Journal articles: 'Taxonomy; Systematics'

1

Small, Ernest. "SYSTEMATICS OF BIOLOGICAL SYSTEMATICS (OR, TAXONOMY OF TAXONOMY)." TAXON 38, no. 3 (August 1989): 335–56. http://dx.doi.org/10.2307/1222265.

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Post, Rory. "Taxonomy and systematics." Parasitology Today 11, no. 6 (June 1995): 224. http://dx.doi.org/10.1016/0169-4758(95)80083-2.

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Gotelli, Nicholas J. "A taxonomic wish–list for community ecology." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 359, no. 1444 (April 29, 2004): 585–97. http://dx.doi.org/10.1098/rstb.2003.1443.

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Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet–based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.

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Klazenga, Niels. "Generic concepts in Australian mosses." Australian Systematic Botany 18, no. 1 (2005): 17. http://dx.doi.org/10.1071/sb04014.

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The impact of changes in generic concepts as a result of changes in philosophy and methodology associated with phylogenetic systematics on the taxonomy of Australian mosses is discussed. It is concluded that, while phylogenetic systematics has already had a significant impact on the taxonomy of Australian mosses, many taxonomic changes that have occurred in recent years are the result of an enormous taxonomic backlog that is being gradually eliminated. The relative impact of phylogenetic systematics is expected to increase in coming years.

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Cracraft, Joel. "Systematics and Taxonomy of Australian Birds." Pacific Conservation Biology 15, no. 2 (2009): 148. http://dx.doi.org/10.1071/pc090148.

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The Australian avifauna is one of most biologically important in the world. For its size, it has the highest diversity and endemism of any continent. Importantly, as a key piece of Gondwana, it was at a crossroads for the early history of modern birds (Neornithes). Indeed, it has phylogenetically deep lineages of palaeognaths, galliforms, anseriforms, caprimulgiforms, parrots, and songbirds. Moreover, patterns of endemism and diversity are well-marked and provide a natural laboratory for the study of speciation and diversification. All of this is why studies of the systematics and taxonomy of Australian birds are so important, for without a clear understanding of the taxonomic limits of taxa and their relationships we cannot hope to make progress toward answering critical evolutionary questions. Nor can we provide the systematic framework for comparative studies in the organismal sciences, especially behaviour, ecology, and conservation biology.

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Cracraft, Joel. "Systematics and Taxonomy of Australian Birds." Pacific Conservation Biology 16, no. 1 (2010): 67. http://dx.doi.org/10.1071/pc100067.

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The Australian avifauna is one of the most biologically important in the world. For its size, it has the highest diversity and endemism of any continent. Importantly, as a key piece of Gondwana, it was at a crossroads for the early history of modern birds (Neornithes). Indeed, it has phylogenetically deep lineages of palaeognaths, galliforms, anseriforms, caprimulgiforms, parrots, and songbirds. Moreover, patterns of endemism and diversity are well-marked and provide a natural laboratory for the study of speciation and diversification. All of this is why studies of the systematics and taxonomy of Australian birds are so important, for without a clear understanding of the taxonomic limits of taxa and their relationships we cannot hope to make progress toward answering critical evolutionary questions. Nor can we provide the systematic framework for comparative studies in the organismal sciences, especially behaviour, ecology, and conservation biology.

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Chun, Jongsik, and Fred A. Rainey. "Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (February 1, 2014): 316–24. http://dx.doi.org/10.1099/ijs.0.054171-0.

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The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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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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Scudder, G. G. E. "The next 25 years: invertebrate systematics." Canadian Journal of Zoology 65, no. 4 (April 1, 1987): 786–93. http://dx.doi.org/10.1139/z87-125.

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A distinction is made between classification, taxonomy, and systematics. Taxonomic studies in most invertebrate groups will not progress beyond the descriptive stages because of the large number of species to be described, the low profile of taxonomy, and the lack of support for museums. Taxonomy and classification must be seen as immediate economic components of modern biology: systematics should be revived in the universities. The limitations of the morphospecies concept make studies on living forms, freshly killed animals, or specially preserved specimens imperative, but these cannot be completed except in very few instances. Hence we are likely to learn more and more about less and less. Nevertheless, more sibling species complexes will undoubtedly be discovered. When these complexes are understood systematically, and population genetics becomes integrated with the study of speciation, more emphasis will likely be given to the multiplicity of speciation models. A pleuralistic definition of species should follow. Cladistic systematics will continue to expand in the invertebrates. More emphasis should be placed on early Metazoan fossils, and attempts made to fit them into classifications. Fossils can be useful in checking various phylogenetic models, even if they are considered useless for determining evolutionary relationships by some cladists. With the current acceptance that the Protista and Protozoa are both polyphyletic, there will be a major revolution in invertebrate systematics. Ultrastructural and biochemical data are needed to clarify the systematics of both the unicellular eukaryotes and multicellular Metazoa. Only after systematic analyses of wider data sets are complete will it be time to consider a new classification for the "invertebrates." However, the resulting scheme will be very different from that which we accept, follow, and teach today.

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WHEELER, QUENTIN D. "Invertebrate systematics or spineless taxonomy?*." Zootaxa 1668, no. 1 (December 21, 2007): 11–18. http://dx.doi.org/10.11646/zootaxa.1668.1.3.

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What progress has been made since these words were written by Wilson more than twenty years ago? The answer is a mixed one. We have so far to go in our inventory of Earth’s species that it is easy to be discouraged by advances measured in hundreds of thousands of new species rather than millions. Yet there has been progress and the potential exists for rapid advances. Excellent work continues to be done as evidenced by this special issue of ZooTaxa and the burgeoning popularity of this e-journal. Innovative new funding has appeared at the U. S. National Science Foundation including the Partnerships to Enhance Expertise in Taxonomy (PEET), Assembling the Tree of Life (AToL), and particularly encouraging, the Revisionary Syntheses in Systematics (RevSys) and Planetary Biodiversity Inventory (PBI) projects that focus specifically on descriptive taxonomy. Most promising is an emerging new field, cybertaxonomy, that represents the convergence of traditional taxonomic goals with new, equally ambitious ones, fueled by the full potential of cyberinfrastructure, digital technology, information science, and computer engineering (Atkins et al. 2003, Page et al. 2005, Wheeler 2004, Wheeler et al. 2004).

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Levanova, L. A., and Yu V. Zakharova. "SYSTEMATICS, TAXONOMY AND CLASSIFICATION OF BACTERIA." Fundamental and Clinical Medicine 2, no. 1 (2017): 91–101. http://dx.doi.org/10.23946/2500-0764-2017-2-1-91-101.

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Kanzaki, N. "Taxonomy and Systematics of Bursaphelenchus Nematodes." Journal of the Japanese Forest Society 88, no. 5 (2006): 392–406. http://dx.doi.org/10.4005/jjfs.88.392.

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13

Astley, W. Graham. "Organizational Systematics: Taxonomy, Evolution, Classification.Bill McKelvey." American Journal of Sociology 91, no. 2 (September 1985): 456–59. http://dx.doi.org/10.1086/228300.

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14

Chesser, R. Terry. "Systematics and Taxonomy of Australian Birds." Systematic Biology 58, no. 6 (October 6, 2009): 659–61. http://dx.doi.org/10.1093/sysbio/syp071.

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15

Martens, Koen, and Hendrik Segers. "Taxonomy and systematics in biodiversity research." Hydrobiologia 542, no. 1 (July 2005): 27–31. http://dx.doi.org/10.1007/s10750-005-0892-z.

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Smith, Gideon F., and Estrela Figueiredo. "Capacity building in taxonomy and systematics." TAXON 58, no. 3 (August 2009): 697–99. http://dx.doi.org/10.1002/tax.583001.

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Michalik, Peter, and Łukasz Michalczyk. "Taxonomy, Systematics and Evolution of Tardigrada." Zoologischer Anzeiger 292 (May 2021): 29. http://dx.doi.org/10.1016/j.jcz.2021.03.001.

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Patterson, David J., David Remsen, William A. Marino, and Cathy Norton. "Taxonomic Indexing—Extending the Role of Taxonomy." Systematic Biology 55, no. 3 (June 1, 2006): 367–73. http://dx.doi.org/10.1080/10635150500541680.

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YEATES, DAVID K., AINSLEY SEAGO, LEIGH NELSON, STEPHEN L. CAMERON, LEO JOSEPH, and JOHN W. H. TRUEMAN. "Integrative taxonomy, or iterative taxonomy?" Systematic Entomology 36, no. 2 (November 22, 2010): 209–17. http://dx.doi.org/10.1111/j.1365-3113.2010.00558.x.

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Hoffman, Joel Christopher, Christy Meredith, Erik Pilgrim, Anett Trebitz, Chelsea Hatzenbuhler, John Russell Kelly, Gregory Peterson, Julie Lietz, Sara Okum, and John Martinson. "Comparison of larval fish detections using morphology-based taxonomy versus high-throughput sequencing for invasive species early detection." Canadian Journal of Fisheries and Aquatic Sciences 78, no. 6 (June 2021): 752–64. http://dx.doi.org/10.1139/cjfas-2020-0224.

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When first introduced, invasive species typically evade detection; DNA barcoding coupled with high-throughput sequencing (HTS) may be more sensitive and accurate than morphology-based taxonomy and thereby improve invasive (or rare) species detection. We quantified the relative error of species detection between morphology-based and HTS-based taxonomic identification of ichthyoplankton collections from the Port of Duluth, Minnesota, an aquatic non-native species introduction “hot-spot” in the Laurentian Great Lakes. We found HTS-based taxonomy identified 28 species and morphology-based taxonomy identified 30 species, of which 27 were common to both. Among samples, 76% of family-level taxonomic assignments agreed; however, only 42% of species assignments agreed. Most errors were attributed to morphology-based taxonomy, whereas HTS-based taxonomy error was low. For this study system, for most non-native fishes, the detection probability by randomized survey for larvae was similar to that by a survey that is optimized for non-native species early detection of juveniles and adults. We conclude that classifying taxonomic errors by comparing HTS results against morphology-based taxonomy is an important step toward incorporating HTS-based taxonomy into biodiversity surveys.

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Lilburn, Timothy G., and George M. Garrity. "Exploring prokaryotic taxonomy." International Journal of Systematic and Evolutionary Microbiology 54, no. 1 (January 1, 2004): 7–13. http://dx.doi.org/10.1099/ijs.0.02749-0.

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Techniques drawn from exploratory data analysis, using tools found in the S-Plus statistical software package, have been used to inspect and maintain the Bergey's Taxonomic Outline and to move towards an automated and community-based means of working on the outline. These techniques can be used to classify sequences from unnamed and uncultured organisms, to visualize errors in the taxonomy or in the curation of the sequences, to suggest emendations to the taxonomy or to the classification of extant species and to complement the visualization of phylogenies based on treeing methods. A dataset of more than 9200 aligned small-subunit rRNA sequences was analysed in the context of the current taxonomic outline. The use of the algorithm in exploring and modifying the taxonomy is illustrated with an example drawn from the family Comamonadaceae.

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Pires, Amanda Ciprandi, and Luciane Marinoni. "DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies." Biota Neotropica 10, no. 2 (June 2010): 339–46. http://dx.doi.org/10.1590/s1676-06032010000200035.

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

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Christoffersen, Martin L. "Cladistic Taxonomy, Phylogenetic Systematics, and Evolutionary Ranking." Systematic Biology 44, no. 3 (September 1995): 440. http://dx.doi.org/10.2307/2413605.

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Last, Peter R. "The state of chondrichthyan taxonomy and systematics." Marine and Freshwater Research 58, no. 1 (2007): 7. http://dx.doi.org/10.1071/mf07003.

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Christoffersen, Martin L. "Cladistic Taxonomy, Phylogenetic Systematics, and Evolutionary Ranking." Systematic Biology 44, no. 3 (September 1995): 440–54. http://dx.doi.org/10.1093/sysbio/44.3.440.

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Miranda, Lucília S., Yayoi M. Hirano, Claudia E. Mills, Audrey Falconer, David Fenwick, Antonio C. Marques, and Allen G. Collins. "Systematics of stalked jellyfishes (Cnidaria: Staurozoa)." PeerJ 4 (May 5, 2016): e1951. http://dx.doi.org/10.7717/peerj.1951.

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Staurozoan classification is highly subjective, based on phylogeny-free inferences, and suborders, families, and genera are commonly defined by homoplasies. Additionally, many characters used in the taxonomy of the group have ontogenetic and intraspecific variation, and demand new and consistent assessments to establish their correct homologies. Consequently, Staurozoa is in need of a thorough systematic revision. The aim of this study is to propose a comprehensive phylogenetic hypothesis for Staurozoa, providing the first phylogenetic classification for the group. According to our working hypothesis based on a combined set of molecular data (mitochondrial markers COI and 16S, and nuclear markers ITS, 18S, and 28S), the traditional suborders Cleistocarpida (animals with claustrum) and Eleutherocarpida (animals without claustrum) are not monophyletic. Instead, our results show that staurozoans are divided into two groups, herein named Amyostaurida and Myostaurida, which can be distinguished by the absence/presence of interradial longitudinal muscles in the peduncle, respectively. We propose a taxonomic revision at the family and genus levels that preserves the monophyly of taxa. We provide a key for staurozoan genera and discuss the evolution of the main characters used in staurozoan taxonomy.

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Ivanyuk, Halyna. "Analysis of “Systematics of Polish Soils”." Visnyk of the Lviv University. Series Geography, no. 44 (November 28, 2013): 122–32. http://dx.doi.org/10.30970/vgg.2013.44.1210.

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The “Systematics of Polish Soils” (SgP, 2011) is very close to WRB and “Soil Taxonomy”. The morphological characteristics of the soils, investigated in the field, rather than soil genesis are diagnostic criteria. The main provisions of the new “Systematics”, properties of soils of higher taxonomic levels have been reviewed. Some diagnostic horizons, which were not borrowed from other classifications, have been described. We tried to find equivalents in the Ukrainian classification for some soils names. The correlation of Poland soils and WRB has been analyzed. Key words: Systematics of Polish Soils, classification, order, soil type, diagnostic horizon, WRB.

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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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CAIRA, JANINE N. "Synergy advances parasite taxonomy and systematics: an example from elasmobranch tapeworms." Parasitology 138, no. 13 (June 9, 2011): 1675–87. http://dx.doi.org/10.1017/s0031182011000643.

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SUMMARYThe synergism facilitated by a series of recent developments has conspired to catalyze rapid advancements in the taxonomy and systematics of elasmobranch tapeworms. These developments are: (1) increased interest in global biodiversity; (2) globalization-facilitated communication; (3) enhanced microscopic and digital technologies; (4) availability of web-based taxonomic resources; (5) ease of use and low cost of molecular techniques and (6) the impressive repertoire of available phylogenetic methods. As a consequence, an estimation of global elasmobranch tapeworm diversity is now within our grasp, as is a basic understanding of the effort and resources required to complete the discovery and description of this fauna globally. The generation of robust hypotheses of the phylogenetic relationships for most elasmobranch-parasitizing cestode orders is also well underway. An international community of cestodologists has emerged and through their sharing of knowledge and specimens is making great strides towards expanding knowledge of the cestode fauna of vertebrates worldwide. It is important that these efforts continue to move forward in a collaborative fashion, integrating morphological and molecular data, but also fully engaging elasmobranch taxonomists and systematists. It is equally important that efforts to characterize and describe global biodiversity are not derailed by such seductive, but ultimately unrewarding impracticable initiatives as molecular taxonomy. Integrated taxonomy is certainly not for the feint of heart, but those with the courage to pursue this strategy will be responsible for maintaining and enhancing the biologically relevant context required for effective species recognition well into the future.

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Ramasamy, Dhamodharan, Ajay Kumar Mishra, Jean-Christophe Lagier, Roshan Padhmanabhan, Morgane Rossi, Erwin Sentausa, Didier Raoult, and Pierre-Edouard Fournier. "A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (February 1, 2014): 384–91. http://dx.doi.org/10.1099/ijs.0.057091-0.

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Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.

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Johnson, Norman F. "A collaborative, integrated and electronic future for taxonomy." Invertebrate Systematics 25, no. 5 (2011): 471. http://dx.doi.org/10.1071/is11052.

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The Platygastroidea Planetary Biodiversity Inventory is a large-scale, multinational effort to significantly advance the taxonomy and systematics of one group of parasitoid wasps. Based on this effort, there are some clear steps that should be taken to increase the efficiency and throughput of the taxonomic process. Increased collaboration among taxonomic specialists can significantly shorten the timeline and add increased rigor to the development of hypotheses of characters and taxa. Species delimitations should make use of multiple data sources, thus providing more nearly independent tests of these hypotheses. Taxonomy should fully embrace electronic media and informatics tools. Particularly, this step requires the development and widespread implementation of community data standards. The barriers to progress in these areas are not technological, but are primarily social. The community needs to see clear evidence of the value added through these changes in procedures and insist upon their use as standard practice.

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Huber, John T., and David W. Langor. "Systematics: Its role in supporting sustainable forest management." Forestry Chronicle 80, no. 4 (August 1, 2004): 451–57. http://dx.doi.org/10.5558/tfc80451-4.

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Understanding the natural world around us requires knowledge of its component parts. From an ecological function perspective, these parts are species. Partitioning the world of living things into distinguishable, universally recognized species, each with a unique scientific name, is difficult, especially when one considers the numerous kinds of microscopic organisms that make up most of the planet's biodiversity. Biosystematics is the study of the origin of biological diversity and the evolutionary relationships among species and higher-level groups (taxa). Taxonomy is the theory and practice of identifying, describing, naming and classifying organisms. Despite the emergence of national and international issues and programs concerning conservation of biodiversity, climate change and invasive alien organisms, all of which demand significant taxonomic input and require an increased investment in systematics, Canada's investment in this discipline has not risen to meet the challenge. Since the mid-1970s the number of taxonomists employed by the federal government has been reduced by about one half. Canada must do more than maintain the inadequate status quo by increasing its investment in systematics in order to meet our nation's obligations, both domestically and internationally. Key words: systematics, taxonomy, definitions, importance for biology, sustainable forestry, biodiversity, invasive pests

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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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Holzenthal, Ralph W., Desiree R. Robertson, Steffen U. Pauls, and Patina K. Mendez. "Taxonomy and systematics: contributions to benthology andJ-NABS." Journal of the North American Benthological Society 29, no. 1 (March 2010): 147–69. http://dx.doi.org/10.1899/08-065.1.

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INGLIS, W. GRANT. "Characters: the central mystery of taxonomy and systematics." Biological Journal of the Linnean Society 44, no. 2 (October 1991): 121–39. http://dx.doi.org/10.1111/j.1095-8312.1991.tb00611.x.

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Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kersters, and J. Swings. "Polyphasic taxonomy, a consensus approach to bacterial systematics." Microbiological reviews 60, no. 2 (1996): 407–38. http://dx.doi.org/10.1128/mmbr.60.2.407-438.1996.

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Vandamme, P., B. Pot, M. Gillis, P. de Vos, K. Kersters, and J. Swings. "Polyphasic taxonomy, a consensus approach to bacterial systematics." Microbiological reviews 60, no. 2 (1996): 407–38. http://dx.doi.org/10.1128/mr.60.2.407-438.1996.

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Sims, Patricia A. "THE FOSSIL GENUSTROCHOSIRA, ITS MORPHOLOGY, TAXONOMY AND SYSTEMATICS." Diatom Research 3, no. 2 (December 1988): 245–57. http://dx.doi.org/10.1080/0269249x.1988.9705037.

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Dunayev, Evgeny A., Evgeniya N. Solovyeva, and Nikolay A. Poyarkov. "Systematics, Phylogeny, and Evolution of Phrynocephalus (Superspecies przewalskii) (Reptilia: Agamidae)." Russian Journal of Herpetology 28, no. 1 (March 5, 2021): 43–59. http://dx.doi.org/10.30906/1026-2296-2021-28-1-43-59.

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The superspecies przewalskii group of Phrynocephalus includes several taxa with unclear taxonomic status. We analyze a fragment of the mitochondrial DNA gene COI and the body patterns of 275 specimens including type specimens. The results resolve the taxonomy and phylogeny of the group and we provide a diagnostic key for the species.

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DAYRAT, BENOÎT. "Towards integrative taxonomy." Biological Journal of the Linnean Society 85, no. 3 (June 24, 2005): 407–15. http://dx.doi.org/10.1111/j.1095-8312.2005.00503.x.

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Page, Rod. "The New Taxonomy." Biological Journal of the Linnean Society 101, no. 3 (October 19, 2010): 757. http://dx.doi.org/10.1111/j.1095-8312.2010.01547.x.

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Zauner, Hans. "Evolving e-taxonomy." BMC Evolutionary Biology 9, no. 1 (2009): 141. http://dx.doi.org/10.1186/1471-2148-9-141.

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Lipscomb, Diana, N. Platnick, and Q. Wheeler. "The intellectual content of taxonomy: a comment on DNA taxonomy." Trends in Ecology & Evolution 18, no. 2 (February 2003): 65–66. http://dx.doi.org/10.1016/s0169-5347(02)00060-5.

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Thiele, K. R., P. H. Weston, and A. R. Mast. "Paraphyly, modern systematics and the transfer of Dryandra into Banksia (Proteaceae): a response to George." Australian Systematic Botany 28, no. 3 (2015): 194. http://dx.doi.org/10.1071/sb15015.

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The transfer of all species of Dryandra into Banksia in 2007, resulting from phylogenetic studies demonstrating that the latter is paraphyletic with respect to the former, generated controversy in some sections of the community. In a recent paper, Alex George, a taxonomist of long standing and monographer of both genera, criticised the transfer, and its subsequent acceptance by the Australian herbarium and plant systematics community. More broadly, George criticised the direction of modern taxonomy, particularly its basis in phylogenetic analysis and monophyly. His criticisms reflect adherence to a largely pre-Darwinian taxonomic tradition, methodology, practice and conceptual framework. This framework, developed in the late 18th and early 19th centuries, and later operationalised as the phenetic method, has for most taxonomists been superseded by the phylogenetic framework for taxonomy developed by and following Willi Hennig. The criticism of the Dryandra transfer by George and colleagues on one hand, and its acceptance by the majority of practicing systematists on the other, is thus an example of competition between differing paradigms rather than George’s claimed specific shortcomings of the transfer or the analyses on which it was based.

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Oren, Aharon. "Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics." International Journal of Systematic and Evolutionary Microbiology 62, no. 2 (February 1, 2012): 263–71. http://dx.doi.org/10.1099/ijs.0.038653-0.

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The halophilic Archaea of the family Halobacteriaceae (36 genera with 129 species with standing in nomenclature as of November 2011) provide an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods have influenced the way in which the taxonomy of a single group of prokaryotes is treated. This review gives an overview of the taxonomy of the family Halobacteriaceae, showing the impact that methods of phenotypic characterization, numerical taxonomy, chemotaxonomy and especially polar lipid analysis, 16S rRNA gene sequence comparisons, multilocus type analysis and comparative genomics have had on their classification.

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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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Miralles, Aurélien, Teddy Bruy, Katherine Wolcott, Mark D. Scherz, Dominik Begerow, Bank Beszteri, Michael Bonkowski, et al. "Repositories for Taxonomic Data: Where We Are and What is Missing." Systematic Biology 69, no. 6 (April 16, 2020): 1231–53. http://dx.doi.org/10.1093/sysbio/syaa026.

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Abstract Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.]

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BRABY, MICHAEL F. "The merging of taxonomy and conservation biology: a synthesis of Australian butterfly systematics (Lepidoptera: Hesperioidea and Papilionoidea) for the 21^st century." Zootaxa 2707, no. 1 (January 22, 2019): 1. http://dx.doi.org/10.11646/zootaxa.2707.1.1.

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Taxonomy is a major scientific discipline that underpins the preservation of biological diversity, but the discipline of taxonomy itself has, until recently, remained somewhat disconnected from conservation biology. Checklists summarise available taxonomic and systematic knowledge and in part provide a framework to optimise efforts and scarce resources for biodiversity conservation. Butterflies have been identified as a key bioindicator group of invertebrates for monitoring, assessing environmental change and for biodiversity conservation. A revised checklist of the butterflies (Hesperioidea: Hesperiidae and Papilionoidea: Papilionidae, Pieridae, Nymphalidae, Riodinidae, Lycaenidae) of Australia is presented, incorporating recent changes to both the higher and lower systematic levels of classification based on review of the literature, mandatory changes of specific epithets to achieve gender agreement, together with recommended common names. A total of 1,134 available species group names are listed, of which 423 are junior synonyms. Currently, 596 valid lower taxa (i.e. species and subspecies) are recognised in the fauna. Of the valid species, 430 are recorded from Australia, of which 404 occur on the mainland and Tasmania and 26 are restricted to remote oceanic islands. Gender changes affect 40 species/subspecies group names, of which 27 are valid taxa and 13 are junior synonyms. Comments are made on the size and composition of the fauna, taxonomic impediment, species concepts and utility of subspecies. Modelling the rate of species accumulation based on taxonomic research effort over the past 100 years using a generalized logistic function suggests that about 91% of the Australian butterfly fauna has been catalogued so far. A detailed review of known problems concerning the taxonomy among the lower systematic levels (i.e. genera, species and subspecies) is presented as candidates for future systematic research. Although Australian butterflies are relatively well-known taxonomically, it is estimated that there are approximately 40 species yet to be formally recorded/recognised and more than 60 problems at the lower systematic levels in which the nomenclature, taxonomic status of species/subspecies or monophyly of genera need to be resolved.

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Ebach, Malte C., Antonio G. Valdecasas, and Quentin D. Wheeler. "Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation." Cladistics 27, no. 5 (February 17, 2011): 550–57. http://dx.doi.org/10.1111/j.1096-0031.2011.00348.x.

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LÜCKING, ROBERT. "Three challenges to contemporaneous taxonomy from a licheno-mycological perspective." Megataxa 1, no. 1 (January 31, 2020): 78–103. http://dx.doi.org/10.11646/megataxa.1.1.16.

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This paper discusses three issues that challenge contemporaneous taxonomy, with examples from the fields of mycology and lichenology, formulated as three questions: (1) What is the importance of taxonomy in contemporaneous and future science and society? (2) An increasing methodological gap in alpha taxonomy: challenge or opportunity? (3) The Nagoya Protocol: improvement or impediment to the science of taxonomy? The importance of taxonomy in society is illustrated using the example of popular field guides and digital media, a billion-dollar business, arguing that the desire to name species is an intrinsic feature of the cognitive component of nature connectedness of humans. While continuous societal support of a critical mass of taxonomists is necessary to catalogue all species on Earth, it is shown that this is a finite task, and a proposal is made how a remaining 10 million species can be catalogued within 40 years by 1,000 well-trained and dedicated taxonomists, with an investment of $4 billion, corresponding to 0.0001% of the annual global GDP or 0.005% of annual military expenditures. Notorious undercitation of actually used taxonomic resources and lack of coverage of impact metrics for monographs and other taxonomic work that cannot be published in indexed journals is discussed and suggestions are made how this problem can be remedied. An increasing methodological gap in approaches to taxonomy, between classic morphological and advanced genomic studies, affects in particular taxonomists in biodiversity-rich countries and amateurs, also regarding proper training to apply advanced methods and concepts. To counterbalance this problem, international collaborations bringing different expertise to the table and undertaking mutual capacitation are one successful remedy. Classic taxonomy still works for many groups and is a first approach to catalogue species and establish taxon hypotheses, but ultimately each taxonomic group needs to be studied with the array of methods proper to the group, including descriptive work. Finally, the Convention on Biological Diversity (CBD) and the Nagoya Protocol has put additional burden on basic biodiversity science. Using lichenology in Latin America and Brazil as an example, it is shown that the spirit of non-monetary benefit-sharing proper to taxonomy and systematics, namely capacitation, joint publications, and shared reference collections, has been increasingly implemented long before the CBD and the Nagoya Protocol, and does not need additional “policing”. Indeed, the Nagoya Protocol puts the heaviest burden on taxonomy and researchers cataloguing biodiversity, whereas for the intended target group, namely those seeking revenue gain from nature, the protocol may not actually work effectively. The notion of currently freely accessible digital sequence information (DSI) to become subject to the protocol, even after previous publication, is misguided and conflicts with the guidelines for ethical scientific conduct. Through its implementation of the Nagoya Protocol, Colombia has set a welcome precedence how to exempt taxonomic and systematic research from “access to genetic resources”, and hopefully other biodiversity-rich countries will follow this example.

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Journal articles on the topic 'Taxonomy; Systematics'

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