scholarly journals Opening Pandora’s Molecular Box

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):  
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.


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.


2015 ◽  
Vol 28 (1) ◽  
pp. 46 ◽  
Author(s):  
David A. Morrison ◽  
Matthew J. Morgan ◽  
Scot A. Kelchner

Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist.


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.


Zootaxa ◽  
2018 ◽  
Vol 4403 (2) ◽  
pp. 378 ◽  
Author(s):  
EUGENYI A. MAKARCHENKO ◽  
MARINA A. MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
DMITRY M. PALATOV

Illustrated descriptions of the adult male, pupa and fourth instar larva, as well as DNA barcoding results of Chaetocladius (Chaetocladius) elisabethae sp. nov. in comparison with closely related species of Chaetocladius s. str. from the Moscow Region are provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation. Comparisons with corresponding regions of COI between C. (s. str.) elisabethae sp. nov. and other species of the subgenus produced K2P genetic distances of 0.11–0.16, values well associated with interspecific variation. The barcodes of the new species were identical to the Chaetocladius sp. 2ES in BOLD systems. Molecular data were also used for the reconstruction of the phylogenetic relationships within the subgenus Chaetocladius s. str. 


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.


Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 461 ◽  
Author(s):  
Carina Carneiro de Melo Moura ◽  
Fabian Brambach ◽  
Kevin Jair Hernandez Bado ◽  
Konstantin V. Krutovsky ◽  
Holger Kreft ◽  
...  

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level.


2009 ◽  
Vol 66 (1) ◽  
pp. 81-95 ◽  
Author(s):  
K. A. Kron ◽  
E. A. Powell

Rhododendron subgenus Tsutsusi (Rhodoreae, Ericoideae, Ericaceae), commonly known as evergreen azaleas, includes approximately 117 deciduous and evergreen species from Japan, China and northeastern Asia. Subgenus Tsutsusi has been divided into two sections, Brachycalyx and Tsutsusi, based on characteristics of the leaves, young twigs and corolla. We obtained molecular data from three chloroplast (matK, ndhF and trnS-trnG) and two nuclear (nrITS and the third intron of rpb2) regions for 30 species of Rhododendron subgenus Tsutsusi and five species of Menziesia. Parsimony, Bayesian and likelihood analyses based on total evidence were used to assess the monophyly of the sections within Rhododendron subgenus Tsutsusi and relationships among the species sampled. In particular, the placement of the problematic Rhododendron tashiroi was addressed. Results support Rhododendron tashiroi as a member of the Rhododendron section Brachycalyx clade. Molecular evidence also supports a clade within Rhododendron section Tsutsusi containing R. indicum, R. tsusiophyllum, R. tschonoskii and R. serpyllifolium, species which were not previously considered closely related.


2004 ◽  
Vol 359 (1444) ◽  
pp. 669-679 ◽  
Author(s):  
Mark L. Blaxter

Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of ‘species’ fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional ‘species’. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re–analysis and meta–analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high–throughput sequencing methodologies, however, place the idea of a universal, multi–locus molecular barcoding system in the realm of the possible.


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