The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions.
Thorough taxon sampling allows the use of more simplistic models of evolution, because multiple changes at each nucleotide site can be appropriately reconstructed through the increased sampling of the tree [ 18].
Our use of those simplistic models is for ease of illustration in a familiar context.
Interestingly, it has been demonstrated that use of such simplistic models is consistent with a decrease in 'observed' mutation rates as distance between samples increases (Calabrese and Sainudiin, 2005).
That sort of simplistic model shouldn't be our framework".
We used an extended dataset of mitochondrial protein genes to reevaluate the phylogeny of Cnidaria, paying attention to common biases in phylogenetic reconstructions resulting from insufficient taxon sampling and using more simplistic models of sequence evolution.
It was later shown in simulations and real data that this can only happen in a very limited number of cases and in general using overly simplistic models should be avoided [ 3, 7, 8].
Besides the use of a rather simplistic model, the study suffered from the use of only two parameters to represent V̇/ Qmismatching; this is a significant limitation, since gas exchange in COPD patients is often characterized by different V̇/Q patterns with two or three modes [12].
