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Monday, 4 August 2014

Bird research this week on PubMed: August 2014 Week 1

PubMed listing for 'bird' OR 'songbird' excluding references to influenza and flu - August 2014 Week 1

1. PLoS One. 2014 Aug 1;9(8):e103367. doi: 10.1371/journal.pone.0103367. eCollection 2014.

Political Systems Affect Mobile and Sessile Species Diversity - A Legacy from the Post-WWII Period.

Cousins SA1, Kaligarič M2, Bakan B3, Lindborg R1.Author information:
1Landscape Ecology, Department of Physical Geography and Quaternary Geology, Stockholm University, Stockholm, Sweden.
2University of Maribor, Biology Department, Faculty of Natural Sciences and Mathematics, Maribor, Slovenia; Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, Hoče, Slovenia.
3University of Maribor, Biology Department, Faculty of Natural Sciences and Mathematics, Maribor, Slovenia.


Political ideologies, policies and economy affect land use which in turn may affect biodiversity patterns and future conservation targets. However, few studies have investigated biodiversity in landscapes with similar physical properties but governed by different political systems. Here we investigate land use and biodiversity patterns, and number and composition of birds and plants, in the borderland of Austria, Slovenia and Hungary. It is a physically uniform landscape but managed differently during the last 70 years as a consequence of the political "map" of Europe after World War I and II. We used a historical map from 1910 and satellite data to delineate land use within three 10-kilometre transects starting from the point where the three countries meet. There was a clear difference between countries detectable in current biodiversity patterns, which relates to land use history. Mobile species richness was associated with current land use whereas diversity of sessile species was more associated with past land use. Heterogeneous landscapes were positively and forest cover was negatively correlated to bird species richness. Our results provide insights into why landscape history is important to understand present and future biodiversity patterns, which is crucial for designing policies and conservation strategies across the world.
PMID: 25084154 [PubMed - as supplied by publisher]
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2. Mol Phylogenet Evol. 2014 Jul 29. pii: S1055-7903(14)00255-3. doi: 10.1016/j.ympev.2014.07.012. [Epub ahead of print]

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

Panero JL1, Freire SE2, Espinar LA3, Crozier BS 4, Barboza GE5, J Cantero J6.
Author information:
1Department of Integrative Biology, The University of Texas, 1 University Station C0930, Austin, TX, 78712, USA. Electronic address:
2Instituto de Botánica Darwinion, Casilla de Correo 22, Labardén 200, San Isidro (B1642HYD), Buenos Aires, Argentina.
3Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Casilla de Correo 495, 5000 Córdoba, Argentina.
4P. O. Box 8315, Santa Fe, New Mexico 87504, USA.
5Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Casilla de Correo 495, 5000 Córdoba, Argentina; Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y M. Allende s.n., Córdoba, Argentina.
6Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC), Casilla de Correo 495, 5000 Córdoba, Argentina; Departamento Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Ruta Nac. 36, Km 601, C.P. X5804BYA, Río Cuarto, Córdoba, Argentina.


A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura + Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae.
Copyright © 2014. Published by Elsevier Inc.
PMID: 25083940 [PubMed - as supplied by publisher]
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3. PeerJ. 2014 Jul 17;2:e488. doi: 10.7717/peerj.488. eCollection 2014.

Automatic large-scale classification of bird sounds is strongly improved by unsupervised feature learning.

Stowell D, Plumbley MD.Author information:
Centre for Digital Music, Queen Mary University of London , UK.


Automatic species classification of birds from their sound is a computational tool of increasing importance in ecology, conservation monitoring and vocal communication studies. To make classification useful in practice, it is crucial to improve its accuracy while ensuring that it can run at big data scales. Many approaches use acoustic measures based on spectrogram-type data, such as the Mel-frequency cepstral coefficient (MFCC) features which represent a manually-designed summary of spectral information. However, recent work in machine learning has demonstrated that features learnt automatically from data can often outperform manually-designed feature transforms. Feature learning can be performed at large scale and "unsupervised", meaning it requires no manual data labelling, yet it can improve performance on "supervised" tasks such as classification. In this work we introduce a technique for feature learning from large volumes of bird sound recordings, inspired by techniques that have proven useful in other domains. We experimentally compare twelve different feature representations derived from the Mel spectrum (of which six use this technique), using four large and diverse databases of bird vocalisations, classified using a random forest classifier. We demonstrate that in our classification tasks, MFCCs can often lead to worse performance than the raw Mel spectral data from which they are derived. Conversely, we demonstrate that unsupervised feature learning provides a substantial boost over MFCCs and Mel spectra without adding computational complexity after the model has been trained. The boost is particularly notable for single-label classification tasks at large scale. The spectro-temporal activations learned through our procedure resemble spectro-temporal receptive fields calculated from avian primary auditory forebrain. However, for one of our datasets, which contains substantial audio data but few annotations, increased performance is not discernible. We study the interaction between dataset characteristics and choice of feature representation through further empirical analysis.
PMID: 25083350 [PubMed]
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4. Science. 2014 Aug 1;345(6196):562-6. doi: 10.1126/science.1252243.

Dinosaur evolution. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds.

Lee MS1, Cau A2, Naish D3, Dyke GJ4.Author information:
1Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia. School of Earth and Environmental Sciences, University of Adelaide 5005, Australia.
2Museo Geologico e Paleontologico "Giovanni Capellini," Via Zamboni 63, 40126 Bologna, Italy. Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Alma Mater Studiorum Università di Bologna, 40126 Bologna, Italy.
3Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK.
4Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK. MTA-DE Lendület Behavioural Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, 4032 Debrecen, Egyetem tér 1, Hungary.

Comment in


Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.
Copyright © 2014, American Association for the Advancement of Science.
PMID: 25082702 [PubMed - in process]
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5. Parasitol Res. 2014 Aug 2. [Epub ahead of print]

Molecular characterisation of Sarcocystis rileyi from a common eider (Somateria mollissima) in Norway.

Gjerde B.Author information:
Department of Food Safety and Infection Biology, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033, Oslo, Norway,


The breast and leg muscles of a common eider (Somateria mollissima; Anatidae: Anseriformes) from northern Norway contained numerous grossly visible cigar-shaped sarcocysts measuring about 5 × 1 mm. Light microscopic examination of isolated sarcocysts revealed that they were encapsulated by a thin fibrous layer, underneath which there was a thin and fairly smooth cyst wall with no visible protrusions. The cystozoites were straight, spindle-shaped and about 13 μm long. Genomic DNA was extracted from 12 excised sarcocysts and each DNA isolate was subjected to PCR amplification of one to four loci: the 18S and 28S ribosomal RNA genes (four isolates), the internal transcribed spacer 1 (ITS1) region (six isolates) and the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) (12 isolates). At the three nuclear loci, the new sequences showed 99.9-100 % sequence identity with previous sequences of Sarcocystis rileyi from the mallard duck in Lithuania and USA, and they could therefore be assigned to this species. At cox1, the new sequences of S. rileyi were most similar to Sarcocystis arctica and Sarcocystis neurona, but the most closely related Sarcocystis spp. in birds have not been sequenced at this locus. There was no sequence variation at any locus between the 4-12 examined isolates of S. rileyi. This is the first genetically verified record of S. rileyi in the common eider, as well as in any bird species in Norway. The phylogenetic placement of S. rileyi was inferred separately from 28S rRNA gene and cox1 sequences, and similar results were obtained in both analyses.
PMID: 25082019 [PubMed - as supplied by publisher]
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6. Curr Protoc Microbiol. 2014 Aug 1;34:15I.1.1-15I.1.33. doi: 10.1002/9780471729259.mc15i01s34.

Avian bornaviruses: diagnosis, isolation, and genotyping.

Guo J1, Payne S, Zhang S, Turner D, Tizard I, Suchodolski P.Author information:
1Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas.


These protocols apply to all currently known genotypes of avian bornavirus (ABV). First, they include four basic protocols for molecular techniques that should enable an investigator to detect ABV infection in a live or dead bird. These include both reverse transcriptase and real-time PCR assays. Second, they include three protocols enabling ABV infections to be diagnosed by serologic techniques including indirect immunofluorescence assays, western blotting, and enzyme-linked immunoassays. Third, they also include methods by which ABV can be isolated from infected bird tissues by culture in primary duck embryo fibroblasts, as well as in other avian cell lines. Finally, as part of a diagnostic workup, any virus detected should be genotyped by sequencing, and a protocol for this is also provided. Curr. Protoc. Microbiol. 34:15I.1.1-15I.1.33. © 2014 by John Wiley & Sons, Inc.
Copyright © 2014 John Wiley & Sons, Inc.
PMID: 25082005 [PubMed - in process]
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7. Zootaxa. 2014 Jul 16;3838(1):127-142. doi: 10.11646/zootaxa.3838.1.8.

A new species and five new records of chewing lice (Insecta: Phthiraptera: Ischnocera) from an isolated population of the solitary tinamou Tinamus solitarius (Aves: Tinamiformes).

Valim MP1, Silveira LF2.Author information:
1Museu de Zoologia, Universidade de São Paulo, Av. Nazaré, 481, Ipiranga, São Paulo, SP 04263-000, Brazil; Email:
2Museu de Zoologia, Universidade de São Paulo, Av. Nazaré, 481, Ipiranga, São Paulo, SP 04263-000, Brazil; Email:


We report the first records of chewing lice from an isolated population of the solitary tinamou (formerly known as Tinamus solitarius pernambucensis Berla, 1946) in the Pernambuco Centre of Endemism (PCE), Brazil. All louse records previously published from the solitary tinamou came from the populations south of the São Francisco River, formerly known as Tinamus solitarius solitarius (Vieillot, 1819). Five known species of the family Heptapsogasteridae were identified from the northern population of this host: Heptarthrogaster grandis Carriker, 1936; Ornicholax alienus (Giebel, 1874); Pterocotes solitarius Guimarães & Lane, 1937; Rhopaloceras oniscus (Nitzsch [in Giebel], 1866); and Strongylocotes wernecki Guimarães & Lane, 1937. Also, the new species Heptagoniodes guimaraesi is described and illustrated from the northern population of this host, and a key for identification of all the species of Heptagoniodes Carriker, 1936 is included. The discovery of H. guimaraesi is the first Brazilian example of a bird ectoparasite represented by two different species of the same genus living on two distinct populations of the same host species. Records of eight louse species and 31 new localities from the southern population of the solitary tinamou in Brazil are given, and an updated list of all the chewing lice known from both host populations [subspecies] is included.
PMID: 25081764 [PubMed - as supplied by publisher]
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8. Dev Neurobiol. 2014 Aug 1. doi: 10.1002/dneu.22220. [Epub ahead of print]

Effects of sex and seasonality on the song control system and FoxP2 protein expression in black-capped chickadees (Poecile atricapillus).

Phillmore LS1, MacGillivray HL, Wilson KR, Martin S.Author information:
1 Departments of Psychology and Neuroscience, Dalhousie University, PO Box 15000, Halifax, Nova Scotia, Canada, B3R 4H2.


Plasticity in behavior is mirrored by corresponding plasticity in the brain in many songbird species. In some species, song system nuclei (Phillmore et al., 2006) are larger in birds in breeding condition than birds in non-breeding condition, possibly due to increased vocal output in spring. FoxP2, a transcription factor associated with language expression and comprehension in humans and song learning in songbirds, also shows plasticity. FoxP2 expression in songbird Area X, a region important for sensorimotor integration, is related to developmental and adult vocal plasticity (Teramitsu et al., 2010, Chen et al., 2013). In this study we examined whether sex and breeding condition affects both song control system volume (HVC, X) and FoxP2 protein expression in black-capped chickadees (Poecile atricapillus). HVC volume was larger in males in breeding condition than males in non-breeding condition, but there were no sex differences. In contrast Area X volume was larger in males than females, regardless of breeding condition, likely reflecting that male and female chickadees produce learned chick-a-dee calls year round, but output of the learned song increases in breeding males. FoxP2 protein levels did not differ between sexes or breeding condition when calculated as a ratio of labeled cells in Area X to labeled cells in the surrounding striato-pallium, however absolute density of FoxP2 in both regions was higher in males than in females. This may indicate that chickadees maintain a level of FoxP2 necessary for plasticity year-round, but males have greater potential for plasticity compared to females. © 2014 Wiley Periodicals, Inc. Develop Neurobiol, 2014.
Copyright © 2014 Wiley Periodicals, Inc., a Wiley company.
PMID: 25081094 [PubMed - as supplied by publisher]
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9. Berl Munch Tierarztl Wochenschr. 2014 Jul-Aug;127(7-8):257-66.

Campylobacter infections in four poultry species in respect of frequency, onset of infection and seasonality.

Weber R, Auerbach M, Jung A, Glünder G.


Over a seven-year period (2001-2007) flocks of four poultry species, 52 broiler flocks, 46 Pekin duck flocks, 22 Muscovy duck flocks, 20 turkey flocks, which were kept on the same farm, were continuously investigated for Campylobacter (C). Altogether 76.1% of the broiler flocks, 59.6% of the Pekin duck flocks, 68.2% of the Muscovy duck flocks and 90.0% turkey flocks were Campylobacter positive. The prevalence during the course of the fattening period increased steadily. There was no specific point of time for the onset of infection. More detailed examination over a one-year period showed the highest isolation rates of C. coli from July to September and a higher isolation rate of the same agent with increasing age, in all species except Muscovy ducks. Moreover, C. coli was isolated more often from the lungs of broilers and Muscovy ducks than from the other two bird species. Flocks of all species housed during the summer months featured a higher prevalence of Campylobacter colonisation than those housed in winter. This was statistically significant for broilers. Another approach for evaluating the seasonality of Campylobacter colonisation was to compare the age of the respective poultry species when the onset occurred in summer and in winter. All poultry species were younger when infection was introduced into a flock in summer. This was statistically significant for broilers and for Pekin ducks.
PMID: 25080818 [PubMed - in process]
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10. J Environ Sci (China). 2014 Jul;26(7):1403-10. doi: 10.1016/j.jes.2014.05.005. Epub 2014 Jun 17.

Methane and nitrous oxide fluxes from four tundra ecotopes in Ny-Ålesund of the High Arctic.

Chen Q1, Zhu R2, Wang Q1, Xu H3.Author information:
11. Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
21. Institute of Polar Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China. Electronic address:
32. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.


During the summers of 2008 and 2009, net methane (CH4) and nitrous oxide (N2O) fluxes were investigated from 4 tundra ecotopes: normal lowland tundra (LT), bird sanctuary tundra (BT), the tundra in an abandoned coal mine (CT) and the tundra in scientific bases (ST) in Ny-Ålesund of the High Arctic. Tundra soils in CT (184.5±40.0μgCH4/(m(2)·hr)) and ST (367.6±92.3μgCH4/(m(2)·hr)) showed high CH4 emissions due to the effects of human activities, whereas high CH4 uptake or low emission occurred in the soils of LT and BT. The lowland tundra soils (mean, -4.4-4.3μgN2O/(m(2)·hr)) were weak N2O sources and even sinks. Bird activity increased N2O emissions from BT with the mean flux of 7.9μgN2O/(m(2)·hr). The mean N2O fluxes from CT (45.4±10.2μgN2O/(m(2)·hr)) and ST (78.8±18.5μgN2O/(m(2)·hr)) were one order of magnitude higher than those from LT and BT, indicating that human activities significantly increased N2O emissions from tundra soils. Soil total carbon and water regime were important factors affecting CH4 fluxes from tundra soils. The N2O fluxes showed a significant positive correlation with ammonia nitrogen (NH4(+)-N) contents (r=0.66, p<0.001) at all the observation sites, indicating that ammonia nitrogen (NH4(+)-N) content acted as a strong predictor for N2O emissions from tundra soils. The CH4 and N2O fluxes did not correspond to the temperature variations of soil at 0-15cm depths. Overall our results implied that human activities might have greater effects on soil CH4 and N2O emissions than current climate warming in Ny-Ålesund, High Arctic.
Copyright © 2014. Published by Elsevier B.V.
PMID: 25079988 [PubMed - in process]
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