainty of the topology and branch lengths of the mammalian phylogeny, I repeated all analyses for 20 species-level phylogenetic trees from Upham et al (2019). The trees were drawn randomly from the posterior distribution.…”

“…Trait numbers correspond to measurements inFigure 1andTable S2. Results are means of replicate analyses using 20 phylogenetic trees(Upham et al 2019). Phylogenetic signal is assessed using Pagel's lambda (λ).Rodent-only pANOVAs were not performed due to a dearth of faunivores in the sample.…”

Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how convergent diets obfuscate traditional morphological taxonomy

“…Given the notable teeth in serrasalmids, it is ironic that their sister taxon, unambiguously identified here as the hemiodontids, have miniscule teeth or are entirely edentulous (Roberts, 1971, 1974). At first glance, serrasalmids would appear to have more in common with their toothier distant relatives, the payaras (Cynodontidae) than hemiodontids; however, we note that our estimates for the divergence among these three clades is Paleocene-Eocene (55-81 mya),enough time for edentulism and near-edentulism to have evolved independently in both aardvarks (Afrotheria) and anteaters (Xenartha) (Upham et al, 2019).…”

A preliminary ecological profile of Kyasanur Forest disease virus hosts among the mammalian wildlife of the Western Ghats, India

“…The Western Ghats region, its biodiversity, and a phylogenetic tree of its mammalian species are presented in Figure 1. The phylogenetic tree was obtained from the VertLife project (Upham et al, 2019). A table of all listed species along with their host susceptibility status is provided in Figshare.…”