Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families

A fundamental challenge in resolving evolutionary relationships across the
Tree of Life is to account for heterogeneity in the evolutionary signal
across loci. Studies of marsupial mammals have demonstrated that this
heterogeneity can be substantial, leaving considerable uncertainty in the
evolutionary timescale and relationships within the group. Using
simulations and a new phylogenomic data set comprising nucleotide
sequences of 1550 loci from 18 of the 22 extant marsupial families, we
demonstrate the power of a method for identifying clusters of loci that
support different phylogenetic trees. We find two distinct clusters of
loci, each providing an estimate of the species tree that matches
previously proposed resolutions of the marsupial phylogeny. We also
identify a well supported placement for the enigmatic marsupial moles
(Notoryctes) that contradicts previous molecular estimates but is
consistent with morphological evidence. The pattern of gene-tree variation
across tree-space is characterized by changes in information content, GC
content, substitution-model adequacy, and signatures of purifying
selection in the data. In a simulation study, we show that incomplete
lineage sorting can explain the division of loci into the two
tree-topology clusters, as found in our phylogenomic analysis of
marsupials. We also demonstrate the potential benefits of minimizing
uncertainty from phylogenetic conflict for molecular dating. Our analyses
reveal that Australasian marsupials appeared in the early Paleocene,
whereas the diversification of present-day families occurred primarily
during the late Eocene and early Oligocene. Our methods provide an
intuitive framework for improving the accuracy and precision of
phylogenetic inference and molecular dating using genome-scale data.