Data from: The virtues of gaps: xenarthran (edentate) monophyly supported by a unique deletion in αA-crystallin

Shared insertions or deletions (indels) in protein-coding DNA can be
strong indicators of the monophyly of a taxon. A three-amino acid deletion
had previously been noted in the eye lens protein αA-crystallin of two
species of sloths and two species of anteaters, which represent the
Pilosa, one of the two infraorders of Xenarthra (Edentata). This deletion
has not been observed in 55 species from 16 other eutherian orders, nor in
two species of marsupials and 34 non-mammalian vertebrates, from birds to
shark. At the genomic level, we have now detected this deletion in two
species of armadillos of the second xenarthran infraorder, Cingulata, as
well as in an additional species of anteater. Phylogenetic trees were
constructed from a 145-bp sequence of the αA-crystallin gene of 39
tetrapod species, supporting xenarthran monophyly with values from 86 to
90%. To quantify the additional support for xenarthran monophyly, as given
by the three-residue deletion, we computed the probabilities for the
occurrence of this deletion per evolutionary time unit for alternative
hypothetical tree topologies. In the obtained estimates, the six trees in
which the xenarthran subgroups are unresolved or paraphyletic give an
increasingly lower likelihood than the two trees which assume xenarthran
monophyly. For the monophyletic trees, the probability that the deletion
observed in the xenarthrans is due to a single event is >0.99.
Thus, this deletion in αA-crystallin gives strong molecular support for
the monophyly of this old and diverse order.