DNA barcoding of Austrian snow scorpionflies (Mecoptera, Boreidae) reveals potential cryptic diversity in Boreus westwoodi

Background Snow scorpionflies (genus Boreus) belong to a family of Mecoptera, Boreidae, that has been vastly neglected by entomological researchers due to their shift in seasonality to the winter months. Their activity during this time is regarded as a strategy for predator avoidance and regular sightings on snow fields suggest that this also facilitates dispersal. However, many aspects about snow scorpionflies, especially systematics, taxonomy, distribution of species, phylogenetics and phylogeography have remained fairly unexplored until today. In this study, we fill some of these gaps by generating a reference DNA barcode database for Austrian snow scorpionflies in the frame of the Austrian Barcode of Life initiative and by characterising morphological diversity in the study region. Methods Initial species assignment of all 67 specimens was based on male morphological characters previously reported to differ between Boreus species and, for females, the shape of the ovipositor. DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene was carried out for all 67 samples and served as a basis for BIN assignment, genetic distance calculations, as well as alternative species delimitation analyses (ABGD, GMYC, bGMYC, bPTP) and a statistical parsimony network to infer phylogenetic relationships among individual samples/sampling sites. Results Morphological investigations suggested the presence of both Boreus hyemalis and Boreus westwoodi in Austria. DNA barcoding also separated the two species, but resulted in several divergent clades, the paraphyly of B. westwoodi in Austria, and high levels of phylogeographic structure on a small geographic scale. Even though the different molecular species delimitation methods disagreed on the exact number of species, they unequivocally suggested the presence of more than the traditionally recognized two Boreus species in Austria, thus indicating potential cryptic species within the genus Boreus in general and especially in B. westwoodi.

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Species Delimitation of Scavenger Flies in the Valley of Mexico

Journal of Medical Entomology ◽

10.1093/jme/tjab094 ◽

2021 ◽

Author(s):

Carlos Pedraza-Lara ◽

Marco A Garduño-Sánchez ◽

Isabel Téllez-García ◽

Stephany Rodríguez-González ◽

Eduardo Nuple-Juárez ◽

...

Keyword(s):

Species Richness ◽

Dna Barcoding ◽

Species Delimitation ◽

Nature Reserve ◽

New Records ◽

Dna Barcode ◽

Coi Gene ◽

Baseline Knowledge ◽

Identification Of Species ◽

Diverse Groups

Abstract Identification of species involved in cadaveric decomposition, such as scavenger Diptera, is a fundamental step for the use of entomological evidence in court. Identification based on morphology is widely used in forensic cases; however, taxonomic knowledge of scavenger fauna is poor for many groups and for many countries, particularly Neotropical ones. A number of studies have documented the utility of a DNA barcoding strategy to assist in the identification of poorly known and diverse groups, particularly in cases involving immature states or fragmented organisms. To provide baseline knowledge of the diversity of scavenger Diptera in the Valley of Mexico, we generated a DNA barcode collection comprised of sequences of the cytochrome c oxidase subunit 1 (COI) gene for all families sampled at a nature reserve located in this region. We collected and identified specimens on the basis of morphology and a species delimitation analysis. Our analyses of 339 individuals delineated 42 species distributed across nine families of Diptera. The richest families were Calliphoridae (9 species), Sarcophagidae (7 species), and Phoridae (6 species). We found many of the species previously recorded for the Valley of Mexico, plus 18 new records for the region. Our study highlights the utility of DNA barcoding as a first-step strategy to assess species richness of poorly studied scavenger fly taxa.

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A DNA barcode reference library of the French Polynesian shore fishes

10.1101/595793 ◽

2019 ◽

Author(s):

Erwan Delrieu-Trottin ◽

Jeffrey T. Williams ◽

Diane Pitassy ◽

Amy Driskell ◽

Nicolas Hubert ◽

...

Keyword(s):

Dna Barcoding ◽

Biological Diversity ◽

Dna Barcode ◽

Reef Fishes ◽

French Polynesia ◽

Morphological Characters ◽

Reference Library ◽

Society Islands ◽

Extensive Collection ◽

I Gene

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

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The Utility of DNA Barcoding for the Species Identification of Larval Fish in the Lower Ing River, Thailand

Turkish Journal of Fisheries and Aquatic Sciences ◽

10.4194/1303-2712-v20_9_02 ◽

2020 ◽

Vol 20 (9) ◽

pp. 671-679

Author(s):

Dutrudi Panprommin ◽

Kanyanat Soontornprasit ◽

Siriluck Tuncharoen ◽

Niti Iamchuen

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Larval Fish ◽

Average Length ◽

Conservation Status ◽

Morphological Characters ◽

Nucleotide Sequences ◽

Coi Gene ◽

Fishery Resource ◽

Sustainable Fishery

The species identification of larval fish is very important for sustainable fishery resource management. However, identification based on morphological characters is very difficult, complex and error-prone. DNA barcoding with the sequence of cytochrome c oxidase I (COI) gene was used to identify larval fish species from 10 stations in the tributaries of the lower Ing River. One hundred and six samples were collected between May 2016 and April 2017. The average length of the COI nucleotide sequences was approximately 640 bp. A total of 99 nucleotide sequences were identified in 35 species, 31 genera, 19 families and 9 orders, with 97-100% identity with entries in both the GenBank and BOLD databases. The genetic distance within species ranged from 0.000 to 0.004. However, seven samples were identified at only the genus level because their sequences had not been reported in any databases. Based on IUCN conservation status, most species were classified as least concern (77.14%). Approximately 69.23% of all species were related to human uses in fisheries, aquaculture or aquariums, whereas 30.77% of species were not assessed. Trichopsis vittata (family Osphronemidae) (90%) had the most frequency of occurrence, followed by Oryzias minutillus (family Adrianichthyidae) (70%) and Trichopodus trichopterus (family Osphronemidae) (70%).

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An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽

10.11646/zootaxa.3104.1.3 ◽

2011 ◽

Vol 3104 (1) ◽

pp. 42 ◽

Cited By ~ 15

Author(s):

MICHELE CESARI ◽

ILARIA GIOVANNINI ◽

ROBERTO BERTOLANI ◽

LORENA REBECCHI

Keyword(s):

Dna Barcoding ◽

Dna Barcode ◽

Intraspecific Variability ◽

Original Description ◽

Morphological Characters ◽

Molecular Data ◽

Integrative Taxonomy ◽

Type Locality ◽

Moss Sample ◽

Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

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DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

Bangladesh Journal of Zoology ◽

10.3329/bjz.v47i2.44344 ◽

2019 ◽

Vol 47 (2) ◽

pp. 333-342

Author(s):

Abu Faiz Md Aslam ◽

Sharmin Sultana ◽

Sumita Rani Das ◽

Abdul Jabber Howlader

Keyword(s):

Dna Barcoding ◽

Tribolium Castaneum ◽

Life Stage ◽

Dna Barcode ◽

Tribolium Confusum ◽

Likelihood Method ◽

Coi Gene ◽

Pest Species ◽

Stored Grain ◽

Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

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Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes

Zootaxa ◽

10.11646/zootaxa.4678.1.1 ◽

2019 ◽

Vol 4678 (1) ◽

pp. 1-75

Author(s):

JIA HUANG ◽

LU GONG ◽

SHUN-CHERN TSAUR ◽

LIN ZHU ◽

KEYING AN ◽

...

Keyword(s):

New Species ◽

Cytochrome C Oxidase ◽

Species Delimitation ◽

Species Complex ◽

Dna Barcode ◽

Sensu Stricto ◽

Coi Gene ◽

Mitochondrial Cytochrome ◽

Dna Barcodes ◽

New Synonyms

A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen & Toda, 1997); P. bipartita (Toda & Peng, 1992); P. biprotrusa (Chen & Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda & Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda & Peng, 1990); P. excrescentiosa (Toda & Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang & Gan, 1986); P. foliata (Chen & Toda, 1997); P. gamma (Toda & Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen & Gao, 2005; P. hainanensis (Chen & Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng & Chen, 2008; P. iota (Toda & Sidorenko, 1996); P. jadete Zhu, Cao & Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda & Peng, 1990); P. latifoliacea Chen & Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen & Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca & Lin, 1993); P. pi (Toda & Peng, 1990); P. protrusa (Zhang & Shi, 1997); P. pseudopi (Toda & Peng, 1990); P. pseudotau (Toda & Peng, 1990); P. psi (Zhang & Gan, 1986); P. rhagolobos Chen & Gao, 2008; P. saeta (Zhang & Gan, 1986); P. setitabula Chen & Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda & Peng, 1990); P. uncinata Chen & Gao, 2005; P. unipetala Chen & Wen, 2005; P. allomega Gong & Chen, sp. nov.; P. archikappa Gong & Chen, sp. nov.; P. dianzangensis Gong & Chen, sp. nov.; P. imbacilia Gong & Chen, sp. nov.; P. liukuni Gong & Chen, sp. nov.; P. tibeta Gong & Chen, sp. nov.; and P. xianfui Gong & Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang & Shi, 1997), syn. nov.; P. antillaria (Chen & Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca & Chen, 1993), syn. nov.; P. shillongensis (Singh & Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca & Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species.

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DNA barcoding implicates 23 species and four orders as potential pollinators of Chinese knotweed (Persicaria chinensis) in Peninsular Malaysia

Bulletin of Entomological Research ◽

10.1017/s0007485315000358 ◽

2015 ◽

Vol 105 (4) ◽

pp. 515-520 ◽

Cited By ~ 6

Author(s):

M.-M. Wong ◽

C.-L. Lim ◽

J.-J. Wilson

Keyword(s):

Dna Barcoding ◽

Honey Bees ◽

Invasive Plant ◽

Dna Barcode ◽

Morphological Diversity ◽

Peninsular Malaysia ◽

Economic Importance ◽

Insect Pollinators ◽

Scant Attention ◽

Barcode Gap

AbstractChinese knotweed (Persicaria chinensis) is of ecological and economic importance as a high-risk invasive species and a traditional medicinal herb. However, the insects associated with P. chinensis pollination have received scant attention. As a widespread invasive plant we would expect P. chinensis to be associated with a diverse group of insect pollinators, but lack of taxonomic identification capacity is an impediment to confirm this expectation. In the present study we aimed to elucidate the insect pollinators of P. chinensis in peninsular Malaysia using DNA barcoding. Forty flower visitors, representing the range of morphological diversity observed, were captured at flowers at Ulu Kali, Pahang, Malaysia. Using Automated Barcode Gap Discovery, 17 morphospecies were assigned to 23 species representing at least ten families and four orders. Using the DNA barcode library (BOLD) 30% of the species could be assigned a species name, and 70% could be assigned a genus name. The insects visiting P. chinensis were broadly similar to those previously reported as visiting Persicaria japonica, including honey bees (Apis), droneflies (Eristalis), blowflies (Lucilia) and potter wasps (Eumedes), but also included thrips and ants.

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Illuminating species diversity of nudibranch in Indonesian coral reef ecosystem using molecular identification

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/944/1/012033 ◽

2021 ◽

Vol 944 (1) ◽

pp. 012033

Author(s):

I G W D Dharmawan ◽

D G Bengen ◽

I Setyobudiandi ◽

B Subhan ◽

I Verawati ◽

...

Keyword(s):

Species Diversity ◽

Genetic Distance ◽

Cytochrome Oxidase ◽

Dna Barcoding ◽

Morphological Characters ◽

Species Level ◽

Coi Gene ◽

Interspecific Genetic Distance ◽

The Difference ◽

Source Of Information

Abstract Nudibranch has high species diversity with complex morphological characters and is challenging to identify at the species level. The lack of knowledge about nudibranchs makes it difficult to identify conventionally using morphological characters. This study aims to identify nudibranchs at the species level using the DNA barcoding method from the mitochondrial cytochrome oxidase 1 (CO1) gen. The results of DNA barcoding using the Cytochrome Oxidase I (COI) gene showed 18 species of 51 samples analyzed. The phylogenetic tree reconstruction revealed 11 main clades belonging to 11 genera. The genetic distance between and within species clearly shows the difference between individuals. Interspecific genetic distance shows the lowest value between species was found between Chromodoris annae and Chromodoris magnifica is 0.075, and the largest genetic distance observed between species Glossodoris rufomarginata and Tritonidae sp is 0.354. This study shows molecular analysis can be used to identify nudibranch up to species level, which will be a source of information in knowing the distribution and the genetic distance.

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Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

European Journal of Taxonomy ◽

10.5852/ejt.2020.704 ◽

2020 ◽

Author(s):

Claudia Isabel Navarro-Rodríguez ◽

Alejandro Valdez-Mondragón

Keyword(s):

New Species ◽

Dna Barcoding ◽

Species Delimitation ◽

Sister Group ◽

Morphological Characters ◽

Integrative Taxonomy ◽

Taxonomic Approach ◽

Morphological Differences ◽

Unique Species ◽

A New Species

Based on an integrative taxonomic approach, a new species of the genus Loxosceles Heineken & Lowe, 1832, is described from the state of Hidalgo, Mexico. Loxosceles tolantongo sp. nov. is described based on DNA barcoding using cytochrome c oxidase subunit 1 (CO1) and internal transcribed spacer 2 (ITS2), and morphology. For species delimitation, four molecular methods were implemented: 1) corrected p-distances under neighbor joining (NJ); 2) automatic barcode gap discovery (ABGD); 3) general mixed yule coalescent model (GMYC) and 4) Bayesian Poisson tree processes (bPTP). The new species morphologically resembles L. jaca, another species from Hidalgo, but there are morphological differences mainly in the tibiae of the male palp, the seminal receptacles of the females and also the high genetic p-distances. CO1 was more informative than ITS2 for the genetic separation; however, both concatenated genes (CO1 + ITS2) present robust evidence for species delimitation. Loxosceles tolantongo sp. nov. is considered a unique species for four reasons: 1) it can be diagnosed and distinguished by morphological characters (of the male palps mainly, but also of the seminal receptacles of the females); 2) the genetic p-distances with CO1 were high (>10%); 3) the molecular species delimitation methods were congruent under CO1 and CO1 + ITS2; and 4) under CO1 and CO1 + ITS2, the new species is a putative sister group of L. jaca + L. tenango.

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Utility of molecular-assisted alpha taxonomy of the genus Cystophora (Fucales, Phaeophyceae) from New Zealand and Australia

10.26686/wgtn.12847595.v1 ◽

2020 ◽

Author(s):

J Buchanan ◽

Giuseppe Zuccarello

Keyword(s):

Species Delimitation ◽

Dna Barcode ◽

Morphological Differentiation ◽

Morphological Characters ◽

Morphological Examination ◽

Species Pairs ◽

Algal Genus ◽

Morphological Species ◽

Independent Species ◽

Genetic Species

© 2018 International Phycological Society. Many brown macroalgal species are difficult to identify because of limited morphological differentiation and/ or high levels of plasticity. Molecular methods for distinguishing species coupled with morphological examination have been useful in clarifying species status in many groups. Cystophora is a species-rich, morphologically complex brown algal genus that has been carefully monographed, and it is ideal for testing the utility of molecular markers for genetic species delimitation. We evaluated the utility of the cytochrome oxidase subunit 1 (COI) DNA-barcode marker, alone and in combination with nuclear-encoded internal transcribed spacer (ITS) rDNA, in delimiting species. We also used several methods to delimit putative genetic species. Our results showed that for consistent species delimitation and species delimitation that approximates morphological species, both markers in combination are necessary. Most species in the genus are morphologically recognizable and genetically distinct but neither COI nor combined COI-ITS data separate Cystophora congesta from Cystophora retroflexa or Cystophora distenta from Cystophora scalaris. We showed that morphological characters used to separate these two species pairs are highly variable among samples, with many intermediates. Thus, we concluded that these are not independent species and synonymize these species. Our data showed that this genus, while widespread, mostly conforms to a morphospecies concept.

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