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Flycatchers in the genus Empidonax are among the most difficult avian taxonomic groups to identify to species. Observers often rely on calls or songs in the field or detailed morphometrics in the hand to identify species. In January and February 2013, we twice captured an Empidonax flycatcher at the Virginia Zoo in Norfolk, Virginia. After being unable to identify the flycatcher to species level using morphometrics and photographs, we extracted DNA from two tail feathers collected during the second encounter to identify the individual genetically. Comparison of cytochrome c oxidase I (COI) with reference sequences in the Barcode of Life Database (BOLD) suggested that the specimen had a >99.8% probability of placement as a Dusky Flycatcher (Empidonax oberholseri). Additional comparisons of NADH dehydrogenase subunit 2 (ND2) to reference sequences in GenBank, however, suggested that the specimen was a Pine Flycatcher (Empidonax affinis), a species not represented in BOLD and confined geographically to a small area in Mexico and Guatemala. After analyzing both COI and ND2 from additional vouchered specimens, the bird caught in Virginia was determined to be a Dusky Flycatcher. We also suspect that some of the sequences in GenBank might derive from incorrectly identified specimens or otherwise could represent overlooked pseudogenes. Because the putative identification, based on GenBank sequences, would have represented the first record of Pine Flycatcher from the United States, our results reinforce the need for carefully vetted and taxonomically comprehensive molecular databases to allow definitive conclusions about sample identity. Further molecular phylogeographic review of this genus is warranted to resolve haplotype ambiguities.

Stomach contents were analyzed using microscopic feather characters and osteological comparisons to document the first record of a Razorbill (Alca torda) being eaten by a Snowy Owl (Bubo scandiacus). Careful comparisons of fragmented morphological evidence in combination with geographic location and other circumstantial data can enhance dietary analyses, especially when it is difficult to obtain DNA sequences from the degraded and digested stomach contents.

Recent genetic studies have shown that introgression rates among loci may greatly vary according to their location in the genome. In particular, several cases of mito-nuclear discordances have been reported for a wide range of organisms. In the present study, we examine the causes of discordance between mitochondrial (mtDNA) and nuclear DNA introgression detected in North American populations of the Great Black-backed Gull (Larus marinus), a Holarctic species, from the Nearctic North American Herring Gull (Larus smithsonianus). Our results show that extensive unidirectional mtDNA introgression from Larus smithsonianus into Larus marinus in North America cannot be explained by ancestral polymorphism but most likely results from ancient hybridization events occurring when Larus marinus invaded the North America. Conversely, our nuclear DNA results based on 12 microsatellites detected very little introgression from Larus smithsonianus into North American Larus marinus. We discuss these results in the framework of demographic and selective mechanisms that have been postulated to explain mito-nuclear discrepancies. We were unable to demonstrate selection as the main cause of mito-nuclear introgression discordance but cannot dismiss the possible role of selection in the observed pattern. Among demographic explanations, only drift in small populations and bias in mate choice in an invasive context may explain our results. As it is often difficult to demonstrate that selection may be the main factor driving the introgression of mitochondrial DNA in natural populations, we advocate that evaluating alternative demographic neutral hypotheses may help to indirectly support or reject hypotheses invoking selective processes.

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 (FST= 0.129), introns (ΦST= 0.185), and mtDNA control region (ΦST= 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.

A nearly complete skeleton of an adult Hawaiian flightless ibis (Apteribis sp.) was recovered from a vaulted dry lava tube in association with remains of contour feathers. This is the first documentation of the genus Apteribis from the island of Lanai and provides the only record of the nature of the plumage in any of the prehistorically extinct species of birds known from the Hawaiian Islands. Light and scanning electron microscope analyses of structure of the pennaceous and plumulaceous (downy) portions of these feathers confirmed their placement with the ibises (Threskiornithidae). Within that family, the microscopic structure of the downy feathers is most similar to that of the New World ibises of the genus Eudocimus, thus corroborating molecular evidence of the derivation of Apteribis from Eudocimus. Plumage color was a combination of brown-black and ivory-beige/light brown suggestive of that of juveniles of Eudocimus. Plumage coloration in Apteribis may thus have evolved through the same processes of paedomorphosis that gave rise to flightlessness.

We identified 25 species of birds representing nine avian Orders from remains in digestive tracts of 85 Burmese pythons (Python molurus bivittatus) collected in Everglades National Park, Florida, USA, from 2003 to 2008. Four species of birds identified in this study are of special concern in Florida and a fifth, the Wood Stork (Mycteria americana), is listed as federally endangered. This represents the first detailed analysis of the avian component of the diet of the introduced Burmese python, now established in Everglades National Park, Florida and highlights the potential for considerable negative impact of this invasive species on native bird populations. Received 9 June 2010. Accepted 27 September 2010.

In the United States alone, over 7400 bird–aircraft collisions (birdstrikes) were reported in 2007. Most of these strikes occurred during takeoff or landing of the flight, and it is during these flight phases that aircraft experience their highest risk of substantial damage after colliding with birds. Birdstrikes carry enormous potential costs in terms of lives and money. Using feather remains and other tissue samples collected from the engines of US Airways Flight 1549, which crash landed in the Hudson River in New York City on 15 January 2009 after a birdstrike, we apply molecular tools and stable hydrogen isotopes to demonstrate that migratory Canada geese were responsible for the crash. Determining whether the geese involved in this birdstrike event were resident or migratory is essential to the development of management techniques that could reduce the risk of future collisions. Currently, the US civil aviation industry is not required to report birdstrikes, yet information on frequency, timing, and ...

We determined effectiveness of using mitochondrial DNA barcodes (cytochrome c oxidase subunit 1 [CO1]) to identify bird–aircraft collision (birdstrike) cases that lacked sufficient feather evidence for morphological diagnosis. From September through December 2006, 821 samples from birdstrike events occurring in the United States were submitted for DNA analysis. We successfully amplified a CO1 DNA barcode product from 554 (67.5%) of the samples; 267 (32.5%) did not contain viable DNA and depended on morphological methods (microscopy) for Order or Family level identification. We deemed 19 cases inconclusive either because the DNA barcode recovered from the sample did not meet our 98% match criteria when compared to the Barcode of Life Database (BoLD) or because the DNA barcode matched to a set of ≥2 closely related species with overlapping barcodes, preventing complete species identification. Age of the sample (≤6 months) did not affect DNA viability, but initial condition of the sample and the col...

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.

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.

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.

AbstractWe examined variation in five microscopic plumulaceous (downy) feather characters of eighteen species of dabbling (Anatini) and diving (Aythyini, Mergini) ducks to quantify the differences between these tribes, and to explain how the plumulaceous feather ultrastructure in ducks may be influenced by different ecological requirements. Over 75% of the variation in feather characters among these ducks was explained by the first two components of a principal components analysis (PCA). Component 1 explained 51% of the variation and was positively correlated with the characters that quantified the number of barbules with expanded nodes and the number of expanded nodes on barbules. The microscopic feather characters of dabbling ducks (Anatini) have triangular-shaped, expanded nodes on most proximal barbules, whereas diving ducks (Aythyini and Mergini) lack expanded nodes on some barbules. Anatini also have a greater density of expanded nodes per barbule, wider nodes, shorter distance between expanded nodes, and longer barbule length. Further analysis of node density across all taxa showed that as dive depths increase, the number of expanded nodes per barbule decreases, and in the deepest divers many of the barbules completely lack expanded nodes. The significantly greater density of expanded nodes in dabbling ducks suggests that the downy nodes may function to trap more air. Diving species have fewer expanded nodes, less buoyant plumage, and are more efficient at foraging in deeper water than dabbling ducks.

1. We examined infrared absorption spectra in contour feathers of 10 species of birds to compare infrared features of the downy and pennaceous regions with the mechanisms of conservation of body heat radiation. 2. At 1700 cm −1 , a sharp increase in transmittance was observed for downy parts, but not for the distal pennaceous regions. 3. The transmittance peak for down may be significant in the conservation of radiation heat: the 1700 cm −1 radiation transmitted by the down is scattered and reflected by the pennaceous region of the contour feather, thereby containing the heat radiation within the feather coat.

One of the traditional methods of determining the dietary preferences of owls relies upon the identification of bony remains of prey contained in regur- gitated pellets. Discovery of a pellet containing a large, complete primary feather from an adult, male Ring-necked Pheasant (Phasianus colchicus) prompted us to examine in detail a small sample of pellets from a Great Horned Owl (Bubo virginianus). Our analyses of feather and hair remains in these pellets docu- mented the presence of three species of birds and two species of mammals, whereas bones in the pellets represented only mammals. This finding indicates an important bias that challenges the reliability of owl pellet studies making use of only osteological remains. Six egested pellets from a Great Horned Owl, Bubo virginianus (Gmelin, 1788), were collected on 13 April 2003 along the northeast side of Blue Marsh Lake, ca. 11 mi north of Reading, Penn Township, Berks County, PA. The pellets were scattered beneath a large black walnut tree (Juglans nigra Linne, 1753) along the edge of a windbreak of trees bordering a grassy, overgrown field just north of Old Church Road and west of Route 183. They are all believed to be from a single individual because of their proximity and their similar size and shape. One of these pellets (catalogue USNM 601957) is unusual because it contains a large (> 190 mm long when extended), complete primary (P-9) feather (Fig. 1) from the right wing of an adult, male Ring-necked Pheasant (Phasianus colchicus Linne, 1758). The pellet also contains large fragments of other feathers, although none with shaft diam- eters as great as the complete P-9. Other than these feathers, the pellet consists primarily of compacted hairs. No bones are apparent on the surface, nor were any revealed by digital x-ray. Our review of the literature on raptor pellets and our discussions with colleagues revealed no previous instances of an item as large as the primary feather being discovered incorporated into the body of a regurgitated pellet. The visual impact of USNM 601957, and the fact that no bones of pheasant were present, encouraged us to examine all of the pellets more closely, paying particular attention to the correspondence among incorpo- rated feathers, hairs, and osteological remains. We identified feathers by direct comparison with museum specimens and by use of microscopic 1

Source: doi: 10.14430/arctic4546 A grave containing the remains of a wooden boat was discovered in 1934 under a low mound in a bog at Øksnes in the Vesterålen islands of northern Norway. The boat grave dates to the 10th century in the Viking Age, and grave goods placed in the boat include an iron axe, a cowhide in which the body was wrapped, and pillow remains consisting of feather stuffing and a wool textile cover. A microscopic analysis of the feathers from a subsample of the pillow fill identified three avian orders: Anseriformes (eider); Suliformes (cormorant), and Charadriiformes (unspecified gull). It was possible to make one species-level identification of Great Cormorant (Phalacrocorax carbo) and to narrow the gull types to the “white-headed” gull group. The sample was composed of a nearly equal mix of downy and pennaceous feather types. Downy feathers from gulls (Laridae) composed the majority of the material in this sample. While it is reported that feathers and down (assumed to be eider) were used in the Late Iron Age, this is the first successful attempt to identify bird species used in these materials and suggests that avian species identifications should be explored in other such burial items to enhance our understanding of human-wildlife interactions throughout Norse history.

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.

Variation in microscopic characters of plumulaceous barbs of six species of Charadrius was studied to quantify characters and test differences among taxa. Pluvialis squatarola was used for intergeneric comparisons. Intraspecific variation in feathers from the sternopectoral tract of C. vociferus was examined to define character parameters and to determine within-vane variation and vane symmetry. A significant difference was observed among the barbs of four regions within each vane of the same feather, but barbs from opposing vanes were not significantly different from one another. Interspecific variation then was studied using discriminant function analysis. Pluvialis separated from all species of Charadrius. Two subgroups were apparent within Charadrius: semipalmatus, vociferus and montanus separated from wilsonia, alexandrinus and melodus.

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.

The Streaked Horned Lark (SHL: Eremophila alpestris strigata) is the Northwest subspecies of the Horned Lark listed as endangered in Washington State, critical in Oregon, and is now being considered for listing as threatened by the US Fish & Wildlife Service. Some of the important breeding areas of SHL are associated with airports in western Washington and Oregon which raises concern over possible collisions between SHLs and aircraft. Here, we report a successful use of mtDNA ND2 gene sequence for identification of SHL feather and tissue remains from a bird collision with a US Air Force F-15-C on 4 October 2012 at Portland International Airport. Due to the conservation status of SHL, documentation of this event and a simple mtDNA-based molecular identification protocol may have management and conservation implications at airfields within the range of this rare subspecies.

Twelve ancient artifacts or fragmented feather samples recovered from melting alpine ice patches in southern Yukon were analyzed in order to identify the species of birds associated with the ice patches or used on weapons recovered from these sites. The identification of bird species used by ancient hunters as long ago as 4500 BP enhances our insight into the customs, culture, and sophistication of life at that time. Downy feather barbs were found on two samples and microscopically identified as duck (Anatidae) and falcon (Falconidae). Further examination and comparisons using museum specimens resulted in a total of six identifications: Anatidae, eagle (Aquila or Haliaeetus), gyrfalcon (Falco rusticolus), white-tailed ptarmigan (Lagopus leucurus), short-eared owl (Asio flammeus), and northern flicker (Colaptes auratus luteus). Three of the feather samples were complete enough to show apparent modification, or notching, along the feather shaft. The identification of non-game birds such as gyrfalcon and eagles, together with evidence of possible worked or notched feathers, indicates that as long as 4500 years ago, Subarctic hunters selected feathers not only for their utility in fletching, but also possibly for symbolic or decorative purposes.

From 1997 through 2007, 821 bat strikes were reported to the U.S. Air Force (USAF) Safety Center by aircraft personnel or ground crew and sent to the National Museum of Natural History, Smithsonian Institution, for identification. Many samples were identified by macroscopic and or microscopic comparisons with bat specimens housed in the museum and augmented during the last 2 years by DNA analysis. Bat remains from USAF strikes during this period were received at the museum from 40 states in the United States and from 20 countries. We confirmed that 46% of the strikes were caused by bats, but we did not identify them further; we identified 5% only to the family or genus level, and 49% to the species level. Fifty-five of the 101 bat-strike samples submitted for DNA analysis have been identified to the species level. Twenty-five bat species have been recorded striking USAF planes worldwide. The Brazilian free-tailed bat (Tadarida brasiliensis; n = 173) is the species most commonly identified in USAF strike impacts, followed by the red bat (Lasiurus borealis; n = 83). Bat strikes peak during the spring and fall, with >57% occurring from August through October; 82% of the reports that included time of strike were recorded between 2100 and 0900 hours. More than 12% of the bat strikes were reported at >300 m above ground level (AGL). Although$825,000 and >50% of this sum was attributable to 5 bat-strike incidents. Only 5 bats from the 10 most damaging bat strikes were identified to the species level, either because we did not receive remains with the reports or the sample was insufficient for identification.

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.

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.

On 25 August, 2007, a Marbled Godwit (Limosa fedoa) was struck by a Southwest Airlines Boeing 737 at 3,700 m. The bird was identified by examination of feather remains recovered from the aircraft and represents an altitude record for this species.

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.

An Egyptian Nightjar (Caprimulgus aegyptius) specimen was salvaged on 5 September 2000 from the landing gear of a DC-10 airliner that had landed at Langley Air Force Base, Virginia. The bird likely collided with the plane during its stop the previous day in Kuwait City, Kuwait, within the typical range of this nightjar. This incident illustrates the importance of proper documentation of specimens and shows that aircraft transport of avian specimens can occur.