A case study of the forensic application of DNA Barcoding to sharkfin identification in the Mexican Pacific

AbstractOne of the problems that arose from the meetings of the Barcode in Mexico project was the urgency of having a method in which Mexican authorities could trust for detecting shark finning. This study examined DNA barcoding as a method to identify 14 dried shark fins confiscated by the Mexican Government in two exportation shipments in Mazatlán and Manzanillo ports. Fins were DNA barcoded using the COI mitochondrial gene and provided matching sequences of six species: Prionace glauca, Carcharhinus falciformis, Carcharhinus limbatus, Alopias pelagicus, Mustelus henlei and Rhizoprionodon longurio. There is no information on DNA barcoding sharkfin trade in the Mexican Pacific and this is the first group effort with Mexican Government Agencies for the conservation of sharks.

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A case study for application of DNA barcoding in identifying species and genetic diversity of fish from the Suez city market, Egypt

Aquatic Living Resources ◽

10.1051/alr/2020012 ◽

2020 ◽

Vol 33 ◽

pp. 11

Author(s):

Omir Abdalwahhab ◽

Asmaa Galal-Khallaf ◽

Samy Abd El-Latif Saber ◽

Alaa GM Osman ◽

Khaled Mohammed-Geba

Keyword(s):

Dna Barcoding ◽

Red Sea ◽

Fish Species ◽

Mitochondrial Gene ◽

Fish Market ◽

Standard Procedures ◽

Gene Coi ◽

Northern Red Sea ◽

Fish Species Diversity

The Red Sea is one of the key areas of biodiversity in the world. It is a hotspot for speciation and biological invasions. In the current work, a pilot, random sampling trial was carried out to characterize some species in the landings reaching the fish market in Suez city, which is one of the largest fish markets in the Northern Red Sea. Samples of different fish species were subjected to the standard procedures of DNA barcoding, applying the sequencing of the cytochrome oxidase subunit 1 mitochondrial gene (COI). DNA barcoding could successfully identify all the targeted fishes to the species-level (>98%). The results exhibited a taxonomically-versatile commercial trends in this market, being the collected species belonging to 7 different fish families and 3 orders. These species were Coris aygula, Papilloculiceps longiceps, Priacanthus sagittarious, Gerres longirostris, Alepes djedaba, Psettodes erumei Cheilinus trilobatus, Calotomus viridescens, and Pardachirus marmoratus. Haplotype diversities in the first six species were moderate. However, their nucleotide diversities were low. This may have resulted from fishing from bottlenecked populations, or from areas that do not hinder the genetic flow. Also, possible cryptic speciation could be detected in P. sagittarius, P. erumei and G. longirostris. Applying the DNA barcoding for species identification in Suez city fish market could then detect various aspects of fish species diversity. More works using the applied analyses can be strongly recommended to aid proper conservation and management of economic fisheries in the Red Sea.

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DNA Barcoding of Economically Important Mushrooms: A Case Study on Lethal Amanitas from China

Plant Diversity and Resources ◽

10.3724/sp.j.1143.2012.12140 ◽

2012 ◽

Vol 34 (6) ◽

pp. 614 ◽

Cited By ~ 8

Author(s):

Qing CAI ◽

Li-Ping TANG ◽

Zhu-Liang YANG

Keyword(s):

Dna Barcoding

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Nutrient flux estimates in a tidal basin: A case study of Magdalena lagoon, Mexican Pacific coast

Estuarine Coastal and Shelf Science ◽

10.1016/j.ecss.2018.03.013 ◽

2018 ◽

Vol 207 ◽

pp. 16-29 ◽

Cited By ~ 6

Author(s):

Oleg Zaytsev ◽

Rafael Cervantes-Duarte

Keyword(s):

Pacific Coast ◽

Nutrient Flux ◽

Tidal Basin ◽

Mexican Pacific

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Molecular Identification of Reptiles from Tabuk Region of Saudi Arabia Through DNA Barcoding: A Case Study

DNA Barcoding and Molecular Phylogeny ◽

10.1007/978-3-030-50075-7_16 ◽

2020 ◽

pp. 253-264

Author(s):

Bishal Dhar ◽

Mohua Chakraborty ◽

Madhurima Chakraborty ◽

Sorokhaibam Malvika ◽

N. Neelima Devi ◽

...

Keyword(s):

Saudi Arabia ◽

Dna Barcoding ◽

Molecular Identification

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The first representatives of the millipede family Glomeridellidae (Diplopoda, Glomerida) recorded from China and Indochina

ZooKeys ◽

10.3897/zookeys.954.54694 ◽

2020 ◽

Vol 954 ◽

pp. 1-15

Author(s):

Weixin Liu ◽

Sergei Golovatch

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Dna Barcoding ◽

Southern China ◽

Mitochondrial Gene ◽

Guizhou Province ◽

The Family ◽

Structural Details ◽

Molecular Phylogenetic ◽

A New Species

A new species of glomeridellid millipede is described from Guizhou Province, southern China: Tonkinomeris huzhengkunisp. nov. This new epigean species differs very clearly in many structural details, being sufficiently distinct morphologically and disjunct geographically from T. napoensis Nguyen, Sierwald & Marek, 2019, the type and sole species of Tonkinomeris Nguyen, Sierwald & Marek, 2019, which was described recently from northern Vietnam. The genus Tonkinomeris is formally relegated from Glomeridae and assigned to the family Glomeridellidae, which has hitherto been considered strictly Euro-Mediterranean in distribution and is thus new to the diplopod faunas of China and Indochina. Tonkinomeris is re-diagnosed and shown to have perhaps the basalmost position in the family Glomeridellidae. Its relationships are discussed, both morphological and zoogeographical, within and outside the Glomeridellidae, which can now be considered as relict and basically Oriental in origin. Because of the still highly limited array of DNA-barcoding sequences of the COI mitochondrial gene available in the GenBank, the first molecular phylogenetic analysis of Glomerida attempted here shows our phylogram to be too deficient to consider meaningful.

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Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China

Chinese Journal of Oceanology and Limnology ◽

10.1007/s00343-010-9131-1 ◽

2010 ◽

Vol 28 (4) ◽

pp. 899-910 ◽

Cited By ~ 7

Author(s):

Hong Zhou ◽

Zhinan Zhang ◽

Haiyan Chen ◽

Renhua Sun ◽

Hui Wang ◽

...

Keyword(s):

Dna Barcoding ◽

Ecological Survey

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Morphological description and DNA barcoding of Chaetocladius (Chaetocladius) elisabethae sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Moscow Region

Zootaxa ◽

10.11646/zootaxa.4403.2.9 ◽

2018 ◽

Vol 4403 (2) ◽

pp. 378 ◽

Cited By ~ 1

Author(s):

EUGENYI A. MAKARCHENKO ◽

MARINA A. MAKARCHENKO ◽

ALEXANDER A. SEMENCHENKO ◽

DMITRY M. PALATOV

Keyword(s):

Dna Barcoding ◽

Mitochondrial Gene ◽

Interspecific Variation ◽

Instar Larva ◽

Molecular Data ◽

Genetic Distances ◽

Moscow Region ◽

Morphological Description ◽

Closely Related Species ◽

Male Pupa

Illustrated descriptions of the adult male, pupa and fourth instar larva, as well as DNA barcoding results of Chaetocladius (Chaetocladius) elisabethae sp. nov. in comparison with closely related species of Chaetocladius s. str. from the Moscow Region are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between C. (s. str.) elisabethae sp. nov. and other species of the subgenus produced K2P genetic distances of 0.11–0.16, values well associated with interspecific variation. The barcodes of the new species were identical to the Chaetocladius sp. 2ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str.

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DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae)

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2007.0062 ◽

2007 ◽

Vol 274 (1619) ◽

pp. 1731-1739 ◽

Cited By ~ 180

Author(s):

T.L Whitworth ◽

R.D Dawson ◽

H Magalon ◽

E Baudry

Keyword(s):

New Species ◽

Dna Barcoding ◽

Mitochondrial Gene ◽

Introgressive Hybridization ◽

Species Number ◽

Closely Related Species ◽

Endosymbiotic Bacteria ◽

Limited Success ◽

Mtdna Introgression ◽

Mtdna Haplotype

In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora , known to be infected with the endosymbiotic bacteria Wolbachia . We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia -associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.

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