scholarly journals Initiating DNA barcoding of Eastern Mediterranean deep-sea biota

2018 ◽  
Author(s):  
GUY PAZ ◽  
YANA YUDKOVSKY ◽  
LEE SHAISH ◽  
NIR STERN ◽  
HADAS LUBINEVSKI ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Deep Sea ◽  
Eastern Mediterranean ◽  
Abundant Species ◽  
Coi Gene ◽  
Pcr Products ◽  
The Common ◽  
Coi Sequences ◽  
First Time ◽  
Deep Sea Fauna

Preliminary results of DNA barcoding survey of deep-sea mega-faunal biota are presented, collected by trawl and gillnet off the Israeli coast (SE Mediterranean, depths 700 to 1500 meters) during 2012-2013. 846 organisms were identified to 37 species, mainly fish and decapod crustaceans. The most abundant species were the blackmouth catshark Galeus melastomus, the cosmopolitan decapod Polycheles typhlops and the bivalve Abra longicallus. Two species were sampled for the first time from the southern Levant- the long armed chiroteuthid squid Chiroteuthis veranyi and the common mora, Mora moro. Four of the 18 fish species and two of the 10 crustacean species were abundant, representing 78% and 61%, respectively, of the organisms collected. Most other species are represented by fewer than 10 individuals. PCR products for the cytochrome c oxidase sub unit I (COI) gene for the 37 species were successfully sequenced. The identified and vouchered individuals are stored at the Steinhardt Museum of Natural History (Tel Aviv University, Israel) and their COI sequences were uploaded into the BoLD universal data center as part of the national marine barcoding project. The COI sequences of Acanthephyra eximia, Gryphus vitreus, Galeodea echinophora, Mesothuria intestinalis and Astropecten irregularis, constitute first records of these species in BoLD. When compared to the COI sequences in BoLD, the present results reveal some inconsistency in species identification, an outcome that should be taken into consideration primarily once the taxonomical verifications of collected taxa are elusive. This study is the first step in DNA barcoding of the Levant’s little-known benthic deep-sea fauna.

scholarly journals Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

2021 ◽  
Vol 15 (2) ◽  
pp. 149-157
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Molecular Genetic ◽  
Species Level ◽  
Coi Gene ◽  
High Similarity ◽  
Coi Sequences ◽  
First Time

Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.

scholarly journals Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

2021 ◽  
Vol 15 (2) ◽  
pp. 149-157
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Molecular Genetic ◽  
Species Level ◽  
Coi Gene ◽  
High Similarity ◽  
Coi Sequences ◽  
First Time

Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.

DNA barcoding and taxonomic validation of Caranx spp. larvae

2021 ◽  
pp. 1-9
Author(s):  
Claudia A. Silva-Segundo ◽  
René Funes-Rodríguez ◽  
Jaime Gómez-Gutiérrez ◽  
Griselda Gallegos-Simental ◽  
Sergio Hernández-Trujillo ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Genetic Similarity ◽  
Fish Larvae ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Nominal Species ◽  
Central Pacific ◽  
Diagnostic Characteristics ◽  
Coi Sequences ◽  
First Time

Abstract Of the five nominal species in the genus Caranx Lacepède 1801 distributed throughout the Eastern Central Pacific, Caranx caballus and Caranx sexfasciatus are the only two that have formal fish larval descriptions based on diagnostic characteristics (morphology, meristics and pigmentation). In this study, the diagnostic characteristics of three Caranx species larvae were validated using DNA barcoding analysis cytochrome c oxidase subunit I (COI; 651 bp). For the first time, the morphological taxonomic assignation of C. caballus fish larvae was confirmed using COI gene partial sequences of adults, with a genetic similarity between 99.8–100%. However, molecular evidence demonstrated that fish larvae previously described as C. sexfasciatus had high genetic similarity (99.7–100%) and low genetic distance (<1%) to Caranx caninus adults. An undescribed larval morphotype collected in the present study genetically matched (100%) with COI sequences of C. sexfasciatus adults. The diagnostic characteristics of this new morphotype were a lack of pigmentation in the supraoccipital crest, over the gut, and at the terminal region of the gut. The combination of diagnostic characteristics and DNA barcoding evidence allowed the discrimination and validation of C. caballus, C. caninus and C. sexfasciatus larvae. The diagnostic characteristics and COI sequences of Caranx lugubris and Caranx melampygus larvae, which are also distributed in the Eastern Central Pacific, remain to be investigated.

scholarly journals Zeiform mouthbrooding in the deepsea – dispelling a myth

2020 ◽  
Author(s):  
Ralf ◽  
G. David Johnson ◽  
Kevin Conway
Keyword(s):  
Deep Water ◽  
Deep Sea ◽  
Developmental Stages ◽  
Extended Period ◽  
Marine Fishes ◽  
Early Developmental Stages ◽  
Water Fish ◽  
First Time ◽  
Early Developmental ◽  
Deep Sea Fauna

Mouthbrooding or oral incubation, the retention of early developmental stages inside of the mouth for an extended period of time, has evolved multiple times in bony fishes1,2. Though uncommon, this form of parental care has been documented and well-studied in several groups of freshwater fishes but is also known to occur in a small number of marine fishes, all inhabiting coastal waters1,2. A recent paper3, reported for the first time mouthbrooding in a deep-water fish species, the zeiform Parazen pacificus, which according to the authors “fills in a gap in the larval literature for this family of fishes and prompts further investigation into other novel reproductive modes of deep-sea fauna.”

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

New records and their associated DNA barcodes of the butterfly family Hesperiidae in Tibet, China

Zootaxa ◽  
2019 ◽  
Vol 4674 (4) ◽  
pp. 426-438
Author(s):  
CHENGLONG CAO ◽  
SIYAO HUANG ◽  
YONGQIANG XU ◽  
HAOMIN WU ◽  
TIANPENG CHEN ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Morphological Study ◽  
New Records ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Species Cluster ◽  
The Family ◽  
Interspecific Genetic Distance ◽  
Coi Sequences ◽  
First Time

The specimens of the family Hesperiidae collected from Tibet during 2016–2018 are identified using morphology. COI sequences of 76 individuals are newly obtained. The result of our morphological study is congruent with COI gene analyses. Maximum likehood (ML) and Bayesina inferences (BI) analyses reveal that individuals identified morphologically as the same species cluster cohesively. The minimum interspecific genetic distance is 1.7% between Halpe aucma and H. filda, and the genetic distance between conspecific individuals ranged from 0 to 0.2% for the genus Halpe. A total of 51 species are recognized, and six of them, Celaenorrhinus consanguineus Leech, 1891, Barca bicolor (Oberthür, 1896), Aeromachus propinquus Alphéraky, 1897, Pedesta bivitta (Oberthür, 1886), Baoris penicillata chapmani Evans, 1937, and Ochlodes brahma Moore, 1878, are reported from Tibet for the first time, and the last species is new to China. 

A test of DNA barcoding in crayfish of the upper James River basin, Virginia

2015 ◽  
Vol 21 (1) ◽  
pp. 179-183
Author(s):  
Paul R. Cabe ◽  
Bradleigh E. Navalsky ◽  
Ainsley K. Bloomer ◽  
Ryan Doherty ◽  
Jordan Edgren ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
Coi Gene ◽  
Test Case ◽  
Accurate Identification ◽  
James River ◽  
Coi Sequences ◽  
Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

The First Danish Deep-Sea Expedition on the Ingolf: 1895 and 1896

2008 ◽  
Vol 27 (2) ◽  
pp. 164-187 ◽  
Author(s):  
Torben Wolff
Keyword(s):  
Deep Sea ◽  
The Arctic ◽  
Parasitic Copepods ◽  
Far North ◽  
The North ◽  
Denmark Strait ◽  
Sea Bottom ◽  
The World ◽  
First Time ◽  
Deep Sea Fauna

The Danish Ingolf Expedition took place in the summer months of 1895 and 1896, with C. F. Wandel as captain, a man with long experience in hydrographical work in the Arctic. The other scientific participants were the zoologists H. Jungersen, W. Lundbeck and H. J. Hansen during the 1895 cruise; C. Wesenberg-Lund replaced Hansen during the 1896 cruise. C. H. Ostenfeld was the botanist and M. Knudsen the hydrographer. The Ingolf (see Figure 1) was a naval cruiser. In both years the voyages were hindered by ice that had moved much further south than normal, even closing most of the Denmark Strait. In 1895, the best results were obtained south of Iceland and in the Davis Strait; in 1896 south and east of Iceland and as far north as Jan Mayen Island. A total of 144 stations were completed, all with soundings, trawlings and (for the first time) continuous hydrographical work associated with the deep-sea trawling (bottom measurements of temperature, salinity, chlorine contents and specific gravity). Eighty of the stations were deeper than 1,000 m. There were more than 800 hydrographical measurements, with about 3,300 registrations recordings added on the basis of the measurements. 138 gas analyses were performed on board with samples from the surface and the sea bottom. The main result of the expedition was the final demonstration of probably the most important threshold boundaries in the world: the Wyville Thompson Ridge from East Greenland to Scotland with maximum depths of 600 m, separating the fauna in the Norwegian and Polar Sea to the north, always with negative below-zero temperatures except close to the Norwegian coast, from the fundamentally different general Atlantic deep-sea fauna to the south of the ridge with positive temperatures. The results are published in the Ingolf Report, with fifteen volumes containing forty-three papers by nineteen Danish authors and fourteen papers by six foreign authors. The sieving technique was excellent—due to an apparatus designed by H. J. Hansen that kept the animals under water until preservation and using the finest silk for sieving. In this way, the expedition collected more smaller animals than had been acquired by previous deep-sea expeditions. Hansen's studies of the peracarid crustaceans and parasitic copepods and Lundbeck's report on the sponges were particularly noteworthy. The 130 photographs taken on board and on land by the ship's doctor William Thulstrup represent a cultural/historical treasure.

scholarly journals First Record of Traumatic Myiasis Obtained From Forest Musk Deer (Moschus Berezovskii) Using DNA Barcoding

2020 ◽  
Author(s):  
Yunyun Gao ◽  
Yajun Fu ◽  
Liping Yan ◽  
Defu Hu ◽  
Benmo Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Animal Husbandry ◽  
First Record ◽  
Coi Gene ◽  
Common Disease ◽  
Human Society ◽  
Musk Deer ◽  
Two Samples ◽  
Nucleotide Divergence ◽  
Coi Sequences

Abstract Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.

Discovery of the genus Claraeola Aczél in Iran with the description of two new species (Diptera: Pipunculidae)

Zootaxa ◽  
2017 ◽  
Vol 4227 (4) ◽  
pp. 563 ◽  
Author(s):  
BEHNAM MOTAMEDINIA ◽  
CHRISTIAN KEHLMAIER ◽  
AZIZOLLAH MOKHTARI ◽  
EHSAN RAKHSHANI ◽  
EBRAHIM GILASIAN
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Identification Key ◽  
Coi Gene ◽  
Palaearctic Species ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Two New Species ◽  
Western Palaearctic ◽  
First Time

The genus Claraeola Aczél is recorded from Iran for the first time. Two new species, Claraeola parnianae Motamedinia & Kehlmaier sp. nov. and Claraeola khorshidae Motamedinia & Kehlmaier sp. nov., are described and illustrated. An updated identification key to the Western Palaearctic species of the genus Claraeola is provided. Both species were characterized morphologically and by DNA barcoding of the mitochondrial COI gene. 

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