scholarly journals Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications

2013 ◽  
Vol 172 (4) ◽  
pp. 478-499 ◽  
Author(s):  
Marco C. Simeone ◽  
Roberta Piredda ◽  
Alessio Papini ◽  
Federico Vessella ◽  
Bartolomeo Schirone
Keyword(s):  
Dna Barcoding ◽  
Nuclear Markers ◽  
Phylogenetic Implications ◽  
Mediterranean Oaks

First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean

Genome ◽  
2020 ◽  
pp. 1-11 ◽  
Author(s):  
Tomasz Rewicz ◽  
Arnold Móra ◽  
Grzegorz Tończyk ◽  
Ada Szymczak ◽  
Michal Grabowski ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Related Species ◽  
Dna Barcode ◽  
Taxonomic Status ◽  
Index Number ◽  
Reference Library ◽  
Nuclear Markers ◽  
Closely Related Species ◽  
Maltese Islands ◽  
Morphological Species

We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.

scholarly journals Deciphering amphibian diversity through DNA barcoding: chances and challenges

2005 ◽  
Vol 360 (1462) ◽  
pp. 1859-1868 ◽  
Author(s):  
Miguel Vences ◽  
Meike Thomas ◽  
Ronald M Bonett ◽  
David R Vieites
Keyword(s):  
Dna Barcoding ◽  
Single Locus ◽  
Universal Primers ◽  
Nuclear Markers ◽  
Amphibian Species ◽  
Interspecific Divergence ◽  
Candidate Species ◽  
Mitochondrial Population ◽  
Tremendous Amount ◽  
Definition Of

Amphibians globally are in decline, yet there is still a tremendous amount of unrecognized diversity, calling for an acceleration of taxonomic exploration. This process will be greatly facilitated by a DNA barcoding system; however, the mitochondrial population structure of many amphibian species presents numerous challenges to such a standardized, single locus, approach. Here we analyse intra- and interspecific patterns of mitochondrial variation in two distantly related groups of amphibians, mantellid frogs and salamanders, to determine the promise of DNA barcoding with cytochrome oxidase subunit I ( cox1 ) sequences in this taxon. High intraspecific cox1 divergences of 7–14% were observed (18% in one case) within the whole set of amphibian sequences analysed. These high values are not caused by particularly high substitution rates of this gene but by generally deep mitochondrial divergences within and among amphibian species. Despite these high divergences, cox1 sequences were able to correctly identify species including disparate geographic variants. The main problems with cox1 barcoding of amphibians are (i) the high variability of priming sites that hinder the application of universal primers to all species and (ii) the observed distinct overlap of intraspecific and interspecific divergence values, which implies difficulties in the definition of threshold values to identify candidate species. Common discordances between geographical signatures of mitochondrial and nuclear markers in amphibians indicate that a single-locus approach can be problematic when high accuracy of DNA barcoding is required. We suggest that a number of mitochondrial and nuclear genes may be used as DNA barcoding markers to complement cox1 .

scholarly journals Hybridisation and introgression in British Helosciadium (Apiaceae).

2020 ◽  
Vol 2 (1) ◽  
pp. 27-42
Author(s):  
Stuart D. Desjardins ◽  
Andrew G. Shaw ◽  
Judith A. Webb
Keyword(s):  
Dna Barcoding ◽  
Parental Species ◽  
Supporting Evidence ◽  
Nuclear Markers ◽  
Early Generation ◽  
The Third ◽  
Chloroplast Marker ◽  
Putative Hybrids

Reticulation between Helosciadium repens (Jacq.) W.D.J. Koch and H. nodiflorum (L.) W.D.J. Koch (Apiaceae) has been the source of much speculation, but until now supporting evidence has remained largely anecdotal. In the current study inter-specific hybridisation and introgression between the two species was confirmed using DNA barcoding. The parentage of three putative hybrids collected from Port Meadow, Oxfordshire (UK) was determined using a maternally-inherited chloroplast marker (rps16-trnK) and two biparentally-inherited nuclear markers (LEAFYi2, ITS). Two of the individuals are early-generation hybrids between H. repens and H. nodiflorum, F1 or otherwise, while the third is most likely a backcross to H. repens. These individuals are the first confirmed hybrids/hybrid derivatives between the two parental species, and represent a new addition to the British flora. The hybrids closely resemble H. nodiflorum var. longipedunculatum F.W. Schultz, and in our view should be treated as H. × longipedunculatum (F.W. Schultz) Desjardins.

scholarly journals DNA barcoding of twelve shrimp species (Crustacea: Decapoda) from Turkish seas reveals cryptic diversity

2014 ◽  
Vol 16 (1) ◽  
pp. 36 ◽  
Author(s):  
R. BILGIN ◽  
M. A. UTKAN ◽  
E. KALKAN ◽  
S. U. KARHAN ◽  
M. BEKBÖLET
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Coastal Waters ◽  
Cryptic Diversity ◽  
Nuclear Markers ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Shrimp Species ◽  
Gene Coi ◽  
First Time ◽  
Mitochondrial Cytochrome Oxidase

DNA barcoding is a useful tool for the identification and potential discovery of new species. In this study, DNA barcoding was employed by sequencing the mitochondrial cytochrome oxidase subunit I gene (COI) to characterize the genetic diversity of 12 shrimp species inhabiting Turkish coastal waters and, when possible, to compare with the genetic data available from different parts of the Mediterranean and eastern Atlantic. This study also comprises the first DNA barcoding study performed in the Turkish Seas using COI. A total of 40 shrimp specimens were collected and analyzed from 9 sites. Generally, the barcoding gap criterion was successful at identifying species; hence COI appeared to be a good marker of choice for DNA barcoding in this group. Out of the 12 species investigated, five were barcoded for the first time. In six species two intraspecific clades were retrieved after the analyses. The results suggest the presence of cryptic diversity in a genetically understudied marine area, Turkish coastal waters, and further investigation in these species using population genetics, taxonomic approaches and nuclear markers is likely to result in designation of new species.

Architecture of Radiolitid Rudist (Mollusca) Shell-Wall Structures and its Phylogenetic Implications

1975 ◽  
Vol 33 ◽  
pp. 686-687
Author(s):  
David H. Sturm ◽  
Bob F. Perkins
Keyword(s):  
Phylogenetic Relationships ◽  
Outer Wall ◽  
Shell Microstructure ◽  
Shell Wall ◽  
Wall Structures ◽  
Phylogenetic Implications ◽  
Cellular Wall ◽  
Superfamily Analysis ◽  
Central Texas

Each of the seven families of rudists (Mollusca, Bivalvia, Hippuritacea) is characterized by distinctive shell-wall architectures which reflect phylogenetic relationships within the superfamily. Analysis of the complex, calcareous, cellular wall of the attached valve of the radiolite rudist Eoradiolites davidsoni (Hill) from the Comanche Cretaceous of Central Texas indicates that its wall architecture is an elaboration of the simpler monopleurid rudist wall and supports possible radiolite-monopleurid relationships.Several well-preserved specimens of E. davidsoni were sectioned, polished, etched, and carbon and gold coated for SEM examination. Maximum shell microstructure detail was displayed by etching with a 0.7% HC1 solution from 80 to 100 seconds.The shell of E. davidsoni comprises a large, thick-walled, conical, attached valve (AV) and a small, very thin, operculate, free valve (FV) (Fig. 1a). The AV shell is two-layered with a thin inner wall, in which original structures are usually obliterated by recrystallization, and a thick, cellular, outer wall.

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