Data from: Phylogenomics uncovers confidence and conflict in the rapid radiation of Australo-Papuan rodents

The estimation of robust and accurate measures of branch support has
proven challenging in the era of phylogenomics. In datasets of potentially
millions of sites, bootstrap support for bifurcating relationships around
very short internal branches can be inappropriately inflated. Such
over-estimation of branch support may be particularly problematic in rapid
radiations, where phylogenetic signal is low and incomplete lineage
sorting severe. Here, we explore this issue by comparing various branch
support estimates under both concatenated and coalescent frameworks, in
the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini).
Using nucleotide sequence data from 1245 independent loci and several
phylogenomic inference methods, we unequivocally resolve the majority of
genus-level relationships within Hydromyini. However, at four nodes we
recover inconsistency in branch support estimates both within and among
concatenated and coalescent approaches. In most cases, concatenated
likelihood approaches using standard fast bootstrap algorithms did not
detect any uncertainty at these four nodes, regardless of partitioning
strategy. However, we found this could be overcome with two-stage
resampling, i.e. across genes and sites within genes (using -bsam GENESITE
in IQtree). In addition, low confidence at recalcitrant nodes was
recovered using UFBoot2, a recent revision to the bootstrap protocol in
IQtree, but this depended on partitioning strategy. Summary coalescent
approaches also failed to detect uncertainty under some circumstances. For
each of four recalcitrant nodes, an equivalent (or close to equivalent)
number of genes were in strong support (> 75% bootstrap) of both
the primary and at least one alternative topological hypothesis,
suggesting notable phylogenetic conflict among loci not detected using
some standard branch support metrics. Recent debate has focused on the
appropriateness of concatenated versus multi-genealogical approaches to
resolving species relationships, but less so on accurately estimating
uncertainty in large datasets. Our results demonstrate the importance of
employing multiple approaches when assessing confidence, and highlight the
need for greater attention to the development of robust measures of
uncertainty in the era of phylogenomics.