scholarly journals African freshwater eel species (Anguilla spp.) identification through DNA barcoding

2020 ◽  
Vol 71 (11) ◽  
pp. 1543
Author(s):  
Céline Hanzen ◽  
Martyn C. Lucas ◽  
Gordon O'Brien ◽  
Colleen T. Downs ◽  
Sandi Willows-Munro
Keyword(s):  
Dna Barcoding ◽  
Environmental Dna ◽  
Western Indian Ocean ◽  
Genetic Distances ◽  
Kwazulu Natal ◽  
Coi Barcoding ◽  
Ocean Region ◽  
Coi Sequences ◽  
Freshwater Eels ◽  
Identification Tool

Freshwater eels (Anguilla spp.) have a long and complex catadromous life cycle. This unique feature, coupled with difficulty in separating species based on morphology, makes them complex targets for conservation. In this study we evaluated the utility of DNA barcoding using cytochrome oxidase I (COI) to delimit the four species of African eels found in the western Indian Ocean region. We collected 76 individual fin clips from the four eel species (A. mossambica, n=51; A. marmorata, n=17; A. bengalensis, n=6; A. bicolor, n=2) in the rivers of KwaZulu–Natal, South Africa, in 2016–18. Phylogenetic analysis of the COI sequences recovered all four species as monophyletic. Barcoding gap analyses were performed and there was no found overlap in inter- and intraspecific genetic distances. Consequently, the use of COI barcoding as an identification tool was found to be reliable for identifying African eels to the species level, which suggests that this marker should be included in future environmental DNA or metabarcoding studies.

scholarly journals Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

2021 ◽  
Author(s):  
Lynne Christianson ◽  
Shannon Johnson ◽  
Darrin Schultz ◽  
Steven Haddock
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Environmental Dna ◽  
Mitochondrial Coi ◽  
Rdna Sequences ◽  
Coi Barcoding ◽  
18S Rdna Sequences ◽  
Mitochondrial Sequences ◽  
Coi Sequences ◽  
Morphological Differences

[Definitive version of this article may be found here] The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI ‘barcoding’ primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata. The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar lobates (Lampocteis sp. ‘V’ stratified by depth, and ‘A’ differentiated by color). The newly described primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyze environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

scholarly journals First report of lionfish prey from Western Florida waters as identified by DNA barcoding

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9922 ◽  
Author(s):  
Carlos A. Santamaria ◽  
James Locascio ◽  
Taylor M. Greenan
Keyword(s):  
Dna Barcoding ◽  
Regional Differences ◽  
Prey Species ◽  
Fish Prey ◽  
Crustacean Species ◽  
First Report ◽  
Eastern Gulf Of Mexico ◽  
Coi Barcoding ◽  
Coi Sequences ◽  
Prey Items

DNA barcoding was used to identify prey fragments recovered from the stomachs of lionfish harvested during the 2016 Sarasota Lionfish Derby. A total of 305 prey fragments were recovered from 50 stomachs (mean = 4.6 per stomach), of which 184 (60.3%) fragments could be identified to either species or genus when Cytochrome Oxidase I (COI) sequences were queried against the Barcode of Life Database. We identified 21 fish prey species which represented fourteen families and accounted for 95.7% of genetically identifiable prey items. The remaining prey items identified corresponded to six crustacean species. The four most common prey taxa in lionfish stomachs were Ptereleotris calliura (24.3%), an unidentified Microgobius species (20.4%), Diplectum formosum (14.3%), and Apogon aurolineatus (12.2%). The most frequently observed crustacean species, Metapenaeopsis goodei, was found in only three stomachs (6.1%). We also report eleven taxa as putative novel lionfish prey species, most of which are common in Florida waters. Sixteen prey items were identified as lionfish (P. volitans); however, it was not definitive whether these detections were due to cross contamination or cannibalization. This represents the first report of lionfish diets from Florida waters in the Eastern Gulf of Mexico based on barcoding efforts. Our results are largely congruent with previous COI barcoding based studies of lionfish diets, indicating these predators to be generalists exhibiting preferences for specific prey traits but with regional differences in their diets.

scholarly journals Species Identification of Marine Fishes in China with DNA Barcoding

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Junbin Zhang
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Introgressive Hybridization ◽  
Genetic Distances ◽  
Gene Coi ◽  
Interspecific Comparisons ◽  
Mitochondrial Cytochrome Oxidase ◽  
Two Parameter ◽  
Identification Tool

DNA barcoding is a molecular method that uses a short standardized DNA sequence as a species identification tool. In this study, the standard 652 base-pair region of the mitochondrial cytochrome oxidase subunit I gene (COI) was sequenced in marine fish specimens captured in China. The average genetic distance was 50-fold higher between species than within species, as Kimura two parameter (K2P) genetic distances averaged 15.742% among congeners and only 0.319% for intraspecific individuals. There are no overlaps of pairwise genetic variations between conspecific and interspecific comparisons apart from the generaPampusin which the introgressive hybridization was detected. High efficiency of species identification was demonstrated in the present study by DNA barcoding. Due to the incidence of cryptic species, an assumed threshold is suggested to expedite discovering of new species and biodiversity, especially involving biotas of few studies.

scholarly journals Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

2021 ◽  
Author(s):  
Lynne Christianson ◽  
Shannon Johnson ◽  
Darrin Schultz ◽  
Steven Haddock
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Environmental Dna ◽  
Mitochondrial Coi ◽  
Rdna Sequences ◽  
Coi Barcoding ◽  
18S Rdna Sequences ◽  
Mitochondrial Sequences ◽  
Coi Sequences ◽  
Morphological Differences

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI ‘barcoding’ primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata. The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar lobates (Lampocteis sp. ‘V’ stratified by depth, and ‘A’ differentiated by color). The newly described primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyze environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

scholarly journals Upeneus floros, a new goatfish from South Africa and Mozambique, with updated taxonomic accounts for U. guttatus and U. pori and a key to Western Indian Ocean Upeneus species (Mullidae)

Zootaxa ◽  
2020 ◽  
Vol 4834 (4) ◽  
pp. 523-555
Author(s):  
FRANZ UIBLEIN ◽  
GAVIN GOUWS ◽  
MARK LISHER ◽  
BERNARDINO S. MALAUENE
Keyword(s):  
South Africa ◽  
Indian Ocean ◽  
Western Indian Ocean ◽  
Similar Species ◽  
Dorsal Fin ◽  
Kwazulu Natal ◽  
Coi Barcoding ◽  
Group Species ◽  
Fin Spines

The highly diverse goatfish genus Upeneus (Mullidae) requires enhanced attention regarding the possible occurrence of undescribed species in insufficiently explored regions. This study focuses on the South-Western Indian Ocean region (SWIO), and on the so-called japonicus-group, a taxonomic species group of Upeneus. Based on in-situ observations and collections in Sodwana Bay, KwaZulu-Natal, South Africa, the Floros goatfish, U. floros n. sp., is described. Detailed comparative studies of colour patterns and morphological characters of all other 13 japonicus-group species were undertaken as well as COI barcoding. The new species occurs in the coastal area between Angoche, N Mozambique and KwaZulu-Natal and partly overlaps in distribution with two similar species, U. guttatus, widely distributed in the Indo-W Pacific, and U. saiab, assumed to be endemic in a small area off Angoche. Two additional japonicus-group species occurring in the SWIO, U. seychellensis from the Seychelles Bank and U. pori from the Mediterranean Sea (as Lessepsian migrant), Northern Red Sea and Madagascar, were also compared. Because specimens as well as in-situ photographs of U. floros have been erroneously identified as either U. guttatus or U. pori during previous studies, updated taxonomic accounts and diagnoses are provided for these species taking size-related and population differences into account. For U. pori, of which a single preserved specimen from SW Madagascar was known so far, a new record from NE Madagascar is reported based on three specimens and a fresh-colour photo. Upeneus floros can be distinguished from U. guttatus and U. pori by a combination of three characters: head length, first dorsal-fin height and number of gill rakers. Upeneus guttatus can be distinguished from the other two species by disproportionally higher anterior dorsal-fin spines vs. a proportional decrease of dorsal-fin spines in height, barbels mostly yellow vs. white or creamy-white, and slightly fewer pectoral-fin rays. COI barcoding detected a clear distinction between U. guttatus and U. floros and U. pori, respectively, but no significant divergence between the two latter species. COI barcoding also failed to differentiate several other Upeneus species which are clearly distinguished morphologically. Possible interrelationships between species distribution patterns and physical oceanography are discussed. An identification key for the 22 WIO Upeneus species is provided. 

DNA Barcoding of Chinese species of the genus Eurydema Laporte, 1833 (Hemiptera: Pentatomidae)

Zootaxa ◽  
2017 ◽  
Vol 4286 (2) ◽  
pp. 151 ◽  
Author(s):  
WANQING ZHAO ◽  
QING ZHAO ◽  
MIN LI ◽  
JIUFENG WEI ◽  
XIANHONG ZHANG ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Genetic Distances ◽  
Morphological Data ◽  
New Combination ◽  
Coi Gene ◽  
Distinct Cluster ◽  
Variation Patterns ◽  
Nj Tree ◽  
Interspecific Distance ◽  
Coi Sequences

The phenotype, as a significant identification character for the bug species Eurydema Laporte, 1833, possesses many variation patterns, making this species difficult to determine. In this context, DNA barcoding provides an efficient method for species identification. In our study, we used distance-based and tree-based methods to assess the effectiveness of COI gene as an additional taxonomic method. We examined COI sequences of 203 specimens collected in China. Intra- and interspecific genetic distances were calculated, and a phylogenetic tree was constructed using the neighbor-joining (NJ) method. The program TaxonDNA was used to calculate the distribution of distances and investigated the barcode gap. DNA barcodes revealed 100% (ABGD), 99.5% (TaxonDNA) and 97.5% (Barcode Index Numbers) successful identification rates. In the NJ tree, all taxonomic species showed monophyletic clusters that were separated from each other by large genetic distances (> 4.3%). Low divergence (< 0.6%) and non-monophyly clusters that included different phenotype variations were found in E. dominulus and E. oleracea. Compared with other Eurydema species, E. sp. had an average interspecific distance of 7.4% that was congeneric distance, and formed a distinct cluster among Eurydema tree clades. We also confirmed a new combination of Eurydema qinlingensis (Zheng, 1982) comb. nov. based on DNA barcoding and morphology data. Overall, our data showed that, despite the little barcode overlap between intra- and interspecific genetic distances, DNA barcoding is a useful and effective method for enhancing morphological data and resolving taxonomic problems. 

“Research in the Western Indian Ocean Region” Conference’: Preliminary Report and Recommendations

1966 ◽  
Vol 9 (01) ◽  
pp. 33-37
Author(s):  
Aidan Southall
Keyword(s):  
Indian Ocean ◽  
Cultural Anthropology ◽  
Western Indian Ocean ◽  
Social Background ◽  
Columbia University ◽  
Indian Ocean Region ◽  
Research Committee ◽  
Northwestern University ◽  
Ocean Region ◽  
Syracuse University

The conference was sponsored by the African Research Committee and was held at the Minnowbrook Conference Center of Syracuse University from October 30 to November 2, 1965. The disciplines represented were social and cultural anthropology, musicology, sociology, social psychology, political science, and history. Participants included Philip Allen (Department of State); Frederick Burke (Syracuse University); Remi Clignet (Northwestern University); L. Gray Cowan (Columbia University); Norma McCloud (Tulane University); John Middleton (Northwestern University); Allen Rawick (Library of Congress); Aidan Southall, Chairman (Syracuse University); and Peter Wilson (Yale University). The conference concentrated its efforts on seeking and sharing a common understanding of the social background of the diverse ocean and island region that includes Madagascar, the Comoros, Mauritius, Réunion, and the Seychelles and on exploring precisely the extent to which linked interdisciplinary and comparative studies would be fruitful. The conference came to a strong and unanimous conclusion that the Western Indian Ocean Region offers the challenging possiblity of a real breakthrough in a number of dissimilar but closely interlocking research interests. The main recommendations of the conference are as follows: 1. That a rather informal clearinghouse should be established which would institute and maintain contact between social scientists interested in the region and keep them up to date on all relevant plans and work in progress. 2. That a careful and detailed application should be drawn up to obtain funds for carrying out a series of well-balanced and integrated studies, attracting graduate students and training them for further work, securing library resources, and forming appropriate ties with interested scholars and academic institutions overseas.

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.

scholarly journals PM 7/129 (1) DNA barcoding as an identification tool for a number of regulated pests

EPPO Bulletin ◽  
2016 ◽  
Vol 46 (3) ◽  
pp. 501-537 ◽  
Keyword(s):  
Dna Barcoding ◽  
Identification Tool
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