scholarly journals PhyloCode und DNA Barcoding - Taxonomische Regeln und Techniken im Wandel?

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.

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.


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.


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.


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.


2019 ◽  
Vol 52 (1) ◽  
Author(s):  
Ibrahim Khan ◽  
Zabta Khan Shinwari ◽  
Nadia Batool Zahra ◽  
Sohail Ahmad Jan ◽  
Shehla Shinwari ◽  
...  

Author(s):  
Anna D. Temraleeva ◽  
Elena S. Krivina ◽  
Yury S. Bukin

The understanding of the impossibility of distinguishing algal species based on morphological features came with the development of DNA sequencing technology, which today is a necessary tool for defining species boundaries and testing traditional species concepts. The paper discusses popular approaches to species identification (DNA barcoding) and the description of new and revision of known species (DNA taxonomy) using molecular genetic methods. The requirements and limitations in their work are given, as well as examples of phylogenetic analysis of green algae from the clade Moewusinia and Parachlorella, including the genus Micractinium.


Genome ◽  
2017 ◽  
Vol 60 (7) ◽  
pp. 618-628 ◽  
Author(s):  
Bhavisha P. Sheth ◽  
Vrinda S. Thaker

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.


Zootaxa ◽  
2011 ◽  
Vol 3025 (1) ◽  
pp. 66 ◽  
Author(s):  
LEANDRO M. SANTOS ◽  
LUIZ R. R. FARIA

The use of DNA sequences, including DNA barcoding, as a taxonomical tool has been happening for some time (Tautz et al., 2003; Hajibabaei et al., 2007; Packer et al., 2009). However, the description of new species based solely on DNA sequences is a new idea (Cook et al., 2010) and a new practice (Brower, 2010). Our aim is not to further polarize the war between advocates of strictly molecular or strictly morphological systematics (following, e.g., Pires & Marinoni 2010). The objectives here are (i) to present some arguments regarding the perils of the proposition of a model (theory) for solely DNA-based descriptions (Cook et al. 2010) and the actual publication (practice) of such descriptions (Brower 2010), (ii) to discuss some reasons why we believe that adopting strictly DNA taxonomy for species description, setting aside everything we have learned from classic taxonomy, may not be the best alternative and (iii) to present the point of view about these matters of a PhD candidate and a recently graduated PhD working with taxonomy in a developing country.


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