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Nodes with support values below 0.95 were collapsed into polytomies and the maximally inclusive subtree was selected where all taxa were represented by no more than one sequence or, in cases where more than one sequence was present for any taxon, all sequences from that taxon formed a monophyletic clade or were part of the same polytomy.

In cases where multiple sequences from the same taxon formed a clade or were part of the same polytomy, all sequences except the longest were deleted.

A final topology was specified as a soft polytomy, with the resolution of the clade of echolocators being resolved by RAxML at runtime, with the rest of the phylogeny remaining constrained.

We therefore adopted the soft polytomy, RAxML resolved version of H as our main bat–dolphin hypothesis.