@ARTICLE{TreeBASE2Ref2175, author = {Link E. Olson and Trina E. Roberts and Eric J. Sargis}, title = {Networks, Trees, and Treeshrews: Assessing Support and Identifying Conflict with Multiple Loci and a Problematic Root.}, year = {2009}, keywords = {}, doi = {10.1093/sysbio/syp025}, url = {}, pmid = {}, journal = {Systematic Biology}, volume = {58}, number = {2}, pages = {257--270}, abstract = {Multiple unlinked genetic loci often provide a more comprehensive picture of evolutionary history than any single gene can, but analyzing multi-gene 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 six 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 to 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 multi-gene 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 mtDNA on other relationships, including the close affinity of T. tana with the enigmatic T. splendidula and of T. belangeri with T. glis. We also discuss the taxonomic and biogeographic implications of these results.} }

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