scholarly journals Application of COI Primers 30F/885R in Rotifers to Regional Species Diversity in (Sub)Tropical China

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 390
Author(s):  
Ya-Nan Zhang ◽  
Shao-Lin Xu ◽  
Qi Huang ◽  
Ping Liu ◽  
Bo-Ping Han
Keyword(s):  
Species Diversity ◽  
Genetic Distance ◽  
Common Species ◽  
Large River ◽  
Coi Gene ◽  
Keratella Cochlearis ◽  
The Common ◽  
The Mean ◽  
Coi Sequences ◽  
Tropical China

Rotifers are the most diverse group in freshwater zooplankton and play an important role in food webs and ecosystems. DNA barcoding has become a useful approach to investigate species diversity at local and regional scales, but its application is still limited by efficient primers for the group. To test a pair of primers 30F/885R recently designed for rotifers, we applied them to investigating regional species diversity in the freshwater of South China. We sequenced the cytochrome c oxidase subunit I (COI) gene of rotifers collected from the investigated 23 reservoirs in a large river basin and obtained 145 COI sequences from 33 species in 14 genera. The mean PCR success rate for all tested species was 50%. The 145 sequenced mtCOI in this study covered 33 of 64 identified morphological taxa, including most of the common species in the basin. The intraspecific genetic distance was calculated with a K2P model for 24 rotifer species occurring in the quantitative samples, in which 15 rotifers, such as Keratella cochlearis and Brachionus calyciflorus, had a genetic distance higher than 5%. The high intraspecific genetic differentiation indicates that cryptic species are probably common in (sub)tropical China.

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. 

Rediscovery and elaborate description of Platycephalus cultellatus Richardson, 1846 collected from the coastal waters of South China Sea

2018 ◽  
Vol 31 ◽  
pp. 32 ◽  
Author(s):  
Zhi Chen ◽  
Na Song ◽  
Jianwei Zou ◽  
Tianxiang Gao
Keyword(s):  
South China Sea ◽  
Genetic Distance ◽  
South China ◽  
Coastal Waters ◽  
Coi Gene ◽  
China Sea ◽  
Dorsal Fin ◽  
Meristic Counts ◽  
The Mean

Platycephalus cultellatus Richardson, 1846 was originally found and named in its type locality, Canton, Guangdong Province, China. However, this species was very rare in the coastal waters of China. Except that Qin et al. simply mentioned the original literature records of this species in 2013, no Chinese taxonomy books or publications have ever recorded or described local P. cultellatus. We collected P. cultellatus individuals from the coastal waters of South China Sea and gave valid identification and detailed descriptions of this species. The diacritically meristic counts were listed as follows: first dorsal fin usually with two small isolated spine anteriorly; second dorsal-fin and anal-fin usually with 13 soft rays; pectoral fin usually with 17–19 soft rays and without very small dark spots; caudal fin with 3–6 horizontal blackish bands, but without yellow marking on the middle when fresh; gill rakers 7–10 and pored lateral line scales 65–76. These conclusive characters were consistent with typical P. cultellatus individuals and could thoroughly separate them from other Platycephalus species. The fragment of cytochrome oxidase subunit I (COI) gene of mitochondrial DNA was also sequenced for the classification of specimens. The mean genetic distance within P. cultellatus was 0.25%, net genetic distance between P. cultellatus and other 14 species of the genus Platycephalus ranged from 11.59 to 25.48%. The phylogenetic analysis supported the validity of P. cultellatus existed in the coastal waters of South China Sea. This study will contribute to species identification within this genus distributed in Chinese seas.

scholarly journals Illuminating species diversity of nudibranch in Indonesian coral reef ecosystem using molecular identification

2021 ◽  
Vol 944 (1) ◽  
pp. 012033
Author(s):  
I G W D Dharmawan ◽  
D G Bengen ◽  
I Setyobudiandi ◽  
B Subhan ◽  
I Verawati ◽  
...  
Keyword(s):  
Species Diversity ◽  
Genetic Distance ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Morphological Characters ◽  
Species Level ◽  
Coi Gene ◽  
Interspecific Genetic Distance ◽  
The Difference ◽  
Source Of Information

Abstract Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to identify nudibranch up to species level, which will be a source of information in knowing the distribution and the 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.

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 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.

Studies on the spatial heterogeneity of shallow water benthos with particular reference to the Chironomidae

1971 ◽  
Vol 49 (7) ◽  
pp. 1013-1019 ◽  
Author(s):  
C. G. Paterson ◽  
C. H. Fernando
Keyword(s):  
Opposite Effect ◽  
Common Species ◽  
Distributional Pattern ◽  
Population Densities ◽  
Benthic Species ◽  
Experimental Examination ◽  
The Common ◽  
The Mean ◽  
Total Fauna ◽  
Behavioral Mechanisms

The examination of numbers of 6-in. Ekman grab samples from areas of 2 m2 or less in a variety of shallow lentic habitats revealed heterogeneity in the spatial distribution of most species of macrobenthos in each habitat. Chironomus abortivus Malloch, Glyptotendipes barbipes (Staeger), Procladius freemani Sublette, and the Oligochaeta were invariably aggregated when their population densities were adequate to determine a distributional pattern. The Chironomidae, considered as a group, also displayed an aggregated distribution in all habitats. Other benthic species had distributional patterns that varied from random to highly aggregated in the different habitats. No evidence was found that any species are normally randomly distributed. Analyses of mean crowding of the common species in each habitat suggest that the species often respond independently to microenvironmental variations. The factors which produce well-defined aggregations of one species may be neutral, or they may have the opposite effect on the distribution of other species. Experimental examination of the possible occurrence of behavioral mechanisms of aggregation in the two chironomids, Chironomus attenuatus Walker and Glyptotendipes barbipes, revealed that they lend to aggregate at low population densities (≈ 1/10 cm2) but are randomly distributed in a uniform environment when present in higher densities. Because of the aggregated nature of most benthic species four 6-in. Ekman grab samples were usually required to obtain a population estimate of the total fauna, total chironomid fauna, and the dominant species within ± 30% of the mean obtained with a larger number of samples.

Comparison of Heffner Criteria and Light Criteria in Differentiating Exudative and Transudative Pleural Effusion

2020 ◽  
Vol 22 (3) ◽  
pp. 141-145
Author(s):  
Krishna Chandra Devkota ◽  
S Hamal ◽  
PP Panta
Keyword(s):  
Pleural Effusion ◽  
Cross Sectional Study ◽  
Pleural Space ◽  
Sectional Study ◽  
Inclusion Criteria ◽  
Cross Sectional ◽  
Medical College ◽  
The Common ◽  
The Mean ◽  
Exudative Pleural Effusion

Pleural effusion is present when there is >15ml of fluid is accumulated in the pleural space. It can be divided into two types; exudative and transudative pleural effusion. Tuberculosis and parapneumonic effusion are the common cause of exudative pleural effusion whereas heart failure accounts for most of the cases of transudative pleural effusion. This study was a hospital based cross sectional study performed at Nepal Medical College during the period of January 2016-December 2016. A total of 50 patients who fulfilled the inclusion criteria were enrolled. Pleural effusion was confirmed by clinical examination and radiology. After confirmation of pleural effusion, pleural fluid was aspirated and was analysed for protein, LDH, cholesterol. The Heffner criteria was compared with Light criteria to classify exudative or transudative pleural effusion. Among 50 patients, 30 were male and 20 were female. The mean age of patient was 45.4±21.85 years. The sensitivity and specificity of using Light criteria to detect the two type of pleural effusion was 100% and 90.9%, whereas using Heffner criteria was 94.87%, 100% respectively(P<0.01). There are variety of causes for development of pleural effusion and no one criteria is definite to differentiate between exudative or transudative effusion. In this study Light criteria was more sensitive whereas Heffner criteria was more specific to classify exudative pleural effusion. Hence a combination of criteria might be useful in case where there is difficulty to identify the cause of pleural effusion.

Of Reformed Versifying

2018 ◽  
Author(s):  
Neil Rhodes
Keyword(s):  
Sixteenth Century ◽  
Faerie Queene ◽  
Classical Literature ◽  
Native Form ◽  
Christian Doctrine ◽  
English Verse ◽  
The Common ◽  
The Mean ◽  
The Faerie Queene ◽  
Stylistic Ideal

This chapter examines how the development of English poetry in the second half of the sixteenth century is characterized by the search for an appropriate style. In this context, ‘reformed versifying’ may be understood as a reconciliation of high and low in which the common is reconfigured as a stylistic ideal of the mean. That development can be traced in debates about prosody where an alternative sense of ‘reformed versifying’ as adapting classical metres to English verse is rejected in favour of native form. At the same time Sidney recuperates poetry by reforming it as an agent of virtue. Reformation and Renaissance finally come together in Spenser, who realizes Erasmus’ aim of harmonizing the values of classical literature with Christian doctrine, and reconciles the foreign and the ‘homewrought’. The Faerie Queene of 1590 represents the triumph of the mean in both style and, through its celebration of marriage, in substance.

scholarly journals Getting information on suspended sediments in a large river from acoustic backscatter

2018 ◽  
Vol 40 ◽  
pp. 04017
Author(s):  
Adrien Vergne ◽  
Céline Berni ◽  
Jérôme Le Coz
Keyword(s):  
Suspended Sediment Concentration ◽  
Spatial Information ◽  
Suspended Sediments ◽  
Sediment Concentration ◽  
Large River ◽  
Acoustic Backscatter ◽  
Qualitative Information ◽  
Sediment Size ◽  
The Common

There has been a growing interest in the last decade in extracting information on Suspended Sediment Concentration (SSC) from acoustic backscatter in rivers. Quantitative techniques are not yet effective, but acoustic backscatter already provides qualitative information on suspended sediments. In particular, in the common case of a bi-modal sediment size distribution, corrected acoustic backscatter can be used to look for sand particles in suspension and provide spatial information on their distribution throughout a river crosssection. This paper presents a case-study where these techniques have been applied.

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