scholarly journals Unravelling taxonomic ambiguity of the Mastacembelidae in the Mekong Delta (Vietnam) through DNA barcoding and morphological approaches

2020 ◽  
Vol 33 (2) ◽  
Author(s):  
Thuy-Yen Duong ◽  
Liem Van Dung Tran ◽  
Ngoc-Tran Thi Nguyen ◽  
Jamsari Amirul Firdaus Jamaluddin ◽  
Mohd Nor Siti Azizah
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Mekong Delta ◽  
The Body ◽  
Coi Gene ◽  
Sister Relationship ◽  
Test Species ◽  
Dorsal Fin ◽  
Mastacembelus Armatus ◽  
Fin Spines

Morphological-based species identification can be problematic for a comparative worldwide survey if taxonomic keys are limited and inconsistent, as illustrated in the family Mastacembelidae. This study combined DNA barcoding and morphological methods to test species identification of Mastacembelidae in the Mekong Delta with emphasis on taxonomic ambiguity of the precise identification of the fish locally known as chach bong. Fish specimens were collected from fishermen in different regions of the delta. Five presumed species within two genera were recorded. Samples were morphologically measured for morphometric and meristic traits. Representative samples of each species were sequenced at the cytochrome c oxidase subunit I (COI) gene. The number of dorsal fin spines and general morphological appearance are distinguishable among the five presumed species. However, morphometric measurements overlapped between Macrognathus semiocellatus and Macrognathus siamensis. K2P distances based on COI sequences among species were high, ranging from 12.4% to 18.7%. All individuals were separated into monophyletic groups of species, clustered into Mastacembelus and two Macrognathus lineages. Chach bong should be recognized as Mastacembelus favus and not Mastacembelus armatus as previously classified. No Mastacembelus armatus was recorded in the Mekong Delta. GenBank sequences of Mastacembelus armatus formed a sister relationship to Mastacembelus favus although both have the same range of number of dorsal fin spines and similar reticulated patterns on the body. Misidentification between these two species has been widely recorded in international databases of species taxonomy and DNA barcodes. Nonetheless, their genetic distance (12.4%) is higher than conspecific distances of samples from other regions, indicating the two species can be differentiated by DNA barcoding.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

Use of molecular methods in identification of species, age and sex of insects useful in forensic entomology

2014 ◽  
Vol 286 ◽  
pp. 66-69
Author(s):  
Joanna Stojak ◽  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Environmental Conditions ◽  
Forensic Entomology ◽  
Sex Identification ◽  
The Body ◽  
Molecular Methods ◽  
Insect Larvae ◽  
Identification Of Species ◽  
Age And Sex

Forensic entomology uses insects to determine the time, cause and place of death. To this end, two entomological methods are used. The development-based method uses the patterns of insect larvae development under the specific thermal and environmental conditions. The succession-based method analyzes the sequence of insect succession on the body in various environmental conditions. The proper insect species identification is essential in both methods. In this article, the molecular methods of species, age and sex identification are presented such as DNA barcoding or DNA-HRM-PCR.

scholarly journals The Utility of DNA Barcoding for the Species Identification of Larval Fish in the Lower Ing River, Thailand

2020 ◽  
Vol 20 (9) ◽  
pp. 671-679
Author(s):  
Dutrudi Panprommin ◽  
Kanyanat Soontornprasit ◽  
Siriluck Tuncharoen ◽  
Niti Iamchuen
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Larval Fish ◽  
Average Length ◽  
Conservation Status ◽  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Coi Gene ◽  
Fishery Resource ◽  
Sustainable Fishery

The species identification of larval fish is very important for sustainable fishery resource management. However, identification based on morphological characters is very difficult, complex and error-prone. DNA barcoding with the sequence of cytochrome c oxidase I (COI) gene was used to identify larval fish species from 10 stations in the tributaries of the lower Ing River. One hundred and six samples were collected between May 2016 and April 2017. The average length of the COI nucleotide sequences was approximately 640 bp. A total of 99 nucleotide sequences were identified in 35 species, 31 genera, 19 families and 9 orders, with 97-100% identity with entries in both the GenBank and BOLD databases. The genetic distance within species ranged from 0.000 to 0.004. However, seven samples were identified at only the genus level because their sequences had not been reported in any databases. Based on IUCN conservation status, most species were classified as least concern (77.14%). Approximately 69.23% of all species were related to human uses in fisheries, aquaculture or aquariums, whereas 30.77% of species were not assessed. Trichopsis vittata (family Osphronemidae) (90%) had the most frequency of occurrence, followed by Oryzias minutillus (family Adrianichthyidae) (70%) and Trichopodus trichopterus (family Osphronemidae) (70%).

scholarly journals New identification of the moray eel Gymnothorax minor (Temminck & Schlegel, 1846) in China (Anguilliformes, Muraenidae)

ZooKeys ◽  
2018 ◽  
Vol 752 ◽  
pp. 149-161 ◽  
Author(s):  
Yuan Li ◽  
Liyan Zhang ◽  
Linlin Zhao ◽  
Ji Feng ◽  
Karhoe Loh ◽  
...  
Keyword(s):  
South China Sea ◽  
Dna Barcoding ◽  
South China ◽  
The South China Sea ◽  
The Body ◽  
Coi Gene ◽  
Valid Species ◽  
Distribution Area ◽  
The South ◽  
China Sea

A new identification of Gymnothoraxminor (Temminck & Schlegel, 1846) is documented based on morphological characteristics and DNA barcoding. Sixty-one individuals of G.minor were collected from the East China Sea and the South China Sea. This species was previously reported as Gymnothoraxreticularis Bloch, 1795 in China because of the similarity in external shape and color. Gymnothoraxminor can be easily distinguished from G.reticularis by its color pattern of 18–20 irregular dark brown vertical bars and the body having scattered small brown spots. Additionally, the teeth are uniserial on both jaws, and the vertebrae number 137–139. By combining congener sequences of the cytochrome oxidase I (COI) gene from GenBank, two groups were detected among all the COI sequences of the currently named G.minor, which further indicated that two valid species were present based on genetic distance. A divergence also occurred on the number of vertebrae between the northern and southern populations. The phylogenetic and morphological analysis strongly supports that the northern and southern populations of G.minor are two different species. Furthermore, the distribution area of the northern G.minor has expanded southward to 5°15'N in the South China Sea. More specimens of G.minor and G.reticularis are crucial in order to define their geographical distribution boundaries and provide the correct DNA barcoding.

scholarly journals Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

2021 ◽  
Author(s):  
Chuanjiang Zhou ◽  
Mengxia Feng ◽  
Yongtao Tang ◽  
Changxing Yang ◽  
Xiaolin Meng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Morphological Characteristics ◽  
Henan Province ◽  
Coi Gene ◽  
Morphological Identification ◽  
Freshwater Shrimp

Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta) based on COI and ITS2 genes in China

2021 ◽  
Author(s):  
Tingting Zhou ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Morphological Identification ◽  
Lumbriculus Variegatus ◽  
Mitochondrial Coi ◽  
Aquatic Oligochaete ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaete could serve as an excellent indicator in aquatic monitoring programs. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial COI gene and nuclear ITS2 gene of 83 specimens belonging to 36 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae, and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree based on ITS2 gene, which was coincident with morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even aquatic oligochaete.

Species identification of DNA barcoding based on COI gene sequences in Bagridae catfishes

2018 ◽  
Vol 25 (4) ◽  
pp. 772
Author(s):  
Hongwei LIANG ◽  
Yan MENG ◽  
Xiangzhong LUO ◽  
Zhong LI ◽  
Guiwei ZOU
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Coi Gene ◽  
Gene Sequences

Two new dwarfgobies from the Southwestern Pacific Ocean (Teleostei: Gobiidae: Eviota)

Zootaxa ◽  
2012 ◽  
Vol 3572 (1) ◽  
pp. 33 ◽  
Author(s):  
DAVID W. GREENFIELD ◽  
RICHARD WINTERBOTTOM
Keyword(s):  
Papua New Guinea ◽  
Pupil Diameter ◽  
The Body ◽  
Sensory Canal ◽  
Dorsal Fin ◽  
Fin Ray ◽  
Fin Rays ◽  
Pectoral Fin Rays ◽  
Fin Spines ◽  
Pelvic Fin

Two species of Eviota with red or orange bars crossing the body, a bifurcated 4th pelvic-fin ray with two long branches,and lacking many or all cephalic sensory-canal pores are described from Palau, Indonesia, and Papua New Guinea. Eviotajewettae has a dorsal/anal fin-ray formula of 8/8, 98% of the specimens lack all cephalic sensory-canal pores, 2–4 lowerpectoral-fin rays branched; non-filamentous dorsal-fin spines; short tubular anterior nares that are not black and are lessthan ½ pupil diameter in length, and five wide bars across the body. Eviota pinocchioi has a dorsal/anal fin-ray formulaof 9/8, always lacks the POP and IT pores and the PITO and AITO pores are fused in about 50% of the specimens, un-branched pectoral-fin rays, males with filamentous dorsal-fin spines, tubular anterior nares black and very long, almost equal to the pupil diameter, and six narrow bars across body.

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 348-357 ◽  
Author(s):  
Luis M. Hernández-Triana ◽  
Fernanda Montes De Oca ◽  
Sean W.J. Prosser ◽  
Paul D.N. Hebert ◽  
T. Ryan Gregory ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Black Flies ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
Species Groups

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

scholarly journals Molecular identification of two gobi fishes of Bangladesh using cytochrome oxidase subunit I (CoI) gene sequences

2017 ◽  
Vol 44 (2) ◽  
pp. 175-184
Author(s):  
Mehnus Tabassum ◽  
Hawa Jahan ◽  
Gulshan Ara Latifa
Keyword(s):  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Molecular Systematic ◽  
Cytochrome Oxidase Subunit I ◽  
Multiple Sequence ◽  
Oxidase Subunit

DNA barcoding has been proposed as a means of quick species identification using a short standardized segment of DNA. Two species (Eleotris fusca and Glossogobius giuris) from the family Gobiidae and Eleotridae were selected for DNA barcoding using samples collected from different regions of Bangladesh. Cytochrome Oxidase Subunit I (COI) gene was sequenced from two different gobi fishes and compared with two previously published similar sequences from the genera Eleotris and Glossogobius. Multiple sequence alignment and the molecular systematic study were performed. The DNA barcode technique identified the two species. The study provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework.Bangladesh J. Zool. 44(2): 175-184, 2016

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