Dendropsophus minutus (Anura: Hylidae) of the Guiana Shield:  using DNA barcodes to assess identity and diversity

Zootaxa ◽  
2007 ◽  
Vol 1540 (1) ◽  
pp. 61-67 ◽  
Author(s):  
MONTY A. HAWKINS ◽  
JACK W. SITES ◽  
BRICE P. NOONAN
Keyword(s):  
Genetic Variation ◽  
Dna Barcode ◽  
Guiana Shield ◽  
Dna Barcodes ◽  
Present Evidence ◽  
Geographic Structure ◽  
Preliminary Examination ◽  
The Status ◽  
Current Sampling ◽  
The Guianas

Herein we discuss the geographic structure of genetic variation of the widely distributed lesser treefrog (Dendropsophus minutus) from the Guianas in a preliminary examination of the status of Guianan populations referred to this taxon. Current sampling is insufficient to determine the status of all lineages of this complex within South America, but our results do indicate the presence of cryptic species within this relatively small portion of the ‘species’ range. Our findings reveal a geographic discontinuity of genetic structure within this region that appears to be correlated with elevation. We also present evidence that supports previous assertions that the conventional DNA barcode locus (COI) is not suitable for amphibians.

scholarly journals DNA barcode identification of commercial fish sold in Mexican markets

Genome ◽  
2018 ◽  
Vol 61 (6) ◽  
pp. 457-466 ◽  
Author(s):  
Stephanie Sarmiento-Camacho ◽  
Martha Valdez-Moreno
Keyword(s):  
Conservation Status ◽  
Dna Barcode ◽  
Common Species ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Commercial Fish ◽  
Sphyrna Lewini ◽  
Pangasianodon Hypophthalmus ◽  
Makaira Nigricans ◽  
The Status

The substitution of high-value fish species for those of lower value is common practice. Although numerous studies have addressed this issue, few have been conducted in Mexico. In this study, we sought to identify fresh fillets of fish, sharks, and rays using DNA barcodes. We analyzed material from “La Viga” in Mexico City, and other markets located on the Gulf and Caribbean coasts of Mexico. From 134 samples, we obtained sequences from 129, identified to 9 orders, 28 families, 38 genera, and 44 species. The most common species were Seriola dumerili, Pangasianodon hypophthalmus, Carcharhinus falciformis, Carcharhinus brevipinna, and Hypanus americanus. Pangasianodon hypophthalmus was most commonly used as a substitute for higher-value species. The substitution rate was 18% of the total. A review of the conservation status of the specimens identified against the IUNC list enabled us to establish that some species marketed in Mexico are threatened: Makaira nigricans, Lachnolaimus maximus, Hyporthodus flavolimbatus, and Isurus oxyrinchus are classified as vulnerable; Lopholatilus chamaeleonticeps and Sphyrna lewini are endangered; and the status of Hyporthodus nigritus is critical. These results will demonstrate to the Mexican authorities that DNA barcoding is a reliable tool for species identification, even when morphological identification is difficult or impossible.

Identity of some recently described Lepidoptera from France—re-assessed with DNA barcodes and morphology

Zootaxa ◽  
2021 ◽  
Vol 4941 (3) ◽  
pp. 301-337
Author(s):  
PETER HUEMER ◽  
ERIK J. VAN NIEUKERKEN
Keyword(s):  
Related Species ◽  
Dna Barcode ◽  
Molecular Data ◽  
Integrative Analysis ◽  
Type Material ◽  
Dna Barcodes ◽  
Closely Related Species ◽  
Diagnostic Characters ◽  
The Status

Seventy-three species of Lepidoptera described from France since 2000, particularly by Jacques Nel and Thierry Varenne, are re-assessed from largely unpublished molecular data. We tried to obtain DNA barcode sequences from 62 holotypes, supplemented by paratypes of eight species and on one case by non-type material, whereas one previously synonymized species was not sequenced. Altogether we obtained 78 DNA barcode sequences for 65 nominal taxa while sequencing failed for six holotypes. An integrative analysis from molecular data and morphology supports the validity of the majority of species but also resulted in the re-assessment of several taxa. The following 13 new synonymies are established: Stigmella cyrneorolandi Nel & Varenne, 2013 syn. nov. of Stigmella rolandi van Nieukerken, 1990; Stigmella thibaulti Varenne & Nel, 2019 syn. nov. of Stigmella nivenburgensis (Preissecker, 1942) (Nepticulidae); Nemapogon peslieri Varenne & Nel, 2017 syn. nov. of Nemapogon inexpectata Varenne & Nel, 2017 (Tineidae); Phyllonorycter acericorsica Varenne & Nel, 2015 syn. nov. of Phyllonorycter ochreojunctella (Klimesch, 1942) (Gracillariidae); Ancylis paraobtusana Varenne, Nel, & Peslier, 2020 syn. nov. of Ancylis comptana (Frölich, 1828) (Tortricidae); Celypha paludicolella Varenne & Nel, 2017 syn. nov. of Celypha doubledayana (Barrett, 1872) (Tortricidae); Cydia oxytropidana Nel & Varenne, 2016 syn. nov. of Cydia oxytropidis (Martini, 1912) (Tortricidae); Sorhagenia orocorsa Varenne & Nel, 2016 syn. nov. of Sorhagenia janiszewskae Riedl, 1962 (Cosmopterigidae); Chionodes cerdanica Peslier, Nel & Varenne, 2020 syn. nov. of Chionodes distinctella (Zeller, 1839) (Gelechiidae); Elachista bidentata Varenne & Nel, 2019 syn. nov. of Elachista orstadii Palm, 1943; Elachista karsticola Varenne & Nel, 2018 syn. nov. of Elachista maculosella Chrétien, 1896 (Elachistidae); Scythris chablaisensis Delmas, 2018 syn. nov. of Scythris laminella ([Denis & Schiffermüller], 1775) (Scythrididae); Epermenia pumila (Buvat & Nel, 2000) syn. nov. of Epermenia profugella (Stainton, 1856) (Epermeniidae). Finally, the status of some taxa still remains unclear due to the lack of DNA barcodes of closely related species and the absence of convincing diagnostic characters in morphology. 

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 637 ◽  
Author(s):  
Mengyue Guo ◽  
Yanqin Xu ◽  
Li Ren ◽  
Shunzhi He ◽  
and Xiaohui Pang
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Identification Accuracy ◽  
Dna Barcodes ◽  
Success Rates ◽  
Data Set ◽  
Herba Epimedii ◽  
Potential Risks ◽  
Medicinal Properties ◽  
Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

scholarly journals Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA

NeoBiota ◽  
2021 ◽  
Vol 70 ◽  
pp. 151-165
Author(s):  
Francesco Zangaro ◽  
Benedetta Saccomanno ◽  
Eftychia Tzafesta ◽  
Fabio Bozzeda ◽  
Valeria Specchia ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Special Focus ◽  
Indigenous Species ◽  
Dna Barcodes ◽  
Identification Of Species ◽  
The Mediterranean ◽  
Taxonomic Groups ◽  
Non Indigenous Species

The biodiversity of the Mediterranean Sea is currently threatened by the introduction of Non-Indigenous Species (NIS). Therefore, monitoring the distribution of NIS is of utmost importance to preserve the ecosystems. A promising approach for the identification of species and the assessment of biodiversity is the use of DNA barcoding, as well as DNA and eDNA metabarcoding. Currently, the main limitation in the use of genomic data for species identification is the incompleteness of the DNA barcode databases. In this research, we assessed the availability of DNA barcodes in the main reference libraries for the most updated inventory of 665 confirmed NIS in the Mediterranean Sea, with a special focus on the cytochrome oxidase I (COI) barcode and primers. The results of this study show that there are no barcodes for 33.18% of the species in question, and that 45.30% of the 382 species with COI barcode, have no primers publicly available. This highlights the importance of directing scientific efforts to fill the barcode gap of specific taxonomic groups in order to help in the effective application of the eDNA technique for investigating the occurrence and the distribution of NIS in the Mediterranean Sea.

scholarly journals DNA barcodes and morphology of P. krempfi, P. mekongensis, and P. elongatus

2016 ◽  
Vol 14 (1) ◽  
pp. 29-37 ◽  
Author(s):  
Dương Thúy Yên ◽  
Nguyễn Kiệt ◽  
Bùi Sơn Nên ◽  
Nguyễn Văn Thường ◽  
Nguyễn Bạch Loan ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Morphological Characteristics ◽  
Mekong Delta ◽  
Genetic Distances ◽  
Dna Barcodes ◽  
Gill Rakers ◽  
Coi Sequences ◽  
Relationship Of ◽  
Metric Traits ◽  
I Gene

Three Pangasius species including P. krempfi, P. elongatus and P. mekongensis, are economically important. They can be mis-identified due to similar external appreance at small sizes. This study aimed to distinguish these species based on their differences in DNA barcode, COI (cytochrome c oxidase subunit I) gene, and morphological characteristics. Fish with various sizes (>90 samples/species) were sampled at the lower Mekong delta region. Kimura-2 parameter genetic distances based on COI sequences of three species (15 samples, in which, 4 unique sequences were assigned Genbank accession numbers from KT289877 to KT289880) are relatively high, ranging 9.33 – 12.10 %. Morphological measurements show that coutanble traits including numbers of fin rays and the first gill rakers vary in similar ranges but ratios of metric traits are significantly different among three species (P<0.01). Principle component analysis using metric traits sets three species apart. P. elongatus is characterized by elongated body, long caudal preduncle, large eyes, and retangle palatine tooth plates. P. krempfi differs from P. mekongesis in characteristics on their head. The number of sections, shape and length of barbel are different among three species. Phylogenetic relationship of three species based on morphology and COI sequences indicate that P. krempfi is closer to P. mekongenis rather than P. elongatus, and that the distance between P. mekongenis and P. elongatus is the largest.

scholarly journals Mekanisme Pembubaran Partai Politik di Indonesia

2020 ◽  
Vol 1 (1) ◽  
pp. 239-242
Author(s):  
Ramot H.P Limbong ◽  
I Gusti Bagus Suryawan ◽  
I Nyoman Sutama
Keyword(s):  
Political Parties ◽  
Criminal Liability ◽  
Primary Source ◽  
Legal Issues ◽  
Constitutional Court ◽  
Legal Research ◽  
Legal Entity ◽  
Preliminary Examination ◽  
The Status ◽  
Legal Arguments

Political parties as legal entities may be subject to criminal liability as they are seen from the characteristic of political parties in accordance with the characteristics of the legal entity. The dissolution of political parties becomes one of the legal issues governed by Indonesian legislation. The problem of this research is: 1) how is the Constitutional Court Authority in the dissolution of political parties in Indonesia? 2) How is the mechanism of dissolution of political parties? The type of research and approach problems used is normative legal research and statutory approaches. The source of the legal material used is the primary source of legal material and the source of secondary legal material. The technique of collecting legal materials is the technique of library study. The collected legal materials are processed and analyzed using legal arguments. The result of this research is the procedure of the dissolution of political parties in the Constitutional Court as follows: Application submission, application registration and trial schedule, preliminary examination, trial examination, meeting Judge, the verdict of the Constitutional Court. The result of the dissolution of political parties may result in external rights and obligations, due to elected positions, due to the status of managers and members and the consequences of internal rights and obligations.

scholarly journals Integrative taxonomy of Nearctic and Palaearctic Aleocharinae: new species, synonymies, and records (Coleoptera, Staphylinidae)

ZooKeys ◽  
2021 ◽  
Vol 1041 ◽  
pp. 27-99
Author(s):  
Adam J. Brunke ◽  
Mikko Pentinsaari ◽  
Jan Klimaszewski
Keyword(s):  
New Species ◽  
North America ◽  
Dna Barcode ◽  
Integrative Taxonomy ◽  
Eastern Canada ◽  
Rove Beetles ◽  
Adventive Species ◽  
The Status ◽  
Taxonomic Studies ◽  
Holarctic Species

A long tradition of separate Nearctic and Palaearctic taxonomic studies of the diverse aleocharine rove beetles (Coleoptera: Staphylinidae) has obscured the recognition of Holarctic species and detection of adventive species in both regions. Recently, integrated study of the two regions through detailed morphological comparisons and development of an authoritatively identified DNA barcode reference library has revealed the degree to which these two aleocharine faunas are interconnected, both naturally and through human activity. Here this approach is adopted to recognize new species, reveal Holarctic species, and recognize adventive species in both North America and Europe. The following new species are described: Isoglossa triangularis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov. from British Columbia; Gnypeta impressicollis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov., from Ontario, Maryland and North Carolina; Aloconota pseudogregaria Klimaszewski, Brunke &amp; Pentinsaari, sp. nov., from Ontario and Virginia; and Philhygra pseudolaevicollis Klimaszewski, Brunke &amp; Pentinsaari, sp. nov. from eastern Canada. Dasygnypeta velata and Philhygra angusticauda are revealed to be Holarctic species, resulting in the following synonymies: Dasygnypeta velata (Erichson, 1839) = Gnypeta minuta Klimaszewski &amp; Webster, 2008, syn. nov. and Philhygra angusticauda (Bernhauer, 1909) = Atheta (Philhygra) pinegensis Muona, 1983, syn. nov. The Nearctic species Hylota ochracea (and genus Hylota), Thecturota tenuissima, and Trichiusa robustula are newly reported from the Palaearctic region as adventive, resulting in the following synonymies: Hylota ochracea Casey, 1906 = Stichoglossa (Dexiogyia) forticornis Strand, 1939, syn. nov.; Thecturota tenuissima Casey, 1893 = Atheta marchii Dodero, 1922, syn. nov.; and Trichiusa robustula Casey, 1893 = T. immigrata Lohse, 1984, syn. nov. The Palaearctic species Amarochara forticornis, Anomognathus cuspidatus, Oligota pumilio, and Parocyusa rubicunda are newly confirmed from the Nearctic region as adventive, resulting in the following synonymies: Parocyusa rubicunda (Erichson, 1837) = Chilopora americana Casey, 1906, syn. nov. and Anomognathus cuspidatus (Erichson, 1839) = Thectura americana Casey, 1893, syn. nov. The genus Dasygnypeta, sensu nov. is newly reported from North America, Paradilacra is newly reported from eastern North America, and Haploglossa is newly reported from Canada, resulting in the following synonymy: Paradilacra densissima (Bernhauer, 1909) = Gnypeta saccharina Klimaszewski &amp; Webster, 2008, syn. nov. Native Cyphea wallisi is newly reported from across Canada and C. curtula is removed from the Nearctic fauna. The status of both Gyrophaena affinis and Homalota plana is uncertain but these species are no longer considered to be adventive in North America. Three new combinations are proposed: Dasygnypeta baranowskii (Klimaszewski, 2020) and D. nigrella (LeConte, 1863) (both from Gnypeta) and Mocyta scopula (Casey, 1893) (from Acrotona). Dolosota Casey, 1910, syn. nov. (type species Eurypronota scopula Casey), currently a subgenus of Acrotona, is therefore synonymized with Mocyta Mulsant &amp; Rey, 1874. Additionally, four new Canadian records and 18 new provincial and state records are reported.

scholarly journals A new species of Litarachna Walter, 1925 (Acari: Hydrachnidia: Pontarachnidae) from Corozal Bay (Belize), described based upon morphology and DNA barcodes

Acarologia ◽  
2021 ◽  
Vol 61 (3) ◽  
pp. 602-613
Author(s):  
Lucia Montes-Ortiz ◽  
Tom Goldschmidt ◽  
Lourdes Vásquez-Yeomans ◽  
Manuel Elías-Gutiérrez
Keyword(s):  
Dna Barcode ◽  
Morphological Description ◽  
Estuarine System ◽  
Dna Barcodes ◽  
Sem Images ◽  
The Family ◽  
Coi Sequences ◽  
First Time ◽  
A New Species ◽  
Electronic Microscope

A new planktonic species of the marine water mites of the family Pontarachnidae Koenike, 1910 is described from Corozal Bay, an estuarine system in Belize. The morphological description includes Scanning Electronic Microscope (SEM) images and is augmented by an analysis of DNA cytochrome c oxidase I (COI) sequences, the DNA barcode, used for the first time for a species description in this group.

Sign in / Sign up

Export Citation Format

Share Document