Acoustic front-end optimization for bird species recognition

2010 ◽  
Author(s):  
Martin Graciarena ◽  
Michelle Delplanche ◽  
Elizabeth Shriberg ◽  
Andreas Stolcke ◽  
Luciana Ferrer
Keyword(s):  
Species Recognition ◽  
Bird Species ◽  
Front End

scholarly journals Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation

2018 ◽  
Vol 285 (1874) ◽  
pp. 20172081 ◽  
Author(s):  
Paola Pulido-Santacruz ◽  
Alexandre Aleixo ◽  
Jason T. Weir
Keyword(s):  
Reproductive Isolation ◽  
Amazon Basin ◽  
Species Recognition ◽  
Bird Species ◽  
Hybrid Zones ◽  
Hybrid Index ◽  
Postzygotic Isolation ◽  
Genome Wide ◽  
Species Pairs ◽  
Hybrid Classes

We possess limited understanding of how speciation unfolds in the most species-rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.

scholarly journals Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ralf C. Mueller ◽  
Nicolai Mallig ◽  
Jacqueline Smith ◽  
Lél Eöery ◽  
Richard I. Kuo ◽  
...  
Keyword(s):  
Bird Species ◽  
Gene Symbol ◽  
Immune Gene ◽  
Command Line ◽  
Biological Processes ◽  
Command Line Interface ◽  
Target List ◽  
Immune Genes ◽  
Front End ◽  
Gene Symbols

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.

Towards the Automatic Acoustical Avian Monitoring System

2017 ◽  
Vol 4 (3) ◽  
pp. 17-38
Author(s):  
Robert Wielgat ◽  
Daniel Król ◽  
Tomasz Potempa ◽  
Paweł Kozioł ◽  
Agnieszka Lisowska-Lis
Keyword(s):  
Computer Program ◽  
Monitoring System ◽  
Power Supply ◽  
Data Transmission ◽  
Species Recognition ◽  
Bird Species ◽  
Solar Panel ◽  
Wireless Data ◽  
Bird Population ◽  
Wireless Data Transmission

One of the crucial aspects of the environmental protection is continuous monitoring of environment. Specific aspect is estimation of the bird species population. It is particularly important for bird species being in danger of extinction. Avian monitoring programs are time and money consuming actions which usually base on terrain expeditions. Certain remedy for this can be automatic acoustical avian monitoring system, described in the paper. Main components of the designed system are: digital audio recorder for bird voices acquisition, computer program automatically recognizing bird species by its signals emitted (voices or others) and object-relational database accessed via the Internet. Optional system components can be: digital camera and camcorder, bird attracting device, wireless data transmission module, power supply with solar panel, portable weather station. The system records bird voices and sends the recordings to the database. Recorded bird voices can be also provoked by the attracting device. Application of wireless data transmission module and power supply with solar panel allows long term operation of digital sound recorder in a hard accessible terrain. Recorded bird voices are analysed by the computer program and labelled with the automatically recognized bird species. Recognition accuracy of the program can be optionally enhanced by an expert system. Besides of labelled sound recordings, database can store also many other information like: photos and films accompanying recorded bird voices/ sounds, information about localization of observation/ recordings (GPS position, description of a place of an observation), information about bird features and behaviour, meteorological information, etc. Database on the base of geographical/ geological digital maps can generate actual maps of bird population (presence, number of individuals of each species). Moreover data-base can trigger alerts in case of rapidly decreasing bird population. It is also possible to obtain new knowledge about bird species with data mining methods. The paper presents collected data on observed bird species (audio recordings, photos and films) as well as results of experiments testing particular components of the automatic acoustical avian monitoring system.

The secretarybird dilemma: identifying a bird species fromthe Temple of Hatshepsut at Deir el-Bahari

2018 ◽  
Vol 27 (2) ◽  
pp. 83-116
Author(s):  
Kamila Braulińska
Keyword(s):  
Personal Experience ◽  
Species Recognition ◽  
Bird Species ◽  
Doctoral Dissertation ◽  
Scientific Discourse ◽  
Theoretical Background ◽  
Ancient Egypt ◽  
Depth Analysis ◽  
Background Material ◽  
The Temple

Known from a few representations in Predynastic Egyptian art, the secretarybird has otherwise been elusive, in the art of Pharaonic Egypt as well as the scientific discourse on iconographic imagery of birds in ancient Egypt. The author's studies of the animal decoration at the Temple for her doctoral dissertation identified three images of birds belonging most likely to the same species, depicted in the context of the expedition of Hatshepsut shown in the Portico of Punt. The zoological identification of the species as the secretarybird (another possibility is the African harrier-hawk) derives from an in-depth analysis of the bird’s systematics, appearance, distribution and habitat, as well as behavior, which are essential for proper species recognition and instrumental for understanding the rationale behind bringing it from the “God’s Land”. Iconographic features contesting this identification and suggesting a different species, that is, the African harrier-hawk, are discussed based on a combination of theoretical background, material analysis, on-site interviews with experts and the author’s personal experience with the species.

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