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Journal articles on the topic 'Molecular taxonomy'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 June 2025

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1

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

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2

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

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3

Tarkhnishvili, David. "Molecular Markers and Taxonomic Explosion in Herpetology: More or Less Robust Taxonomy? True and False Advantages of DNA Markers." International Journal of Zoology and Animal Biology 7, no. 2 (2024): 1–14. http://dx.doi.org/10.23880/izab-16000569.

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Despite the increasing deficit of taxonomic expertise, the number of newly described species since the early 2010s has grown exponentially. This growth is related to the increased use of DNA markers in taxonomic descriptions. However, routine use of DNA markers in taxonomy did not bring practical taxonomy closer to the theory. Species are unique lineages with irreversible evolutionary pathways, and only the presence of distinct populations within the same geographic range, or at least the presence of narrow hybrid zones between the parapatric ranges is a conclusive evidence of evolutionary irreversibility. In the case of allopatric populations, only very high genetic distances, suggesting several tens of millions of years of independent evolution, can be used for validation of species status. This problem cannot be solved by the broader introduction of genomic phylogenies, which also fail to provide robust criteria for evolutionary irreversibility. We can hardly suppose that robust validation of species status is applicable to all or most of hundreds of thousands of animal species, including 20,000 amphibians and reptiles. Instead, practical taxonomy should concentrate on describing recognizable species, maintaining a trade-off between sufficiently detailed descriptions of world biodiversity and the applicability of these descriptions for practical use and metaanalyses, not pretending that formally described species reflect real lineages with independent and irreversible evolutionary pathways. Simultaneously, the non-critical elevation of the taxonomic status of individual geographic populations, contrary to the declared purpose of better-focusing conservation efforts, often has the opposite effect, leaving many formally described taxa outside the conservation umbrella.

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4

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 (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 (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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6

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 (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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7

Shelke, Rahul G., Yogesh Lahane, Priyanka Ingle, et al. "Advances in Plant Molecular Taxonomy: Techniques, Challenges, and Applications." PLANT CELL BIOTECHNOLOGY AND MOLECULAR BIOLOGY 26, no. 3-4 (2025): 89–110. https://doi.org/10.56557/pcbmb/2025/v26i3-49210.

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Advances in plant molecular taxonomy have revolutionized species identification and classification, overcoming the limitations of traditional morphology-based approaches. These challenges include cryptic species, hybridization, and phenotypic plasticity complicate the distinction of closely related taxa. Molecular techniques, including DNA barcoding and plastid genome analysis, have emerged as powerful tools to address these issues. DNA barcoding, utilizing standardized genetic markers such as rbcL, matK, and ITS regions, has become indispensable for species identification, biodiversity assessment, and conservation efforts. The integration of NGS technologies has further enhanced molecular taxonomy, enabling large-scale genomic and transcriptomic studies. Plastid genome sequencing has provided deeper insights into plant phylogenetics, resolving complex evolutionary relationships and taxonomic ambiguities. Despite challenges like limited marker variability and incomplete databases, advancements in NGS, third-generation sequencing, and bioinformatics are expanding the frontiers of molecular taxonomy. Emerging technologies, including SNP analysis, RAD-seq, and machine learning are offering new opportunities for exploring plant diversity. Future directions will focus on expanding genomic databases, integrating phenotypic and molecular data, and applying these tools for large-scale biodiversity monitoring. These efforts will ensure continued progress in plant taxonomy, systematics, and conservation, particularly in the face of global environmental change.

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8

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

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9

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

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10

Venu, Potharaju, and Munivenkatappa Sanjappa. "Morpho-taxonomy and molecular intrusion!" Current Science 127, no. 12 (2024): 1397. https://doi.org/10.18520/cs/v127/i12/1397-1402.

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11

Banushree CS. "Molecular taxonomy of gastric carcinoma." Indian Journal of Pathology and Oncology 11, no. 3 (2024): 218–19. http://dx.doi.org/10.18231/j.ijpo.2024.049.

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12

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

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13

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

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14

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

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15

Mandal, Fatik Baran. "Hurdle in taxonomy: A case of malaria parasites and other Haemosporidia." Open Veterinary Science 2, no. 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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16

ZHANG, ZHI-QIANG. "Contributing to the progress of descriptive taxonomy." Zootaxa 1968, no. 1 (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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17

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

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18

Walter, Helmut E., and Pablo C. Guerrero. "Towards a unified taxonomic catalogue for the Chilean cacti: assembling molecular systematics and classical taxonomy." Phytotaxa 550, no. 2 (2022): 79–98. https://doi.org/10.11646/phytotaxa.550.2.1.

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Walter, Helmut E., Guerrero, Pablo C. (2022): Towards a unified taxonomic catalogue for the Chilean cacti: assembling molecular systematics and classical taxonomy. Phytotaxa 550 (2): 79-98, DOI: 10.11646/phytotaxa.550.2.1

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19

Arrigoni, Roberto, Jarosław Stolarski, Tullia I. Terraneo, et al. "Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae." Contributions to Zoology 92, no. 2 (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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20

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 (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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21

Koren, Anamarija, Vladimir Sikora, Biljana Kiprovski, et al. "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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22

Samson, Robert A. "Constraints associated with taxonomy of biocontrol fungi." Canadian Journal of Botany 73, S1 (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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23

Canino, Alexis, Agnès Bouchez, Christophe Laplace-Treyture, Isabelle Domaizon, and Frédéric Rimet. "Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations." Metabarcoding and Metagenomics 5 (December 15, 2021): e74096. https://doi.org/10.3897/mbmg.5.74096.

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Methods for biomonitoring of freshwater phytoplankton are evolving rapidly with eDNA-based methods, offering great complementarity with microscopy. Metabarcoding approaches have been more commonly used over the last years, with a continuous increase in the amount of data generated. Depending on the researchers and the way they assigned barcodes to species (bioinformatic pipelines and molecular reference databases), the taxonomic assignment obtained for HTS DNA reads might vary. This is also true for traditional taxonomic studies by microscopy with regular adjustments of the classification and taxonomy. For those reasons (leading to non-homogeneous taxonomies), gap-analyses and comparisons between studies become even more challenging and the curation processes to find potential consensus names are time-consuming. Here, we present a web-based application (Phytool), developed with ShinyApp (Rstudio), that aims to make the harmonisation of taxonomy easier and in a more efficient way, using a complete and up-to-date taxonomy reference database for freshwater microalgae. Phytool allows users to homogenise and update freshwater phytoplankton taxonomical names from sequence files and data tables directly uploaded in the application. It also gathers barcodes from curated references in a user-friendly way in which it is possible to search for specific organisms. All the data provided are downloadable with the possibility to apply filters in order to select only the required taxa and fields (e.g. specific taxonomic ranks). The main goal is to make accessible to a broad range of users the connection between microscopy and molecular biology and taxonomy through different ready-to-use functions. This study estimates that only 25% of species of freshwater phytoplankton in Phytobs are associated with a barcode. We plead for an increased effort to enrich reference databases by coupling taxonomy and molecular methods. Phytool should make this crucial work more efficient. The application is available at https://caninuzzo.shinyapps.io/phytool_v1/

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24

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

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25

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

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26

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

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27

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

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28

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

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29

Mahmoud, Mahmoud Gaber, and Asmaa Ahmed Abdelbaset. "Molecular Taxonomy Toward Personalized MDS Management." Sohag Medical Journal 29, no. 2 (2025): 35–48. https://doi.org/10.21608/smj.2025.346164.1519.

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30

Cai, Feng, and Irina S. Druzhinina. "In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma." Fungal Diversity 107, no. 1 (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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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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32

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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Mou, Feng-Juan, Xiu Hu, Bui Thu Ha, and Nguyen Manh Cuong. "Taxonomic revision of Bergera J.Koenig ex L. (Rutaceae) based on the molecular phylogeny and morphology." European Journal of Taxonomy 860 (March 1, 2023): 141–80. https://doi.org/10.5852/ejt.2023.860.2057.

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Mou, Feng-Juan, Hu, Xiu, Ha, Bui Thu, Cuong, Nguyen Manh (2023): Taxonomic revision of Bergera J.Koenig ex L. (Rutaceae) based on the molecular phylogeny and morphology. European Journal of Taxonomy 860: 141-180, DOI: 10.5852/ejt.2023.860.2057

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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 (2023): 245–451. http://dx.doi.org/10.21608/jpp.2023.209588.1240.

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Elkan, G. H. "Taxonomy of the rhizobia." Canadian Journal of Microbiology 38, no. 6 (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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Liu, Jing, Huixin Xu, Ziqing Wang, et al. "Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini)." Insects 15, no. 7 (2024): 508. http://dx.doi.org/10.3390/insects15070508.

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To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.

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Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.

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(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.

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Galimberti, Andrea, Martina Spada, Danilo Russo, et al. "Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy." PLoS ONE 7, no. 6 (2012): e40122. https://doi.org/10.5281/zenodo.13484858.

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(Uploaded by Plazi for the Bat Literature Project) Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy.

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Florence, Rousseau, Gey Delphine, and Kurihara Akira. "Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus." European Journal of Taxonomy 269 (December 31, 2017): 1–19. https://doi.org/10.5852/ejt.2017.269.

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Florence Rousseau, Delphine Gey, Akira Kurihara (2017): Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus. European Journal of Taxonomy 269: 1-19, DOI: 10.5852/ejt.2017.269

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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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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 (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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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 (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, et al. "A refined molecular taxonomy of breast cancer." Oncogene 31, no. 9 (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 (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 (2006): 101–3. http://dx.doi.org/10.1080/13102818.2006.10817349.

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Abeshouse, Adam, Jaeil Ahn, Rehan Akbani, et al. "The Molecular Taxonomy of Primary Prostate Cancer." Cell 163, no. 4 (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 (2016): 73–82. http://dx.doi.org/10.1016/j.clon.2015.11.001.

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