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Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

The feather beta ([beta]) keratins of the white leghorn chicken (order Galliformes, Gallus gallus domesticus) are the products of a multigene family that includes claw, feather, feather-like, and scale genes (Presland et al. 1989a). Here we characterize the feather [beta]-keratin genes in additional bird species. We designed primers for polymerase chain reactions (PCR) using sequences available from chicken, cloned the resulting amplicons to isolate individual copies, and sequenced multiple clones from each PCR reaction for which we obtained amplicons of the expected size. Feather [beta]-keratins of 18 species from eight avian orders demonstrate DNA sequence variation within and among taxa, even in the protein-coding regions of the genes. Phylogenies of these data suggest that Galliformes (fowl-like birds), Psittaciformes (parrots), and possibly Falconiformes (birds of prey) existed as separate lineages before duplication of the feather [beta]-keratin gene began in Ciconiiformes (herons, storks, and allies), Gruiformes (cranes, rails, and allies), and Piciformes (woodpeckers and allies). Sequences from single species of Coraciiformes (kingfishers) and Columbiformes (pigeons) are monophyletic and strikingly divergent, suggesting feather [beta]-keratin genes in these birds also diverged after these species last shared a common ancestor with the other taxa investigated. Overall, these data demonstrate considerable variation in this structural protein in the relatively recent history of birds, and raise questions concerning the origin and homology of claw, feather-like, and scale [beta]-keratins of birds and the reptilian [beta]-keratins.

Abstract Background The epidermal appendages of reptiles and birds are constructed of beta (β) keratins. The molecular phylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes of the chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β-keratins, but to study their molecular evolution in archosaurians. Results The subfamilies (claw, feather, feather-like, and scale) of β-keratin genes are clustered in the same 5' to 3' order on microchromosome 25 in chicken and zebra finch, although the number of claw and feather genes differs between the species. Molecular phylogenies show that the monophyletic scale genes are the basal group within birds and that the monophyletic avian claw genes form the basal group to all feather and feather-like genes. Both species have a number of feather clades on microchromosome 27 that form monophyletic groups. An additional monophyletic cluster of feather genes exist on macrochromosome 2 for each species. Expression sequence tag analysis for the chicken demonstrates that all feather β-keratin clades are expressed. Conclusions Similarity in the overall genomic organization of β-keratins in Galliformes and Passeriformes suggests similar organization in all Neognathae birds, and perhaps in the ancestral lineages leading to modern birds, such as the paravian Anchiornis huxleyi. Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral β-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the β-keratin multigene family expanded, novel β-keratin genes were selected for novel functions within appendages such as feathers.

Dinosaur fossils possessing integumentary appendages of various morphologies, interpreted as feathers, have greatly enhanced our understanding of the evolutionary link between birds and dinosaurs, as well as the origins of feathers and avian flight. In extant birds, the unique expression and amino acid composition of proteins in mature feathers have been shown to determine their biomechanical properties, such as hardness, resilience, and plasticity. Here, we provide molecular and ultrastructural evidence that the pennaceous feathers of the Jurassic nonavian dinosaur Anchiornis were composed of both feather β-keratins and α-keratins. This is significant, because mature feathers in extant birds are dominated by β-keratins, particularly in the barbs and barbules forming the vane. We confirm here that feathers were modified at both molecular and morphological levels to obtain the biomechanical properties for flight during the dinosaur-bird transition, and we show that the patterns and timing of adaptive change at the molecular level can be directly addressed in exceptionally preserved fossils in deep time. [ABSTRACT FROM AUTHOR]

The integuments of extant vertebrates display a variety of epidermal appendages whose patterns, morphology and terminal differentiation (epidermal keratins) depend upon interactions between ectodermal (epidermis) and mesodermal (dermis) tissues. In reptiles and birds, appendage morphogenesis precedes terminal differentiation. Studies have demonstrated that appendage morphogenesis influences the expression of the appendage specific keratin genes. However, little is known about the nature of the structural genes expressed by the epidermal appendages of reptiles. How pattern formation and/or appendage morphogenesis influence terminal differentiation of reptilian appendages is not known. The epidermal appendages of reptiles and birds are characterized by the presence of both alpha ([Alpha]) and beta ([Beta]) type keratin proteins. Studies have focused on the genes of avian [Beta] keratins because they are the major structural proteins of feathers. The occurrence of [Beta] keratin proteins in the scales and claws of both birds and reptiles and their immunological cross-reactivity suggest that the genes for reptilian [Beta] keratins may be homologous with those of birds. In bird appendages, the [Beta] keratins are the products of a large family of homologous genes. Specific members of this gene family are expressed during the development of each appendage. Recent sequence analyses of feather [Beta] keratins, from different orders of birds, demonstrate that there is more diversity at the DNA level than was implied by earlier protein sequencing studies. Immunological techniques show that the same antibodies that react with the epidermal [Beta] keratins of the chicken (Gallus domesticus) react with the epidermal [Beta] keratins of American alligators (Alligator mississippiensis). Furthermore, a peptide sequence (20 amino acids) from an alligator claw [Beta] keratin is similar to a highly conserved region of avian claw, scale, feather, and feather-like [Beta] keratins. These observations suggest that the [Beta] keratin genes of avian epidermal appendages have homologues in the American alligator. Understanding the origin and evolution of the [Beta] keratin gene families in reptiles and birds will undoubtedly add to our understanding of the evolution of skin appendages such as scales and feathers.

The cornified epidermal appendages of birds consist primarily of highly insoluble, cysteine rich, 3nm fibrous proteins of relatively low molecular weight which give a beta-type X-ray diffraction pattern. In the chicken these unique proteins, known as beta-keratins, are the products of a large multi-gene family including the claw, scale, feather and feather-like keratin gene clusters. Although these genes have been sequenced for the chicken, no information is available for other taxa. The recent discovery of feathered dinosaurs suggests an ancient origin for these genes. Thus, we have undertaken the characterization of the beta-keratins in extant archosaurs to elucidate their diversity, age, and origins.