Journal articles: 'Molecular taxonomy'

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Deák, T. "MOLECULAR TAXONOMY OF YEASTS." Acta Microbiologica et Immunologica Hungarica 46, no. 2-3 (May 1999): 181–86. http://dx.doi.org/10.1556/amicr.46.1999.2-3.3.

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Wink, M., E. Käss, and M. Kaufmann. "Molecular versus Chemical Taxonomy." Planta Medica 59, S 1 (December 1993): A594—A595. http://dx.doi.org/10.1055/s-2006-959803.

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Gómez Daglio, Liza, and Michael N. Dawson. "Integrative taxonomy: ghosts of past, present and future." Journal of the Marine Biological Association of the United Kingdom 99, no. 06 (April 26, 2019): 1237–46. http://dx.doi.org/10.1017/s0025315419000201.

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AbstractDescribing species has been a formal, intellectually rich and influential applied and basic area of study for many of the past 260 years. While formally described eukaryotic diversity still falls short of estimated eukaryotic species diversity by many hundreds of thousands of species, some recent accounts have suggested a growing number of taxonomists are within reach of describing all extant species. We present a case study that illustrates, to the contrary, a recent ‘taxonomic impediment’ in part attributable to derogation of taxonomy as a scientific discipline: contemporary practice has re-interpreted taxonomy largely as an endeavour in enumerating species. We argue that challenges lie in (1) a poor understanding of taxonomy's epistemology; (2) excessive displacement of interest toward ecological or molecular studies; (3) over-interpretation of the contributions of multiple authors describing a species; and (4) perspectives that are strongly influenced by well-known taxa. The historical and recent literature on scyphozoans reveal ghosts of taxonomy's past that persist in the present, but suggest also that a renaissance enabled by integrative taxonomy is possible in the (near) future.

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Akram, Seemab, Shamsul Khamis, Shahrizim Zulkifly, Rishzuan Talib, and Nurul Izza Ab Ghani. "Phylogeny Study of 20 Selected Species of Zingiberaceae from Ex situ Collections in Peninsular Malaysia." Pertanika Journal of Tropical Agricultural Science 46, no. 1 (February 22, 2023): 329–45. http://dx.doi.org/10.47836/pjtas.46.1.18.

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Zingiberaceae is widely distributed in Malaysia, with 750 species and 31 genera. This family comprises a different number of subfamilies and genera according to different taxonomic classification methods — classical taxonomy: one subfamily and four tribes vs molecular taxonomy: four subfamilies and six tribes. However, the taxonomic classification of Zingiberaceae is still debated, especially the classical taxonomy. It is due to some Zingiberaceae species showing cryptic morphologies that make it difficult to classify them through classical taxonomy, which refers to the unique morphological characteristics of a tribe/species. Therefore, accurate taxonomic classification is required by using a molecular approach. In this study, 20 selected species of Zingiberaceae collected from the Agricultural Conservatory Park, Institute of Bioscience (IBS), Universiti Putra Malaysia (UPM) were taxonomically classified using a molecular method with the help of three random amplified polymorphic DNA (RAPD) and three inter simple sequence repeat (ISSR) markers until the tribe level. The combined RAPD and ISSR unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree was comparable to Zingiberaceae’s current molecular and classical taxonomy. The 20 selected species were grouped into three tribes (Alpinieae, Zingiberaceae, and Globbeae). This finding has contributed additional biological information to better manage the 20 Zingiberaceae species in the Agricultural Conservatory Park, IBS, UPM. Further studies are needed to explore the genetic diversities and properties of Zingiberaceae species.

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HÖFLING, José F., Edvaldo A. R. ROSA, Mirian J. BAPTISTA, and Denise M. P. SPOLIDÓRIO. "New Strategies on Molecular Biology Applied to Microbial Systematics." Revista do Instituto de Medicina Tropical de São Paulo 39, no. 6 (November 1997): 345–52. http://dx.doi.org/10.1590/s0036-46651997000600007.

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Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint

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Guého, Eveline, M. C. Leclerc, G. S. Hoog, and B. Dupont. "Molecular taxonomy and epidemiology ofBlastomycesandHistoplasmaspecies." Mycoses 40, no. 3-4 (September 1997): 69–81. http://dx.doi.org/10.1111/j.1439-0507.1997.tb00191.x.

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Méndez-Álvarez, Sebastián, Sergio Ramírez-Moreno, and Núria Gaju. "Molecular Taxonomy of the GenusChlorobium." Critical Reviews in Microbiology 27, no. 1 (January 2001): 9–24. http://dx.doi.org/10.1080/20014091096675.

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Harley, E. H. "DNA APPROACHES TO MOLECULAR TAXONOMY." Transactions of the Royal Society of South Africa 46, no. 4 (January 1988): 283–90. http://dx.doi.org/10.1080/00359198809520131.

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Lahbib-Mansais, Yvette, Mireille Mata, and Paul Ritzenthaler. "Molecular taxonomy of Lactobacillus phages." Biochimie 70, no. 3 (March 1988): 429–35. http://dx.doi.org/10.1016/0300-9084(88)90217-9.

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10

Kurtzman, Cletus P. "Molecular taxonomy of the yeasts." Yeast 10, no. 13 (December 1994): 1727–40. http://dx.doi.org/10.1002/yea.320101306.

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Masuda, Shinobu. "Breast cancer pathology: The impact of molecular taxonomy on morphological taxonomy." Pathology International 62, no. 5 (March 16, 2012): 295–302. http://dx.doi.org/10.1111/j.1440-1827.2012.02790.x.

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Mandal, Fatik Baran. "Hurdle in taxonomy: A case of malaria parasites and other Haemosporidia." Open Veterinary Science 2, no. 1 (January 1, 2021): 40–54. http://dx.doi.org/10.1515/ovs-2020-0110.

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Abstract A crucial progress in taxonomy matches with the growth of various branches of biological sciences. This validates the taxonomic positions of many organisms. Haemoproteus, Leucocytozoon and Plasmodium, the members of the Haemosporidia, are the well recognized parasitic genera. Revisiting the progress in animal taxonomy appears to be important to evaluate our studies. Haemosporidia being microscopic, their taxonomy specially the morphotaxonomy has sometimes created confusion. Therefore, analysis of progression of the taxonomy of the avian Haemosporidia demands special attention. Modern phylogenetic analyses revealed a wealth of information, which is undoubtedly useful for protozoology and other related sciences. Techniques of molecular taxonomy are applied to draw the phylogeny covering members of Haemosporidia. The study of the life cycles of both hosts and parasites are absorbing. Besides, analysis of their evolution through molecular phylogenetics appears to be vital in studying haemosporidians and to gain insight for basic and applied sciences. This article examines the potential of molecular phylogenetics in refining systematics of avian Haemosporidia and to explain a holistic view of the group.

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ZHANG, ZHI-QIANG. "Contributing to the progress of descriptive taxonomy." Zootaxa 1968, no. 1 (December 22, 2008): 65–68. http://dx.doi.org/10.11646/zootaxa.1968.1.7.

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One of the fundamental quests of biology is discovering how many species inhabit the Earth. Yet the vast majority of the world’s animal species are waiting to be discovered, named and described—estimates of the total number vary from 5 to 30 million. Most biologists would agree that taxonomy is important and fundamental to credible biology, and descriptive taxonomy is the most important task of taxonomy (Wheeler 2007). Unfortunately, the reality is that descriptive taxonomy has been marginalized since the mid-1950s and has sustained serious losses in funding and academic positions in universities and museums around the world, especially since phylogenetic and molecular studies became popular in the last twenty years. During this period, there has also been an important historical trend in taxonomic publishing—many journal publishers/editors have been making increasing demands on authors to provide phylogenetic analysis, molecular systematics, and other modern types of information in taxonomic papers. In addition, there are long publication delays and/or increasing page charges for many journals that do publish descriptive taxonomic papers. Zootaxa was founded in 2001 to provide a much-needed outlet for descriptive taxonomic papers and monographs that are difficult to publish elsewhere, and as a result has received tremendous support from taxonomists worldwide, despite the fact that it is a grass-roots project without support from government and institutions (Zhang 2006a). Zootaxa satisfied the publishing need of many zoological taxonomists, and sustained a period of rapid growth during 2001 to 2006 (Zhang 2006b). During the last two years, it has continued to grow in size, and especially in its impact, and has become a major force in reviving descriptive taxonomy on a global scale. Here I summarize some encouraging data on the growth of Zootaxa and its impact. I also comment on its contribution to the progress of descriptive taxonomy.

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Koren, Anamarija, Vladimir Sikora, Biljana Kiprovski, Milka Brdar-Jokanovic, Milica Acimovic, Bojan Konstantinovic, and Dragana Latkovic. "Controversial taxonomy of hemp." Genetika 52, no. 1 (2020): 1–13. http://dx.doi.org/10.2298/gensr2001001k.

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Hemp (Cannabis sativa L.) was one of the earliest domesticated plant species. Biological classification (taxonomy or systematization) manifests evolutional relationships between taxons according to trait similarities. When it comes to taxonomy, hemp is one of the most controversial plant species due to significant effects of environmental conditions on hemp phenology and expression of quantitative traits as well as different levels of gender expression observed in hemp plants. Controversial taxonomy of hemp has gone through several phases throughout history. The attitude on the number of species within the genus Cannabis and the criteria used in taxonomic units division were under dispute. Initially focused on morphological characteristics and geographical origin, the approach was greatly amended by the development of molecular and biochemical techniques. The main cause of taxonomic uncertainties is the inbreeding ability of all wild Cannabis populations, resulting in continual variability of quantitative traits. The aim of the paper is to review the history of Cannabis classification including different approaches to this scientific issue.

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Cai, Feng, and Irina S. Druzhinina. "In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma." Fungal Diversity 107, no. 1 (February 5, 2021): 1–69. http://dx.doi.org/10.1007/s13225-020-00464-4.

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AbstractModern taxonomy has developed towards the establishment of global authoritative lists of species that assume the standardized principles of species recognition, at least in a given taxonomic group. However, in fungi, species delimitation is frequently subjective because it depends on the choice of a species concept and the criteria selected by a taxonomist. Contrary to it, identification of fungal species is expected to be accurate and precise because it should predict the properties that are required for applications or that are relevant in pathology. The industrial and plant-beneficial fungi from the genus Trichoderma (Hypocreales) offer a suitable model to address this collision between species delimitation and species identification. A few decades ago, Trichoderma diversity was limited to a few dozen species. The introduction of molecular evolutionary methods resulted in the exponential expansion of Trichoderma taxonomy, with up to 50 new species recognized per year. Here, we have reviewed the genus-wide taxonomy of Trichoderma and compiled a complete inventory of all Trichoderma species and DNA barcoding material deposited in public databases (the inventory is available at the website of the International Subcommission on Taxonomy of Trichodermawww.trichoderma.info). Among the 375 species with valid names as of July 2020, 361 (96%) have been cultivated in vitro and DNA barcoded. Thus, we have developed a protocol for molecular identification of Trichoderma that requires analysis of the three DNA barcodes (ITS, tef1, and rpb2), and it is supported by online tools that are available on www.trichokey.info. We then used all the whole-genome sequenced (WGS) Trichoderma strains that are available in public databases to provide versatile practical examples of molecular identification, reveal shortcomings, and discuss possible ambiguities. Based on the Trichoderma example, this study shows why the identification of a fungal species is an intricate and laborious task that requires a background in mycology, molecular biological skills, training in molecular evolutionary analysis, and knowledge of taxonomic literature. We provide an in-depth discussion of species concepts that are applied in Trichoderma taxonomy, and conclude that these fungi are particularly suitable for the implementation of a polyphasic approach that was first introduced in Trichoderma taxonomy by John Bissett (1948–2020), whose work inspired the current study. We also propose a regulatory and unifying role of international commissions on the taxonomy of particular fungal groups. An important outcome of this work is the demonstration of an urgent need for cooperation between Trichoderma researchers to get prepared to the efficient use of the upcoming wave of Trichoderma genomic data.

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Gajdács, Márió. "Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists." Acta Pharmaceutica Hungarica 89, no. 4 (March 7, 2020): 99–108. http://dx.doi.org/10.33892/aph.2019.89.99-108.

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Taxonomy is the science of the classification of various living organisms consisting of three independent, but interrelated disciplines, namely classification, nomenclature and identification. With the advent of molecular biological methods and sequencing, a revolution is currently occurring with regards to the reporting of novel taxa and changes in the taxonomy of already described bacterial species. The applications of taxonomic changes can be broad ranging: they may impact the clinical care of patients, through variations in choosing the appropriate antimicrobial susceptibility testing standards or data interpretation, or even their clinical relevance and epidemiology. The aim of this paper was to aid healthcare professionals and pharmaceutical scientists to navigate through the ‘maze’ of bacterial taxonomy, and to aid in finding authentic information regarding the description of taxonomic changes and to present some examples of changes in bacterial taxonomy which have proven to be clinically significant.

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Miller, R. F., and A. E. Wakefield. "Pneumocystis carinii: molecular taxonomy and epidemiology." Journal of Medical Microbiology 45, no. 4 (October 1, 1996): 233–35. http://dx.doi.org/10.1099/00222615-45-4-233.

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Holt, Ben G., and Knud Andreas Jønsson. "Reconciling Hierarchical Taxonomy with Molecular Phylogenies." Systematic Biology 63, no. 6 (August 19, 2014): 1010–17. http://dx.doi.org/10.1093/sysbio/syu061.

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Momen, Hooman. "BRIEF REPORT Molecular Taxonomy of Trypanosomatids." Archives of Medical Research 33, no. 4 (July 2002): 413–15. http://dx.doi.org/10.1016/s0188-4409(02)00369-7.

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Hergueta-Redondo, Marta, José Palacios, Amparo Cano, and Gema Moreno-Bueno. "“New” molecular taxonomy in breast cancer." Clinical and Translational Oncology 10, no. 12 (December 2008): 777–85. http://dx.doi.org/10.1007/s12094-008-0290-x.

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Sjödahl, Gottfrid, Martin Lauss, Kristina Lövgren, Gunilla Chebil, Sigurdur Gudjonsson, Srinivas Veerla, Oliver Patschan, et al. "A Molecular Taxonomy for Urothelial Carcinoma." Clinical Cancer Research 18, no. 12 (May 2, 2012): 3377–86. http://dx.doi.org/10.1158/1078-0432.ccr-12-0077-t.

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Elkan, G. H. "Taxonomy of the rhizobia." Canadian Journal of Microbiology 38, no. 6 (June 1, 1992): 446–50. http://dx.doi.org/10.1139/m92-075.

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Extensive cross testing on a relatively few legume hosts led initially to a taxonomic characterization of rhizobia based on bacteria–plant cross–inoculation groups. This has gradually become less acceptable, and has been replaced by taxonomic groupings derived from numerical taxonomy, carbohydrate metabolism, antibiotic susceptiblities, serology, and various molecular techniques. It has long been recognized that there are two distinct groups of rhizobia based on growth rate. The fast-growing genus Rhizobium includes R. leguminosarum, R. meliloti, R. loti, R. galegae, R. tropici, and R. huakuii. The slow-growing genus Bradyrhizobium contains only one recognized species, B. japonicum. Two new genera have been recognized: Azorhizobium, with one recognized species (A. caulinadans), and Sinorhizobium, with two species (S. fredii and S. xinjiangensis). Genetic studies of both the fast- and slow-growing groups show unacceptably wide intrageneric and intergeneric diversity. Although there have been some elegant studies of some of the genetic relationships among rhizobia, overall there has (have) not been the comprehensive study(ies) needed to allow a conclusive taxonomic scheme. Because proposals for revision are accelerating, minimum standards have been proposed by the International Subcommittee for the Taxonomy of Rhizobium and Agrobacterium. Key words: Rhizobium taxonomy, classification of rhizobia, interrelationships of rhizobia.

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Abd El-Aziz,, El-S., and A. Awad. "Molecular Taxonomy Matches Pollen Grains Taxonomy in Differentiation Between Some Caesalpinioideae Taxa." Journal of Plant Production 14, no. 5 (May 1, 2023): 245–451. http://dx.doi.org/10.21608/jpp.2023.209588.1240.

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Samson, Robert A. "Constraints associated with taxonomy of biocontrol fungi." Canadian Journal of Botany 73, S1 (December 31, 1995): 83–88. http://dx.doi.org/10.1139/b95-229.

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An increasing number of fungi are being collected and screened for the biological control of pests, but nomenclature, taxonomy, and correct identification of many of them remain problematic. Trichoderma spp. and the rust fungi are promising candidates for biocontrol agents, yet they present serious taxonomic problems. Several groups of entomopathogenic fungi are also potential biocontrol sources of agents. Genera such as Cordyceps, Aschersonia, Verticillium, Beauveria, and Metarhizium are in need of urgent revision. Before their release can be considered, all details of their complex life cycles and taxonomy have to be elucidated to satisfy quarantine authorities. Formerly, the taxonomy and identification of biocontrol fungi has been based largely on morphological structures, but molecular techniques have been introduced to provide more objective criteria. Beauveria and Metarhizium spp. have been subjected to several molecular techniques that have resolved phylogeny and species concepts. In Metarhizium, a high degree of genetic diversity is present. Incorrect typification, lack of holotypes, and poorly resolved life cycles and unclear teleomorph – (syn)anamorph connections are serious taxonomic contraints. Only a small fraction of the fungi that can be used for biological control has been examined. The destruction of habitats and ecosystems for these fungi will result in the disappearance of fungal germ plasm of potential value, not only for biological control but also as a source of novel metabolites. This loss and the decline of taxonomic expertise in the fungi are major problems. Key words: biocontrol, taxonomy, Trichoderma, Beauveria, Metarhizium, Cordyceps.

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Bruno, Laura, Daniela Billi, and Patrizia B. Albertano. "Optimization of molecular techniques applied to the taxonomy of epilithic Leptolyngbya strains." Algological Studies/Archiv für Hydrobiologie, Supplement Volumes 117 (October 1, 2005): 197–207. http://dx.doi.org/10.1127/1864-1318/2005/0117-0197.

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Arrigoni, Roberto, Jarosław Stolarski, Tullia I. Terraneo, Bert W. Hoeksema, Michael L. Berumen, Claude Payri, Simone Montano, and Francesca Benzoni. "Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae." Contributions to Zoology 92, no. 2 (March 13, 2023): 130–71. http://dx.doi.org/10.1163/18759866-bja10041.

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Abstract The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.

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Ohira, Hajime, Shingo Kaneko, Leanne Faulks, and Tadaaki Tsutsumi. "Unexpected species diversity within Japanese Mundochthonius pseudoscorpions (Pseudoscorpiones : Chthoniidae) and the necessity for improved species diagnosis revealed by molecular and morphological examination." Invertebrate Systematics 32, no. 2 (2018): 259. http://dx.doi.org/10.1071/is17036.

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Using the complementary approaches of morphological and molecular taxonomy is essential to further our understanding of invertebrate diversity, including the identification of cryptic species. Although the species classification of a widespread group of arachnids, the pseudoscorpions, has been based on traditional diagnostic characters for a long time, recent taxonomic studies have suggested that some of these are unreliable for distinguishing species. Thus, the application of molecular taxonomy may be particularly useful in this group. Here, we performed molecular phylogenetic analyses and species delimitation analyses based on partial sequences of mitochondrial DNA cytochrome c oxidase I and nuclear DNA 18S rRNA genes to assess the taxonomy of species and the reliability of morphological characteristics for distinguishing species in the Japanese soil-dwelling genus Mundochthonius (Chthoniidae). Our results revealed the existence of seven major genetic clades, likely corresponding to three described species and four cryptic species. Although two described species, M. kiyoshii and M. itohi, were represented by single clades in the phylogenetic analysis, a third, M. japonicus, was composed of multiple clades, highlighting inconsistencies between phylogenetic relationships and current species classifications using traditional morphological diagnostics. This study exemplifies the need for further exploration of pseudoscorpion taxonomy and species diversity. In particular, detailed morphological examinations are expected to help determine differences among cryptic species.

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Zhang, Feng, Daoyuan Yu, Mark I. Stevens, and Yinhuan Ding. "Colouration, chaetotaxy and molecular data provide species-level resolution in a species complex of Dicranocentrus (Collembola : Entomobryidae)." Invertebrate Systematics 32, no. 6 (2018): 1298. http://dx.doi.org/10.1071/is18019.

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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.

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Samper, Cristián. "Taxonomy and environmental policy." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1444 (April 29, 2004): 721–28. http://dx.doi.org/10.1098/rstb.2004.1476.

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In 1992, with the United Nations Conference on Environment and Development in Rio de Janeiro and the subsequent Convention on Biological Diversity (CBD), the world changed for the science of taxonomy. Many taxonomists appear not to have noticed this change, but it has significantly altered the political climate in which taxonomic research is undertaken. By the late 1990s it was clear that effective implementation of the CBD needed the participation of and funding for the taxonomic community. In this paper, I chart the rise of the Global Taxonomy Initiative (GTI), review some of its goals and explore how it interacts with the CBD. The interactions of the GTI with the Global Environment Facility, a potential funding body, are explored, as are the possible synergies between the GTI and the many other global initiatives linking to taxonomy. Finally, I explore some of the challenges ahead as taxonomy begins to take a front seat in the implementation of environmental policy on the world stage.

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Hunter, Philip. "Viral taxonomy." EMBO reports 18, no. 10 (September 6, 2017): 1693–96. http://dx.doi.org/10.15252/embr.201744982.

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Pardo-Diaz, Carolina, Alejandro Lopera Toro, Sergio Andrés Peña Tovar, Rodrigo Sarmiento-Garcés, Melissa Sanchez Herrera, and Camilo Salazar. "Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy." PeerJ 7 (August 5, 2019): e7332. http://dx.doi.org/10.7717/peerj.7332.

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Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses.

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Wheeler, Quentin D. "Taxonomic triage and the poverty of phylogeny." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1444 (April 29, 2004): 571–83. http://dx.doi.org/10.1098/rstb.2003.1452.

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Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis–driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high–throughput species hypothesis–testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age.

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Gräser, Y., A. F. A. Kuijpers, W. Presber, and G. S. de Hoog. "Molecular Taxonomy of the Trichophyton rubrum Complex." Journal of Clinical Microbiology 38, no. 9 (2000): 3329–36. http://dx.doi.org/10.1128/jcm.38.9.3329-3336.2000.

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The validity of taxa around Trichophyton rubrum was evaluated by a combination of phenetic and molecular methods. Morphological and physiological features were compared to results of sequencing of the internal transcribed spacer region of the ribosomal operon, PCR fingerprinting, and amplified fragment length polymorphism analysis. The 15 species and varieties investigated (Trichophyton circonvolutum, Trichophyton fischeri,Trichophyton fluviomuniense, Trichophyton glabrum, Trichophyton gourvilii, Trichophyton kanei, Trichophyton kuryangei, Trichophyton megninii, Trichophyton pedis, Trichophyton raubitschekii, Trichophyton rodhaini,Trichophyton rubrum var. nigricans,Trichophyton soudanense, Trichophyton violaceumvar. indicum, and Trichophyton yaoundei) were reclassified or synonymized as T. rubrum or T. violaceum.

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Graser, Y., M. El Fari, W. Presber, A. F. A. Kuijpers, and G. S. De Hoog. "Molecular and conventional taxonomy of theMicrosporum caniscomplex." Medical Mycology 38, no. 2 (January 2000): 143–53. http://dx.doi.org/10.1080/mmy.38.2.143.153.

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Guedj, M., L. Marisa, A. de Reynies, B. Orsetti, R. Schiappa, F. Bibeau, G. MacGrogan, et al. "A refined molecular taxonomy of breast cancer." Oncogene 31, no. 9 (July 25, 2011): 1196–206. http://dx.doi.org/10.1038/onc.2011.301.

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Wilson, Kenneth H. "Molecular Biology as a Tool for Taxonomy." Clinical Infectious Diseases 20, Supplement_2 (June 1, 1995): S117—S121. http://dx.doi.org/10.1093/clinids/20.supplement_2.s117.

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Irwin, Peter J. "Canine babesiosis: from molecular taxonomy to control." Parasites & Vectors 2, Suppl 1 (2009): S4. http://dx.doi.org/10.1186/1756-3305-2-s1-s4.

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Kantardjiev, T., V. Levterova, S. Panaiotov, I. Ivanov, and E. Hristozova. "Molecular Taxonomy ofCryptococcus NeoformansVarieties Displaying Phenotypic Similarities." Biotechnology & Biotechnological Equipment 20, no. 2 (January 2006): 101–3. http://dx.doi.org/10.1080/13102818.2006.10817349.

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Abeshouse, Adam, Jaeil Ahn, Rehan Akbani, Adrian Ally, Samirkumar Amin, Christopher D. Andry, Matti Annala, et al. "The Molecular Taxonomy of Primary Prostate Cancer." Cell 163, no. 4 (November 2015): 1011–25. http://dx.doi.org/10.1016/j.cell.2015.10.025.

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Biswas, S., D. Holyoake, and T. S. Maughan. "Molecular Taxonomy and Tumourigenesis of Colorectal Cancer." Clinical Oncology 28, no. 2 (February 2016): 73–82. http://dx.doi.org/10.1016/j.clon.2015.11.001.

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Jarrard, David F., and Wei Huang. "The New Age of Molecular Taxonomy Approaches." European Urology 69, no. 4 (April 2016): 561–62. http://dx.doi.org/10.1016/j.eururo.2015.11.011.

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Durkin, Louisa, Tobias Jansson, Marisol Sanchez, Maryia Khomich, Martin Ryberg, Erik Kristiansson, and R. Henrik Nilsson. "When mycologists describe new species, not all relevant information is provided (clearly enough)." MycoKeys 72 (September 10, 2020): 109–28. http://dx.doi.org/10.3897/mycokeys.72.56691.

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Taxonomic mycology struggles with what seems to be a perpetual shortage of resources. Logically, fungal taxonomists should therefore leverage every opportunity to highlight and visualize the importance of taxonomic work, the usefulness of taxonomic data far beyond taxonomy, and the integrative and collaborative nature of modern taxonomy at large. Is mycology really doing that, though? In this study, we went through ten years’ worth (2009–2018) of species descriptions of extant fungal taxa – 1,097 studies describing at most ten new species – in five major mycological journals plus one plant journal. We estimated the frequency at which a range of key words, illustrations, and concepts related to ecology, geography, taxonomy, molecular data, and data availability were provided with the descriptions. We also considered a range of science-demographical aspects such as gender bias and the rejuvenation of taxonomy and taxonomists as well as public availability of the results. Our results show that the target audience of fungal species descriptions appears to be other fungal taxonomists, because many aspects of the new species were presented only implicitly, if at all. Although many of the parameters we estimated show a gradual, and in some cases marked, change for the better over time, they still paint a somewhat bleak picture of mycological taxonomy as a male-dominated field where the wants and needs of an extended target audience are often not understood or even considered. This study hopes to leave a mark on the way fungal species are described by putting the focus on ways in which fungal taxonomy can better anticipate the end users of species descriptions – be they mycologists, other researchers, the public at large, or even algorithms. In the end, fungal taxonomy, too, is likely to benefit from such measures.

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ZIMMERMANN, BIANCA LAÍS, IVANKLIN SOARES CAMPOS-FILHO, GIOVANNA MONTICELLI CARDOSO, SANDRO SANTOS, JOSÉ OTÁVIO AGUIAR, and PAULA BEATRIZ ARAUJO. "Two new species of Atlantoscia Ferrara & Taiti, 1981 (Isopoda: Oniscidea: Philosciidae) from southern Brazil described in the light of integrative taxonomy." Zootaxa 4482, no. 3 (September 19, 2018): 551. http://dx.doi.org/10.11646/zootaxa.4482.3.7.

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The use of molecular data in association with classical taxonomy has helped to alleviate the taxonomic impediment through the discovery, delimitation and description of new species. Terrestrial isopods are the largest suborder of Isopoda; however, there are very few active taxonomists in this group and a representative part of the terrestrial isopods world diversity remains unexplored. The genus Atlantoscia comprises five species in which diagnostic characters are few and show subtle differences among the species. The objective of this study was to delimit and describe two new species of the genus Atlantoscia from southern Brazil by using traditional taxonomy coupled with genetic information. Specimens were analyzed morphologically and by the aid of two molecular markers, mitochondrial COI and nuclear 18S rRNA. The validity of the new species Atlantoscia antennamaculata sp. nov. and Atlantoscia australis sp. nov. was corroborated, unambiguously, by morphological approach, phylogenetic analysis and species delimitation methods. Our study reinforces the fact that, despite the undeniable importance of comparative morphology in species discovery, new methods and data, particularly molecular ones, are becoming prominent and an integrative part of the taxonomy practice.

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Shackleton, M. E., K. A. Dafforn, N. P. Murphy, P. Greenfield, M. Cassidy, and C. H. Besley. "How does molecular taxonomy for deriving river health indices correlate with traditional morphological taxonomy?" Ecological Indicators 125 (June 2021): 107537. http://dx.doi.org/10.1016/j.ecolind.2021.107537.

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Hirose, Mamiko, Tetsuya Tochikubo, and Euichi Hirose. "Taxonomic significance of tunic spicules in photosymbiotic ascidians: a quantitative and molecular evaluation." Journal of the Marine Biological Association of the United Kingdom 90, no. 5 (December 9, 2009): 1065–71. http://dx.doi.org/10.1017/s0025315409991263.

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Many didemnid ascidians have calcareous spicules in the tunic. Since the spicules of each species have a specific shape and size-range, they are often regarded as an important character for taxonomy. To evaluate the taxonomic significance of tunic spicules, a quantitative survey of spicule size and shape was combined with a molecular phylogeny inferred from the partial sequence of the cytochrome c oxidase subunit I (COI) gene in some groups of didemnid species that are supposedly closely related. This study revealed the presence of substantial intraspecific variations in the shape and size of tunic spicules. The spicules are, therefore, not always crucial features discriminating species, particularly among related species. Although tunic spicules are potentially valuable features for didemnid taxonomy, their intraspecific variation should be carefully considered before they are used as a key character for species identification.

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Rosselló-Mora, Ramon. "Updating Prokaryotic Taxonomy." Journal of Bacteriology 187, no. 18 (September 15, 2005): 6255–57. http://dx.doi.org/10.1128/jb.187.18.6255-6257.2005.

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van Staden, Michaela, David A. Ebert, Enrico Gennari, Rob W. Leslie, Meaghen E. McCord, Matthew Parkinson, Ralph G. A. Watson, Sabine Wintner, Charlene da Silva, and Aletta E. Bester-van der Merwe. "Molecular Taxonomy of South Africa’s Catsharks: How Far Have We Come?" Diversity 15, no. 7 (July 1, 2023): 828. http://dx.doi.org/10.3390/d15070828.

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The ability to correctly identify specimens at the species level is crucial for assessing and conserving biodiversity. Despite this, species-specific data are lacking for many of South Africa’s catsharks due to a high level of morphological stasis. As comprehensive and curated DNA reference libraries are required for the reliable identification of specimens from morphologically similar species, this study reviewed and contributed to the availability of cytochrome c oxidase subunit I (COI) and nicotinamide adenine dehydrogenase subunit 2 (NADH2) sequences for South Africa’s catsharks. A molecular taxonomic approach, implementing species delimitation and specimen assignment methods, was used to assess and highlight any taxonomic uncertainties and/or errors in public databases. The investigated species were summarised into 47 molecular operational taxonomic units (MOTUs), with some conflicting specimen assignments. Two Apristurus specimens sampled in this study remained unidentified, revealing the presence of previously undocumented genetic diversity. In contrast, haplotype sharing within Haploblepharus—attributed to nucleotide ambiguities—resulted in the delimitation of three congeners into a single MOTU. This study reveals that molecular taxonomy has the potential to flag undocumented species and/or misidentified specimens, and further highlights the need to implement integrated taxonomic assessments on catsharks that represent an irreplaceable component of biodiversity in the region.

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Balkrishna, Acharya, Ajay Kumar Gautam, Shubhi Avasthi, Mekala Niranjan, Rajnish Kumar Verma, Vedpriya Arya, Ashwani Kumar, Samantha C. Karunarathna, and Nakarin Suwannarach. "A Comprehensive Account of the Rust Genus Skierka (Skierkaceae)." Journal of Fungi 8, no. 12 (November 24, 2022): 1243. http://dx.doi.org/10.3390/jof8121243.

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The rust genus Skierka belonging to the phylum Basidiomycota was described in 1900 by Raciborski with Skierka canarii as the type species. The published literature on this rust genus reveals its ambiguity in taxonomic placement. It was challenging to taxonomically delineate and precisely identify each species within this genus due to the species sharing some common characteristics. The latest studies based on morphology taxonomy and molecular characteristics, however, have solved this puzzle now and placed this genus in its new family Skierkaceae. To understand all about the genus Skierka, this compilation was carried out to unveil the general characteristics, history, diversity, distribution, ecology, morphology and molecular taxonomy of different species of Skierka. After exploring 14 species of Skierka, it was observed that this genus is distributed in seven plant families in 19 countries all over the world. The genus appears to be well-represented in Asian and South American counties. This rust has not been reported from any European countries to date. The morpho-taxonomy of all species is well studied, but molecular analyses are still required. Only two species of the genus namely S. robusta and S. diploglottidis were identified based molecular analyses. Therefore, further studies should be focused on epitypifying the taxa that are too old and updating their taxonomy based on molecular, biochemical, and physiological aspects along with morphological characteristics. Multiple analytical methods should be considered when dealing with multi-locus datasets. This will increase our understanding of the diversity, distribution, and identification of these rust fungi.

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Raven, Peter H. "Taxonomy: where are we now?" Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1444 (April 29, 2004): 729–30. http://dx.doi.org/10.1098/rstb.2004.1462.

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Mirza, Zeeshan A., Editorial office H. T. Lalremsanga, Harshal Bhosale, Gaurang Gowande, Harshil Patel, Sabira S. Idiatullina, and Nikolay A. Poyarkov. "Systematics of Trimeresurus popeiorum Smith, 1937 with a revised molecular phylogeny of Asian pitvipers of the genus Trimeresurus Lacépède, 1804 sensu lato." Evolutionary Systematics 7, no. 1 (February 24, 2023): 91–104. http://dx.doi.org/10.3897/evolsyst.7.97026.

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The pit viper snake genus Trimeresurus Lacépède, 1804 sensu lato, is a diverse group of nocturnal serpents comprising over 61 species. The genus is morphologically heterogeneous and has been divided into several subgenera. We present an updated phylogeny of Asian pitvipers and propose a revised classification. Additionally, we revise the taxonomy of T. popeiorum Smith, 1937 and propose taxonomic changes with support from molecular and morphological data. We restrict T. popeiorumsensu stricto to northeastern India, Bangladesh, southern China, and northern Myanmar; populations beyond these areas require further assessment. We also synonymize T. yingjiangensisChen et al., 2019 with T. popeiorum based on overlapping morphological characters, molecular data, and distribution. The findings shed new light on the taxonomy of T. popeiorum, warranting the need for assessing the population of T. popeiorum from southeast Asia.

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Journal articles on the topic 'Molecular taxonomy'

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