Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles.

BACKGROUND: Vertebrate skin appendages are constructed of keratins produced by multigene families. Alpha (α) keratins are found in all vertebrates, while beta (β) keratins are found exclusively in reptiles and birds. We have studied the molecular evolution of these gene families in the genomes of 48 phylogenetically diverse birds and their expression in the scales and feathers of the chicken. RESULTS: We found that the total number of α-keratins is lower in birds than mammals and non-avian reptiles, yet two α-keratin genes (KRT42 and KRT75) have expanded in birds. The β-keratins, however, demonstrate a dynamic evolution associated with avian lifestyle. The avian specific feather β-keratins comprise a large majority of the total number of β-keratins, but independently derived lineages of aquatic and predatory birds have smaller proportions of feather β-keratin genes and larger proportions of keratinocyte β-keratin genes. Additionally, birds of prey have a larger proportion of claw β-keratins. Analysis of α- and β-keratin expression during development of chicken scales and feathers demonstrates that while α-keratins are expressed in these tissues, the number and magnitude of expressed β-keratin genes far exceeds that of α-keratins. CONCLUSIONS: These results support the view that the number of α- and β-keratin genes expressed, the proportion of the β-keratin subfamily genes expressed and the diversification of the β-keratin genes have been important for the evolution of the feather and the adaptation of birds into multiple ecological niches.

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. RESULTS: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. CONCLUSIONS: We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

Structural function and evolution of the subarctometatarsus

Compares the metatarsal structural design (subarctometatarsus) of recently discovered Chinese feathered dinosaurs with the metatarsus (arctometatarsus) possessed by more advanced theropod dinosaurs and the metatarsus of more primitive forms. The subarctometatarsus was proved to be an intermediate structure. Additionally the metatarsus appears to co-incide with the evolution of the avian feather suggesting a possible relationship between the subarctometatarsus's evolution and the evolution of avian flight.

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.

BACKGROUND: While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS: Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS: Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.

Low frequency of paleoviral infiltration across the avian phylogeny.

BACKGROUND: Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insights into the patterns and processes of endogenous viral element evolution. RESULTS: Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae, Bornaviridae, Circoviridae, and Parvoviridae. All nonretroviral endogenous viral elements are present at low copy numbers and in few species, with only endogenous hepadnaviruses widely distributed, although these have been purged in some cases. We also provide the first evidence for endogenous bornaviruses and circoviruses in avian genomes, although at very low copy numbers. A comparative analysis of vertebrate genomes revealed a simple linear relationship between endogenous viral element abundance and host genome size, such that the occurrence of endogenous viral elements in bird genomes is 6- to 13-fold less frequent than in mammals. CONCLUSIONS: These results reveal that avian genomes harbor relatively small numbers of endogenous viruses, particularly those derived from RNA viruses, and hence are either less susceptible to viral invasions or purge them more effectively.

Identifying the African wintering grounds of hybrid flycatchers using a multi-isotope (δ2H, δ13C, δ15N) assignment approach

Migratory routes and wintering grounds can have important fitness consequences, which can lead to divergent selection on populations or taxa differing in their migratory itinerary. Collared (Ficedula albicollis) and pied (F. hypoleuca) flycatchers breeding in Europe and wintering in different sub-Saharan regions have distinct migratory routes on the eastern and western sides of the Sahara desert, respectively. In an earlier paper, we showed that hybrids of the two species did not incur reduced winter survival, which would be expected if their migration strategy had been a mix of the parent species' strategies potentially resulting in an intermediate route crossing the Sahara desert to different wintering grounds. Previously, we compared isotope ratios and found no significant difference in stable-nitrogen isotope ratios (δ15N) in winter-grown feathers between the parental species and hybrids, but stable-carbon isotope ratios (δ13C) in hybrids significantly clustered only with those of pied flycatchers. We followed up on these findings and additionally analyzed the same feathers for stable-hydrogen isotope ratios (δ2H) and conducted spatially explicit multi-isotope assignment analyses. The assignment results overlapped with presumed wintering ranges of the two species, highlighting the efficacy of the method. In contrast to earlier findings, hybrids clustered with both parental species, though most strongly with pied flycatcher.

The bright incubate at night: sexual dichromatism and adaptive incubation division in an open-nesting shorebird

Ornamentation of parents poses a high risk for offspring because it reduces cryptic nest defence. Over a century ago, Wallace proposed that sexual dichromatism enhances crypsis of open-nesting females although subsequent studies found that dichromatism per se is not necessarily adaptive. We tested whether reduced female ornamentation in a sexually dichromatic species reduces the risk of clutch depredation and leads to adaptive parental roles in the red-capped plover Charadrius ruficapillus, a species with biparental incubation. Males had significantly brighter and redder head coloration than females. During daytime, when visually foraging predators are active, colour-matched model males incurred a higher risk of clutch depredation than females, whereas at night there was no difference in depredation risk between sexes. In turn, red-capped plovers maintained a strongly diurnal/nocturnal division of parental care during incubation, with males attending the nest largely at night when visual predators were inactive and females incubating during the day. We found support for Wallace's conclusion that reduced female ornamentation provides a selective advantage when reproductive success is threatened by visually foraging predators. We conclude that predators may alter their prey's parental care patterns and therefore may affect parental cooperation during care.

Skull and mandible formation in the cuckoo (Aves, Cuculidae): Contributions to the nomenclature in avian osteology and systematics

The study of the contributions of different bones to the formation of the skeleton in birds is necessary: (1) to establish homologies in comparative anatomy; (2) to delimit each bone structure correctly, mainly in relation to the skull and mandible where the bones are fused to each other in adults; and (3) to standardize nomenclature in avian osteology. In this paper at least one young specimen belonging to each sub-family of Cuculidae was examined in order to identify each bone in terms of boundaries and contributions to skull and mandible formation. These cuckoos specimens were also compared with adults and young of turacos and hoatzin. The results show little variation of skull and jaw among the young cuckoos studied compared with the variations among adult specimens. However, it provides new suggestions for the boundaries and nomenclature of certain osseous structures in the skull and mandible of birds, specifically fissura zona flexoria craniofacialis, prominetia frontoparietalis, crista temporalis transversa, processus squamosalis, fossa laterosphenoidalis, tuberculum laterosphenoidale and processus retroangularis. This study also provides more reliable homologies for use in cladistic analysis and above all it contributes to the phylogenetic position of Cuculidae within Neognathae, specifically the skull formation suggest that turacos and hoatzin are more similar to each other than either is to the cuckoos. © 2005 Taylor & Francis.

Wind-assisted flight of Archaeopteryx

Archaeopteryx may be envisaged as an occasional or opportunistic flier that maintained an essentially dinosaurian life style on the shore but took to the air when circumstances were favourable. Such an interpretation is fully consistent with what is known of the anatomy, the taphonomy and the habitat of Archaeopteryx.

A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): spectral tuning and light-activated kinetics

Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for non-mammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.

A bibliography of birds; with special reference to anatomy, behavior, biochemistry, embryology, pathology, physiology, genetics, ecology, aviculture, economic ornithology, poultry culture, evolution, and related subjects ...

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