scholarly journals The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia

2018 ◽  
Vol 6 ◽  
Author(s):  
Bruno Cancian de Araujo ◽  
Stefan Schmidt ◽  
Olga Schmidt ◽  
Thomas von Rintelen ◽  
Rosichon Ubaidillah ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
National Park ◽  
Large Scale ◽  
Dna Barcode ◽  
Cost Benefit ◽  
Good Picture ◽  
Large Scale Assessment ◽  
Indonesian Archipelago ◽  
Technological Advances ◽  
Malaise Traps

The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.

scholarly journals ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

scholarly journals Expedited Assessment of Terrestrial Arthropod Diversity by Coupling Malaise Traps with DNA Barcoding

2017 ◽  
Author(s):  
JR deWaard ◽  
V Levesque-Beaudin ◽  
SL deWaard ◽  
NV Ivanova ◽  
JTA McKeown ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
National Park ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
List Type ◽  
Arthropod Diversity ◽  
Sequencing Technologies ◽  
Data Release ◽  
Speed And Accuracy ◽  
Malaise Traps

SummaryMonitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches.The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance.Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 20,000 specimens representing 2200 species.These protocols can support arthropod monitoring programs at regional, national, and continental scales.

scholarly journals DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9641 ◽  
Author(s):  
Nur Fadli ◽  
Siti Azizah Mohd Nor ◽  
Ahmad Sofiman Othman ◽  
Hizir Sofyan ◽  
Zainal A. Muchlisin
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Reef Fishes ◽  
Morphological Identification ◽  
Species Discovery ◽  
Indonesian Archipelago ◽  
Aceh Province ◽  
Commercially Important ◽  
Catch Composition ◽  
Fisheries Statistics

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 85-95 ◽  
Author(s):  
Jeremy R. deWaard ◽  
Valerie Levesque-Beaudin ◽  
Stephanie L. deWaard ◽  
Natalia V. Ivanova ◽  
Jaclyn T.A. McKeown ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
National Park ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Arthropod Diversity ◽  
Sequencing Technologies ◽  
Data Release ◽  
Speed And Accuracy ◽  
Malaise Traps

Monitoring changes in terrestrial arthropod communities over space and time requires a dramatic increase in the speed and accuracy of processing samples that cannot be achieved with morphological approaches. The combination of DNA barcoding and Malaise traps allows expedited, comprehensive inventories of species abundance whose cost will rapidly decline as high-throughput sequencing technologies advance. Aside from detailing protocols from specimen sorting to data release, this paper describes their use in a survey of arthropod diversity in a national park that examined 21 194 specimens representing 2255 species. These protocols can support arthropod monitoring programs at regional, national, and continental scales.

scholarly journals Extensive sampling reveals the phenology and habitat use of Afrotropical parasitoid wasps (Hymenoptera: Ichneumonidae: Rhyssinae)

2019 ◽  
Vol 6 (8) ◽  
pp. 190913 ◽  
Author(s):  
Tapani Hopkins ◽  
Heikki Roininen ◽  
Ilari E. Sääksjärvi
Keyword(s):  
National Park ◽  
Large Scale ◽  
Parasitoid Wasp ◽  
Primary Forest ◽  
Parasitoid Wasps ◽  
Sampling Effort ◽  
Ecological Data ◽  
Adult Lifespan ◽  
First Results ◽  
Malaise Traps

Tropical invertebrates, such as the ichneumonids of tropical forests, are poorly known. Here, we report the first results of extensive sampling at Kibale National Park, Uganda, by providing some of the first tropical ecological data for the ichneumonid subfamily Rhyssinae. We sampled ichneumonids with 34 Malaise traps for a year in 10 sites, in habitats ranging from primary forest to farmland. We also gathered weather and vegetation data. The total sampling effort was 373 trap months and we caught 444 rhyssines in six species. We caught the most rhyssines in dry weather, and towards the end of the sampling year. The rhyssines showed a clear preference for decaying logs and for primary forest. We fitted a model which can be used to predict future catches at the site, and draw conclusions on when rhyssines emerge and on their adult lifespan. Sampling extensively gave us a wealth of ecological data on a poorly known parasitoid wasp subfamily. We recommend that future tropical sampling collect ecological data, and that existing data from previous large-scale surveys be used for ecological analyses.

scholarly journals Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data

ZooKeys ◽  
2018 ◽  
Vol 757 ◽  
pp. 85-152 ◽  
Author(s):  
Daniel G. Mulcahy ◽  
Justin L. Lee ◽  
Aryeh H. Miller ◽  
Mia Chand ◽  
Myint Kyaw Thura ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Rapid Assessment ◽  
Dna Barcode ◽  
Taxonomic Diversity ◽  
Efficient Manner ◽  
Number Of Species ◽  
Technological Advances ◽  
Species Complexes ◽  
Life On Earth ◽  
History Database

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophiscf.kohtaoensis andChalcoranaeschatia) and three snakes (Ahaetullamycterizans,Boigadendrophila, andBoigadrapiezii).

scholarly journals DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project

2019 ◽  
Vol 7 ◽  
Author(s):  
Bruno Cancian de Araujo ◽  
Stefan Schmidt ◽  
Olga Schmidt ◽  
Thomas von Rintelen ◽  
Kristina von Rintelen ◽  
...  
Keyword(s):  
Information System ◽  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Index Number ◽  
Diversity Assessment ◽  
Data Release ◽  
Family Level ◽  
Canopy Fogging ◽  
Biodiversity Information

We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere.

scholarly journals A Rapid Colorimetric Assay for On-Site Authentication of Cephalopod Species

Biosensors ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 190
Author(s):  
Giuseppina Tatulli ◽  
Paola Cecere ◽  
Davide Maggioni ◽  
Andrea Galimberti ◽  
Pier Paolo Pompa
Keyword(s):  
Dna Barcoding ◽  
Genomic Dna ◽  
Large Scale ◽  
Colorimetric Assay ◽  
Dna Barcode ◽  
Mitochondrial Coi ◽  
Cephalopod Species ◽  
Accurate Design ◽  
Relevant Group ◽  
Species Specific

A colorimetric assay, exploiting the combination of loop-mediated isothermal amplification (LAMP) with DNA barcoding, was developed to address the authentication of some cephalopod species, a relevant group in the context of seafood traceability, due to the intensive processing from the fishing sites to the shelf. The discriminating strategy relies on accurate design of species-specific LAMP primers within the conventional 5’ end of the mitochondrial COI DNA barcode region and allows for the identification of Loligo vulgaris among two closely related and less valuable species. The assay, coupled to rapid genomic DNA extraction, is suitable for large-scale screenings and on-site applications due to its easy procedures, with fast (30 min) and visual readout.

scholarly journals Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kaomud Tyagi ◽  
Vikas Kumar ◽  
Shantanu Kundu ◽  
Avas Pakrashi ◽  
Priya Prasad ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Global Database ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
Tree Topologies ◽  
Multiple Species

Abstract Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

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