Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers. By analysing 48 bird genomes, we identified millions of avian-specific highly conserved elements (ASHCEs) that predominantly (>99%) reside in non-coding regions. Many ASHCEs show differential histone modifications that may participate in regulation of limb development. Comparative embryonic gene expression analyses across tetrapod species suggest ASHCE-associated genes have unique roles in developing avian limbs. In particular, we demonstrate how the ASHCE driven avian-specific expression of gene Sim1 driven by ASHCE may be associated with the evolution and development of flight feathers. Together, these findings demonstrate regulatory roles of ASHCEs in the creation of avian-specific traits, and further highlight the importance of cis-regulatory rewiring during macroevolutionary changes.

BackgroundFlight feathers, a type of feather that is unique to extant/extinct birds and some non-avian dinosaurs, are the most evolutionally advanced type of feather. In general, feather types are formed in the second or later generation of feathers at the first and following molting, and the first molting begins at around two weeks post hatching in chicken. However, it has been stated in some previous reports that the first molting from the natal down feathers to the flight feathers is much earlier than that for other feather types, suggesting that flight feather formation starts as an embryonic event. The aim of this study was to determine the inception of flight feather morphogenesis and to identify embryological processes specific to flight feathers in contrast to those of down feathers.ResultsWe found that the second generation of feather that shows a flight feather-type arrangement has already started developing by chick embryonic day 18, deep in the skin of the flight feather-forming region. This was confirmed by shh gene expression that shows barb pattern, and the expression pattern revealed that the second generation of feather development in the flight feather-forming region seems to start by embryonic day 14. The first stage at which we detected a specific morphology of the feather bud in the flight feather-forming region was embryonic day 11, when internal invagination of the feather bud starts, while the external morphology of the feather bud is radial down-type.ConclusionThe morphogenesis for the flight feather, the most advanced type of feather, has been drastically modified from the beginning of feather morphogenesis, suggesting that early modification of the embryonic morphogenetic process may have played a crucial role in the morphological evolution of this key innovation. Co-optation of molecular cues for axial morphogenesis in limb skeletal development may be able to modify morphogenesis of the feather bud, giving rise to flight feather-specific morphogenesis of traits.

Stable tris-, bis- and mono[9-(azuleno[1,2-b]thienyl)]methyl cations (7a, 8a and 9a) and their derivatives, with a 6-isopropyl substituent on each azuleno[1,2-b]thiophene ring (7b, 8b and 9b) were prepared by the hydride abstraction reaction of the corresponding methane derivatives. The bonding situation of these compounds including the methane derivatives was examined by analysis of the 3J(H,H) values for the seven-membered ring from the 1H NMR spectra. The methane derivatives exhibited a significant alternating pattern in the 3J(H,H) values, which indicated that the pi-system of the azulene core is perturbed by the fused thiophene ring, showing a tendency towards a localized heptafulvene substructure. The 3J(H,H) values of 7b and 8b in the seven-membered ring revealed that the alternating C-C bond lengths in the azulene core still existed. The cations 9a and 9b, which exhibited nearly equal 3J(H,H) values in the seven-membered ring, exhibit the development of a delocalized tropylium substructure in the azulene core. X-ray crystal analysis of 6-isopropylazuleno[1,2-b]thiophene revealed substantial bond-length alternation in the seven-membered ring. Significant bond-length equalization in the seven-membered ring was also confirmed by the X-ray crystal analysis of 9b. The stability of these carbocations was examined by measurement of the pKR+ values and the redox potentials, which revealed that the bond-length alternation in the azulene core does not significantly affect the stability of the carbocations.