Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA

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Molecular phylogenetics of Vespoidea indicate paraphyly of the superfamily and novel relationships of its component families and subfamilies (2008, background): “…well appreciated, particularly when rates of evolution or depths of divergence are such that multiple substitutions at a given site may obscure phylogenetic signal and mislead the analysis (Simon et al. 1994, 2006; Swofford et al. 1996; Philippe & Laurent 1998; Steel 2005; Sullivan & Joyce 2005).”
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. (2012, background): “However, the accuracy of molecular phylogenetic inference depends on having an appropriate model of molecular evolution (Sullivan and Joyce 2005; Simon et al. 2006).”
How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research (2014, background): “While it is common to design species-specific primers for long PCR, it is not necessary and primer sets conserved at various taxonomic scales – for example, all animals (Simon et al., 2006), arthropods (Yamauchi et al.”
The influence of rate heterogeneity among sites on the time dependence of molecular rates. (2012, background): “It is well known that some positions of an alignment evolve at a substantially faster rate than others, and the impact of this among-site rate variation on phylogenetic reconstruction have been clearly demonstrated (Yang 1996; Simon et al. 2006).”