In reply to the comments of Professor Pettigrew, the paraphyly of micro-bats is indeed assumed to be correct in our paper. This arrangement is supported by numerous independent genetic studies from across the globe. Analyses that account for potential compositional biases have not altered the result, and other independent molecular evidence supporting microbat paraphyly cannot be confounded by such biases, such as the15 bp deletion in BRCA1 and the 7 bp deletion in PLCB4 that unites all the Yangochiroptera (PNAS, 2002, 99:1431–1436) or chromosome banding patterns that support Yinpterochiroptera (Chromosome Research, 2007, 15:257–267).

In our paper we constrained the tree topology in order to measure rates of substitution long each branch, however, the unconstrained FoxP2 gene tree (which we did not show but which can be seen following the link below) also supports microbat paraphyly and the Yinpterochiroptera-Yangochiroptera division, in line with other recent genetic papers. It is therefore our view that the amino acids in FoxP2 that are shared between the echolocating bats are almost certainly derived. In terms of derived amino acids, there is no more support for the traditional arrangement of bats than for the revised one.

Professor Pettigrew warns against the recognition of Yinpterochiroptera on the basis that there is not a “single character from outside DNA that supports a link between rhinolophoids and mega-bats”. We agree this is frustrating but perhaps not that strange. A more extreme case is seen in the Afrotheria, where overwhelming DNA evidence (including strong data from SINEs) has united morphologically distinct taxa such as golden moles, tenrecs and elephants. Recognition of the Afrotheria has led to the rejection the old group Insectivora, thus revealing previously diagnostic traits as convergent. Yet only in the past year has an unambiguous morphological synapomorphy been offered for afrotherians. Flight in bats means that they are subject to greater physical and evolutionary constraint in body plan than afrotherians, so perhaps it’s not so surprising that morphological synapomorphies for yinpterochiropterans that exclude yangochiropterans will be even harder to find.

The suggestion that the ancient origin of bats could account for the comparatively high variation in FoxP2 in bats, rather than accelerated evolution, does not make sense to us. Although bats are very old, their radiation is still predated by that of the main mammalian lineages, and bats show more variation than between members of different super clades of mammals.

Steve Rossiter


link to gene tree:
http://www.plosone.org/at...