scholarly journals DNA Barcoding approach reveals 17 exploited fish species, including an unrecognised species of the yellow-lined snapper complex

2021 ◽  
Vol 4 ◽  
Author(s):  
ADIBAH ABU BAKAR ◽  
Siti Mohd Nor
Keyword(s):  
Dna Barcoding ◽  
Species Level ◽  
Fisheries Resources ◽  
Taxonomic Description ◽  
Accurate Knowledge ◽  
Colour Patterns ◽  
Catch Composition ◽  
Fisheries Statistics ◽  
Biogeographical Pattern ◽  
Bigeye Snapper

Management of wild fisheries resources requires accurate knowledge on which species are being routinely exploited, but it can be hard to identify fishes to species level, especially in speciose fish groups where colour patterns vary with age. Snappers of the genus Lutjanus represent one such group, where fishes can be hard to identify and as a result fisheries statistics fail to capture species-level taxonomic information. This study employs DNA barcoding approaches to identify adult and juvenile Lutjanus species harvested in Malaysian wild-capture fishery. We uncovered two divergent groups of bigeye snapper ('Lutjanus lutjanus') distributed on either side of the Malay Peninsula, displaying a biogeographical pattern similar to distributions observed for many co-occurring reef distributed fish groups. One of these bigeye snapper groups almost certainly represents an unrecognized species in need of taxonomic description. The study demonstrates the utility of DNA barcoding in identifying overlooked diversity and for assessing species catch composition in a complicated but economically important taxonomic group.

scholarly journals DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9641 ◽  
Author(s):  
Nur Fadli ◽  
Siti Azizah Mohd Nor ◽  
Ahmad Sofiman Othman ◽  
Hizir Sofyan ◽  
Zainal A. Muchlisin
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Reef Fishes ◽  
Morphological Identification ◽  
Species Discovery ◽  
Indonesian Archipelago ◽  
Aceh Province ◽  
Commercially Important ◽  
Catch Composition ◽  
Fisheries Statistics

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

scholarly journals DNA barcoding and phylogenetic relationships in Omphalogramma (Primulaceae) from the Hengduan Mountain region of China

Phytotaxa ◽  
2019 ◽  
Vol 402 (2) ◽  
pp. 97
Author(s):  
YUAN HUANG ◽  
XIONG CHEN ◽  
JIAHUI CHEN ◽  
ZHIMIN LI
Keyword(s):  
Dna Barcoding ◽  
Dna Markers ◽  
Internal Transcribed Spacer ◽  
Mean Value ◽  
Species Level ◽  
Discrimination Power ◽  
Taxonomic Description ◽  
The Mean ◽  
Chloroplast Dna Markers ◽  
Intraspecific Distance

One nuclear and three chloroplast DNA markers (internal transcribed spacer [ITS], rbcL, matK, and trnH-psbA) were evaluated from 39 accessions of Omphalogramma (Primulaceae) from the Hengduan Mountains, representing seven species. The discrimination power of the markers at the species level was 14.3% (rbcL), 28.4% (trnH-psbA), 42.9% (matK), and 100% (ITS). The mean value of genetic distance between species for ITS was more than 3-fold that of intraspecific distance; all species were distinguished. Species were differentiated by unique characters, and phylogenetic analysis showed that the Omphalogramma species formed two clear monophyletic clades comprising O. vincaeflora (bootstrapping: 96.8%) and remaining Omphalogramma species (bootstrapping: 97.5%). This study indicated that DNA barcoding is a useful technique in the phylogenetic and taxonomic description of Omphalogramma species.

scholarly journals Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1298 ◽  
Author(s):  
Feng Zhang ◽  
Daoyuan Yu ◽  
Mark I. Stevens ◽  
Yinhuan Ding
Keyword(s):  
Species Complex ◽  
Instar Larva ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Integrative Approach ◽  
Gene Markers ◽  
Late Neogene ◽  
Taxonomic Approach ◽  
Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

scholarly journals SUMBER DAYA IKAN PERAIRAN UMUM DARATAN DI INDONESIA-TERABAIKAN

2017 ◽  
Vol 1 (1) ◽  
pp. 1 ◽  
Author(s):  
Endi Setiadi Kartamihardja ◽  
Kunto Purnomo ◽  
Chairulwan Umar
Keyword(s):  
Local Government ◽  
Monitoring And Evaluation ◽  
Ecological Function ◽  
Inland Waters ◽  
Flood Plains ◽  
Fisheries Resources ◽  
Natural Lakes ◽  
Function Management ◽  
Fisheries Statistics ◽  
Potential Area

Perairan umum daratan Indonesia mempunyai luas 13,85 juta ha yang terdiri atas 12,0 juta ha sungai dan paparan banjiran (flood plains), 1,8 juta ha danau alam (natural lakes) dan 0,05 juta ha danau buatan (man made lakes) atau waduk (reservoirs). Potensi perikanan tangkap di perairan umum daratan ditaksir mencapai 3.034.934 ton per tahun. Perairan umum daratan berperan penting sebagai sumber protein dan ketahanan pangan, sumber ekonomi masyarakat, sumber lapangan kerja, sumber plasma nutfah dan genetik, sumber devisa dan pendapatan asli daerah, serta obyek wisata alam (ecoturism). Perairan umum daratan yang terabaikan akan berdampak terhadap penurunan potensi luasnya, keanekaragaman jenis ikan, produksi ikan, kesempatan dan peluang kerja (peningkatan pengangguran), pendapatan asli daerah, dan fungsi estetika. Pengelolaan perairan umum dengan benar akan berpengaruh terhadap peningkatan produksi minimal 20% dan fungsi ekologis, sehingga perikanan perairan umum daratan dapat dijadikan tumpuan pembangunan perekonomian masyarakat, khususnya nelayan. Berbagai upaya yang dilakukan untuk membangun perikanan perairan umum daratan antara lain mempromosikan akan penting dan peranan sub sektor perikanan, memberikan perhatian terhadap riset di bidang sumber daya perikanan, melakukan valuasi sumber daya, melaksanakan monitoring dan evaluasi (termasuk perbaikan statistik perikanan), mengembangkan ko manajemen dan kapasitas sumber daya manusia.Inland waters of Indonesia has a total area of 13.85 million ha composing of 12.0 million ha rivers and flood plains, 1.8 million ha natural lakes and 0.05 million ha man made lakes/ reservoirs. Total of fish potential yields of the inland waters was estimated to be 3,034,934 ton per yr. The inland waters plays an important role as source of protein and food security, source of economic and supporting livelihood of the peoples, source of employment, sources of genetics and germ plasm, contributing to foreign exchange and local government earning, and eco-tourism. The neglecting inland waters has affected on the decreasing potential area, fish potential yields, fish species diversity, employment opportunity, and local government earning and the ecological function. Management of the resources could impact on the increasing fish yields at least 20% and its ecological function, so that the inland waters fisheries can be used as a based of economic development of the peoples especially for the fishers. Some efforts which should be done in development of the inland waters fisheries are promotion of the role and importance of fisheries between other sectors, prioritizing research on fisheries resources, valuation of inland waters fisheries, monitoring and evaluation (including fisheries statistics), development of fisheries co-management and capacity building of the human resources.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

scholarly journals Strategies of the small-scale fisheries on the Central Amazon floodplain

2002 ◽  
Vol 32 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Carlos Edwar de Carvalho FREITAS ◽  
Vandick da Silva BATISTA ◽  
Antonio José INHAMUNS
Keyword(s):  
Hydrological Cycle ◽  
Small Scale ◽  
Good Tool ◽  
Central Amazon ◽  
Small Scale Fisheries ◽  
Fisheries Resources ◽  
Patterns Of Use ◽  
Target Fish ◽  
Catch Composition ◽  
High Level

A multivariate approach was applied to data of small-scale fisheries developed in Central Amazon, using information about catch composition, environment, fishing gear and season of the hydrological cycle. The correspondence analysis demonstrated to be a good tool for the analysis related multispecies fisheries. The analysis identified patterns of use of fisheries resources by the riverine communities, showing the correlation between the environmental factors and the fishing strategy for the capture of target fish species, indicating the high level of empiric knowledge about the environment and fisheries.

scholarly journals Species composition and diversity of cast net fisheries in New Calabar River, Niger Delta, Nigeria

2018 ◽  
Vol 4 (1) ◽  
pp. 19-26 ◽  
Author(s):  
HE Dienye ◽  
OA Olopade ◽  
SA Toby
Keyword(s):  
Decapod Crustacean ◽  
Abundant Species ◽  
Diversity Indices ◽  
Fish Stock ◽  
Base Line ◽  
Fisheries Resources ◽  
Fish Samples ◽  
Catch Composition ◽  
Rivers State ◽  
Management And Conservation

A study on the catch composition and diversity of cast net fisheries was conducted between May and August, 2017 in the New Calabar River, Rivers state, using cast net of varying mesh sizes (1.5mm and 2.5mm). Fish samples were collected from three sampling stations, viz. Station1- Aluu, Station 2- Choba and Station 3- Iwofe. The fish species recorded comprised of 26 species under 11 families, and one decapod crustacean. The three most abundant species were; Coptodon guineensis (25.11%), Coptodon zilli (18.56%) both from the Cichlidae family, and Penaeus nitialis (10.90%) from the Penaeidae family, while the least abundant species was Liza grandisquamis (0.13%) from the Mugilidae family. The diversity indices showed that station 2 recorded the highest number of species (21) while station 1 recorded the lowest with (12) species. Simpson’s indexes of diversity, Simpson’s reciprocal index, Shannon- weiner index, and Pielou’s evenness index, were estimated. This study serves as a base line data which will assist relevant bodies in the management and conservation of fisheries resources in the New Calabar River. It is therefore recommended that for an improved and sustainable exploitation and management of fisheries resources of the New Calabar River, proper monitoring and management for fish stock must be done.J. Biodivers. Conserv. Bioresour. Manag. 2018, 4(1): 19-26

scholarly journals Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group

ZooKeys ◽  
2018 ◽  
Vol 751 ◽  
pp. 1-40 ◽  
Author(s):  
Alice Laciny ◽  
Herbert Zettel ◽  
Alexey Kopchinskiy ◽  
Carina Pretzer ◽  
Anna Pal ◽  
...  
Keyword(s):  
Species Complex ◽  
Mandibular Gland ◽  
Species Group ◽  
The Philippines ◽  
Species Level ◽  
Model Species ◽  
Species Identity ◽  
Taxonomic Description ◽  
Biological Studies ◽  
Taxonomic Changes

A taxonomic description of all castes of Colobopsisexplodens Laciny & Zettel, sp. n. from Borneo, Thailand, and Malaysia is provided, which serves as a model species for biological studies on “exploding ants” in Southeast Asia. The new species is a member of the Colobopsiscylindrica (COCY) group and falls into a species complex that has been repeatedly summarized under the name Colobopsissaundersi (Emery, 1889) (formerly Camponotussaundersi). The COCY species group is known under its vernacular name “exploding ants” for a unique behaviour: during territorial combat, workers of some species sacrifice themselves by rupturing their gaster and releasing sticky and irritant contents of their hypertrophied mandibular gland reservoirs to kill or repel rivals. This study includes first illustrations and morphometric characterizations of males of the COCY group: Colobopsisexplodens Laciny & Zettel, sp. n. and Colobopsisbadia (Smith, 1857). Characters of male genitalia and external morphology are compared with other selected taxa of Camponotini. Preliminary notes on the biology of C.explodens Laciny & Zettel, sp. n. are provided. To fix the species identity of the closely related C.badia, a lectotype from Singapore is designated. The following taxonomic changes within the C.saundersi complex are proposed: Colobopsissolenobia (Menozzi, 1926), syn. n. and Colobopsistrieterica (Menozzi, 1926), syn. n. are synonymized with Colobopsiscorallina Roger, 1863, a common endemic species of the Philippines. Colobopsissaginata Stitz, 1925, stat. n., hitherto a subspecies of C.badia, is raised to species level.

scholarly journals The DNA Barcoding of Several Commercial Fish from Simeulue Islands Coast of Aceh Using Cytochrome Oxidase Sub Unit I (COI) Gene Marker

2019 ◽  
Vol 1 (1) ◽  
pp. 62-70
Author(s):  
Edwarsyah Edwarsyah ◽  
Muhammad Nasir ◽  
Muhammad Banda Selamat
Keyword(s):  
Dna Barcoding ◽  
Species Level ◽  
Dna Bases ◽  
Coi Gene ◽  
Gene Marker ◽  
Base Pairs ◽  
Commercial Fish ◽  
Morphological Approach ◽  
Mitochodrial Dna ◽  
The Right

Simeulue is a cluster of islands that rich of commercial fisheries in Aceh waters. Management of the fisheries products is highly related to species identification in order to ascertain the appropriate steps to manage the resources sustainably. Identification using DNA barcoding tools is the right answer for the problem that have not been able to be resolved even by morphological approach. Some of 11 individual samples were taken from 6 sampling points based on lobster’s catchment and cultivation areas. All of the samples were identified using COI mitochodrial DNA resulting 6 species including Scomber scombus, Scomberomorus plurilineatus, Octopus cyanea, Taeniura Lymna, Sympterygia bonapartii and Panulirus versicolor. The DNA bases were aligned using MEGA application and Neigbour- Joining method, Kimura 2 parameters resulting a 690 base pairs nucleotides. Reconstruction of philogenetic tree shows that the species of Simeulue were conjoined into one clade with the sequences downloaded from genebank. It shows that those species were closely related genetically indicating by the bootstrap value of Scomber scombus (100), Scomberomorus plurilineatus (100), Octopus cyanea (100). The results of the study shows that the DNA barcoding tools can explicate not only the identification up to the species level but also the genetic relationship that can be seen from the interspecies bases composition.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

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