scholarly journals Validity of Pampus liuorum Liu & Li, 2013, Revealed by the DNA Barcoding of Pampus Fishes (Perciformes, Stromateidae)

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 618
Author(s):  
Jiehong Wei ◽  
Renxie Wu ◽  
Yongshuang Xiao ◽  
Haoran Zhang ◽  
Laith A. Jawad ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Valid Species ◽  
Dna Barcodes ◽  
Operational Taxonomic Units ◽  
Barcoding Gap ◽  
Coi Barcoding ◽  
Commercially Important ◽  
Coi Sequences ◽  
Morphological Species ◽  
Fishery Species

The genus Pampus contains seven valid species, which are commercially important fishery species in the Indo-Pacific area. Due to their highly similar external morphologies, Pampus liuorum has been proposed as a synonym of Pampus cinereus. In this study, partial sequences of COI (582 bp) and Cytb (1077 bp) were presented as potential DNA barcodes of six valid Pampus species and the controversial species P. liuorum. A species delimitation of the seven Pampus species was performed to verify their validities. Explicit COI barcoding gaps were found in all assessed species, except for P. liuorum and P. cinereus, which resulted from their smaller interspecific K2P distance (0.0034–0.0069). A Cytb barcoding gap (0.0200) of the two species was revealed, with a K2P distance ranging from 0.0237 to 0.0277. The longer Cytb fragment is thus a more suitable DNA barcode for the genus Pampus. In the genetic tree, using concatenated Cytb and COI sequences, the seven species reciprocally formed well-supported clades. Species delimitations with ABGD, GMYC, and bPTP models identified seven operational taxonomic units, which were congruent with the seven morphological species. Therefore, all of the seven analyzed species, including P. liuorum, should be kept as valid species.

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 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.

scholarly journals DNA barcodes identify medically important tick species in Canada

Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcode ◽  
Nearest Neighbour ◽  
Cryptic Diversity ◽  
Dna Barcodes ◽  
Genetic Cluster ◽  
Potential Health ◽  
Intraspecific Divergence ◽  
Coi Sequences ◽  
I Gene ◽  
Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

Revalidation and redescription of Serranus knysnaensis Gilchrist, 1904, (Perciformes: Serranidae) with a new distribution record

Zootaxa ◽  
2021 ◽  
Vol 5057 (1) ◽  
pp. 99-113
Author(s):  
YONELA SITHOLE ◽  
ELAINE HEEMSTRA ◽  
MONICA MWALE
Keyword(s):  
Dna Barcode ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Genetic Distances ◽  
Valid Species ◽  
Eastern Atlantic Ocean ◽  
Coi Sequences ◽  
Morphological And Molecular Data ◽  
Gill Raker ◽  
Distribution Record

A southwestern Indian Ocean (SWIO) percoid fish Serranus knysnaensis Gilchrist, 1904, was long synonymised with the comber, Serranus cabrilla (Linnaeus, 1758), from the eastern Atlantic Ocean, Mediterranean and Black Sea. However, when the species was brought out of synonymy by Heemstra & Heemstra (2004), reasons for this decision were not given. This study aims to revalidate the present taxonomic status of S. knysnaensis using morphological and molecular assessments. The two species are distinguished by the number of circumpeduncular scales (26–34 in S. knysnaensis versus 34–38 in S. cabrilla) and total gill rakers (18–22 versus 22–24). Serranus knysnaensis is also distinct from S. novemcinctus Kner, 1864, the other SWIO species of Serranus, based on total gill raker counts (18–22 versus 31–35). Genetic analysis of mitochondrial DNA barcode (COI) sequences for 17 Serranus species revealed three closely-related monophyletic clusters corresponding to S. cabrilla, S. novemcinctus and S. knysnaensis that were supported (P <0.001) by species delimitation methods. Even though the genetic distances among the three species were the lowest in the genus (1.60−1.99%), these species may be ecomorphs or lineages that have only recently diverged from each other. These three species also have allopatric distributions and our morphological and molecular data thus confirm that S. knysnaensis is a valid species.  

scholarly journals Splitting the leafmining shield-bearer moth genus Antispila Hübner (Lepidoptera, Heliozelidae): North American species with reduced venation placed in Aspilanta new genus, with a review of heliozelid morphology

ZooKeys ◽  
2020 ◽  
Vol 957 ◽  
pp. 105-161
Author(s):  
Erik J. van Nieukerken ◽  
Charles S. Eiseman
Keyword(s):  
Central America ◽  
New Genus ◽  
Dna Barcode ◽  
Single Species ◽  
Dna Barcodes ◽  
Host Family ◽  
Main Host ◽  
Candidate Species ◽  
Coi Sequences ◽  
Rich Fauna

The new genus Aspilantagen. n. is described to harbour Nearctic heliozelid moths with reduced venation, previously placed in Antispila Hübner, 1825, with type species Antispila oinophylla van Nieukerken &amp; Wagner, 2012. The erection of this genus has become possible now that monophyly has been supported by a recent phylotranscriptomics analysis. Six species are combined in this genus: Aspilanta oinophylla (van Nieukerken &amp; Wagner, 2012), comb. n., A. hydrangaeella (Chambers, 1874), comb. n., A. ampelopsifoliella (Chambers, 1874), comb. n., A. voraginella (Braun, 1927), comb. n., A. argentifera (Braun, 1927), comb. n., A. viticordifoliella (Clemens, 1860), comb. n. and two candidate species are recognised. DNA barcode COI sequences of Malaise trapped specimens suggest a rich fauna of Aspilanta in Central America. All are leafminers, with Vitaceae as main host family, and single species feeding respectively on Hydrangeaceae and Myricaceae. The species are briefly diagnosed, and data on biology, DNA barcodes and distribution are provided. To place the genus in context, a review of heliozelid morphology and phylogeny is presented and a key to Nearctic genera is given. The genus is confined to North and Central America, possibly also occurring in South America. Aspilanta oinophylla is also an invasive species on grapevine in Italy. The genus is sister to Coptodisca Walsingham, 1895. Another species is removed from Antispila: Heliozela eugeniella (Busck, 1900), comb. n., feeding on Eugenia (Myrtaceae), from Florida.

scholarly journals Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy

2020 ◽  
Vol 8 ◽  
Author(s):  
Dagoberto Venera-Pontón ◽  
Amy Driskell ◽  
Sammy De Grave ◽  
Darryl Felder ◽  
Justin Scioli ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Dna Sequences ◽  
Marine Invertebrates ◽  
Graduate Training ◽  
Dna Barcode ◽  
Reference Database ◽  
Diagnostic Features ◽  
Operational Taxonomic Units ◽  
As Species ◽  
Coi Sequences

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

scholarly journals DNA barcodes of birds from northern Colombia

2021 ◽  
Vol 9 ◽  
Author(s):  
Paulo Pulgarín-R ◽  
Martha Olivera-Angel ◽  
Luisa Ortíz ◽  
Duván Nanclares ◽  
Sara Velásquez-Restrepo ◽  
...  
Keyword(s):  
South America ◽  
Tropical Forest ◽  
Dna Barcode ◽  
Bird Species ◽  
Taxonomic Identification ◽  
Dna Barcodes ◽  
Laboratory Methods ◽  
Blood Samples ◽  
Lowland Tropical Forest ◽  
Coi Sequences

DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 26 COI sequences from 18 species, 10 families and three orders and found that barcodes largely matched (but not always) phenotypic identification (&gt; 90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.

LSU rDNA D5 region: the DNA barcode for molecular classification and identification of Demodex

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 295-304 ◽  
Author(s):  
Li Hu ◽  
Yae Zhao ◽  
Yuanjun Yang ◽  
Dongling Niu ◽  
Rui Yang
Keyword(s):  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Its Region ◽  
Molecular Classification ◽  
Ribosomal Genes ◽  
Lsu Rdna ◽  
Dna Barcodes ◽  
Barcoding Gap ◽  
Demodex Folliculorum

Whether ribosomal genes can be used as DNA barcodes for molecular identification of Demodex (Acariformes: Demodicidae) is unclear. To examine this, Demodex folliculorum, D. brevis, D. canis, and D. caprae were collected for DNA extraction, rDNA fragments amplification, sequencing, and analysis. The V2 and V4 regions of SSU rDNA; D5, D6, and D8 regions of LSU rDNA; and ITS region were obtained from the four morphospecies. BLAST analysis showed that the obtained sequences matched those of Demodex or Aplonobia (Acariformes: Tetranychidae) in Raphignathae. Phylogenetic trees derived from V2, V4, D5, D6, and D8 regions, but not from ITS region, showed that the four species of Demodex clustered independently. Sequence divergence analysis further demonstrated that D5, D6, and D8 regions had obvious barcoding gap between intraspecific and interspecific divergences, with the gap of D5 (16.91%) larger than that of D6 (11.82%) and D8 (4.66%). The V2 and V4 regions did not have a barcoding gap, as the intraspecific and interspecific divergences partially overlapped. For the ITS region, intraspecific and interspecific divergences completely overlapped. These results suggest that the D5, D6, and D8 regions of LSU rDNA, especially D5, are suitable DNA barcodes for Demodex.

Three Oriental species of Pseudoaerumnosa Rudzinski (Diptera, Sciaridae) from China

Zootaxa ◽  
2021 ◽  
Vol 4969 (3) ◽  
pp. 551-562
Author(s):  
ZULUAN CHEN ◽  
XUE YANG ◽  
FRANK MENZEL ◽  
HONG WU ◽  
JUNHAO HUANG
Keyword(s):  
Genetic Distances ◽  
Species Concepts ◽  
Dna Barcodes ◽  
Neighbor Joining ◽  
Coi Sequences ◽  
Morphological Species

Three Oriental species of the genus Pseudoaerumnosa Rudzinski, 2006 from China are described and illustrated: P. regularis sp. n., P. tianmushana sp. n. and P. tkoci Vilkamaa, Halenius & Ševčík, 2019. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of Pseudoaerumnosa species were analyzed and a neighbor-joining tree was constructed, based on 37 sequences of nine species. 

scholarly journals DNA barcodes from northern birds of Colombia

2021 ◽  
Author(s):  
Paulo Pulgarín-R ◽  
Martha Olivera-Angel ◽  
Luisa Ortíz ◽  
Duván Nanclares ◽  
Sara Velásquez-Restrepo ◽  
...  
Keyword(s):  
South America ◽  
Tropical Forest ◽  
Dna Barcode ◽  
Bird Species ◽  
Taxonomic Identification ◽  
Dna Barcodes ◽  
Laboratory Methods ◽  
Blood Samples ◽  
Lowland Tropical Forest ◽  
Coi Sequences

DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood sampled birds in a lowland tropical forest with various degrees of intervention using standard 10 × 12 mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 28 COI sequences from 19 species, 10 families and 3 orders and found that barcodes largely matched (but not always) phenotypic identification (>90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.

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