?Funeral for the Flying Primate Hypothesis:
 
 

John Allman, Bob Martin and Todd Preuss, three authorities in primate evolution, recently pronounced the hypothesis dead, or at least "severely disabled". Since the revealed basis for these opinions did not seem to take into account the full range of evidence, I thought it worthwhile to draw attention to the key issues that appear to have been overlooked by each of these experts.

  Molecular Evidence: Bob Martin (Nature 399:426,1999) thinks that the "molecular evidence now overwhelmingly indicates that bats are monophyletic".

Check:  The reader can check out the validity of this pronouncement by referring to my summary of the available molecular evidence.

Vote Tally or Consideration?  There are about one dozen sequence studies of the bat problem. A simple-minded tally of votes for and against would perhaps give a slim majority to bat monophyly (see Table)........ but note that there are large inconsistencies.

12SrDNA Now Supportive of Diphyly: To take one glaring example, parts of the 12SrDNA gene have been sequenced 4 times in separate pursuits of the answer to the bat problem.   3 studies support bat monophyly, while the latest study, with around 10 times as much data as the other 3 put together, splits megabats from microbats! Does one give a vote to each study? Or does one pay more attention to the study with the largest data set?

Perhaps Bob is doing the democratic thing and giving a vote each to the small studies, but one would need to justify how it is possible to ignore the much larger data set when it more satisfactorily deals with deep branches in the mammalian tree..... as well as splitting the bats.

All these inconsistencies and paradoxes are part of the current realisation that phylogenies based on DNA sequencing are not trouble-free, expecially for genomes with biases, like the bat genomes.

Base Biases: In fact, the field is still waiting for an answer to the challenge that the molecular data on bats are so far completely corrupted by base compositional biases (Pettigrew 1994). The confident assertion that bats are monophyletic on the basis of molecular data can be placed on the same rank as the similar statements made about Dictyostelium and Amphioxus, two well-studied taxa recently placed in unlikely phylogenies by much more extensive DNA sequence data than has ever been brought to bear on the bat problem.

Can you imagine how a biologist would react to an arrogant assertion, based on DNA sequence data, that the lancelet, Amphioxus was not a cephalochordate, or that the eucaryoye slime mould Dictyostelium is really a procaryote?!?

These aberrant phylogenies, created with high confidence limits and exhaustive bootstrapping by computer reconstructions of massive DNA data sets, could only be corrected by attention to particular biases in the DNA data sets.
  In the case of Dictyostelium, a eucaryote slime mould with around 100Kb of DNA sequence data available , DNA "overwhelmingly" indicates that it is not a eucaryote at all, instead linking it to the base of the "tree of life" with procaryotes!! A closer look,..... translation of the DNA codons into amino acid sequence, ........and other adjustments,        resulted in Dictyostelium moving 4-5 nodes "up" the phylogeny toward the yeasts where it "belongs". In this case the anomalous position can be attributed largely to this slime mould's extreme base compositional bias (85% A+T), that links it spuriously to other taxa with similar biases (see Loomis in Pettigrew 1994).
 

In the case of Amphioxus, the chordate lancelet, DNA data place it unambiguously outside both cephalochordates and echinoderms, a crazy result that is nevertheless "overwhelmingly" supported by the sequence data. The anomalous result is not a product of deficient data.
  Amphioxus can be placed satisfactorily on the molecular phylogeny, next to its chordate cousins, but only if the misleading signal in the sequence data is dealt with (see Naylor GJP & Brown WM Syst. Biol. 47, 61-77 1998). The problem is that the DNA data have the power positively to mislead, because adaptive evolution creates DNA similarities that are not the result of shared ancestry, just like the convergences that are well known at the morphological level.
  Michael Lee (see Lee, M. TREE 14, 177-178 1999).has put this case eloquently in print, succour to my wounded soul following the Science editorial,( complete with derisory cartoon,) that mocked my suggestion of adaptive evolution in DNA as an explanation for AT-biased microbat-megabat DNA similarities

Back to bats: All megabats have an extreme base compositional bias in their DNA (they have the highest A+T content of any vertebrate DNA!) and so do many microbats (certainly most microbat taxa so far used for DNA sequence studies....the latest 12SrDNA study used the microbat Myotis, which lacks an extreme A+T bias, perhaps explaining the differences from previous studies of bats with this gene).  So all that the sequence studies so far show is that both kinds of bats have an A+T bias in their DNA !
  Since this fact was already well-known before DNA sequencing came along, it does not make me very popular to point it out! Nevertheless, I am not aware of any study on the bat problem that has yet solved this problem. Certainly no sequence data have appeared on the bat problem that deal adequately with base composition bias. DNA-DNA hybridisation studies that have taken A+T bias into account have emphasised how serious this problem is. Taken at face value, the molecular data presently split the microbats into two groups........ hardly a triumph for monophyly! (see papers with Kirsch below)
  It remains to be shown whether high A+T was independently acquired in microbat DNA ........ .as well as megabat DNA ..........or whether each kind of bat acquired the bias from a common flying ancestor, as monophyly predicts. The fact that a number of microbats do not have A+T biases (?connected to torpor and different metabolism) is hard to reconcile with a common origin, as is the frequent independent evolution of large A+T biases in diverse, unrelated taxa.
 
 

?Conflicting Evidence from the Midbrain: Allman (Evolving Brains, Sci. Amer. 1999) and Preuss do not seem to be so swayed by the molecular evidence as by the apparently conflicting findings in the midbrain of two different megabats (flying foxes or "fruit bats"), Pteropus and Rousettus. In Pteropus there is a clear decussation in retino-tectal pathway to the midbrain..a primate characteristic, found unexpectedly in a megabat, that was the impetus for the last decade's resurgence of interest in the old primate-bat connection first raised by Linnaeus. In contrast to the two studies showing a clear midbrain decussation with a variety of techniques in Pteropus (Pettigrew 1986, Rosa and Schmid 1992), a study in Rousettus, a smaller cave-roosting species, appeared to show the primitive pattern, without a primatelike decussation (Thiele et al ).
  There are a number of ways to deal with this discrepancy:-

1. Look at the global picture rather than rely exclusively on this character to make a decision. There are many other primate characters that have been found in megabats. The original hypothesis stimulated a large number of studies that found primate similarities in megabats (LGN, hippocampus, motor pathways, reproductive system, eye, serum proteins..see Pettigrew 1995)

2. Methodological Difficulties: Rosa and Schmid (1992) offer a technical explanation for the discrepancy. Thiele et al placed Rousettus in the frame with the long axis of the skull horizontal, an orientation that places the visual axis looking up at a large angle. In flying foxes the normal orientation of the snout during flight is tipped downwards at 40-50 deg.
  This orientation during mapping may have resulted in an exploration of the far inferior field where the decussation is both hard to define and misleadingly shifted. Even an anthropoid primate is hard to diagnose from the retinotectal decussation if one uses only the far inferior field, setting aside the fact that "lower" primates have fuzzier decussations, so we would expect a possible primate sister taxon like a flying fox to be even fuzzier still.
 

3. Rousettus may be genuinely different, having lost some of its visual specialisations perhaps as a result of its cavernicolous habits. Most megabats roost in the open. Rousettus has a number of apparently derived features such as cave roosting and tongue-clicking echolocation that have sometimes led to a questionable association of this megabat with microbats, which latter are very often cave roosting and all of which echolocate (by laryngeal sonar instead of tongue-clicking).
 

  Whichever view one adopts on the question of Rousettus' apparent lack of a primate-like midbrain, it seems premature to dismiss a hypothesis that has generated so much interest and new studies.
 

  In conclusion it is worth noting that the "flying primate" hypothesis spans many current areas of controversy and tumult:- phylogenetic reconstruction using different data sets; the use of brain for phylogenetic reconstruction; misleading signals from base composition and non-polar amino acids in molecular phylogeny; the problem of distinguishing convergence from shared ancestry.
  Given the intense interest in the flying primate hypothesis, and its clear stimulating effect on the generation of new studies, it seems premature to cast the hypothesis aside based on evidence from methodologies that are themselves in tumult.
 
 

  Social Aspects of the Flying Primate Controversy: It is curious how passionate scientists become over phylogeny, especially when one considers that phylogenetic hypotheses can never be verified in the usual experimental ways. The passion rises further when the phylogeny concerns our own twig......the primates!
 There have been vigorous "punch-ups" in the past over a possible primate-flying fox connection, long before I came along and stirred up the American Museum of Natural History (NY) on this subject. Linnaeus obviously thought that there was something in it, perhaps because he examined a flying fox rather than a microbat before he put bats in his Order Primates. In the nineteenth century Leche and Winge had a heated debate, and in the 1970s, James Dale Smith took on the" bat monophyly establishment", winning plenty of scientific points but finally losing out in the complex US scientific social scene where open discussion of this topic is often constrained or biased (I was told of a meeting where a striking detailed resemblance of primate and flying fox laryngeal structure was described, with the microbat larynx apparently completely different, . But, according to the author, this was "not up for discussion"!)

  I think that the social scientific aspects of the flying primate debate would make a wonderful PhD topic for someone interested in the sociology of science, irrespective of the rights and wrongs of the proponents on each side.

 An Anecdote about Bob Martin: Since Bob has gone out of his way to pour cold water on "flying primates" using some biased and fragmentary and biased DNA sequence data (until the recent study that splits the bats, only about 10Kb of DNA sequence data, spread across 7 studies), I thought that it would be appropriate to provide some evidence gleaned from Bob's Right hemisphere (which, as Damasio showed, often gets the correct answer quite a long while before the Left hemisphere knows how to put it into words!).
  I first met Bob in 1986, soon after the flying primate idea was published. Bob told me that he had gone straightway to the British Museum and asked the late John Hill to show him a flying fox skull. I knew John Hill, having spent plenty of time in the Museum measuring bat wings and X-raying bat feet. John told me that he gave Bob a large, mature male flying fox skull (Pteropus), and John verified Bob's account.
  Bob was so staggered by the lemur-like similarity of the flying fox skull that he felt a bit weak on his feet and had to sit down.
  The strong post-orbital bar and the general configuration of the skull and jaw are very lemur-like, at first glance. Upon consideration, a good student soon realises that the flying fox's cranium is smaller than the lemur's (although few would easily see this without the lemur skull also being present for comparision). In addition, if the ventral side is turned up there is a "dead giveaway" in that the flying fox has no complete osseus bulla. The few boney fragments in the largely cartilaginous structure of the flying fox bulla tend to be lost in preparation.
  The smaller cranium and less-developed bulla are both features that one might expect from a less-advanced primate sister taxon.
  Bob did publish this remarkable primate similarity of the flying fox skull in Nature. In fact, the cranial features are one of the reasons why John Hill was always a proponent of the flying primate idea, even though he was reluctant to take up the cudgels on its behalf, being a quiet and gentle man. Bob's initial emotional reaction to the fact is perhaps worth recording, to contrast with the more abstract analyses by others that have tried to argue in exactly the opposite direction (that flying fox skulls are not like primates but are like microbats, an argument I was never able to understand, given the strange, elaborate and unique cranial features of microbats). Bob never argued against the cranial similarity, arguing instead for convergent evolution between primates and flying foxes as a result of their shared life-style in the trees.
  I think that there are too many shared similarities, in systems quite separate from the visual system, to be accounted for by convergent evolution of flying foxes and primates. Nor is there any plausible reason to account for all these similarities, in contrast to the special demands of flight that can account for the detailed similarities between microbats and flying foxes. Virtually all the noteable similarities between microbats and flying foxes can be linked to flight, whereas there is no single explanation for the shared primate-flying fox features. The two kinds of bats show dramatic differences (see the list of over 50 such differences in( Pettigrew 1995) in all systems that have been studied except for those connected to flight (even the hooked milk teeth shared by both kinds of baby bats are arguably linked to the inverted posture that comes with flight, a point-of-view that is supported by significant differences in the detailed structure of the barbs and hooks in microbat and megabat milk teeth.

"Quantitative" Brain Characters Support Bat Monophyly, .......but Primate Polyphyly!

Lapointe F-J, Baron G and Legendre P 1999 Brain Behav. Evol. 54: 119-126
Encephalisation, adaptation and evolution of Chiroptera: A statistical analysis with further evidence of bat monophyly.

This is a puzzling paper. The authors expect the reader to take the conclusions about bat monophyly seriously when their own tools were unable to unite the primates!

Given the evidence linking megabats to primates, it would be a realistic expectation that any method addressing the bat problem would make a reasonable fist of the primates, whose monophyly has never been questioned, but which are scattered all over the trees put forward in this paper.

How could they make any statments about monophyly of bats when their own data show that they were incapable of making a monophyletic group out of smaller subsets of taxa?
For example, they triumphantly join the megabats and microbats together in a single tree.....then one has a closer look to find that this same tree also contains scattered primates!

Taken literally, the results would have us believe that flight originated only once, but that there were a number of cases of "fallen angels" where a winged primate lost is flight powers! This is a poetic scenario that won me lots of correspondence from literati when I first put it forward in 1989 for the sake of discussion only.....but this is the first time that it forms the implicit key to a serious discussion about bat origins.

Lapointe's group has previously shown good examples of convergence in overall brain dimensions of different bats, particularly the frugivorous phyllostomids and pteropodids (megabats) that no bat researcher thinks are closely related. In other words, the quantitative traits used do not enable one to make the distinction between the brain of a phyllostomid microbat and that of a megabat. Yet examination of the thalamus or the pyramidal tract or hippocampus or brainstem auditory nuclei (qualitative characters in the terminology of this group) enables this distinction easily to be made. My colleagues and I find it quite extraordinary that this group has so much trouble distinguishing microbat brains from megabat brains when there are are so many obvious points of dissimilarity (e.g. the position of the rhinal fissure is sufficient to distinguish most of them at the gross morphological level, microbats having the primitive insectivore arrangement with the fissure exposed on the dorsal surface to separate neo- from archi-cortex,.......compared with the "tucked under" rhinal fissure of the megabat brain which is dominated by neocortex)..

It appears that the size of brain parts can shift around according to ecology (as shown by this group), while qualitative new features, such as LGN lamination, zonation of the hippocampus, decussation of the retinotectal fibres and the pyramidal tract  etc. may provide a better guide to phylogeny. At least the latter characters can succesfully order all primates together, as well as subdividing them into accepted groupings (with the exception of the controversial Tarsius) as I have shown in my papers.
 
 

Megabats, Fruit Bats or Flying Foxes? Elsewhere I have expressed my unhappiness for the ambiguous term "fruit bat". Bob Martin insists on using this term, and an Internet search under "fruit bat" will show how popular it is. Such a search will also reveal my objection to this loose term.....it makes no distinction between the group of Neotropical microbats who eat fruit (as well as other kinds of food) and the whole megachiroteran sub-Order (flying foxes, megabats, flughundes etc), all of whom are exclusively phytophagous (i.e. eating plant material.....flowers, pollen and fruit). If bats are monophyletic, one might say that it does not matter to confuse some phyllostomid fruit bats in the Neotropics with their distant megachiropteran relatives in Africa. But it is precisely this kind of confusion that has held up any real progress in the difficult problem of sorting out the relationships of the bats. A common example of this is to link microbats and megabats together using Rousettus, a small cave-roosting megabat (flying fox, ?fruit bat) because it echolocates in a primitive way using tongue-clicking. The important fact that this kind of echolocation is completely different from the sophisticated laryngeal, frequency-modulated sonar of microbats, and certainly evolved quite independently, gets lost in such crude comparisons. Likewise, I think that it is not helpful to muddy the distinction between New World phyllostomid bats that eat fruit and the Old World megabats, particularly when megabats are not well known from life in the US. The eyes of microbats, even the phyllostomid fruit bats, as well as their visual brains, are small compared with all megabats. For this reason it is often a surprise when a student of bats handles his/her first megabat and is "looked in the eye" by it. We are often bound by the limitations of language...so I would urge that we use precise terms where possible. Of course, I can also see that counter-revolutionaries, resisting moves to split the bats, might welcome any terms, such as "fruit bats", that blur the distinction between microbats and megabats.