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Monday, 26 October 2015

What's new for 'birdRS' in PubMed. October 2015, Week 3

birdRS-Latest News

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

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

PubMed Results

1. PLoS One. 2015 Oct 22;10(10):e0141059. doi: 10.1371/journal.pone.0141059.   

An Ornithopod-Dominated Tracksite from the Lower Cretaceous Jiaguan Formation (Barremian-Albian) of Qijiang, South-Central China: New Discoveries, Ichnotaxonomy, Preservation and Palaeoecology.   
Xing L(1), Lockley MG(2), Marty D(3), Zhang J(1), Wang Y(4), Klein H(5), McCrea RT(6), Buckley LG(6), Belvedere M(7), Mateus O(8), Gierliński GD(9), Piñuela L(10), Persons WS 4th(11), Wang F(12), Ran H(13), Dai H(14), Xie X(12). Author information: (1)School of Earth Sciences Resources, China University of Geosciences, Beijing 100083, China. (2)Dinosaur Trackers Research Group, University of Colorado at Denver, Colorado, United States of America. (3)Naturhistorisches Museum Basel, Augustinergasse 2, CH-4001 Basel, Switzerland. (4)Institute of Geology and Paleontology, Linyi University, Linyi, Shandong 276000, China. (5)Saurierwelt Paläontologisches Museum, Alte Richt 7, D-92318 Neumarkt, Germany. (6)Peace Region Palaeontology Research Centre, Box 1540, Tumbler Ridge, British Columbia, V0C 2W0, Canada. (7)Museum für Naturkunde, Invalidenstrasse 43, 10115 Berlin, Germany. (8)Departamento de Ciências da Terra (CICEGe-FCT), Universidade Nova de Lisboa, Lisbon 2530-157, Portugal. (9)Moab Giants Tracks Museum, 112 W, SR 313, Moab, Utah, United States of America. (10)Museo del Jurásico de Asturias MUJA (Jurassic Museum of Asturias), Colunga E-33328, Spain. (11)Department of Biological Sciences, University of Alberta 11455 Saskatchewan Drive, Edmonton, Alberta T6G 2E9, Canada. (12)Qijiang District Bureau of Land Resources, Chongqing 401420, China. (13)Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guilin 541004, China. (14)No.208 Hydrogeological and Engineering Geological Team, Chongqing Bureau of Geological and Mineral Resource Exploration and Development, Chongqing 400700, China.   

The historically-famous Lotus Fortress site, a deep 1.5-3.0-meter-high, 200-meter-long horizonal notch high up in near-vertical sandstone cliffs comprising the Cretaceous Jiaguan Formation, has been known since the 13th Century as an impregnable defensive position. The site is also extraordinary for having multiple tetrapod track-bearing levels, of which the lower two form the floor of part of the notch, and yield very well preserved asseamblages of ornithopod, bird (avian theropod) and pterosaur tracks. Trackway counts indicate that ornithopods dominate (69%) accounting for at least 165 trackmakers, followed by bird (18%), sauropod (10%), and pterosaur (3%). Previous studies designated Lotus Fortress as the type locality of Caririchnium lotus and Wupus agilis both of which are recognized here as valid ichnotaxa. On the basis of multiple parallel trackways both are interpreted as representing the trackways of gregarious species. C. lotus is redescribed here in detail and interpreted to indicate two age cohorts representing subadults that were sometimes bipedal and larger quadrupedal adults. Two other previously described dinosaurian ichnospecies, are here reinterpreted as underprints and considered nomina dubia. Like a growing number of significant tetrapod tracksites in China the Lotus Fortress site reveals new information about the composition of tetrapod faunas from formations in which the skeletal record is sparse. In particular, the site shows the relatively high abundance of Caririchium in a region where saurischian ichnofaunas are often dominant. It is also the only site known to have yielded Wupus agilis. In combination with information from other tracksites from the Jiaguan formation and other Cretaceous formations in the region, the track record is proving increasingly impotant as a major source of information on the vertebrate faunas of the region. The Lotus Fortress site has been developed as a spectacular, geologically-, paleontologically- and a culturally-significant destination within Qijiang National Geological Park. PMID: 26492525 [PubMed - as supplied by publisher]     

2. Biodivers Data J. 2015 Sep 24;(3):e6360. doi: 10.3897/BDJ.3.e6360. eCollection 2015.   

Ecology and phylogeny of birds foraging at outdoor restaurants in Sweden.   
Haemig PD(1), Sjöstedt de Luna S(2), Blank H(1), Lundqvist H(1). Author information: (1)Naturavdelningen, Länsstyrelsen i Jönköpings Län (English Translation: Nature Division, Governing Board of Jönköping Province), Jönköping, Sweden. (2)Institutionen för Matematik och Matematisk Statistik, Umeå Universitet (English Translation: Department of Mathematics and Mathematical Statistics, Umeå University), Umeå, Sweden.   

BACKGROUND: Birds frequently visit the outdoor serving areas of restaurants to feed on scraps of food and leftovers. Although this feeding association between humans and birds is widespread and could have significant effects, both positive and negative, for all taxa involved, the authors know of no published studies that have investigated restaurant bird communities. To lay the foundation for future research, the authors conducted a basic study of birds at 80 outdoor restaurants in Sweden, identifying which species and taxonomic clades of birds visited the restaurants and comparing restaurant birds in urban and rural environments. NEW INFORMATION: Thirteen species of birds visited the outdoor restaurants. Eight of these species were predominant, i.e. accounting for 51% or more of bird presence (sum of minutes of all individual birds) at one or more restaurants. Every restaurant studied had a predominant species, but species often differed from each other in frequency of predominance in different landscapes. No endangered species were seen visiting restaurants. However, three farmland bird species (House Sparrow Passer domesticus, White Wagtail Motacilla alba, Eurasian Tree Sparrow Passer montanus), whose numbers are reported to be declining in the countryside, were predominant at the majority of restaurants in rural areas, suggesting that rural restaurants might be able to contribute to the conservation of these species. The thirteen species of restaurant-visiting birds belonged to five monophyletic clades. Ninety percent of all restaurants had, as their predominant species, birds from either Clade A (Passeridae, Motacillidae, Fringillidae) or Clade C (Corvidae). Statistical testing revealed that Clade A and Clade C were distributed differently in environments along the urban-rural gradient. At all spatial scales measured, birds of Clade C were predominant at the majority of restaurants in urban areas, while birds of Clade A were the predominant clade at the majority of restaurants in rural areas. The authors use this evidence, and observations of birds foraging in association with other primates, to hypothesize that the outdoor serving areas of modern restaurants may be helping to preserve and nurture ancient human-bird symbioses that have been part of human ecology since antiquity. PMID: 26491395 [PubMed]     

3. Biodivers Data J. 2015 Oct 5;(3):e6351. doi: 10.3897/BDJ.3.e6351. eCollection 2015.   

A new species of Neossos Malloch (Diptera: Heleomyzidae) from the Yukon Territory, Canada, and a revised key to the Nearctic species.   
Solecki AM(1), Wheeler TA(1). Author information: (1)McGill University, Ste-Anne-de-Bellevue, Canada.   

BACKGROUND: The rarely collected genus Neossos Malloch contains three Nearctic and one western European species. Most known specimens have been collected from bird nests. Two specimens of an undescribed species of Neossos were collected by sweeping in subarctic tundra and a mesic meadow in the Yukon Territory, Canada. This represents a significant northward extension of the known Nearctic range of the genus. NEW INFORMATION: Neossos tombstonensis sp. n. is described from the Yukon Territory. This represents the fourth described Nearctic species of Neossos. Although the type specimens were collected by sweeping, the species is predicted to be associated with bird nests, based on habits of other members of the genus. A revised key to the Nearctic species of Neossos is provided. PMID: 26491394 [PubMed]     

4. Proc Biol Sci. 2015 Oct 22;282(1817). pii: 20152033. doi: 10.1098/rspb.2015.2033.   

Hidden keys to survival: the type, density, pattern and functional role of emperor penguin body feathers.   
Williams CL(1), Hagelin JC(2), Kooyman GL(3). Author information: (1)Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 91697, USA Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA (2)Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775, USA. (3)Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA.   

Antarctic penguins survive some of the harshest conditions on the planet. Emperor penguins breed on the sea ice where temperatures drop below -40°C and forage in -1.8°C waters. Their ability to maintain 38°C body temperature in these conditions is due in large part to their feathered coat. Penguins have been reported to have the highest contour feather density of any bird, and both filoplumes and plumules (downy feathers) are reported absent in penguins. In studies modelling the heat transfer properties and the potential biomimetic applications of penguin plumage design, the insulative properties of penguin plumage have been attributed to the single afterfeather attached to contour feathers. This attribution of the afterfeather as the sole insulation component has been repeated in subsequent studies. Our results demonstrate the presence of both plumules and filoplumes in the penguin body plumage. The downy plumules are four times denser than afterfeathers and play a key, previously overlooked role in penguin survival. Our study also does not support the report that emperor penguins have the highest contour feather density. © 2015 The Author(s). PMID: 26490794 [PubMed - in process]     

5. Proc Biol Sci. 2015 Oct 22;282(1817). pii: 20151585. doi: 10.1098/rspb.2015.1585.   

Conflict between biotic and climatic selective pressures acting on an extended phenotype in a subarctic, but not temperate, environment.   
Rohwer VG(1), Bonier F(2), Martin PR(2). Author information: (1)Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6 (2)Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6.   

Climatic selective pressures are thought to dominate biotic selective pressures at higher latitudes. However, few studies have experimentally tested how these selective pressures differentially act on traits across latitudes because traits can rarely be manipulated independently of the organism in nature. We overcame this challenge by using an extended phenotype-active bird nests-and conducted reciprocal transplant experiments between a subarctic and temperate site, separated by 14° of latitude. At the subarctic site, biotic selective pressures (nest predation) favoured smaller, non-local temperate nests, whereas climatic selective pressures (temperature) favoured larger local nests, particularly at colder temperatures. By contrast, at the temperate site, climatic and biotic selective pressures acted similarly on temperate and subarctic nests. Our results illustrate a functional trade-off in the subarctic between nest morphologies favoured by biotic versus climatic selective pressures, with climate favouring local nest morphologies. At our temperate site, however, allocative trade-offs in the time and effort devoted to nest construction favour smaller, local nests. Our findings illustrate a conflict between biotic and climatic selective pressures at the northern extremes of a species geographical range, and suggest that trade-offs between trait function and trait elaboration act differentially across latitude to create broad geographic variation in traits. © 2015 The Author(s). PMID: 26490789 [PubMed - in process]     

6. N Z Vet J. 2015 Oct 22:1-14. [Epub ahead of print]   

Network analysis of wildlife translocations in New Zealand.   
Van Andel M(1), McInnes K(2), Tana T(1), French NP(3). Author information: (1)a Ministry for Primary Industries , PO Box 40742, Upper Hutt 5140 , New Zealand. (2)b Department of Conservation , PO Box 10420, Wellington 6011 , New Zealand. (3)c mEpiLab, Infectious Disease Research Centre, Institute of V9+eterinary, Animal and Biomedical Sciences , Massey University , Palmerston North , New Zealand.   

AIMS: To identify network measures with relevance to disease spread in a network of movements derived from the Department of Conservation (DOC) translocation records from 1970 to mid-2014, and to identify conservation sites that should be prioritised for surveillance activities and improvements to data collection to make the best use of network analysis techniques in the future. METHODS: Data included the source and destination of translocated specimens, the species and the dates the translocations were expected to occur. The data were used to construct a directed, non-weighted network in which a translocation event represented a tie in the network. Network density, in-degree (movements entering a node of interest) and out-degree (movements leaving a node of interest) and reciprocity were calculated. RESULTS: The data analysed consisted of 692 unique translocations between 307 sites, with the majority (518; 73%) being for birds. The constructed network for bird, reptile and frog translocations comprised 260 nodes, with 34/260 (13%) having two-way movements and 47/260 (18%) non-reciprocal movements. The median degree score (sum of in- and out-degree) was two (min 0, max 36) with a mean of 3.5 in a right skewed distribution. Most sites acted as receivers or senders of consignments with only a few having both high in- and high out-degree, and thus had characteristics that made them sites of interest for surveillance activities. These included the National Wildlife Centre at Mount Bruce, Tiritiri Matangi Island and Te Kakahu (Chalky Island). CONCLUSIONS: The presence of linking sites that join larger clusters within the network creates the potential for rapid disease spread if a pathogen were to be introduced. The important sites that supply or receive specimens for translocations are already well-recognised by those performing translocations in New Zealand, and this paper provides further information by quantifying their role within the network. PMID: 26490218 [PubMed - as supplied by publisher]     

7. PLoS One. 2015 Oct 21;10(10):e0139034. doi: 10.1371/journal.pone.0139034. eCollection 2015.   

Presence of Zea luxurians (Durieu and Ascherson) Bird in Southern Brazil: Implications for the Conservation of Wild Relatives of Maize.   
Silva NC(1), Vidal R(2), Costa FM(1), Vaio M(3), Ogliari JB(1). Author information: (1)Departamento de Fitotecnia, Centro de Ciências Agrárias (CCA), Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brasil. (2)Departamento de Fitotecnia, Centro de Ciências Agrárias (CCA), Universidade Federal de Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brasil; Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay. (3)Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay.   

Records of the occurrence of wild relatives of maize in South American lowlands are unprecedented, especially in sympatric coexistence with landraces. This fact is relevant, because regions of occurrence of wild relatives of cultivated plants should be a priority for conservation, even if they do not correspond to the center of origin of the species. The aim of this study was to identify and characterize the wild relatives of maize in the Far West of Santa Catarina, southern Brazil. Therefore, phenotypic characterization was performed for five populations, based on 22 morphological traits deemed as fundamental for classifying the species of the genus Zea, and validated through the characterization of chromosomal knobs of two populations. The occurrence and distribution of teosinte populations were described through semi-structured interviews applied to a sample of 305 farmers. A total of 136 teosinte populations were identified; 75% of them occur spontaneously, 17% are cultivated populations, and 8% occur both ways, for the same farm. Populations that were characterized morphologically had trapezoidal fruits mostly, upright tassel branch (4-18), non-prominent main branch and glabrous glumes, with two protruding outer ribs and 8 inner ribs, on average. Cytogenetic analysis identified 10 pairs of homologous chromosomes (2n = 20) with 26 knobs, located in the terminal region of all chromosomes. The similarity of these results with the information reported in the literature indicates that the five populations of wild relatives of maize in this region of Santa Catarina belong to the botanical species Zea luxurians. PMID: 26488577 [PubMed - in process]     

8. J Med Entomol. 2015 Oct 19. pii: tjv149. [Epub ahead of print]   

A Preliminary Investigation on Ticks (Acari: Ixodidae) Infesting Birds in Kızılırmak Delta, Turkey.   
Keskin A(1), Erciyas-Yavuz K(2). Author information: (1)Department of Biology, Faculty of Science & Art, Gaziosmanpasa University, Tasliciftlik, Tokat, Turkey 60250 (, (2)Ornithology Research Center, Ondokuz Mayis University, Atakum, Samsun, Turkey 55137 (   

Ticks are mandatory blood-feeding ectoparasites of mammals, birds, reptiles, and even amphibians. Turkey has a rich bird fauna and is located on the main migration route for many birds. However, information on ticks infesting birds is very limited. In the present study, we aimed to determine ticks infesting birds in Kızılırmak Delta, Turkey. In 2014 autumn bird migration season, a total of 7,452 birds belonging to 79 species, 52 genera, 35 families, and 14 orders were examined for tick infestation. In total, 287 (234 larvae, 47 nymphs, 6♀) ticks were collected from 54 passerine birds (prevalence = 0.72%) belonging to 12 species. Ticks were identified as Amblyomma sp., Dermacentor marginatus (Sulzer), Haemaphysalis concinna Koch, Haemaphysalis punctata Canestrini and Fanzago, Hyalomma sp., Ixodes frontalis (Panzer), and Ixodes ricinus (L). The most common tick species were I. frontalis (223 larvae, 23 nymphs, 6♀) followed by I. ricinus (3 larvae, 12 nymphs) and H. concinna (4 larvae, 6 nymphs). Based on our results, it can be said that Erithacus rubecula (L.) is the main host of immature I. frontalis, whereas Turdus merula L. is the most important carrier of immature stages of some ticks in Kızılırmak Delta, Turkey. To the best of our knowledge, most of the tick-host associations found in this study have never been documented in the literature. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: PMID: 26487249 [PubMed - as supplied by publisher]     

9. Genome Biol. 2015 Oct 21;16(1):215. doi: 10.1186/s13059-015-0780-4.   

The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures.   
Chung O(1), Jin S(2), Cho YS(3,)(4), Lim J(5), Kim H(6), Jho S(7), Kim HM(8), Jun J(9), Lee H(10), Chon A(11), Ko J(12), Edwards J(13), Weber JA(14), Han K(15,)(16), O'Brien SJ(17,)(18,)(19), Manica A(20), Bhak J(21,)(22,)(23), Paek WK(24). Author information: (1)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (2)National Institute of Ecology, Seocheon, 325-813, Republic of Korea. (3)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (4)The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. (5)National Science Museum, Daejeon, 305-705, Republic of Korea. (6)The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. (7)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (8)The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. (9)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (10)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (11)The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. (12)Theragen BiO Institute, TheragenEtex, Suwon, 443-270, Republic of Korea. (13)Department Chemistry and Chemical Biology, Molecular Genetics and Microbiology, and Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, New Mexico, USA. (14)Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA. (15)Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea. (16)DKU-Theragen institute for NGS analysis (DTiNa), Cheonan, 330-714, Republic of Korea. (17)Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University St. Petersburg, Petersburg, 199004, Russia. (18)Oceanographic Center, 8000 N. Ocean Drive, Dania Beach, USA. (19)Nova Southeastern University Ft Lauderdale, Fort Lauderdale, Florida, 33004, USA. (20)Department of Zoology, Evolutionary Ecology Group, University of Cambridge, Cambridge, UK. (21)Personal Genomics Institute, Genome Research Foundation, Osong, 361-951, Republic of Korea. (22)The Genomics Institute, Biomedical Engineering Department, UNIST, Ulsan, Republic of Korea. (23)Geromics, Ulsan, 689-798, Republic of Korea. (24)National Science Museum, Daejeon, 305-705, Republic of Korea.   

BACKGROUND: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging. RESULTS: We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome, a close relative with a divergence time of 18 million years. By comparing the cinereous vulture to other avian genomes, we find positively selected genetic variations in this species associated with respiration, likely linked to their ability of immune defense responses and gastric acid secretion, consistent with their ability to digest carcasses. Comparisons between the Old World and New World vulture groups suggest convergent gene evolution. We assemble the cinereous vulture blood transcriptome from a second individual, and annotate genes. Finally, we infer the demographic history of the cinereous vulture which shows marked fluctuations in effective population size during the late Pleistocene. CONCLUSIONS: We present the first genome and transcriptome analyses of the cinereous vulture compared to other avian genomes and transcriptomes, revealing genetic signatures of dietary and environmental adaptations accompanied by possible convergent evolution between the Old World and New World vultures. PMID: 26486310 [PubMed - in process]     

10. Ecol Appl. 2015 Jul;25(5):1213-25.   

Estimating wind-turbine-caused bird and bat fatality when zero carcasses are observed.   
Huso MM, Dalthorp D, Dail D, Madsen L.   

Many wind-power facilities in the United States have established effective monitoring programs to determine turbine-caused fatality rates of birds and bats, but estimating the number of fatalities of rare species poses special difficulties. The loss of even small numbers of individuals may adversely affect fragile populations, but typically, few (if any) carcasses are observed during monitoring. If monitoring design results in only a small proportion of carcasses detected, then finding zero carcasses may give little assurance that the number of actual fatalities is small. Fatality monitoring at wind-power facilities commonly involves conducting experiments to estimate the probability (g) an individual will be observed, accounting for the possibilities that it falls in an unsearched area, is scavenged prior to detection, or remains undetected even when present. When g < 1, the total carcass count (X) underestimates the total number of fatalities (M). Total counts can be 0 when M is small or when M is large and g << 1. Distinguishing these two cases is critical when estimating fatality of a rare species. Observing no individuals during searches may erroneously be interpreted as evidence of absence. We present an approach that uses Bayes' theorem to construct a posterior distribution for M, i.e., P(M \ X, ĝ), reflecting the observed carcass count and previously estimated g. From this distribution, we calculate two values important to conservation: the probability that M is below a predetermined limit and the upper bound (M*) of the 100(1 - α)% credible interval for M. We investigate the dependence of M* on α, g, and the prior distribution of M, asking what value of g is required to attain a desired M for a given α. We found that when g < -0.15, M* was clearly influenced by the mean and variance of ĝ and the choice of prior distribution for M, but the influence of these factors is minimal when g > -0.45. Further, we develop extensions for temporal replication that can inform prior distributions of M and methods for combining information across several areas or time periods. We apply the method to data collected at a wind-power facility where scheduled searches yielded X = 0 raptor carcasses. PMID: 26485950 [PubMed - in process]     

11. Ecol Appl. 2015 Jul;25(5):1175-86.   

Evaluating the impact of gas extraction infrastructure on the occupancy of sagebrush-obligate songbirds.   
Mutter M, Pavlacky DC Jr, Van Lanen NJ, Grenyer R.   

Development associated with natural gas extraction may have negative effects on wildlife. Here we assessed the effects of natural gas development on the distributions of three sagebrush-obligate birds (Brewer's Sparrow, Spizella breweri; Sagebrush Sparrow, Amphispiza belli; and Sage Thrasher, Oreoscoptes montanus) at a natural gas extraction site in Wyoming, USA. Two drivers of habitat disturbance were investigated: natural gas well pads and roadways. Disturbances were quantified on a small scale (minimum distance to a disturbance) and a large scale (landscape density of a disturbance). Their effects on the study species' distributions were assessed using a multi-scale occupancy model. Minimum distances to wells and roadways were found to not have significant impacts on small-scale occupancy. However, roadway and well density at the landscape-scale significantly impacted the large-scale occupancy of Sagebrush Sparrows and Sage Thrashers. The results confirmed our hypotheses that increasing road density negatively affects the landscape-scale occupancy rates of Sagebrush Sparrow and Sage Thrasher, but did not confirm our hypothesis that increasing well density would negatively impact large-scale occupancy. We therefore suggest that linear features that affect patch size may be more important than point features in determining sagebrush-obligate songbird occupancy when compared to structural effects such as habitat fragmentation and increased predation. We recommend that future well construction be focused along existing roadways, that horizontal drilling be used to reduce the need for additional roads, and that deactivation and restoration of roadways be implemented upon the deactivation of wells, we also recommend a possible mitigation strategy when new roads are to be built. PMID: 26485947 [PubMed - in process]     

12. Proc Natl Acad Sci U S A. 2015 Oct 19. pii: 201512599. [Epub ahead of print]   

The evolution of parental cooperation in birds.   
Remeš V(1), Freckleton RP(2), Tökölyi J(3), Liker A(4), Székely T(5). Author information: (1)Department of Zoology and Laboratory of Ornithology, Palacky University, 77146 Olomouc, Czech Republic; (2)Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom; (3)MTA-DE "Lendület" Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, 4032 Debrecen, Hungary; (4)Department of Limnology, University of Pannonia, H-8201 Veszprém, Hungary; (5)Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom; State Key Laboratory of Biocontrol and College of Ecology and Evolution, Sun Yat-sen University, Guangzhou 5102275, China.   

Parental care is one of the most variable social behaviors and it is an excellent model system to understand cooperation between unrelated individuals. Three major hypotheses have been proposed to explain the extent of parental cooperation: sexual selection, social environment, and environmental harshness. Using the most comprehensive dataset on parental care that includes 659 bird species from 113 families covering both uniparental and biparental taxa, we show that the degree of parental cooperation is associated with both sexual selection and social environment. Consistent with recent theoretical models parental cooperation decreases with the intensity of sexual selection and with skewed adult sex ratios. These effects are additive and robust to the influence of life-history variables. However, parental cooperation is unrelated to environmental factors (measured at the scale of whole species ranges) as indicated by a lack of consistent relationship with ambient temperature, rainfall or their fluctuations within and between years. These results highlight the significance of social effects for parental cooperation and suggest that several parental strategies may coexist in a given set of ambient environment. PMID: 26483476 [PubMed - as supplied by publisher]     

13. BMC Genomics. 2015 Oct 19;16(1):816. doi: 10.1186/s12864-015-2016-0.   

Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek's disease is predominantly determined by transcriptional regulation.   
Cheng HH(1), Perumbakkam S(2,)(3), Pyrkosz AB(2), Dunn JR(2), Legarra A(4), Muir WM(5). Author information: (1)USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA. (2)USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA. (3)Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. (4)INRA, Animal Genetics, GenPhySE, Castanet Tolosan, 31326, France. (5)Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA.   

BACKGROUND: Marek's disease (MD) is a lymphoproliferative disease of poultry induced by Marek's disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout the chicken genome. METHODS: Hypothesizing that variants located in transcriptional regulatory regions are the main mechanism underlying this complex trait, a genome-wide association study was conducted by genotyping a ~1,000 bird MD resource population derived from experimental inbred layers with SNPs containing 1,824 previously identified allele-specific expression (ASE) SNPs in response to MDV infection as well as 3,097 random SNPs equally spaced throughout the chicken genome. Based on the calculated associations, genomic predictions were determined for 200 roosters and selected sires had their progeny tested for Marek's disease incidence. RESULTS: Our analyses indicate that these ASE SNPs account for more than 83 % of the genetic variance and exhibit nearly all the highest associations. To validate these findings, 200 roosters had their genetic merit predicted from the ASE SNPs only, and the top 30 and bottom 30 ranked roosters were reciprocally mated to random hens. The resulting progeny showed that after only one generation of bidirectional selection, there was a 22 % difference in MD incidence and this approach gave a 125 % increase in accuracy compared to current pedigree-based estimates. CONCLUSIONS: We conclude that variation in transcriptional regulation is the major driving cause for genetic resistance to MD, and ASE SNPs identify the underlying genes and are sufficiently linked to the causative polymorphisms that they can be used for accurate genomic prediction as well as help define the underlying molecular basis. Furthermore, this approach should be applicable to other complex traits. PMID: 26481588 [PubMed - in process]     

14. J Appl Microbiol. 2015 Oct 19. doi: 10.1111/jam.12972. [Epub ahead of print]   

Effect of Bacillus subtilis CGMCC 1.1086 on the growth performance and intestinal microbiota of broilers.   
Li Y(1), Xu Q(1), Huang Z(1), Lv L(1), Liu X(1), Yin C(1), Yan H(1), Yuan J(2). Author information: (1)School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China. (2)State Key Laboratory for Animal Nutrition, China Agricultural University, Beijing, 100193, China.   

AIMS: Probiotics have been proved to be the most preferred and effective alternative to antibiotics as growth promoter and pathogens inhibitor in poultry industry. In this study Bacillus subtilis CGMCC 1.1086 as a probiotic bacterium was administered in diet and its effects on both the growth performance and the cecal microbiota of broilers were evaluated. METHODS AND RESULTS: A total of 240 male Arbor Acres (AA) broilers were randomly allocated into 2 treatment groups of basal diet without any addition of probiotics and basal diet containing B. subtilis CGMCC 1.1086. The body weight of broilers was measured individually at 32, 39 and 46 d of bird age. Furthermore MiSeq high-throughput sequencing analysis of 16S rRNA were used to investigate the bacterial community structure in the ceca of broilers. The results indicated that broilers receiving diet supplemented with B. subtilis CGMCC 1.1086 showed 27.7% higher daily weight gain than those of control during two weeks. The feed conversion ratio (FCR) of B. subtilis CGMCC 1.1086 group was also improved by 10.3%. In the ceca of broilers fed with B. subtilis CGMCC 1.1086, the relative abundance of Alistipes, Odoribacter, Ruminococcus, Blautia and Desulfovibrio were higher, while the potential pathogens such as Staphylococcus and Escherichia-Shigella were lower than those of control. CONCLUSIONS: The probiotic B. subtilis CGMCC 1.1086 can effectively improve the growth performance and FCR of broilers via the beneficial modulation of cecal microbiota. SIGNIFICANCE AND IMPACT OF STUDY: The effect of B. subtilis on growth performance of broilers was evaluated and the relationship between growth and cecal microbiota was revealed. The results of this study help to promote application of probiotics in poultry industry. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved. PMID: 26480894 [PubMed - as supplied by publisher]     

15. Animals (Basel). 2015 Jul 9;5(3):495-511. doi: 10.3390/ani5030368.   

Air Quality in Alternative Housing Systems May Have an Impact on Laying Hen Welfare. Part I-Dust.   
David B(1), Moe RO(2), Michel V(3), Lund V, Mejdell C(4). Author information: (1)Norwegian Veterinary Institute, P.O. Box 750 Sentrum, Oslo 0106, Norway. (2)Norwegian University of Life Sciences, P.O. Box 8146 Dep., Oslo 0033, Norway. (3)French Agency for Food, Environmental and Occupational Health Safety (Anses), P.O.Box 53, Ploufragan 22440, France. (4)Norwegian Veterinary Institute, P.O. Box 750 Sentrum, Oslo 0106, Norway.   

The new legislation for laying hens in the European Union put a ban on conventional cages. Production systems must now provide the hens with access to a nest, a perch, and material for dust bathing. These requirements will improve the behavioral aspects of animal welfare. However, when hens are kept with access to litter, it is a concern that polluted air may become an increased threat to health and therefore also a welfare problem. This article reviews the literature regarding the health and welfare effects birds experience when exposed to barn dust. Dust is composed of inorganic and organic compounds, from the birds themselves as well as from feed, litter, and building materials. Dust may be a vector for microorganisms and toxins. In general, studies indicate that housing systems where laying hens have access to litter as aviaries and floor systems consistently have higher concentrations of suspended dust than caged hens with little (furnished cages) or no access to litter (conventional cages). The higher dust levels in aviaries and floor housing are also caused by increased bird activity in the non-cage systems. There are gaps in both the basic and applied knowledge of how birds react to dust and aerosol contaminants, i.e., what levels they find aversive and/or impair health. Nevertheless, high dust levels may compromise the health and welfare of both birds and their caretakers and the poor air quality often found in new poultry housing systems needs to be addressed. It is necessary to develop prophylactic measures and to refine the production systems in order to achieve the full welfare benefits of the cage ban. PMCID: PMC4598690 PMID: 26479370 [PubMed]     

16. Animals (Basel). 2015 Apr 10;5(2):214-25. doi: 10.3390/ani5020214.   

The Efficiency of an Integrated Program Using Falconry to Deter Gulls from Landfills.   
Thiériot E(1), Patenaude-Monette M(2), Molina P(3), Giroux JF(4). Author information: (1)Groupe de Recherche en Écologie Comportementale et Animale, Département des sciences biologiques, Université du Québec à Montréal, P.O. Box 8888 Station Centre-ville, Montréal, QC H3C 3P8, Canada. (2)Groupe de Recherche en Écologie Comportementale et Animale, Département des sciences biologiques, Université du Québec à Montréal, P.O. Box 8888 Station Centre-ville, Montréal, QC H3C 3P8, Canada. (3)Falcon Environmental Services, P.O. Box 1018, St-Lazare, QC J7T 2Z7, Canada. (4)Groupe de Recherche en Écologie Comportementale et Animale, Département des sciences biologiques, Université du Québec à Montréal, P.O. Box 8888 Station Centre-ville, Montréal, QC H3C 3P8, Canada.   

Gulls are commonly attracted to landfills, and managers are often required to implement cost-effective and socially accepted deterrence programs. Our objective was to evaluate the effectiveness of an intensive program that integrated the use of trained birds of prey, pyrotechnics, and playback of gull distress calls at a landfill located close to a large ring-billed gull (Larus delawarensis) colony near Montreal, Quebec, Canada. We used long-term survey data on bird use of the landfill, conducted behavioral observations of gulls during one season and tracked birds fitted with GPS data loggers. We also carried out observations at another landfill located farther from the colony, where less refuse was brought and where a limited culling program was conducted. The integrated program based on falconry resulted in a 98% decrease in the annual total number of gulls counted each day between 1995 and 2014. A separate study indicated that the local breeding population of ring-billed gulls increased and then declined during this period but remained relatively large. In 2010, there was an average (±SE) of 59 ± 15 gulls/day using the site with falconry and only 0.4% ± 0.2% of these birds were feeding. At the other site, there was an average of 347 ± 55 gulls/day and 13% ± 3% were feeding. Twenty-two gulls tracked from the colony made 41 trips towards the landfills: twenty-five percent of the trips that passed by the site with falconry resulted in a stopover that lasted 22 ± 7 min compared to 85% at the other landfill lasting 63 ± 15 min. We concluded that the integrated program using falconry, which we consider more socially acceptable than selective culling, was effective in reducing the number of gulls at the landfill. PMCID: PMC4494414 PMID: 26479231 [PubMed]     

17. Exp Appl Acarol. 2015 Oct 17. [Epub ahead of print]   

The natural infection of birds and ticks feeding on birds with Rickettsia spp. and Coxiella burnetii in Slovakia.   
Berthová L(1), Slobodník V(2), Slobodník R(3), Olekšák M(4), Sekeyová Z(1), Svitálková Z(5), Kazimírová M(5), Špitalská E(6). Author information: (1)Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovakia. (2)State Nature Conservancy of the Slovak Republic, Dlhá 3, 971 01, Prievidza, Slovakia. (3)Raptor Protection of Slovakia, Kuklovská 5, 841 04, Bratislava, Slovakia. (4)National Park Slovak Karst, Hámossyho 188, 049 51, Brzotín, Slovakia. (5)Institute of Zoology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 06, Bratislava, Slovakia. (6)Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovakia.   

Ixodid ticks (Acari: Ixodidae) are known as primary vectors of many pathogens causing diseases in humans and animals. Ixodes ricinus is a common ectoparasite in Europe and birds are often hosts of subadult stages of the tick. From 2012 to 2013, 347 birds belonging to 43 species were caught and examined for ticks in three sites of Slovakia. Ticks and blood samples from birds were analysed individually for the presence of Rickettsia spp. and Coxiella burnetii by PCR-based methods. Only I. ricinus was found to infest birds. In total 594 specimens of bird-attached ticks were collected (451 larvae, 142 nymphs, 1 female). Altogether 37.2 % (16/43) of bird species were infested by ticks and some birds carried more than one tick. The great tit, Parus major (83.8 %, 31/37) was the most infested species. In total, 6.6 and 2.7 % of bird-attached ticks were infected with Rickettsia spp. and C. burnetii, respectively. Rickettsia helvetica predominated (5.9 %), whereas R. monacensis (0.5 %) was only sporadically detected. Coxiella burnetii was detected in 0.9 %, Rickettsia spp. in 8.9 % and R. helvetica in 4.2 % of bird blood samples. The great tit was the bird species most infested with I. ricinus, carried R. helvetica and C. burnetti positive tick larvae and nymphs and was found to be rickettsaemic in its blood. Further studies are necessary to define the role of birds in the circulation of rickettsiae and C. burnetii in natural foci. PMID: 26477038 [PubMed - as supplied by publisher]     

18. Horm Behav. 2015 Oct 14. pii: S0018-506X(15)30102-1. doi: 10.1016/j.yhbeh.2015.10.005. [Epub ahead of print]   

Developmental effects of vasotocin and nonapeptide receptors on early social attachment and affiliative behavior in the zebra finch.   
Baran NM(1), Sklar NC(2), Adkins-Regan E(3). Author information: (1)Department of Psychology, Cornell University, Ithaca, NY, USA. Electronic address: (2)Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA. (3)Department of Psychology, Cornell University, Ithaca, NY, USA; Department of Neurobiology & Behavior, Cornell University, Ithaca, NY, USA.   

Zebra finches demonstrate selective affiliation between juvenile offspring and parents, which, like affiliation between pair partners, is characterized by proximity, vocal communication and contact behaviors. This experiment tested the hypothesis that the nonapeptide arginine vasotocin (AVT, avian homologue of vasopressin) and nonapeptide receptors play a role prior to fledging in the development of affiliative behavior. Zebra finch hatchlings of both sexes received daily intracranial injections (post-hatch days 2-8) of either AVT, Manning Compound (MC, a potent V1a receptor antagonist) or saline (vehicle control). The social development of both sexes was assessed by measuring responsiveness to isolation from the family and subsequent reunion with the male parent after fledging. In addition, we assessed the changes in affiliation with the parents, unfamiliar males, and unfamiliar females each week throughout juvenile development. Compared to controls, MC subjects showed decreased attachment to the parents and MC males did not show the normal increase in affiliative interest in opposite sex individuals as they reached reproductive maturity. In contrast, AVT subjects showed a sustained affiliative interest in parents throughout development, and males showed increased interest in opposite sex conspecifics as they matured. These results provide the first evidence suggesting that AVT and nonapeptide receptors play organizational roles in social development in a bird. Copyright © 2015. Published by Elsevier Inc. PMID: 26476409 [PubMed - as supplied by publisher]

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