On the use of ultrasonic detectors for bat species identification and the calibration of QMC Mini Bat Detectors

1984 ◽  
Vol 62 (12) ◽  
pp. 2677-2679 ◽  
Author(s):  
Donald W. Thomas ◽  
Stephen D. West
Keyword(s):  
Species Identification ◽  
Species Level ◽  
Ultrasonic Detection ◽  
Echolocation Call ◽  
Echolocation Calls ◽  
Reliable Identification ◽  
Level Identification

Several ultrasonic detection and analysis systems are currently used to provide information on the echolocation calls of bats, in many cases permitting species-level identification. This note briefly describes these systems and alerts potential users of the inaccuracies of the simplest device, the superheterodyne QMC Mini Bat Detector. Without adequate calibration, the error in this latter detector is such that reliable identification of bats by echolocation call characteristics cannot be achieved.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Variability in echolocation call design of 26 Swiss bat species: consequences, limits and options for automated field identification with a synergetic pattern recognition approach

Mammalia ◽  
2004 ◽  
Vol 68 (4) ◽  
Author(s):  
Martin K. Obrist ◽  
Ruedi Boesch ◽  
Peter F. Flückiger
Keyword(s):  
Pattern Recognition ◽  
Species Identification ◽  
Automated Systems ◽  
Echolocation Call ◽  
Echolocation Calls ◽  
Recognition Algorithms ◽  
Field Identification ◽  
Pattern Recognition Approach ◽  
Species Specific ◽  
Independent Species

Pattern recognition algorithms offer a promising approach to recognizing bat species by their echolocation calls. Automated systems like synergetic classifiers may contribute significantly to operator-independent species identification in the field. However, it necessitates the assembling of an appropriate database of reference calls, a task far from trivial. We present data on species specific flexibility in call parameters of all Swiss bat species (except

scholarly journals Assessing the reliability of medicinal Dendrobium sequences in GenBank for botanical species identification

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hoi-Yan Wu ◽  
Kwun-Tin Chan ◽  
Grace Wing-Chiu But ◽  
Pang-Chui Shaw
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Species Level ◽  
Research Groups ◽  
Voucher Specimen ◽  
Botanical Species ◽  
Promising Tool ◽  
Chloroplast Genomes ◽  
Level Identification ◽  
Annotation Quality

AbstractDNA-based method is a promising tool in species identification and is widely used in various fields. DNA barcoding method has already been included in different pharmacopoeias for identification of medicinal materials or botanicals. Accuracy and validity of DNA-based methods rely on the accuracy and taxonomic reliability of the DNA sequences in the database to be compared against. Here we evaluated the annotation quality and taxonomic reliability of selected barcode loci (rbcL, matK, psbA-trnH, trnL-trnF and ITS) of 41 medicinal Dendrobium species downloaded from GenBank. Annotations of most accessions are incomplete. Only 53.06% of the 2041 accessions downloaded contain a reference to a voucher specimen. Only 31.60% and 4.8% of the entries are annotated with country of origin and collector or assessor, respectively. Taxonomic reliability of the sequences was evaluated by a Megablast search based on similarity to sequences submitted by other research groups. A small number of sequences (211, 7.14%) was regarded as highly doubted. Moreover, 10 out of 60 complete chloroplast genomes contain highly doubted sequences. Our findings suggest that sequences of GenBank should be used with caution for species-level identification. The scientific community should provide more important information regarding identity and traceability of the sample when they deposit sequences to public databases.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

2018 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species level molecular identification methods, we tested six DNA barcodes viz. ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa, ITS2+matK+rbcLa for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Integrative Description of Cryptic Tigriopus Species From Korea Using MALDI-TOF MS and DNA Barcoding

2021 ◽  
Vol 8 ◽  
Author(s):  
Jisu Yeom ◽  
Nayeon Park ◽  
Raehyuk Jeong ◽  
Wonchoel Lee
Keyword(s):  
Species Identification ◽  
Species Level ◽  
Morphological Comparison ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Low Costs ◽  
A New Species ◽  
Level Identification ◽  
Tof Ms

MALDI Time-of-Flight Mass Spectrometry (MALDI-TOF MS) provides a fast and reliable alternative method for species-level identification of pathogens and various metazoans. Compared to the commonly used mitochondrial cytochrome c oxidase subunit I (mtCOI) barcoding, advantages of MALDI-TOF MS are rapid species identifications and low costs. In this study, we used MALDI-TOF MS to determine whether spectra patterns of different species can be used for species identification. We obtained a total of 138 spectra from individual specimens of Tigriopus, which were subsequently used for various cluster analyses. Our findings revealed these spectra form three clear clusters with high AU value support. This study validates the viability of MALDI-TOF MS as a methodology for higher-resolution species identification, allowing detection of cryptic species of harpacticoida. In addition, we propose a new species, Tigriopus koreanus sp. nov. by utilizing integrative methods such as morphological comparison, mtCOI barcoding, and MALDI-TOF MS.

scholarly journals First Report of a Gall Midge Species (Diptera: Cecidomyiidae) Associated With Pistachios

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Farshid O Sirjani ◽  
Edwin E Lewis
Keyword(s):  
Gall Midge ◽  
Species Level ◽  
Plant Tissues ◽  
First Report ◽  
Branch Dieback ◽  
First Time ◽  
Level Identification

Abstract A new dipterous pest is reported, for the first time, on commercial pistachios from Sirjan, Kerman province, Iran. The genus of the insect was determined to be Resseliella Seitner (Diptera: Cecidomyiidae). Adults are light brown to brown in color and 0.8–1.5 mm in length with females, generally, slightly larger than males. Females have an elongated ovipositor, which is characteristic of the genus. Larvae are orange in color, 2–3 mm in length in the later instars, feed under bark without inducing galls, and cause branch dieback on trees of various ages. Brown to black discolorations are observed on plant tissues under bark where the larvae feed. Infestations observed on current and the previous—year’s growths, ranged from 0.5 to 1.2 cm in diameter, and all located in outer branches. Dry leaves and fruit clusters on infested branches remain attached, which may be used to recognize infestation by the gall midge. Dark-colored, sunken spots with splits on the bark located at the base of the wilted sections of the shoots also are symptoms of Resseliella sp. larval activity. Species-level identification of the gall midge is currently underway.

scholarly journals Description of Echolocation Call Parameters for Urban Bats in Vietnam as a Step Towards a More Integrated Acoustic Monitoring of Urban Wildlife in Southeast Asia

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 18
Author(s):  
Long Kim Pham ◽  
Bang Van Tran ◽  
Quy Tan Le ◽  
Trung Thanh Nguyen ◽  
Christian C. Voigt
Keyword(s):  
Discriminant Function ◽  
Discriminant Function Analysis ◽  
Function Analysis ◽  
Quantitative Description ◽  
Southeast Asian ◽  
Asian Countries ◽  
Echolocation Call ◽  
Echolocation Calls ◽  
Pilot Work ◽  
Southeast Asian Countries

This study is the first step towards more systematic monitoring of urban bat fauna in Vietnam and other Southeast Asian countries by collecting bat echolocation call parameters in Ho Chi Minh and Tra Vinh cities. We captured urban bats and then recorded echolocation calls after releasing in a tent. Additional bat’s echolocation calls from the free-flying bats were recorded at the site where we captured bat. We used the obtained echolocation call parameters for a discriminant function analysis to test the accuracy of classifying these species based on their echolocation call parameters. Data from this pilot work revealed a low level of diversity for the studied bat assemblages. Additionally, the discriminant function analysis successfully classified bats to four bat species with an accuracy of >87.4%. On average, species assignments were correct for all calls from Taphozous melanopogon (100% success rate), for 70% of calls from Pipistrellus javanicus, for 80.8% of calls from Myotis hasseltii and 67.3% of calls from Scotophilus kuhlii. Our study comprises the first quantitative description of echolocation call parameters for urban bats of Vietnam. The success in classifying urban bats based on their echolocation call parameters provides a promising baseline for monitoring the effect of urbanization on bat assemblages in Vietnam and potentially also other Southeast Asian countries.

scholarly journals Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus

2016 ◽  
Vol 10 (1) ◽  
pp. 202-208 ◽  
Author(s):  
Marisa Almuzara ◽  
Claudia Barberis ◽  
Viviana Rojas Velázquez ◽  
Maria Soledad Ramirez ◽  
Angela Famiglietti ◽  
...  
Keyword(s):  
Extraction Methods ◽  
Species Level ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Genus Level ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Level Identification ◽  
Gram Positive Cocci ◽  
Tof Ms

Objective:To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates.Methods:All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and <1.700 no reliable identification) and lower cut-off scores (≥1.500 for genus level, ≥ 1.700 for species-level and score <1.500 no reliable identification) were considered for identification. A minimum difference of 10% between the top and next closest score was required for a different genus or species.MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result.When both methods gave discordant results, the 16S rDNA orsodAgenes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S orsodA identification were considered incorrect.Results:Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained.Conclusion:The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis asHelcococcus,Abiotrophia,Granulicatella, among others. Nevertheless, expansion of the library, especially including more strains with different spectra on the same species might overcome potential “intraspecies” variability problems. Moreover, a decrease of the identification scores for species and genus-level identification must be considered since it may improve the MALDI-TOF MS accuracy.

scholarly journals Don’t believe the mike: behavioural, directional, and environmental impacts on recorded bat echolocation call measures

2018 ◽  
Vol 96 (4) ◽  
pp. 283-288 ◽  
Author(s):  
J.M. Ratcliffe ◽  
L. Jakobsen
Keyword(s):  
Environmental Impacts ◽  
Acoustic Signals ◽  
Bird Song ◽  
Great Flexibility ◽  
Echolocation Call ◽  
Echolocation Calls ◽  
Acoustic Information ◽  
Species Overlap ◽  
Actual Signal ◽  
Nocturnal Mammals

Echolocation calls produced by bats in their larynges allow these flying, nocturnal mammals to orient and find food at night. The acoustic signals are not like bird song, and even individual bats exhibit great flexibility in call design and between-species overlap is common. As a result, identifying bats to species by their echolocation calls even in communities with few bat species can be difficult. Unfortunately, the situation is worse still. As a result of several factors — some to do with microphones, some with environment, some with bats, and the calls themselves — acoustic information transmitted to and transduced by microphones can be dramatically different from the actual signal produced by the bat and as would be recorded on axis, close to its mouth using ideal microphones under ideal conditions. We outline some of these pitfalls and discuss ways to make the best of a bad situation. Overall, however, we stress that many of these factors cannot be ignored and do impact our recordings.

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