Model Selection in Phylogenetics

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Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification (2012, background): “Although it has been noted that barcode variation within species is generally low (Ward 2009; Hebert et al. 2010), it is not clear whether simple measures could systematically bias results by underestimating change (Sullivan & Joyce 2005).”
Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. (2010, methodology): “Recent advances in model-based phylogenetics have suggested that it is often preferable to apply partition-specific rate models instead of using a single gamma distribution to describe the heterogeneity of the substitution process across multiple-gene regions and codon positions (Sullivan and Joyce ”
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA (2006, background): “Posada & Buckley (2004) and Sullivan & Joyce (2005) discuss the need for models in science and phylogenetics, review the properties of molecular evolutionary models, and/or compare and contrast methods of model selection.”