Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA.

Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection

Rapid and high throughput molecular identification of diverse mosquito species by igh resolution melting analysis

Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the Anopheles gambiae and Culex pipiens complexes. We validated the use of PCR-HRM analyses to differentiate species within Anopheles and within each of six genera of culicine mosquitoes, comparing primers targeting cytochrome b (cyt b), NADH dehydrogenase subunit 1 (ND1), intergenic spacer region (IGS) and cytochrome c oxidase subunit 1 (COI) gene regions. HRM analyses of amplicons from all the six primer pairs successfully differentiated two or more mosquito species within one or more genera (Aedes (Ae. vittatus from Ae. metallicus), Culex (Cx. tenagius from Cx. antennatus, Cx. neavei from Cx. duttoni, cryptic Cx. pipiens species), Anopheles (An. gambiae s.s. from An. arabiensis) and Mansonia (Ma. africana from Ma. uniformis)) based on their HRM profiles. However, PCR-HRM could not distinguish between species within Aedeomyia (Ad. africana and Ad. furfurea), Mimomyia (Mi. hispida and Mi. splendens) and Coquillettidia (Cq. aurites, Cq. chrysosoma, Cq. fuscopennata, Cq. metallica, Cq. microannulatus, Cq. pseudoconopas and Cq. versicolor) genera using any of the primers. The IGS and COI barcode region primers gave the best and most definitive separation of mosquito species among anopheline and culicine mosquito genera, respectively, while the other markers may serve to confirm identifications of closely related sub-species. This approach can be employed for rapid identification of mosquitoes

A new benchmark dataset with production methodology for short text semantic similarity algorithms

This research presents a new benchmark dataset for evaluating Short Text Semantic Similarity (STSS) measurement algorithms and the methodology used for its creation. The power of the dataset is evaluated by using it to compare two established algorithms, STASIS and Latent Semantic Analysis. This dataset focuses on measures for use in Conversational Agents; other potential applications include email processing and data mining of social networks. Such applications involve integrating the STSS algorithm in a complex system, but STSS algorithms must be evaluated in their own right and compared with others for their effectiveness before systems integration. Semantic similarity is an artifact of human perception; therefore its evaluation is inherently empirical and requires benchmark datasets derived from human similarity ratings. The new dataset of 64 sentence pairs, STSS-131, has been designed to meet these requirements drawing on a range of resources from traditional grammar to cognitive neuroscience. The human ratings are obtained from a set of trials using new and improved experimental methods, with validated measures and statistics. The results illustrate the increased challenge and the potential longevity of the STSS-131 dataset as the Gold Standard for future STSS algorithm evaluation. © 2013 ACM 1550-4875/2013/12-ART17 15.00

The identification of several dipterocarpaceae and fagaceae trees by barcode dna coupled with high-resolution melting analysis

The loss of forests is a major environmental, social, and economic problem. The disappear-ance has been occurring to an extreme degree in many parts of Southeast Asia, including Thailand. Logging and clearing of forests for agriculture, cash crops, and food production has destroyed much of the tropical forests in Thailand. Floristic inventory could provide essential information for forest conservation but species identification as a part of inventory creating could be challenging in some cases. Barcode DNA coupled with High Resolution Melting analysis (Bar-HRM) was used here in aiding species identification of plant in Dipterocarpaceae (Dipterocarpus alatus, D. costatu, D. intricatus, D. obtusifolius, Hopea ferrea, H. odorata, Shorea guiso, S. obtuse, S. roxburghii, and S. siamensis) and Fagaceae (Castanopsis echinocarpa, C. inermis, Lithocarpus wallichianus, Quercus aliena and Q. oidocarpa) families. Two main experiments were conducted including: (1) a comparing method for primer design and (2) testing the robustness of the Bar-HRM by trying to identify tree samples that did not have sequences in the GenBank. In experiment 1, the manual design primer pair was found to be the best fit for the work. Of key importance is finding the primers which give the most nucleotide variations within the generated amplicon; this is a parameter that cannot be set in any web-based tools. Next, in experiment 2, Bar-HRM using primers of ITS1 and ITS2 regions were able to discriminate all 10 tested tree species without any problem, even when there were no sequences of the samples to be analysed before performing the HRM. Here, Bar-HRM poses potential to be a game-changer in tropical forest conservation, as it will be useful for species identification. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Environmental DNA detection of giant snakehead in Thailand’s major rivers for wild stock assessment

Capture-based aquaculture is now gaining much attention in Southeast Asia. This system was used to produce several fish species with social and economic implications, including the giant snakehead (Channa micropeltes). As wild harvesting of organisms for seed stock is one of main practices in capture-based aquaculture, abundance and distribution of the wild stock are essential for both environmental impact evaluation and stock management. Mark and recapture, visual observation and physical capture of target species are costly, ineffective, and labour intensive for fish surveys in several cases. Detection of target organisms using eDNA (environmental DNA) could be a good alternative as it has proved to be a non-invasive, rapid, and sensitive method for aquatic species monitoring and surveying. Here, we developed a TaqMan assay that targets the 16S region of giant snakehead DNA to amplify eDNA captured in water samples. 300 µl of water samples were collected from 15 sites located in the Chao Phraya River Basin (Ping, Wang, Yom, Nan, and Chao Phraya River) and filtered with 0.7 µm glass fibre membrane filter. Giant snakehead eDNA was detected in most tributaries (60%) with concentrations ranging from 74.0 copies/ml in Wang River sites to 7.4 copies/ml in Nan River sites. As intensification of capture-based aquaculture could lead to depleting of wild fish stocks, urgent management is needed. However, the existing conventional approaches for assessment of fish overexploitation, survey and monitoring have several limitations. Copyright: © 2022 Osathanunkul, Madesis. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Rapid analysis for the identification of the seagrass Halophila ovalis (Hydrocharitaceae)

Seagrasses are considered as one of the most important species as they play key ecological roles in various types of ecosystems and also provide a food source for endangered animal species. There are two main  characteristics of seagrasses that hinder efforts to correctly identify species based on conventional identification keys alone: i) the variability of  morphological characteristics and ii) lack of needed morphological  characters especially flowers. A taxonomically unresolved complex such as Halophila spp. is reported. Plant DNA barcoding regions (rbcL and trnH-psbA) were used to confirm species of collected seagrasses from the southern coast of Thailand. Small and big-leaved samples of Halophila spp. were analysed in this study. The big-leaved samples were identified on the field as Halophila ovalis whilst it was uncertain whether the small-leaved samples belonged to H. ovalis. DNA analysis revealed that the small-leaved samples could be H. ovalis. We also coupled PCR with high resolution melt (HRM) to more cost-effectively identify individuals of H. ovilis than using barcoding alone. Using HRM to resolve differences in the sequence of two genes showed that the two unknown seagrasses belonged to the same species as H. ovalis.  In conclusion, using HRM proved to pose great potential in seagrass identification. Key words: DNA barcoding, Halophila ovalis, rbcL, trnH-psbA, species identification

Bar-HRM for Species Confirmation of Native Plants Used in Forest Restoration in Northern Thailand

Plant species confirmation is a crucial step in using native plant species for forest restoration. To enhance this, a hybrid method of DNA barcoding and high-resolution melting analysis (Bar-HRM) was investigated in this study. In total, 12 native plant species samples were collected from forest restoration sites in Nan, a province in Northern Thailand. Simulation HRM analysis was performed to find the most appropriate region for in vitro Bar-HRM analysis. After that, in vitro Bar-HRM was carried out to validate the performance of native plant species. Results from both simulation and in vitro analyses revealed that the nuclear ribosomal internal transcribed spacer (ITS) region can be used as a primer set that can clearly discriminate native plant species in this study. With our study, Bar-HRM was proved of use in native plant species confirmation, even if that species had no molecular data available. In this con-text, Bar-HRM would be useful for the identification of native plant species used in tropical forest restoration not only in Thailand but also in any areas with similar plant groups. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

DNA-based species identification of Greek macromycetes

Fungi comprise one of the largest and diverse groups of eukaryotes. Macromycetes, which are commonly known as mushrooms, include species in Basidiomycota and Ascomycota. Macromycetes are essential for ecosystem functioning and have high commercial value owing to their nutritional and medicinal properties. Despite the importance of macrofungi for the ecosystem and human welfare, macromycete diversity and phylogeny are poorly characterized, owing to the lack of molecular-based biodiversity descriptors supporting phenotypic classifications, especially for biodiversity rich countries such as Greece. In this study, we implemented a multi-marker DNA barcoding approach, utilizing the Internal Transcribed Spacer 1 (ITS1) and part of the 28S nuclear ribosomal Large Subunit (nrLSU) rDNA regions, for the molecular identification of representative Greek macromycetes. Our analysis involved 103 Greek macromycetes covering seven genera of Basidiomycota (Agaricus, Amanita, Boletus, Cantharellus, Lactarius, Pleurotus, and Russula) and one genus of Ascomycota (Morchella). Phylogenetic inference based on the generated rDNA sequences, revealed high DNA divergence among most of the examined macromycete genera, which formed discrete monophyletic groups. Our phylogenetic analysis, in accordance with previous studies in the field, further supports the early divergence of the Cantharellus clade, followed by the subsequent split of the Russulaceae from a sister clade formed by the Agaricus, Amanita, Boletus and Pleurotus genera. © 2021. Current Research in Environmental and Applied Mycology. All Rights Reserved