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.