scholarly journals DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia

2021 ◽  
Vol 11 (2) ◽  
pp. 151-160
Author(s):  
Yanti Ariyanti ◽  
◽  
Ika Rini ◽  
Indah Oktaviani ◽  
Sovia Leksikowati ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
National Park ◽  
Conservation Status ◽  
Genetic Distances ◽  
Coi Gene ◽  
Species Discovery ◽  
Mitochondrial Coi ◽  
Identification Of Species ◽  
Way Kambas National Park

Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.

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.

Morphological description and DNA barcoding of Hydrobaenus golovinensis sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Russian Far East

Zootaxa ◽  
2017 ◽  
Vol 4286 (2) ◽  
pp. 277
Author(s):  
EUGENYI A. MAKARCHENKO ◽  
MARINA A. MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
OLEG A. VELIAEV
Keyword(s):  
Dna Barcoding ◽  
Russian Far East ◽  
Far East ◽  
Instar Larva ◽  
Genetic Distances ◽  
Coi Gene ◽  
Morphological Description ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
The Russian Far East

Illustrated descriptions of adult male, pupa and fourth instar larva, as well as DNA barcoding results of Hydrobaenus golovinensis sp. nov. in comparison with closely related species H. majus Makarchenko et Makarchenko and H. sikhotealinensis Makarchenko et Makarchenko from the Russian Far East are provided. Partial mitochondrial COI gene (DNA barcoding) of the new species has been sequenced and uploaded to GenBank. Comparisons with corresponding regions of COI between H. golovinensis and other species in the genus produce K2P genetic distances of 10.3–14.3%, the values well above those associated with intraspecific variation. In contrast, genetic distances among 18 specimens are all within the range of 0–3.5%. The ML tree is also constructed using DNA barcodes obtained in the present study and those of other species of Hydrobaenus Fries from GenBank. 

scholarly journals DNA barcoding of Deltocephalus Burmeister leafhoppers (Cicadellidae, Deltocephalinae, Deltocephalini) in China

ZooKeys ◽  
2019 ◽  
Vol 867 ◽  
pp. 55-71 ◽  
Author(s):  
Hong Zhang ◽  
Yalin Zhang ◽  
Yani Duan
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Distinct Species ◽  
Genetic Distances ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Chinese Populations ◽  
The Status ◽  
Morphological Variants

We investigated the feasibility of using the DNA barcode region in identifying Deltocephalus from China. Sequences of the barcode region of the mitochondrial COI gene were obtained for 98 specimens (Deltocephalusvulgaris – 88, Deltocephaluspulicaris – 5, Deltocephalusuncinatus – 5). The average genetic distances among morphological and geographical groups of D.vulgaris ranged from 0.9% to 6.3% and among the three species of Deltocephalus ranged from 16.4% to 21.9% without overlap, which effectively reveals the existence of a “DNA barcoding gap”. It is important to assess the status of these morphological variants and explore the genetic variation among Chinese populations of D.vulgaris because the status of this species has led to taxonomic confusion because specimens representing two distinct morphological variants based on the form of the aedeagus are often encountered at a single locality. Forty-five haplotypes (D.vulgaris – 36, D.pulicaris – 5, D.uncinatus – 4) were defined to perform the phylogenetic analyses; they revealed no distinct lineages corresponding either to the two morphotypes of D.vulgaris or to geographical populations. Thus, there is no evidence that these variants represent genetically distinct species.

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.

DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene

2020 ◽  
Vol 31 (2) ◽  
pp. 73-80
Author(s):  
Rui Zou ◽  
Cong Liang ◽  
Mengmeng Dai ◽  
Xiaodong Wang ◽  
Xiuyue Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene

scholarly journals Caridina biyiga sp. nov., a new freshwater shrimp (Crustacea: Decapoda: Atyidae) from Leichhardt Springs, Kakadu National Park, Australia, based on morphological and molecular data, with a preliminary illustrated key to Northern Territory Caridina

Zootaxa ◽  
2019 ◽  
Vol 4695 (1) ◽  
pp. 1-25
Author(s):  
JOHN W. SHORT ◽  
TIMOTHY J. PAGE ◽  
CHRISTOPHER L. HUMPHREY
Keyword(s):  
New Species ◽  
16S Rdna ◽  
National Park ◽  
Strong Support ◽  
Molecular Data ◽  
Genetic Distances ◽  
Northern Territory ◽  
Coi Gene ◽  
Gene Fragment ◽  
Morphological And Molecular Data

Caridina biyiga sp. nov. is described from Leichhardt Springs, Kakadu National Park, Northern Territory, Australia, based on morphological and molecular data. The new species is highly distinctive among its congeners in having the dactylus of pereiopod 5 similar to the dactyli of pereiopods 3–4 and lacking the comb-like row of spiniform setae typical of the genus. The branchial formula is also distinctive for the genus in lacking an arthrobranch at the base of pereiopod 1 and in having a vestigial epipod on maxilliped 1.                Despite the distinctive morphology of the new species, the molecular data did not provide strong support for the recognition of a new genus. Phylogenetic analyses of Australian Caridina using the mitochondrial 16S rDNA gene fragment placed the new species in a well-supported clade containing at least one typical species of Caridina. Within this clade, referred to as the ‘thermophila’ group, Kimura 2-parameter (K2P) genetic distances of 16S rDNA between the new species and sister taxa ranged from 5.1–6.0%. Analyses using the mitochondrial 3’ COI gene fragment from species of the ‘thermophila’ group yielded K2P genetic distances between the new species and its sister taxa ranging from 10.4–15.1%.                A preliminary illustrated key to Northern Territory Caridina is provided. The conservation significance of Leichhardt Springs and its aquatic fauna are also briefly discussed. 

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%).

DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries

Zootaxa ◽  
2008 ◽  
Vol 1839 (1) ◽  
pp. 1 ◽  
Author(s):  
MANUEL ELÍAS-GUTIÉRREZ ◽  
FERNANDO MARTÍNEZ JERÓNIMO ◽  
NATALIA V. IVANOVA ◽  
MARTHA VALDEZ-MORENO ◽  
PAUL D. N. HEBERT
Keyword(s):  
Dna Barcoding ◽  
Classification Systems ◽  
Coi Gene ◽  
Aquatic Environments ◽  
Dna Barcodes ◽  
Chydorus Sphaericus ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Current Classification ◽  
Excellent Tool

DNA barcoding, based on sequence diversity in the mitochondrial COI gene, has proven an excellent tool for identifying species in many animal groups. Here, we report the first barcode studies for freshwater zooplankton from Mexico and Guatemala and discuss the taxonomic and biological implications of this work. Our studies examined 61 species of Cladocera and 21 of Copepoda, about 40% of the known fauna in this region. Sequence divergences among conspecific individuals of cladocerans and copepods averaged 0.82% and 0.79%, respectively, while sequence divergences among congeneric taxa were on average 15-20 times as high. Barcodes were successful in discriminating all species in our study, but sequences for Mexican Daphnia exilis overlapped with those of D. spinulata from Argentina. Our barcode data revealed evidence of many species overlooked by current classification systems —for example, based on COI genotypes the Diapahanosoma birgei group appears to include 5 species, while Ceriodaphnia cf. rigaudi, Moina cf. micrura, Mastigodiaptomus albuquerquensis and Mastigodiaptomus reidae all include 2–3 taxa. The barcode results support recent taxonomic revisions, such as recognition of the genus Leberis, and the presence of several species in the D. birgei and Chydorus sphaericus complexes. The present results indicate that DNA barcoding will provide powerful new insights into both the incidence of cryptic species and a better understanding of zooplankton distributions, aiding evaluation of the factors influencing competitive outcomes, and the colonization of aquatic environments.

Sign in / Sign up

Export Citation Format

Share Document