References for Commentary on FoxP2 in Bats:

1. Li G, Wang J, Rossiter SJ, Jones G, Zhang S (2007) Accelerated FoxP2 Evolution in Echolocating Bats. PLoS ONE 2(9): e900. doi:10.1371/journal.pone.0000900

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0000900

2. Pettigrew, J.D. and Kirsch, J.A.W. (1998)  The bat problem. I. DNA-hybridisation melting curves based on DNA enriched for AT- or GC-content.  Phil. Trans. Roy. Soc. B, 353: 369-379.

3. Kirsch, J. A. W. & Pettigrew, J. D.  (1998)  Base compositional biases and the bat  problem. II.  DNA-hybridisation trees based on tracers enriched for AT- or GC- content.  Phil. Trans. Roy. Soc. B, 353: 381-388

These two papers use a technique suggested by Roy Britten to melt  DNA at different temperatures so that fractions could be obtained at a range of temperatures.  High temperatures yielded GC-rich DNA, since G &C are joined by 3 hydrogen bonds and so require higher temperatures to dissociate or melt, while lower temperatures yielded AT-rich DNA, since A&T are joined by only two hydrogen bonds and melt at a lower temperature.  Such fractions showed that there was a large error in estimating the rhinolophoid-megabat distance because these two groups of bats share the highest AT content in vertebrate DNA. This distance increased when GC-rich DNA was used, showing that uncorrected measurements of that distance were under-estimated by a large margin that would lead to an artifactual association between rhinolophoids and megabats.

4. Hutcheon, J.M., Kirsch, J.A.W., & Pettigrew, J.D. (1998) Base-compositional biases  and the bat problem. III. the question of microchiropteran monophyly Phil. Trans.  Roy. Soc. B, 353:607-617
 
This paper is often quoted in support of microbat paraphyly, even though it completely ignores the evidence from [3 &4] that the rhinolophoid-megabat affinity is an artifact of the high AT content of these two otherwise dissimilar groups of bats. This study made no effort to correct for this artifact during data collection. The late John Kirsch mischievously set this paper as a trap, to see who would be influenced more by the tree with pictured taxa in this paper than by the hard evidence for a biasing effect of high AT content from the previous two papers by the same lab.
 
5. Teeling EC, Springer MS, Madsen O, Bates P, O'brien SJ, Murphy WJ. 2005
 A molecular phylogeny for bats illuminates biogeography and the fossil record.  Science. 2005 Jan 28;307(5709):580-4.
 
6. Jones G, Teeling EC.
 The evolution of echolocation in bats. Trends Ecol Evol. 2006 Mar;21(3):149-56
 
7. Teeling EC, Madsen O, Van den Bussche RA, de Jong WW, Stanhope MJ, Springer MS.
 Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1431-6.
 
Papers 5, 6 & 7 put forward a radical new  phylogeny of bats, paraphyly, that is unsupported  by virtually every other discipline  apart from DNA sequence data. The association  of megabats and rhinolophoid microbats is put forward as fact despite the absence of any supporting evidence from other disciplines and despite the fact that the association is contradicted by molecular evidence from proteins such as serum proteins [8], hemoglobin,alpha-crystallin, etc.  It would not be possible to find any bats that are more different than megabats and rhinolophoids, so it is not surprising that morphological studies emphatically support the molecular protein data in contradicting paraphyly  (e.g. Jones KE, Purvis A, MacLarnon A, Bininda-Emonds, Simmons NB.(2002)  A phylogenetic supertree of the bats (Mammalia: Chiroptera).Biol Rev Camb Philos Soc. 77(2):223-59). The source of the error is not hard to find, since megabats and rhinolophoids have the most modified genomes of any vertebrate. Seen in the light of the isochore phenomenon, these two groups of bats will have extremely similar DNA sequences in many genes that are not otherwise protected in the H3 isochore, like FoxP2. Convergent similarity of DNA sequences is a real phenomenon, despite derisory comments to the contrary, and is an unpleasant feature that requires uusual measures to overcome it, such as the use of translated protein sequence data or innovative distance techniques. The cursory measurements of overall base composition that were used  in studies 5 & 7 would not be adequate to uncover the site -specific changes in DNA base composition underlying isochore formation.
 
8. Schreiber A Bauer D and Bauer K 1994 Mammalian evolution from serum protein epitopes Biological Journal of  the Linnaean Society51:359-376
 
This is an example of the many studies using proteins that are quite incompatible with the new paraphyly of microbats that links rhinolophoids to megabats. While not all such studies explicitly address the bat problem, it is obvious that protein sequence data from hemoglobin, alpha-crystallin, opsins, etc fail to make this anomalous linkage between the two most contrasting of any bat groups. One wonders why the protein is ignored in favour of the DNA, which is strongly biased in these two groups of bats. It is worth noting that conversion to amino acid codons can overcome DNA biases, a correction not applied in any of the DNA sequence studies that claim a paraphyletic arrangement between rhinolophoid microbats and megabats.
 
9. Frances E. Arrighi1, William Z. Lidicker Jr.2, Manley Mandel1 and Janet Bergendahl1Biochemical Genetics 6: 27-30 Heterogeneity in CsCl buoyant densities of chiropteran DNA
 
10. Sabeur G, Macaya G, Kadi F, Bernardi G   The isochore patterns of mammalian genomes and their phylogenetic implications. J Mol Evol. 1993 Aug;37(2):93-108

 
<>11. Naylor GJP, Brown WM SYSTEMATIC BIOLOGY  47: (1) 61-76 MAR 1998
Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
 
12. Loomis WF, Smith DW. 1995 Experientia.51: 1110-1115 Consensus phylogeny of Dictyostelium.
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14. Yager, David D. (1989) Audition in the praying mantis,Mantis religiosa L.: identification of an interneuron mediating ultrasonic hearing. Journal of Comparative Physiology A 165(4)
 
<> 15. L F. GÁLL  LF1 and. TIFFNEY BF 1983 Science 219: 507-509 A Fossil Noctuid Moth Egg from the Late Cretaceous of Eastern North America
 
<> 16. Pierson, ED. 1986 Molecular Systematics of the Microchiroptera: Higher taxon relations and biogeography. PhD Thesis. UC Berkeley.
 
<> 17. Summary of FoxP2 substitutions in bats.
 
 2 Pteropus            V  L
 7 Cynopterus        I V M H G G I
 6 Rhinolophus     A P A S A T
 6 Asellicus           I D P M S T
 3 Hipposideros    I T M
 9 Coelops            V I D M D T A L S
 13 Megaderma    N T S S A A P A T V N T S
 3 Taphozous       L G  L
 8 Nycteris           A T A A F E V S
 3 Pteronotus        I  M T
 4 Carollia            M L T S
 12 Vesper bats    M  V I V N L N A V L P M
   1 Chaerophon   V
 
3 Whales             P A M
 
If microbats diverged 100 MyA and whales ~40 MyA,
then there should be 7-8 substitutions in
microbats. Actual value is:-MEAN =  5.7 (range 1-13). The prediction
would be more accurate if it were known whether
all the whales inherited their complement of
FoxP2 changes from an ancestor (as seems likely, since both echolocating odontocetes and non-echolocating mystecetes have the same three FoxP2 substitutions). The older age of this ancestor would align the prediction. Note that these calculations would make some microbats very old indeed, such as the vespertilionids, rhinolophoids, megadermatids and nycterids. No wonder there is so much strife in elucidating a phylogeny for some microbats!