Paleoproteomic identification of the species used in fourteenth century gut-skin garments from the archaeological site of Nuulliit, Greenland.

Until recently, the identification of the species of origin for skin and fur materials used in the production of archaeological clothing has been based on the analysis of macro- and microscopic morphological features and on the traditional knowledge of Indigenous groups. This approach, however, is not always applicable due to the deterioration of the archaeological objects. Paleoproteomics was used as an alternative approach to identify the species of origin of fifteen samples of various tissues from approximately 600-year-old garments found in Nuulliit, northern Greenland. Proteomics revealed that a limited group of marine and terrestrial mammals were used for clothing production. The results obtained from the analysis of multiple types of clothing and elements, such as sinew thread and gut skin, suggest that their applications were based on their properties. When conclusive assignment of a sample to a species via proteomics was not possible, the observation by transmitted light microscopy of feather and hair micromorphology, if not affected by diagenesis, was used to improve the identification. The proteomic characterization of animal materials used for clothing production in the Nuulliit archaeological context provides an insight into the practical knowledge and the strategies adopted by the local Indigenous community to exploit natural resources.

How seabirds plunge-dive without injuries.

In nature, several seabirds (e.g., gannets and boobies) dive into water at up to 24 m/s as a hunting mechanism; furthermore, gannets and boobies have a slender neck, which is potentially the weakest part of the body under compression during high-speed impact. In this work, we investigate the stability of the bird's neck during plunge-diving by understanding the interaction between the fluid forces acting on the head and the flexibility of the neck. First, we use a salvaged bird to identify plunge-diving phases. Anatomical features of the skull and neck were acquired to quantify the effect of beak geometry and neck musculature on the stability during a plunge-dive. Second, physical experiments using an elastic beam as a model for the neck attached to a skull-like cone revealed the limits for the stability of the neck during the bird's dive as a function of impact velocity and geometric factors. We find that the neck length, neck muscles, and diving speed of the bird predominantly reduce the likelihood of injury during the plunge-dive. Finally, we use our results to discuss maximum diving speeds for humans to avoid injury.

Recurrent hybridization and recent origin obscure phylogenetic relationships within the 'white-headed' gull (Larus sp.) complex.

Species complexes that have undergone recent radiations are often characterized by extensive allele sharing due to recent ancestry and (or) introgressive hybridization. This can result in discordant evolutionary histories of genes and heterogeneous genomes, making delineating species limits difficult. Here we examine the phylogenetic relationships among a complex group of birds, the white-headed gulls (Aves: Laridae), which offer a unique window into the speciation process due to their recent evolutionary history and propensity to hybridize. Relationships were examined among 17 species (61 populations) using a multilocus approach, including mitochondrial and nuclear intron DNA sequences and microsatellite genotype information. Analyses of microsatellite and intron data resulted in some species-based groupings, although most species were not represented by a single cluster. Considerable allele and haplotype sharing among white-headed gull species was observed; no locus contained a species-specific clade. Despite this, our multilocus approach provided better resolution among some species than previous studies. Interestingly, most clades appear to correspond to geographic locality: our BEAST analysis recovered strong support for a northern European/Icelandic clade, a southern European/Russian clade, and a western North American/canus clade, with weak evidence for a high latitude clade spanning North America and northwestern Europe. This geographical structuring is concordant with behavioral observations of pervasive hybridization in areas of secondary contact. The extent of allele and haplotype sharing indicates that ecological and sexual selection are likely not strong enough to complete reproductive isolation within several species in the white-headed gull complex. This suggests that just a few genes are driving the speciation process.

Seeking carotenoid pigments in amber-preserved fossil feathers.

Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.

Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis.

The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin-1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence.

Hybridization among Arctic white-headed gulls (Larus spp.) obscures the genetic legacy of the Pleistocene.

We studied the influence of glacial oscillations on the genetic structure of seven species of white-headed gull that breed at high latitudes (Larus argentatus, L. canus, L. glaucescens, L. glaucoides, L. hyperboreus, L. schistisagus, and L. thayeri). We evaluated localities hypothesized as ice-free areas or glacial refugia in other Arctic vertebrates using molecular data from 11 microsatellite loci, mitochondrial DNA (mtDNA) control region, and six nuclear introns for 32 populations across the Holarctic. Moderate levels of genetic structure were observed for microsatellites (F(ST)= 0.129), introns (Φ(ST)= 0.185), and mtDNA control region (Φ(ST)= 0.461), with among-group variation maximized when populations were grouped based on subspecific classification. Two haplotype and at least two allele groups were observed across all loci. However, no haplotype/allele group was composed solely of individuals of a single species, a pattern consistent with recent divergence. Furthermore, northernmost populations were not well differentiated and among-group variation was maximized when L. argentatus and L. hyberboreus populations were grouped by locality rather than species, indicating recent hybridization. Four populations are located in putative Pleistocene glacial refugia and had larger τ estimates than the other 28 populations. However, we were unable to substantiate these putative refugia using coalescent theory, as all populations had genetic signatures of stability based on mtDNA. The extent of haplotype and allele sharing among Arctic white-headed gull species is noteworthy. Studies of other Arctic taxa have generally revealed species-specific clusters as well as genetic structure within species, usually correlated with geography. Aspects of white-headed gull behavioral biology, such as colonization ability and propensity to hybridize, as well as their recent evolutionary history, have likely played a large role in the limited genetic structure observed.

Comment on "A diverse assemblage of Late Cretaceous dinosaur and bird feathers from Canadian amber".

McKellar et al. (Reports, 16 September 2011, p. 1619) analyzed Late Cretaceous amber specimens from Canada and identified some filaments as dinosaurian protofeathers. We argue that their analysis and data do not provide sufficient evidence to conclude that such filaments are feather-like structures. Further investigation, including destructive sampling, must be carried out for more convincing conclusions.

Towards a comprehensive model of feather regeneration.

Understanding of the regeneration of feathers, despite a 140 year tradition of study, has remained substantially incomplete. Moreover, accumulated errors and mis-statements in the literature have confounded the intrinsic difficulties in describing feather regeneration. Lack of allusion to Rudall's (Rudall [1947] Biochem Biophys Acta 1:549-562) seminal X-ray diffraction study that revealed two distinct keratins, beta- and alpha-, in a mature feather, is one of the several examples where lack of citation long inhibited progress in understanding. This article reviews and reevaluates the available literature and provides a synthetic, comprehensive, morphological model for the regeneration of a generalized, adult contour feather. Particular attention is paid to several features that have previously been largely ignored. Some of these, such as the beta-keratogenic sheath and the alpha-keratogenic, supra-umbilical, pulp caps, are missing from mature, functional feathers sensu stricto because they are lost through preening, but these structures nevertheless play a critical role in development. A new developmental role for a tissue unique to feathers, the medullary pith of the rachis and barb rami, and especially its importance in the genesis of the superior umbilical region (SUR) that forms the transition from the spathe (rachis and vanes) to the calamus, is described. It is postulated that feathers form through an intricate interplay between cyto- and histodifferentiative processes, determined by patterning signals that emanate from the dermal core, and a suite of interacting biomechanical forces. Precisely regulated patterns of loss of intercellular adhesivity appear to be the most fundamental aspect of feather morphogenesis and regeneration: rather than a hierarchically branched structure, it appears more appropriate to conceive of feathers as a sheet of mature keratinocytes that is "full of holes.

Prevalence and diversity of avian hematozoan parasites in Asia: a regional survey.

Tissue samples from 699 birds from three regions of Asia (Myanmar, India, and South Korea) were screened for evidence of infection by avian parasites in the genera Plasmodium and Haemoproteus. Samples were collected from November 1994 to October 2004. We identified 241 infected birds (34.0%). Base-on-sequence data for the cytochrome b gene from 221 positive samples, 34 distinct lineages of Plasmodium, and 41 of Haemoproteus were detected. Parasite diversity was highest in Myanmar followed by India and South Korea. Parasite prevalence differed among regions but not among host families. There were four lineages of Plasmodium and one of Haemoproteus shared between Myanmar and India and only one lineage of Plasmodium shared between Myanmar and South Korea. No lineages were shared between India and South Korea, although an equal number of distinct lineages were recovered from each region. Migratory birds in South Korea and India originate from two different migratory flyways; therefore cross-transmission of parasite lineages may be less likely. India and Myanmar shared more host species and habitat types compared to South Korea. Comparison between low-elevation habitat in India and Myanmar showed a difference in prevalence of haematozoans.

Comprehensive DNA barcode coverage of North American birds.

DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.

Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers.

We used ancient DNA analysis of seven museum specimens of the endangered North American ivory-billed woodpecker (Campephilus principalis) and three specimens of the species from Cuba to document their degree of differentiation and their relationships to other Campephilus woodpeckers. Analysis of these mtDNA sequences reveals that the Cuban and North American ivory bills, along with the imperial woodpecker (Campephilus imperialis) of Mexico, are a monophyletic group and are roughly equidistant genetically, suggesting each lineage may be a separate species. Application of both internal and external rate calibrations indicates that the three lineages split more than one million years ago, in the Mid-Pleistocene. We thus can exclude the hypothesis that Native Americans introduced North American ivory-billed woodpeckers to Cuba. Our sequences of all three woodpeckers also provide an important DNA barcoding resource for identification of non-invasive samples or remains of these critically endangered and charismatic woodpeckers.