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

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.