Morphological characters and DNA barcoding of Syngnathus schlegeli in the coastal waters of China
7
Citation
39
Reference
10
Related Paper
Citation Trend
Keywords:
DNA Barcoding
The development of DNA barcoding has been of great benefit for taxonomy. The simplicity,speed and high precision of this technique has made it widely used in species identification. The Hymenoptera is the 3rd most diverse order of insects,and presents a huge and difficult task for taxonomists. DNA barcoding has already been widely used in Hymenopteran taxonomy. The applications of barcoding to species identification, cryptic species recognition and biodiversity are summarized.
DNA Barcoding
Barcode
Molecular taxonomy
Identification
Cite
Citations (0)
Since Linnæus (1735) proposed a now globally adopted classification scheme, taxonomists have benefited greatly from the ‘Linnæan Binomial Enterprise’. Ebach’s (2011) concerns, particularly that taxonomy “is slowly dying off”, were around well before DNA barcoding began. Here we discuss the integrative potential of DNA barcoding with morphology, which contrary to Ebach’s comments, has proved a useful addition to the taxonomists tool-kit; such molecular applications to taxonomy are not new and have been widely used by taxonomists for over 30 years (e.g., Kitchener et al. 1984).
DNA Barcoding
Molecular taxonomy
Cite
Citations (32)
Many issues in DNA barcoding need to be solved before it can reach its goal to become a general database for species identification. While species delimitations are more or less well established in several taxa, there are still many groups where this is not the case. Without the proper taxonomic background/knowledge and corroboration with other kinds of data, the DNA barcoding approach may fail to identify species accurately. The classification and taxonomy of phylum Nemertea (nemerteans, ribbon worms) are traditionally based on morphology, but are not corroborated by an increasing amount of genetic data when it comes to classification either into species or into higher taxa. The taxonomy of the phylum needs to be improved before the full potential of DNA barcoding can be utilized to make sure that valid Linnean names accompany the barcode sequences. We illustrate the problematic situation in the phylum Nemertea by a case study from the genus Cerebratulus.
DNA Barcoding
Barcode
Genetic data
Taxonomic rank
Identification
Cite
Citations (32)
Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica. This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0-2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids. Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors. DNA barcoding - the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species - was added to the taxonomic identification process in 2003. Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps. Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible. No specimen with a full barcode was misidentified when its barcode was compared with the barcode library. Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species. Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to 'variation' or thought to be insignificant for species-level recognition. Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
DNA Barcoding
Barcode
Species complex
Tachinidae
Cite
Citations (343)
DNA barcoding has been widely used in species identification and biodiversity research because it has been shown that in many groups, including insects, interspecific variation in DNA sequences of some genes is much higher than intraspecific and this provided an opportunity to use DNA sequences for species identification. Cytochrome oxidase I (COI) barcoding sequences can be used to discover cryptic, closely related and morphologically similar species. DNA barcoding has gained increased recognition as a molecular tool for species identification in various groups of organisms. A study was, therefore, undertaken to barcode five fly species prevalent in poultry farms in and around Bengaluru districts in Karnataka state. The barcoding of COI gene of Musca domestica, Chrysomya megacephala, Hydrotaea capensis, Hermetia illucens and Sarcophaga ruficornis yielded an amplified fragment of 658 bp sequence. Barcode for all 5 species was generated using Bold_Systems v3 and submitted to GenBank and accession numbers were obtained. In the present study, identification of five different fly species based on morphology was also confirmed by DNA barcoding to prove their correct identity.
DNA Barcoding
Barcode
Chrysomya megacephala
Species complex
Cite
Citations (3)
Abstract DNA barcoding is a system designed to provide species identification by using standardized gene regions as internal species tag. Foreseen since its earlier development as a solution to speed up the pace of species discovery, DNA barcoding has established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics. Initially proposed as a tool for species identification, DNA barcoding has also been applied in taxonomy routines for automated species delineation. Species identification and species delineation, however, should be considered as distinct activities relying on different theoretical and methodological backgrounds. The aim of the present review is to provide an overview of the use of DNA sequences in taxonomy, since the earliest development of molecular taxonomy until the development of DNA barcoding. We further present the differences between procedures of species identification and species delineation and highlight how DNA barcoding proposed a new paradigm that helps promote more sustainable practices in taxonomy.
DNA Barcoding
Identification
Species Identification
Molecular taxonomy
Cite
Citations (151)
DNA barcoding is a technique proposed by Hebert and co-workers in 2003 for discriminating species through analysis of a single gene barcode locus. It aims to obtain a better taxonomic resolution than that achieved through morphological studies, and to avoid the decline in taxonomic knowledge. Today DNA barcoding is a global enterprise, and the implementation of the idea has seen a rapid rise (more than 1900 papers published to date on different organisms). Nonetheless, controversy still arises regarding barcoding and taxonomy. It is important to note that DNA barcoding does not focus on building a tree-of-life or on doing DNA taxonomy, even though sometimes it has been used for these purposes. DNA barcoding rather focuses on producing a universal molecular identification key based on strong taxonomic knowledge that should be included in the barcode reference library. In the phylum Tardigrada, DNA barcoding represents a recent approach to species identification and to help in solving taxonomic problems, especially considering the diminutive size of these animals and the paucity of morphological characters useful for taxonomy. In the framework of the MoDNA Project (Morphology and DNA), carried out by our research group in collaboration with several colleagues, we are combining the study of a fragment of the mitochondrial cytochrome c oxidase subunit I gene (cox1) with morphological data, in a wide sense (cuticular structures, chromosomes, data on sex ratio and reproduction), to form an integrative taxonomy approach for tardigrade species identification. We believe that without verified reference sequences from voucher specimens that have been authenticated by qualified taxonomists, there is no reliable library for newly generated sequences with which to be compared. Methods and protocols for standardized results are focused on obtaining tight correspondence between tardigrade morphology (and egg shell morphology, when useful), possibly both light and scanning electron microscopy images, and molecular sequence. This approach is particularly useful in describing new species, and important when applied on material collected in species type localities. Results using this approach are presented, primarily focusing on a number of species from the so-called Macrobiotus hufelandi group.
DNA Barcoding
Barcode
Tardigrade
Identification
Taxonomic rank
Species Identification
Cite
Citations (18)
[Objectives] To explore the feasibility of DNA barcoding and establishing a local DNA barcoding library for the identification of moths, the COⅠ genes of 82 samples from 10 Noctuidae species in Baoding and Langfang(Hebei Province) were amplified using universal barcoding primers. [Methods] Tree-based, distance-based, threshold-based and character-based methods. [Results] The results show that DNA-based classification was generally consistent with that of traditional methods. However, sample LF110802.008 was misclassified as Maliattha signifera, which differs from the morphological results. Using character-based methods to analyze the 28S gene produced results were consistent with the morphological taxonomy. The effect of sample sizes on the number of diagnostic characters was investigated. Character-based methods are relatively effective, even in the case of small sample sizes. We propose the establishment of a local DNA barcoding library in order to make species identification is more effective. [ConcIusion] DNA barcoding produces good classification results and a local DNA barcoding library would be useful for moth identification.
DNA Barcoding
Barcode
Identification
Species Identification
Cite
Citations (1)
DNA Barcoding
Barcode
Identification
Cite
Citations (3)
哺乳動物には,2種類のゲノム,核DNAとミトコンドリアDNA(mtDNA)が存在している.mtDNAの遺伝様式は,母性遺伝と急調分離に代表されるように,核DNAとは大きく異なる. mtDNAは古くから母性遺伝をすることが信じられてきた.なぜなら,哺乳動物では卵に存在するmtDNAコピー数が精子よりも103-4倍多く,極微量の精子由来mtDNAが次世代へと伝達されることが考えにくかったためである.しかし,当時の技術ではこの極微量の"精子由来のmtDNA"が検出されず,父親由来のmtDNAが子孫へ伝達している可能性が残されていた.その後,高感度なPCR法を用いることで,マウス精子のmtDNAが前核期後期までに消失することが示され,幾つかの特殊な事例を除き,mtDNAは完全に母性遺伝することが,実験的に証明された.形態学的解析からもマウスでは受精時に卵細胞質内に侵入した精子由来ミトコンドリアが2細胞期までにほぼ消失する様子が観察されており,ユビキチン‐プロテアソーム分解系の関与が報告されている. 一方,急調分離とはmtDNAの状態がヘテロプラズミーからホモプラズミーへ速やかに移行する遺伝現象である.mtDNAは体細胞では103-4コピー存在しており,核DNAの約1-10倍も変異を起こしやすい.このことから,ヘテロプラズミーの方がホモプラズミーより起こりやすいことが想定されるが,実際はその逆で一つの細胞に複数のmtDNA分子種が存在することは極めて稀である.このホモプラズミー維持の機構が「ボトルネック効果」であり,これまで「雌性生殖系の細胞中のmtDNA数が極端に減少する」としたモデルが広く受入れられてきた.ところが,実際にmtDNA分子数を我々が測定するとそのコピー数に極端な減少は無く,ホモプラズミーの維持はコピー数減少以外の機構によってmtDNAの分離単位の実効数が小さくなるためと考えられる.
mtDNA control region
Cite
Citations (1)