DOI: 10.5061/dryad.tb03d03
title: Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

description: 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.
description: <b>S1
 Data. </b><b>Details of the DNA cleaning steps and updated
 master taxonomy of mammals used in this study.</b> Three multi-tab
 Excel files, including the per-gene sampling in the final supermatrix,
 initial gene lengths, NCBI accession numbers, and the authors of each
 sequence. (ZIP) <b>S2 Data.
 </b><b>Per-gene DNA alignments for 31 genes and gene tree
 outputs from RAxML.</b> Includes PDF plots of each gene tree along
 with the newick tree file and the DNA alignments in phylip format.
 (ZIP) <b>S3 Data.
 </b><b>Global ML tree for 4098 species of mammals built from
 the 31-gene supermatrix. </b>Includes the full 31-gene supermatrix
 alignment, taxonomy file, newick tree file and PDF plotting of global
 RAxML tree, and R code for dividing the tree into patch clade segments for
 scaffolding the subsequent Bayesian analyses. (ZIP)
 <b>S4
 Data. </b><b>Results of 28 patch clade phylogenies delimited
 across Mammalia.</b> Maximum clade credibility (MCC) trees for each
 of the patch clade runs, both as nexus and PDF plots, and details of the
 species and gene sampling in each patch clade.
 (ZIP) <b>S5 Data.
 </b><b>Results and run files for backbone divergence-time
 analyses in MrBayes.</b> Maximum clade credibility (MCC) trees for
 each of the three backbone dating analyses in nexus format, as well as the
 run files and details of taxon sampling and node constraints.
 (ZIP) <strong>**Additional files** [not
 referenced in the main text due to large file
 sizes]:</strong> <b>S6 Data. Patch clade run
 files for MrBayes with constraints constructed using PASTIS.</b>
 Nexus files ready for execution, both for the DNA-only patches (‘freeOut’)
 and the completed patches (‘cons’), as well as the other input files used
 by the PASTIS R package for forming the topological constraints to place
 DNA-missing species within given taxa. (ZIP) <b>S7 Data.
 </b><b>Credible tree sets of Mammalia species-level
 evolutionary history.</b> Four credible sets of 10,000 trees each
 are provided for the DNA-only and completed data sets and the node- and
 tip-dated backbones. Also provided are the maximum clade credibility (MCC)
 trees for the DNA-only data sets in PDF and newick formats, and the
 species-level tip DR calculations summarized across 10,000 completed trees
 (note that MCC trees and tip DR calculations only make sense for the
 DNA-only and completed data sets, respectively).
 (ZIP) <b>S8 Data.
 </b><b>Plotting code and corresponding data for all
 figures.</b> The R code, source data, and intermediate files are
 provided for each figure in the main text and supplement to promote re-use
 of these resources.  This file will be updated
 at https://github.com/n8upham/MamPhy_v1
 (ZIP)