Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Fig 2
Building the backbone-and-patch Mammalia phylogenies.
(a) Schematic overview of DNA sequence gathering from NCBI, taxonomic matchup, iterative error checking, and estimating a global ML tree from the resulting supermatrix (31 genes by 4,098 species [49]). Patch phylogenies were then delimited, estimated using Bayesian inference [50], and joined to fossil-calibrated backbone trees (node- or tip-dated). The resulting posterior samples of 10,000 fully dated phylogenies either had the global ML tree topology constrained (completed trees of 5,911 species, “TopoCons”) or no topology constraints (DNA-only trees, “TopoFree”). (b, c) Comparison of results from the time-calibrated backbones as pruned to the 28 patch clade representatives. The tip-dated analysis uses fossil taxa as extinct tips in the tree (left side) and then pruned (right side), whereas the node-dated approach uses exponential priors from minimum to soft-max ages. Trees are maximum clade credibility summaries of 10,000 trees. Circles at nodes indicate PP values according to the legend. (d) Topological and age uncertainty in the backbones included the unresolved base of Placentalia, which slightly favors the Atlantogenata hypothesis (blue) versus Exafroplacentalia (red; shown for the node-dated backbone). (e) Bayesian phylogenies of 28 patch clades were separately estimated in relative-time units for rescaling to representative divergence times on the backbone. Combining sets of backbones and patch clades yielded four posterior distributions for analysis. Dryad data: https://doi.org/10.5061/dryad.tb03d03; phylogeny subsets: http://vertlife.org/phylosubsets. Carbonif., Carboniferous; Cisu., Cisuralian; FBD, fossilized birth–death; Guad., Guadalupian; Lopi., Lopingian; Marsup., Marsupialia; mis-ID, misidentification; Miss., Mississippian; ML, maximum-likelihood; Monotr., Monotremata; NCBI, National Center for Biotechnology Information; Nioge., Neogene; PASTIS, Phylogenetic Assembly with Soft Taxonomic Inferences; Penn., Pennsylvanian; PP, posterior probability; RAxML, Randomized Axelerated Maximum Likelihood. Artwork from phylopic.org and open source fonts (see S1 Text, section 9 for detailed credits).