DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

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Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

Zootaxa ◽

10.11646/zootaxa.4286.1.4 ◽

2017 ◽

Vol 4286 (1) ◽

pp. 93 ◽

Cited By ~ 18

Author(s):

OLGA KLISHKO ◽

MANUEL LOPES-LIMA ◽

ELSA FROUFE ◽

ARTHUR BOGAN ◽

LYUDMILA VASILIEV ◽

...

Keyword(s):

Freshwater Mussel ◽

Integrated Approach ◽

Molecular Data ◽

Coi Gene ◽

Data Set ◽

Widespread Species ◽

Molecular Analyses ◽

Morphological Variations ◽

Mtdna Coi ◽

Morphological And Molecular Data

The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio, in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus. Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al. (2004) and Bogatov & Kijashko (2016).

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New free-living nematode species and records (Chromadorea: Plectida and Desmodorida) from the edge and axis of Kermadec Trench, Southwest Pacific Ocean

PeerJ ◽

10.7717/peerj.12037 ◽

2021 ◽

Vol 9 ◽

pp. e12037

Author(s):

Daniel Leduc

Keyword(s):

Nematode Species ◽

Distinct Species ◽

Abundant Species ◽

Molecular Data ◽

Weddell Sea ◽

Body Contour ◽

Southwest Pacific ◽

Free Living Nematode ◽

Strong Resemblance ◽

Morphological And Molecular Data

One new nematode species is described and two new species records are provided from the edge (6,080 m depth) and axis (7,132 m) of Kermadec Trench, Southwest Pacific. Leptolaimus hadalis sp. nov. is characterised by medium body 587–741 μm long, labial region not offset from body contour, inconspicuous labial sensilla, amphid located 12–19 μm from anterior end, female without supplements, male with four tubular precloacal supplements (alveolar supplements absent), tubular supplements almost straight with dentate tip, arcuate spicules and weakly cuticularized dorsal gubernacular apophyses strongly bent distally. In a previously published ecological survey of Kermadec Trench, L. hadalis sp. nov. was the most abundant species in a core obtained at 8,079 m water depth and third most abundant species in a core obtained at 7,132 m, while only one individual was found at 6,096 m depth, and none at 9,175 m depth (Leduc & Rowden, 2018). Alaimella aff. cincta and Desmodora aff. pilosa are recorded for the first time from the Southwest Pacific region. Prior to the present study, Alaimella had only been recorded from coastal locations and from the Weddell sea to a depth of 2,000 m. The record of Desmodora aff. pilosa at 6,080 m depth is the deepest record of a Desmodora species to date, although unidentified Desmodora specimens have been found as deep as 6,300 m in the South Sandwich Trench. The morphology of the Kermadec Trench Alaimella aff. cincta and Desmodora aff. pilosa specimens bear a strong resemblance to their respective type populations from the Northern Hemisphere, but further morphological and molecular data are required to ascertain whether they in fact represent distinct species.

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First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

Acta Biologica Sibirica ◽

10.3897/abs.6.e52836 ◽

2020 ◽

Vol 6 ◽

pp. 1-4

Author(s):

Stanislav K Korb

Keyword(s):

Nucleotide Sequence ◽

Cytochrome C ◽

Dna Barcoding ◽

Cytochrome C Oxidase ◽

Coi Gene ◽

First Results ◽

The Difference ◽

Coi Sequences ◽

Lepidoptera Noctuidae ◽

Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

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A new crenobiontic water mite species of the genus Atractides Koch, 1837 from Montenegro and Bulgaria, based on morphological and molecular data (Acariformes, Hydrachnidia, Hygrobatidae)

Systematic and Applied Acarology ◽

10.11158/saa.25.10.12 ◽

2020 ◽

Vol 25 (10) ◽

pp. 1889-1900

Author(s):

Vladimir Pešić ◽

Andrzej Zawal ◽

Aleksandra Bańkowska ◽

Milica Jovanović ◽

Miroslawa Dabert

Keyword(s):

New Species ◽

Morphological Analysis ◽

Molecular Data ◽

Mite Species ◽

The Novel ◽

Molecular Tools ◽

Mtdna Coi ◽

Coi Sequences ◽

Morphological And Molecular Data ◽

A New Species

A new species of water mites from Montenegro and Bulgaria, Atractides anae Pešić sp. nov., is described, combining traditional morphological techniques with the analysis of partial mtDNA COI sequences (DNA-barcodes). Based on our molecular and morphological analysis, the new species is most closely related to the crenobiontic A. pennatus (K. Viets 1920) from which it differs by 6.4 (SD = 1.12)% K2P distance. A dataset including the novel COI sequences of 10 Atractides species from Montenegro and Iran is assembled in order to facilitate further studies on the genus by using molecular tools.

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Caridina biyiga sp. nov., a new freshwater shrimp (Crustacea: Decapoda: Atyidae) from Leichhardt Springs, Kakadu National Park, Australia, based on morphological and molecular data, with a preliminary illustrated key to Northern Territory Caridina

Zootaxa ◽

10.11646/zootaxa.4695.1.1 ◽

2019 ◽

Vol 4695 (1) ◽

pp. 1-25

Author(s):

JOHN W. SHORT ◽

TIMOTHY J. PAGE ◽

CHRISTOPHER L. HUMPHREY

Keyword(s):

New Species ◽

16S Rdna ◽

National Park ◽

Strong Support ◽

Molecular Data ◽

Genetic Distances ◽

Northern Territory ◽

Coi Gene ◽

Gene Fragment ◽

Morphological And Molecular Data

Caridina biyiga sp. nov. is described from Leichhardt Springs, Kakadu National Park, Northern Territory, Australia, based on morphological and molecular data. The new species is highly distinctive among its congeners in having the dactylus of pereiopod 5 similar to the dactyli of pereiopods 3–4 and lacking the comb-like row of spiniform setae typical of the genus. The branchial formula is also distinctive for the genus in lacking an arthrobranch at the base of pereiopod 1 and in having a vestigial epipod on maxilliped 1. Despite the distinctive morphology of the new species, the molecular data did not provide strong support for the recognition of a new genus. Phylogenetic analyses of Australian Caridina using the mitochondrial 16S rDNA gene fragment placed the new species in a well-supported clade containing at least one typical species of Caridina. Within this clade, referred to as the ‘thermophila’ group, Kimura 2-parameter (K2P) genetic distances of 16S rDNA between the new species and sister taxa ranged from 5.1–6.0%. Analyses using the mitochondrial 3’ COI gene fragment from species of the ‘thermophila’ group yielded K2P genetic distances between the new species and its sister taxa ranging from 10.4–15.1%. A preliminary illustrated key to Northern Territory Caridina is provided. The conservation significance of Leichhardt Springs and its aquatic fauna are also briefly discussed.

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A test of DNA barcoding in crayfish of the upper James River basin, Virginia

Freshwater Crayfish ◽

10.5869/fc.2015.v21-1.179 ◽

2015 ◽

Vol 21 (1) ◽

pp. 179-183

Author(s):

Paul R. Cabe ◽

Bradleigh E. Navalsky ◽

Ainsley K. Bloomer ◽

Ryan Doherty ◽

Jordan Edgren ◽

...

Keyword(s):

Dna Barcoding ◽

River Basin ◽

Native Species ◽

Biological Diversity ◽

Coi Gene ◽

Test Case ◽

Accurate Identification ◽

James River ◽

Coi Sequences ◽

Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

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First Record of Traumatic Myiasis Obtained From Forest Musk Deer (Moschus Berezovskii) Using DNA Barcoding

10.21203/rs.3.rs-106294/v1 ◽

2020 ◽

Author(s):

Yunyun Gao ◽

Yajun Fu ◽

Liping Yan ◽

Defu Hu ◽

Benmo Jiang ◽

...

Keyword(s):

Dna Barcoding ◽

Animal Husbandry ◽

First Record ◽

Coi Gene ◽

Common Disease ◽

Human Society ◽

Musk Deer ◽

Two Samples ◽

Nucleotide Divergence ◽

Coi Sequences

Abstract Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.

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Diversity and distribution of Epeorus (Caucasiron) (Ephemeroptera, Heptageniidae) in Iran, with descriptions of three new species

ZooKeys ◽

10.3897/zookeys.947.51259 ◽

2020 ◽

Vol 947 ◽

pp. 71-102

Author(s):

Ľuboš Hrivniak ◽

Pavel Sroka ◽

Jindřiška Bojková ◽

Roman J. Godunko ◽

Javid Imanpour Namin ◽

...

Keyword(s):

New Species ◽

Habitat Preferences ◽

Molecular Data ◽

Central Iran ◽

Integrative Approach ◽

Northern Iran ◽

Coi Sequences ◽

Morphological And Molecular Data ◽

Three New Species ◽

First Time

Combining morphological and molecular data in an integrative approach, three new mayfly species of Epeorus (Caucasiron) are described. These include Epeorus (Caucasiron) alborzicus Hrivniak & Sroka, sp. nov. and Epeorus (Caucasiron) shargi Hrivniak & Sroka, sp. nov. from northern Iran, and Epeorus (Caucasiron) zagrosicus Hrivniak & Sroka, sp. nov. from central Iran. They are unambiguously delimited using both distance-based and likelihood-based approaches in the analyses of barcode COI sequences. Each new species is compared with other species of the subgenus and morphological diagnostic characters are provided. Based on extensive sampling of streams throughout the country, the distribution and habitat preferences of all Caucasiron species in Iran are assessed. Altogether, there are now six species recorded, among them also E. (C.) nigripilosus Sinitshenkova, 1976 is reported for the first time in Iran. Five species are distributed in the Alborz Mts. in northern Iran, one species was found in the Zagros Mts. in central Iran.

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New insight into the taxonomic resolution of the genus Bythotrephes Leydig (Crustacea: Cladocera) based on molecular data from Central Europe

Scientific Reports ◽

10.1038/s41598-021-02648-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maciej Karpowicz ◽

Magdalena Świsłocka ◽

Joanna Moroz ◽

Łukasz Sługocki

Keyword(s):

Genetic Analysis ◽

Central Europe ◽

Taxonomic Status ◽

Molecular Data ◽

Coi Gene ◽

Taxonomic Resolution ◽

Monotypic Genus ◽

Mtdna Coi ◽

Xix Century ◽

Insight Into

AbstractThe taxonomic status of the genus Bythotrephes Leydig (Crustacea: Cladocera) has been debated since the second half of the XIX century. The most widespread view of recent decades has been that Bythotrephes is a monotypic genus, which was support by preliminary molecular data. However, the recent detailed morphological revision of this genus clearly distinguishes at least seven species. Therefore, we performed a multi-lake survey in Central Europe to give new insight into the taxonomic status of Bythotrephes by combining genetic analysis with traditional morphology-based taxonomy. Based on the morphology we identified two species in Central Europe, B. brevimanus and B. lilljeborgi, as well as hybrid forms. For the genetic analysis, we used newly obtained 113 sequences of mtDNA COI gene of the 535-bp length Bythotrephes from Central Europe and sequences downloaded from GenBank. There were no significant differences between all analyzed sequences, which supports the hypothesis that Bythotrephes is a monotypic genus, with only one highly polymorphic species. On the other hand, the results of our work could point out that the COI gene is insufficient to evaluate the taxonomic status of Bythotrephes. Nonetheless, we have identified 29 new haplotypes of mtDNA COI, and one which was the same as the haplotype found in North America and Finland. Furthermore, this haplotype was the source variant from which most other haplotypes were derived.

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Perlidae (Plecoptera) from the Paranapiacaba Mountains, Atlantic Forest, Brazil: Diversity and implications of the integrative approach and teneral specimens on taxonomy

PLoS ONE ◽

10.1371/journal.pone.0243393 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0243393

Author(s):

Lucas Henrique de Almeida ◽

Pitágoras da Conceição Bispo

Keyword(s):

New Record ◽

Molecular Data ◽

Integrative Taxonomy ◽

Coi Gene ◽

Southeastern Brazil ◽

Integrative Approach ◽

South American ◽

Neighbor Joining ◽

Previous Record ◽

Coi Sequences

The study of complementary sources of biological variation (e.g. morphological, molecular) has allowed a better understanding of biodiversity through the construction of an integrative taxonomy. Using this approach, specimens from the Paranapiacaba Mountains, southeastern Brazil, were studied to update the knowledge on the stonefly family Perlidae from the region, characterize the species, and make associations between nymphs and adults using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The study also discusses the implications of integrative taxonomy and teneral specimens for the study of South American Perlidae. The molecular data were analyzed using Bayesian inference, Neighbor-joining, and delimiting species methods. Our results revealed that, in general, there was a morphological and molecular congruence between species. In the Paranapiacaba Mountains, three genera and 15 species were recorded: Anacroneuria boraceiensis Froehlich 2004, A. debilis (Pictet 1841) (new record), A. fiorentini De Ribeiro and Froehlich 2007 (new record), A. flintorum Froehlich 2002, A. iporanga Bispo and Froehlich 2004, A. itajaimirim Bispo and Froehlich 2004, A. polita (Burmeister 1913), A. subcostalis Klapálek 1921, A. tupi Bispo and Froehlich 2004 (with a description of the nymph), Kempnyia auberti Froehlich 1996, K. colossica (Navás 1934), K. flava Klapálek 1916, K. neotropica (Jacobson and Bianchi 1905) (including its new junior synonym K. petersorum Froehlich 1996), Kempnyia sp., and Macrogynoplax veneranda Froehlich 1984. COI sequences were obtained for 11 species, five of which had nymphs associated with adults. Among the five associated nymphs, the nymph of A. tupi is described here. The results of this study indicate that the color of adult teneral specimens differs from that of mature specimens. Given this, the synonym of K. neotropica and K. petersorum was proposed since these species have high morphological and molecular similarities and differ only in color patterns. In addition, the previous record of A. petersi Froehlich 2002 from the Paranapiacaba Mountains was invalidated since it was considered a teneral specimen of A. flintorum. These results suggest that the development of an integrative taxonomy is essential to continue advancing the study of Perlidae diversity in South America.

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