Data from: Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root

Multiple unlinked genetic loci often provide a more comprehensive picture
of evolutionary history than any single gene can, but analyzing multigene
data presents particular challenges. Differing rates and patterns of
nucleotide substitution, combined with the limited information available
in any data set, can make it difficult to specify a model of evolution. In
addition, conflict among loci can be the result of real differences in
evolutionary process or of stochastic variance and errors in
reconstruction. We used 6 presumably unlinked nuclear loci to investigate
relationships within the mammalian family Tupaiidae (Scandentia),
containing all but one of the extant tupaiid genera. We used a
phylogenetic mixture model to analyze the concatenated data and compared
this with results using partitioned models. We found that more complex
models were not necessarily preferred under tests using Bayes factors and
that model complexity affected both tree length and parameter variance. We
also compared the results of single-gene and multigene analyses and used
splits networks to analyze the source and degree of conflict among genes.
Networks can show specific relationships that are inconsistent with each
other; these conflicting and minority relationships, which are implicitly
ignored or collapsed by traditional consensus methods, can be useful in
identifying the underlying causes of topological uncertainty. In our data,
conflict is concentrated around particular relationships, not widespread
throughout the tree. This pattern is further clarified by considering
conflict surrounding the root separately from conflict within the ingroup.
Uncertainty in rooting may be because of the apparent evolutionary
distance separating these genera and our outgroup, the tupaiid genus
Dendrogale. Unlike a previous mitochondrial study, these nuclear data
strongly suggest that the genus Tupaia is not monophyletic with respect to
the monotypic Urogale, even when uncertainty about rooting is taken into
account. These data concur with mitochondrial DNA on other relationships,
including the close affinity of Tupaia tana with the enigmatic Tupaia
splendidula and of Tupaia belangeri with Tupaia glis. We also discuss the
taxonomic and biogeographic implications of these results.