Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species

Abstract Background Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm. Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database. Utility and discussion The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.

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Edge effects on the distribution and abundance of birds in a southern Victorian forest

Wildlife Research ◽

10.1071/wr00057 ◽

2001 ◽

Vol 28 (3) ◽

pp. 239 ◽

Cited By ~ 19

Author(s):

Lainie Berry

Keyword(s):

Habitat Fragmentation ◽

Bird Species ◽

Forest Edge ◽

Bird Communities ◽

Forest Edges ◽

Forest Interior ◽

Open Country ◽

Habitat Edge ◽

Malurus Cyaneus ◽

Grey Shrike

An important consequence of habitat fragmentation for wildlife communities is the effect of an increase in the ratio of habitat edge to interior. This study compares the bird communities at forest/farmland edges and in forest interior at Bunyip State Park, Victoria. Overall, there was a significantly higher number of bird species and individuals in forest edge than in forest interior sites. The greater diversity of species at edge sites appeared to be due to an increase in forest-edge specialists, as opposed to an influx of open-country species. Four bird species: the white-throated treecreeper (Cormobates leucophaeus), the superb fairy-wren (Malurus cyaneus), the grey shrike-thrush (Colluricincla harmonica) and the grey fantail (Rhipidura fuliginosa) were significantly more abundant in edge sites. There were no species that were significantly more abundant in interior sites. Differences between the bird communities in edge and interior sites were attributed to increased foraging opportunities in the open country adjacent to forest edges.

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Vegetation on and around large-scale buildings positively influences native tropical bird abundance and bird species richness

Urban Ecosystems ◽

10.1007/s11252-018-0808-0 ◽

2018 ◽

Vol 22 (2) ◽

pp. 213-225 ◽

Cited By ~ 3

Author(s):

Richard N. Belcher ◽

Keren R. Sadanandan ◽

Emmanuel R. Goh ◽

Jie Yi Chan ◽

Sacha Menz ◽

...

Keyword(s):

Species Richness ◽

Large Scale ◽

Bird Species ◽

Bird Abundance ◽

Bird Species Richness ◽

Tropical Bird

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Unraveling the Effects of Selection and Demography on Immune Gene Variation in Free-Ranging Plains Zebra (Equus quagga) Populations

PLoS ONE ◽

10.1371/journal.pone.0050971 ◽

2012 ◽

Vol 7 (12) ◽

pp. e50971 ◽

Cited By ~ 7

Author(s):

Pauline L. Kamath ◽

Wayne M. Getz

Keyword(s):

Immune Gene ◽

Gene Variation ◽

Free Ranging ◽

Plains Zebra

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Males of a single-brooded tropical bird species do not show increases in testosterone during social challenges

Hormones and Behavior ◽

10.1016/j.yhbeh.2008.02.003 ◽

2008 ◽

Vol 54 (1) ◽

pp. 115-124 ◽

Cited By ~ 25

Author(s):

Sharon A. Gill ◽

Lauren M. Costa ◽

Michaela Hau

Keyword(s):

Bird Species ◽

Social Challenges ◽

Tropical Bird

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Habitat fragmentation reduces occupancy of nest boxes by an open-country raptor

Bird Conservation International ◽

10.1017/s0959270913000415 ◽

2014 ◽

Vol 24 (3) ◽

pp. 364-378 ◽

Cited By ~ 6

Author(s):

JESSI L. BROWN ◽

MICHAEL W. COLLOPY ◽

JOHN A. SMALLWOOD

Keyword(s):

Habitat Fragmentation ◽

Landscape Structure ◽

Spatial Scales ◽

Bird Species ◽

Probability Of Detection ◽

American Kestrel ◽

Open Habitat ◽

Nest Boxes ◽

Time Period ◽

Time Periods

SummaryDespite the recent rapid decline of many grassland bird species, the relative importance of habitat configuration to population persistence is unclear. We used Southeastern American KestrelsFalco sparverius paulusin north-central Florida as a model system to explore the relative influence of landscape structure components on site occupancy patterns at two spatial scales, and for two different time periods. We focused on the dynamic processes of site-level population expansion or contraction. We modelled the occupancy of 131 American Kestrel nest boxes with Bayesian state-space dynamic occupancy models that considered both the partially observed process of true occupancy and the probability of detection of occupancy. We used reversible jump Markov chain Monte Carlo (RJMCMC) algorithms to identify variables that described the continued occupancy of nest boxes, or ϕ, and the probability of colonisation of nest boxes between time periods, or γ3. Changes in open habitat patch isolation at a fine scale, as estimated by the variability of nearest neighbour distance, predicted site colonisation between decades, and patch shape variability was related to ϕ during the early time period (1992–93). We found no strong effects of landscape structure on ϕ during the later time period (2008–2010). We also found no evidence for effects of loss of open habitat on box occupancy or colonization. Our results indicate that continued habitat fragmentation would be deleterious for this threatened subspecies. Additionally, certain land cover management practices recommended for the Florida sandhills, such as frequent low-intensity controlled burns, will likely help conservation attempts.

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Breeding Bird Communities in a Naturally Fragemented Forest Ecosystem in Grand Teton National Park

The UW National Parks Service Research Station Annual Reports ◽

10.13001/uwnpsrc.1998.3359 ◽

1998 ◽

Vol 22 ◽

pp. 37-37

Author(s):

Gregory Schrott

Keyword(s):

Habitat Fragmentation ◽

National Park ◽

Bird Species ◽

Bird Communities ◽

Western North America ◽

Breeding Bird ◽

Grand Teton National Park ◽

Bird Populations ◽

Natural Processes

This project examined the bird species breeding in the morainal forests on the valley floor in Grand Teton National Park. These forests are very patchily distributed and range in size from less than 1 hectare to over 700 hectares, allowing for a unique opportunity to study the responses of the local bird species to a forest system that has been fragmented for centuries through natural processes. This information can be useful for predicting the potential long-term impacts of human-caused forest fragmentation on bird populations in western North America. Until quite recently very little was known of the tolerances of western forest bird species to habitat fragmentation and this project could represent an important step towards understanding their needs in this regard.

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