scholarly journals Faunistic survey of the zooplankton community in an oligotrophic sinkhole, Cenote Azul (Quintana Roo, Mexico), using different sampling methods, and documented with DNA barcodes

2018 ◽  
Author(s):  
Lucia Montes-Ortiz ◽  
Manuel Elias-Gutierrez
Keyword(s):  
Dna Barcoding ◽  
High Throughput Sequencing ◽  
Sampling Methods ◽  
Fish Larvae ◽  
Zooplankton Community ◽  
Quintana Roo ◽  
Essential Difference ◽  
Dna Barcodes ◽  
Light Traps ◽  
Freshwater System

This study is the first faunistic inventory of a zooplankton community from an open, karstic and oligotrophic aquatic sinkhole in the south of the Yucatan Peninsula (Mexico), we describe the richness of the zooplankton collected with the combination of plankton nets and light traps of our own design, using morphological and molecular characters to identify the species and demonstrate the effectiveness of only one set of primers to sequence all taxa. Recently, it has been demonstrated that different sampling methods can increase the number of zooplankton species from tropical and temperate systems dramatically. These more effective methods together with DNA barcoding can give a new and more realistic picture of the species dwelling in a freshwater system. In total, we sequenced 268 specimens, and the list of species known in this sinkhole increased from 13 to 77 taxa, with a projection of 87 in total, including cladocerans, copepods, ostracods, fish larvae, tadpoles, rotifers, chironomids, water mites, among others. From the 77 taxa identified by us, 72 BINS (Barcode Index Numbers, equivalent to putative species) were assigned by the BOLD Database (boldsystems.org), and 30 of them are new records for both, BOLD and GenBank (www.ncbi.nlm.nih.gov). There was an essential difference in the number of taxa collected with the plankton nets and the light traps. Only 23 taxa were registered in the nets, representing between 28 and 29% of the total richness, while 67 were present in the light traps representing 87% of the species found. From these, 46 taxa were exclusive to this sampling method. Light traps are an effective method for rapid evaluation of zooplankton. In the future, combining DNA barcoding and high-throughput sequencing methods with more  efficient collecting will enable us to perform quick and precise biomonitoring of any aquatic ecosystem, enabling the detection of changes in zooplankton composition resulting from climate change and anthropogenic disturbances. Nevertheless, as a first step it is fundamental to establish a baseline of DNA barcodes for the species in these ecosystems.

scholarly journals eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eva Garcia-Vazquez ◽  
Oriane Georges ◽  
Sara Fernandez ◽  
Alba Ardura
Keyword(s):  
High Throughput Sequencing ◽  
Fish Larvae ◽  
Early Stage ◽  
Zooplankton Community ◽  
Coi Gene ◽  
Fish Diet ◽  
Commercial Fish ◽  
Tropical Waters ◽  
Small Water ◽  
Sampling Protocols

AbstractZooplankton community inventories are the basis of fisheries management for containing fish larvae and their preys; however, the visual identification of early-stage larvae (the “missing biomass”) is difficult and laborious. Here, eDNA metabarcoding was employed to detect zooplankton species of interest for fisheries from open and coastal waters. High-Throughput sequencing (HTS) from environmental samples using small water volumes has been proposed to detect species of interest whose DNA is the most abundant. We analyzed 6-L water samples taken from subtropical and tropical waters using Cytochrome oxidase I (COI) gene as metabarcode. In the open ocean, several commercial fish larvae and invertebrate species important in fish diet were found from metabarcodes and confirmed from individual barcoding. Comparing Atlantic, Mediterranean, Red Sea, and Pacific samples we found a lower taxonomic depth of OTU assignments in samples from tropical waters than in those from temperate ones, suggesting large gaps in reference databases for those areas; thus a higher effort of zooplankton barcoding in tropical oceans is highly recommended. This and similar simplified sampling protocols could be applied in early detection of species important for fisheries.

scholarly journals High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Genetic Identification ◽  
Dna Barcodes ◽  
Biological Quality ◽  
Dna Metabarcoding ◽  
Morphological Approach

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

scholarly journals Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

scholarly journals Preliminary Study on Fish Larvae at Selected Coastal Waters of Sarawak

1970 ◽  
Vol 4 (2) ◽  
pp. 1-8
Author(s):  
Norhakimi Muhamad ◽  
Siti Akmar Khadijah Ab Rahim
Keyword(s):  
Coastal Waters ◽  
Intertidal Zone ◽  
Larval Dispersal ◽  
Sampling Methods ◽  
Fish Larvae ◽  
Mesh Size ◽  
Subtidal Zone ◽  
Preliminary Study ◽  
Study Sites

A survey were carried out from April to November 2012 at five study sites namely Teluk Pandan beach, Rambungan beach, Puteri beach, Sampadi Island and Satang Besar Island, Sarawak. This survey was carried out in order to obtain early documentation of fish larvae at selected coastal waters of Sarawak. Seine net (1 mm mesh size) which was pulled by two persons at intertidal zone; and bridle net (0.5 mm mesh size) that was towed by boat at subtidal zone (Sampadi Island only) were used to collect the samples. A total of 2,562 fish larvae which comprise 25 families were obtained from both sampling methods. A total of 16 families of fish larvae were caught by seine net from the intertidal zone. The same number of families was collected at the subtidal zone of Sampadi Island by bridle net. Ambassidae, Clupeidae, Engraulidae and Gerreidae found to be dominant families in the study sites. Clupeidae and Gerreidae shown a wide larval dispersal area because they were collected at all study sites. These findings seem to indicate that the subtidal zone of Sampadi support more species of fish larvae.

scholarly journals Parasitic wasps as natural enemies of aphid populations in the Mashhad region of Iran: New data from DNA barcodes and SEM

2011 ◽  
Vol 63 (4) ◽  
pp. 1225-1234 ◽  
Author(s):  
Reyhaneh Darsouei ◽  
Javad Karimi ◽  
Mehdi Modarres-Awal
Keyword(s):  
Dna Barcoding ◽  
Modern Method ◽  
Diaeretiella Rapae ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Parasitic Wasps ◽  
Pome Fruit ◽  
Initial Attempt ◽  
Morphometric Characters ◽  
Preliminary Identification

DNA barcoding is a modern method for the identification of different species, including insects. Among animals, the major emphasis of DNA barcoding is on insects. Due to this global trend we addressed this approach for surveying a group of insects. The parasitic wasps (including primary and hyperparasitoids) of pome fruit orchard aphids were collected from Iran-Mashhad during 2009-2010. Preliminary identification of this group was performed by using morphological and morphometric characters and SEM. The COI gene in the specimens was amplified and sequenced. In this survey, Aphidius matricariae, Binodoxys angelicae, Diaeretiella rapae, Ephedrus persicae, Lysiphlebus fabarum and Praon volucre parasitoids and Alloxysta sp., Asaphes suspensus, Dendrocerus carpenteri, Pachyneuron aphidis, Syrphophagus aphidivorus hyperparasitoids were studied. Based on intra-interspecies distances and phylogenetic analysis using NJ, all species possess diagnostic barcode sequences. The results of this study show that the COI sequence could be useful in identification study of this group of insects. Here we have provided the first GenBank data for the COI gene of the above-mentioned hyperparasitoids as well as an initial attempt toward preparing DNA barcodes for Iranian parasitoid and hyperparasitoid aphids.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

scholarly journals A Review of Recent Phytomedicinal Investigations and the Need for DNA Barcoding of Endemic Plants of Northern Cyprus

2020 ◽  
pp. 61-70
Author(s):  
Dudu Özkum Yavuz ◽  
Mustapha Bulama- Modu
Keyword(s):  
Quality Control ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Pharmacological Properties ◽  
Endemic Plants ◽  
Dna Barcodes ◽  
Inclusion Criteria ◽  
Ovid Medline ◽  
Northern Cyprus ◽  
Medicinal Properties

Aims: To review the phytomedicinal researches on endemic plants of Northern Cyprus and to assess the plants of their DNA barcoding status. Study Design: A review. Methodology: This work reviewed available and accessible original articles in EBSCO, Ovid MEDLINE®, PubMed®, ScienceDirectTM, Scopus® and Web of ScienceTM databases on phytomedicinal investigations and BOLD System, MMDBD version 1.5 and GenBank® on DNA barcodes of the endemic plants of Northern Cyprus until May, 2020. Using keywords searches related to phytochemistry, biological activity and DNA barcoding, DNA Sequences and the data obtain evaluated and the information that does not meet the inclusion criteria were excluded. We believe that this information would tentatively help researchers to ethically explore these plants for their Medicinal and Aromatic potentials. Results: Only 6 of the 20 endemic plants of Northern Cyprus were phytopharmaceutically investigated, while DNA sequences of 5 were found to be deposited in the publicly accessible databases accounting for 30% and 25% of the total plants respectively. Conclusion: Endemism is related to uniqueness in features including the phytomedicinal features, thus Northern Cyprus endemic plants hold ample of such. However the results of this review showed that only few were harnessed for their medicinal properties and hence the need for their pharmacological properties and comprehensive barcoding for proper authentication, detection of adulteration, and quality control.

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