Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly<i>Astraptes fulgerator</i>

Hebert, Paul D. N.; Penton, Erin H.; Burns, John M.; Janzen, Daniel H.; Hallwachs, Winnie

doi:10.1073/pnas.0406166101

Cited by 3,079 publications

(2,585 citation statements)

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“…Finally, the accuracy of the DNA-based identifications is tightly dependent on the coverage of the DNA barcode reference libraries used to assign the sequences generated through NGS to known taxa [e.g. 17,21,28,189,[205][206][207][208][209].…”

Section: Resultsmentioning

confidence: 99%

“…Compared to morphological characters, DNA barcodes presents several advantages: (1) intraspecific phenotypic variation often These detailed specimens and barcode records ensure the reproducibility of the PCR and sequencing protocols by providing contact of the peoples involved in generating DNA barcodes. In addition, it enables the continuous updating of the identification of specimens by the community of users and facilitates the use of DNA barcodes for further taxonomic studies [21,[27][28][29][30][31]183]. To further improve the quality of DNA barcode data, the BARCODE data standard as been implemented in GenBank for the records that are compliant with the following requirements: 1.…”

Section: Dna Barcoding: a Solution To The Taxonomic Impediment?mentioning

confidence: 99%

“…The dominant families, however, varies among biogeographical provinces as Sundaland is dominated by the Cyprinidae (231 species; changes during ontogeny, fish identification is not an easy task. After almost a decade, it has become evident that DNA barcoding presents several advantages compared to morphological characters for species identification including: (1) intraspecific phenotypic variation often overlaps that of sister taxa in nature, which can lead to incorrect identifications or species delineations [21,22], (2) DNA barcodes are effective whatever the life stages under scrutiny [23,24] or available biological materials for identification [25,26], (3) spectacular levels of cryptic diversity have been frequently reported using DNA barcoding [21,[27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

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DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

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With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.

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Section: Resultsmentioning

confidence: 99%

Section: Dna Barcoding: a Solution To The Taxonomic Impediment?mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

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“…Afterwards they were centrifuged for 10 s at 3,000 r.p.m. The primers used were: for COI (676 bp) LCO 1490 (5′-GGTCAACAAATCATAA AGATATTGG-3′) 34 and Nancy (5′-CCCGGTAAAATTAAAATATAAACTTC-3′) 35 , or (658 bp) LepF1 (5′-ATTCAACCAATCATAAAGATATTGG-3) and LepR1 (5′-TAAACTTCTGGATGTCCAAAAAATCA-3′) 36 ; for ND1 (790-794 bp) 5′-CTGTTCGATCATTAAAATCTTAC-3′ (forward) 37 and 5′-ATCAAAAG GAGCTCGATTAGTTTC-3′ (reverse) 38 ; for ITS2 (684 bp) ITS3 (5′-GCATCGAT GAAGAACGCAGC-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) 39 ; for Wg (403 bp) Wg1 (5′-GARTGYAARTGYCAYGGYATGTCTGG-3′) and Wg2 (5′-ACTICGCRCACCARTGGAATGTRCA-3′) 40 ; for CAD (571 bp) CADFa (5′-GDATGGTYGATGAAAATGTTAA-3′) and CADRa (5′-CTCATRTCGTAAT CYGTRCT-3′). Double-stranded DNA was amplified in 25 µl volume reactions: 13.22 µl ultra pure (HPLC quality) water, 2.5 µl 10× buffer, 4.5 µl 25 mM MgCl 2 , 0.25 µl 100 mM dNTP, 1.2 µl of each primer (10 mM), 0.13 µl Taq DNA Gold Polymerase (Qiagen) and 2 µl of extracted DNA.…”

Section: Methodsmentioning

confidence: 99%

Unexpected layers of cryptic diversity in wood white Leptidea butterflies

et al. 2011

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uncovering cryptic biodiversity is essential for understanding evolutionary processes and patterns of ecosystem functioning, as well as for nature conservation. As European butterflies are arguably the best-studied group of invertebrates in the world, the discovery of a cryptic species, twenty years ago, within the common wood white Leptidea sinapis was a significant event, and these butterflies have become a model to study speciation. Here we show that the so-called 'sibling' Leptidea actually consist of three species. The new species can be discriminated on the basis of either DnA or karyological data. such an unexpected discovery challenges our current knowledge on biodiversity, exemplifying how a widespread species can remain unnoticed even within an intensely studied natural model system for speciation. G iven the global biodiversity crisis [1][2][3] , cataloguing the earth's species has become a race against time. Several studies have highlighted the presence and importance of cryptic biodiversity, which might represent a substantial proportion of Earth's natural capital. An estimate of cryptic species diversity is important to better understand evolutionary processes and patterns of ecosystem functioning, while also having deep implications for nature conservation 4,5 . The recent increase in the number of reported cryptic species is, in large part, owing to an increasing amount of studies incorporating DNA-based techniques, including large-scale approaches such as DNA barcoding 6 , which often provide resolution beyond the boundaries of morphological information. However, documenting cryptic diversity based on DNA data alone is generally not sufficient, prompting calls for integrative morphological, ecological and molecular approaches 7,8 . Recent estimates on the distribution of cryptic diversity are contradictory, and are based on a thin empirical foundation 4,9 . In any case, it is to be expected that the highest number of yet-to-be-discovered cryptic species is concentrated in the most biodiverse and least explored regions of our planet (that is, tropical areas). In temperate regions such as Europe, it is assumed that the level of unrecognized diversity is low, not only because of lower species richness, but also because taxonomic research has been intense for many groups of organisms. Such a case is represented by butterflies, probably the best-studied group of invertebrates, which have become a flagship for insect conservation efforts in Europe 10,11 .The discovery of a new European species of wood white (Leptidea sp.) at the end of the twentieth century was an important event in butterfly systematics. Leptidea sinapis (Linnaeus, 1758), a common butterfly with Palaearctic distribution was found to 'hide' a cryptic species, Leptidea reali (Reissinger, 1989) 12,13 . After the two species were shown to be separable based on their genitalia-but not on their wing morphology 13 -several studies revealed that L. reali is often sympatric with L. sinapis and that its distribution is almost as wide as that ...

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“…2011) or barcode gaps lead to the recognition of new species upon further study (Hebert et al. 2004; Bickford et al. 2007).…”

Section: Introductionmentioning

confidence: 99%

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

Hill

2016

Ecology and Evolution

149

178

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Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population‐specific mitonuclear coadaptations create between‐population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.

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Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterflyAstraptes fulgerator

Cited by 3,079 publications

References 31 publications

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Unexpected layers of cryptic diversity in wood white Leptidea butterflies

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

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