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Message: <blockquote data-quote="alytothrix" data-source="post: 2266774" data-attributes="member: 96832">The paper is discussing pairwise sequence divergence, which is different than the branches lengths found from phylogenetic methods like maximum parsimony and Bayesian inference. Phylogenetic methods use a number of taxa (a minimum of 4) to calculate trees, while distance methods just compare pairs of two sequences against each other.The p-distance referred to is simply the proportion of sites differing between two sequences. Models like the TrN+Γ model referred to in the abstract or the K2P model almost universally used in barcoding papers attempt to correct for unobserved changes between the sequences (eg. if a nucleotide changes from C->G->T, p-distance will only count one difference, even though two evolutionary events occurred). The paper seems to be arguing that selecting the correct model is important when using distances rather than assuming that p-distance or K2P are fine.</blockquote>