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.

scholarly journals The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

2018 ◽  
Vol 109 (1-2) ◽  
pp. 301-323 ◽  
Author(s):  
Emanuel TSCHOPP ◽  
Paul UPCHURCH
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Parsimony ◽  
Large Scale ◽  
Intraspecific Variability ◽  
Species Level ◽  
A Posteriori ◽  
Operational Taxonomic Units ◽  
Vertebrate Palaeontology ◽  
Tree Topologies ◽  
Parsimony Criterion

ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

scholarly journals ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

scholarly journals DNA Barcoding of the Solanaceae Family in Puerto Rico Including Endangered and Endemic Species

2019 ◽  
Vol 144 (5) ◽  
pp. 363-374 ◽  
Author(s):  
Lumariz Hernandez Rosario ◽  
Juan O. Rodríguez Padilla ◽  
Desiree Ramos Martínez ◽  
Alejandra Morales Grajales ◽  
Joel A. Mercado Reyes ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Puerto Rico ◽  
Dna Barcoding ◽  
Endemic Species ◽  
Phylogenetic Trees ◽  
Dna Barcode ◽  
Pairwise Distance ◽  
Greater Antilles ◽  
Solanaceae Species ◽  
Solanaceae Family

The Solanaceae family is one of the largest and well-distributed plant families in the world. It contains species of agricultural and economical importance, such as Solanum tuberosum, Solanum melongena, Solanum lycopersicum, Nicotiana tabacum, and Capsicum annuum. In Puerto Rico, there are ≈46 species of Solanaceae of which six are endemic: Brunfelsia densifolia, Brunfelsia lactea, Brunfelsia portoricensis, Goetzea elegans, Solanum ensifolium, and Solanum woodburyi. Our objective was to use DNA barcoding to identify the Solanaceae species in Puerto Rico, including the endemics, and to assess the species relationships between them. To accomplish our objective, two chloroplast regions (psbA-trnH and matK) and a nuclear region [internal transcribed spacer (ITS)] were assessed. Pairwise distance and phylogenetic analysis demonstrate that DNA barcoding can be used to discriminate at the species level among these taxa in Puerto Rico. For all three markers, the genus that showed the highest pairwise distance between represented species was Solanum, whereas the genus that displayed the least was Capsicum. Phylogenetic trees of single and concatenated regions were generated from sequences obtained in this study and from data downloaded from the National Center for Biotechnology Information database. Our results show that this technique can be used to identify species with one, two, or three combinations of DNA barcode markers depending on the taxon. In addition, this is the first study to include the endemic species S. woodburyi in a molecular phylogenetic analysis, and it was found to have a close relationship with S. ensifolium, also endemic to Puerto Rico, and to Solanum bahamense from the Bahamas and Greater Antilles. Therefore, we suggest that S. woodburyi might be part of the Bahamense clade.

scholarly journals DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9641 ◽  
Author(s):  
Nur Fadli ◽  
Siti Azizah Mohd Nor ◽  
Ahmad Sofiman Othman ◽  
Hizir Sofyan ◽  
Zainal A. Muchlisin
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Reef Fishes ◽  
Morphological Identification ◽  
Species Discovery ◽  
Indonesian Archipelago ◽  
Aceh Province ◽  
Commercially Important ◽  
Catch Composition ◽  
Fisheries Statistics

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 641-660 ◽  
Author(s):  
Daniel H. Janzen ◽  
Winnie Hallwachs
Keyword(s):  
Costa Rica ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Data Systems ◽  
Species Discovery ◽  
Life Data ◽  
And Behavior ◽  
Specimen Identification ◽  
Biodiversity Information

The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

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 DNA barcoding of different Triticum species

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Samira A. Osman ◽  
Walaa A. Ramadan
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Phylogenetic Tree ◽  
Dna Barcoding ◽  
Critical Role ◽  
Dna Barcode ◽  
Species Group ◽  
Amino Acid Sequences ◽  
Pairwise Distance ◽  
Multiple Sequence

Abstract Background The genus Triticum L. includes diploid, tetraploid, and hexaploid species. DNA barcoding is a new method to identify plant taxa by using short sequences of DNA and within a short time. In this investigation, we determined a phylogenetic analysis of 20 different Triticum species by partial chloroplast Maturase encoding gene (matK). Materials and methods Twenty accessions of different Triticum species diploid, tetraploid, and hexaploid were obtained from different countries. Genomic DNA was isolated from young leaves of studied samples and then used as a template for PCR reaction. PCR products were checked by electrophoresis, purified, sequenced, and submitted in the GenBank nucleotide sequence database, the nucleotide sequence was translated into an amino acid sequence. The nucleotide and amino acid sequences were aligned with Clustal W multiple sequence alignment programs to obtain the phylogenetic tree depending on two statistical data analysis such as bootstrapping and pairwise distance from both nucleotide and amino acid sequences. Results The phylogenetic tree obtained from both nucleotide and amino acid sequences divided the 20 Triticum species into two groups, A and B. Group A represented the diploid Triticum species. Group B was divided into two subgroup, I and II. Subgroup I represented the hexaploid Triticum species and subgroup II represented the tetraploid species. Conclusion The matK gene sequence has a critical role in discriminating the closely related Triticum species. So these sequences could be used as a DNA barcode for detecting the evolutionary history of Triticum species.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

scholarly journals Mini-barcodes are equally useful for species identification and more suitable for large-scale species discovery in Metazoa than full-length barcodes

2019 ◽  
Author(s):  
Darren Yeo ◽  
Amrita Srivathsan ◽  
Rudolf Meier
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Species Level ◽  
Full Length ◽  
New Techniques ◽  
Species Discovery ◽  
Operational Taxonomic Units ◽  
The Mean ◽  
Window Approach ◽  
Moderate Length

AbstractNew techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens and 5,500 species, as well as six clade-specific datasets from GenBank covering ca. 98,000 specimens for over 20,000 species. All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 – 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5’ end of the Folmer region. The mean congruence between morphospecies and mOTUs is ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.

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.

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