scholarly journals Comment on Falade et al. (2016) DNA-barcoding of Clarias gariepinus, Coptedon zillii and Sarotherodon melanotheron from Southwestern Nigeria

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2654
Author(s):  
Jeremy A. Miller ◽  
Isolde van Riemsdijk ◽  
Mohd Zacaery Khalik ◽  
David J. Scager ◽  
Menno Schilthuizen

A publication by Falade et al. was selected for discussion by a Naturalis Biodiversity Center-Leiden University Journal Club. The study focused on the identification of fish from Southwestern Nigeria using a DNA barcoding approach. Questions raised during the discussion led to a reanalysis and reinterpretation of the data presented. The authors characterize the process of deriving a taxonomic identification from their sequence data as straightforward, but we were concerned that their approach made it nearly impossible to fail to obtain a taxonomic name for each sequence. The value of sophisticated DNA taxonomy, as well as the pitfalls of its naïve application, are discussed. We suggest that journal discussion groups may be an untapped resource for expanding rigorous peer review, particularly for journals that have adopted an open review model.

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1268 ◽  
Author(s):  
Mofolusho O. Falade ◽  
Anthony J. Opene ◽  
Otarigho Benson

DNA barcoding has been adopted as a gold standard rapid, precise and unifying identification system for animal species and provides a database of genetic sequences that can be used as a tool for universal species identification. In this study, we employed mitochondrial genes 16S rRNA (16S) and cytochrome oxidase subunit I (COI) for the identification of some Nigerian freshwater catfish and Tilapia species. Approximately 655 bp were amplified from the 5′ region of the mitochondrial cytochrome C oxidase subunit I (COI) gene whereas 570 bp were amplified for the 16S rRNA gene. Nucleotide divergences among sequences were estimated based on Kimura 2-parameter distances and the genetic relationships were assessed by constructing phylogenetic trees using the neighbour-joining (NJ) and maximum likelihood (ML) methods. Analyses of consensus barcode sequences for each species, and alignment of individual sequences from within a given species revealed highly consistent barcodes (99% similarity on average), which could be compared with deposited sequences in public databases. The nucleotide distance between species belonging to different genera based on COI ranged from 0.17% between Sarotherodon melanotheron and Coptodon zillii to 0.49% between Clarias gariepinus and C. zillii, indicating that S. melanotheron and C. zillii are closely related. Based on the data obtained, the utility of COI gene was confirmed in accurate identification of three fish species from Southwest Nigeria.


2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
D. E. Lebonah ◽  
A. Dileep ◽  
K. Chandrasekhar ◽  
S. Sreevani ◽  
B. Sreedevi ◽  
...  

Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.


Author(s):  
Daniel Lukic ◽  
Jonas Eberle ◽  
Jana Thormann ◽  
Carolus Holzschuh ◽  
Dirk Ahrens

DNA-barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affect the accuracy and performance of DNA-barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical data set sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivore chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analysed for a total of 186 individuals of 56 morphospecies. Tree based and distance based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. PTP and TCS prevailingly over-splitted morphospecies, while 3% clustering and ABGD also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs were discussed in the context of historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.


Zootaxa ◽  
2011 ◽  
Vol 2946 (1) ◽  
pp. 60 ◽  
Author(s):  
MALTE C. EBACH ◽  
MARCELO R. DE CARVALHO ◽  
DAVID M. WILLIAMS

Mooi & Gill (2010) have prised open the cap of the molecular systematics vial and caused a debate to take-off in the ichthyological community. Molecular trees and their supporting evidence are the first two items to leave this Pandora’s box, closely followed by DNA barcoding and DNA taxonomy. In short, the debate is fuelled by the nature of molecular data: can nucleotide sequences provide the necessary evidence for relationship? The majority (Wiley et al., 2011) believe that DNA contains informative data; however, in our view, they have failed to ascertain the truth of their claim. Not all data are informative. Data may provide supporting evidence, conflicting evidence, or no evidence at all. Assuming that all data are informative apriori to analysis is a theoretical position, not an empirical one. We claim that systematics is, quite the contrary, empirical, and relies on evidence rather than on implicit measurements of data. Consequently, this assertion leads back to the original question of evidence in molecular systematics, namely molecular homology.


Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.


2005 ◽  
Vol 360 (1462) ◽  
pp. 1969-1974 ◽  
Author(s):  
Mikhail V Matz ◽  
Rasmus Nielsen

DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability.


Parasitology ◽  
2017 ◽  
Vol 145 (5) ◽  
pp. 574-584 ◽  
Author(s):  
JAN ŠLAPETA

SUMMARYCryptosporidiumspp. (Apicomplexa) causing cryptosporidiosis are of medical and veterinary significance. The genusCryptosporidiumhas benefited from the application of what is considered a DNA-barcoding approach, even before the term ‘DNA barcoding’ was formally coined. Here, the objective to define the DNA barcode diversity ofCryptosporidiuminfecting mammals is reviewed and considered to be accomplished. Within theCryptosporidiumliterature, the distinction between DNA barcoding and DNA taxonomy is indistinct. DNA barcoding and DNA taxonomy are examined using the latest additions to the growing spectrum of namedCryptosporidiumspecies and within-species and between-species identity is revisited. Ease and availability of whole-genome DNA sequencing of the relatively smallCryptosporidiumgenome offer an initial perspective on the intra-host diversity. The opportunity emerges to apply a metagenomic approach to purified field/clinicalCryptosporidumisolates. The outstanding question remains a reliable definition ofCryptosporidiumphenotype. The complementary experimental infections and metagenome approach will need to be applied simultaneously to addressCryptosporidiumphenotype with carefully chosen clinical evaluations enabling identification of virulence factors.


2016 ◽  
Author(s):  
Ziheng Yang ◽  
Bruce Rannala

A number of methods have been developed to use genetic sequence data to identify and delineate species. Some methods are based on heuristics, such as DNA barcoding which is based on a sequence-distance threshold, while others use Bayesian model comparison under the multispecies coalescent model. Here we use mathematical analysis and computer simulation to demonstrate large differences in statistical performance of species identification between DNA barcoding and Bayesian inference under the multispecies coalescent model as implemented in the bpp program. We show that a fixed genetic-distance threshold as used in DNA barcoding is problematic for delimiting species, even if the threshold is "optimized", because different species have different population sizes and different divergence times, and therefore display different amounts of intra-species versus inter-species variation. In contrast, bpp can reliably delimit species in such situations with only one locus and rarely supports a wrong assignment with high posterior probability. While under-sampling or rare specimens may pose problems for heuristic methods, bpp can delimit species with high power when multi-locus data are used, even if the species is represented by a single specimen. Finally we demonstrate that bpp may be powerful for delimiting cryptic species using specimens that are misidentified as a single species in the barcoding library.


F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.


Author(s):  
Peter Nagel

Die Begriffe PhyloCode und DNA Barcoding stehen für innerhalb der Wissenschaftsgemeinschaft heftig diskutierte, jüngere Entwicklungen, die insbesondere für die Taxonomie (Systematik) und unmittelbar darauf aufbauende Disziplinen wie die Biogeographie grosse Relevanz haben. Der PhyloCode wurde als internationales Regelwerk für die phylogenetische Nomenklatur gegründet. Seine Ziele beinhalten die Einführung eines universell für alle Organismen gültigen Systems auf der Basis der phylogenetischen Beziehungen. Existierende Normen wie die Internationalen Regeln für die zoologische Nomenklatur (ICZN) sind primär merkmals- und rang-basiert und ermöglichen kein detailliertes Abbild der phylogenetischen Beziehungen. Der PhyloCode nennt Regeln für die Benennung von Monophyla und anderen Kladen, verzichtet aber auf jede Information über die relative hierarchische Position der Abstammungsgemeinschaften. Die angeblich im Gegensatz zu den existierenden Regelwerken vorhandene Stabilität der Nomenklatur kann nicht nachvollzogen werden, da sich die als Begründungen verwendeten Synapomorphien bei Revisionen als Homoplasien herausstellen können. Auch die Prüfung weiterer Punkte des PhyloCode ergab keine Hinweise auf belegbare Vorteile im Vergleich zu einem System wie dem ICZN, das durchaus Defizite in Bezug auf die Erkenntnisfortschritte der phylogenetischen Forschung aufzuweisen hat, das sich aber im Prinzip seit 250 Jahren und als offizielles Regelwerk seit 100 Jahren bewährt hat. - Das DNA Barcoding („Strichcode des Lebens“), steht für eine Genabschnitt-Methode zur Kennzeichnung aller Arten. Das mitochondriale Gen COI wurde als der DNA-Abschnitt bestimmt, mit dessen Hilfe sich theoretisch jeder Organismus eindeutig beschreiben und identifizieren lassen soll. Die Analyse und Datenbank-speicherung der COI-Sequenz aller Arten wurde als effektivere Methode zur Beschreibung der taxonomischen Biodiversität bezeichnet als die derzeit verwendeten, oft nicht-molekularen Methoden der traditonellen Taxonomen. Allerdings ist die COI-bezogene molekulare Analyse sämtlicher bekannter Arten utopisch. Weiterhin können sich die Basensequenzen der Proben von zwei identischen Taxa so sehr unterscheiden, dass eine sichere Bestimmung nicht immer möglich ist. Die für einige Taxa bereits intensiv betriebene COI-Analyse kommt auch der integrativen Taxonomie zugute, die bereits seit längerem schon molekulargenetische neben den traditionellen Methoden verwendet. Das Ziel des DNA Barcoding, nämlich das automatische Identifizieren von Taxa, ist nur in manchen Fällen eindeutig möglich und kann die integrativ arbeitenden Taxonomen nicht ersetzen.Stichwörterclade, DNA Barcoding, DNA taxonomy, ICZN, PhyloCode, phylogenetics, molecular systematics.


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