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Anybody know which traits of bird plumage are accurate indicators of a birds health? For example feather coloration, feather brightness, amount of feather wear, number of feathers, moult timing, moult duration etc.
This resource provides a short list of which general components of plumage are good indicators of a healthy bird.
Your pet's plumage should be…
Soft - feathers should be strong, yet flexible.
Smooth - no rough feather shafts; no uneven or split edges
Glossy - sheen extends over the entire coat
Full - thick, where it needs to be
Vivid - color should be deep, bright and uniform
Clean - free of dust, dander, waste, or soil
Parasite-Free - no lice or mites
Also, this website page discusses the signs of malnutrition or disease in plumage in more detail.
Stress bars, dark lines which transect a feather, are directly caused by an inefficient absorption or lack of required nutrients. Stress bars can be found on all feathers during the period of malnutrition, and remain even after this period.
Assymetrical moulting is also a sign of bad health. There should not be any bald patches present during the moult.
The resource states that if a moult is delayed due to malnutrition, an incorrect photoperiod or a metabolic problem, plumage will become depigmented. However, the appearance of "dirty" feathers can also be due to overpreening or damage done to feathers by physical contact.
Finally, a change in the usual plumage color of the bird in question is indicative of a lack or oversupply of a particular nutrient.
Bird Plumage Variations and Abnormalities
Male Painted Bunting in his spectacular plumage : Tim Hopwood
Variations in plumage can be based on the sex of the bird, its age, or seasonal changes caused by molting. Molting patterns are complex and even the experts do not have all the answers about how this process is controlled. This basic introduction to molting will provide you with a glimpse into the challenge and fun of studying molting patterns and the range of molting behaviors. Several plumage patterns can be observed in birds. The molting process can be either very obvious or difficult to detect, depending on the species and its plumage pattern.
The Delight of Watching Birds on the Streets of New York
It&rsquos springtime, and the city feels especially glorious it felt like a winter on top of a winter this year. But, if we reflect on what brought joy during this challenging time, birds enjoyed a top spot on the happy list for many. Especially those we saw out our windows&mdashor, in New York City, on the street.
Three species in particular dominate the sidewalks, asphalt, tops of buildings, fire escapes, window ledges and air conditioners: house sparrows (the small brown and gray birds, males with a black beak and bib underneath), pigeons (which need no introduction) and starlings (the medium-sized dark iridescent birds that are quick, crafty and ubiquitous). All three of these species are invasive. Domesticated pigeons came from France around 1600, and escaped. House sparrows were introduced to Brooklyn around 1851 and starlings were successfully released in Central Park in 1890 and 1891.
The house sparrow and starling introductions were the work of the American Acclimatization Society, an organization founded in 1871 whose mission was to bring species that were &ldquouseful or interesting&rdquo from Europe to North America. House sparrows, for example, were imported to control insect pests. But starlings have another story. It&rsquos widely believed that they were brought to the U.S. by the society&rsquos president, Eugene Schieffelin, as part of an effort to introduce all of the birds mentioned by Shakespeare. But while Schieffelin was responsible for the starlings, there&rsquos no contemporary evidence for the Shakespeare-starling connection&mdashit&rsquos not mentioned in any official document from the society. Though the story, which is a good one, continues to be told.
At the time of these introductions, the scientific fields of ecology and conservation were virtually nonexistent and now we know that either for pest control or homage to the great playwright, this was a terrible idea. Today, house sparrows and starlings are the most widespread invasive birds in the world, also deliberately introduced to South Africa, Australia, New Zealand, Argentina and other locations. But I would add a qualifier to that terrible idea by calling it, what the Grinch would consider, &ldquoa wonderful, awful&rdquo idea.
I have been studying starlings in New York City since 2016. I do so formally in museums and labs, but in between my research I watch them informally on the street. It&rsquos turning out to be a whole starling life. I was initially captivated by their adaptability to the urban landscape, especially their dietary flexibility. They will eat a pile of yellow rice on Columbus Ave, a soft pretzel on Central Park West and a flattened apple pie in the parking lot of a Costco in Queens. Pigeons and house sparrows often hover and hop around them but cannot compete with their quickness. For a bird, they are good at walking on the ground. I have seen one saunter up a ramp of a Checks Cashed or fly low just across the street and then start walking again seconds later.
The sounds they make are so varied that you might not recognize that they are coming from the same species. If you listen closely, you can hear their up-and-down whistling, whirring and even an early video game laser&ndashlike sound. You may not consider it beautiful enough to be called a song, but it&rsquos a song nonetheless. And when you stare at them, as I have many times, they never ever appear to look at you, but it is obvious they see you because they respond incredibly rapidly to absolutely any movement or disturbance. They are off in a flash, always faster than I can draw my phone out for a good picture. Their beaks and plumage change color with the seasons. In fall and winter, their feathers are flecked with white and their beaks are a deep brown.
In early spring, their beaks change color to a bright yellow (thanks to hormones signaling pigment molecules), and their plumage is shiny and iridescent, not black but the deepest darkest greens, grays and purples. The males are especially shiny, very slightly larger than females and have longer feathers on the front of their neck. And any day now, the all-gray juveniles will be out of their nests learning to fly and begging their parents for food.
But despite the quirky qualities that make them especially good for urban bird-watching, each year starlings cause millions of dollars of damage to farms across the country by decimating agricultural crops, stealing substantial quantities of food meant for domesticated animals and spreading diseases to livestock in their guano. And if that weren&rsquot enough, starlings also fly into aircraft and compete with native birds for nesting sites. They build their nests in tree holes and on stone window ledges. Because of their invasive status, and the agricultural, ecological and economic issues that they cause, they are either ignored or downright hated, especially by bird-lovers who are &ldquoin the know.&rdquo
In fact, hating starlings is often an early sign that you are now identifying as someone who knows about birds. Sometimes, I wish I didn&rsquot know about what else they do across the country, or why they arrived here, and could just enjoy watching them in a quiet ignorance. And I wonder if you can know about their paths of destruction and still appreciate aspects of their biology and behavior. Especially those two individuals keeping me company at the bus stop.
There is a great deal more avian diversity in New York City than just pigeons, house sparrows and starlings. If you go into the parks, you will see tufted titmice, robins, red-tailed hawks, mourning doves, cardinals and, if you were lucky a few weeks ago, the fabulous snowy owl. Central Park is also a major migration flyway for many bird species in springtime, which bring an additional group of temporary and exciting passersby. But this diversity is not distributed evenly in this fragmented urban landscape. So, what if, like spring last year, you didn&rsquot feel safe walking into the park crowded with people, so you looked out the window instead?
Or what if you were out there working, not in your pajamas like some, and just didn&rsquot have time to bring your binoculars for a stroll in the park? A park is a privilege sometimes. But does the opportunity to enjoy birds also have to be? A growing body of research has quantified the health benefits from spending time in nature. A short walk in a natural green space can result in anxiety reduction, reduced negative rumination and increased feelings of well-being. So, what if that nature spills out onto the sidewalk is it any less uplifting? And don&rsquot species like starlings buoy us with their resilience in the face of the sometimes absurd ugliness of a city?
At times this winter, the world felt particularly dreary, and nothing in the built environment even came close to reminding me of life or the natural world sprawling storage facilities, scaffolding, for-rent signs and restaurant structures struggling under snow. And then way up in that bit of sky, beside the water tower, I spotted five of them. I know their triangular wings, and their quick and suspicious behavior, anywhere. And then as they flew up and out of my sight they left in their wake, hope: of bluer skies and future springtimes.
Analysis of the influences on plumage condition in laying hens: How suitable is a whole body plumage score as an outcome?
An important indicator of the health and behavior of laying hens is their plumage condition. Various scoring systems are used, and various risk factors for feather damage have been described. Often, a summarized score of different body parts is used to describe the overall condition of the plumage of a bird. However, it has not yet been assessed whether such a whole body plumage score is a suitable outcome variable when analyzing the risk factors for plumage deterioration. Data collected within a German project on farms keeping laying hens in aviaries were analyzed to investigate whether and the extent to which information is lost when summarizing the scores of the separate body parts. Two models were fitted using multiblock redundancy analysis, in which the first model included the whole body score as one outcome variable, while the second model included the scores of the individual body parts as multiple outcome variables. Although basically similar influences could be discovered with both models, the investigation of the individual body parts allowed for consideration of the influences on each body part separately and for the identification of additional influences. Furthermore, ambivalent influences (a factor differently associated with 2 different outcomes) could be detected with this approach, and possible dilutive effects were avoided. We conclude that influences might be underestimated or even missed when modeling their explanatory power for an overall score only. Therefore, multivariate methods that allow for the consideration of individual body parts are an interesting option when investigating influences on plumage condition.
Keywords: farm management laying hen multiblock redundancy analysis risk factor analysis whole body plumage score.
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Materials and methods
We captured hatch year house finches Carpodacus mexicanusMüller in Auburn, Alabama, USA from early July through August. Upon capture, we took 100 μl of blood from each bird. Blood was spun to separate plasma and red blood cells, which were stored in TNE buffer at–80°C. Plasma was stored at 4°C for serological analysis (see below). In juvenile plumage, male and female house finches cannot be distinguished morphologically, so we used a molecular-sexing technique to determine the sex of the birds that we captured. Briefly, the DNA was extracted from stored red blood cells using a standard phenol/chloroform technique (Quinn and White,1987 Westneat,1993). Extracted DNA was resuspended in TE buffer and stored at–20°C. We identified the sex of the hatch year birds using P2 and P8 microsatellite primers and the PCR protocol outlined by Griffiths et al.(1998). These primers amplify introns on the CHD1-W and CHD1-Z genes. Two bands are present in females, which are the heterogametic sex, whereas males as the homogametic sex have a single band(Griffiths et al., 1998). PCR products were separated on a 1.5% agarose gel laced with ethidium bromide by electrophoresis at 150 V for 2 h.
Males were housed in small cages with 2 birds per cage for the duration of the experiment. Birds within a cage received the same experimental treatment–either infected or not infected (see below). They were held near windows so they experienced a natural light cycle. All birds had ad libitum access to a canary pellet diet (canary maintenance, Avi-Sci Inc.,St Johns, Michigan, USA). Through the molt period, we added one part tangerine juice (100% pure juice, not from concentrate, never frozen) to one part drinking water for all birds. Tangerine juice tended to spoil at room temperature so tangerine juice/water was changed every 24 h.
To ensure that none of the birds in our experiments had been previously exposed to MG, we tested the serum of each bird for antibodies to MG using a serum plate agglutination assay as described in Roberts et al.(2001). We also tested birds for the presence of MG by polymerase chain reaction (PCR Roberts et al., 2001). We collected samples for analysis by PCR by swabbing the choanal cleft using a micro-tip swab (Becton Dickinson and Co. Maryland, USA). Any birds that were found to have antibodies to MG or that were PCR-positive were excluded from the study. Coccidiosis is another widespread disease of house finches that is known to affect expression of carotenoid coloration(Brawner et al., 2000). To be certain that coccidiosis did not confound the effects of mycoplasmosis in this experiment, we added sulfadimethoxine to the water of all birds to ensure that they remained free of coccidiosis (Brawner et al., 2000)
We cultured MG from symptomatic wild house finches caught in Auburn,Alabama. We infected the birds in the MG treatment group by dropping 10 μl of SP4 medium containing 1×10 6 color-changing units ml –1 into each eye for a total dose of 2×10 4 color-changing units. This dose of MG has been effective in previous studies in inducing a modest infection among captive house finches(Roberts et al., 2001). Birds in the uninfected treatment group were sham infected with the same amount of sterile SP4. We monitored the birds daily for onset of disease. Disease was measured for each eye on a five-point scale, where 0=normal eye and 4=blindness caused by swelling (Roberts et al., 2001). We captured all birds three weeks post-inoculation to collect blood for serology and swabs for MG detection by PCR.
Following molt, we measured plumage coloration of all males using a Colortron reflectance spectrophotometer(Hill, 1998). Male house finches display carotenoid-based plumage coloration on their crown, breast and rump, and a technician with no knowledge of the experiment scored plumage color by taking three measurements in each of these areas. We averaged these measurements to obtain an overall hue, saturation and brightness for each male. We photographed the breast patch of each male along with a size standard and used Sigma Scan 5.0 to measure breast patch size. We calibrated each picture using the size standard and then traced the breast patch three times and used the average size in all analyses.
All infection protocols carried out in this study were approved by the Institutional Animal Care and Use Committee (IACUC) at Auburn University. We used the smallest sample of birds that would give us reasonable power to detect differences among groups.
The morphological data for the birds are given in Table 1. Birds with trains performed 4.6±0.7 flights and birds without trains performed 4.8±0.9 flights.
The velocity of the bird at take-off and the flight velocity of the peafowl at the end of the second wingstroke were not significantly different between the two treatments (Table 2). The overall velocity decreased during the flight the rate of loss of kinetic energy was similar across the two treatments (Table 2). The rate of change of potential energy was not significantly different between the two conditions (Table 2). Note that in all birds the rate of increase in potential energy far exceeded the rate of loss of kinetic energy hence, net positive mechanical power is required from the flight muscles to move the centre of mass of the body (CoM) of the bird. The total mass-specific power of the centre of mass of the body (PCoM calculated relative to pectoralis muscle mass) was not significantly different between birds with and without trains (train PCoM=222.6±43.3 W kg −1 no train PCoM=210.0±25.5 W kg −1 t4=0.41, ns Fig. 1A,C, Table 2).
Morphological data for peafowl Pavo cristatus
Aerodynamic forces on the peafowl train
The drag on the train increased linearly with increasing air velocity for each angle and was highest at steeper angles (Fig. 2). At the mean flight velocity for birds (4 m s −1 ) possessing a train, the drag on the train ranged from 0.12 N (level) to 0.15 N (−10 deg): during take-off, the train was held at an angle of between 0 and −10 deg relative to the angle of elevation of the flight trajectory of the bird. A small vertical lift force was produced when the train was held at angles below the horizontal (0.04 N at a train angle of −10 deg at 4 m s −1 ). This was less than 0.08% of body weight and was ignored in the calculation of induced power.
The total power requirement of take-off (Paero) was not significantly different between the two conditions (train Paero=414.1±31.2 W kg −1 no train Paero=393.3±27.1 W kg −1 t4=0.55, ns Fig. 1B, Table 2). Parasite drag was significantly higher in birds with a train compared with birds following the train's removal (Table 2). Profile power and the power required to generate the induced velocity were not significantly different between the two conditions (Table 2).
Subadult Tree Swallows from the PCB-contaminated population along the upper Hudson River had an increased amount of adult-type blue-green color in their normally brown dorsal plumage (Fig. 1). This conclusion is based on comparisons of estimates of the extent of iridescent blue-green feathers in the plumage of wild-caught subadults from the Hudson River with those of museum specimens from throughout the species' range. Although this is a simple method of estimating color, it proved to be highly repeatable for museum specimens and wild-caught birds because one person scored both samples of birds, variability among observers was not a factor.
Based on previous work with individuals of known age ( Hussell 1983), it is likely that most of the females with intermediate-colored plumage are yearlings with excessive adult-type blue-green color. Some intermediate females are older adults with abnormal amounts of brown plumage. However, this does not change our conclusion that the proportion of intermediate females is greater along the Hudson River.
Previous studies from elsewhere provide additional support for the conclusion that female Tree Swallows along the Hudson River have an abnormal pattern of color in their subadult plumage. In his study in Ontario, Hussell (1983) found that 12 of 76 (16%) of the subadult females he examined had adult-type blue-green feathers over at least 50% of their upperparts (“intermediates”). Cohen (1980) examined 67 subadult females from Colorado and estimated that 19% of his sample were “approximately 50%” blue-green, and another 6% had more extensive adult-type feathers. If half of the birds classified as “approximately 50%” were no more than 50% blue-green (the classification used by Hussell ), then 15.5% of Colorado subadults would have had ≥50% blue-green plumage, and the remainder would have had <50%. Both of these studies are consistent with our estimates of plumage color in museum specimens where 14% (11 of 80) of the subadults were given plumage scores ≥50%. In contrast, 46% (29 of 63) of the Hudson River Tree Swallows were classified as ≥50% blue-green.
It is not known if this association between PCB contamination and plumage color of females exists in other populations of Tree Swallows. Previous studies of Tree Swallows have reported much lower levels of PCB contamination than found along the Hudson River ( Ankley et al. 1993, Bishop et al. 1995, Nichols et al. 1995, Secord et al. 1999). The high concentrations of PCBs in the Hudson River, combined with the size of the contaminated area, have created a situation where such effects on populations would be more easily detected. Because the Hudson River dominates the landscape in the study area, it is likely that individuals from a large surrounding area are exposed to PCBs while feeding over the river prior to and during migration. This may not be true of other sites where contamination is more localized and where only birds breeding adjacent to the source of contaminants will be exposed.
Plumage color is important in the biology of birds in that it mediates a wide variety of interactions among individuals ( Butcher and Rohwer 1989, Andersson 1994, Savalli 1995), including mate choice ( Norris 1990, Hill 1990) and territoriality ( Stutchbury 1991). Evidence from several species indicates that variation in plumage characters may be an indicator of an individual's social status ( Rohwer 1977, Jarvi and Bakken 1984, Möller 1987) and genetic or physiological quality ( Hill 1991, 1992 Norris 1993). The function of subadult plumage in Tree Swallows is not fully understood, but plumage color may act as a signal of age and sex to conspecifics, reducing levels of aggression directed at brown subadult females ( Lyon and Montgomerie 1986, Stutchbury and Robertson 1987). Numerous studies have shown that brown subadult females have smaller clutch sizes and lower reproductive success ( De Steven 1978, Lombardo 1984, Stutchbury and Robertson 1988, Wheelwright and Schultz 1994, Winkler and Allen 1996 but see Lozano and Handford 1995), both because they are smaller and have lower fat and protein reserves than adult females ( Lozano and Handford 1995), and because high-quality males may preferentially mate with iridescent blue-green adults.
Although these previous studies have documented differences between brown subadult females and older blue-green females, to our knowledge no study has examined the implications of variation among subadults. We found no relationship between the color of subadults and reproductive success as measured by number of fledglings or fledglings per egg, but brighter females bred significantly earlier in the season and laid larger clutches (Fig. 3). A robust relationship exists between early breeding and reproductive success in a wide range of birds (see Price et al. 1988, Winkler and Allen 1996), suggesting that breeding date is an important indicator of other aspects of an individual's quality. More colorful subadult females lay larger clutches, but this is confounded by the relationship between breeding date and clutch size in this and other Tree Swallow populations ( Stutchbury and Robertson 1988, Winkler and Allen 1996). Multivariate analysis that included female color and breeding date suggests that the relationship between breeding date and color is responsible for differences in clutch size among subadults (Fig. 3).
The differences in subadult color we report are unlikely to result from natural differences among subpopulations because no subspecies of Tree Swallows have been recognized, nor has geographic variation in plumage been described. Moreover, birds from Ontario ( Hussell 1983), Colorado ( Cohen 1980), and the rest of North America (this study) generally had consistent patterns of plumage color, as did museum specimens collected in New York.
It also is unlikely that the difference between museum specimens and the Hudson River birds results from fading or other changes in museum specimens because the blue-green color of Tree Swallows is structural in origin, rather than pigment-based. Examination of male Tree Swallows more than 100 years old showed no signs of fading, and we found no relationship between the age of a museum specimen and its color score (Fig. 2). Another valid concern is that museum specimens represent a biased sample of the wild population (e.g. a collector might have avoided taking intermediate females). However, the fact that collections at two different museums, as well as the results of two independent field studies ( Cohen 1980, Hussell 1983), consist of low numbers of intermediate females makes it highly unlikely that the patterns presented here result from a collection bias against intermediate females.
The one obvious difference between the Hudson River and elsewhere in the range of Tree Swallows where museum specimens have been collected is that the Hudson River is the most heavily contaminated PCB site in the United States ( Limburg 1986). The locations where most of the adults in this study were born are not known. However, available data indicate that natal dispersal in Tree Swallows is limited and that the majority of surviving nestlings breed within 20 km of their natal nest site ( Cohen et al. 1989, Robertson et al. 1992), suggesting that most of the individuals we captured were born in the Hudson River Valley.
During both the prebreeding and postbreeding period, we observed large concentrations of Tree Swallows feeding on the abundant insects emerging from the Hudson River. It is likely that birds from a wide area are exposed to PCBs from the Hudson River prior to and during molt. Molt in female Tree Swallows occurs after the breeding season and generally before migration ( Stutchbury and Rohwer 1990). The persistent nature of PCBs in the body means that even individuals molting months after exposure to Hudson River PCBs will be contaminated ( Stickel et al. 1984).
Field biologists usually focus on traits such as reproductive success or gross morphological changes when screening for effects of environmental contaminants on wildlife. Although a relationship appears to exist between PCB contamination and reproductive success and behavior in this population of Tree Swallows ( McCarty and Secord 1999a,b), changes in plumage color may prove to be a reliable means of screening for effects of contamination. Environmental disturbances may have a stronger effect on ornamental traits, such as the plumage dimorphism in Tree Swallows, than on traits under strong natural selection ( Møller 1993, Hill 1995). In condition-dependent traits such as tail length, pigments derived from food sources, or the degree of asymmetry in bilateral traits, the quality of ornamental traits is expected to decrease under environmental stress. The direction of effects on ornamental traits that are not condition dependent, such as subadult plumage, cannot be predicted without a detailed understanding of the mechanisms that determine the expression of the trait. The patterns described here are consistent with hormonal abnormalities that result in the early expression of an adult trait.
We report a positive correlation between plumage color and timing of breeding and suggest a role for PCBs in increasing the average color of subadult females, but it is important to note that this does not suggest that PCB contamination leads to overall higher reproductive success in Tree Swallows. Indeed, we have evidence that Tree Swallows in this population suffer from decreased reproductive success ( McCarty and Secord 1999b). Any positive benefits to individual subadult females associated with their abnormally bright plumage color simply acts to moderate the other negative effects of contamination, such as reduced hatchability of eggs. In fact, evidence for an adaptive benefit of brown plumage in young females ( Lyon and Montgomerie 1986, Stutchbury and Robertson 1987) emphasizes that abnormally colorful plumage in young birds is likely to be detrimental.
The correlational nature of our study makes it impossible to establish a causal relationship between PCB contamination and female plumage color. Logistical and ethical difficulties associated with experimentally introducing toxins into the environment make establishing causality difficult in most field studies of effects of contamination on behavior ( Peakall 1996). However, a plausible link exists between PCBs and plumage color because PCBs are suspected to interfere with normal functioning of the endocrine system ( Guillette et al. 1995, Eisler and Belisle 1996). The hormonal basis for subadult plumage in Tree Swallows has not been studied, but sex-specific differences in plumage generally are under hormonal control ( Fivizzani et al. 1990, Collis and Borgia 1992, Owens and Short 1995, Lank et al. 1999). Although field studies such as ours seldom have been able to demonstrate a causal link between contaminants and their effects, they have been important in identifying possible effects of contaminants that would not be identified from carefully controlled laboratory experiments ( Blus and Henny 1997).
X-rays reveal new picture of 'dinobird' plumage patterns
The first complete chemical analysis of feathers from Archaeopteryx, a famous fossil linking dinosaurs and birds, reveals that the feathers of this early bird were patterned - light in colour, with a dark edge and tip to the feather ­­- rather than all black, as previously thought.
The findings came from X-ray experiments undertaken by a team from the University of Manchester, working with colleagues at the US Department of Energy's (DOE) SLAC National Accelerator Laboratory. The scientists were able to find chemical traces of the original 'dinobird' and dilute traces of plumage pigments in the 150 million-year-old fossil.
"This is a big leap forward in our understanding of the evolution of plumage and also the preservation of feathers," said Dr Phil Manning, a palaeontologist at The University of Manchester and lead author of the report in the June 13 issue of the Journal of Analytical Atomic Spectrometry (Royal Society of Chemistry).
Only 11 specimens of Archaeopteryx have been found, the first one consisting of a single feather. Until a few years ago, researchers thought minerals would have replaced all the bones and tissues of the original animal during fossilisation, leaving no chemical traces behind, but two recently developed methods have turned up more information about the dinobird and its plumage.
The first is the discovery of melanosomes - microscopic 'biological paint pot' structures in which pigment was once made, but are still visible in some rare fossil feathers. A team led by researchers at Brown University announced last year that an analysis of melanosomes in the single Archaeopteryx feather indicated it was black. They identified the feather as a covert - a type of feather that covers the primary and secondary wing feathers - and said its heavy pigmentation may have strengthened it against the wear and tear of flight, as it does in modern birds.
However, that study examined melanosomes from just a few locations in the fossilised feather, explained SLAC's Dr Uwe Bergmann: "It's actually quite a beautiful paper," he said, "but they took just tiny samples of the feather, not the whole thing."
The second is a method that Drs Bergmann, Manning and Roy Wogelius have developed for rapidly scanning entire fossils and analysing their chemistry with an X-ray beam at SLAC's Stanford Synchrotron Radiation Lightsource (SSRL) in the USA.
Over the past three years, the team used this method to discover chemical traces locked in the dinobird's bones, feathers and in the surrounding rock, as well as pigments from the fossilised feathers of two specimens of another species of early bird. This allowed the team to recreate the plumage pattern of an extinct bird for the very first time.
In the latest study, the team scanned the entire fossil of the first Archaeopteryx feather with the SSRL X-ray beam. They found trace-metals that have been shown to be associated with pigment and organic sulphur compounds that could only have come from the animal's original feathers.
"The fact that these compounds have been preserved in-place for 150 million years is extraordinary," said Dr Manning said. "Together, these chemical traces show that the feather was light in colour with areas of darker pigment along one edge and on the tip.
"Scans of a second fossilised Archaeopteryx, known as the Berlin counterpart, also show that the trace-metal inventory supported the same plumage pigmentation pattern."
Co-author Dr Roy Wogelius, also based in Manchester's School of Earth, Atmospheric and Environmental Sciences, said: "This work refines our understanding of pigment patterning in perhaps the most important known fossil. Our technique shows that complex patterns were present even at the very earliest steps in the evolution of birds."
The team's results show that the chemical analysis provided by synchrotron X-ray sources, such as SSRL, is crucial when studying the fossil remains of such pivotal species. The plumage patterns can begin to help scientists review their possible role in the courtship, reproduction and evolution of birds and possibly shed new light on their health, eating habits and environment.
Dr Manning added: "It is remarkable that x-rays brighter than a million suns can shed new light on our understanding of the processes that have locked elements in place for such vast periods of time. Ultimately, this research might help inform scientists on the mechanisms acting during long-term burial, from animal remains to hazardous waste. The fossil record has potential to provide the experimental hindsight required in such studies."
The research team included scientists from The University of Manchester (UK) SLAC (USA) the Black Hills Institute of Geological Research in South Dakota (USA) and the Museum für Naturkunde in Berlin (Germany), which provided the stunning Archaeopteryx fossils for analysis.
We developed a novel approach to evaluating condition of California brown pelicans in the field following oil spill rehabilitation and release. We found that it was possible to locate adequate samples of post-spill birds without the aid of electronic tracking devices, although it required a lot of survey effort at roost sites that were both heavily used and conducive to close observations. Our results suggest that there were subtle lingering physiological effects of pollution exposure and rehabilitation in the first year after the spill that caused significant differences in crown and gular pouch appearance, contrary to the null hypothesis. Condition-dependent signals represent the sum of environmental pressures on an animal . In this case, the burden of wearing electronic transmitters appeared to be a hindrance to recovery of previously oiled, rehabilitated pelicans and confounded the results of the study. While GPS-PTT tagged birds survived and initially appeared to move normally [50, 56], there was evidently ongoing stress that resulted in a general failure to express gular redness prior to the breeding season for both oiled and non-oiled birds bearing the tags. We recommend that a similar study be repeated without the additional variable of electronic transmitters and with a focus on documenting gular pouch redness in the pre-breeding phase.
Although our results were unexpected with regard to the strong influence of the GPS-PTT tags , broad literature reviews have concluded that transmitters negatively affect most aspects of bird behavior and ecology to some degree and may bias resulting data [60, 61]. Kesler et al.  found that mallards (Anas platyrhynchos) fitted with dummy transmitters attached with Teflon ribbon harness had lower body mass than controls without equipment. Fitted mallards also tended to avoid water, presumably due to greater energetic expenditure to thermoregulate in cold weather and compromised feather insulation caused by the equipment. In our study, one of the equipment-related stressors for pelicans was likely similar bodily heat loss due to plumage disruption around the chest harness and transmitter (see Fig 2B) an issue that may have become aggravated over time.
The fact that there was no discernible difference in plumage quality with respect to waterproofing between previously oiled pelicans marked with leg band-only and the general population was an important finding. Current rehabilitation methods include techniques to ensure that plumage integrity is restored through washing and self-preening and are not released until the birds have met restored waterproofing criteria . This is a major advance compared to the early days of seabird oil-spill rehabilitation, when plumage restoration seemed impossible to achieve .
Plumage phase differences between oiled and non-oiled birds could indicate stressors associated with oil exposure, rehabilitation, and/or tracking equipment. A wide range of debilitating sublethal impacts following oil exposure have been previously described [4, 8, 13, 26], but impacts on subsequent feather replacement have not been specified. Our finding that post-spill pelicans moved through the prebasic hindneck plumage transition (from brown to white feathering) at a rate insignificantly different from the general population indicated that this molt process proceeded normally despite the trauma of the spill event.
Sexual signals, including plumage colors that depend on antioxidants such as carotenoids, offer a more sensitive measure of the immunological and nutritional state of animals, since bodily antioxidants tend to be directed to other functions related to survival at the expense of the expression of the sexual traits [64–67]. The less frequent occurrence of yellow crown plumage observed in post-spill pelicans in this study seemed to indicate such a trade-off, but we could not determine if lack of yellow was due to lagging molt or absence of pigmentation in emerged feathers. In addition, brown pelican head rubbing on the uropygial gland may increase the crown’s golden appearance due to adventitious coloring from the sebaceous oils after yellow feathers have emerged [34, 35]. It seems important to note that some of the behaviors we observed in the field suggested that the backpack transmitters may have obstructed normal access to the preen gland by the head, which could result in a less intense yellow hue to the crown and represent another negative impact. Color deficiencies in ornamental plumage may affect mate acquisition and subsequent breeding success . Future field researchers may be able to improve methodology by using calibrated photographs and spectrometers to distinguish variation in the crown’s yellow hue .
If one assumes that the red gular pouch provides a positive measure of health in the California brown pelican, our results suggest that, although not equal to the general population, the post-spill birds released with only bands were in relatively good condition going into the first breeding season after the spill, that numerous complex interacting physiological mechanisms were functioning, and that many of these birds could afford the additional costs of color display [46, 69]. Developing and maintaining bright gular coloration in the brown booby (Sula leucogaster) apparently incurs oxidative costs for both sexes . Perhaps most importantly, our finding that post-spill pelicans with redder pouches tended to be encountered at a higher rate in subsequent years suggests that gular color may also predict overall survival. Parasite load, nutritional status, and immunocompetence are some of the possible links between survival and color of a dynamic avian integument feature [70–72]. The gular pouch will probably reflect a pelican’s current condition better than plumage color during the pre-breeding season. Dey et al.  found that a bare-part ornament was a more reliable status signal than plumage color in a cooperatively breeding bird and recommended an increased focus on bare-parts to expand understanding of animal communication.
Relationships between body condition, integument color, and breeding success are relatively well-known for several seabird species but are not fully understood in the brown pelican. Investigation of the underlying mechanisms surrounding gular pouch color expression and how it relates to pelican fitness would increase the utility of using pouch color in future studies. In the sexually dimorphic great frigatebird, for example, the male displays a bright red inflated throat pouch during courtship that rapidly fades to orange at the onset of incubation. Astaxanthin, a carotenoid pigment, has been found in very high concentrations in the outer dermal layer of the pouch . The spectral pattern of color and the vascularization of the pouch suggests that along with carotenoids, increased blood flow and the presence of hemoglobin may contribute substantially to the overall coloration of the pouch during the display period . Variation in displaying male frigatebird pouch color has been positively correlated to breeding success . The blue and green gular skin color in both sexes of breeding brown boobies is thought to be due to a combination of structural color mechanisms and allocation of carotene pigments . Males expressing greener gular color were found to have increased parental investment in chicks [47, 75]. Kittiwakes in good body condition displayed brighter carotenoid based integument colors around the eye, gape and tongue, than those in poor condition . Pouch color of other brown pelican subspecies varies but none are typically red [35, 36] adding interest to questions surrounding color mechanism and signaling function of the gular pouch in this species.
Targeted field surveys with large sample sizes and from wide geographic ranges are also needed to better establish or update baseline patterns and variation in molt and seasonal color change for California brown pelicans. Schreiber et al.  noted that there were many questions surrounding brown pelican molt, including how food supply, region of residence, age, sex, and the interaction between these and other factors, may affect feather replacement these questions also apply to gular pouch color. For example, we found that gular pouch redness occurred three months earlier than previously described [34, 35]. We saw many birds with red pouches by September at nonbreeding communal roosts, where pouch displays are often used in social interactions .
Chronology and outcome of annual breeding effort can affect timing of avian molt [34, 38] but it is not clear how that may have factored into our study results. During the period 2014–2016 there was unprecedented breeding failure throughout much of California brown pelican range due to environmental conditions . Electronic tracking results  suggest that pelicans oiled in the Refugio spill included birds from Mexican breeding colonies that had failed or forgone breeding in 2015, and were migrating north along the California coast when caught in the spill. Although pelicans with GPS-PTT tags visited breeding colonies in 2016, none were known to successfully breed .
Despite the challenges, field tracking and visual assessment of plumage and gular pouch color of marked brown pelicans has good potential for future ecotoxicology and post-release studies. The expression of gular pouch redness likely plays a role in behavioral ecology at non-breeding communal roosts, as well as breeding colonies, and may provide a valuable window into many aspects of California brown pelican health and fitness. This study also serves as a reminder to use caution when interpreting data based on animals bearing a significant equipment burden and will hopefully help encourage development of improved remote tracking techniques for brown pelicans.