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Friday, 11 December 2015

What's new for 'birdRS' in PubMed. December Week 2, 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. PLoS One. 2015 Dec 4;10(12):e0143241. doi: 10.1371/journal.pone.0143241. 

Breeding Bird Community Continues to Colonize Riparian Buffers Ten Years after Harvest. 
Pearson SF(1), Giovanini J(2), Jones JE(2), Kroll AJ(2). Author information: (1)Wildlife Research Division, Washington Department of Fish and Wildlife, Olympia, Washington, United States of America. (2)Weyerhaeuser, Federal Way, Washington, United States of America. 

Abstract Riparian ecosystems integrate aquatic and terrestrial communities and often contain unique assemblages of flora and fauna. Retention of forested buffers along riparian habitats is a commonly employed practice to reduce potential negative effects of land use on aquatic systems. However, very few studies have examined long-term population and community responses to buffers, leading to considerable uncertainty about effectiveness of this practice for achieving conservation and management outcomes. We examined short- (1-2 years) and long-term (~10 years) avian community responses (occupancy and abundance) to riparian buffer prescriptions to clearcut logging silvicultural practices in the Pacific Northwest USA. We used a Before-After-Control-Impact experimental approach and temporally replicated point counts analyzed within a Bayesian framework. Our experimental design consisted of forested control sites with no harvest, sites with relatively narrow (~13m) forested buffers on each side of the stream, and sites with wider (~30m) and more variable width unharvested buffer. Buffer treatments exhibited a 31-44% increase in mean species richness in the post-harvest years, a pattern most evident 10 years post-harvest. Post-harvest, species turnover was much higher on both treatments (63-74%) relative to the controls (29%). We did not find evidence of local extinction for any species but found strong evidence (no overlap in 95% credible intervals) for an increase in site occupancy on both Narrow (short-term: 7%; long-term 29%) and Wide buffers (short-term: 21%; long-term 93%) relative to controls after harvest. We did not find a treatment effect on total avian abundance. When assessing relationships between buffer width and site level abundance of four riparian specialists, we did not find strong evidence of reduced abundance in Narrow or Wide buffers. Silviculture regulations in this region dictate average buffer widths on small and large permanent streams that range from ~22-25 m. Guidelines for this region are within the range of buffers included in our study, in which we observed no evidence for avian species loss or for a decline in species abundance (including riparian associated species). PMID: 26637120 [PubMed - as supplied by publisher] 


 2. Genet Mol Res. 2015 Nov 30;14(4):15331-8. doi: 10.4238/2015.November.30.10. 

Genome-wide association study of growth traits in the Jinghai Yellow chicken. 
Zhang GX(1), Fan QC(1), Zhang T(1), Wang JY(2), Wang WH(1), Xue Q(1), Wang YJ(3). Author information: (1)College of Animal Science and Technology, Yangzhou University, Yangzhou, China. (2)College of Animal Science and Technology, Yangzhou University, Yangzhou, China jywang@yzu.edu.cn. (3)Jiangsu Jinghai Industry Poultry Group Co., Ltd., Jiangsu Nantong, China. 

Abstract
Growth is one of the most economically important traits in the poultry industry. In this study, we identified single-nucleotide polymorphisms (SNPs) and candidate genes associated with growth traits of the Jinghai Yellow chicken. Genome-wide association studies were conducted using the Illumina 60 K SNP Chicken array to genotype 400 Jinghai Yellow chickens. For each bird, the body weights at hatching and at 2, 4, 6, 8, 12, 14, and 16 weeks were recorded. The SNPs that were significantly associated with the growth traits were identified using the general linear regression model. The results revealed a total of 18 SNPs that reached Bonferroni genome-wide significance (P < 1.80E-6). Three proximal genes (BTRC, NLK, and NF1) were found to participate in the Wnt-signaling pathway and mitogen-activated protein kinase signaling pathway. Haplotype analysis identified 19 significant haplotypes and identified a region 152.4-156.3M on GGA1 affecting 3 growth traits (BW4, BW14, and BW16). These results may help identify the exact locations of body weight quantitative trait loci on a genome level and indicate variants that can be used for subsequent investigations for Jinghai Yellow chicken. PMID: 26634498 [PubMed - in process] 


3. Langmuir. 2015 Dec 3. [Epub ahead of print] 

From Beetles in Nature to the Lab: Actuating Underwater Locomotion on Hydrophobic Surfaces. 
Pinchasik BS, Steinkuehler J, Wuytens PC, Skirtach AG, Fratzl P, Möhwald H. 

Abstract
Controlled wetting and de-wetting of surfaces is a primary mechanism used by beetles in nature such as the lady bird and the leaf beetle for underwater locomotion. Their adhesion to surfaces underwater is enabled through the attachment of bubbles entrapped in their setae covered legs. Locomotion, however, is done by applying mechanical forces on the bubbles in order to move, attach and detach them in a controlled manner. In synthetic conditions, however, when a bubble is bound to a surface, it is merely impossible to maneuver without the use of external stimuli. Thus, actuated wetting and de-wetting of surfaces remain challenges. Here, electrowetting on dielectrics (EWOD) is used for the manipulation of bubble-particle complexes on unpatterned surfaces. Bubbles nucleate on catalytic Janus disks adjacent to a hydrophobic surface. By changing the wettability of the surface through electrowetting the bubbles show a variety of reactions, depending on the shape and periodicity of the electric signal. Time resolved (µs) imaging of bubble radial oscillations reveals the possible mechanisms for lateral mobility of bubbles on a surface under electrowetting: bubble instability is induced when electric pulses are carefully adjusted. This instability is adjusted to control the surface bound bubble locomotion and described in terms of the change in surface energy. It is shown that a deterministic force applied normal can lead to a random walk of micrometer-sized bubbles by exploiting the phenomenon of contact angle hysteresis. Finally, bubble use in nature for underwater locomotion and the actuated bubble locomotion presented in this study are compared. PMID: 26633751 [PubMed - as supplied by publisher] 


4. Parasitol Int. 2015 Nov 26. pii: S1383-5769(15)00193-2. doi: 10.1016/j.parint.2015.11.009. [Epub ahead of print] 

Phylogenetic analysis of nasal avian schistosomes (Trichobilharzia) from aquatic birds in Mazandaran province, northern Iran. 
Fakhar M(1), Ghobaditara M(1), Brant SV(2), Karamian M(3), Gohardehi S(1), Bastani R(1). Author information: (1)Molecular and Cell Biology Research Center, Department of Parasitology and Mycology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. (2)Museum of Southwestern Biology Division of Parasites, Department of Biology, University of New Mexico, Albuquerque, USA. (3)Cellular and Molecular Research Center, Department of Microbiology, Birjand University of Medical Sciences, Birjand, Iran. Electronic address: karamianm@yahoo.com. 

Abstract
Nasal schistosomes are trematodes in the family Schistosomatidae, many members of which are causative agents of human cercarial dermatitis (HCD). Little is known about the species diversity and distribution of nasal dwelling schistosomes of water birds, particularly in countries outside of Europe; even less is known in countries like Iran. Nasal schistosomes are of particular interest since these species migrate via the central nervous system to the nasal cavity once they penetrate their host. Thus, there must be efforts to determine the incidence of HCD due to nasal schistosomes. HCD outbreaks are reported seasonally in Mazandaran Province, northern Iran, an area well known for rice cultivation leading to increased person contact with water and infected snails. Such places include favorable habitat for both domestic ducks year round, and wild migratory ducks in the winter through spring. Recent reports have detected the presence of both nasal and visceral schistosomes in ducks in this area but with little species characterization. In this study, we examine a diversity of aquatic birds to determine the distribution, prevalence and bird host use of nasal schistosomes. We apply for the first time a molecular identification and phylogenetic analysis of these schistosomes. From 2012 to 2014, the nasal cavity of 508 aquatic birds from Mazandaran Province were examined that included species in Anseriformes, Gruiformes, Charadriiformes and Phoenicopteriformes. Nasal schistosomes were found in 45 (8.9%) birds belonging to Anseriformes (Anas platyrhynchos and A. clypeata). Phylogenetic analysis of the nuclear internal transcribed spacer 1 rDNA and the mitochondrial cytochrome oxidase1 gene of isolated eggs revealed that all samples grouped in a sister clade to the European Trichobilharzia regenti. However, Trichobilharzia from this study were more similar to a unique haplotype of Trichobilharzia, isolated from the nasals of an A. clypeata in France. The genetic and phenotypic differences between the species found herein and T. regenti from Europe, may prove with additional data to be a distinct species of Trichobilharzia. Copyright © 2015. Published by Elsevier Ireland Ltd. PMID: 26631753 [PubMed - as supplied by publisher] 


5. Proc Biol Sci. 2015 Dec 7;282(1820). pii: 20151786. doi: 10.1098/rspb.2015.1786. 

Preys' exploitation of predators' fear: when the caterpillar plays the Gruffalo. 
Castellano S(1), Cermelli P(2). Author information: (1)Department of Life Science and Systems Biology, University of Turin, via Accademia Albertina 13, Turin 10123, Italy sergio.castellano@unito.it. (2)Department of Mathematics, University of Turin, Via Carlo Alberto 10, Turin 10123, Italy. 

Abstract
Alike the little mouse of the Gruffalo's tale, many harmless preys use intimidating deceptive signals as anti-predator strategies. For example, several caterpillars display eyespots and face-like colour patterns that are thought to mimic the face of snakes as deterrents to insectivorous birds. We develop a theoretical model to investigate the hypothesis that these defensive strategies exploit adaptive cognitive biases of birds, which make them much more likely to confound caterpillars with snakes than vice versa. By focusing on the information-processing mechanisms of decision-making, the model assumes that, during prey assessment, the bird accumulates noisy evidence supporting either the snake-escape or the caterpillar-attack motor responses, which compete against each other for execution. Competition terminates when the evidence for either one of the responses reaches a critical threshold. This model predicts a strong asymmetry and a strong negative correlation between the prey- and the predator-decision thresholds, which increase with the increasing risk of snake predation and assessment uncertainty. The threshold asymmetry causes an asymmetric distribution of false-negative and false-positive errors in the snake-caterpillar decision plane, which makes birds much more likely to be deceived by the intimidating signals of snake-mimicking caterpillars than by the alluring signals of caterpillar-mimicking snakes. © 2015 The Author(s). PMID: 26631561 [PubMed - in process] 


6. Cold Spring Harb Protoc. 2015 Dec 2;2015(12):pdb.corr091009. doi: 10.1101/pdb.corr091009. 

Corrigendum: A Method for Exploring Adult Neurogenesis in the Songbird Brain. 
Asik K, Rao JL, Kirn JR. Erratum for Cold Spring Harb Protoc. 2014 Dec;2014(12):1259-66. PMID: 26631118 [PubMed - in process] 


7. PLoS One. 2015 Dec 2;10(12):e0143996. doi: 10.1371/journal.pone.0143996. eCollection 2015. 

Determinants of Mammal and Bird Species Richness in China Based on Habitat Groups. 
Xu H(1), Cao M(1), Wu J(1), Cai L(2), Ding H(1), Lei J(3), Wu Y(3), Cui P(1), Chen L(1), Le Z(1), Cao Y(1,)(4). Author information: (1)Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China. (2)Department of Natural Ecology Conservation, Ministry of Environmental Protection, Beijing 100035, China. (3)College of Forest Resources and Environment, Nanjing Forestry University, Nanjing 210037, China. (4)Department of Biology, Nanjing University, Nanjing 210093, China. 

Abstract
Understanding the spatial patterns in species richness is a central issue in macroecology and biogeography. Analyses that have traditionally focused on overall species richness limit the generality and depth of inference. Spatial patterns of species richness and the mechanisms that underpin them in China remain poorly documented. We created a database of the distribution of 580 mammal species and 849 resident bird species from 2376 counties in China and established spatial linear models to identify the determinants of species richness and test the roles of five hypotheses for overall mammals and resident birds and the 11 habitat groups among the two taxa. Our result showed that elevation variability was the most important determinant of species richness of overall mammal and bird species. It is indicated that the most prominent predictors of species richness varied among different habitat groups: elevation variability for forest and shrub mammals and birds, temperature annual range for grassland and desert mammals and wetland birds, net primary productivity for farmland mammals, maximum temperature of the warmest month for cave mammals, and precipitation of the driest quarter for grassland and desert birds. Noteworthily, main land cover type was also found to obviously influence mammal and bird species richness in forests, shrubs and wetlands under the disturbance of intensified human activities. Our findings revealed a substantial divergence in the species richness patterns among different habitat groups and highlighted the group-specific and disparate environmental associations that underpin them. As we demonstrate, a focus on overall species richness alone might lead to incomplete or misguided understanding of spatial patterns. Conservation priorities that consider a broad spectrum of habitat groups will be more successful in safeguarding the multiple services of biodiversity. PMID: 26629903 [PubMed - in process] 


8. PLoS One. 2015 Dec 2;10(12):e0144232. doi: 10.1371/journal.pone.0144232. eCollection 2015. 

Spatial Distribution and Temporal Patterns of Cassin's Auklet Foraging and Their Euphausiid Prey in a Variable Ocean Environment. 
Manugian S(1), Elliott ML(1), Bradley R(1), Howar J(1), Karnovsky N(2), Saenz B(3), Studwell A(1,)(4), Warzybok P(1), Nur N(1), Jahncke J(1). Author information: (1)California Current Group, Point Blue Conservation Science, Petaluma, California, United States of America. (2)Department of Biology, Pomona College, Claremont, California, United States of America. (3)Department of Biology, University of South Florida, Tampa, Florida, United States of America. (4)Department of Geography, San Francisco State University, San Francisco, California, United States of America. 

Abstract
Krill (Euphausiids) play a vital ecosystem role in many of the world's most productive marine regions, providing an important trophic linkage. We introduce a robust modeling approach to link Cassin's auklet (Ptychoramphus aleuticus) abundance and distribution to large-scale and local oceanic and atmospheric conditions and relate these patterns to similarly modeled distributions of an important prey resource, krill. We carried out at-sea strip transect bird surveys and hydroacoustic assessments of euphausiids (2004-2013). Data informed separate, spatially-explicit predictive models of Cassin's auklet abundance (zero-inflated negative binomial regression) and krill biomass (two-part model) based on these surveys. We established the type of prey responsible for acoustic backscatter by conducting net tows of the upper 50 m during surveys. We determined the types of prey fed to Cassin's auklet chicks by collecting diet samples from provisioning adults. Using time-depth-recorders, we found Cassin's auklets utilized consistent areas in the upper water column, less than 30 m, where krill could be found (99.5% of dives were less than 30 m). Birds primarily preyed upon two species of euphausiids, Euphausia pacifica and Thysanoessa spinifera, which were available in the upper water column. Cassin's auklet abundance was best predicted by both large scale and localized oceanic processes (upwelling) while krill biomass was best predicted by local factors (temperature, salinity, and fluorescence) and both large scale and localized oceanic processes (upwelling). Models predicted varying krill and bird distribution by month and year. Our work informs the use of Cassin's auklet as a valuable indicator or krill abundance and distribution and strengthens our understanding of the link between Cassin's auklet and its primary prey. We expect future increases in frequency and magnitude of anomalous ocean conditions will result in decreased availability of krill leading to declines in the Farallon Islands population of Cassin's auklets. PMID: 26629818 [PubMed - in process] 


 9. Avian Dis. 2015 Dec;59(4):472-4. doi: 10.1637/11089-041115-Reg.1. 

Persistence of Two Isolates of Trichomonas gallinae in Simulated Bird Baths With and Without Organic Material. 
Purple KE(1,)(2), Gerhold RW(1). Author information: (1)A Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Dr., Room A205, Knoxville, TN 37996. (2)B Comparative and Experimental Medicine, University of Tennessee, Knoxville, TN 37996. 

Abstract
Trichomonas gallinae, a well-documented protozoan parasite of avian hosts, has been implicated in major passerine mortality events recently and historically throughout the literature. It has been suggested that bird baths and artificial water sources could serve as a source of infection for naive birds; however, trichomonad persistence in water is not well understood. We measured the persistence of T. gallinae isolates from two avian hosts in distilled water and distilled water with the addition of organic material. We inoculated plastic containers in a laboratory setting with 1 × 10(6) trichomonads and then sampled 500 μl from each container at various time points postinoculation (0-20 hr). The 500-μl aliquots were inoculated into flasks with 5 ml of modified Diamond media at each time point. Flasks were incubated at 37 C and examined by light microscopy for five consecutive days for the characteristic movements of live trichomonads. The maximum persistence was 16 hr with a Cooper's hawk (Accipiter cooperii) isolate in the organic material treatment, far longer than the 1 hr persistence previously reported. We show that T. gallinae isolates are capable of persisting for long periods of time in water, illustrating that bird baths may be validated as a potential source of transmission in epidemics. PMID: 26629619 [PubMed - in process] 


10. Proteome Sci. 2015 Dec 1;13:29. 

The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata). 
Mann K(1). Author information: (1)Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, D-82152 Martinsried, Am Klopferspitz 18 Germany. 

Abstract
BACKGROUND: The proteins of avian eggshell organic matrices are thought to control the mineralization of the eggshell in the shell gland (uterus). Proteomic analysis of such matrices identified many candidates for such a role. However, all matrices analyzed to date come from species of one avian family, the Phasianidae. To analyze the conservation of such proteins throughout the entire class Aves and to possibly identify a common protein toolkit enabling eggshell mineralization, it is important to analyze eggshell matrices from other avian families. Because mass spectrometry-based in-depth proteomic analysis still depends on sequence databases as comprehensive and accurate as possible, the obvious choice for a first such comparative study was the eggshell matrix of zebra finch, the genome sequence of which is the only songbird genome published to date. RESULTS: The zebra finch eggshell matrix comprised 475 accepted protein identifications. Most of these proteins (84 %) were previously identified in species of the Phasianidae family (chicken, turkey, quail). This also included most of the so-called eggshell-specific proteins, the ovocleidins and ovocalyxins. Ovocleidin-116 was the second most abundant protein in the zebra finch eggshell matrix. Major proteins also included ovocalyxin-32 and -36. The sequence of ovocleidin-17 was not contained in the sequence database, but a presumptive homolog was tentatively identified by N-terminal sequence analysis of a prominent 17 kDa band. The major proteins also included three proteins similar to ovalbumin, the most abundant of which was identified as ovalbumin with the aid of two characteristic phosphorylation sites. Several other proteins identified in Phasianidae eggshell matrices were not identified. When the zebra finch sequence database contained a sequence similar to a missing phasianid protein it may be assumed that the protein is missing from the matrix. This applied to ovocalyxin-21/gastrokine-1, a major protein of the chicken eggshell matrix, to EDIL3 and to lactadherin. In other cases failure to identify a particular protein may be due to the absence of this protein from the sequence database, highlighting the importance of better, more comprehensive sequence databases. CONCLUSIONS: The results indicate that ovocleidin-116, ovocleidin-17, ovocalyxin-36 and ovocalyxin-32 may be universal avian eggshell-mineralizing proteins. All the more important it is to elucidate the role of these proteins at the molecular level. This cannot be achieved by proteomic studies but will need application of other methods, such as atomic force microscopy or gene knockouts. However, it will also be important to analyze more eggshell matrices of different avian families to unequivocally identify other mineralization toolkit proteins apart from ovocleidins and ovocalyxins. Progress in this respect will depend critically on the availability of more, and more comprehensive, sequence databases. The development of faster and cheaper nucleotide sequencing methods has considerably accelerated genome and transcriptome sequencing, but this seems to concur with frequent publication of incomplete and fragmented sequence databases. PMCID: PMC4666066 PMID: 26628892 [PubMed - as supplied by publisher] 


11. Poult Sci. 2015 Dec 1. pii: pev323. [Epub ahead of print] 

Potential environmental benefits of prospective genetic changes in broiler traits. 
Leinonen I(1), Williams AG(2), Kyriazakis I(3). Author information: (1)School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK ilkka.leinonen@newcastle.ac.uk. (2)School of Energy, Environment and Agri-Food, Cranfield University, Bedford, MK43 0AL, UK. (3)School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK. 

Abstract
A system approach-based Life Cycle Assessment (LCA) framework, combined with a simple mechanistic model of bird energy balance was used to predict the potential effects of 15 y prospective broiler breeding on the environmental impacts of the standard UK broiler production system. The year 2014 Ross 308 genotype was used as a baseline, and a future scenario was specified from rates of genetic improvement predicted by the industry. The scenario included changes in the traits of growth rate (reducing the time to reach a target weight 2.05 kg from 34 d to 27 d), body lipid content, carcass yield, mortality and the number of chicks produced by a breeder hen. Diet composition was adjusted in order to accommodate the future nutrient requirements of the birds following the genetic change. The results showed that predicted changes in biological performance due to selective breeding could lead to reduced environmental impacts of the broiler production chain, most notably in the Eutrophication Potential (by 12%), Acidification Potential (by 10%) and Abiotic Resource Use (by 9%) and Global Warming Potential (by 9%). These reductions were mainly caused by the reduced maintenance energy requirement and thus lower feed intake, resulting from the shorter production cycle, together with the increased carcass yield. However, some environmental benefits were limited by the required changes in feed composition (e.g., increased inclusion of soy meal and vegetable oil) as a result of the changes in bird nutrient requirements. This study is the first one aiming to link the mechanistic animal modeling approach to predicted genetic changes in order to produce quantitative estimates of the future environmental impacts of broiler production. Although a more detailed understanding on the mechanisms of the potential changes in bird performance and their consequences on feeding and husbandry would be still be needed, the modeling framework produced in this study provides a starting point for predictions of the effects of prospective genetic progress. © 2015 Poultry Science Association Inc. PMID: 26628347 [PubMed - as supplied by publisher] 


12. Environ Microbiol. 2015 Dec 2. doi: 10.1111/1462-2920.13164. [Epub ahead of print] 

Co-infections and transmission dynamics in a tick-borne bacterium community exposed to songbirds. 
Heylen D(1), Fonville M(2), van Leeuwen AD(2), Sprong H(2). Author information: (1)Evolutionary Ecology Group, Department of Biology, University of Antwerp, Belgium. (2)Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and Environment (RIVM), Bilthoven, the Netherlands. 

Abstract
We investigated the transmission dynamics of a community of tick-borne pathogenic bacteria in a common European songbird (Parus major). Tick-naïve birds were infested with three successive batches (spaced five days apart) of field-collected Ixodes ricinus nymphs, carrying the following tick-borne bacteria: Ricketssia helvetica (16.9 %), Borrelia garinii (1.9 %), Borrelia miyamotoi (1.6 %), Anaplasma phagocytophylum (1.2 %), and Candidatus Neoehrlichia mikurensis (0.4 %). Fed ticks were screened for the pathogens after moulting to the next developmental phase. We found evidence for early transmission (within 2.75 days after exposure) of R. helvetica and B. garinii, and to a lesser extent of A. phagocytophylum based on the increased infection rates of ticks during the first infestation. The proportion of ticks infected with R. helvetica remained constant over the three infestations. In contrast, the infection rate of B. garinii in the ticks increased over the three infestations, indicating a more gradual development of host tissue infection. No interactions were found among the different bacterium species during transmission. Birds did not transmit or amplify the other bacterial species. We show that individual birds can transmit several pathogenic bacterium species at the same time using different mechanisms, and that the transmission facilitation by birds increases the frequency of co-infections in ticks. This article is protected by copyright. All rights reserved. PMID: 26627444 [PubMed - as supplied by publisher] 


13. BMC Res Notes. 2015 Dec 1;8(1):736. doi: 10.1186/s13104-015-1749-9. 

Development of microsatellite markers for Hyacinth macaw (Anodorhynchus hyacinthinus) and their cross-amplification in other parrot species. 
da Silva HE(1), Presti FT(2), Wasko AP(3), Pinhal D(4). Author information: (1)Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618-970, Brazil. helder.eliasilva@gmail.com. (2)Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618-970, Brazil. flapresti@hotmail.com. (3)Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618-970, Brazil. awasko@ibb.unesp.br. (4)Department of Genetics, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, 18618-970, Brazil. dlpinhal@ibb.unesp.br. 

Abstract
BACKGROUND: Hyacinth macaw Anodorhynchus hyacinthinus is the largest parrot of the world and is considered vulnerable to extinction due to its habitat loss and illegal trade associated to the international pet market demand. Genetic studies on this species are still incipient to generate a consistent characterization of the population dynamics and to develop appropriate conservation strategies. In this sense, microsatellite markers may support the detection of a population genetic structure for this bird species. However, at this time, none Hyacinth macaw species-specific primers for microsatellite loci have been so far established. This study aimed to develop and characterize polymorphic microsatellite markers for A. hyacinthinus and to check for their cross-amplification in other parrot species. FINDINGS: Sequences containing repeated dinucleotide motifs were prospected and optimized from a genomic library that was enriched for microsatellites using magnetic beads. The analyses of 43-57 samples from wild individuals of three distinct Brazilian subpopulations led to the characterization of five polymorphic microsatellite loci. Allele richness per locus ranged from two to 12. Three loci exhibited observed heterozygosity values higher than 50 %, but the overall average value among all loci was close to 45 %. In addition, successful primer cross-amplification was verified in seven other investigated species of Neotropical parrots. CONCLUSIONS: The newly developed markers have shown to be potentially useful for in situ and ex situ population studies to support future conservation actions of Hyacinth macaw and other parrots. PMCID: PMC4665848 PMID: 26626138 [PubMed - in process] 


14. PLoS One. 2015 Dec 1;10(12):e0144098. doi: 10.1371/journal.pone.0144098. eCollection 2015. 

Nest Predation Deviates from Nest Predator Abundance in an Ecologically Trapped Bird. 
Hollander FA(1), Van Dyck H(1), San Martin G(1,)(2), Titeux N(1,)(3,)(4). Author information: (1)Behavioural Ecology & Conservation Group, Biodiversity Research Centre, Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium. (2)Unité Protection des plantes et écotoxicologie, Département des Sciences du Vivant, Centre wallon de Recherche agronomiques, Gembloux, Belgium. (3)Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg. (4)InForest Joint Research Unit (CSIC-CTFC-CREAF), Forest Sciences Centre of Catalonia (CEMFOR-CTFC), Solsona, Spain. 

Abstract
In human-modified environments, ecological traps may result from a preference for low-quality habitat where survival or reproductive success is lower than in high-quality habitat. It has often been shown that low reproductive success for birds in preferred habitat types was due to higher nest predator abundance. However, between-habitat differences in nest predation may only weakly correlate with differences in nest predator abundance. An ecological trap is at work in a farmland bird (Lanius collurio) that recently expanded its breeding habitat into open areas in plantation forests. This passerine bird shows a strong preference for forest habitat, but it has a higher nest success in farmland. We tested whether higher abundance of nest predators in the preferred habitat or, alternatively, a decoupling of nest predator abundance and nest predation explained this observed pattern of maladaptive habitat selection. More than 90% of brood failures were attributed to nest predation. Nest predator abundance was more than 50% higher in farmland, but nest predation was 17% higher in forest. Differences between nest predation on actual shrike nests and on artificial nests suggested that parent shrikes may facilitate nest disclosure for predators in forest more than they do in farmland. The level of caution by parent shrikes when visiting their nest during a simulated nest predator intrusion was the same in the two habitats, but nest concealment was considerably lower in forest, which contributes to explaining the higher nest predation in this habitat. We conclude that a decoupling of nest predator abundance and nest predation may create ecological traps in human-modified environments. PMID: 26624619 [PubMed - in process] 


15. Zootaxa. 2015 Oct 30;4034(3):401-44. doi: 10.11646/zootaxa.4034.3.1. 

The feather mites of the hoatzin Opisthocomus hoazin (Müller) (Aves: Opisthocomiformes), with the description of two new genera and six new species (Acari: Analgoidea, Pterolichoidea). 
Hernandes FA(1), Mironov SV(2). Author information: (1)Departamento de Zoologia, Avenida 24-A, 1515, 13506-900, Universidade Estadual Paulista, Rio Claro, SP, Brazil.; Email: abakashi@gmail.com. (2)Zoological Institute, Russian Academy of Sciences, Universitetskaya embankment 1, 199034, Saint Petersburg, Russia.; Email: sergei.mironov@zin.ru. 

Abstract
Six new species and two new genera of feather mites are described from the hoatzin Opisthocomus hoazin (Müller) (Opisthocomiformes: Opisthocomidae) in Brazil: Gymnolichus lacrimosus sp. n., G. latihumeralis sp. n. (Xolalgidae), Temnalges hoazin sp. n., T. atelodiscus sp. n. (Psoroptoididae), Ciganalichus boasfilhoi gen. n., sp. n., and Hoazinacarus anisosetus gen. n., sp. n. (Pterolichidae). Illustrations of two previously known species, Opisthocomacarus umbellifer (Trouessart, 1899) and Stakyonemus hystrix (Trouessart, 1899) are provided. We show that the hoatzin bears a much richer feather mite fauna than previously thought and presently includes eight mite species from three families: Xolalgidae, Psoroptoididae (Analgoidea) and Pterolichidae (Pterolichoidea). They represent two morpho-ecological groups: (1) mites inhabiting the wing and tail feathers, and (2) mites living in downy and body contour feathers. We hypothesize that these mites represent a native feather mite fauna of the hoatzin, inherited from its ancestors and existing on this bird for a long time. The controversial and unresolved relationships of this bird with other bird taxa are briefly discussed in the light of the new acarofauna discovered. PMID: 26624451 [PubMed - in process] 


16. Zootaxa. 2015 Oct 29;4034(2):342-50. doi: 10.11646/zootaxa.4034.2.6.

Trypanosoma naviformis sp. nov. (Kinetoplastidae: Trypanosomatidae) from widespread African songbirds, the Olive sunbird (Cyanomitra olivacea) and Yellow-whiskered greenbul (Andropadus latirostris). 
Sehgal RN(1), Iezhova TA(2), Marzec T(3), Valkiūnas G(4). Author information: (1)Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, California, 94132.; Email: sehgal@sfsu.edu. (2)Nature Research Centre, Institute of Ecology, Akademijos 2, LT-08412, Vilnius, Lithuania.; Email: tatjana@ekoi.lt. (3)Department of Biology, San Francisco State University, 1600 Holloway Ave., San Francisco, California, 94132.; Email: timothymarzec@gmail.com. (4)Nature Research Centre, Institute of Ecology, Akademijos 2, LT-08412, Vilnius, Lithuania.; Email: gedvalk@ekoi.lt. 

Abstract
Trypanosoma naviformis n. sp. is described from the African olive sunbird Cyanomitra olivacea in Ghana based on the morphology of its hematozoic trypomastigotes and partial sequences of the small subunit ribosomal RNA gene. This parasite belongs to the group of small non-striated avian trypanosomes (&lt; 30 µm in length in average) with the kinetoplast situated close to the posterior end of the body. Trypanosoma naviformis can be distinguished from other small avian trypanosomes due to its poorly visible flagellum, central position of its nucleus, and the symmetrically (in relation to the nucleus) narrowing of both ends of the hematozoic trypomastigotes, which are boat-like in shape. Illustrations of trypomastigotes of the new species are given, and SSU rDNA lineages associated with this parasite are documented. This parasite has been reported in Ghana and Cameroon and was also found in the yellow-whiskered greenbul, Andropadus latirostris in these countries. It appears to be widespread in its range given the distribution of these bird species in Africa. PMID: 26624445 [PubMed - in process] 


17. Zootaxa. 2015 Oct 16;4032(3):251-63. doi: 10.11646/zootaxa.4032.3.1. 

Cryptic speciation in the Lesser Elaenia Elaenia chiriquensis (Aves: Passeriformes: Tyrannidae). 
Rheindt FE(1), Krabbe N(2), Wee AK(3), Christidis L(4). Author information: (1)Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; Email: dbsrfe@nus.edu.sg. (2)Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark; Email: unknown. (3)Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543; Email: unknown. (4)National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW Australia 2450; Email: unknown. 

Abstract
Tyrant-flycatchers (Tyrannidae) are a taxonomically confusing bird group containing a large degree of cryptic diversity that has only recently begun to be unraveled through the application of acoustic and molecular methods. We investigated all three subspecies of the Lesser Elaenia, Elaenia chiriquensis Lawrence, across their range using sound recordings as well as nuclear and mitochondrial markers. We show that two of the three subspecies, the nominate race from southern Central America and the widespread South American subspecies E. c. albivertex Pelzeln, have undergone very low levels of vocal and molecular differentiation across their fragmented range. In contrast, the isolated taxon E. c. brachyptera Berlepsch, endemic to the western and also, as recently shown, eastern slopes of the northern Andes, is phylogenetically and vocally distinct from other Lesser Elaenias, indicating that it constitutes a separate biological species. PMID: 26624360 [PubMed - in process] 


18. Zootaxa. 2015 Sep 8;4013(2):252-64. doi: 10.11646/zootaxa.4013.2.6. 

Towards completion of the early Eocene aviary: A new bird group from the Messel oil shale (Aves, Eopachypterygidae, fam. nov.). 
Mayr G(1). Author information: (1)Senckenberg Research Institute and Natural History Museum Frankfurt, Ornithological Section, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.; Email: Gerald.Mayr@senckenberg.de. 

Abstract
A new avian species is described from the early Eocene Messel fossil site in Germany. Eopachypteryx praeterita, gen. et sp. nov. is a small bird and exhibits a characteristic morphology with a short and robust beak, a distinctively shaped coracoid, stout humerus, robust pectoral girdle skeleton, and short hindlimbs. Although similarities to the Paleogene Eocuculus as well as to some extant telluravian and strisorine taxa are noted, the phylogenetic affinities of the new species are unresolved. To account for the fact that the new species is clearly distinguished from any of the known fossil or extant avian taxa, it is here assigned to the new taxon Eopachypterygidae, fam. nov.. Eopachypteryx praeterita is represented by three partial skeletons. A further partial skeleton from Messel belongs to a second, unnamed species, which is tentatively referred to Eopachypteryx. PMID: 26623896 [PubMed - in process] 


19. PeerJ. 2015 Oct 20;3:e1328. 

Replacement of native by non-native animal communities assisted by human introduction and management on Isla Victoria, Nahuel Huapi National Park. 
Martin-Albarracin VL(1), Nuñez MA(2), Amico GC(1). Author information: (1)Laboratorio Ecotono, INIBIOMA, CONICET-Universidad Nacional del Comahue , Bariloche, Río Negro , Argentina. (2)Grupo de Ecologia de Invasiones, INIBIOMA, CONICET-Universidad Nacional del Comahue , Bariloche, Río Negro , Argentina. 

Abstract
One of the possible consequences of biological invasions is the decrease of native species abundances or their replacement by non-native species. In Andean Patagonia, southern Argentina and Chile, many non-native animals have been introduced and are currently spreading. On Isla Victoria, Nahuel Huapi National Park, many non-native vertebrates were introduced ca. 1937. Records indicate that several native vertebrates were present before these species were introduced. We hypothesize that seven decades after the introduction of non-native species and without appropriate management to maintain native diversity, non-native vertebrates have displaced native species (given the known invasiveness and impacts of some of the introduced species). We conducted direct censuses in linear transects 500 m long (n = 10) in parallel with camera-trapping (1,253 camera-days) surveys in two regions of the island with different levels of disturbance: high (n = 4) and low (n = 6) to study the community of terrestrial mammals and birds and the relative abundances of native and non-native species. Results show that currently non-native species are dominant across all environments; 60.4% of census records and 99.7% of camera trapping records are of non-native animals. We detected no native large mammals; the assemblage of large vertebrates consisted of five non-native mammals and one non-native bird. Native species detected were one small mammal and one small bird. Species with the highest trapping rate were red and fallow deer, wild boar, silver pheasant (all four species are non-native) and chucao (a native bird). These results suggest that native species are being displaced by non-natives and are currently in very low numbers. PMCID: PMC4662593 PMID: 26623176 [PubMed - as supplied by publisher] 20. Otolaryngol Head Neck Surg. 2015 Dec;153(6):1082. doi: 10.1177/0194599815617481. Corrigendum. [No authors listed] Erratum for Otolaryngol Head Neck Surg. 2015 Nov;153(5):865-74. Rudmik L, Bird C, Dean S, Dort JC, Schorn R, Kukec E. Geographic variation of endoscopic sinus surgery in Canada: an Alberta-based small area variation analysis. Otolaryngol Head Neck Surg. 2015;153:865-874. (Original DOI: 10.1177/0194599815602679). © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015. PMID: 26621933 [PubMed - in process]

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