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Wednesday, 30 December 2015

What's new for 'birdRS' in PubMed, Christmas 2015

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).

PubMed Results

1. Chemosphere. 2015 Dec 15. pii: S0045-6535(15)30443-4. doi: 10.1016/j.chemosphere.2015.11.112. [Epub ahead of print] 

A novel pollution pattern: Highly chlorinated biphenyls retained in Black-crowned night heron (Nycticorax nycticorax) and Whiskered tern (Chlidonias hybrida) from the Yangtze River Delta. 
Zhou Y(1), Yin G(2), Asplund L(3), Qiu Y(4), Bignert A(5), Zhu Z(6), Zhao J(6), Bergman Å(7). Author information: (1)State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Analytical and Toxicology Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE-10691 Stockholm, Sweden. (2)Analytical and Toxicology Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE-10691 Stockholm, Sweden. Electronic address: ge.yin@aces.su.se. (3)Analytical and Toxicology Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE-10691 Stockholm, Sweden. (4)Key Laboratory of Yangtze River Water Environment (Ministry of Education), College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China. (5)State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, Sweden. (6)State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China. (7)State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Analytical and Toxicology Chemistry Unit, Department of Environmental Science and Analytical Chemistry, Stockholm University, SE-10691 Stockholm, Sweden; Swedish Toxicology Sciences Research Center, Forskargatan 20, SE-15136 Södertälje, Sweden. 

Abstract
Contamination of organochlorine pesticides (OCPs), polychlorinated diphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), hydroxylated polybrominated diphenyl ethers (OH-PBDEs) and their methylated counterparts (MeO-PBDEs) were determined in Black-crowned night heron (Nycticorax nycticorax) and Whiskered tern (Chlidonias hybrida) from two drinking water sources, e.g. Tianmu lake and East Tai lake in Yangtze River Delta, China. A novel PCBs contamination pattern was detected, including 11% and 6.9% highly chlorinated biphenyls (PCBs with eight to ten chlorines) in relation to total PCB concentrations in the Black-crowned night heron and Whiskered tern eggs, respectively. The predominating OCPs detected in the present study were 4,4'-DDE, with concentration range 280-650 ng g(-1) lw in Black-crowned night heron and 240-480 ng g(-1) lw in Whiskered tern, followed by β-HCH and Mirex. 6-MeO-BDE-90 and 6-MeO-BDE-99 are the two predominant congeners of MeO-PBDEs whereas 6-OH-BDE-47 contributes mostly to the OH-PBDEs in both species. Contamination level was considered as median or low level compared global data. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved. PMID: 26705146 [PubMed - as supplied by publisher] 


2. PLoS One. 2015 Dec 23;10(12):e0144445. doi: 10.1371/journal.pone.0144445. 

Avitourism and Australian Important Bird and Biodiversity Areas. 
Steven R(1), Morrison C(2), Arthur JM(3), Castley JG(1). Author information: (1)Environmental Futures Research Institute, Griffith School of Environment, Gold Coast campus, Griffith University, Gold Coast, Queensland, 4222, Australia. (2)Griffith School of Environment, Gold Coast campus, Griffith University, Gold Coast, Queensland, 4222, Australia. (3)Australian Rivers Institute, Griffith School of Environment, Griffith University, Gold Coast, Queensland, Australia. 

Abstract
Formal protected areas will not provide adequate protection to conserve all biodiversity, and are not always designated using systematic or strategic criteria. Using a systematic process, the Important Bird and Biodiversity Area (IBA) network was designed to highlight areas of conservation significance for birds (i.e. IBA trigger species), and more recently general biodiversity. Land use activities that take place in IBAs are diverse, including consumptive and non-consumptive activities. Avitourism in Australia, generally a non-consumptive activity, is reliant on the IBA network and the birds IBAs aim to protect. However, companies tend not to mention IBAs in their marketing. Furthermore, avitourism, like other nature-based tourism has the potential to be both a threatening process as well as a conservation tool. We aimed to assess the current use of IBAs among Australian-based avitour companies' marketing, giving some indication of which IBAs are visited by avitourists on organised tours. We reviewed online avitour itineraries, recorded sites featuring in descriptions of avitours and which IBA trigger species are used to sell those tours. Of the 209 avitours reviewed, Queensland is the most featured state (n = 59 tours), and 73% feature at least one IBA. Daintree (n = 22) and Bruny Island (n = 17) IBAs are the most popular, nationally. Trigger species represent 34% (n = 254 out of 747) of species used in avitour descriptions. The most popular trigger species' are wetland species including; Brolga (n = 37), Black-necked Stork (n = 30) and Magpie Goose (n = 27). Opportunities exist to increase collaboration between avitour companies and IBA stakeholders. Our results can provide guidance for managing sustainability of the avitourism industry at sites that feature heavily in avitour descriptions and enhance potential cooperation between avitour companies, IBA stakeholders and bird conservation organisations. PMID: 26701779 [PubMed - as supplied by publisher] 


3. Biol Lett. 2015 Dec;11(12). pii: 20150777. Epub 2015 Dec 23. 

Activity profiles and hook-tool use of New Caledonian crows recorded by bird-borne video cameras. 
Troscianko J(1), Rutz C(2). Author information: (1)School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK. (2)Department of Zoology, University of Oxford, Oxford OX1 3PS, UK christian.rutz@st-andrews.ac.uk. 

Abstract
New Caledonian crows are renowned for their unusually sophisticated tool behaviour. Despite decades of fieldwork, however, very little is known about how they make and use their foraging tools in the wild, which is largely owing to the difficulties in observing these shy forest birds. To obtain first estimates of activity budgets, as well as close-up observations of tool-assisted foraging, we equipped 19 wild crows with self-developed miniature video cameras, yielding more than 10 h of analysable video footage for 10 subjects. While only four crows used tools during recording sessions, they did so extensively: across all 10 birds, we conservatively estimate that tool-related behaviour occurred in 3% of total observation time, and accounted for 19% of all foraging behaviour. Our video-loggers provided first footage of crows manufacturing, and using, one of their most complex tool types-hooked stick tools-under completely natural foraging conditions. We recorded manufacture from live branches of paperbark (Melaleuca sp.) and another tree species (thought to be Acacia spirorbis), and deployment of tools in a range of contexts, including on the forest floor. Taken together, our video recordings reveal an 'expanded' foraging niche for hooked stick tools, and highlight more generally how crows routinely switch between tool- and bill-assisted foraging. © 2015 The Authors. PMID: 26701755 [PubMed - as supplied by publisher] 


4. PLoS One. 2015 Dec 23;10(12):e0144089. doi: 10.1371/journal.pone.0144089. 

Implications of Climate Change for Bird Conservation in the Southwestern U.S. under Three Alternative Futures. 
Friggens MM(1), Finch DM(1). Author information: (1)United States Forest Service, Rocky Mountain Research Station, Albuquerque, New Mexico, United States of America. 

Abstract
Future expected changes in climate and human activity threaten many riparian habitats, particularly in the southwestern U.S. Using Maximum Entropy (MaxEnt3.3.3) modeling, we characterized habitat relationships and generated spatial predictions of habitat suitability for the Lucy's warbler (Oreothlypis luciae), the Southwestern willow flycatcher (Empidonax traillii extimus) and the Western yellow-billed cuckoo (Coccyzus americanus). Our goal was to provide site- and species-specific information that can be used by managers to identify areas for habitat conservation and/or restoration along the Rio Grande in New Mexico. We created models of suitable habitat for each species based on collection and survey samples and climate, biophysical, and vegetation data. We projected habitat suitability under future climates by applying these models to conditions generated from three climate models for 2030, 2060 and 2090. By comparing current and future distributions, we identified how habitats are likely to change as a result of changing climate and the consequences of those changes for these bird species. We also examined whether land ownership of high value sites shifts under changing climate conditions. Habitat suitability models performed well. Biophysical characteristics were more important that climate conditions for predicting habitat suitability with distance to water being the single most important predictor. Climate, though less important, was still influential and led to declines of suitable habitat of more than 60% by 2090. For all species, suitable habitat tended to shrink over time within the study area leaving a few core areas of high importance. Overall, climate changes will increase habitat fragmentation and reduce breeding habitat patch size. The best strategy for conserving bird species within the Rio Grande will include measures to maintain and restore critical habitat refugia. This study provides an example of a presence-only habitat model that can be used to inform the management of species at intermediate scales. PMID: 26700871 [PubMed - as supplied by publisher] 


5. Biodivers Data J. 2015 Nov 20;(3):e6604. doi: 10.3897/BDJ.3.e6604. eCollection 2015. 

Birds from the Azores: An updated list with some comments on species distribution. 
Barcelos LM(1), Rodrigues PR(2), Bried J(3), Mendonça EP(1), Gabriel R(1), Borges PA(1). Author information: (1)CE3C - Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group and Universidade dos Açores, Azores, Portugal. (2)Universidade dos Açores, Ponta Delgada, Portugal. (3)na, Biarritz, France. 

Abstract
BACKGROUND: An updated checklist of the Birds of the Azores is presented based on information compiled from Rodrigues et al. (2010) and from the websites, Azores Bird Club. (2014), Aves dos Açores (2014) Azores Bird Sightings (2014) and Vittery (2014), since 2010. NEW INFORMATION: The checklist has a total of 414 species, including 38 new species. Almost half of the species and subspecies that occur in the Azores have a Palearctic origin, the remaining ones being essentialy Nearctic and Holarctic species. São Miguel is the island with the highest number of bird species, followed by Terceira, Corvo and Flores islands. PMCID: PMC4678808 PMID: 26696765 [PubMed] 


6. Glob Chang Biol. 2015 Dec 22. doi: 10.1111/gcb.13154. [Epub ahead of print] 

The pace of past climate change vs. potential bird distributions and land use in the United States.
Bateman BL(1), Pidgeon AM(1), Radeloff VC(1), VanDerWal J(2,)(3), Thogmartin WE(4), Vavrus SJ(5), Heglund PJ(6). Author information: (1)SILVIS Lab, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA. (2)Centre for Tropical Biodiversity and Climate Change Research, School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. (3)Division of Research and Innovation, James Cook University, Townsville, Qld, 4811, Australia. (4)U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, 54603, USA. (5)Center for Climate Research, University of Wisconsin-Madison, Madison, WI, 53706, USA. (6)U.S. Fish and Wildlife Service, La Crosse, WI, 54603, USA. 

Abstract
Climate change may drastically alter patterns of species distributions and richness, but predicting future species patterns in occurrence is challenging. Significant shifts in distributions have already been observed, and understanding these recent changes can improve our understanding of potential future changes. We assessed how past climate change affected potential breeding distributions for landbird species in the conterminous United States. We quantified the bioclimatic velocity of potential breeding distributions, that is, the pace and direction of change for each species' suitable climate space over the past 60 years. We found that potential breeding distributions for landbirds have shifted substantially with an average velocity of 1.27 km yr(-1) , about double the pace of prior distribution shift estimates across terrestrial systems globally (0.61 km yr(-1) ). The direction of shifts was not uniform. The majority of species' distributions shifted west, northwest, and north. Multidirectional shifts suggest that changes in climate conditions beyond mean temperature were influencing distributional changes. Indeed, precipitation variables that were proxies for extreme conditions were important variables across all models. There were winners and losers in terms of the area of distributions; many species experienced contractions along west and east distribution edges, and expansions along northern distribution edges. Changes were also reflected in the potential species richness, with some regions potentially gaining species (Midwest, East) and other areas potentially losing species (Southwest). However, the degree to which changes in potential breeding distributions are manifested in actual species richness depends on landcover. Areas that have become increasingly suitable for breeding birds due to changing climate are often those attractive to humans for agriculture and development. This suggests that many areas might have supported more breeding bird species had the landscape not been altered. Our study illustrates that climate change is not only a future threat, but something birds are already experiencing. © 2015 John Wiley & Sons Ltd. PMID: 26691721 [PubMed - as supplied by publisher] 


7. Glob Chang Biol. 2015 Dec 22. doi: 10.1111/gcb.13150. [Epub ahead of print] 

North by north-west: climate change and directions of density shifts in birds. 
Lehikoinen A(1), Virkkala R(2). Author information: (1)The Helsinki Lab of Ornithology, Finnish Museum of Natural History, University of Helsinki, P. O. Box 17, FI-00014, Helsinki, Finland. (2)Natural Environment Centre, Finnish Environment Institute, Mechelininkatu 34 a, P.O. Box 140, FI-00251, Helsinki, Finland. 

Abstract
There is increasing evidence that climate change shifts species distributions towards poles and mountain tops. However, most studies are based on presence-absence data, and either abundance or the observation effort has rarely been measured. In addition, hardly any studies have investigated the direction of shifts and factors affecting them. Here, we show using count data on a 1000 km south-north gradient in Finland, that between 1970-1989 and 2000-2012, 128 bird species shifted their densities, on average, 37 km towards the north north-east. The species-specific directions of the shifts in density were significantly explained by migration behaviour and habitat type. Although the temperatures have also moved on average towards the north north-east (186 km), the species-specific directions of the shifts in density and temperature did not correlate due to high variation in density shifts. Findings highlight that climate change is unlikely the only driver of the direction of species density shifts, but species-specific characteristics and human land-use practices are also influencing the direction. Furthermore, the alarming results show that former climatic conditions in the north-west corner of Finland have already moved out of the country. This highlights the need for an international approach in research and conservation actions to mitigate the impacts of climate change. © 2015 John Wiley & Sons Ltd. PMID: 26691578 [PubMed - as supplied by publisher] 


8. Protoplasma. 2015 Dec 21. [Epub ahead of print] 

Development of mechanical papillae of the tongue in the domestic goose (Anser anser f. domestica) during the embryonic period. 
Skieresz-Szewczyk K(1), Jackowiak H(2). Author information: (1)Department of Histology and Embryology, Poznań University of Life Sciences, Wojska Polskiego 71 C, 60-625, Poznań, Poland. skieresz@up.poznan.pl. (2)Department of Histology and Embryology, Poznań University of Life Sciences, Wojska Polskiego 71 C, 60-625, Poznań, Poland. 

Abstract
Three types of mechanical papillae, i.e., conical, filiform, and hair-like papillae, are present on the tongue in the domestic goose. Within conical papillae, we distinguish three categories: large and small conical papillae on the body and conical papillae on the lingual prominence. The arrangement of mechanical papillae on the tongue in Anseriformes is connected functionally with different feeding mechanisms such as grazing and filter-feeding. The present work aims to determine whether morphology of three types of mechanical papillae in goose at the time of hatching is the same as in an adult bird and if the tongue is prepared to fulfill feeding function. Our results revealed that the primordia of the large conical papillae start to develop during the differentiation stage. The primordia of the small conical papillae and conical papillae of the lingual papillae start to develop during the growth stage. At the end of the growth stage, only large conical papillae, three pairs of small conical papillae, and conical papillae of the lingual prominence have similar arrangement as in an adult bird. The shape and arrangement of the remaining small conical papillae probably will be changed after hatching. During embryonic period, the filiform papillae and hair-like papillae are not formed. The embryonic epithelium that covered the mechanical papillae undergoes transformation leading to the formation of multilayered epithelium. During prehatching stage, epithelium becomes orthokeratinized epithelium. In conclusion, the tongue of the domestic goose after hatching is well prepared only for grazing. The filtration of food from water is limited due to the lack of filiform papillae. PMID: 26689409 [PubMed - as supplied by publisher] 


9. Bull Math Biol. 2015 Dec 18. [Epub ahead of print] 

Impact of Spring Bird Migration on the Range Expansion of Ixodes scapularis Tick Population. 
Wu X(1), Röst G(2), Zou X(3). Author information: (1)Department of Mathematics, Shanghai Maritime University, Shanghai, 201306, China. xtwu@shmtu.edu.cn. (2)Bolyai Institute, University of Szeged, Szeged, H6720, Hungary. rost@math.u-szeged.hu. (3)Department of Applied Mathematics, Western University, London, ON, N6A 5B7, Canada. xzou@uwo.ca. 

Abstract
Many observational studies suggest that seasonal migratory birds play an important role in spreading Ixodes scapularis, a vector of Lyme disease, along their migratory flyways, and they are believed to be responsible for geographic range expansion of I. scapularis in Canada. However, the interplay between the dynamics of I. scapularis on land and migratory birds in the air is not well understood. In this study, we develop a periodic delay meta-population model which takes into consideration the local landscape for tick reproduction within patches and the times needed for ticks to be transported by birds between patches. Assuming that the tick population is endemic in the source region, we find that bird migration may boost an already established tick population at the subsequent region and thus increase the risk to humans, or bird migration may help ticks to establish in a region where the local landscape is not appropriate for ticks to survive in the absence of bird migration, imposing risks to public health. This theoretical study reveals that bird migration plays an important role in the geographic range expansion of I. scapularis, and therefore our findings may suggest some strategies for Lyme disease prevention and control. PMID: 26688012 [PubMed - as supplied by publisher] 


10. Microb Ecol. 2015 Dec 21. [Epub ahead of print] 

Wild Birds, Frequent Carriers of Extended-Spectrum β-Lactamase (ESBL) Producing Escherichia coli of CTX-M and SHV-12 Types. 
Alcalá L(1), Alonso CA(2), Simón C(1), González-Esteban C(3), Orós J(1), Rezusta A(4), Ortega C(1), Torres C(5). Author information: (1)Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain. (2)Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain. (3)Centro de Recuperación de Fauna Silvestre de La Alfranca, Departamento de Agricultura, Ganadería y Medio Ambiente, Gobierno de Aragón, Spain. (4)Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Universidad de Zaragoza, IIS Aragón, Spain. (5)Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Madre de Dios 51, 26006, Logroño, Spain. carmen.torres@unirioja.es. 

Abstract
To get a better insight into the role of birds as reservoirs of extended-spectrum β-lactamase (ESBL) and plasmidic AmpC β-lactamase (pAmpC) Escherichia coli producers, 100 fecal samples belonging to 15 different wild avian species from Northern Spain were analyzed. Cefotaxime-resistant (CTX(R)) E. coli isolates were identified in 16 of the 100 tested birds, which corresponded to 9 animal species (Gyps fulvus-griffon vulture, Larus michahellis-yellow-legged gull, Milvus migrans-black kite, Milvus milvus-red kite, Ciconia ciconia-white stork, Sturnus unicolor-spotless starling, Aquila chrysaetos-golden eagle, Cuculus canorus-common cuckoo, Tyto alba-barn owl). Fifteen isolates harbored ESBL or pAmpC-encoding genes (number of isolates): bla SHV-12 (9), bla CTX-M-1 (3), bla CTX-M-14 (2), and bla CMY-2 (1). The last CTX(R) isolate presented a -42-point-mutation in the chromosomal ampC promoter. Eleven out of 15 ESBL/pAmpC E. coli isolates were multiresistant (most common resistance phenotype: β-lactams-quinolones-tetracycline-sulfamethoxazole/trimethoprim). A plasmid-mediated quinolone resistance determinant (qnrS1) was identified in one E. coli from a barn owl. High genetic diversity was observed among ESBL/pAmpC E. coli isolates, with 12 different sequence types (STs), including several strains of STs frequently detected among human clinical isolates (ST38/D, ST131/B2, ST155/B1, ST10/A). The ST131 isolate belonged to the emergent ciprofloxacin-resistant H30R subclone. This study reveals a high percentage of bird as carriers of ESBL/pAmpC E. coli isolates in Spain, highlighting the elevated rate among storks, kites, and vultures. Wild birds can contribute to the global spread of ESBL/pAmpC-producing E. coli in natural ecosystems. PMID: 26687342 [PubMed - as supplied by publisher] 


11. Sci Rep. 2015 Dec 21;5:18317. doi: 10.1038/srep18317. 

Spatially modulated structural colour in bird feathers. 
Parnell AJ(1), Washington AL(1,)(2), Mykhaylyk OO(3), Hill CJ(4), Bianco A(2), Burg SL(1), Dennison AJ(5,)(6), Snape M(1), Cadby AJ(1), Smith A(7), Prevost S(8), Whittaker DM(1), Jones RA(1), Fairclough JP(2), Parker AR(9). Author information: (1)Department of Physics and Astronomy, The University of Sheffield, S3 7RH, UK. (2)Department of Mechanical Engineering, The University of Sheffield, S3 7HQ, UK. (3)Department of Chemistry, The University of Sheffield, S3 7HF, UK. (4)Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN. (5)University Grenoble-Alpes, IBS, 38044, France. (6)Institut Laue-Langevin, 38042 Grenoble Cedex 9, France. (7)Beamline I22 Diamond Light Source, Oxfordshire, UK. (8)ID02 Beamline, European Synchrotron Radiation Facility (ESRF), F38043, Grenoble, France. (9)Department of Zoology, Natural History Museum, London SW7 5BD, UK. 

Abstract
Eurasian Jay (Garrulus glandarius) feathers display periodic variations in the reflected colour from white through light blue, dark blue and black. We find the structures responsible for the colour are continuous in their size and spatially controlled by the degree of spinodal phase separation in the corresponding region of the feather barb. Blue structures have a well-defined broadband ultra-violet (UV) to blue wavelength distribution; the corresponding nanostructure has characteristic spinodal morphology with a lengthscale of order 150 nm. White regions have a larger 200 nm nanostructure, consistent with a spinodal process that has coarsened further, yielding broader wavelength white reflectance. Our analysis shows that nanostructure in single bird feather barbs can be varied continuously by controlling the time the keratin network is allowed to phase separate before mobility in the system is arrested. Dynamic scaling analysis of the single barb scattering data implies that the phase separation arrest mechanism is rapid and also distinct from the spinodal phase separation mechanism i.e. it is not gelation or intermolecular re-association. Any growing lengthscale using this spinodal phase separation approach must first traverse the UV and blue wavelength regions, growing the structure by coarsening, resulting in a broad distribution of domain sizes. PMID: 26686280 [PubMed - in process] 


12. J Exp Biol. 2015 Dec 18. pii: jeb.126532. [Epub ahead of print] 

Lingual articulation in songbirds. 
Suthers RA(1), Rothgerber JR(2), Jensen KK(3). Author information: (1)School of Medicine, Jordan Hall, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA suthers@indiana.edu. (2)School of Medicine, Jordan Hall, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA. (3)Starkey Hearing Technologies, 6600 Washington Avenue S., Eden Prairie, MN 55344, USA. 

Abstract
Lingual articulation in humans is one of the primary means of vocal tract resonance filtering that produces the characteristic vowel formants of speech. In songbirds, the function of the tongue in song has not been thoroughly examined, although recent research has identified the oropharyngeal-esophageal cavity as a resonance filter that is actively tuned to the frequency of the song. In northern cardinals (Cardinalis cardinalis), the volume of this cavity is inversely proportional to the frequency of the song above 2 kHz. However, cardinal song extends below this range, leaving the question of if and how the vocal tract is tracking these low frequencies. We investigated the possible role of the tongue in vocal tract filtering using X-ray cineradiography of northern cardinals. Below 2 kHz, there was prominent tongue elevation in which the tip of the tongue was raised until it seemed to touch the palate. These results suggest that tongue elevation lowers the resonance frequency below 2 kHz by reducing the area of the passage from the oral cavity into the beak. This is consistent with a computational model of the songbird vocal tract in which resonance frequencies are actively adjusted by both changing the volume of the oropharyngeal-esophageal cavity and constricting the opening into the beak. © 2015. Published by The Company of Biologists Ltd. PMID: 26685174 [PubMed - as supplied by publisher] 


13. J Am Vet Med Assoc. 2016 Jan 1;248(1):67-71. doi: 10.2460/javma.248.1.67. 

Evaluation of the mydriatic effects of topical administration of rocuronium bromide in Hispaniolan Amazon parrots (Amazona ventralis). 
Petritz OA, Guzman DS, Gustavsen K, Wiggans KT, Kass PH, Houck E, Murphy CJ, Paul-Murphy J. 

Abstract
OBJECTIVE To determine the mydriatic effects of topical rocuronium bromide administration in Hispaniolan Amazon parrots (Amazona ventralis) and to identify any adverse effects associated with treatment. DESIGN Randomized crossover study. ANIMALS 8 healthy adult Hispaniolan Amazon parrots. PROCEDURES Rocuronium bromide (20 μL/eye; 10 mg/mL) or saline (20 μL/eye; 0.9% NaCl) solution was administered in both eyes of each bird with a 26-day washout period. The birds were manually restrained in lateral recumbency with the apex of the cornea positioned upward for 2 minutes following administration in each eye. Infrared pupillometry and direct pupillary light reflex measurements were used to evaluate the mydriatic effects. Pupillary measurements were recorded prior to administration and every 20 minutes for 2 hours after administration, then hourly for a total of 7 hours. A brief physical examination was performed, direct pupillary light reflex was tested, and fluorescein staining was performed on each eye of each bird 24 hours after administration. RESULTS A significant difference in pupillary diameter for the active versus control treatment group was noted from 20 to 360 minutes after drug administration, but not at 420 minutes. Minimal adverse effects were noted. Three birds had transient inferior eyelid paresis noted in both eyes after receiving rocuronium; 24 hours after the treatment, no differences in ocular measurements existed between the active and control treatments. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that topical rocuronium bromide administration may be safely used for pupillary dilation in Hispaniolan Amazon parrots and could be used for clinical evaluation, fundus imaging, and surgical interventions involving the lens and posterior segment in this species. PMID: 26684093 [PubMed - in process] 


14. PLoS One. 2015 Dec 18;10(12):e0145433. doi: 10.1371/journal.pone.0145433. eCollection 2015. 

Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wisła Forest District: Genetic Assessments of Captive and Reintroduced Populations. 
Strzała T(1), Kowalczyk A(2), Łukaszewicz E(2). Author information: (1)Department of Genetics, Faculty of Biology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland. (2)Division of Poultry Breeding, Institute of Animal Breeding, Faculty of Biology, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland. 

Abstract
The Western capercaillie (Tetrao urogallus) is a specific bird species, which, despite its very broad distribution and large global population size, is highly endangered in many Western and Central European countries. According to the species situation, in many countries (including Poland), breeding and reintroduction programmes have been started. One of the most complex and large-scale reintroduction programmes was started in Bory Dolnośląskie Forest, and the Capercaillie Breeding Centre in Wisła Forest District was used as one of the sources of individuals for reintroduction. As genetic tools provide essential knowledge about species biodiversity, which is crucially important during the breeding process and reintroduction, both captive and reintroduced grouse populations were genetically analysed. We were particularly interested in genetic diversity of the individuals in both populations and the genetic relationship between them, as well as between them and other capercaillie representatives from their current range. To fulfil these goals we determined nine microsatellite loci along with a fragment of the mitochondrial control region. Genetic diversity parameters were moderate to high compared to populations from other Central and Western European countries. Both populations were clustered into three distinct genetic clades based on microsatellites. Phylogenetic analysis placed all mitochondrial haplotypes we revealed in the Eurasian clade. The present results will play an important role as they will help to preserve and maximize genetic diversity in captive populations, and will provide a basis for future monitoring of the reintroduction process. PMID: 26682897 [PubMed - in process] 


15. PLoS One. 2015 Dec 18;10(12):e0145168. doi: 10.1371/journal.pone.0145168. eCollection 2015. 

Vertebral Pneumaticity in the Ornithomimosaur Archaeornithomimus (Dinosauria: Theropoda) Revealed by Computed Tomography Imaging and Reappraisal of Axial Pneumaticity in Ornithomimosauria. 
Watanabe A(1,)(2), Eugenia Leone Gold M(1,)(2), Brusatte SL(3), Benson RB(4,)(5), Choiniere J(5), Davidson A(1), Norell MA(1,)(2). Author information: (1)Division of Paleontology, American Museum of Natural History, New York, New York, United States of America. (2)Richard Gilder Graduate School, American Museum of Natural History, New York, New York, United States of America. (3)School of GeoSciences, University of Edinburgh, Scotland, United Kingdom. (4)Department of Earth Sciences, University of Oxford, Oxford, United Kingdom. (5)Evolutionary Studies Institute and DST/NRF Centre of Excellence in Palaeosciences, University of the Witwatersrand, Johannesburg, South Africa. 

Abstract
Among extant vertebrates, pneumatization of postcranial bones is unique to birds, with few known exceptions in other groups. Through reduction in bone mass, this feature is thought to benefit flight capacity in modern birds, but its prevalence in non-avian dinosaurs of variable sizes has generated competing hypotheses on the initial adaptive significance of postcranial pneumaticity. To better understand the evolutionary history of postcranial pneumaticity, studies have surveyed its distribution among non-avian dinosaurs. Nevertheless, the degree of pneumaticity in the basal coelurosaurian group Ornithomimosauria remains poorly known, despite their potential to greatly enhance our understanding of the early evolution of pneumatic bones along the lineage leading to birds. Historically, the identification of postcranial pneumaticity in non-avian dinosaurs has been based on examination of external morphology, and few studies thus far have focused on the internal architecture of pneumatic structures inside the bones. Here, we describe the vertebral pneumaticity of the ornithomimosaur Archaeornithomimus with the aid of X-ray computed tomography (CT) imaging. Complementary examination of external and internal osteology reveals (1) highly pneumatized cervical vertebrae with an elaborate configuration of interconnected chambers within the neural arch and the centrum; (2) anterior dorsal vertebrae with pneumatic chambers inside the neural arch; (3) apneumatic sacral vertebrae; and (4) a subset of proximal caudal vertebrae with limited pneumatic invasion into the neural arch. Comparisons with other theropod dinosaurs suggest that ornithomimosaurs primitively exhibited a plesiomorphic theropod condition for axial pneumaticity that was extended among later taxa, such as Archaeornithomimus and large bodied Deinocheirus. This finding corroborates the notion that evolutionary increases in vertebral pneumaticity occurred in parallel among independent lineages of bird-line archosaurs. Beyond providing a comprehensive view of vertebral pneumaticity in a non-avian coelurosaur, this study demonstrates the utility and need of CT imaging for further clarifying the early evolutionary history of postcranial pneumaticity. PMID: 26682888 [PubMed - in process] 


16. BMC Res Notes. 2015 Dec 18;8(1):799. doi: 10.1186/s13104-015-1683-x. 

Evolutionary significance and diversification of the phosphoglucose isomerase genes in vertebrates. 
Tine M(1,)(2). Author information: (1)Molecular Zoology Laboratory, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa. tine@mpgpz.mpg.de. (2)Genome Centre Cologne at MPI for Plant Breeding Research, 22 Carl-von-Linné-Weg 10, 50829, Cologne, Germany. tine@mpgpz.mpg.de. 

Abstract
BACKGROUND: Phosphoglucose isomerase (PGI) genes are important multifunctional proteins whose evolution has, until now, not been well elucidated because of the limited number of completely sequenced genomes. Although the multifunctionality of this gene family has been considered as an original and innate characteristic, PGI genes may have acquired novel functions through changes in coding sequences and exon/intron structure, which are known to lead to functional divergence after gene duplication. A whole-genome comparative approach was used to estimate the rates of molecular evolution of this protein family. RESULTS: The results confirm the presence of two isoforms in teleost fishes and only one variant in all other vertebrates. Phylogenetic reconstructions grouped the PGI genes into five main groups: lungfishes/coelacanth/cartilaginous fishes, teleost fishes, amphibians, reptiles/birds and mammals, with the teleost group being subdivided into two subclades comprising PGI1 and PGI2. This PGI partitioning into groups is consistent with the synteny and molecular evolution results based on the estimation of the ratios of nonsynonymous to synonymous changes (Ka/Ks) and divergence rates between both PGI paralogs and orthologs. Teleost PGI2 shares more similarity with the variant found in all other vertebrates, suggesting that it has less evolved than PGI1 relative to the PGI of common vertebrate ancestor. CONCLUSIONS: The diversification of PGI genes into PGI1 and PGI2 is consistent with a teleost-specific duplication before the radiation of this lineage, and after its split from the other infraclasses of ray-finned fishes. The low average Ka/Ks ratios within teleost and mammalian lineages suggest that both PGI1 and PGI2 are functionally constrained by purifying selection and may, therefore, have the same functions. By contrast, the high average Ka/Ks ratios and divergence rates within reptiles and birds indicate that PGI may be involved in different functions. The synteny analyses show that the genomic region harbouring PGI genes has independently undergone genomic rearrangements in mammals versus the reptile/bird lineage in particular, which may have contributed to the actual functional diversification of this gene family. PMCID: PMC4684624 PMID: 26682538 [PubMed - in process] 


17. Evol Psychol. 2015 Apr 29;13(2):339-59. 

Human preferences for colorful birds: Vivid colors or pattern? 
Lišková S(1), Landová E(2), Frynta D(3). Author information: (1)National Institute of Mental Health, Klecany, Czech Republic.. (2)Department of Zoology, Faculty of Science, Charles University, Praha 2, Czech Republic; National Institute of Mental Health, Klecany, Czech Republic.. (3)Department of Zoology, Faculty of Science, Charles University, Praha 2, Czech Republic; National Institute of Mental Health, Klecany, Czech Republic. 

Abstract
In a previous study, we found that the shape of a bird, rather than its color, plays a major role in the determination of human preferences. Thus, in the present study, we asked whether the preferences of human respondents towards uniformly shaped, colorful birds are determined by pattern rather than color. The experimental stimuli were pictures of small passerine birds of the family Pittidae possessing uniform shape but vivid coloration. We asked 200 participants to rank 43 colored and 43 identical, but grayscaled, pictures of birds. To find the traits determining human preferences, we performed GLM analysis in which we tried to explain the mean preference ranks and PC axes by the following explanatory variables: the overall lightness and saturation, edges (pattern), and the portion of each of the basic color hues. The results showed that the mean preference ranks of the grayscale set is explained mostly by the birds' pattern, whereas the colored set ranking is mostly determined by the overall lightness. The effect of colors was weaker, but still significant, and revealed that people liked blue and green birds. We found no significant role of the color red, the perception of which was acquired relatively recently in evolution. PMID: 25920889 [PubMed - indexed for MEDLINE]


Monday, 21 December 2015

What's new for 'birdRS' in PubMed. December Week 4, 2015

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. Glob Change Biol Bioenergy. 2015 Jul 1;7(4):741-751. 

Balance between climate change mitigation benefits and land use impacts of bioenergy: conservation implications for European birds. 
Meller L(1), Thuiller W(2), Pironon S(3), Barbet-Massin M(4), Hof A(5), Cabeza M(6). Author information: (1)Metapopulation Research Group, Department of Biosciences, P.O. Box 65, 00014 University of Helsinki, Finland; tel. +35844-5377193; laura.meller@helsinki.fi ; Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J. Fourier, Grenoble I, BP 53, 38041 Grenoble Cedex 9, France. (2)Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J. Fourier, Grenoble I, BP 53, 38041 Grenoble Cedex 9, France. (3)Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J. Fourier, Grenoble I, BP 53, 38041 Grenoble Cedex 9, France ; Instituto Pirenaico de Ecología (CSIC), 50080 Zaragoza, Spain. (4)Muséum National d'Histoire Naturelle, UMR 7204 MNHN-CNRS-UPMC, Centre de Recherches sur la Biologie des Populations d'Oiseaux, CP 51, 55 Rue Buffon, 75005, Paris, France ; Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520-8106, USA. (5)PBL Netherlands Environmental Assessment Agency, Bilthoven, The Netherlands. (6)Metapopulation Research Group, Department of Biosciences, P.O. Box 65, 00014 University of Helsinki, Finland; tel. +35844-5377193; laura.meller@helsinki.fi. 

Abstract
Both climate change and habitat modification exert serious pressure on biodiversity. Although climate change mitigation has been identified as an important strategy for biodiversity conservation, bioenergy remains a controversial mitigation action due to its potential negative ecological and socio-economic impacts which arise through habitat modification by land-use change. While the debate continues, the separate or simultaneous impacts of both climate change and bioenergy on biodiversity have not yet been compared. We assess projected range shifts of 156 European bird species by 2050 under two alternative climate change trajectories: a baseline scenario, where the global mean temperature increases by 4°C by the end of the century, and a 2 degrees scenario, where global concerted effort limits the temperature increase to below 2°C. For the latter scenario, we also quantify the pressure exerted by increased cultivation of energy biomass as modelled by IMAGE2.4, an integrated land-use model. The global bioenergy use in this scenario is in the lower end of the range of previously estimated sustainable potential. Under the assumptions of these scenarios, we find that the magnitude of range shifts due to climate change is far greater than the impact of land conversion to woody bioenergy plantations within the European Union, and that mitigation of climate change reduces the exposure experienced by species. However, we identified potential for local conservation conflict between priority areas for conservation and bioenergy production. These conflicts must be addressed by strict bioenergy sustainability criteria that acknowledge biodiversity conservation needs beyond existing protected areas and apply also to biomass imported from outside the European Union. PMID: 26681982 [PubMed] 


2. Mitochondrial DNA. 2015 Dec 18:1-2. [Epub ahead of print] 
The complete mitochondrial genome of the green-backed tit Parus monticolus (Passeriformes: Paridae). 
Wen L(1), Fu Y(1), Dai B(1), Liao J(1). Author information: (1)a Sichuan Institute Key Laboratory for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University , Leshan , People's Republic of China. 

Abstract
The complete mitochondrial genome of the green-backed tit Parus monticolus was assembled from Illumina sequencing reads. The genome is 16 771 bp long, and harbors 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region. All PCGs are initiated with the ATG codon except for COX1 with GTG as its start codon. Five distinct types of stop codons are inferred, i.e. AGA (ND1 and ND5), AGG (COX1), TAA (ATP6, ATP8, COX2, ND3 and ND4L), TAG (ND6), and the incomplete codon T/TA (COX3, CYTB, ND2 and ND4). The 22 tRNAs range in size from 66 to 75 bp. The 12S and 16S rRNAs are 982 and 1601 bp long, respectively, and are separated by tRNA-Val gene. The putative control region is located between tRNA-Glu and tRNA-Phe with a length of 1187 bp. Phylogenetic analysis indicated that this species is closely related to its congener P. major. PMID: 26681602 [PubMed - as supplied by publisher] 3. Genetica. 2015 Dec 17. [Epub ahead of print] Gene structure and evolution of transthyretin in the order Chiroptera. Khwanmunee J(1), Leelawatwattana L(1), Prapunpoj P(2). Author information: (1)Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand. (2)Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand. porntip.p@psu.ac.th. Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested. PMID: 26681450 [PubMed - as supplied by publisher] 


4. Mitochondrial DNA. 2015 Dec 18:1-2. [Epub ahead of print] 

The complete mitochondrial genome sequence of Japanese murrelet (Aves: Alcidae) and its phylogenetic position in Charadriiformes. 
Eo SH(1), An J(2). Author information: (1)a Department of Forest Resources , Kongju National University , Chungnam , Republic of Korea and. (2)b Animal Resources Division, National Institute of Biological Resources , Incheon , Republic of Korea. 

Abstract
The Japanese murrelet (Synthliboramphus wumizusume) is a threatened bird endemic to Japan, Korea, and Russia. We generated the complete mitochondrial genome sequence to provide molecular genetic information for phylogeny and conservation of the species. The S. wumizusume mitochondrial genome is 16 714 bp in length and comprises 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, a non-coding control region, and a repeat region. Gene composition and order in the genome is consistent with that of other mitochondrial genomes of the order Charadriiformes currently available in the GenBank. Phylogenetic analysis using all available Charadriiform mitochondrial genomes revealed that interfamilial relationships of the birds based on mitochondrial genes were in agreement with those based on multilocus nuclear genes. The complete mitochondrial genome of S. wumizusume we sequenced might be a useful genetic resource for phylogenetic relationships, evolutionary biology, and conservation of the species. PMID: 26680731 [PubMed - as supplied by publisher] 


5. Res Vet Sci. 2015 Dec;103:87-95. doi: 10.1016/j.rvsc.2015.09.015. Epub 2015 Sep 25. 

Drinking water application of Denagard® Tiamulin for control of Brachyspira pilosicoli infection of laying poultry.
Woodward MJ(1), Mappley L(1), Le Roy C(1), Claus SP(1), Davies P(2), Thompson G(2), La Ragione RM(3). Author information: (1)Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights Parks, P.O. Box 226, Reading RG6 6AP, UK. (2)Animal Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK. (3)Animal Health Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK; School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK. 

Abstract
Avian intestinal spirochaetosis (AIS) caused by Brachyspira spp., and notably Brachyspira pilosicoli, is common in layer flocks and reportedly of increasing incidence in broilers and broiler breeders. Disease manifests as diarrhoea, increased feed consumption, reduced growth rates and occasional mortality in broilers and these signs are shown in layers also associated with a delayed onset of lay, reduced egg weights, faecal staining of eggshells and non-productive ovaries. Treatment with Denagard® Tiamulin has been used to protect against B. pilosicoli colonisation, persistence and clinical presentation of AIS in commercial layers, but to date there has been no definitive study validating efficacy. Here, we used a poultry model of B. pilosicoli infection of layers to compare the impact of three doses of Denagard® Tiamulin. Four groups of thirty 17week old commercial pre-lay birds were all challenged with B. pilosicoli strain B2904 with three oral doses two days apart. All birds were colonised within 2days after the final oral challenge and mild onset of clinical signs were observed thereafter. A fifth group that was unchallenged and untreated was also included for comparison as healthy birds. Five days after the final oral Brachypira challenge three groups were given Denagard® Tiamulin in drinking water made up following the manufacturer's recommendations with doses verified as 58.7ppm, 113ppm and 225ppm. Weight gain body condition and the level of diarrhoea of birds infected with B. pilosicoli were improved and shedding of the organism reduced significantly (p=0.001) following treatment with Denagard® Tiamulin irrespective of dose given. The level and duration of colonisation of organs of birds infected with B. pilosicoli was also reduced. Confirming previous findings we showed that the ileum, caeca, colon, and both liver and spleen were colonised and here we demonstrated that treatment with Denagard® Tiamulin resulted in significant reduction in the numbers of Brachyspira found in each of these sites and dramatic reduction in faecal shedding (p<0.001) to approaching zero as assessed by culture of cloacal swabs. Although the number of eggs produced per bird and the level of eggshell staining appeared unaffected, egg weights of treated birds were greater than those of untreated birds for a period of approximately two weeks following treatment. These data conclusively demonstrate the effectiveness of Denagard® Tiamulin in reducing B. pilosicoli infection in laying hens. Copyright © 2015 Elsevier Ltd. All rights reserved. PMID: 26679801 [PubMed - in process] 


6. Mitochondrial DNA. 2015 Dec 18:1-2. [Epub ahead of print] 

The complete mitochondrial genome of the white-browed laughing thrush Garrulax sannio (Passeriformes: Leiothrichidae). 
Wen L(1,)(2), Wang Y(2), Fu Y(1), Dai B(1). Author information: (1)a Sichuan Institute Key Laboratory for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University , Leshan , People's Republic of China and. (2)b Department of Biological and Environmental Sciences , Alabama A&M University , Normal , AL , USA. 

Abstract
The complete mitochondrial genome of the white-browed laughing thrush Garrulax sannio was assembled using next-generation sequencing (NGS) technology. The double-stranded circular genome is 17 848 bp in length, including 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and 2 putative control region. All PCGs are initiated with the ATG codon except for COX1 with GTG as its start codon. Five distinct types of stop codons are present, i.e., AGA (ND5), AGG (COX1 and ND1), TAA (ATP6, ATP8, COX2, CYTB, and ND4L), TAG (ND6), and the incomplete codon T/TA (COX3, ND2, ND3, and ND4). The nucleotide composition is moderately asymmetric (28.94% A, 32.82% C, 15.00% G, and 23.24% T) with an overall GC content of 47.82% ("light strand"). Phylogenetic analysis indicated a close genetic relationship between this species and its congeners G. perspicillatus, G. cineraceus, and G. canorus. PMID: 26679731 [PubMed - as supplied by publisher] 


7. Mitochondrial DNA. 2015 Dec 18:1-2. [Epub ahead of print] 

The assembly and annotation of the complete Rufous-bellied thrush mitochondrial genome. 
Gomes de Sá P(1), Veras A(1), Fontana CS(2), Aleixo A(3), Burlamaqui T(1), Mello CV(4), de Vasconcelos AT(5), Prosdocimi F(6), Ramos R(1), Schneider M(1), Silva A(1). Author information: (1)a Institute of Biological Sciences, Federal University of Pará , Belem, Pará , Brazil ; (2)b PUCRS - Museu De Ciências E Tecnologia (MCT), Graduate Program in Zoology Pontifícia Universidade Católica Do Rio Grande Do Sul (PUCRS) , Porto Alegre , Rio Grande Do Sul , Brazil ; (3)c Museu Paraense Emílio Goeldi , Belém , Pará , Brazil ; (4)d Department of Behavioral Neuroscience , Oregon Health and Science University , Portland , OR , USA ; (5)e Bioinformatics Laboratory , National Laboratory of Scientific Computation (LNCC/MCTI) , Petrópolis , Rio De Janeiro , Brazil ; (6)f Genomics and Biodiversity Laboratory , Medical Biochemical Institute Leopoldo De Meis, Federal University of Rio De Janeiro , Rio De Janeiro , Brazil. 

Abstract
Among known bird species, oscines are one of the few groups that produce complex vocalizations due to vocal learning. One of the most conspicuous oscine passerines in southeastern South America is the Rufous-bellied Thrush, Turdus rufiventris. The complete mitochondrial genome of this species was sequenced with the Illumina HiSeq platform (Illumina Inc., San Diego, CA), assembled using MITObim software and annotated by MITOS web server and Artemis software. This mitogenome contained 16 669 bases, organized as 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (d-loop). The sequencing of the Rufous-bellied Thrush mitochondrial genome is of particular interest for better understanding of population genetics and phylogeography of the Turdidae family. PMID: 26679427 [PubMed - as supplied by publisher] 


8. Mol Ecol. 2015 Dec 17. doi: 10.1111/mec.13519. [Epub ahead of print] 

Evidence from Pyrosequencing Indicates that Natural Variation in Animal Personality is Associated with DRD4 DNA Methylation. 
Verhulst EC(1,)(2), Mateman CA(1), Zwier MV(3), Caro SP(1), Verhoeven KJ(2), van Oers K(1). Author information: (1)Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands. (2)Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands. (3)Center for Liver, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Digestive and Metabolic Diseases, Groningen, The Netherlands. 

Abstract
Personality traits are heritable and respond to natural selection, but are at the same time influenced by the ontogenetic environment. Epigenetic effects, such as DNA methylation, have been proposed as a key mechanism to control personality variation. However, to date little is known about the contribution of epigenetic effects to natural variation in behaviour. Here we show that great tit (Parus major) lines artificially selected for divergent exploratory behaviour for four generations differ in their DNA methylation levels at the Dopamine Receptor D4 (DRD4) gene. This D4 receptor is statistically associated with personality traits in both humans and non-human animals, including the great tit. Previous work in this songbird failed to detect functional genetic polymorphisms within DRD4 that could account for the gene-trait association. However, our observation supports the idea that DRD4 is functionally involved in exploratory behaviour but that its effects are mediated by DNA methylation. While the exact mechanism underlying the transgenerational consistency of DRD4 methylation remains to be elucidated, this study shows that epigenetic mechanisms are involved in shaping natural variation in personality traits. We outline how this first finding provides a basis for investigating the epigenetic contribution to personality traits in natural systems and its subsequent role for understanding the ecology and evolution of behavioural consistency. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26678756 [PubMed - as supplied by publisher] 


9. Mitochondrial DNA. 2015 Dec 18:1-2. [Epub ahead of print] 

Complete mitochondrial genome and phylogenetic relationship analysis of Garrulax affinis (Passeriformes, Timaliidae). 
Huang R(1), Zhou Y(2), Yao Y(2), Zhao B(2), Zhang Y(2), Xu HL(1). Author information: (1)a College of Life Science, Sichuan Agricultural University , Ya'an , China and. (2)b College of Animal Science and Technology, Sichuan Agricultural University , Chengdu , China. 

Abstract
Garrulax affinis was a medium-sized bird of Timaliidae, and we got its complete mitochondrial genome by the polymerase chain reaction method (PCR). The genome (17 856 in length), it contained 13 protein-coding genes, 2 rRNA (12S and 16S) genes, 2 tRNA genes, 2 control regions (D-loop). All protein-coding, rRNA, and tRNA genes were similar to other Passeriformes in gene arrangement and composition. In 13 PCGs, 12 were initiated with ATG, only COI was GTG, and stopped by five types of stop codons. We constructed a phylogenetic tree based on 13 PCGs of G. affinis and other nine Timaliidae species, found that the species belong to the same Passeriformes all cluster together. PMID: 26678550 [PubMed - as supplied by publisher] 


10. Parasitol Res. 2015 Dec 17. [Epub ahead of print] 

Hemosporidian parasites of free-living birds in the São Paulo Zoo, Brazil. 
Chagas CR(1), Guimarães LO(2), Monteiro EF(2), Valkiūnas G(3), Katayama MV(4), Santos SV(5), Guida FJ(1), Simões RF(2), Kirchgatter K(6). Author information: (1)São Paulo Zoological Park Foundation, Av. Miguel Estéfano 4241, São Paulo, SP, 04301-905, Brazil. (2)Malaria Research Center, Superintendence for Endemic Disease Control, São Paulo Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, São Paulo, SP, 05403-000, Brazil. (3)Nature Research Centre, Akademijos 2, Vilnius, 08412, Lithuania. (4)Post-Graduate Program of Ecology and Natural Resources, Department of Ecology and Evolutionary Biology, Federal University of São Carlos, Rodovia Washington Luis km 235, São Carlos, SP, 13565-905, Brazil. (5)Post-Graduate Program of Infectology, Federal University of São Paulo, Rua Sena Madureira 1500, São Paulo, SP, 04021-001, Brazil. (6)Malaria Research Center, Superintendence for Endemic Disease Control, São Paulo Institute of Tropical Medicine, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar 470, São Paulo, SP, 05403-000, Brazil. karink@usp.br. 

Abstract
Numerous studies addressed the diversity of bird Plasmodium and Haemoproteus parasites. However, a few have been carried out in continental avian hotspot regions such as Brazil, a country with markedly different biomes, including Amazon, Brazilian Savanna, Atlantic Forest, Caatinga, Pantanal, and Pampas. We present the first study on hemosporidian (Haemosporida) parasites in free-living birds from an Atlantic Forest fragment where more than 80 avian species have been reported. Within this area, the São Paulo Zoo locates, and it is the fourth largest zoo in the world and the largest in Latin America. A total of 133 free-living bird samples representing 12 species were collected in the zoo, with the overall hemosporidian prevalence of 18 % by PCR-based diagnostics. Twenty-four positive PCR signals were reported from four different bird species, including migratory ones. Columba livia, an urban species, considered nowadays a pest in big cities, showed 100 % prevalence of Haemoproteus spp., mainly Haemoproteus columbae. We discuss the epidemiological importance of new parasites introduced by migratory birds in the São Paulo Zoo area and the risk it poses to the captive species, which are natives or exotics. We also warn about the influence these parasites can have on the biodiversity and the structure of host populations by altering the competitive interaction between the free-living and the captive birds. PMID: 26677094 [PubMed - as supplied by publisher] 


11. Environ Monit Assess. 2016 Jan;188(1):34. doi: 10.1007/s10661-015-5017-1. Epub 2015 Dec 16. 

Sediment contaminant surveillance in Milford Haven Waterway. 
Little DI(1), Bullimore B(2), Galperin Y(3), Langston WJ(4). Author information: (1)Environmental Consultancy, Swavesey, Cambridge, CB24 4RL, UK. david.i.little@btinternet.com. (2)Deep Green Seas, Marine Environmental Consultancy, Tiers Cross, Haverfordwest, SA62 3DG, UK. (3)Environmental Geochemistry Consulting, Moorpark, CA, 93021, USA. (4)Marine Biological Association, Citadel Hill, Plymouth, PL1 2PB, UK. 

Abstract
Sediment contaminants were monitored in Milford Haven Waterway (MHW) since 1978 (hydrocarbons) and 1982 (metals), with the aim of providing surveillance of environmental quality in one of the UK's busiest oil and gas ports. This aim is particularly important during and after large-scale investment in liquefied natural gas (LNG) facilities. However, the methods inevitably have changed over the years, compounding the difficulties of coordinating sampling and analytical programmes. After a review by the MHW Environmental Surveillance Group (MHWESG), sediment hydrocarbon chemistry was investigated in detail in 2010. Natural Resources Wales (NRW) contributed their MHW data for 2007 and 2012, collected to assess the condition of the Special Area of Conservation (SAC) designated under the European Union Habitats Directive. Datasets during 2007-2012 have thus been more comparable. The results showed conclusively that a MHW-wide peak in concentrations of sediment polycyclic aromatic hydrocarbons (PAHs), metals and other contaminants occurred in late 2007. This was corroborated by independent annual monitoring at one centrally located station with peaks in early 2008 and 2011. The spatial and temporal patterns of recovery from the 2007 peak, shown by MHW-wide surveys in 2010 and 2012, indicate several probable causes of contaminant trends, as follows: atmospheric deposition, catchment runoff, sediment resuspension from dredging, and construction of two LNG terminals and a power station. Adverse biological effects predictable in 2007 using international sediment quality guidelines were independently tested by data from monitoring schemes of more than a decade duration in MHW (starfish, limpets) and in the wider SAC (grey seals). Although not proving cause and effect, many of these potential biological receptors showed a simultaneous negative response to the elevated 2007 contamination following intense dredging activity in 2006. Wetland bird counts were typically at a peak in the winter of 2005-2006 previous to peak dredging. In the following winter 2006-2007, shelduck in the Pembroke River showed their lowest winter count, and spring 2007 was the largest ever drop in numbers of shelduck broods across MHW between successive breeding seasons. Wigeon counts in the Pembroke River were low in 2006-2007 and in late 2012 after further dredging nearby. These results are strongly supported by PAH data reported previously from invertebrate bioaccumulation studies in MHW 2007-2010, themselves closely reflecting sediment trends for PAHs in the Pembroke River and Angle Bay. PMID: 26676410 [PubMed - in process] 


12. Braz J Biol. 2015 Nov;75(4):1008-17. doi: 10.1590/1519-6984.05714. Epub 2015 Nov 10. 

The impact of anthropogenic food supply on fruit consumption by dusky-legged guan (Penelope obscura Temminck, 1815): potential effects on seed dispersal in an Atlantic forest area. 
Vasconcellos-Neto J(1), Ramos RR(1), Pinto LP(1). Author information: (1)Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. 

Abstract
Frugivorous birds are important seed dispersers and influence the recruitment of many plant species in the rainforest. The efficiency of this dispersal generally depends on environment quality, bird species, richness and diversity of resources, and low levels of anthropogenic disturbance. In this study, we compared the sighting number of dusky-legged guans (Penelope obscura) by km and their movement in two areas of Serra do Japi, one around the administrative base (Base) where birds received anthropogenic food and a pristine area (DAE) with no anthropogenic resource. We also compared the richness of native seeds in feces of birds living in these two areas. Although the abundance of P. obscura was higher in the Base, these individuals moved less, dispersed 80% fewer species of plants and consumed 30% fewer seeds than individuals from DAE. The rarefaction indicated a low richness in the frugivorous diet of birds from the Base when compared to the populations from DAE. We conclude that human food supply can interfere in the behavior of these birds and in the richness of native seeds dispersed. PMID: 26675919 [PubMed - in process] 


13. Braz J Biol. 2015 Nov;75(4):953-62. doi: 10.1590/1519-6984.03414. Epub 2015 Nov 10. 

Hematological, morphological and morphometric characteristics of blood cells from rhea, Rhea Americana (Struthioniformes: Rheidae): a standard for Brazilian birds. 
Gallo SS(1), Ederli NB(2), Bôa-Morte MO(1), Oliveira FC(1). Author information: (1)Laboratório de Sanidade Animal, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, RJ, Brazil. (2)Universidade Federal do Pará, Marajó-Breves, PA, Brazil. 

Abstract
Blood exams are an indispensable tool in bird medicine. This study aimed at describing values and aspects of rheas' hematology, Rhea americana, as well as analyzing the morphology and morphometry of all blood cells. Fifty eight adult rheas of both sexes from two farms, one in Cachoeiro de Itapemirim, Espírito Santo State and the other in São Carlos, São Paulo State, were selected. Blood samples were taken and RBC count, PCV and Hb levels measured and used in hematimetric indexes calculations. The total and differentiated leukocyte counts, as well as the TPP and fibrinogen were determined. Erythrocytes, leukocytes and thrombocytes were identified and characterized morphologically. The values for the red series and hematimetric indexes were: RBC (2.81±0.15×106/μL), PCV (44.20±2.86%), Hb (12.12±0.74 g/dL), MCV (15.75±0.89 fL), MCH (43.18±1.82 pg), MCHC (27.44±0.80 g/dL); the values of white series were: WBC (12.072±4116/μL), heterophils (64.10±9.90%), eosinophils (2.05±2.06%), monocytes (6.40±2.99%), lymphocytes (26.93±9.62%), basophils (0.52±1.27%). One may conclude that on average, rheas' blood cells are larger than those of other birds, but these cells in smears cannot be differentiated only by their size. Besides rheas' leukocytes have different components and coloring as in other bird species, however, there are no components or staining aspects unique to the species. PMID: 26675913 [PubMed - in process] 


14. Braz J Biol. 2015 Nov;75(4):932-5. doi: 10.1590/1519-6984.02914. Epub 2015 Nov 10. 

Trace elements concentrations in Buff-breasted Sandpiper sampled in Lagoa do Peixe National Park, Southern Brazil. 
Scherer JF(1), Scherer AL(1), Barbieri E(2), Petry MV(1), Valiati VH(1). Author information: (1)Centro de Ciências da Saúde, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil. (2)Instituto de Pesca, Cananéia, SP, Brazil. 

Abstract
Cadmium, cobalt, chromium, copper, manganese, nickel, zinc and lead concentrations were detected in feathers of Buff-breasted Sandpipers (Calidris subruficollis) captured during the non-breeding season and analyzed with relationship to body mass. Of these metals tested for, only copper levels (2.28 µg/g) were positively correlated with bird body mass. Zinc levels showed higher concentration (67.97 µg/g) than the other metals, and cadmium levels showed the lowest concentration (0.14 µg/g). Trace element concentrations were below toxicity levels for all tested chemicals and we suggest that this probably reflects that essential elements are maintained there by normal homeostatic mechanism and that no excessive environmental exposure to these elements during migration or on the wintering area is suggested by these results. PMID: 26675909 [PubMed - in process] 


15. PLoS One. 2015 Dec 15;10(12):e0144949. doi: 10.1371/journal.pone.0144949. eCollection 2015. 

Asymmetric Response of Costa Rican White-Breasted Wood-Wrens (Henicorhina leucosticta) to Vocalizations from Allopatric Populations. 
Pegan TM(1), Rumelt RB(1), Dzielski SA(1), Ferraro MM(1), Flesher LE(1), Young N(1), Class Freeman A(2), Freeman BG(1,)(2). Author information: (1)Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America. (2)Cornell Laboratory of Ornithology, Ithaca, NY, United States of America. 

Abstract
Divergence in song between allopatric populations can contribute to premating reproductive isolation in territorial birds. Song divergence is typically measured by quantifying divergence in vocal traits using audio recordings, but field playback experiments provide a more direct way to behaviorally measure song divergence between allopatric populations. The White-breasted Wood-Wren (Henicorhina leucosticta; hereafter "WBWW") is an abundant Neotropical species with four mitochondrial clades (in Central America, the Darién, the Chocó and the Amazon) that are deeply divergent (~5-16% sequence divergence). We assessed the possibility that the WBWW as currently defined may represent multiple biological species by conducting both statistical analysis of vocal characters and field playback experiments within three clades (Central America, Chocó and Amazon). Our analysis of vocal traits revealed that Central American songs overlapped in acoustic space with Chocó songs, indicating vocal similarity between these two populations, but that Central American songs were largely divergent from Amazonian songs. Playback experiments in the Caribbean lowlands of Costa Rica revealed that Central American WBWWs typically responded aggressively to songs from the Chocó population but did not respond to playback of songs from the Amazonian population, echoing the results of the vocal trait analysis. This marked difference in behavioral response demonstrates that the songs of Central American and Amazonian WBWWs (but not Central American and Chocó WBWWs) have diverged sufficiently that Central American WBWWs no longer recognize song from Amazonian WBWWs as a signal to elicit territorial defense. This suggests that significant premating reproductive isolation has evolved between these two populations, at least from the perspective of the Central American population, and is consistent with the possibility that Central American and Amazonian populations represent distinct biological species. We conclude by advocating for the further use of field playback experiments to assess premating reproductive isolation (and species limits) between allopatric songbird populations, a situation where behavioral systematics can answer questions that phylogenetic systematics cannot. PMID: 26671001 [PubMed - in process] 


16. Br Poult Sci. 2015 Dec 15. [Epub ahead of print] 

Predicted optimum ambient temperatures for broiler chickens to dissipate metabolic heat do not affect performance or improve breast muscle quality. 
Zahoor I(1,)(2), Mitchell MA(3), Hall S(3), Beard PM(1), Gous RM(4), de Koning DJ(1,)(5), Hocking PM(1). Author information: (1)a Roslin Institute and R(D)SVS , University of Edinburgh , Easter Bush, Midlothian , EH25 9RG , UK . (2)b University of Veterinary and Animal Sciences , Lahore , Pakistan . (3)c SRUC , Easter Bush, Midlothian , EH25 9RG , UK . (4)d University of KwaZulu-Natal , Private Bag X01, Scottsville 3209 , South Africa. (5)e Department of Animal Breeding and Genetics , Swedish University of Agricultural Sciences , 750 07 Uppsala , Sweden. 

Abstract
1. An experiment was conducted to test the hypothesis that muscle damage in fast growing broiler chickens is associated with an ambient temperature that does not permit the birds to lose metabolic heat resulting in physiological heat stress and a reduction in meat quality. 2. The experiment was performed in 4 climate chambers and was repeated in two trials using a total of 200 male broiler chickens. Two treatments compared the recommended temperature profile and a cool regimen. The cool regimen was defined by a theoretical model that determined the environmental temperature that would enable heat generated by the bird to be lost to the environment. 3. There were no differences in growth rate or feed intake between the two treatments. Breast muscles from birds on the recommended temperature regimen were lighter, less red and more yellow than those from the cool temperature regimen. There were no differences in moisture loss or shear strength but stiffness was greater in breast muscle from birds housed in the cool compared to the recommended regimen. 4. Histopathological changes in the breast muscle were similar in both treatments and were characterised by mild to severe myofibre degeneration and necrosis with regeneration, fibrosis and adipocyte infiltration. There was no difference in plasma creatine kinase activity, a measure of muscle cell damage, between the two treatments consistent with the absence of differences in muscle pathology. 5. It was concluded that breast muscle damage in fast growing broiler chickens was not the result of an inability to lose metabolic heat at recommended ambient temperatures. The results suggest that muscle cell damage and breast meat quality concerns in modern broiler chickens are related to genetic selection for muscle yields and that genetic selection to address breast muscle integrity in a balanced breeding programme is imperative. PMID: 26670305 [PubMed - as supplied by publisher] 


17. Epidemiol Infect. 2015 Dec 16:1-7. [Epub ahead of print] 

Managing a cluster outbreak of psittacosis in Belgium linked to a pet shop visit in The Netherlands. 
DE Boeck C(1), Dehollogne C(2), Dumont A(1), Spierenburg M(3), Heijne M(4), Gyssens I(5), VAN DER Hilst J(5), Vanrompay D(1). Author information: (1)Laboratory for Immunology and Animal Biotechnology,Faculty of Bioscience Engineering,Ghent University,Ghent,Belgium. (2)Flemish Agency for Care and Health,Hasselt,Belgium. (3)Netherlands Food and Consumer Product Safety Authority,Utrecht,The Netherlands. (4)Central Veterinary Institute of Wageningen University and Research Centre,Lelystad,The Nederlands. (5)Department of Infectious Diseases and Immunity,Jessa Hospital,Hasselt,Belgium;Hasselt University,Hasselt,Belgium. 

Abstract
In July 2013, a Belgian couple were admitted to hospital because of pneumonia. Medical history revealed contact with birds. Eleven days earlier, they had purchased a lovebird in a pet shop in The Netherlands. The bird became ill, with respiratory symptoms. The couple's daughter who accompanied them to the pet shop, reported similar symptoms, but was travelling abroad. On the suspicion of psittacosis, pharyngeal swabs from the couple were taken and sent to the Belgian reference laboratory for psittacosis. Culture and nested polymerase chain reaction (PCR) tests were positive for the presence of Chlamydia psittaci, and ompA genotyping indicated genotype A in both patients. The patients were treated with doxycycline and the daughter started quinolone therapy; all three recovered promptly. Psittacosis is a notifiable disease in Belgium and therefore local healthcare authorities were informed. They contacted their Dutch colleagues, who visited the pet shop. Seven pooled faecal samples were taken and analysed using PCR by the Dutch national reference laboratory for notifiable animal diseases for the presence of Chlamydia psittaci. Four (57%) samples tested positive, genotyping revealed genotype A. Enquiring about exposure to pet birds is essential when patients present with pneumonia. Reporting to health authorities, even across borders, is warranted to prevent further spread. PMID: 26669637 [PubMed - as supplied by publisher] 


18. Ecol Evol. 2015 Oct 5;5(20):4696-705. doi: 10.1002/ece3.1743. eCollection 2015. 

Bioacoustics for species management: two case studies with a Hawaiian forest bird. 
Sebastián-González E(1), Pang-Ching J(1), Barbosa JM(2), Hart P(1). Author information: (1)Department of Biology University of Hawai'i at Hilo 96720 Hilo Hawai'i. (2)Department of Global Ecology Carnegie Institution for Science 94305 Stanford California. 

Abstract
The management of animal endangered species requires detailed information on their distribution and abundance, which is often hard to obtain. When animals communicate using sounds, one option is to use automatic sound recorders to gather information on the species for long periods of time with low effort. One drawback of this method is that processing all the information manually requires large amounts of time and effort. Our objective was to create a relatively "user-friendly" (i.e., that does not require big programming skills) automatic detection algorithm to improve our ability to get basic data from sound-emitting animal species. We illustrate our algorithm by showing two possible applications with the Hawai'i 'Amakihi, Hemignathus virens virens, a forest bird from the island of Hawai'i. We first characterized the 'Amakihi song using recordings from areas where the species is present in high densities. We used this information to train a classification algorithm, the support vector machine (SVM), in order to identify 'Amakihi songs from a series of potential songs. We then used our algorithm to detect the species in areas where its presence had not been previously confirmed. We also used the algorithm to compare the relative abundance of the species in different areas where management actions may be applied. The SVM had an accuracy of 86.5% in identifying 'Amakihi. We confirmed the presence of the 'Amakihi at the study area using the algorithm. We also found that the relative abundance of 'Amakihi changes among study areas, and this information can be used to assess where management strategies for the species should be better implemented. Our automatic song detection algorithm is effective, "user-friendly" and can be very useful for optimizing the management and conservation of those endangered animal species that communicate acoustically. PMCID: PMC4670053 PMID: 26668733 [PubMed]