DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

@article{Kekkonen2014DNABD,
  title={DNA barcode-based delineation of putative species: efficient start for taxonomic workflows},
  author={Mari Kekkonen and Paul D. N. Hebert},
  journal={Molecular Ecology Resources},
  year={2014},
  volume={14},
  pages={706 - 715}
}
The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by… Expand
Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths
TLDR
Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. Expand
DNA barcoding as a screening tool for cryptic diversity: an example from Caryocolum, with description of a new species (Lepidoptera, Gelechiidae)
TLDR
Deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3% are observed in Caryocolum amaurella, indicating possible cryptic diversity and the taxonomy of these taxa has to be re-assessed in the future. Expand
One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire
TLDR
The results suggest that sequences as short as 56 bp can often provide valuable taxonomic information and support significant taxonomic oversplitting of species in the Elachista dispunctella complex. Expand
DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera, Papilionidae)
TLDR
An explicit flow chart is provided describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. Expand
Does a Barcoding Gap Exist in Prokaryotes? Evidences from Species Delimitation in Cyanobacteria
TLDR
The main message of the results is a call for caution in the estimate of diversity from 16S sequences only, given that different subjective choices in the method to delimit units could provide different results. Expand
Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera
TLDR
It is suggested that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors. Expand
DNA barcoding of the rodent genus Oligoryzomys (Cricetidae: Sigmodontinae): mitogenomic-anchored database and identification of nuclear mitochondrial translocations (Numts)
TLDR
The GMYC delimitations and DNA barcode gap results highlight the need for further work that integrate molecular, karyotypic, and morphological analyses, as well as additional sampling, to tackle persistent problems in the taxonomy of Oligoryzomys. Expand
DNA barcode based delineation of freshwater fishes from northern Western Ghats of India, one of the world’s biodiversity hotspots
TLDR
This is the first effort to generate the DNA barcode reference library of freshwater fishes from northern Western Ghats of India, one of the world’s biodiversity hotspots, and will provide valuable measures to prove the efficiency of molecular species delimitation methods in taxonomic discrimination which aid conservation of biodiversity. Expand
A DNA barcode library for the butterflies of North America
TLDR
A DNA barcode reference library is assembled for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study, and to provide new perspectives on the incidence of both cryptic and potentially over-split species. Expand
DNA barcoding techniques used to identify the shared ichthyofauna between the Pantanal floodplain and Upper Parana River
TLDR
The results demonstrate that human interventions possibly participated in the distribution of some lineages and suggest that the number of species that are present in these two basins is underestimated and that human actions can irreversibly affect the natural history of the species in these regions. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 71 REFERENCES
A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
TLDR
A persistent, species-level taxonomic registry for the animal kingdom is developed based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. Expand
DNA barcodes distinguish species of tropical Lepidoptera.
TLDR
It is shown that cytochrome c oxidase I DNA barcodes effectively discriminate among species in three Lepidoptera families from Area de Conservación Guanacaste in northwestern Costa Rica, suggesting DNA barcoding will significantly aid species identification and discovery in tropical settings. Expand
ABGD, Automatic Barcode Gap Discovery for primary species delimitation
TLDR
Automatic Barcode Gap Discovery is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach. Expand
Sequence-based species delimitation for the DNA taxonomy of undescribed insects.
Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence dataExpand
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
TLDR
It is shown that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity, while estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. Expand
A DNA ‘Barcode Blitz’: Rapid Digitization and Sequencing of a Natural History Collection
TLDR
This study reveals the speed with which DNA barcoding workflows can mobilize biodiversity data, often providing the first web-accessible information for a species, and suggests that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity – insects. Expand
DNA Barcoding the Geometrid Fauna of Bavaria (Lepidoptera): Successes, Surprises, and Questions
TLDR
The present study provides a comprehensive DNA barcode library for the Geometridae, one of the most diverse of insect families, and emphasizes the effectiveness of DNA barcoding as a tool for monitoring biodiversity. Expand
A comparison of DNA‐based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy
TLDR
Gaussian clustering produced the classifications with the highest concordance with the morphological classification of all approaches applied in this study, both with single‐locus sequences and with binary multilocus data. Expand
Molecular-based rapid inventories of sympatric diversity: A comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians
TLDR
Evaluating the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clades-based barcode data, while a promising coalescent-based method performed poorly on symp atric data. Expand
Allopatry as a Gordian Knot for Taxonomists: Patterns of DNA Barcode Divergence in Arctic-Alpine Lepidoptera
TLDR
DNA barcodes have great potential to both increase taxonomic resolution and to make decisions concerning the taxonomic status of allopatric populations more objective. Expand
...
1
2
3
4
5
...