scholarly journals DNA barcode reference library for Iberian butterflies enables a continental-scale preview of potential cryptic diversity

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Vlad Dincă ◽  
Sergio Montagud ◽  
Gerard Talavera ◽  
Juan Hernández-Roldán ◽  
Miguel L. Munguira ◽  
...  

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Vlad Dincă ◽  
Leonardo Dapporto ◽  
Panu Somervuo ◽  
Raluca Vodă ◽  
Sylvain Cuvelier ◽  
...  

AbstractThe study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.



Botany ◽  
2010 ◽  
Vol 88 (7) ◽  
pp. 639-667 ◽  
Author(s):  
Gary W. Saunders ◽  
Brian McDonald

The DNA barcode (COI-5P) was used to investigate cryptic diversity among Rhodymenia spp. in southern Australia. Whereas eight species are currently recognized, we uncovered ca. 20 genetic species groups, phylogenetically assigned to four genera in two families. Procumbent specimens with molecular and anatomical signatures of the Fryeellaceae are assigned to Pseudohalopeltis tasmanensis gen. et sp. nov. Collections from Lord Howe Island recorded in the field as Rhodymenia / Fauchea sp. are assigned to the poorly known genus Microphyllum as Microphyllum robustum sp. nov. A cluster of species with distinct molecular and anatomical attributes is included in a resurrected Halopeltis J.G. Agardh, including Halopeltis australis (J. Agardh) comb. nov. (type species); Halopeltis austrina (Womersley) comb. nov.; Halopeltis cuneata (Harvey) comb. nov. [including Rhodymenia halymenioides (J. Agardh) Womersley]; Halopeltis gracilis sp. nov.; Halopeltis prostrata sp. nov.; and Halopeltis verrucosa (Womersley) comb. nov. Four additional species of Halopeltis from Lord Howe Island (LH1, LH2), Tasmania (TAS), and Western Australia are not characterized further. For Rhodymenia sensu stricto, similar levels of cryptic diversity were noted. Samples tentatively field-identified as “ Rhodymenia sonderi ,” but having affiliations to Rhodymenia rather than Halopeltis, are referred to Rhodymenia novahollandica sp. nov. Collections field-identified as R. obtusa are genetically distinct from that species and are assigned to Rhodymenia wilsonis (Sonder) comb. nov. Two highly divergent species currently identified as Rhodymenia leptophylla (LH from Lord Howe Island; TAS from Tasmania), as well as two additional cryptic previously unnamed taxa from South Australia (SA) and Victoria (VIC), are not characterized further.



2019 ◽  
Author(s):  
Erwan Delrieu-Trottin ◽  
Jeffrey T. Williams ◽  
Diane Pitassy ◽  
Amy Driskell ◽  
Nicolas Hubert ◽  
...  

AbstractThe emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.



2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen

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.



2021 ◽  
Vol 43 (1) ◽  
pp. 141-145
Author(s):  
C Fagg ◽  
NL Phair ◽  
L Claassens ◽  
RSK Barnes ◽  
S von der Heyden


2017 ◽  
Vol 8 ◽  
Author(s):  
Jinxin Liu ◽  
Linchun Shi ◽  
Jingyuan Song ◽  
Wei Sun ◽  
Jianping Han ◽  
...  


2015 ◽  
Vol 15 (6) ◽  
pp. 1366-1374 ◽  
Author(s):  
Chao Xu ◽  
Wenpan Dong ◽  
Shuo Shi ◽  
Tao Cheng ◽  
Changhao Li ◽  
...  


Genome ◽  
2017 ◽  
Vol 60 (1) ◽  
pp. 74-84 ◽  
Author(s):  
Danielle A. Ondrejicka ◽  
Kevin C. Morey ◽  
Robert H. Hanner

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.



2016 ◽  
Vol 3 ◽  
Author(s):  
Vieira Pedro ◽  
Gomes Nuno ◽  
Lobo Jorge ◽  
Borges Luisa ◽  
Queiroga Henrique ◽  
...  


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