Biological Identifications Through DNA Barcodes

Ramadan, Hassan A. I.; Baeshen, Nabih A.

doi:10.5772/49967

Cited by 4 publications

(5 citation statements)

References 23 publications

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“…In this study, genetic distance was calculated with MEGA 5.0 (Tamura et al, 2011) with the default parameters and 1,000 bootstrap replicates under K2P model. The early studies proposed that levels of neutral mitochondrial DNA sequence diversity play a prominent role in alpha taxonomy, with divergence thresholds of approximately 3% widely being accepted as indicative of species differences (Chappell, Trewick, & Morganrichards, 2011;Hebert, Cywinska, Ball, & DeWaard, 2003;Johnston, Morikawa, Ntie, & Anthony, 2011). In this study, we reviewed all case in which haplogroups separated from the closest neighboring haplogroup by a nucleotide distance larger than the threshold (3%) and considered them to potentially represent additional cryptic species.…”

Section: Phylogenetic Analyses and Genetic Distancementioning

confidence: 99%

“…In most situations, genetic distances between individuals from different species are supposed to be greater than the intraspecific variation, revealing a noncontinuous distribution (Hebert et al, 2003).…”

Section: Dna Taxonomymentioning

confidence: 99%

“…Our phylogenetic relationships within the opsariichthine group were mostly concordant with previous studies (Huang, Wang, & Wang, 2017), and three main groups were found: the Candidia-Parazacco-Nipponocypris group with one longitudinal stripe on the flanks, the Zacco group with an indistinct vertical stripe or band on the side of the body, and the Opsariichthys group with several distinct vertical stripes or bands along its body. Earlier studies proposed that the levels of mitochondrial DNA sequence diversity play a prominent role in taxonomy, with divergence thresholds of approximately 3% widely being accepted as indicative of species differences (Chappell et al, 2011;Hebert et al, 2003 MOTUs in the Zacco group, and 29 MOTUs in the Opsariichthys group. Even though the results of the three methods were not identical, all of them showed that there should be more valid species in the opsariichthine group than the present description.…”

Section: High Species Diversity In the Opsariichthine Groupmentioning

confidence: 99%

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Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Wang

Liu

et al. 2019

Ecology and Evolution

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Opsariichthine (sensu Oceanologi Et Limnologia Sinica , 1982, 13, 293–298) is a cyprinid group consisting of five genera and endemic to East Asia. Previous studies suggested that there may be many possible cryptic species in this group, but this has not been confirmed. In this study, using mitochondrial cyt b sequences on 1,388 samples and 739 haplotypes, we showed very high species diversity within this group. The results showed that phylogenetic relationships of the opsariichthine group were as ([ Nipponocypris ‐ Parazacco ‐ Candidia ] + [ Zacco + Opsariichthys ]), and there were multiple deep lineages within several species, flagging putative cryptic species. When a 3% genetic distance was used as a threshold for species delimitation, 35 haplogroups were found, nine haplogroups in Candidia ‐ Parazacco ‐ Nipponocypris group, six haplogroups in the Zacco group, and 20 haplogroups in the Opsariichthys group. We consider all of them to be putative until determination of distinct species based on the tree topology, geographic distributions, or a combination of both. In addition, two kinds of species delimitation tools, ABGD and PTP, were applied to construct molecular operational taxonomic units (MOTUs). The ABGD method revealed nine MOTUs in Candidia ‐ Parazacco ‐ Nipponocypris group, two MOTUs in the Zacco group, and 17 MOTUs in the Opsariichthys group. And the PTP method revealed 10 MOTUs in Candidia ‐ Parazacco ‐ Nipponocypris group, 10 MOTUs in the Zacco group, and 29 MOTUs in the Opsariichthys group. Therefore, there should be more species in the opsariichthine group than presently described. Based on the molecular data and morphological characteristics, we proposed Opsariichthys macrolepis as a valid species and described its morphological diagnostic characters.

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Section: Phylogenetic Analyses and Genetic Distancementioning

confidence: 99%

Section: Dna Taxonomymentioning

confidence: 99%

Section: High Species Diversity In the Opsariichthine Groupmentioning

confidence: 99%

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Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Wang

Liu

et al. 2019

Ecology and Evolution

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show abstract

“…To reduce ambiguity in morphological identification criteria and minimize variance in results among different observers, species identification begins to rely on gene sequencing through a metabarcoding process of environmental DNA (eDNA) [17,18]. Environmental DNA (eDNA) refers to DNA derived from organisms present in the water, soil, and atmosphere.…”

Section: Introductionmentioning

confidence: 99%

Environmental DNA in a Biofilm Can Be Used to Assess Diatom Ecological Health in Stream Water Ecology

Kim,

Cho,

Kim

et al. 2023

Diversity

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In urban and agricultural streams, assessing aquatic ecosystem health is critical due to widespread pollution. Traditional methods for evaluating attached diatoms crucial for ecosystem monitoring face limitations such as species misidentification and sample damage. This study was conducted in the Miho River within the Geum River system and highlights the effectiveness of environmental DNA (eDNA) techniques for more accurate and efficient genetic-based analysis than conventional microscopic analysis methods. When eDNA-based assessments were compared with traditional microscopic methods, this study found that eDNA analysis often revealed poorer ecosystem health. Notably, eDNA assessments showed a stronger correlation with phosphorus concentrations, underlining their precision and importance in ecological studies. These findings suggest that eDNA has potential as a valuable tool for comprehensive biomonitoring. However, the use of international genetic barcode databases in eDNA analysis could lead to the identification of unrecorded species in Korea. Therefore, this study recommends developing a localized genetic barcode database and constructing eDNA information through meta-barcoding, focusing on native species. This approach is crucial for enhancing the accuracy and applicability of eDNA-based health assessments in national biomonitoring efforts.

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“…Molecular markers have proven to be an efficient method for identifying plants and typically show enough variation to allow different species to be distinguished (Hebert et al, 2003). The principal benefit of applying a method based on DNA is that samples can be identified without the need for expertise in taxonomy, while the tissue samples used can be very small and may be obtained from any part of the organism in question.…”

Section: Introductionmentioning

confidence: 99%

Research Article A modified non-liquid nitrogen protocol for extraction of high-quality genomic DNA from the inner bark tissues of <i>Dalbergia</i> <i>cochinchinensis</i> (Fabaceae)

Mo¹,

Wangsomnuk²

2021

Genet. Mol. Res.

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Dalbergia cochinchinensis (Fabaceae) is known as Thai rosewood. It is a Thai native and widespread throughout Thailand. Due to it being a hardwood tree, it became a valuable hardwood tree species for its commercial value for luxury furniture and as a first-class prime timber, which has made it a potentially endangered species. For genetic studies of this tree, we tested four protocols of genomic DNA extraction from the inner bark based on the sodium dodecyl sulfate method and two protocols of the cetyltrimethyl ammonium bromide method. We evaluated the quantity, purity, and integrity of the extracted genomic DNA from 15 genotypes of D. cochinchinensis using PCR amplification and restriction enzyme digestion to develop a protocol for this species. We found that optimal concentrations of lithium chloride and polyvinylpyrrolidone could improve the quantity and quality of DNA in the extraction buffer without using liquid nitrogen. The highest concentration of high-quality DNA was obtained with protocol M5 (392 ng/µL DNA and a purity ratio of A 260 /A 280 equal to 1.96). In contrast, the commercial Nucleospin Plant II Mini Kit provided the lowest yield of 13.94 ng/µL DNA, with a low purity ratio of A 260 /A 280 (1.58). Start codon targeted and sequence-related amplified polymorphism fingerprints further demonstrated that protocol M5 developed for inner ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (2): gmr18836 X.C. Mo et al. 2 bark tissue samples gives good DNA quality and quantity for genetic studies of D. cochinchinensis.

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Biological Identifications Through DNA Barcodes

Cited by 4 publications

References 23 publications

Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Mitochondrial divergence suggests unexpected high species diversity in the opsariichthine fishes (Teleostei: Cyprinidae) and the revalidation of Opsariichthys macrolepis

Environmental DNA in a Biofilm Can Be Used to Assess Diatom Ecological Health in Stream Water Ecology

Research Article A modified non-liquid nitrogen protocol for extraction of high-quality genomic DNA from the inner bark tissues of <i>Dalbergia</i> <i>cochinchinensis</i> (Fabaceae)

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