Search birdRS Box

Search birdRS blog posts

Browse the Blog Posts

Or scan through the blog archive below for items of interest as only the latest post is shown below, thanks.

Monday, 8 September 2014

Bird research this week on PubMed: September 2014 Week 2

PubMed listing for 'bird' OR 'songbird' excluding references to influenza and flu - September 2014 Week 2

1. PLoS One. 2014 Sep 5;9(9):e106649. doi: 10.1371/journal.pone.0106649. eCollection 2014.

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies.

Card DC1, Schield DR1, Reyes-Velasco J1, Fujita MK1, Andrew AL1, Oyler-McCance SJ2, Fike JA2, Tomback DF3, Ruggiero RP4, Castoe TA1.Author information:
1Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America.
2United States Geological Survey - Fort Collins Science Center, Fort Collins, Colorado, United States of America.
3Department of Integrative Biology, University of Colorado Denver, Denver, Colorado, United States of America.
4Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America.


As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.
PMID: 25192061 [PubMed - as supplied by publisher]
2. J Vet Med Sci. 2014 Sep 3. [Epub ahead of print]

Experimental Final Hosts of Metagonimus hakubaensis (Trematoda: Heterophyidae) and Their Suitability to the Fluke.

Kudo N1, Ota C, Saka F, Ikeda Y, Tomihisa Y , Itoi Y, Oyamada T.Author information:
1Department of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University.


Seven laboratory mammal and bird species were orally inoculated with 200-1,000 encysted Metagonimus hakubaensis metacercariae that had been isolated from naturally infected lampreys (Lethenteron reissneri) captured in Aomori Prefecture. At 8 and 15 days post-infection, adult flukes were recovered from all of the laboratory animals tested, and therefore, hamster, rat, mouse, dog, cat, chicken and quail were considered as final hosts of M. hakubaensis. Recovery rates of the fluke were higher in dogs and hamsters than in cats, rats, mice, chickens and quails. The flukes recovered from dogs and hamsters showed increased body length and higher fecundity than those recovered from the other hosts. These results indicate that the suitability of dogs and hamsters for M. hakubaensis infection is higher than that of the other laboratory animals.
Free Article
PMID: 25187303 [PubMed - as supplied by publisher]

Icon for J-STAGE, Japan Science and Technology Information Aggregator, Electronic

3. N Z Vet J. 2014 Sep 4:1-10. [Epub ahead of print]

Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection.

White D1, Hall R, Jakob-Hoff R, Wang J, Jackson B, Tompkins D.Author information:
Landcare Research , Private Bag 92170, Auckland Mail Centre , Auckland.


Abstract AIM: To investigate the initiating causes of cloacitis (inflammation of the cloaca) in kakapo (Strigops habroptilus).


Metagenomics using unbiased RNA or DNA sequencing, was applied to faecal material from an 11-year-old female kakapo with exudative cloacitis, and a pool of eight birds (male and female aged 1-20 years) with no current signs or history of the disease. Faecal material from the diseased bird was collected pre- and post- treatment. Extracted RNA/DNA was subject to DNase, and the remaining RNA reverse transcribed to cDNA and subject to multiple displacement amplification prior to sequencing.


No significant alignment to any known avian virus sequence was obtained from any faecal samples. However significant BLAST alignments to five bacteriophages known to infect enterobacteria were obtained. Strong evidence was obtained for the presence of the bacteriophage Escherichia phage TL-2011b, a bacteriophage known to occur in Escherichia coli causing outbreaks of foodborne disease in humans, in the sample from the diseased bird, but not the non-diseased pool. Differences in E. coli community structure between the diseased bird and the non-diseased pool were also apparent.


Escherichia coli infection of human origin is suggested as a possible cause of exudative cloacitis, although confirmatory work is required to test this hypothesis.
PMID: 25186371 [PubMed - as supplied by publisher]

Icon for Atypon

4. Oecologia. 2014 Sep 4. [Epub ahead of print]

The control of rank-abundance distributions by a competitive despotic species.

Mac Nally R1, McAlpine CA, Possingham HP, Maron M.Author information:
1Institute for Applied Ecology, The University of Canberra, Canberra, ACT, 2617, Australia,


Accounting for differences in abundances among species remains a high priority for community ecology. While there has been more than 80 years of work on trying to explain the characteristic S shape of rank-abundance distributions (RADs), there has been recent conjecture that the form may not depend on ecological processes per se but may be a general phenomenon arising in many unrelated disciplines. We show that the RAD shape can be influenced by an ecological process, namely, interference competition. The noisy miner (Manorina melanocephala) is a hyperaggressive, 'despotic' bird that occurs over much of eastern Australia (>10km2). We compiled data for bird communities from 350 locations within its range, which were collected using standard avian survey methods. We used hierarchical Bayesian models to show that the RAD shape was much altered when the abundance of the strong interactor exceeded a threshold density; RADs consistently were steeper when the density of the noisy miner ≥2.5 birds ha-1. The structure of bird communities at sites where the noisy miner exceeded this density was very different from that at sites where the densities fell below the threshold: species richness and Shannon diversity were much reduced, but mean abundances and mean avian biomass per site did not differ substantially.
PMID: 25185775 [PubMed - as supplied by publisher]

Icon for Springer

5. Parasitol Res. 2014 Sep 4. [Epub ahead of print]

From cuckoos to chickens: a caught-in-the-act case of host shift in feather mites (Arachnida: Acari: Psoroptoididae).

Hernandes FA1, Pedroso LG, Mironov SV.Author information:
1Departamento de Zoologia, Universidade Estadual Paulista, Rio Claro, SP, 13506-900, Brazil,


Feather mites are highly specialized permanent ectosymbionts recorded from all recently recognized bird orders. These mites, specialized to live in the plumage of their hosts, rarely cause any visible damage to their specific hosts. Recently described feather mite Allopsoroptoides galli Mironov (Acariformes: Psoroptoididae) was reported to cause severe mange in chickens in Brazil, leading to unprecedented economic losses. Until now, the natural host of A. galli remained unknown. In this paper, we report its true wild host, the Guira cuckoo Guira guira (Cuculiformes: Cuculidae). In addition, a previously unknown heteromorphic form of males is described from the mite population distributed on its natural host. We also speculate a possible scenario by which this mite species could have been horizontally transferred from the wild populations of the natural host to the secondary hosts.
PMID: 25185669 [PubMed - as supplied by publisher]

Icon for Springer

6. Oecologia. 2014 Sep 3. [Epub ahead of print]

Functional importance of avian seed dispersers changes in response to human-induced forest edges in tropical seed-dispersal networks.

Saavedra F1, Hensen I, Beck SG, Böhning-Gaese K, Lippok D, Töpfer T, Schleuning M.Author information:
1Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108, Halle (Saale), Germany,


Although seed-dispersal networks are increasingly used to infer the functioning of ecosystems, few studies have investigated the link between the properties of these networks and the ecosystem function of seed dispersal by animals. We investigate how frugivore communities and seed dispersal change with habitat disturbance and test whether relationships between morphological traits and functional roles of seed dispersers change in response to human-induced forest edges. We recorded interaction frequencies between fleshy fruited plants and frugivorous bird species in tropical montane forests in the Bolivian Andes and recorded functional bird traits (body mass, gape width and wing tip length) associated with quantitative (seed-removal rate) and qualitative (seed-deposition pattern) components of seed-dispersal effectiveness. We found that the abundance and richness of frugivorous birds were higher at forest edges. More fruits were removed and dispersed seeds were less clustered at edges than in the interior. Additionally, functional and interaction diversity were higher at edges than in the interior, but functional and interaction evenness did not differ. Interaction strength of bird species increased with body mass, gape width and wing tip length in the forest interior, but was not related to bird morphologies at forest edges. Our study suggests that increases in functional and interaction diversity and an even distribution of interaction strength across bird morphologies lead to enhanced quantity and tentatively enhanced quality of seed dispersal. It also suggests that the effects of species traits on ecosystem functions can vary along small-scale gradients of human disturbance.
PMID: 25182931 [PubMed - as supplied by publisher]

Icon for Springer

7. Oecologia. 2014 Sep 3. [Epub ahead of print]

Importance of intraspecifically gregarious species in a tropical bird community.

Sridhar H1, Shanker K.Author information:
1Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India,


In both single- and mixed-species social groups, certain participants are known to play important roles in providing benefits. Identifying these participants is critical for understanding group dynamics, but is often difficult with large roving social groups in the wild. Here, we develop a new approach to characterize roles in social groups and apply it to mixed-species bird flocks (flocks hereafter) in an Indian tropical evergreen forest. Two types of species, namely intraspecifically gregarious and sallying species, are thought to play important roles in flocks because studies have shown they attract other flock participants. However, it is unclear why these types are attractive and whether they are essential for flock formation. We address these questions by focusing on the composition of the subset of flocks containing only two species each. In two-species flocks, it is reasonable to assume that at least one species obtains some kind of benefit. Therefore, only those species combinations that result in benefit to at least one species should occur as two-species flocks. Using data from 540 flocks overall, of which 158 were two-species flocks, we find that intraspecifically gregarious species are disproportionately represented in two-species flocks and always lead flocks when present, and that flocks containing them are joined significantly more by other species. Our results suggest that intraspecifically gregarious species are likely to be the primary benefit providers in flocks and are important for tropical flock formation. Our study also provides a new approach to understanding importance in other mixed-species and single-species social groups.
PMID: 25182930 [PubMed - as supplied by publisher]

Icon for Springer

8. Comp Biochem Physiol C Toxicol Pharmacol. 2014 Aug 23. pii: S1532-0456(14)00109-4. doi: 10.1016/j.cbpc.2014.08.004. [Epub ahead of print]

Effects of early-life lead exposure on oxidative status and phagocytosis activity in great tits (Parus major).

Rainio MJ1, Eeva T2, Lilley T3, Stauffer J 4, Ruuskanen S5.Author information:
1Department of Biology, University of Turku, FI-20014 Turku, Finland. Electronic address:
2Department of Biology, University of Turku, FI-20014 Turku, Finland. Electronic address:
3Department of Biology, University of Turku, FI-20014 Turku, Finland. Electronic address:
4Department of Biology, University of Turku, FI-20014 Turku, Finland. Electronic address:
5Department of Biology, University of Turku, FI-20014 Turku, Finland; Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands. Electronic address:


Lead is a highly poisonous metal with a very long half-life, distributing throughout the body in blood and accumulating primarily in bones and kidney. We studied the short and long-term effects of early-life lead exposure on antioxidant defense and phagocytosis activity in a small passerine bird, the great tit (Parus major) by manipulating dietary lead levels of the nestlings. We had three experimental groups, exposed to environmentally relevant lead concentrations; high (4μg/g body mass), low (1μg/g body mass) and control (0μg/g body mass) group. As a comparison, a great tit population breeding in the vicinity of a metal smelter was included to the experimental set-up. We measured glutathione, the ratio of reduced and oxidized glutathione, and the antioxidant enzymes: glutathione peroxidase, glutathione-S-transferase, catalase and superoxide dismutase together with protein carbonylation and phagocytosis activity to study the effects of lead on the oxidative status and immune function of birds. We found differences in enzyme activities between the study groups, but in most cases the smelter group differed from the other groups. Despite the differences observed in antioxidant enzymes, our results indicate only minor short-term effects of lead exposure on oxidative status, since either glutathione ratio or protein carbonylation were not affected by lead. Phagocytosis activity was not linked to higher lead concentrations either. Interestingly, protein carbonylation was positively associated with enzyme activities and glutathione level. Our results did not show major long-term effects of lead on the oxidative status of great tits.
Copyright © 2014 Elsevier Inc. All rights reserved.
PMID: 25182672 [PubMed - as supplied by publisher]

9. Mil Med. 2014 Sep;179(9):e1059-61. doi: 10.7205/MILMED-D-14-00020.

Cryptococcal Meningitis Caused by Cryptococcus neoformans in an Immunocompetent Soldier.

Newsome J, Nguyen D.Author information:
Department of Family Medicine, Womack Army Medical Center, 2817 Reilly Road, Fort Bragg, NC 28310.



Cryptococcus neoformans is an encapsulated yeast that commonly causes disease in individuals in the setting of immunocompromised states. It is rarely reported in immunocompetent patients in the literature.


An active duty service member with no significant medical history presented with persistent headache, nausea, vomiting, weight loss, and nocturnal fevers for 2 months. The patient was admitted to the hospital where a lumbar puncture was performed showing an elevated white blood cell count, low glucose, and elevated protein. Subsequent cerebral spinal fluid analysis yielded cryptococcal antigen latex screen and culture which speciated C. neoformans. The patient received fluconazole and flucytosine, and completed a 10-week course to result in a full recovery.


C. neoformans is found throughout the world in soil contaminated with bird droppings and usually causes infection and disease in individuals who are immunosuppressed. Rare case reports exist where C. neoformans causes central nervous infection in immunocompetent hosts. This fungal etiology should be considered in all patients presenting with meningitis symptoms and a cerebral spinal fluid panel with low glucose and high protein, or without a clear bacterial etiology. This case illustrates the importance of broadening the differential when previously healthy service members present with common or nonspecific symptoms.
Reprint & Copyright © 2014 Association of Military Surgeons of the U.S.
PMID: 25181727 [PubMed - in process]

10. Parasit Vectors. 2014 Sep 1;7(1):415. [Epub ahead of print]

An inverse association between West Nile virus serostatus and avian malaria infection status.

Medeiros MC, Anderson TK, Higashiguchi JM, Kitron UD, Walker ED, Brawn JD, Krebs BL, Ruiz MO, Goldberg TL, Ricklefs RE, Hamer GL.



Various ecological and physiological mechanisms might influence the probability that two or more pathogens may simultaneously or sequentially infect a host individual. Concurrent infections can have important consequences for host condition and fitness, including elevated mortality risks. In addition, interactions between coinfecting pathogens may have important implications for transmission dynamics.


Here, we explore patterns of association between two common avian pathogens (West Nile virus and avian malaria parasites) among a suburban bird community in Chicago, IL, USA that share mosquito vectors. We surveyed 1714 individual birds across 13 species for both pathogens through established molecular protocols.


Field investigations of haemosporidian and West Nile virus (WNV) infections among sampled birds yielded an inverse association between WNV serostatus and Plasmodium infection status. This relationship occurred in adult birds but not in juveniles. There was no evidence for a relationship between Haemoproteus infection and WNV serostatus. We detected similar prevalence of Plasmodium among birds captured with active WNV infections and spatiotemporally paired WNV-naive individuals of the same species, demonstrating that the two pathogens can co-infect hosts.


Mechanisms explaining the negative association between WNV serostatus and Plasmodium infection status remain unclear and must be resolved through experimental infection procedures. However, our results highlight potential interactions between two common avian pathogens that may influence their transmission among hosts. This is especially relevant considering that West Nile virus is a common zoonotic pathogen with public health implications. Moreover, both pathogens are instructive models in infectious disease ecology, and infection with either has fitness consequences for their avian hosts.
Free Article
PMID: 25178911 [PubMed - as supplied by publisher]

Icon for BioMed Central

No comments:

Post a comment