scholarly journals DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation

Genome ◽  
2017 ◽  
Vol 60 (7) ◽  
pp. 618-628 ◽  
Author(s):  
Bhavisha P. Sheth ◽  
Vrinda S. Thaker
Keyword(s):  
Dna Barcoding ◽  
Biodiversity Conservation ◽  
Biological Diversity ◽  
Integrated Approach ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Conservation Practice ◽  
Dna Taxonomy ◽  
Research Areas ◽  
Traditional Taxonomy

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.

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
Keyword(s):  
Dna Barcoding ◽  
Molecular Systematics ◽  
Molecular Data ◽  
Supporting Evidence ◽  
Dna Taxonomy ◽  
Theoretical Position ◽  
Conflicting Evidence ◽  
Original Question ◽  
Molecular Homology ◽  
Molecular Trees

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.

scholarly journals Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra

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 ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Evolutionary Rate ◽  
Molecular Data ◽  
Morphological Identification ◽  
Chloroplast Gene ◽  
Taxonomic Level ◽  
Morphological Taxonomy ◽  
Traditional Taxonomy ◽  
Lowland Forests ◽  
Interspecific Genetic Distance

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.

scholarly journals DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies

2010 ◽  
Vol 10 (2) ◽  
pp. 339-346 ◽  
Author(s):  
Amanda Ciprandi Pires ◽  
Luciane Marinoni
Keyword(s):  
Dna Barcoding ◽  
Financial Incentives ◽  
Scientific Community ◽  
New Technologies ◽  
Integrative Taxonomy ◽  
Taxonomic Impediment ◽  
Traditional Taxonomy

The taxonomic crisis, emphasized in recent years, is marked by the lack of popularity (lack of interest in taxonomy) and financial incentives to study biodiversity. This situation, coupled with the issues involved with the necessity of knowing many yet undiscovered species, has meant that new technologies, including the use of DNA, have emerged to revitalize taxonomy. Part of the scientific community, however, has rejected the use of these innovative ideas. DNA barcoding has especially been the target of numerous criticisms regarding its application, as opposed to the use of morphology. This paper aims to highlight the inconsistency of the debate involving DNA versus morphology, since there is a proposal for the integration of traditional taxonomy and DNA barcoding - the integrative taxonomy. The positive and negative points of this proposal will be discussed, as well as its validity and application. From it, the importance of morphology is recognized and the revitalization of traditional taxonomy is achieved by the addition of technologies to overcome the taxonomic impediment.

An example of problems associated with DNA barcoding in tardigrades: a novel method for obtaining voucher specimens

Zootaxa ◽  
2011 ◽  
Vol 3104 (1) ◽  
pp. 42 ◽  
Author(s):  
MICHELE CESARI ◽  
ILARIA GIOVANNINI ◽  
ROBERTO BERTOLANI ◽  
LORENA REBECCHI
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Intraspecific Variability ◽  
Original Description ◽  
Morphological Characters ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Type Locality ◽  
Moss Sample ◽  
Voucher Specimens

We have in recent papers revealed that an integrative taxonomy approach helps to solve taxonomic problems in tardigrades. However, whole tardigrades are required for DNA work, which leaves no hologenophore voucher specimens with adult morphology. Using a novel methodology for the Tardigrada, we introduce the practice of collecting high quality maximum magnification light microscopy images of recently thawed animals to act as hologenophore voucher specimens of animals later used for DNA barcode sequencing. Within the framework of a DNA barcoding project on tardigrades, we collected a moss sample from the type locality of Macrobiotus terminalis Bertolani & Rebecchi, 1993 (Castelsantangelo, Central Apennines, Italy), a species of the “Macrobiotus hufelandi group”. Within the moss sample we found several animals and eggs with a morphology that corresponded to the original description of M. terminalis, while others were attributable to Macrobiotus macrocalix Bertolani & Rebecchi, 1993. In this study, molecular (cox1 mtDNA) analyses demonstrated no intraspecific variability in M. terminalis from the type locality but very large interspecific differences when compared with M. macrocalix and GenBank data for other species within the M. “hufelandi group”. There was also a large difference between our M. terminalis sequences and the GenBank data of a specimen attributed to the same species. The GenBank sequence originated from a population in the Northern Apennines, whose morphology appeared to be like that of the specimens of the locus typicus. This confirmed the importance in utilising material from the type locality for linking molecular data to the species’ morphological characters. Our paper underlines the importance of an integrative taxonomy in species diagnoses and demonstrates a scenario where morphological observations alone are not always sufficient. Lastly, this work adds reliable information to the sequence reference library that provides a useful building block for further studies on similar and related tardigrade taxa.

scholarly journals The biodiversity crisis in Canada: failures and challenges of federal and sub-national strategic and legal frameworks

FACETS ◽  
2021 ◽  
Vol 6 ◽  
pp. 1044-1068
Author(s):  
Justina C. Ray ◽  
Jaime Grimm ◽  
Andrea Olive
Keyword(s):  
Decision Making ◽  
Biodiversity Conservation ◽  
Biological Diversity ◽  
Integrated Approach ◽  
Legal Framework ◽  
Convention On Biological Diversity ◽  
Governance Capacity ◽  
Financial Investment ◽  
Economic Wealth ◽  
Biodiversity Crisis

Negative biodiversity trends are evident in Canada, in spite of its ecological and economic wealth and high governance capacity. We examined the current implementation of Canada’s national biodiversity strategy—the planning instrument to the United Nations Convention on Biological Diversity—through its existing legal framework. We did this by evaluating biodiversity-related strategies and plans and 201 federal, provincial, and territorial laws. We found that while most jurisdictions claim dedicated attention to biodiversity, there is little evidence of an integrated approach within provinces and territories and across the federation. Biodiversity conservation led by governments underscores the need for considerations of species and ecosystem services to be mainstreamed into economic and development decision-making. Key challenges to this include Canada’s unusual degree of decentralized constitutionally ascribed authority over natural assets and its historical and continued economic emphasis on extraction of natural resources—a conflict of interest for jurisdictions. Transitioning to scale-appropriate planning and integrated decision-making that can address the pressures and causes of biodiversity conservation in Canada will require transformative change. Law reform, while necessary, will not succeed unless accompanied by a whole-of-government approach, a shift to a bio-centric mindset, innovative governance (particularly Indigenous-led conservation), and federal leadership with strong levels of financial investment.

scholarly journals Shell and appendages variability in two allopatric ostracod species seen through the light of molecular data

2020 ◽  
Vol 89 (3) ◽  
pp. 247-269
Author(s):  
Ivana Karanovic ◽  
Pham Thi Minh Huyen ◽  
Hyunsu Yoo ◽  
Yuriko Nakao ◽  
Akira Tsukagoshi
Keyword(s):  
Evolutionary Biology ◽  
Intraspecific Variability ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Shell Shape ◽  
Closely Related Species ◽  
Traditional Taxonomy ◽  
Brackish Water Species ◽  
A New Species ◽  
Water Species

Ostracod crustaceans are among the most abundant microfossil animals. Understanding intra- and interspecific variability of their shell is of pivotal importance for the interpretation of paleontological data. In comparison to appendages, ostracod shell displays more intraspecific variability (in shape, size, and ornamentation), often as a response to environmental conditions. Shell variability has been studied with sophisticated methods, such as geometric morphometrics (GM), but the conspecificity of examined specimens and populations was never tested. In addition, there are no GM studies of appendages. We build on previously published high cytochrome c oxidase subunit I (COI) divergence rates among populations of a brackish water species, Ishizakiella miurensis (Hanai, 1957). With landmark-based GM analyses of its shell and appendages, and additional genetic markers (ITS, 28S, 18S), we test if the genetic variability is structured in morphospace. This approach is the core of integrative taxonomy paradigm which has been proposed to bring the gap between traditional taxonomy and other disciplines such as evolutionary biology. The results show that it is the shell shape, and not the shape of appendages, that mirrors the molecular phylogeny, and we describe a new species. Our results suggest that the landmark-based GM studies may be useful in paleontological datasets for closely related species delineation. We implement molecular clock and population statistics to discuss speciation processes and phylogeography of the two congeners in Korea and Japan.

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.

scholarly journals Toward a More Expansive Discourse in a Changing World: An Analysis of Political Leaders’ Speeches on Biodiversity

2021 ◽  
Vol 13 (5) ◽  
pp. 2899
Author(s):  
Sang Hun Lee ◽  
Yi Hyun Kang ◽  
Rong Dai
Keyword(s):  
Biodiversity Conservation ◽  
Policy Process ◽  
Biological Diversity ◽  
Convention On Biological Diversity ◽  
Decision Making Process ◽  
Political Leaders ◽  
Host Countries ◽  
Global Pandemic ◽  
The Subject ◽  
High Level

Speeches delivered in the Conference of the Parties (COPs) to the Convention on Biological Diversity represent leading discourses about biodiversity conservation. The discourse shared by high-level politicians is especially influential in the financing and decision-making process of global biodiversity governance. However, the speeches given in the COPs have not been the subject of systematic analyses until now. This study analyzes the host countries’ speeches given at the six most recent COPs and investigates which discourses have been expressed in the speeches. The regulatory discourse that views nature as a resource was found to be the dominant discourse, while other discourses that view nature as a scientific object or a spiritual entity were represented only marginally. As the need for a transformational policy for biodiversity conservation is growing amid a global pandemic, it is essential to deepen our understanding of the dynamics and complexity of nature and reflect it in the policy process. This study suggests that more balanced discourse on biodiversity may earn broader audiences’ consensus on biodiversity conservation.

scholarly journals Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1298 ◽  
Author(s):  
Feng Zhang ◽  
Daoyuan Yu ◽  
Mark I. Stevens ◽  
Yinhuan Ding
Keyword(s):  
Species Complex ◽  
Instar Larva ◽  
Molecular Data ◽  
Integrative Taxonomy ◽  
Species Level ◽  
Integrative Approach ◽  
Gene Markers ◽  
Late Neogene ◽  
Taxonomic Approach ◽  
Colour Patterns

Integrative taxonomic approaches are increasingly providing species-level resolution to ‘cryptic’ diversity. In the absence of an integrative taxonomic approach, formal species validation is often lacking because of inadequate morphological diagnoses. Colouration and chaetotaxy are the most commonly used characters in collembolan taxonomy but can cause confusion in species diagnoses because these characters often have large intraspecific variation. Here, we take an integrative approach to the genus Dicranocentrus in China where four species have been previously recognised, but several members of the genus have been morphologically grouped as a species complex based on having paired outer teeth on unguis and seven colour patterns. Molecular delimitations based on distance- and evolutionary models recovered four candidate lineages from three gene markers and revealed that speciation events likely occurred during the late Neogene (4–13million years ago). Comparison of intact dorsal chaetotaxy, whose homologies were erected on the basis of first instar larva, further validated these candidates as formal species: D. gaoligongensis, sp. nov., D. similis, sp. nov., D. pallidus, sp. nov. and D. varicolor, sp. nov., and increase the number of Dicranocentrus species from China to eight. Our study further highlights the importance of adequate taxonomy in linking morphological and molecular characters within integrative taxonomy.

Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

Zootaxa ◽  
2017 ◽  
Vol 4286 (1) ◽  
pp. 93 ◽  
Author(s):  
OLGA KLISHKO ◽  
MANUEL LOPES-LIMA ◽  
ELSA FROUFE ◽  
ARTHUR BOGAN ◽  
LYUDMILA VASILIEV ◽  
...  
Keyword(s):  
Freshwater Mussel ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Data Set ◽  
Widespread Species ◽  
Molecular Analyses ◽  
Morphological Variations ◽  
Mtdna Coi ◽  
Morphological And Molecular Data

The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio, in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus. Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al. (2004) and Bogatov & Kijashko (2016). 

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