Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict.The phylogenetic information inherent in sequence data from different genes can be combined to yield a species phylogeny rather than gene trees. The gene data for these phylogenies are mainly collected following two strategies: (a) using only genes that provide full information, i.e., cover all taxa of interest (e.g. [1]) or (b) using all available genes that are present in some taxa and fulfill special overlap conditions (e.g. [2-4]). The latter approach is able to use many more genes and taxa, since it allows for missing data. It can also be applied for phylogeny reconstruction from expressed sequence tags (ESTs, e.g. [5]). Before the gene alignments are obtained, two important steps can influence the phylogeny result: First, orthologs must be assigned correctly (see e.g. [6,7] for method comparisons). Second, these orthologs need to be aligned with sufficient accuracy (see e.g. [8] for a review and [9] for an example of the impact of alignment accuracy on phylogeny reconstruction).After reliable alignments are obtained, different methods are available to combine the original data at different points along the way from the underlying sequences to the final tree [4,10]: First, superalig