The identity of the digits of the bird wing is a classic problem of evolutionary biology, born out of apparently contradictory developmental and morphological evidence. If we follow the criterion of homology by embryological position of origin, we find that the wing digits develop from embryological positions corresponding to those of digits 2, 3 and 4 of crocodilians 
. Crocodilians are bird's closest living relatives 
and thus the optimal reference point for developmental comparisons to the bird wing. In the alligator forelimb (as in mouse) the first cartilaginous digital condensation to form is spatially in line with the ulnare and ulna (, top row), and develops into digit 4 (, bottom row). The spatial alignment of these elements is referred to as the “primary axis”, indicated by a red line in . In the wing, the primary axis develops into the posterior digit, indicating the digits develop at positions 2, 3 and 4 
(). However, the wing digits of early birds like Archaeopteryx
are morphologically similar to digits 1, 2, and 3 of crocodilians, presenting 2, 3 and 4 phalanges, respectively (). We arrive at the same conclusion if we compare Archaeopteryx
to early dinosaurs, lizards, and even early branches of amniotes (, See Captorhinus
). Wing digits are labeled 1,2,3 in the fields of phylogenetic systematics and comparative anatomy 
As an explanation to this apparent contradiction with the embryological evidence, Wagner and Gauthier 
suggested that a homeotic frame shift of digital identity had occurred in the evolution of the bird wing, such that in birds digits 1, 2 and 3 develop from embryological positions 2, 3 and 4 ().
Three levels to the avian digit homology problem: embryology, gene expression, and morphology.
The evolution of digit morphology.
Consistent with this hypothesis, the embryological position of HoxD gene expression appears to be shifted in the bird wing. The posterior HoxD genes (i.e. HoxD-10
, and HoxD-13
) are well known for their expression and function in developing digits 
. In the bird wing HoxD-10
, -11 and -12
are absent only at the most anterior digit 
(embryological position 2, ). Because the same is true only for digit 1 of the mouse 
, Vargas and Fallon 
argued that HoxD gene expression in the wing suggests a digit 1 develops at the embryological position of digit 2. If the comparison of digit 1 of the mouse to the anterior wing digit is correct, we should expect closer relatives of birds to show no expression of these genes only in digit 1 (The predicted expression for alligator is shown in gray shading in ). If we do not assume a frame shift, but rather that wing digits develop directly into digits 2,3 and 4, expression in crocodilian forelimbs could be absent in digit 2. To test these predictions, we investigate HoxD-11
expression in crocodilians (bird's closest living relatives). If expression in crocodilians is not uniquely absent in digit 1 (as in mouse), HoxD-11
would provide no support for the homeotic frame shift hypothesis. We cloned a fragment of exon 1 of HoxD-11
of the crocodilian Alligator mississippiensis
and observed its transcription in developing digits. We found that, as in the mouse, in alligator forelimbs HoxD-11
mRNA is absent only at digit 1. We discuss the relevance of this result for the hypothesis of a homeotic frame shift in the bird wing.