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Monday, 12 October 2015

What's new for 'birdRS' in PubMed: October 2015, Week 1

birdRS-Latest News

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).

View complete results in PubMed (results may change over time).


PubMed Results


1. PLoS One. 2015 Oct 9;10(10):e0139600. doi: 10.1371/journal.pone.0139600. 

Can Observation Skills of Citizen Scientists Be Estimated Using Species Accumulation Curves? 
Kelling S(1), Johnston A(2), Hochachka WM(1), Iliff M(1), Fink D(1), Gerbracht J(1), Lagoze C(3), La Sorte FA(1), Moore T(4), Wiggins A(5), Wong WK(4), Wood C(1), Yu J(4). Author information: (1)Cornell Lab of Ornithology, Cornell University, Ithaca, New York, United States of America. (2)British Trust for Ornithology, Thetford, Norfolk, England, United Kingdom. (3)School of Information, University of Michigan, Ann Arbor, Michigan, United States of America. (4)School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, United States of America. (5)College of Information Studies, University of Maryland, College Park, Maryland, United States of America. 

Abstract
Volunteers are increasingly being recruited into citizen science projects to collect observations for scientific studies. An additional goal of these projects is to engage and educate these volunteers. Thus, there are few barriers to participation resulting in volunteer observers with varying ability to complete the project's tasks. To improve the quality of a citizen science project's outcomes it would be useful to account for inter-observer variation, and to assess the rarely tested presumption that participating in a citizen science projects results in volunteers becoming better observers. Here we present a method for indexing observer variability based on the data routinely submitted by observers participating in the citizen science project eBird, a broad-scale monitoring project in which observers collect and submit lists of the bird species observed while birding. Our method for indexing observer variability uses species accumulation curves, lines that describe how the total number of species reported increase with increasing time spent in collecting observations. We find that differences in species accumulation curves among observers equates to higher rates of species accumulation, particularly for harder-to-identify species, and reveals increased species accumulation rates with continued participation. We suggest that these properties of our analysis provide a measure of observer skill, and that the potential to derive post-hoc data-derived measurements of participant ability should be more widely explored by analysts of data from citizen science projects. We see the potential for inferential results from analyses of citizen science data to be improved by accounting for observer skill. PMID: 26451728 [PubMed - as supplied by publisher] 



2. Vet Anaesth Analg. 2015 Oct 9. doi: 10.1111/vaa.12305. [Epub ahead of print] 

Pilot study of long-term anaesthesia in broiler chickens. 
O'Kane PM(1), Connerton IF(1), White KL(2). Author information: (1)Division of Food Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, UK. (2)School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK. 

Abstract
OBJECTIVE: To provide stable anaesthesia of long duration in broiler chickens in order to perform a terminal caecal ligated loop procedure. STUDY DESIGN: Prospective experimental study. ANIMALS: Seven clinically healthy broiler chickens (Gallus domesticus) aged 27-36 days, weighing 884-2000 g. METHODS: Anaesthesia was induced and maintained with isoflurane in oxygen. All birds underwent intermittent positive pressure ventilation for the duration. End-tidal carbon dioxide, peripheral haemoglobin oxygen saturation, heart rate and oesophageal temperature were monitored continuously. All birds received intraosseous fluids. Butorphanol (2 mg kg(-1) ) was administered intramuscularly at two hourly intervals. Euthanasia by parenteral pentobarbitone was performed at the end of procedure. RESULTS: Stable anaesthesia was maintained in four chickens for durations ranging from 435 to 510 minutes. One bird died and one was euthanized after 130 and 330 minutes, respectively, owing to surgical complications and another died from anaesthetic complication after 285 minutes. CONCLUSIONS AND CLINICAL RELEVANCE: Long-term, stable anaesthesia is possible in clinically healthy chickens, provided complications such as hypothermia and hypoventilation are addressed and vital signs are carefully monitored. There are no known previous reports describing monitored, controlled anaesthesia of this duration in chickens. © 2015 The Authors Veterinary Anaesthesia and Analgesia published by John Wiley & Sons Ltd on behalf of Association of Veterinary Anaesthetists and the American College of Veterinary Anesthesia and Analgesia. PMID: 26449623 [PubMed - as supplied by publisher] 


3. Gen Comp Endocrinol. 2015 Oct 5. pii: S0016-6480(15)30003-4. doi: 10.1016/j.ygcen.2015.10.002. [Epub ahead of print] 

A state of non-specific tension in living matter? Stress in Australian Animals. 
Bradshaw D(1). Author information: (1)School of Animal Biology, The University of Western Australia, Perth, WA, Australia 6009. Electronic address: Don.Bradshaw@uwa.edu.au. 

Abstract
Evidence of stress responses in Australian animals is reviewed through a series of case studies involving desert frogs and lizards, small carnivorous marsupials, desert wallabies, a dwarf kangaroo species, the quokka wallaby and a small nectarivorous bird. An operational definition of stress as "the physiological resultant of demands that exceed an animal's homeostatic capacities" is used to identify instances of stress responses in the field, and to gauge their intensity. Clear evidence of stress responses is found in small dasyurid marsupial carnivores, and desert agamid lizards, both of which are semelparous. Other instances of seasonal stress responses include the Rottnest Island quokka, the barrow Island euro kangaroo and a small nectarivorous bird, the Silvereye. The review also highlights the high level of physiological adaptation of some desert wallabies, such as the Spectacled hare wallaby, which is able to maintain physiological homeostasis in the field when challenged by conditions of extreme drought. The importance of thermal and hygric refugia for the long-term survival or rock wallabies, which apparently lack any hormonal control of renal function, is also highlighted. Copyright © 2015. Published by Elsevier Inc. PMID: 26449159 [PubMed - as supplied by publisher] 


4. Environ Sci Technol. 2015 Oct 8. [Epub ahead of print] 

Assessing the risk of fipronil treated seed ingestion and associated adverse effects in the red-legged partridge. 
Lopez-Antia A, Ortiz-Santaliestra ME, Camarero PR, Mougeot F, Mateo R. 

Abstract
Fipronil is an insecticide commonly used in agriculture, but there are growing concerns over its environment impacts (e.g. harmful effects on pollinators). Fipronil-treated seed ingestion might threaten granivorous farmland birds, in particular Gallinaceous birds that are particularly sensitive to this insecticide. We report here on exposure risk and effects in a game bird of high socio-economic importance, the red-legged partridge (Alectoris rufa). We fed captive birds with untreated maize (controls) or with a mixture of untreated-treated maize (ratio 80:20; exposed birds) during 10 days at the beginning of the breeding period (n=12 pairs in each group). We first show that exposed partridges did not reject treated seeds, but reduced food intake and lost body condition. We further studied the effects of treated seed ingestion on adult survival, oxidative balance, plasma biochemistry, carotenoid-based coloration, cellular immune response, steroid hormone levels and reproduction. Fipronil exposure altered blood biochemistry and sexual hormone levels, reduced cellular immune response, antioxidant levels and carotenoid-based coloration. Exposed pairs also had reduced egg fecundation rate, produced eggs with fewer antioxidants and offspring that had reduced cellular immune response. These negative effects on adult partridges, their reproductive performance and offspring quality highlight that fipronil-treated seed ingestion is a significant threat to wild birds. PMID: 26448319 [PubMed - as supplied by publisher] 


5. PLoS One. 2015 Oct 8;10(10):e0140145. doi: 10.1371/journal.pone.0140145. eCollection 2015. 

Marshes as "Mountain Tops": Genetic Analyses of the Critically Endangered São Paulo Marsh Antwren (Aves: Thamnophilidae). 
de Camargo C(1), Gibbs HL(2), Costa MC(3), Del-Rio G(4), Silveira LF(5), Wasko AP(1), Francisco MR(3). Author information: (1)Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Distrito de Rubião Júnior, s/n, CEP 18618-970, Botucatu, São Paulo, Brazil. (2)Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio 43210-1293, United States of America. (3)Departamento de Ciências Ambientais, Universidade Federal de São Carlos, Campus de Sorocaba, Rod. João Leme dos Santos, km 110, CEP 18052-780, Sorocaba, São Paulo, Brazil. (4)Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana 70803, United States of America. (5)Seção de Aves, Museu de Zoologia da Universidade de São Paulo, Caixa Postal 42494, CEP 04218-970, São Paulo, São Paulo, Brazil. 

Abstract
Small populations of endangered species can be impacted by genetic processes such as drift and inbreeding that reduce population viability. As such, conservation genetic analyses that assess population levels of genetic variation and levels of gene flow can provide important information for managing threatened species. The São Paulo Marsh Antwren (Formicivora paludicola) is a recently-described and critically endangered bird from São Paulo State (Brazil) whose total estimated population is around 250-300 individuals, distributed in only 15 isolated marshes around São Paulo metropolitan region. We used microsatellite DNA markers to estimate the population genetic characteristics of the three largest remaining populations of this species all within 60 km of each other. We detected a high and significant genetic structure between all populations (overall FST = 0.103) which is comparable to the highest levels of differentiation ever documented for birds, (e.g., endangered birds found in isolated populations on the tops of African mountains), but also evidence for first-generation immigrants, likely from small local unsampled populations. Effective population sizes were small (between 28.8-99.9 individuals) yet there are high levels of genetic variability within populations and no evidence for inbreeding. Conservation implications of this work are that the high levels of genetic structure suggests that translocations between populations need to be carefully considered in light of possible local adaptation and that remaining populations of these birds should be managed as conservation units that contain both main populations studied here but also small outlying populations which may be a source of immigrants. PMID: 26447791 [PubMed - in process] 


6. Br Poult Sci. 2015 Oct 8. [Epub ahead of print] 

Optimisation of broiler chicken responses from 0 to 7 days of age to dietary leucine, iso-leucine and valine using Taguchi and mathematical methods. 
Sedghi M(1), Golian A(1), Kolahan F(2), Afsar A(3). Author information: (1)a Animal Science Department, Faculty of Agriculture , Ferdowsi University of Mashhad , Mashhad , Iran. (2)b Department of Mechanical Engineering , Ferdowsi University of Mashhad , Tehran , Iran. (3)c Evonik Degussa Iran AG , Tehran , Iran. 

Abstract
1. Three experiments were conducted to evaluate the applicability of the Taguchi method (TM) and optimisation algorithms to optimise the branch chain amino acids (BCAA) requirements in 0 to 7 d broiler chicks. 2. In the first experiment, the standardised digestible amino acids (SID) and AME values of maize, wheat and soya bean meal were evaluated. 3. In the second experiment, three factors including Leucine (Leu), Isoleucine (Ile) and Valine (Val), each at 4 levels, were selected, and an orthogonal array layout of L16 (4(3)) using TM was performed. After data collection, optimisation of average daily gain (ADG) and feed conversion ratio (FCR) were obtained using TM. The multi-objective genetic algorithm (MOGA) and random search algorithm (RSA) were also applied to predict the optimal combination of BCAA for broiler performance. 4. In the third experiment a growth study was conducted to evaluate the applicability of obtained optimum BCAA requirements data by TM, MOGA and RSA and results were compared to those of birds fed with a diet formulated according to Ross 308 recommendation. 5. In the second experiment, the TM resulted in 13.45 g/kg SID Leu, 8.5 g/kg SID Ile and 10.45 g/kg SID Val as optimum level for maximum ADG (21.57 g/bird/d) and minimum FCR (1.11 g feed/g gain) in 0 to 7 d old broiler chickens. MOGA predicted the following combinations: SID Leu = 14.8, SID Ile = 9.1 and SID Val = 10.3 for maximum ADG (22.05) and minimum FCR (1.11). The optimisation using RSA predicted Leu = 16.0, Ile = 9.5 and Val = 10.2 for maximum ADG (22.67), and Leu = 15.5, Ile = 9.0 and Val = 10.4 to achieve minimum FCR (1.08). 6. The validation experiment confirmed that TM, MOGA and RSA yielded optimum determination of dietary amino acid requirements and improved ADG and FCR as compared to Aviagen recommendations. However based on the live animal validation trial MOGA and RSA over-predicted the optimum requirement as compared to TM. In general, the results of these studies showed that the TM may be used to optimise nutrient requirements for poultry. PMID: 26447759 [PubMed - as supplied by publisher] 


7. PLoS One. 2015 Oct 7;10(10):e0137997. doi: 10.1371/journal.pone.0137997. eCollection 2015. 

A Landscape-Scale, Applied Fire Management Experiment Promotes Recovery of a Population of the Threatened Gouldian Finch, Erythrura gouldiae, in Australia's Tropical Savannas. 
Legge S(1), Garnett S(2), Maute K(3), Heathcote J(1), Murphy S(4), Woinarski JC(2), Astheimer L(5). Author information: (1)Australian Wildlife Conservancy, PO Box 8070, Subiaco East, WA, 6008, Australia. (2)Research Institute for the Environment and Livelihoods and Threatened Species Recovery Hub of the National Environmental Science Programme, Charles Darwin University, NT, 0909, Australia. (3)Australian Wildlife Conservancy, PO Box 8070, Subiaco East, WA, 6008, Australia; Institute of Conservation Biology and Environmental Management, University of Wollongong, Wollongong, NSW, 2522, Australia. (4)Australian Wildlife Conservancy, PO Box 8070, Subiaco East, WA, 6008, Australia; Bush Heritage Australia, Collins St, Melbourne, VIC, Australia. (5)Deakin University, DVC Research Office, Locked Bag 20000, Geelong, VIC, 3220, Australia. 

Abstract
Fire is an integral part of savanna ecology and changes in fire patterns are linked to biodiversity loss in savannas worldwide. In Australia, changed fire regimes are implicated in the contemporary declines of small mammals, riparian species, obligate-seeding plants and grass seed-eating birds. Translating this knowledge into management to recover threatened species has proved elusive. We report here on a landscape-scale experiment carried out by the Australian Wildlife Conservancy (AWC) on Mornington Wildlife Sanctuary in northwest Australia. The experiment was designed to understand the response of a key savanna bird guild to fire, and to use that information to manage fire with the aim of recovering a threatened species population. We compared condition indices among three seed-eating bird species-one endangered (Gouldian finch) and two non-threatened (long-tailed finch and double-barred finch)-from two large areas (> 2,830 km2) with initial contrasting fire regimes ('extreme': frequent, extensive, intense fire; versus 'benign': less frequent, smaller, lower intensity fires). Populations of all three species living with the extreme fire regime had condition indices that differed from their counterparts living with the benign fire regime, including higher haematocrit levels in some seasons (suggesting higher levels of activity required to find food), different seasonal haematocrit profiles, higher fat scores in the early wet season (suggesting greater food uncertainty), and then lower muscle scores later in the wet season (suggesting prolonged food deprivation). Gouldian finches also showed seasonally increasing stress hormone concentrations with the extreme fire regime. Cumulatively, these patterns indicated greater nutritional stress over many months for seed-eating birds exposed to extreme fire regimes. We tested these relationships by monitoring finch condition over the following years, as AWC implemented fire management to produce the 'benign' fire regime throughout the property. The condition indices of finch populations originally living with the extreme fire regime shifted to resemble those of their counterparts living with the benign fire regime. This research supports the hypothesis that fire regimes affect food resources for savanna seed-eating birds, with this impact mediated through a range of grass species utilised by the birds over different seasons, and that fire management can effectively moderate that impact. This work provides a rare example of applied research supporting the recovery of a population of a threatened species. PMID: 26445496 [PubMed - in process] 


8. PLoS One. 2015 Oct 7;10(10):e0139734. doi: 10.1371/journal.pone.0139734. eCollection 2015. 

The Hoopoe's Uropygial Gland Hosts a Bacterial Community Influenced by the Living Conditions of the Bird. 
Rodríguez-Ruano SM(1), Martín-Vivaldi M(2), Martín-Platero AM(1), López-López JP(1), Peralta-Sánchez JM(1), Ruiz-Rodríguez M(3), Soler JJ(3), Valdivia E(1), Martínez-Bueno M(1). Author information: (1)Departamento de Microbiología, Universidad de Granada, Granada, Spain. (2)Departamento de Zoología, Universidad de Granada, Granada, Spain. (3)Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas (CSIC), Almería, Spain. 

Abstract
Molecular methods have revealed that symbiotic systems involving bacteria are mostly based on whole bacterial communities. Bacterial diversity in hoopoe uropygial gland secretion is known to be mainly composed of certain strains of enterococci, but this conclusion is based solely on culture-dependent techniques. This study, by using culture-independent techniques (based on the 16S rDNA and the ribosomal intergenic spacer region) shows that the bacterial community in the uropygial gland secretion is more complex than previously thought and its composition is affected by the living conditions of the bird. Besides the known enterococci, the uropygial gland hosts other facultative anaerobic species and several obligated anaerobic species (mostly clostridia). The bacterial assemblage of this community was largely invariable among study individuals, although differences were detected between captive and wild female hoopoes, with some strains showing significantly higher prevalence in wild birds. These results alter previous views on the hoopoe-bacteria symbiosis and open a new window to further explore this system, delving into the possible sources of symbiotic bacteria (e.g. nest environments, digestive tract, winter quarters) or the possible functions of different bacterial groups in different contexts of parasitism or predation of their hoopoe host. PMID: 26445111 [PubMed - in process] 


9. PLoS One. 2015 Oct 7;10(10):e0138295. doi: 10.1371/journal.pone.0138295. eCollection 2015. 

Territory Quality and Plumage Morph Predict Offspring Sex Ratio Variation in a Raptor. 
Chakarov N(1), Pauli M(1), Mueller AK(1), Potiek A(1), Grünkorn T(2), Dijkstra C(3), Krüger O(1). Author information: (1)Department of Animal Behaviour, Bielefeld University, PO Box 10 01 31, 33501, Bielefeld, Germany. (2)BioConsult SH, Brinckmannstr. 31, 25813, Husum, Germany. (3)Behavioural Biology, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands. 

Abstract
Parents may adapt their offspring sex ratio in response to their own phenotype and environmental conditions. The most significant causes for adaptive sex-ratio variation might express themselves as different distributions of fitness components between sexes along a given variable. Several causes for differential sex allocation in raptors with reversed sexual size dimorphism have been suggested. We search for correlates of fledgling sex in an extensive dataset on common buzzards Buteo buteo, a long-lived bird of prey. Larger female offspring could be more resource-demanding and starvation-prone and thus the costly sex. Prominent factors such as brood size and laying date did not predict nestling sex. Nonetheless, lifetime sex ratio (LSR, potentially indicative of individual sex allocation constraints) and overall nestling sex were explained by territory quality with more females being produced in better territories. Additionally, parental plumage morphs and the interaction of morph and prey abundance tended to explain LSR and nestling sex, indicating local adaptation of sex allocation However, in a limited census of nestling mortality, not females but males tended to die more frequently in prey-rich years. Also, although females could have potentially longer reproductive careers, a subset of our data encompassing full individual life histories showed that longevity and lifetime reproductive success were similarly distributed between the sexes. Thus, a basis for adaptive sex allocation in this population remains elusive. Overall, in common buzzards most major determinants of reproductive success appeared to have no effect on sex ratio but sex allocation may be adapted to local conditions in morph-specific patterns. PMID: 26445010 [PubMed - in process] 


10. Nature. 2015 Oct 7. doi: 10.1038/nature15697. [Epub ahead of print] 

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. 
Prum RO(1,)(2), Berv JS(3), Dornburg A(1,)(2,)(4), Field DJ(2,)(5), Townsend JP(1,)(6), Lemmon EM(7), Lemmon AR(8). Author information: (1)Department of Ecology &Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA. (2)Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA. (3)Department of Ecology and Evolutionary Biology, Fuller Evolutionary Biology Program, Cornell University, and Cornell Laboratory of Ornithology, Ithaca, New York 14853, USA. (4)North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27601, USA. (5)Department of Geology &Geophysics, Yale University, New Haven, Connecticut 06520, USA. (6)Department of Biostatistics, and Program in Computational Biology and Bioinformatics, Yale University, NewHaven, Connecticut 06520, USA. (7)Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA. (8)Department of Scientific Computing, Florida State University, Tallahassee, Florida 32306, USA. 

Abstract
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves-a clade that encompasses nearly all living bird species-remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades-Columbea and Passerea-were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction. PMID: 26444237 [PubMed - as supplied by publisher] 


11. Front Psychol. 2015 Sep 28;6:1416. doi: 10.3389/fpsyg.2015.01416. eCollection 2015. 

Social coordination in animal vocal interactions. Is there any evidence of turn-taking? The starling as an animal model. 
Henry L(1), Craig AJ(2), Lemasson A(3), Hausberger M(1). Author information: (1)Laboratoire d'éthologie animale et humaine, Centre National de la Recherche Scientifique, UMR 6552, Université de Rennes 1 Rennes, France. (2)Department of Zoology and Entomology, Rhodes University Grahamstown, South Africa. (3)Laboratoire d'éthologie animale et humaine, Centre National de la Recherche Scientifique, UMR 6552, Université de Rennes 1 Rennes, France ; Laboratoire d'éthologie animale et humaine, Centre National de la Recherche Scientifique, UMR 6552, Station Biologique, Université de Rennes 1 Paimpont, France. 

Abstract
Turn-taking in conversation appears to be a common feature in various human cultures and this universality raises questions about its biological basis and evolutionary trajectory. Functional convergence is a widespread phenomenon in evolution, revealing sometimes striking functional similarities between very distant species even though the mechanisms involved may be different. Studies on mammals (including non-human primates) and bird species with different levels of social coordination reveal that temporal and structural regularities in vocal interactions may depend on the species' social structure. Here we test the hypothesis that turn-taking and associated rules of conversations may be an adaptive response to the requirements of social life, by testing the applicability of turn-taking rules to an animal model, the European starling. Birdsong has for many decades been considered as one of the best models of human language and starling songs have been well described in terms of vocal production and perception. Starlings do have vocal interactions where alternating patterns predominate. Observational and experimental data on vocal interactions reveal that (1) there are indeed clear temporal and structural regularities, (2) the temporal and structural patterning is influenced by the immediate social context, the general social situation, the individual history, and the internal state of the emitter. Comparison of phylogenetically close species of Sturnids reveals that the alternating pattern of vocal interactions varies greatly according to the species' social structure, suggesting that interactional regularities may have evolved together with social systems. These findings lead to solid bases of discussion on the evolution of communication rules in relation to social evolution. They will be discussed also in terms of processes, at the light of recent neurobiological findings. PMCID: PMC4585254 PMID: 26441787 [PubMed] 


12. Elife. 2015 Oct 6;4. doi: 10.7554/eLife.07770. 

Patterns of call communication between group-housed zebra finches change during the breeding cycle. 
Gill LF(1), Goymann W(1), Ter Maat A(1), Gahr M(1). Author information: (1)Max Planck Institute for Ornithology, Seewiesen, Germany. 

Abstract
Vocal signals such as calls play a crucial role for survival and successful reproduction, especially in group-living animals. However, call interactions and call dynamics within groups remain largely unexplored because their relation to relevant contexts or life-history stages could not be studied with individual-level resolution. Using on-bird microphone transmitters, we recorded the vocalisations of individual zebra finches (Taeniopygia guttata) behaving freely in social groups, while females and males previously unknown to each other passed through different stages of the breeding cycle. As birds formed pairs and shifted their reproductive status, their call repertoire composition changed. The recordings revealed that calls occurred non-randomly in fine-tuned vocal interactions and decreased within groups while pair-specific patterns emerged. Call-type combinations of vocal interactions changed within pairs and were associated with successful egg-laying, highlighting a potential fitness relevance of calling dynamics in communication systems. PMCID: PMC4592938 PMID: 26441403 [PubMed - in process] 


13. Folia Biol (Praha). 2015;61(4):125-33. 

Expression of Prostaglandin-Synthesizing Enzymes (Cyclooxygenase 1, Cyclooxygenase 2) in the Ovary of the Quail (Coturnix japonica). 
Rodler D(1), Sinowatz F(1). Author information: (1)Institute of Anatomy, Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians University Munich, Germany. 

Abstract
Cyclooxygenase is known to be the ratelimiting enzyme in the production of prostaglandins. So far, in different bird species there have been found two isoforms of cyclooxygenases (COX), cyclooxygenase 1 (COX-1) and cyclooxygenase 2 (COX-2). These isoforms along with prostaglandins are regarded to possess a determining influence on the success in female reproduction. Only in a few bird species the expression sites of cyclooxygenases have been investigated. In this study we report on the expression of COX-1 and COX-2 in the ovary of the quail (Coturnix japonica) using PCR, immunohistochemistry and non-radioactive in situ hybridization techniques. Using real time-polymerase chain reaction (RT-PCR), a distinct signal for COX-1 and COX-2 could be shown in small and large follicles of quail ovary. Antibodies to COX-1 distinctly labelled smooth muscle cells of the stroma, whereas COX-2 showed marked immunostaining in the thecal glands and the ovarian surface epithelium. In the same location, a signal of the corresponding mRNAs of COX-1 and COX-2 was found using in situ hybridization. This expression pattern in the quail is therefore completely different from the localization of COX-1 and COX-2 in the hen and ostrich, which suggests different functions of the cyclooxygenases in this small galliform avian species. According to our results, in quails COX-2 is involved in the synthesis of prostaglandins in the ovary's interstitial glands, which until now have been considered mainly as steroid-secreting cells. COX-1, which is expressed in the smooth muscles of the stroma, possibly plays a role in ovulation. PMID: 26441201 [PubMed - in process] 


14. J Appl Anim Welf Sci. 2015 Oct 8;18 Suppl 1:S11-7. doi: 10.1080/10888705.2015.1075832. 

Bird-Window Collisions: A Critical Animal Welfare and Conservation Issue. 
Klem D Jr(1). Author information: (1)a Acopian Center for Ornithology, Department of Biology , Muhlenberg College. 

Abstract
Sheet glass and plastic in the form of clear and reflective windows are universally lethal to birds. Reasonable interpretation of available scientific evidence describes windows as a principal human-associated avian mortality factor that is an indiscriminant killer of common species as well as species of conservation concern. A conservative toll estimates 1 billion or more annual fatalities in the United States alone. The injury and death from birds striking windows are foreseeable and preventable, but the most promising legal measures and commercial products are not being applied or made available to protect defenseless victims. Avian window casualties are important for birds and people, and they have nonhuman animal welfare, biodiversity, sustainability, legal, and ethical and moral value justifying responsible human action. Preventing this unintended and unwanted lethal hazard for free-flying birds should be an obligation. Short-term solutions include retrofitting existing panes with a variety of proven measures that among others include applying various materials to cover the outside surface of windows. Long-term solutions include current and proposed bird-safe sheet glass and plastic for remodeling and new construction that have patterns that transform windows into barriers that birds see and avoid. PMID: 26440494 [PubMed - in process] 


15. Sci Rep. 2015 Oct 6;5:14864. doi: 10.1038/srep14864.

Soft-tissue and dermal arrangement in the wing of an Early Cretaceous bird: Implications for the evolution of avian flight. 
Navalón G(1,)(2), Marugán-Lobón J(2,)(3), Chiappe LM(3), Luis Sanz J(2), Buscalioni ÁD(2). Author information: (1)School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol, BS8 1RJ, UK. (2)Unidad de Paleontología, Facultad de Ciencias, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain. (3)Dinosaur Institute, Natural History Museum of Los Angeles, 900 Exposition Boulevard, Los Angeles, CA 90007, USA. 

Abstract
Despite a wealth of fossils of Mesozoic birds revealing evidence of plumage and other soft-tissue structures, the epidermal and dermal anatomy of their wing's patagia remain largely unknown. We describe a distal forelimb of an enantiornithine bird from the Lower Cretaceous limestones of Las Hoyas, Spain, which reveals the overall morphology of the integument of the wing and other connective structures associated with the insertion of flight feathers. The integumentary anatomy, and myological and arthrological organization of the new fossil is remarkably similar to that of modern birds, in which a system of small muscles, tendons and ligaments attaches to the follicles of the remigial feathers and maintains the functional integrity of the wing during flight. The new fossil documents the oldest known occurrence of connective tissues in association with the flight feathers of birds. Furthermore, the presence of an essentially modern connective arrangement in the wing of enantiornithines supports the interpretation of these primitive birds as competent fliers. PMID: 26440221 [PubMed - in process] 


16. Nat Commun. 2015 Oct 6;6:8514. doi: 10.1038/ncomms9514. 

Hydrodynamic schooling of flapping swimmers. 
Becker AD(1), Masoud H(1), Newbolt JW(1), Shelley M(1), Ristroph L(1). Author information: (1)Applied Math Lab, Courant Institute, New York University, 251 Mercer Street, New York, New York 10012, USA. 
 
Abstract
Fish schools and bird flocks are fascinating examples of collective behaviours in which many individuals generate and interact with complex flows. Motivated by animal groups on the move, here we explore how the locomotion of many bodies emerges from their flow-mediated interactions. Through experiments and simulations of arrays of flapping wings that propel within a collective wake, we discover distinct modes characterized by the group swimming speed and the spatial phase shift between trajectories of neighbouring wings. For identical flapping motions, slow and fast modes coexist and correspond to constructive and destructive wing-wake interactions. Simulations show that swimming in a group can enhance speed and save power, and we capture the key phenomena in a mathematical model based on memory or the storage and recollection of information in the flow field. These results also show that fluid dynamic interactions alone are sufficient to generate coherent collective locomotion, and thus might suggest new ways to characterize the role of flows in animal groups. PMID: 26439509 [PubMed - in process] 


17. BMC Genomics. 2015 Oct 6;16(1):751. doi: 10.1186/s12864-015-1924-3. 

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds. 
Borges R(1,)(2), Khan I(3,)(4), Johnson WE(5), Gilbert MT(6), Zhang G(7,)(8), Jarvis ED(9,)(10), O'Brien SJ(11,)(12), Antunes A(13,)(14). Author information: (1)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal. ruiborges23@gmail.com. (2)Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. ruiborges23@gmail.com. (3)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal. btimran@gmail.com. (4)Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. btimran@gmail.com. (5)Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA. johnsonwe@si.edu. (6)Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350, Copenhagen, Denmark. mtpgilbert@gmail.com. (7)China National GeneBank, BGI-Shenzhen, Shenzen, 518083, China. zhanggj@genomics.cn. (8)Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark. zhanggj@genomics.cn. (9)Department of Neurobiology, Duke University Medical Center Durham, Box 3209, North Carolina, 27710, USA. jarvis@neuro.duke.edu. (10)Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA. jarvis@neuro.duke.edu. (11)Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia. lgdchief@gmail.com. (12)Oceanographic Center, Nova Southeastern University, 8000 N. Ocean Drive, Ft Lauderdale, Florida, 33004, USA. lgdchief@gmail.com. (13)CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal. aantunes@ciimar.up.pt. (14)Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. aantunes@ciimar.up.pt. 

Abstract
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. PMCID: PMC4595237 PMID: 26438339 [PubMed - in process] 


18. PLoS One. 2015 Oct 5;10(10):e0139390. doi: 10.1371/journal.pone.0139390. eCollection 2015. 

The Foraging Ecology of the Endangered Cape Verde Shearwater, a Sentinel Species for Marine Conservation off West Africa. 
Paiva VH(1), Geraldes P(2), Rodrigues I(3), Melo T(3), Melo J(3), Ramos JA(1). Author information: (1)MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal. (2)SPEA - Sociedade Portuguesa para o Estudo das Aves, Lisboa, Portugal. (3)Biosfera I, Mindelo, São Vicente, Cabo Verde. 

Abstract
Large Marine Ecosystems such as the Canary Current system off West Africa sustains high abundance of small pelagic prey, which attracts marine predators. Seabirds are top predators often used as biodiversity surrogates and sentinel species of the marine ecosystem health, thus frequently informing marine conservation planning. This study presents the first data on the spatial (GPS-loggers) and trophic (stable isotope analysis) ecology of a tropical seabird-the endangered Cape Verde shearwater Calonectris edwardsii-during both the incubation and the chick-rearing periods of two consecutive years. This information was related with marine environmental predictors (species distribution models), existent areas of conservation concern for seabirds (i.e. marine Important Bird Areas; marine IBAs) and threats to the marine environment in the West African areas heavily used by the shearwaters. There was an apparent inter-annual consistency on the spatial, foraging and trophic ecology of Cape Verde shearwater, but a strong alteration on the foraging strategies of adult breeders among breeding phases (i.e. from incubation to chick-rearing). During incubation, birds mostly targeted a discrete region off West Africa, known by its enhanced productivity profile and thus also highly exploited by international industrial fishery fleets. When chick-rearing, adults exploited the comparatively less productive tropical environment within the islands of Cape Verde, at relatively close distance from their breeding colony. The species enlarged its trophic niche and increased the trophic level of their prey from incubation to chick-rearing, likely to provision their chicks with a more diversified and better quality diet. There was a high overlap between the Cape Verde shearwaters foraging areas with those of European shearwater species that overwinter in this area and known areas of megafauna bycatch off West Africa, but very little overlap with existing Marine Important Bird Areas. Further investigation on the potential nefarious effects of fisheries on seabird communities exploiting the Canary Current system off West Africa is needed. Such negative effects could be alleviated or even dissipated if the 'fisheries-conservation hotspots' identified for the region, would be legislated as Marine Protected Areas. PMID: 26436804 [PubMed - in process] 


19. J Environ Qual. 2015 Sep;44(5):1657-66. doi: 10.2134/jeq2015.02.0099. 

Alum and Rainfall Effects on Ionophores in Runoff from Surface-Applied Broiler Litter. 
Doydora SA, Franklin D, Sun P, Cabrera M, Thompson A, Love-Myers K, Rema J, Calvert V, Pavlostathis SG, Huang CH. 

Abstract
Polyether ionophores, monensin, and salinomycin are commonly used as antiparasitic drugs in broiler production and may be present in broiler litter (bird excreta plus bedding material). Long-term application of broiler litter to pastures may lead to ionophore contamination of surface waters. Because polyether ionophores break down at low pH, we hypothesized that decreasing litter pH with an acidic material such as aluminum sulfate (alum) would reduce ionophore losses to runoff (i.e., monensin and salinomycin concentrations, loads, or amounts lost). We quantified ionophore loss to runoff in response to (i) addition of alum to broiler litter and (ii) length of time between litter application and the first simulated rainfall event. The factorial experiment consisted of unamended (∼pH 9) vs. alum-amended litters (∼pH 6), each combined with simulated rainfall at 0, 2, or 4 wk after litter application. Runoff from alum-amended broiler litter had 33% lower monensin concentration ( < 0.01), 57% lower monensin load ( < 0.01), 48% lower salinomycin concentration ( < 0.01), and 66% lower salinomycin load ( < 0.01) than runoff from unamended broiler litter when averaged across all events of rainfall. Ionophore losses to runoff were also less when rainfall was delayed for 2 or 4 wk after litter application relative to applying rainfall immediately after litter application. While the weather is difficult to predict, our data suggest that ionophore losses in runoff can be reduced if broiler litter applications are made to maximize dry time after application. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc. PMID: 26436282 [PubMed - in process] 

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