Molecular evolution of beta (beta) keratins in three bird species and divergence time estimates for the avian beta-keratin subfamilies

The origin and evolution of feathers has fascinated the general public and researchers for many years. Interest in the evolution of feathers is frequently fueled by discoveries of feathered dinosaurs, such as the recently discovered Anchiornis huxleyi, which displays pennaceous feathers on all four limbs and is dated to the early Middle Jurassic (∼155 Ma). One way researchers may study the evolution of feathers is through the use of genetic information, such as whole genomes, to understand the molecular evolution of proteins involved in the formation of these novel structures. Beta (beta) keratins are structural proteins found solely in reptiles (including birds) and comprise epidermal appendages such as claws and scales in reptiles and feathers and beaks in birds. In the avian lineage, the beta-keratins make up a multigene family containing at least four major subfamilies (scale, claw, feather-like and feather beta-keratins). Three avian genomes, the chicken (Gallus gallus), zebra finch (Taeniopygia guttata) and the turkey (Meleagris gallopavo), have recently been published and through the knowledge of divergence times and molecular differences between these birds, a better understanding of beta-keratin evolution can be achieved and applied to the study of feather evolution. It has been found that tandem arrays of beta-keratins reside on several syntenic loci in the three avian genomes. In the chicken and zebra finch, a cluster comprising representatives of all four subfamilies is located on microchromosome 25 and two clusters of feather beta-keratins are localized on chromosome 2 and microchromosome 27. While the turkey genome contains a much reduced number of beta-keratins (32) as compared to either the chicken (111) or zebra finch (108), the three major genomic loci are mostly conserved and indicate a Neognathae origin for these three loci. Phylogenetic analyses of avian beta-keratins from these three species suggest that the scale and claw beta-keratins are basal to the monophyletic beta-keratins from cultured keratinocytes, which are basal to the feather and feather-like beta-keratins. Also, the feather beta-keratins form multiple monophyletic clades, which correlate with their genomic loci in each species. Within the Family Phasianidae (chicken and turkey), beta-keratins form multiple orthologous relationships within each unique feather beta-keratin clade and beta-keratin subfamily. Using molecular dating methods, it is shown that the feather beta-keratins started diverging into their unique subfamily ∼143 Ma, which is after the appearance of Anchiornis huxleyi (∼155 Ma) with pennaceous feathers on all four limbs. These results indicate that primitive feathers were made of beta-keratins more similar to the basal scale and claw beta-keratins than those of the feather beta-keratin subfamily seen in today's birds. The feather beta-keratins may have arisen through multiple duplication events and became fixed in the lineage leading to modern birds due to the structural demands on feathers for flight.