Objections to the Flying Primate Theory:
This is a significant objection. In fact one of my Brisbane colleagues jumped ship because he felt that the megabat geniculate was too like a rodent, sitting on the dorsolateral aspect of the thalamus instead of being rotated than 100 deg outward to lie on the ventral aspect of the thalamus.
Remember that it is not a hypothesis about ³flying anthropoids². All the evidence points to a very early branch from the primate line. The megabat skull is very similar to a lemur, so similar it gave Bob Martin a shock, as I have already related. But the megabat cranium is clearly smaller than a comparable-sized lemur skull, and there is no ossified auditory bulla, two features indicating that megabats are more primitive primates than lemurs.
Labeling studies lessen the difficulties, since the lamination pattern of the megabat LGN is the same as that of primates, with, for example the ipsi and contra magnocellular layers lying externally, under the optic tract. This leaves the very much reduced rotation of the megabat LGN to deal with.
It is generally accepted that the extreme outward rotation of the primate LGN in development is brought about by the elaboration of the pulvinar and related visual thalamus. These visual nuclei, whose functions are still not well understood, lie medially to the LGN and therefore cause the LGN to rotate outward as they increase in size.
Even the doyens of primate LGN evolution such as Jon Kaas and Jon Allman would have to admit that there is a huge gap between the organization of the primate LGN and that of other mammals. The megabat visual thalamus could fill that gap with more research. For example, the details of the megabat pulvinar can be worked out, despite its much smaller size compared with the primate pulvinar. Such details could then illuminate the process of expansion and the consequent rotation of the adjacent LGN.
2. The primate pattern of retinotectal connections has evolved independently in primates and megabats (Bob Martin, John Allman).
This objection is easier to dismiss than 1. Martin and Allman are probably being misled by their bias, which is that the primate visual connections are an adaptation to predation in the ³fine branch niche². I think that this is unlikely to be correct, but even if true, it does not explain the selection pressure that would have operated to bring this about in phytophagous taxa like megabats and the colugos, both of which have the primate pattern but are not predators in the fine branch niche.
Apart from the absence of a selective explanation for independent evolution of these traits in different groups, there is the long string of derived characters shared by megabats and primates in brain (modulatory nuclei, motor system), proteins (hemoglobin, alpha-crystallin, FoxP2, serum proteins), reproduction (genital anatomy, menstrual cycle) and morphology.
One can develop a much better argument for the independent evolution of flight-related characters in megabats and microbats than for the independent evolution of a decussated retinotectal pathway in megabats and primates.
3. It is not parsimonious to postulate that flight evolved twice in mammals (Many Reviewers).
Gliding flight has evolved independently 7 different times in mammals, if we include 140 MyA Volaticotherium along with the 3 different marsupial families, the two different rodent families and the colugo. Š..not to mention gliding flight in geckoes, lizards, frogs and snakes, as well as powered flight in pterosaurs and birds. While they are not examples of true powered flight, both the colugo and Volaticotherium had a gliding membrane that enclosed the digits and so could represent the predecessor of true powered flight with a handwing like microbats and megabats. In these terms, flight is not extremely rare. The similarity of megabat and microbat wings is remarkable in dried museum skins, but does not hold in life, where the two kinds of bats have quite different wing strokes. Moreover, the handwings of both megabats and microbats can easily be separated by a single measurement of the digits, without any overlap, raising doubts that they had a common origin.
4. Molecular data show that megabats and microbats are monophyletic.
This is true only for DNA sequence data. Protein sequence data consistently split these two kinds of bats (haemoglobun, alpha-crystallin, Foxp2, opsins). An immunological study involving 26 separate monoclonal antibodies raised against serum protein epitopes not only splits megabats from microbats, but shows that megabats are the closest sister taxa to primates, with microbats far away on the tree, outside the carnivores.
Nor do the DNA data provide the strong support for monophyly that is claimed. The bootstrap support may be high, but it is based on a compositional artifact. Analysis with this possibility in mind shows that DNA places rhinolophoid microbats and megabats artificially close, at half the distance given by other methods.
5. Both morphology and molecular data support monophyly:
The recent molecular and morphological trees of bats are mutually exclusive of each other, with the megabats basal in the morphological tree but nested high in the molecular tree alongside the rhinolophoid microbats.
It is fallacious to claim support for monophyly from both data sets in this way, even if the fallacy manages to get past Nature reviewers. Two mutually exclusive propositions cannot be used to support a third thesis, since only one of them can be correct. Indeed, although they both cannot be correct, the published molecular and morphological trees could both be wrong, as they almost certainly are. The inclusion in the morphological data set of the very strong brain data (from visual pathways and from the modulatory nuclei) would remove the megabats from their position at the base of the morphological tree, an undesirable outcome apparently, given the unexplained exclusion of the brain data. Removing the megabats from the DNA tree of microbats is more complicated because of the convergent similarity of DNA sequences in megabats and rhinolophoids. Nevertheless, this removal can be accomplished quantitatively. The split of megabats from microbats and the sister relationship to primates in a DNA tree is strongly supported by molecular sequence data from proteins, which have been largely neglected in the recent studies proposing ³microbat paraphyly² but which are are less affected by the convergent DNA biases of bats.