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Monday, 30 March 2015

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

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
Items 1 - 20 of 24

1. PLoS One. 2015 Mar 26;10(3):e0122264. doi: 10.1371/journal.pone.0122264.

Do Bird Assemblages Predict Susceptibility by E-Waste Pollution? A Comparative Study Based on Species- and Guild-Dependent Responses in China Agroecosystems.

Zhang Q1, Wu J2, Sun Y2, Zhang M1, Mai B2, Mo L2, Lee TM3, Zou F1.
Author information:
Guangdong Entomological Institute/South China Institute of Endangered Animals, Guangzhou, China.
Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China.
Department of Ecology, Evolution, and Environmental Biology and Earth Institute, Columbia University, New York, New York, United States of America.


Indirect effects of electronic waste (e-waste) have been proposed as a causal factor in the decline of bird populations, but analyses of the severity impacts on community assembly are currently lacking. To explore how population abundance/species diversity are influenced, and which functional traits are important in determining e-waste susceptibility, here we surveyed breeding and overwintering birds with a hierarchically nested sampling design, and used linear mixed models to analyze changes in bird assemblages along an exposure gradient in South China. Total bird abundance and species diversity decreased with e-waste severity (exposed < surrounding < reference), reflecting the decreasing discharge and consequent side effects. Twenty-five breeding species exclusively used natural farmland, and nine species decreased significantly in relative abundance at e-waste polluted sites. A high pairwise similarity between exposed and surrounding sites indicates a diffuse effect of pollutants on the species assembly at local scale. We show that sensitivity to e-waste severity varies substantially across functional guild, with the prevalence of woodland insectivorous and grassland specialists declining, while some open farmland generalists such as arboreal frugivores, and terrestrial granivores were also rare. By contrast, the response of waterbirds, omnivorous and non-breeding visitors seem to be tolerable to a wide range of pollution so far. These findings underscore that improper e-waste dismantling results in a severe decline of bird diversity, and the different bird assemblages on polluted and natural farmlands imply species- and guild-dependent susceptibility with functional traits. Moreover, a better understanding of the impact of e-waste with different pollution levels, combined multiple pollutants, and in a food-web context on bird is required in future.
PMID: 25811881 [PubMed - as supplied by publisher]

2. PLoS One. 2015 Mar 26;10(3):e0119213. doi: 10.1371/journal.pone.0119213.

Acquired Alterations of Hypothalamic Gene Expression of Insulin and Leptin Receptors and Glucose Transporters in Prenatally High-Glucose Exposed Three-Week Old Chickens Do Not Coincide with Aberrant Promoter DNA Methylation.

Rancourt RC1, Schellong K1, Ott R1, Bogatyrev S2, Tzschentke B2, Plagemann A1.
Author information:
Clinic of Obstetrics, Division of 'Experimental Obstetrics', Charité-University Medicine Berlin, Campus Virchow-Klinikum, Berlin, Germany.
Humboldt-University of Berlin, Institute of Biology, Berlin, Germany.



Prenatal exposures may have a distinct impact for long-term health, one example being exposure to maternal 'diabesity' during pregnancy increasing offspring 'diabesity' risk. Malprogramming of the central nervous regulation of body weight, food intake and metabolism has been identified as a critical mechanism. While concrete disrupting factors still remain unclear, growing focus on acquired epigenomic alterations have been proposed. Due to the independent development from the mother, the chicken embryo provides a valuable model to distinctively establish causal factors and mechanisms.


The aim of this study was to determine the effects of prenatal hyperglycemia on postnatal hypothalamic gene expression and promoter DNA methylation in the chicken.


To temporarily induce high-glucose exposure in chicken embryos, 0.5 ml glucose solution (30 mmol/l) were administered daily via catheter into a vessel of the chorioallantoic egg membrane from days 14 to 17 of incubation. At three weeks of postnatal age, body weight, total body fat, blood glucose, mRNA expression (INSR, LEPR, GLUT1, GLUT3) as well as corresponding promoter DNA methylation were determined in mediobasal hypothalamic brain slices (Nucleus infundibuli hypothalami). Although no significant changes in morphometric and metabolic parameters were detected, strongly decreased mRNA expression occurred in all candidate genes. Surprisingly, however, no relevant alterations were observed in respective promoter methylation.


Prenatal hyperglycemia induces strong changes in later hypothalamic expression of INSR, LEPR, GLUT1, and GLUT3 mRNA. While the chicken provides an interesting approach for developmental malprogramming, the classical expression regulation via promoter methylation was not observed here. This may be due to alternative/interacting brain mechanisms or the thus far under-explored bird epigenome.
PMID: 25811618 [PubMed - as supplied by publisher]

3. Am Nat. 2015 Apr;185(4):443-451. Epub 2015 Feb 17.

Color Patterns of Closely Related Bird Species Are More Divergent at Intermediate Levels of Breeding-Range Sympatry.

Martin PR1, Montgomerie R, Lougheed SC.
Author information:
Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada.


Closely related species of birds often differ markedly in their color patterns. Here we examine the influence of breeding-range overlap (breeding sympatry) on the evolution of color pattern differences in a sample of closely related bird species. We used a sister-lineage method to analyze 73 phylogenetically independent comparisons among 246 species and 39 families of birds worldwide. We found that divergence of color patterns among closely related species was greater between sympatric than between allopatric lineages, but only at intermediate levels of sympatry (50%-80% breeding-range overlap). This pattern suggests that closely related species incur costs at intermediate levels of sympatry if they exhibit similar color patterns-costs that could include hybridization, interspecific aggression, competition for signaling space, or ecological interactions that secondarily influence color patterns. The decline in color pattern divergence with further increase in sympatry suggests either the relaxation of divergent selection, increased impediment of gene flow, or an increased role for counteracting selection at higher levels of sympatry. We also found that the differences in color pattern between sympatric and allopatric sister species were greatest at lower latitudes. The global scale and broad taxonomic coverage in our study suggest that the divergence of color patterns between sympatrically breeding closely related species is widespread in birds.
PMID: 25811081 [PubMed - as supplied by publisher]

4.Bioinspir Biomim. 2015 Mar 25;10(2):025001. doi: 10.1088/1748-3190/10/2/025001.

Folding in and out: passive morphing in flapping wings.

Stowers AK1, Lentink D.
Author information:
Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.


We present a new mechanism for passive wing morphing of flapping wings inspired by bat and bird wing morphology. The mechanism consists of an unactuated hand wing connected to the arm wing with a wrist joint. Flapping motion generates centrifugal accelerations in the hand wing, forcing it to unfold passively. Using a robotic model in hover, we made kinematic measurements of unfolding kinematics as functions of the non-dimensional wingspan fold ratio (2-2.5) and flapping frequency (5-17 Hz) using stereo high-speed cameras. We find that the wings unfold passively within one to two flaps and remain unfolded with only small amplitude oscillations. To better understand the passive dynamics, we constructed a computer model of the unfolding process based on rigid body dynamics, contact models, and aerodynamic correlations. This model predicts the measured passive unfolding within about one flap and shows that unfolding is driven by centrifugal acceleration induced by flapping. The simulations also predict that relative unfolding time only weakly depends on flapping frequency and can be reduced to less than half a wingbeat by increasing flapping amplitude. Subsequent dimensional analysis shows that the time required to unfold passively is of the same order of magnitude as the flapping period. This suggests that centrifugal acceleration can drive passive unfolding within approximately one wingbeat in small and large wings. Finally, we show experimentally that passive unfolding wings can withstand impact with a branch, by first folding and then unfolding passively. This mechanism enables flapping robots to squeeze through clutter without sophisticated control. Passive unfolding also provides a new avenue in morphing wing design that makes future flapping morphing wings possibly more energy efficient and light-weight. Simultaneously these results point to possible inertia driven, and therefore metabolically efficient, control strategies in bats and birds to morph or recover within a beat.
PMID: 25807583 [PubMed - in process]

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5. PLoS One. 2015 Mar 25;10(3):e0119919. doi: 10.1371/journal.pone.0119919. eCollection 2015.

Perceptual strategies of pigeons to detect a rotational centre-a hint for star compass learning?

Alert B1, Michalik A1, Helduser S2, Mouritsen H1, Güntürkün O2.
Author information:
Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, D-26111, Oldenburg, Germany; Research Centre Neurosensory Science, University of Oldenburg, D-26111, Oldenburg, Germany.
Department of Psychology, Institute of Cognitive Neuroscience, Biopsychology, Ruhr-University Bochum, D-44780, Bochum, Germany.


Birds can rely on a variety of cues for orientation during migration and homing. Celestial rotation provides the key information for the development of a functioning star and/or sun compass. This celestial compass seems to be the primary reference for calibrating the other orientation systems including the magnetic compass. Thus, detection of the celestial rotational axis is crucial for bird orientation. Here, we use operant conditioning to demonstrate that homing pigeons can principally learn to detect a rotational centre in a rotating dot pattern and we examine their behavioural response strategies in a series of experiments. Initially, most pigeons applied a strategy based on local stimulus information such as movement characteristics of single dots. One pigeon seemed to immediately ignore eccentric stationary dots. After special training, all pigeons could shift their attention to more global cues, which implies that pigeons can learn the concept of a rotational axis. In our experiments, the ability to precisely locate the rotational centre was strongly dependent on the rotational velocity of the dot pattern and it crashed at velocities that were still much faster than natural celestial rotation. We therefore suggest that the axis of the very slow, natural, celestial rotation could be perceived by birds through the movement itself, but that a time-delayed pattern comparison should also be considered as a very likely alternative strategy.
Free Article
PMID: 25807499 [PubMed - in process]

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6. J Appl Anim Welf Sci. 2015 Mar 25:1-16. [Epub ahead of print]

Companion Rabbit and Companion Bird Management Practices Among a Representative Sample of Guardians in Victoria, Australia.

Howell TJ1, Mornement K, Bennett PC.
Author information:
1 Anthrozoology Research Group, School of Psychological Science, La Trobe University , Bendigo , Victoria , Australia.


Although companion animal management practices used by caregivers can influence the welfare of the companion animals, there is little existing information about the ways in which people attempt to meet their companion animals' needs. A representative sample of rabbit guardians (n = 93, representing 63,000 people) and bird guardians (n = 203, representing 157,000 people) in Victoria, Australia, completed an online survey. Items were related to the environmental, diet/exercise, behavioral, social, and health management practices used by guardians. Guardians sometimes meet their companion animals' welfare needs, but they do not always engage in best practices. Most (79%) bird guardians reported that they interacted with their birds daily, but only 68% of rabbit guardians did the same. Likewise, 32% of rabbit guardians and 55% of bird guardians never had their companion animals vaccinated. These results may be used for educational campaigns for improving companion animal welfare.
PMID: 25807325 [PubMed - as supplied by publisher]

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7. Parasitology. 2015 Mar 25:1-10. [Epub ahead of print]

Molecular characterization of Trichomonas gallinae isolates recovered from the Canadian Maritime provinces' wild avifauna reveals the presence of the genotype responsible for the European finch trichomonosis epidemic and additional strains.

McBurney S1, Kelly-Clark WK1, Forzán MJ1, Lawson B2, Tyler KM3, Greenwood SJ4.
Author information:
Department of Pathology & Microbiology,Atlantic Veterinary College, University of Prince Edward Island,550 University Avenue,Charlottetown,PE,C1A 4P3,Canada Prince Edward Island,Canada.
Institute of Zoology, Zoological Society of London,Regents Park,London NW1 4RY,UK.
Norwich Medical School, University of East Anglia,Norwich NR4 7TJ,UK.
Department of Biomedical Sciences,Atlantic Veterinary College, University of Prince Edward Island,550 University Avenue,Charlottetown,PE,C1A 4P3,Canada Prince Edward Island,Canada.


Finch trichomonosis, caused by Trichomonas gallinae, emerged in the Canadian Maritime provinces in 2007 and has since caused ongoing mortality in regional purple finch (Carpodacus purpureus) and American goldfinch (Carduelis tristis) populations. Trichomonas gallinae was isolated from (1) finches and rock pigeons (Columbia livia) submitted for post-mortem or live-captured at bird feeding sites experiencing trichomonosis mortality; (2) bird seed at these same sites; and (3) rock pigeons live-captured at known roosts or humanely killed. Isolates were characterized using internal transcribed spacer (ITS) region and iron hydrogenase (Fe-hyd) gene sequences. Two distinct ITS types were found. Type A was identical to the UK finch epidemic strain and was isolated from finches and a rock pigeon with trichomonosis; apparently healthy rock pigeons and finches; and bird seed at an outbreak site. Type B was obtained from apparently healthy rock pigeons. Fe-hyd sequencing revealed six distinct subtypes. The predominant subtype in both finches and the rock pigeon with trichomonosis was identical to the UK finch epidemic strain A1. Single nucleotide polymorphisms in Fe-hyd sequences suggest there is fine-scale variation amongst isolates and that finch trichomonosis emergence in this region may not have been caused by a single spill-over event.
PMID: 25804862 [PubMed - as supplied by publisher]

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8. Tierarztl Prax Ausg K Kleintiere Heimtiere. 2015 Mar 25;43(3). [Epub ahead of print]

First detection of Macrorhabdus ornithogaster in wild Eurasian Siskins (Carduelis spinus) in Germany. A case study.

Legler M1, Stelter R, Jung A, Wohlsein P, Kummerfeld N.
Author information:
Dr. Marko Legler, Clinic for Exotic Pets, Reptiles and Birds, University of Veterinary Medicine Hannover, Foundation, Bünteweg 9, 30559 Hannover, Germany, Email:



The colonization of the gastric ascomycetous yeast Macrorhabdus (M.) ornithogaster could be associated with a chronic wasting disease in several bird species in captivity. The prevalence and clinical relevance of M. ornithogaster in wild birds is unknown in detail.


In the wintering season 2012/13 injured Eurasian Siskins (Carduelis spinus, n = 8) from the area of Hannover, Lower Saxony, Germany were examined microbiologically and pathologically.


In six out of eight injured Eurasian Siskins M. ornithogaster were detected. The yeast was diagnosed microscopically in wet smears from the gastric isthmus and/or in faecal samples. Histopathological examination (n = 4) of the macroscopically slightly enlarged proventriculus in infected birds demonstrated the growth of M. ornithogaster in the mucosal surface and in the ducts of the glands without an inflammatory reaction. As a possible sign of a lowered fitness, all six infected siskins had a reduced body weight (mean: 11.8 ± 1.64 g) in the lower normal weight range compared to the two injured Eurasian Siskins without M. ornithogaster (15.0 g) as well as to data from the literature. Concurrent intestinal bacterial infections comprised Escherichia coli, Clostridium perfringens or Salmonella Typhimurium, that are regarded as an abnormal bacterial flora for Eurasian Siskins.


Infections with M. ornithogaster can be found in the wild population of Eurasian Siskins in Germany. The frequent occurrence of secondary bacterial infections associated with M. ornithogaster infections should be considered in the treatment and rehabilitation of finches.
PMID: 25804259 [PubMed - as supplied by publisher]

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9. PLoS One. 2015 Mar 24;10(3):e0121672. doi: 10.1371/journal.pone.0121672. eCollection 2015.

Characterization of the avian trojan gene family reveals contrasting evolutionary constraints.

Petrov P1, Syrjänen R1, Smith J2, Gutowska MW2, Uchida T3, Vainio O1, Burt DW2.
Author information:
Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland; Nordlab Oulu, Oulu University Hospital, Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.
Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom.
Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.


"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.
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PMID: 25803627 [PubMed - in process]

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10. PeerJ. 2015 Mar 19;3:e853. doi: 10.7717/peerj.853. eCollection 2015.

Patterns of evolution of MHC class II genes of crows (Corvus) suggest trans-species polymorphism.

Eimes JA1, Townsend AK2, Sepil I3, Nishiumi I4, Satta Y1.
Author information:
Department of Evolutionary Studies of Biosystems, Graduate University for Advanced Studies (SOKENDAI) , Hayama , Japan.
Department of Biology, Hamilton College , Clinton, NY , USA.
Department of Zoology, University of Oxford , Oxford , UK.
Department of Zoology, National Museum of Nature and Science , Tsukuba , Japan.


A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed using non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.
PMCID: PMC4369332 Free PMC Article
PMID: 25802816 [PubMed]
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11. Trop Biomed. 2015 Mar;32(1):11-6.

Prevalence of Ascaridia galli in white leghorn layers and Fayoumi-Rhode Island red crossbred flock at government poultry farm Dina, Punjab, Pakistan.

Hafiz AB1, Muhammad AR2, Muhammad AA3, Imran AK4, Abdul A4, Zahid M5, Shaukat HM5.
Author information:
Government Poultry Farm Dina, Punjab, Pakistan.
University of Agriculture, Faisalabad (Sub-campus Dera Ghazi Khan), Pakistan.
Poultry Research Institute, Rawalpindi, Pakistan.
Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan.
Faculty of Medicine and Allied Medical Sciences, Isra University, Islamabad, Pakistan.


Poultry farming not only provides high nutritious food but also creates employment opportunity for rural masses. Documented evidences elaborates that helminth parasitism is most deciduous problem of chickens especially in developing world. Ascaridia (A.) galli, a nematode of small intestine, has been considered as the most common and important parasite of chicken. The present study was carried out to investigate prevalence and severity of A. galli in White Leghorn layers (housing type: battery cage and deep litter, 50 each) and Fayoumi-Rhode Island Red crossbred (male and female: 50 each) flock rearing at Government Poultry Farm, Dina, Punjab, Pakistan. Two hundred faecal samples were examined by using standard parasitological and McMaster egg counting technique. The overall prevalence was 24.5% at farm, 13% in White leghorn layer (battery cage=2%, deep litter=24%) and 36% in Fayoumi-Rhode Island Red (male=34%, female=38%). It was also observed that White leghorn layer rearing in deep litter had more severe infection (EPG=1920) of A. galli compare with battery cages birds (EPG=500). Parasite prevalence was significantly related with sex (P<0.05) in Fayoumi-Rhode Island Red and male birds had less number of average parasites (0.34±0.47) as compared to females (0.38±0.490). Additionally, female birds were under serious threat of infection (EPG=2270) compared with its counterpart (EPG=1250). Given the high infection rates, particular attention should be paid to management and provision of feed supplement to White leghorn layer housing in deep litter and female bird of Fayoumi-Rhode Island Red crossbred.
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PMID: 25801250 [PubMed - in process]

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12. Cell Rep. 2015 Mar 19. pii: S2211-1247(15)00235-1. doi: 10.1016/j.celrep.2015.02.058. [Epub ahead of print]

Origins and Impacts of New Mammalian Exons.

Merkin JJ1, Chen P2, Alexis MS3, Hautaniemi SK2, Burge CB4.
Author information:
Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Research Programs Unit, Genome-Scale Biology and Institute of Biomedicine, University of Helsinki, 00014 Helsinki, Finland.
Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:


Mammalian genes are composed of exons, but the evolutionary origins and functions of new internal exons are poorly understood. Here, we analyzed patterns of exon gain using deep cDNA sequencing data from five mammals and one bird, identifying thousands of species- and lineage-specific exons. Most new exons derived from unique rather than repetitive intronic sequence. Unlike exons conserved across mammals, species-specific internal exons were mostly located in 5' UTRs and alternatively spliced. They were associated with upstream intronic deletions, increased nucleosome occupancy, and RNA polymerase II pausing. Genes containing new internal exons had increased gene expression, but only in tissues in which the exon was included. Increased expression correlated with the level of exon inclusion, promoter proximity, and signatures of cotranscriptional splicing. Altogether, these findings suggest that increased splicing at the 5' ends of genes enhances expression and that changes in 5' end splicing alter gene expression between tissues and between species.
Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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PMID: 25801031 [PubMed - as supplied by publisher]

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13. PLoS One. 2015 Mar 23;10(3):e0119674. doi: 10.1371/journal.pone.0119674. eCollection 2015.

The response of farmland bird communities to agricultural intensity as influenced by its spatial aggregation.

Teillard F1, Jiguet F2, Tichit M1.
Author information:
INRA-AgroParisTech, UMR 1048 SAD APT, Paris, France.
MNHN-CNRS-UPMC, UMR 7204 CRBPO, Paris, France.


The shape of the relationship between biodiversity and agricultural intensity determines the range of intensities that should be targeted by conservation policies to obtain the greatest environmental benefits. Although preliminary evidence of this relationship exists, the influence of the spatial arrangement of intensity on biodiversity remains untested. We conducted a nationwide study linking agricultural intensity and its spatial arrangement to a farmland bird community of 22 species. Intensity was described with a continuous indicator based on Input Cost per hectare, which was relevant for both livestock and crop production. We used the French Breeding Bird Survey to compute several descriptors of the farmland bird community along the intensity gradient and tested for the significance of an interaction effect between intensity and its spatial aggregation on these descriptors. We found that the bird community was comprised of both winner and loser species with regard to intensity. The community composition descriptors (trophic level, specialisation, and specialisation for grassland indices) displayed non-linear relationships to intensity, with steeper slopes in the lower intensity range. We found a significant interaction effect between intensity and its spatial aggregation on the grassland specialisation index of the bird community; the effect of agricultural intensity was strengthened by its spatial aggregation. We suggest that an opportunity to improve the effectiveness of conservation policies exists by targeting measures in areas where intensity is moderate to low and aggregated. The effect of the aggregation of agricultural intensity on biodiversity should be considered in other scales and taxa when developing optimal policy targeting and intensity allocation strategies.
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PMID: 25799552 [PubMed - in process]

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14. PLoS One. 2015 Mar 23;10(3):e0119906. doi: 10.1371/journal.pone.0119906. eCollection 2015.

Birds flush early and avoid the rush: an interspecific study.

Samia DS1, Blumstein DT2.
Author information:
Laboratory of Theoretical Ecology and Synthesis, Department of Ecology, Federal University of Goiás, Goiânia, Goiás, Brazil.
Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America.


Since 1986, studies about the escape decisions made by prey are grounded in optimal escape theory (OET) which states that prey will initiate escape when the risk of remaining and the costs of leaving are equal. However, a recent hypothesis, Flush Early and Avoid the Rush (FEAR), acknowledged that the cost of monitoring approaching predators might be a ubiquitous cost. The FEAR hypothesis predicts that prey will generally flee soon after they detect a predator so as to minimize the costs incurred by monitoring the predator. Knowing whether animals flee to reduce monitoring costs is of applied interest because wildlife managers use escape behavior to create set-back zones to reduce human-wildlife conflict. Here we provide the most comprehensive assessment of the FEAR hypothesis using data collected from 178 bird species representing 67 families from two continents. The FEAR hypothesis explains escape behavior in 79% of studied species. Because the FEAR hypothesis is a widespread phenomenon that drives escape behavior in birds, alert distance must be systematically incorporated into the design of set-back zones to protect vulnerable species.
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PMID: 25799238 [PubMed - in process]

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15. PLoS One. 2015 Mar 23;10(3):e0120933. doi: 10.1371/journal.pone.0120933. eCollection 2015.

Two Novel Vocalizations Are Used by Veeries (Catharus fuscescens) during Agonistic Interactions.

Belinsky KL1, Nemes CE2, Schmidt KA3.
Author information:
  • 1Biology Department, State University of New York New Paltz, New Paltz, New York, United States of America.
  • 2Department of Biology, Ball State University, Muncie, Indiana, United States of America.
  • 3Department of Biological Sciences, Texas Tech University, Lubbock, Texas United States of America.

  • Abstract

    Avian vocalizations are common examples of the complex signals used by animals to negotiate during agonistic interactions. In this study, we used two playback experiments to identify agonistic signals in a songbird species with several acoustically complex songs and calls, the veery. In the first experiment, we compared veery singing behavior in response to simulated territorial intrusions including playback of three variations of veery song: 1) song alone as a control, 2) songs with added whisper calls, and 3) songs with introductory notes removed. In the second experiment, we used multimodal stimuli including songs, whisper calls and songs with introductory notes removed, along with a robotic veery mount. Focal males readily responded to all of the playback stimuli, approached the speaker and/or robotic mount, and vocalized. Male veeries gave more whisper calls, and sang more songs without the introductory note in response to all types of playback. However, veeries responded similarly to all types of stimuli presented, and they failed to physically attack the robotic mount. These results indicate that rival veeries use two different types of novel vocalizations: whisper calls and songs lacking the introductory note as agonistic signals, but do not allow us to discern the specific functions of these two vocalizations.
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    PMID: 25798825 [PubMed - in process]

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    16. Mol Phylogenet Evol. 2015 Mar 19. pii: S1055-7903(15)00061-5. doi: 10.1016/j.ympev.2015.03.005. [Epub ahead of print]

    Phylogeny and biogeography of the New World siskins and goldfinches: Rapid, recent diversification in the Central Andes.

    Beckman EJ1, Witt CC2.
    Author information:
    Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA. Electronic address:
    Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131-0001, USA.


    Time-calibrated molecular phylogenies can help us to understand the origins of the diverse and unique Andean avifauna. Previous studies have shown that the tempo of diversification differed between the Andes and adjacent lowland regions of South America. Andean taxa were found to have speciated more recently and to have avoided the decelerated diversification that is typical of Neotropical lowland clades. The South American siskins, a Pleistocene finch radiation, may typify this Andean pattern. We investigated the phylogenetic biogeography of all the New World siskins and goldfinches in new detail. To understand the specific role of the Andes in siskin diversification, we asked: (1) Was diversification faster in Andean siskin lineages relative to non-Andean ones? (2) Did siskin lineages move into and out of the Andes at different rates? We found that siskin lineages in the Andes had higher diversification rates and higher outward dispersal rates than siskin lineages outside the Andes. We conclude that páramo expansion and contraction in response to Pleistocene climatic cycles caused accelerated diversification and outward dispersal in Andean siskins. The younger average age of bird species in the Andes compared to lowland South America may be attributable to bursts of recent diversification in siskins and several other vagile, open-habitat clades.
    Copyright © 2015 Elsevier Inc. All rights reserved.
    PMID: 25796324 [PubMed - as supplied by publisher]

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    17. Exp Parasitol. 2015 Mar 17. pii: S0014-4894(15)00058-2. doi: 10.1016/j.exppara.2015.03.005. [Epub ahead of print]

    Morphological and molecular characterization of Eimeria haematodi, coccidian parasite (Apicomplexa:Eimeriidae) in a rainbow lorikeet (Trichoglossus haematodus).

    Yang R1, Brice B2, Ryan U3.
    Author information:
    School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia, 6150. Electronic address:
    Kanyana Wildlife Rehabilitation Centre, 120 Gilchrist Road, Lesmurdie, Western Australia, 6076.
    School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia, 6150.


    Eimeria haematodi was first described in 1977 from the rainbow lorikeet (Trichoglossus haematodus) in Papua New Guinea. In the present study, we re-describe this coccidian species morphologically and molecularly from a rainbow lorikeet bird in Western Australia (WA). The oocysts were ovoid to slightly piriform and measured 28.5 to 37.8 by 25.8 to 33.0 µm (33.3 by 28.1 µm). Oocyst wall was approximately 1.5 µm thick and bilayered. Micropyle (5 to 7 µm) and oocyst residuum (8.0 to 10.0 µm) present; polar granule was absent. Sporocysts ellipsoidal, 11.8 to 13.6 by 8.0 to 9.6 µm (12.2 by 8.3 µm), with thin convex Stieda body and granular sporocyst residuum (4.0 to 5.0 µm). Molecular characterization of E. haematodi was conducted at 18S ribosomal RNA and the mitochondrial cytochrome oxidase gene (COI) loci. At the 18S ribosomal RNA locus, E. haematodi shared 98.1% genetic similarity to E. alabamensis from cattle in New South Wales, Australia. At COI locus, E. haematodi was closest (92.3% similarity) to E. praecox from domestic chickens (Gallus gallus domesticus) from Canada and China.
    Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.
    PMID: 25795281 [PubMed - as supplied by publisher]

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