scholarly journals Molecular Identification of Mudskipper Fish (Periophthalmus spp.) from Baros Beach, Bantul, Yogyakarta

2021 ◽  
Vol 6 (3) ◽  
pp. 66391
Author(s):  
Katon Waskito Aji ◽  
Tuty Arisuryanti
Keyword(s):  
Genetic Distance ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Fish Species ◽  
Mitochondrial Gene ◽  
Universal Primers ◽  
Molecular Approaches ◽  
Morphological Studies ◽  
The Family ◽  
Pcr Method

Mudskipper fish is amphibious fish belonging to the family Gobiidae. Coastal communities widely consume mudskipper to meet their animal protein needs. Mudskipper is primarily cryptic species that are morphologically difficult to identify and distinguish from other mudskipper fish species. Consequently, it can be confused with the naming of mudskipper fish species and can affect the conservation efforts of the fish in their habitat. One of the molecular approaches that can be used to identify the fish species quickly and accurately is DNA barcoding using the COI mitochondrial gene. However, the research on the identification of mudskipper fish in Indonesia is still very limited. Therefore, this study aimed to identify 26 mudskipper fish from Baros Beach, Bantul, Yogyakarta, using COI mitochondrial gene as a molecular marker for DNA barcoding. The method used in this study was a PCR method with universal primers, FishF2 and FishR2. The data obtained were then analyzed using GeneStudio, DNASTAR, BLAST, Identification Engine, Mesquite, MEGAX, and BEAST. The analysis was conducted to obtain similarity, genetic distance and reconstruct a phylogenetic tree. The result revealed that all 26 samples of mudskippers collected from Baros Beach were identified in one genus, namely Periophthalmus, and consisted of 3 species, namely P. kalolo (16 samples), P. argentilineatus (9 samples), and P. novemradiatus (1 sample). Furthermore, this study also discovered a suspected cryptic species in P. argentilineatus with a genetic distance of 5.46-5.96% between clade E, F compared with clade G. Further morphological studies are needed to confirm the species status of these three clades before solidly proclaim that they are cryptic species. 

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

ZooKeys ◽  
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.

scholarly journals The 16S and COI Mitochondrial DNA Nucleotide Composition of Stripped Snakehead (Channa striata Bloch,1793) from Lake Sentani, Jayapura, Papua

2019 ◽  
Vol 20 (2) ◽  
pp. 57
Author(s):  
Christine Bawaeda Sitandung Kombong ◽  
Tuty Arisuryanti
Keyword(s):  
Mitochondrial Dna ◽  
Fish Species ◽  
Nutritional Value ◽  
Genetic Characterization ◽  
Mitochondrial Gene ◽  
Nucleotide Composition ◽  
Omega 3 ◽  
Channa Striata ◽  
Pcr Method

Stripped snakehead (Channa striata Bloch,1793) has potency to be developed in Indonesia due to high nutritional value including omega 3 which is useful for children growth. However, study on composition of mitochondrial DNA nucleotide as a part of study on genetic characterization of stripped snakehead fish in Indonesia is poorlyunderstood. Genetic characterization of stripped snakehead is important to obtain data information that can be applied for breeding and conservation program. Therefore, the objective of this study was to determine the 16S and COI mitochondrial DNA nucleotide of stripped snakehead collected from Lake Sentani, Jayapura, Papua. Method used in this research is PCR method using primer 16Sar and 16Sbr for 16S mitochondrial gene, and FishF2 and FishR2 for COI mitochondrial gene. The results showed that composition of 16S mtDNA nucleotide from 616 bp was T=21.92%, C=25.49%, A=30.19%, dan G=22.40%, whereas composition of A+T=52.11% and G+C=47.89%. In addition, composition of COI mtDNA nucleotide from 705 bp was T=29.93%, C=28.65%, A=24.26%, and G=17.16% while composition of A+T=54.48% and G+C=45.52%. Data of 16S and COI mitochondrial DNA nucleotide composition of the stripped snakehead collected from Lake Sentani gained in this study are to be expected to complete genetic information of the fish species which is useful to improve breeding program of this fish species in the future.

DNA barcoding Australian macroinvertebrates for monitoring programs: benefits and current short comings

2016 ◽  
Vol 67 (3) ◽  
pp. 380 ◽  
Author(s):  
Michael Shackleton ◽  
Gavin N. Rees
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Sequence Data ◽  
Aquatic Environments ◽  
Molecular Approaches ◽  
Monitoring Programs ◽  
Online Databases ◽  
Murray Darling Basin ◽  
Freshwater Fauna ◽  
Australian Freshwater

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.

DNA barcoding reflects the diversity and variety of brooding traits of fish species in the family Syngnathidae along China’s coast

2017 ◽  
Vol 185 ◽  
pp. 137-144 ◽  
Author(s):  
Yan-Hong Zhang ◽  
Geng Qin ◽  
Hui-Xian Zhang ◽  
Xin Wang ◽  
Qiang Lin
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
The Family

DNA barcoding and phylogeny in the family Mactridae (Bivalvia: Heterodonta): Evidence for cryptic species

2012 ◽  
Vol 44 ◽  
pp. 164-172 ◽  
Author(s):  
Lehai Ni ◽  
Qi Li ◽  
Lingfeng Kong ◽  
Shuqing Huang ◽  
Lujing Li
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
The Family

scholarly journals DNA barcoding Australia's fish species

2005 ◽  
Vol 360 (1462) ◽  
pp. 1847-1857 ◽  
Author(s):  
Robert D Ward ◽  
Tyler S Zemlak ◽  
Bronwyn H Innes ◽  
Peter R Last ◽  
Paul D.N Hebert
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
Codon Position ◽  
Phylogenetic Signal ◽  
Gc Content ◽  
Morphological Evidence ◽  
Separate Species ◽  
Operational Taxonomic Units ◽  
The Family ◽  
Taxonomic Groups

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene ( cox1 ). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus , flatheads of the family Platycephalidae, and tunas of the genus Thunnus —were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species.

Contributions to the millipede genus Nepalella Shear, 1979 from China, with four new species and first results on phylogeny based on DNA-barcoding (Diplopoda, Chordeumatida, Megalotylidae)

Zootaxa ◽  
2017 ◽  
Vol 4243 (3) ◽  
pp. 455 ◽  
Author(s):  
WEIXIN LIU ◽  
THOMAS WESENER ◽  
SERGEI GOLOVATCH ◽  
MINGYI TIAN
Keyword(s):  
New Species ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Southern China ◽  
Mitochondrial Gene ◽  
First Results ◽  
First Time

Four new species of the chordeumatidan millipede genus Nepalella Shear, 1979, family Megalotylidae, are described from caves in southern China: N. troglodytes sp. nov., N. lobata sp. nov., N. jinfoshan sp. nov., and N. wangi sp. nov. Three of them (except N. lobata sp. nov.) are presumed troglobites. Additional locality records of two cave congeners, N. caeca Shear, 1999 and N. grandoides Golovatch, Geoffroy & Mauriès, 2006, are also provided. DNA-barcoding based on the COI mitochondrial gene is documented in this genus and for species of the order Chordeumatida outside Europe for the first time. Interspecific p-distances between Nepalella species amount to 8.5–15.9%, while intraspecific p-distances are 0–6.8%. The species of Nepalella are found to show a surprisingly low genetic distance from the European genus Atractosoma Fanzago, 1876, family Craspedosomatidae Gray in Jones, 1843, potentially based on the very limited number of barcoding sequences of the order Chordeumatida being available. 

Discrimination of Cricotopus species (Diptera: Chironomidae) by DNA barcoding

2008 ◽  
Vol 98 (6) ◽  
pp. 555-563 ◽  
Author(s):  
C.S. Sinclair ◽  
S.E. Gresens
Keyword(s):  
Water Quality ◽  
Cytochrome Oxidase ◽  
Dna Barcoding ◽  
Mitochondrial Gene ◽  
Accurate Method ◽  
Taxonomic Resolution ◽  
Molecular Approaches ◽  
Putative Species ◽  
Sequence Variations ◽  
Wide Range

AbstractChironomids (Diptera) typically comprise the most abundant group of macroinvertebrates collected in water quality surveys. Species in the genus Cricotopus display a wide range of tolerance for manmade pollutants, making them excellent bioindicators. Unfortunately, the usefulness of Cricotopus is overshadowed by the difficulty of accurately identifying larvae using current morphological keys. Molecular approaches are now being used for identification and taxonomic resolution in many animal taxa. In this study, a sequence-based approach for the mitochondrial gene, cytochrome oxidase I (COI), was developed to facilitate identification of Cricotopus species collected from Baltimore area streams. Using unique COI sequence variations, we developed profiles for seven described Cricotopus sp., four described Orthocladius sp., one described Paratrichocladius sp. and one putative species of Cricotopus. In addition to providing an accurate method for identification of Cricotopus, this method will make a useful contribution to the development of keys for Nearctic Cricotopus.

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

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.

scholarly journals Molecular phylogeny of cave dwelling Eremogryllodes crickets (Orthoptera, Myrmecophilidae) across Zagros Mountains and Southern Iran

2021 ◽  
Vol 50 (2) ◽  
pp. 213-221
Author(s):  
Mohadeseh Sadat Tahami ◽  
Mina Hojat-Ansari ◽  
Anna Namyatova ◽  
Saber Sadeghi
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Zagros Mountains ◽  
High Similarity ◽  
Molecular Approaches ◽  
Rrna Tree ◽  
The Family ◽  
Geographical Locations

Recently, several new species and subspecies from the genus Eremogryllodes Chopard, 1929 (Insecta: Orthoptera: Myrmecophilidae) inhabiting caves of Iran, have been described based on morphology. The high variation of genitalia structure along with high similarity of external morphology between populations hamper the precise species identification. Thus, molecular approaches are critical to determine the taxonomic positions of species/subspecies of this genus. Here we provide the molecular phylogeny, based on the 16S rRNA mitochondrial gene, of recently described species of Eremogryllodes along with some unidentified specimens from the same region. The results support the monophyly of the family Myrmecophilidae. The topology of the 16S rRNA tree did not completely support the five morpho-species. The three main recovered clades mainly grouped specimens by their geographical locations. Our study suggests the possibility of more than one species in one cave and the presence of cryptic species among cave dwelling crickets, based on the 16S rRNA marker.

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