Comparison of branch lengths estimated under group-specific matrices and an overall matrix.

<p>Reduced datasets were used to investigate the impact of model-choice on branch lengths. <b>A</b>. A phylogenetic tree for 21 fish taxa. <b>B</b>. A plot showing differences between branch lengths estimated under partition-specific matrices and the mtFishR0 matrix. <b>C</b>. A plot showing the differences between the corrected branch lengths under a mixture of the partition specific matrices and mtFishR0 for the whole data. Differences between branch lengths (Bl) are measured as (Bl_<i>R_i/</i>Bl_<i>R₀</i>) – 1, where Bl_<i>R_i</i> denotes branch lengths obtained using a partition specific matrix, and Bl_<i>R₀</i> denotes branch lengths obtained using the reference matrix (mtFishR0). This measure centers the difference between branch lengths on 0, with values above 0 indicating branches that were larger under the partition-specific matrix and values below 0 indicating branches that were shorter under the partition-specific matrix. A value of zero indicates no difference between branch lengths.