After alignment, ambiguous regions (i.e. containing gaps and/or poorly aligned) were removed with GBLOCKS (v0.91b) using the following parameters: minimum length of a block after gap cleaning of 10, no gap positions were allowed in the final alignment, all segments with contiguous non-conserved positions bigger than 8 were rejected and minimum number of sequences for a flank position: 85%.
After alignment, ambiguous regions (i.e. containing gaps and/or are poorly aligned) were removed with Gblocks (v0.91b, [ 39]) using the following parameters: minimum length of a block after gap cleaning = 10; no gap positions were allowed in the final alignment; all segments with contiguous nonconserved positions bigger than 8 were rejected; minimum number of sequences for a flank position = 85%.
Minimum length of a block after gap cleaning was set at 10; no gap positions were allowed in the final alignment.
Parameters used were the following: matches allow no gap, a minimum length of 40 nucleotides and no more than one mismatch.
For a sub-pattern P', which is derived by deleting one block of length c from P in between two inter-block gaps of lengths a and b and of relative flexibilities f a and f b respectively, the maximum length of the resultant new inter-block gap equals to a×(1 + f a) + b×(1 + f b) + c, and the minimum length of the resultant inter-block gap equals a×(1 - f a) + b×(1 - f b) + c.
Protein alignments were then parsed to remove poorly aligned regions using the Gblocks algorithm [45] with the following criteria; maximum number of contiguous non-conserved positions = 10, minimum length of a block = 5, gap positions allowed in all sequences.
Parameters used were: minimum number of sequences for a conserved position = 41, minimum number of sequences for a flank position: 41, maximum number of contiguous non-conserved positions: 8, minimum length of a block: 10, allowed gap positions: with half, use similarity matrix: yes.
We used the following settings for the 50 species dataset: minimum number for a conserved position: 26; minimum number for a flank position: 26; maximum number of non-conserved positions: 8; minimum length of a block: 10; allowed gap positions: with half.
Ambiguously aligned positions in both mt tRNA and rRNA gene alignments were excluded with Gblocks v.0.19b [ 56] using the following settings: minimum number of sequences for a conserved position 31, minimum number of sequences for a flanking position 36, maximum number of contiguous non-conserved positions 5, minimum length of a block 10, allowed gap positions with half.
For the large dataset non-conserved sites were excluded from likelihood analyses making use of the Gblocks software [ 52], with the following parameter settings: minimum number of sequences for a conserved position: 55; minimum number of sequences for a flanking position: 55; maximum number of contiguous nonconserved positions: 8; minimum length of a block: 10; allowed gap positions: with half.
