scholarly journals DNA Barcoding of Mullets (Family Mugilidae) from Pakistan Reveals Surprisingly High Number of Unknown Candidate Species

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 232
Author(s):  
Ariba Hasan ◽  
Pirzada Jamal Ahmed Siddiqui ◽  
Shabir Ali Amir ◽  
Jean-Dominique Durand
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Morphological Examination ◽  
Operational Taxonomic Units ◽  
Phylogenetic Studies ◽  
Management Measures ◽  
Morphological Criteria ◽  
Candidate Species

The mullets are a widespread group of ecologically and economically important fishes of disputed taxonomy due to their uniform external morphology. Barcoding and phylogenetic studies from various locations around the world largely highlighted the species diversity underestimation using morphological criteria used to establish the taxonomy of the family. Here, we investigated the mullet species diversity from Pakistan, a biogeographic area where nearly no mullet species were genetically characterized. Morphological examination of 40 mullets reveals 6 known species (Planiliza macrolepis, P. klunzingeri, P. subviridis, Crenimugil seheli, Ellochelon vaigiensis, and Mugil cephalus). Using a references DNA barcode library, the DNA barcode-based species identification flagged eight molecular operational taxonomic units (MOTUs) belonging to five genera (Crenimugil, Ellochelon, Mugil, Osteomugil, and Planiliza). Among these MOTUs, only one was already present in Barcode of Life Data system, all other representing new Barcode Index Numbers (BIN). These results emphasize the importance of the recognition of cryptic species and the necessity to re-evaluate the overall diversity by the genetic characterization of different species of this family. DNA barcoding is an effective tool to reveal cryptic species that need to be considered in conservation and management measures of fisheries in Pakistan.

DNA barcoding of a complex genus, Aesculus L. (Sapindaceae) reveals lack of species-level resolution

Botany ◽  
2019 ◽  
Vol 97 (9) ◽  
pp. 503-512 ◽  
Author(s):  
Deniz Aygoren Uluer ◽  
Rahma Alshamrani
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Its Region ◽  
Species Level ◽  
Species Discrimination ◽  
Phylogenetic Studies ◽  
Taxonomic Confusion ◽  
Low Levels ◽  
Trees And Shrubs ◽  
Small Genus

Aesculus L. is a small genus of horticulturally important trees and shrubs, comprising 13–19 species. Frequent hybridization among species, particularly in cultivation, has contributed to taxonomic confusion and difficulties in the identification of plants. In this study, we evaluated three widely employed plant DNA barcode loci, matK, and the entire ITS region (ITS1+5.8S+ITS2) as well as subunit ITS2 for 50 individuals representing 13 species of Aesculus, excluding only A. wangii (=A. assamica). In contrast to the plastid matK region, both the ITS and ITS2 loci displayed low levels of species discrimination, especially in our “first hit” BLASTn searches. We also presented the phylogeny of Aesculus based on matK and the entire ITS region, with additional matK and ITS sequences from GenBank. Our results show that Aesculus chinensis, A. flava, A. glabra, A. pavia, and A. sylvatica are probably not monophyletic. Furthermore, with the widest taxon coverage until now, the current study highlights the importance of sampling multiple individuals, not only for DNA barcoding, but also for phylogenetic studies.

A DNA barcode examination of the red algal family Dumontiaceae in Canadian waters reveals substantial cryptic species diversity. 1. The foliose Dilsea–Neodilsea complex and WeeksiaThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 773-789 ◽  
Author(s):  
Gary W. Saunders
Keyword(s):  
Species Diversity ◽  
Dna Barcoding ◽  
Life Histories ◽  
Dna Barcode ◽  
Genetic System ◽  
Marine Macroalgae ◽  
Accurate Identification ◽  
Additional Species ◽  
Large Numbers ◽  
Red Algal

The field of DNA barcoding is working towards generating a genetic system for the quick and accurate identification of eukaryotic species. For the more systematic minded, however, DNA barcoding offers a new approach towards screening and uniting large numbers of biological specimens in genetic groups as a first step towards assigning them to species and genera in an approach best termed “molecular-assisted alpha taxonomy”. This approach is particularly amenable in organisms with simple morphologies, a propensity for convergence, extensive phenotypic plasticity, and life histories with an alternation of heteromorphic generations. It is hard to imagine a group of organisms better defined by all of these traits than the marine macroalgae. In an effort to assess the utility of the DNA barcode (COI-5′) for testing the current concepts of biodiversity of marine macroalgae in Canada, a study to assess species diversity in the red algal family, Dumontiaceae, was initiated. Through this work I confirm the presence in Canadian waters of Dilsea californica (J. Agardh) Kuntze, Dilsea integra (Kjellman) Rosenvinge, and Neodilsea borealis (I.A. Abbott) Lindstrom of the Dilsea–Neodilsea complex, and Weeksia coccinea (Harvey) Lindstrom for the genus Weeksia . However, our work has uncovered two additional species of the former complex, Dilsea lindstromiae Saunders sp. nov. and Dilsea pygmaea (Setchell) Setchell, and an additional species of the latter, Weeksia reticulata Setchell, effectively doubling representation of these foliose dumontiacean genera in Canadian waters.

scholarly journals Defining operational taxonomic units using DNA barcode data

2005 ◽  
Vol 360 (1462) ◽  
pp. 1935-1943 ◽  
Author(s):  
Mark Blaxter ◽  
Jenna Mann ◽  
Tom Chapman ◽  
Fran Thomas ◽  
Claire Whitton ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Population Genetic ◽  
Dna Barcode ◽  
Scientific Programme ◽  
Operational Taxonomic Units ◽  
Significant Challenge ◽  
Complete Catalogue ◽  
Diversity Of Life

Abstract The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene ‘for’ speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to ‘species’, and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.

scholarly journals Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

2021 ◽  
Author(s):  
Chuanjiang Zhou ◽  
Mengxia Feng ◽  
Yongtao Tang ◽  
Changxing Yang ◽  
Xiaolin Meng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Morphological Characteristics ◽  
Henan Province ◽  
Coi Gene ◽  
Morphological Identification ◽  
Freshwater Shrimp

Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

DNA-barcoding of sympatric species of ectoparasitic gastropods of the genusCerithiopsis(Mollusca: Gastropoda: Cerithiopsidae) from Croatia

2012 ◽  
Vol 93 (4) ◽  
pp. 1059-1065 ◽  
Author(s):  
M.V. Modica ◽  
P. Mariottini ◽  
J. Prkić ◽  
M. Oliverio
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Genetic Data ◽  
Distinct Species ◽  
Sympatric Species ◽  
Species Level ◽  
Colour Pattern ◽  
Coi Sequences

The ectoparasitic gastropod genusCerithiopsisForbes & Hanley, 1850 was nominally based onMurex tubercularisMontagu, 1803. We have used the DNA barcode COI sequences to assay sympatric samples of morphotypes recently described as distinct species of theCerithiopsis tubercularis-complex. Our results demonstrated that, in the Croatian waters, the gastropods usually calledC. tubercularisin fact comprise a complex of cryptic species, which can be reliably diagnosed only by examining the soft parts. In the present study we have demonstrated that the colour pattern of the head-foot is diagnostic at the species level in this complex and, coupled with genetic data, may provide a sounding base for a revision of the cerithiopsids of the European coasts.

scholarly journals Hiding in plain sight: DNA barcoding suggests cryptic species in all ‘well-known’ Australian flower beetles (Scarabaeidae: Cetoniinae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9348
Author(s):  
Andrew Mitchell ◽  
Christian H. Moeseneder ◽  
Paul M. Hutchinson
Keyword(s):  
Cryptic Species ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Undescribed Species ◽  
Species Discovery ◽  
Multiple Clusters ◽  
High Diversity

DNA barcode data is presented for Australian cetoniine flower beetles to aid with species discovery and guide revisionary taxonomy. Sequences of the COI gene’s DNA barcode region were acquired from 284 cetoniine specimens, covering 68 described species and 33 genera. This equates to 48% of the known species and 83% of the genera which occur in Australia. Results suggest up to 27 putative undescribed species in our sample, only 11 of which were suspected to be undescribed before this study, leaving 16 unexpected (“cryptic”) species. The Australian cetoniine fauna may hence be increased by up to 19%. An unanticipated result of the work is that each of the five most visible and commonly collected Australian cetoniine species, Eupoecila australasiae (Donovan, 1805), Neorrhina punctatum (Donovan, 1805), Glycyphana (Glycyphaniola) stolata (Fabricius, 1781), Chondropyga dorsalis (Donovan, 1805) and Bisallardiana gymnopleura (Fischer, 1823), have unexpectedly high diversity in DNA barcode sequences and were consequently split into multiple clusters, possibly indicating the presence of cryptic species.

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.

Unexpected species diversity within Japanese Mundochthonius pseudoscorpions (Pseudoscorpiones : Chthoniidae) and the necessity for improved species diagnosis revealed by molecular and morphological examination

2018 ◽  
Vol 32 (2) ◽  
pp. 259 ◽  
Author(s):  
Hajime Ohira ◽  
Shingo Kaneko ◽  
Leanne Faulks ◽  
Tadaaki Tsutsumi
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Molecular Taxonomy ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Morphological Examination ◽  
Species Classification ◽  
Invertebrate Diversity

Using the complementary approaches of morphological and molecular taxonomy is essential to further our understanding of invertebrate diversity, including the identification of cryptic species. Although the species classification of a widespread group of arachnids, the pseudoscorpions, has been based on traditional diagnostic characters for a long time, recent taxonomic studies have suggested that some of these are unreliable for distinguishing species. Thus, the application of molecular taxonomy may be particularly useful in this group. Here, we performed molecular phylogenetic analyses and species delimitation analyses based on partial sequences of mitochondrial DNA cytochrome c oxidase I and nuclear DNA 18S rRNA genes to assess the taxonomy of species and the reliability of morphological characteristics for distinguishing species in the Japanese soil-dwelling genus Mundochthonius (Chthoniidae). Our results revealed the existence of seven major genetic clades, likely corresponding to three described species and four cryptic species. Although two described species, M. kiyoshii and M. itohi, were represented by single clades in the phylogenetic analysis, a third, M. japonicus, was composed of multiple clades, highlighting inconsistencies between phylogenetic relationships and current species classifications using traditional morphological diagnostics. This study exemplifies the need for further exploration of pseudoscorpion taxonomy and species diversity. In particular, detailed morphological examinations are expected to help determine differences among cryptic species.

scholarly journals Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuchi Chen ◽  
Xiaocheng Zhu ◽  
Panayiotis Loukopoulos ◽  
Leslie A. Weston ◽  
David E. Albrecht ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Native Species ◽  
Management Strategies ◽  
Dna Barcode ◽  
Cost Effective ◽  
Species Level ◽  
Morphological Examination ◽  
South Wales ◽  
Interspecific Distance ◽  
Genotypic Identification

AbstractAustralia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.

scholarly journals Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kaomud Tyagi ◽  
Vikas Kumar ◽  
Shantanu Kundu ◽  
Avas Pakrashi ◽  
Priya Prasad ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Pairwise Distance ◽  
Global Database ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
Tree Topologies ◽  
Multiple Species

Abstract Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

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