Taxonomy and fossils: a critical appraisal (original) (raw)
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Extinct Taxa in an Extant World: Working towards better fossil taxonomic representation
Biodiversity Information Science and Standards
Paleontology collections face many similar challenges mobilizing taxonomic data as extant collections disciplines: from complex nomenclatural histories to incomplete taxonomic authorities to questionable specimen identifications. These challenges exist within the information management of an individual institution and are amplified at the level of data aggregation, where a minor misspelling of authorship or a historic name can completely erase the discoverability of a specimen. In addition to those challenges shared with extant taxonomy, fossil taxonomy must also address uncertainty in far more detail and at many levels. It may be impossible to assign a name into the traditional Linnaean hierarchy or to provide classification at higher ranks due to uncertainty in our understanding of how the specimen is related to other known taxa. Moreover, some branches of paleontology prefer not to use Linnaean ranks at all, making it even more difficult to map concepts and/or clade names to term...
Palynology, 2021
Effective communication of taxonomic concepts is crucial to meaningful application in all biological sciences, and thus the development and following of best practices in taxonomy and the formulation of clear and practical rules of nomenclature underpin a wide range of scientific studies. The International Code of Nomenclature for algae, fungi and plants (the Code), currently the Shenzhen Code of 2018, provides these rules. Although early versions of the Code were designed mainly with extant plants in mind, the Code has been increasingly used for fossil 2 plants and, in recent decades, for organic-walled microfossils, the study of which is called palaeopalynology, or simply palynology. However, rules embodied in the Code do not fully reflect the needs and practices of this discipline; and taxonomic practices between fossil applications, especially in palynology, have tended to diverge from practices for extant plants. Differences in these rules and practices present specific challenges. We therefore review the Shenzhen Code as it applies to palynology, clarifying procedures and recommending approaches based on best practices, for example, in the designation and use of nomenclatural types. The application of nomenclatural types leads to taxonomic stability and precise communication, and lost or degraded types are therefore problematic because they remove the basis for understanding a taxon. Such problems are addressed using examples from the older European literature in which type specimens are missing or degraded. A review of the three most important conventions for presenting palynological taxonomic information, synonymies, diagnoses/descriptions and illustrations, concludes with recommendations of best practices. Palynology continues to play an important role in biostratigraphy, basin analysis, and evolutionary studies, and is contributing increasingly to our understanding of past climates and ocean systems. To contribute with full potential to such applied studies, consistent communication of taxonomic concepts, founded upon clear rules of nomenclature, is essential.
Naming taxa from cladograms: some confusions, misleading statements, and necessary clarifications
Cladistics, 2007
on the taxonomy and nomenclature of American ranid frogs. His paper consists not only in a reply to my paper, as it contains in fact three distinct kinds of statements: (1) an attempt to ''save'' the new generic nomina proposed by from being considered nomina nuda under the Code; (2) another plea for the superiority of the Phylocode over the Code, especially as regards the absence of a Rule of Coordination and the substitution of ''phylogenetic definition'' of nomina to the use of onomatophores for the allocation of nomina to taxa; (3) a plea for ''taxonomic stability'' in order not to upset the traditional use of nomina and to please users of electronic data bases. These three points are here commented, as follows: (1) even with the best goodwill, under the rules of the Code it is possible to ''save'' only three or four of the seven new nomina of Hillis and Wilcox , the others being indeed nomina nuda; furthermore, three of these seven nomina are definitively useless and redundant, being junior objective synonyms of other generic nomina; (2) the well-known arguments against the Phylocode do not need to be repeated in detail once again, the most important one being that replacement of a secular nomenclatural system by another one, whose theoretical and practical superiority is highly questionable, would cause considerable chaos and detract taxonomists from their urgent task of accelerating the collection, study and description of the living species of our planet; (3) the claim for taxonomic and nomenclatural stability ignores the importance of the taxonomic impediment and sends a misleading message to the scientific community and to society as a whole: in the present situation of our knowledge, taxonomic stability is ignorance, and the science of taxonomy would have much to lose to adapt its concepts and practices to the needs of databases at the expense of scientific quality. It is once again stressed that, for the quality and accuracy of communication between evolutionary biologists, and above all with other biologists and non-biologists, it is urgent that scientific periodicals impose the use of different systems of notation of nomina following distinct nomenclatural systems, such as the Code and the Phylocode.
To name or not to name: Criteria to promote economy of change in Linnaean classification schemes
Zootaxa, 2013
The Linnaean classification system provides the universal reference system for communicating about the diversity of life and its hierarchic history. Several limitations that challenge the stability of this system have been identified and, as a result, alternative systems have been proposed since its early inception. The revolution caused by molecular phylogenetics has, more than ever, exemplified that Linnaean classification schemes are subject to a degree of instability that may hamper their significance and communication power. Our analysis of recent changes in the classification of several groups of organisms, with a focus on amphibians and reptiles, reveals two main sources of instability: (i) revisionary, objective (empirical) changes based on the discovery of unambiguous instances of non-monophyly and on progress in the Globe's species inventory, and (ii) subjective changes based on author preferences or on a poor analysis of the advantages and limitations of new classification schemes. To avoid subjective taxonomic instability, we review and elaborate proposals for the assignment of Linnaean rank to clades, and thereby for the naming of these clades as Linnaean taxa (Taxon Naming Criteria: TNCs). These are drafted from the perspective of practicing taxonomists and can help choosing among alternative monophyly-based classifications under a premise of economy of change. We provide a rationale for each TNC along with real and theoretical examples to illustrate their practical advantages and disadvantages. We conclude that not all TNCs lead to equally informative and stable taxonomies. Therefore, we order the various TNCs by the generality of their implications and provide a workflow scheme to guide the procedure of taxonomic decisions concerning the creation or modification of supraspecific classifications. The following criteria are considered primary when naming taxa: (i) Monophyly of the taxon in an inferred species tree; (ii) Clade Stability, i.e., the monophyly of a clade to be named as taxon should be as strongly supported as possible by various methods of tree inference, tests of clade robustness, and different data sets; and (iii) Phenotypic Diagnosability, i.e., ranked supraspecific taxa should be those that are phenotypically most conspicuous although in phenotypically cryptic groups of organisms it can be warranted to name taxa based on molecular differences alone. We consider various other criteria as secondary (i.e., the Time Banding, Biogeography, Adaptive Zone, and Hybrid Viability TNCs) and refute using them as sole arguments for the modification of established classifications or proposal of new ones. Taxonomists are encouraged to be explicit and consistent when applying TNCs for creating or modifying classifications. We emphasize that, except for monophyly, the priority TNCs are not proposed as mandatory requisites of a Linnaean taxon but as yardsticks to allow for an informed choice among various clades in a tree that could alternatively be named as Linnaean taxa. Despite a need for plurality, classifications should avoid deliberately violating any of the three primary TNCs because taxa of unstable monophyly or poor diagnosability reduce the information content and hence the utility of the Linnaean system.
2018
Morphology, or shapes, particularly of bones, is important for understanding how animals vary and, therefore, for understanding diversity. Comparison of morphology in animals can be used to make inferences on fossil organisms. At its base, fossil specimens are described and compared with other fossil and modern specimens, often to determine if they represent a new and distinct species, thereby increasing observed biodiversity through time. Dromaeosaurids (family Dromaeosauridae) are a group of dynamic, swift predatory dinosaurs, that have a sparse fossil record, particularly at the time of their extinction near the Cretaceous-Paleogene boundary. A recently recovered specimen from the latest Cretaceous of New Mexico represents a new genus and species and is the first diagnostic dromaeosaurid from the Maastrichtian of the southern United States (southern Laramidia). The specimen also reveals aspects of this dinosaurs behavior, including potential wounds or injuries consistent with an active predatory lifestyle, features that would have made it agile, and the presence of feathers on its forelimbs. The evolutionary relationships of this dinosaur were explored through phylogenetic analysis and shows multiple lineages of these dinosaurs at the end of the Cretaceous in North America. Additionally, the Maastrichtian members of these dinosaurs would have also been living in the same environments as the largest terrestrial predators known, the tyrannosaurids, with different species in the north and south living alongside different tyrannosaurid species, creating complex ecosystems with different sized predators presumably utilizing different predatory methods. Emydids (family Emydidae) are the most diverse and widespread family of turtles in the New World. Their fossil record is relatively well known, but more complete fossils are less common and little work has been done to understand the relationships of potential fossil members. New species within both subfamilies (Deirochelyinae and Emydinae) from approximately 5 million years ago increase our knowledge of the past biodiversity of the group. A new painted turtle helps show how Chrysemys has migrated through time and part of these biogeographic changes are controlled by temperature and climate conditions. A new species of Emydoidea represents the southern-most occurrence of the genus and suggests the physiological requirements of the species have changed through time. A new species of Terrapene shows features consistent with an aquatic or semi-aquatic lifestyle, and its position basally within the genus lends further credence to the hypothesis that the genus evolved from aquatic or semiaquatic ancestors and has evolved to become more terrestrial through time. The new species also help researchers better understand previously known fossil species. Several fossil species considered to represent Chrysemys are found to be basally within the subfamily and potentially outside Chrysemys. Emydoidea lies phylogenetically close to Emys and is part of a clade of emydine turtles that can at least partially close their shells. Features of stem Terrapene species suggest features of T. ornata are basal and further suggests terrestrially has evolved multiple times in the genus or that there have been multiple reinvasions of the water. These studies look at morphological variation to determine the distinct nature of several new fossil species and use phylogenetic analyses to hypothesize evolutionary relationships. This information can be used to make inferences of the direct groups studied and closely related groups, but also can be used to investigate ancient ecosystems and local and regional habitats and climates, along with more generalized larger-scale conditions. These continue to add to our knowledge of biodiversity and increases the information and data we have to use toward further future studies as well.