scholarly journals Challenging species delimitation in Collembola: cryptic diversity among common springtails unveiled by DNA barcoding

2012 ◽  
Vol 26 (6) ◽  
pp. 470 ◽  
Author(s):  
D. Porco ◽  
A. Bedos ◽  
Penelope Greenslade ◽  
C. Janion ◽  
D. Skarżyński ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Functional Groups ◽  
Species Delimitation ◽  
Sequence Divergence ◽  
Cryptic Diversity ◽  
Congeneric Species ◽  
Nuclear Marker ◽  
Accurate Identification ◽  
Intraspecific Divergence

Collembola is one of the major functional groups in soil as well as a model taxon in numerous disciplines. Therefore the accurate identification of specimens is critical, but could be jeopardised by cases of cryptic diversity. Several populations of six well characterised species of springtails were sequenced using the COI barcode fragment as a contribution to the global Collembola barcoding campaign. Each species showed high intraspecific divergence, comparable to interspecific sequence divergence values observed in previous studies and in 10 congeneric species barcoded here as a reference. The nuclear marker, 28S, confirmed all the intraspecific lineages found with COI, supporting the potential specific status of these entities. The implications of this finding for taxonomy and for disciplines relying on species names, such as evolution and ecology, are discussed.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3516 ◽  
Author(s):  
Sohath Z. Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation forLucilia eximia, Lucilia retroversa, Lucilia ricaandChloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals Variation and Diagnostic Power of the Internal Transcribed Spacer 2 in Mediterranean and Atlantic Eolid Nudibranchs (Mollusca, Gastropoda)

2021 ◽  
Vol 8 ◽  
Author(s):  
Matteo Garzia ◽  
Paolo Mariottini ◽  
Daniele Salvi ◽  
Giulia Furfaro
Keyword(s):  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Marine Biodiversity ◽  
Cryptic Diversity ◽  
Nuclear Marker ◽  
Nuclear Markers ◽  
Closely Related Species ◽  
Internal Transcribed Spacer 2 ◽  
Mitochondrial Markers

Mediterranean marine biodiversity is still underestimated especially for groups such as nudibranchs. The identification of nudibranchs taxa is challenging because few morphological characters are available and among them chromatic patterns often do not align with species delimitation. Molecular assessments helped unveiling cryptic diversity within nudibranchs and have been mostly based on mitochondrial markers. Fast evolving nuclear markers are much needed to complement phylogenetic and systematic assessments at the species and genus levels. Here, we assess the utility of the nuclear Internal Transcribed Spacer 2 (ITS2) to delimit species in the eolid nudibranchs using both primary and secondary structures. Comparisons between the variation observed at the ITS2 and at the two commonly used mitochondrial markers (COI and 16S) on 14 eolid taxa from 10 genera demonstrate the ability of ITS2 to detect congeneric, closely related, species. While ITS2 has been fruitfully used in several other mollusc taxa, this study represents the first application of this nuclear marker in nudibranchs.

DNA barcoding of forensically important flies in the Western Cape, South Africa

Genome ◽  
2018 ◽  
Vol 61 (12) ◽  
pp. 823-828 ◽  
Author(s):  
Tenielle Cooke ◽  
Kyle Kulenkampff ◽  
Marise Heyns ◽  
Laura Jane Heathfield
Keyword(s):  
South Africa ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
The Body ◽  
Western Cape ◽  
Accurate Identification ◽  
Intraspecific Divergence ◽  
Post Mortem Interval ◽  
Interspecific Divergence

Forensic entomology aids the determination of post mortem interval based on arthropods associated with a deceased body. This relies on the accurate identification of insects that visit the body, particularly first colonisers such as Calliphoridae (Diptera). Traditional species identification though morphological keys can be challenging as immature or closely related specimens can look similar. Some of these challenges have been overcome through “DNA barcoding”, which involves the sequencing of informative regions within a species’ DNA and comparison to a database of reference sequences. However, reference DNA sequences of blow fly species in South Africa is currently limited. In this study, adult blow flies representing four species common to the Western Cape, South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, Lucilia sericata) were examined using morphological keys and DNA barcoding of two regions: COI and ITS2. These DNA sequences were then used as references for the successful identification of seven unknown immature specimens. Intraspecific divergence showed a maximum of 0.36% and 2.25% for COI and ITS2, respectively; interspecific divergence showed a minimum of 6.14% and 64.6% for COI and ITS2, respectively. According to these results, COI and ITS2 have sufficient discriminatory power for species-level identification for the four species studied.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

2017 ◽  
Author(s):  
Sohath Z Yusseff-Vanegas ◽  
Ingi Agnarsson
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Morphological Data ◽  
Caribbean Region ◽  
Reference Database ◽  
Correct Identification ◽  
Accurate Identification ◽  
The Caribbean

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identify immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean; we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

scholarly journals Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Robert G. Young ◽  
Cathryn L. Abbott ◽  
Thomas W. Therriault ◽  
Sarah J. Adamowicz
Keyword(s):  
Dna Barcoding ◽  
Species Delimitation ◽  
Graphical Method ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Threshold Value ◽  
Quantitative Comparison ◽  
Data Set ◽  
Pairwise Sequence Divergence ◽  
Marine Realm

DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value. With these thresholds, and using a newly generated planktonic marine data set, we quantify the degree of concordance using a bidirectional analysis and discuss different analytical methods for sequence-based species delimitation (e.g., BIN, ABGD, jMOTU, UPARSE, Mothur, PTP, and GMYC). Our results support a COI-5P threshold between 2.1% and 2.6% p-distance across methods for these crustacean taxa, yielding molecular groupings largely concordant with traditional, morphologically defined species. The adoption of internal methods for clustering verification enables rapid biodiversity studies and the exploration of unknown faunas using DNA barcoding. The approaches taken here for concordance assessment also provide a more quantitative comparison of clustering results (as contrasted with “success/failure” of barcoding), and we recommend their further consideration for barcoding studies.

scholarly journals Species delimitation of Melia dubia Cav. from Melia azedarach L. complex based on DNA barcoding

Botany ◽  
2018 ◽  
Vol 96 (5) ◽  
pp. 329-336 ◽  
Author(s):  
Irusappan Sivaraj ◽  
Stalin Nithaniyal ◽  
Varadharajan Bhooma ◽  
Umapathy Senthilkumar ◽  
Madasamy Parani
Keyword(s):  
Dna Barcoding ◽  
Distinct Species ◽  
Melia Azedarach ◽  
Nuclear Marker ◽  
Intraspecific Divergence ◽  
Interspecific Divergence ◽  
Medicinal Properties ◽  
Melia Dubia ◽  
Chloroplast Dna Markers ◽  
Suitable Marker

The genus Melia L., which belongs to the “Mahogany” family Meliaceae, is a source of important phytochemicals with marked medicinal properties. Species identification in Melia is complex due to the existence of overlapping morphological features. Although Melia dubia Cav. is listed as a synonym of Melia azedarach L., it is not clear from the available literature whether they are the same species or different, and the species complexity still remains unresolved. In the present study, 10 accessions of M. dubia and M. azedarach were analysed by DNA barcoding using three chloroplast DNA markers (rbcL, matK, and trnH–psbA), and one nuclear marker (ITS2). Intraspecific divergence was not found in any of the four markers. However, the interspecific divergence between M. azedarach and M. dubia ranged between 0.3% (rbcL) and 4.7% (ITS2) for individual markers, and for the combined dataset, it was 8.5%. Among the four markers, ITS2 was found to be the most suitable marker for differentiating M. azedarach and M. dubia. Parsimony analysis of the DNA barcoding data showed a clear segregation between M. azedarach and M. dubia as distinct monophyletic clades in all the markers, except the rbcL marker. Our results based on Bayesian analysis of the concatenated dataset strongly support the view that M. dubia be considered a distinct species; not a synonym of M. azedarach.

scholarly journals Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang
Keyword(s):  
Biological Control ◽  
Species Delimitation ◽  
Southern China ◽  
Insect Pest ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Accurate Identification ◽  
Phenacoccus Solenopsis

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.

Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico

2020 ◽  
Vol 150 ◽  
pp. 106880
Author(s):  
Tonatiuh Ramírez-Reyes ◽  
Christopher Blair ◽  
Oscar Flores-Villela ◽  
Daniel Piñero ◽  
Amy Lathrop ◽  
...  
Keyword(s):  
Molecular Species ◽  
Species Delimitation ◽  
Cryptic Diversity
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