Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)

Marine bird populations have been declining globally with the factors driving this decline not fully understood. Viral diseases, including those caused by poxviruses, are a concern for endangered seabird species. In this study we have characterised a novel avipoxvirus, tentatively designated albatrosspox virus (ALPV), isolated from a skin lesion of an endangered New Zealand northern royal albatross (Diomedea sanfordi). The ALPV genome was 351.9 kbp in length and contained 336 predicted genes, seven of which were determined to be unique. The highest number of genes (313) in the ALPV genome were homologs of those in shearwaterpox virus 2 (SWPV2), while a further 10 were homologs to canarypox virus (CNPV) and an additional six to shearwaterpox virus 1 (SWPV1). Phylogenetic analyses positioned the ALPV genome within a distinct subclade comprising recently isolated avipoxvirus genome sequences from shearwater, penguin and passerine bird species. This is the first reported genome sequence of ALPV from a northern royal albatross and will help to track the evolution of avipoxvirus infections in this endangered species.

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Impacts of deforestation on passerine avifauna in the Opunohu Valley of Mo'orea, French Polynesia

10.7287/peerj.preprints.2672 ◽

2016 ◽

Author(s):

Vanessa M. ZoBell ◽

Brett J Furnas

Keyword(s):

Detection Probability ◽

Bird Species ◽

Canopy Cover ◽

French Polynesia ◽

Passerine Bird ◽

Oceanic Islands ◽

Bird Populations ◽

Green Fruit ◽

Discrete Nature ◽

Acoustic Recording

Human expansion has negatively impacted biodiversity. Oceanic islands have some of the most diverse, endemic biodiversity. Endemism leads to vulnerability due to the isolated and discrete nature of oceanic islands. Birds are indicator species that adapt to change very quickly. By analyzing birds, we can investigate how changes in behavior and abundance may occur for different species in the future. Nine passerine bird species were studied with automated acoustic recording devices. Recording devices were places in agricultural, forest, and mixed habitats. Three invasive species preferred agriculture areas and low canopy cover, based on call frequency and detection probability. Native bird detectability was significantly lower than invasive bird detectability. Occupancy was above 0.8 for all species, except for the gray-green fruit dove that was >0.6. Native bird populations are at risk, based on their calling number and detection probability.

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Impacts of deforestation on passerine avifauna in the Opunohu Valley of Mo'orea, French Polynesia

10.7287/peerj.preprints.2672v1 ◽

2016 ◽

Author(s):

Vanessa M. ZoBell ◽

Brett J Furnas

Keyword(s):

Detection Probability ◽

Bird Species ◽

Canopy Cover ◽

French Polynesia ◽

Passerine Bird ◽

Oceanic Islands ◽

Bird Populations ◽

Green Fruit ◽

Discrete Nature ◽

Acoustic Recording

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Biomass, abundances, and abundance and geographical range size relationship of birds along a rainforest elevational gradient in Papua New Guinea

PeerJ ◽

10.7717/peerj.9727 ◽

2020 ◽

Vol 8 ◽

pp. e9727 ◽

Cited By ~ 1

Author(s):

Katerina Sam ◽

Bonny Koane

Keyword(s):

Papua New Guinea ◽

Bird Species ◽

New Guinea ◽

Elevational Gradient ◽

Passerine Bird ◽

Range Size ◽

Geographical Range ◽

Feeding Guilds ◽

Bird Assemblages ◽

Bird Populations

The usually positive inter-specific relationship between geographical range size and the abundance of local bird populations comes with exceptions. On continents, the majority of these exceptions have been described from tropical montane areas in Africa, where geographically-restricted bird species are unusually abundant. We asked how the local abundances of passerine and non-passerine bird species along an elevational gradient on Mt. Wilhelm, Papua New Guinea relate to their geographical range size. We collected data on bird assemblages at eight elevations (200–3,700 m, at 500 m elevational increments). We used a standardized point-counts at 16 points at each elevational study site. We partitioned the birds into feeding guilds, and we obtained data on geographical range sizes from the Bird-Life International data zone. We observed a positive relationship between abundance and geographical range size in the lowlands. This trend changed to a negative one towards higher elevations. The total abundances of the assemblage showed a hump-shaped pattern along the elevational gradient, with passerine birds, namely passerine insectivores, driving the observed pattern. In contrast to abundances, the mean biomass of the bird assemblages decreased with increasing elevation. Our results show that montane bird species maintain dense populations which compensate for the decreased available area near the top of the mountain.

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Biomass, abundances, and abundance and geographical range size relationship of birds along a rainforest elevational gradient in Papua New Guinea

10.1101/651422 ◽

2019 ◽

Author(s):

Katerina Sam ◽

Bonny Koane

Keyword(s):

Papua New Guinea ◽

Bird Species ◽

New Guinea ◽

Elevational Gradient ◽

Passerine Bird ◽

Range Size ◽

Geographical Range ◽

Feeding Guilds ◽

Bird Assemblages ◽

Bird Populations

AbstractThe usually positive inter-specific relationship between geographical range size and the abundance of local bird populations comes with exceptions. On continents, the majority of these exceptions have been described from tropical montane areas in Africa, where geographically-restricted bird species are unusually abundant. We asked how the local abundances of passerine and non-passerine bird species along an elevational gradient on Mt. Wilhelm, Papua New Guinea relate to their geographical range size. We collected data on bird assemblages at eight elevations (200 – 3,700 m, at 500 m elevational increments). We used a standardized point-counts at 16 points at each elevational study site. We partitioned the birds into feeding guilds, and we obtained data on geographical range sizes from Bird-Life International data zone. We observed a positive relationship between abundance and geographical range size in the lowlands. This trend changed to a negative one towards higher elevations. The total abundances of the assemblage showed a hump-shaped pattern along the elevational gradient, with passerine birds, namely passerine insectivores, driving the observed pattern. In contrast to abundances, the mean biomass of the bird assemblages decreased with increasing elevation. Our results show that montane bird species maintain dense populations which compensate for the decreased available area near the top of the mountain.

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Corrigendum to “Polycyclic aromatic compounds (PACs) and trace elements in four marine bird species from northern Canada in a region of natural marine oil and gas seeps” [Sci. Total Environ. 744 (2020) 140959]

The Science of The Total Environment ◽

10.1016/j.scitotenv.2020.144682 ◽

2021 ◽

pp. 144682

Author(s):

Jennifer F. Provencher ◽

Philippe J. Thomas ◽

Bruce Pauli ◽

Birgit M. Braune ◽

Ryan P. Franckowiak ◽

...

Keyword(s):

Trace Elements ◽

Aromatic Compounds ◽

Oil And Gas ◽

Bird Species ◽

Polycyclic Aromatic Compounds ◽

Marine Bird ◽

Marine Oil ◽

Northern Canada ◽

Polycyclic Aromatic ◽

Gas Seeps

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Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽

10.3390/v13061017 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1017

Author(s):

Hirohisa Mekata ◽

Tomohiro Okagawa ◽

Satoru Konnai ◽

Takayuki Miyazawa

Keyword(s):

Phylogenetic Analyses ◽

Foamy Virus ◽

Pcr Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Whole Genome Analysis ◽

Virus Family ◽

Bovine Foamy Virus ◽

Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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Cognitive flexibility in the wild: Individual differences in reversal learning are explained primarily by proactive interference, not by sampling strategies, in two passerine bird species

Learning & Behavior ◽

10.3758/s13420-021-00505-1 ◽

2022 ◽

Author(s):

Julie Morand-Ferron ◽

Michael S. Reichert ◽

John L. Quinn

Keyword(s):

Individual Differences ◽

Proactive Interference ◽

Cognitive Flexibility ◽

Reversal Learning ◽

Bird Species ◽

Passerine Bird ◽

Sampling Strategies ◽

In The Wild ◽

Wild Individual

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A global phylogenetic analysis of Japanese tonsil-derived Epstein–Barr virus strains using viral whole-genome cloning and long-read sequencing

Journal of General Virology ◽

10.1099/jgv.0.001549 ◽

2021 ◽

Author(s):

Misako Yajima ◽

Risako Kakuta ◽

Yutaro Saito ◽

Shiori Kitaya ◽

Atsushi Toyoda ◽

...

Keyword(s):

Viral Genome ◽

Epstein Barr Virus ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Regional Distribution ◽

Genome Sequences ◽

Barr Virus ◽

Endemic Areas ◽

Epstein Barr ◽

Genome Heterogeneity

Epstein–Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.

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