Accounting for gene rate heterogeneity in phylogenetic inference.
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Syst Biol 56 (2): 194--205 (July 2007)

Traditionally, phylogenetic analyses over many genes combine data into a contiguous block. Under this concatenated model, all genes are assumed to evolve at the same rate. However, it is clear that genes evolve at very different rates and that accounting for this rate heterogeneity is important if we are to accurately infer phylogenies from heterogeneous multigene data sets. There remain open questions regarding how best to incorporate gene rate parameters into phylogenetic models and which properties of real data correlate with improved fit over the concatenated model. In this study, two methods of accounting for gene rate heterogeneity are compared: the n-parameter method, which allows for each of the n gene partitions to have a gene rate parameter, and the alpha-parameter method, which fits a distribution to the gene rates. Results demonstrate that the n-parameter method is both computationally faster and in general provides a better fit over the concatenated model than the alpha-parameter method. Furthermore, improved model fit over the concatenated model is highly correlated with the presence of a gene with a slow relative rate of evolution.
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