Linnaean Ranks Research Articles

Extinct Taxa in an Extant World: Working towards better fossil taxonomic representation

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 terms in the Linnaean-based Darwin Core standard (DwC, Darwin Core Task Group 2009). Incomplete preservation of fossil specimens also makes it difficult or impossible to identify many specimens to the extant gold standard rank of species. While these specimens are often recorded as precisely as possible (e.g., to a secondary Linnaean rank like subfamily) in local collection management systems, the data are obscured when shared with global aggregators since these ranks do not exist in the DwC framework. The paleontology collections community has been facilitating efforts to address these challenges for many years in an attempt to improve the quality of our data and the treatment of taxonomic information for fossil specimens by aggregators. Most recently, the Paleo Data Working Group has been focusing on the practical matters of digitizing, mobilizing, and promoting the use of specimen data from our collections, and further assessing possible community-sourced solutions that could increase the discoverability of our specimens from a taxonomic entry point. In this talk, we share our explorations into the past and current state of fossil taxonomy in the global landscape (including notable gaps) and its use in paleontology collections, and we also report on possible paths forward. Understanding some of the historical issues with fossil taxonomy in the global landscape has led to a better understanding of root differences between extant and fossil taxonomic data models. The Paleo Data Working Group (Krimmel et al. 2021) has reviewed fossil taxonomic data as it is published through aggregators like the Global Biodiversity Information Facility (GBIF), and identified concrete issues in order to classify systematic pain points. We have discussed existing sources of taxonomic data and the agency of collections professionals to take an active role in working toward new solutions for enhancing and evolving these systems. Opportunities for intentional action have been identified across a spectrum of local to global efforts, and from individual capacity to collaboration across stakeholder groups, connecting with those who can more directly address a particular gap or combine expertise. On the individual scale, we are promoting the adoption of best practices for recording taxonomic data in collections information systems and subsequent mapping to DwC. Through coordination with stakeholder groups, we are hoping to enable paleontologists to provide taxonomic authority information to Catalogue of Life for certain fossil groups in new ways. Working within this space, we have tested new systems for collaborative taxonomic data curation and produced updated community data guidelines for use in paleontology collections, to improve the consistency and quality of mobilized data. Accurately representing extinct taxa in an extant world is a moving target, affected by constantly evolving data standards and technical capacity. For instance, GBIF is moving to an operational model where Catalogue of Life provides the taxonomic backbone, but fossil names are problematic in Catalogue of Life because they cannot always integrate into the single tree of life perspective. Seeking solutions that are inclusive of fossil taxonomy will enable our global corpus of biodiversity data to extend back into deep time and promote new opportunities for synergy and cooperation.

Zoological nomenclature: Suggestions to increase stability and facilitate the naming of Clades.

Taxon names are at the core of communication related to biodiversity. Thus, systems that regulate such names should prevent unnecessary changes. Unfortunately, the current regulatory codes have some articles that produce confusion or, even, generate name instability. To promote nomenclatural stability, while maintaining a system that effectively conveys information about biological diversity and its evolution, we argue in favor of emendations to the current International Code of Zoological Nomenclature (ICZN). We propose that taxon names should be created within an evolutionary framework; ideally, this would mean including a phylogenetic tree or, at the very least, formulating a hypothesis in words based on explicit arguments (homologous traits) for the evolutionary relatedness of taxa, avoiding subjective perceptions. Additionally, we consider that some relatively minor changes of the ICZN would greatly increase name stability; the most relevant modifications that would facilitate long-term stability are: (i) immutability of the species epithet of species names, (ii) intercalation of unranked taxa between formal Linnaean ranks, (iii) elimination of homonyms in taxon names at the genus-group level, and (iv) inclusion of flexible phylogenetic definitions when supraspecific taxa are named.

The meaning of categorical ranks in evolutionary biology

Despite having been utilized for over 250 years, Linnaean ranks are periodically dismissed by some systematists and evolutionary biologists. Here, we discuss recent criticisms and point out that they are often the result of a misunderstanding of both the meaning and the intent of such ranks. Although arbitrary in some cases, ranks contain meaningful taxonomic information, facilitate communication, and serve as proxies for a fully resolved and correctly dated tree of life. Ranks favor communication and evolutionary comparisons, but they do not make assumptions about equal age or diversity for any two taxa with the same Linnaean category.

A taxonomic revision of boas (Serpentes: Boidae).

Large molecular datasets including many species and loci have greatly improved our knowledge of snake phylogeny, particularly within the group including boas (Table 1). Recent taxonomic revisions using molecular phylogenies have clarified some of the previously contentious nomenclature of the group (Wilcox et al. 2002; Lawson et al. 2004; Burbrink 2005; Noonan & Chippindale 2006), resulting in a robust taxonomy that is mostly concordant with the phylogeny as currently known, which includes ~85% of described, extant species (Pyron et al. 2013; Reynolds et al. 2014). However, a few unresolved issues remain, related primarily to the rules of the International Code of Zoological Nomenclature (the Code hereafter) and the application of Linnaean ranks (International Commission on Zoological Nomenclature et al. 1999).

Time to Standardize Taxonomies

Taxonomic assignments are grossly nonstandardized in current biological classifications. For example, some genera such as Drosophila are an order of magnitude older than others such as Pan or Gorilla; and, further more, because of an apples-versus-oranges problem, a genus-level (or any other) designation for particular assemblages of fruit flies and primates provides almost no information on whether such disparate groups en compass comparable amounts of phenotypic, genetic, or evolutionary variation. Another aspect of nonstandard ization is that some taxa (e.g., Reptilia) are paraphyletic as traditionally delimited, whereas others (e.g., Aves) are monophyletic. Although it is sometimes proclaimed that taxa afforded the same taxonomic rank should in prin ciple be more or less equivalent by some criterion (Van Valen, 1973; Minelli, 2000), what that universal criterion might be and how to implement it have received scant attention (Dubois, 2005). In principle, a strategy (Hennig, 1966; Avise and Johns, 1999) for classification could rem edy this situation by moving taxonomy closer to both of its two ideal functions (Mayr, 1982): to provide a univer sal system for information storage and retrieval and to encapsulate an evolutionary interpretation of biological (Jiversity. For any phylogenetic tree with internal nodes reliably dated (from molecular clocks, biogeographic data, fossils, or other evidence), extant species compris ing any clade would be assigned a taxonomic rank de termined by the temporal window (band) in which the basal node for that clade resides. (Although nodal dates can be notoriously difficult to estimate, rapid progress is being made for many clades thanks especially to the availability of extensive molecular sequence data; e.g., Springer et al, 2003; Moreau et al, 2006.) Because clades in any phylogeny are hierarchically arranged, each re sulting classification would also be hierarchical (as un der traditional Linnaean schemes) but with the added benefit of now being calibrated and standardized by a universal yardstick: evolutionary time. Temporal banding could provide a simple way to equilibrate taxonomic ranks across any extant forms of life. The boundaries of the temporal windows to be associated with each rank are inherently arbitrary. However, once formally ratified by a consensus among systematists, they would thereafter provide an objec tive and universal standard for classifying any group of extant organisms for which a well-dated phylogeny is available. A serious problem with the temporal-banding scheme (as formulated above) is that it would necessitate dra matic rank changes for many taxa. Taxonomic stabil ity is also important in biology (Godfray and Knapp, 2004), so any wholesale taxonomic revision would be counterproductive if it complicated more so than fa cilitated effective communication and information re trieval. Here we suggest a simple and straightforward taxonomic tactic by which the epistemological advan tages of temporal banding could be achieved without abandoning tried-and-comfortable Linnaean ranks and nomenclatures. Although we prefer the retention of rank ing hierarchies in biological classifications, our current proposal could also be implemented in rank-free sys tems such as PhyloCode (see de Queiroz and Gauthier, 1992).

Taxonomy and phylogeny in the earliest diverging pleurocarps: square holes and bifurcating pegs

The extant members of the earliest diverging pleurocarpous moss lineages comprise few species but span a wide range of structural and molecular diversity, most of it restricted to temperate and high-altitude tropical forests in the Southern Hemisphere. We present the most comprehensive molecular phylogenetic study of these lineages to date, based on parsimony and Bayesian analyses of four regions from the chloroplast and mitochondrial genomes. In addition to corroborating the findings of parsimony methods in this and previous studies, the results of heterogeneous Bayesian analyses provide strong support for sub-topologies that are also consistently found under parsimony, but are rarely well supported. Careful model specification and investigation of potential sources of error increase confidence in the Bayesian results, which provide the basis for a substantially revised classification reflecting the best currently available hypothesis of evolutionary history. The genera previously classified in the Rhizogoniaceae, together with Orthodontium, Orthodontopsis, Aulacomnium and Calomnion, are recognized in three families, the Orthodontiaceae, Rhizogoniaceae and Aulacomniaceae, and three monofamilial orders, the Orthodontiales ord. nov., Rhizogoniales and Aulacomniales ord. nov. Many of the species previously recognized in Hypnodendron are placed in Sciadocladus, Touwiodendron gen. nov., Dendro-hypnum or Mniodendron. These genera, with the exception of Sciadocladus, are placed in the Hypnodendraceae together with Spiridens, Franciella, Cyrtopus and Bescherellia. Braithwaitea is excluded from the Hypnodendraceae and recognized in the monogeneric Braithwaiteaceae fam. nov., while Sciadocladus is placed with Pterobryella and Cyrtopodendron in the Pterobryellaceae. The Hypnodendraceae, Pterobryellaceae, Braithwaiteaceae and Racopilaceae are recognized in the order Hypnodendrales comb. et stat. nov. We discuss the advantages and limitations of ranked classification systems and propose the abandonment of intercalated Linnaean ranks between order and class levels in Bryopsida. Three node-based informal names, the Pleurocarpids, the Core Pleurocarps and the Homocostate pleurocarps, are defined to represent evolutionarily significant clades within the pleurocarpous group.

Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.

Character‐based phylogenetic Linnaean classification: taxa should be both ranked and monophyletic

Three primary philosophical positions have emerged among systematists concerning the relationship between phylogenetic analysis and biological classification. The first of these, expressed in a letter to Taxon in February 2005, coordinated by I. Nordal and B. Stedje and signed by 148 additional botanists (Nordal & Stedje, 2005), maintains that paraphyletic should be accepted because of the alleged logical incompatibility between the strict requirement of monophyly and the use of Linnaean ranks, and the claim that with monophyletic taxa results in classifications that are solely on descent at the expense of modification. According to this view, phylogenetic analysis and taxonomy are complete ly separate endeavors that may inform one another but that should not be strictly linked in any necessary way. The second view, held by proponents of phylogenetic nomenclature (e.g., De Queiroz & Gauthier, 1992) as exemplified by the PhyloCode (http://www.ohiou.edu/ phylo code/), is that should be monophyletic by def inition and that the only way to make classification sys tems adequately and satisfactorily phylogenetic is to abandon Linnaean ranks completely. In this view, phylo genetic analysis is used not to test the monophyly of but to reveal their identities and membership, which therefore could only be known with certainty if we could reconstruct with certainty the true tree of all life. The third, intermediate position, the one to which we sub scribe and which we believe is the prevailing view among systematists, states that monophyly and Linnaean ranks are not only compatible but complementary and that should be both ranked according to the so-called Linnaean system and circumscribed so as to reflect puta tive monophyletic groups based on current evidence. In this view, taxonomy and phylogenetic analysis are dis tinct but tightly linked endeavors: each taxon is a human construct whose membership is determined by taxono mists based on character state distributions, and phyloge netic analyses simultaneously provide information about which groups are and are not monophyletic and which character states are and are not homologous. In a twist that we find both ironic and unfortunate, the first two positions described above have come to be considered complementary because they are united in claiming that the criterion of monophyly and the use of Linnaean ranks are incompatible, and at least some mem bers of each of these two camps have suggested that we should have two parallel systems of classification, one that is Linnaean but not strictly phylogenetic and a sec ond that is strictly phylogenetic but not Linnaean. We find these suggestions deeply disturbing and believe that to adopt either or both of these systems would be coun terproductive and detrimental to systematics as a science. It is our view that the so-called obsession with monophyly is part of a historical and intellectual pro gression, in which, as methods to understand and classi fy knowledge of biological diversity?fundamental human endeavors?have improved, those methods have been incorporated into the science of systematics. We are therefore obsessed with monophyly for the same rea sons we are obsessed with explaining diversity by Darwin's theory of evolution by natural selection or with formulating and testing hypotheses according to the sci entific method. To abandon any of these would represent a step backwards in scientific progress. On the other hand, the same can be said about the so-called Linnaean hierarchy and the rules of nomenclature put forward in the ICBN (Greuter & al., 2000), which also represent progress in the science of taxonomy. Moreover, as has been pointed out repeatedly, abandoning the system that has served us well for over 200 years would cause mas sive and completely unnecessary confusion. We further contend that the arguments put forward by proponents of both of the first two positions described above are based on misconceptions, misinterpretations, and misguided logic. The claim that paraphyletic groups are inevitable in the Linnaean system is based on the inappropriate (and impossible) desire to construct classifications from phy logenetic trees rather than cladograms, and the corre sponding assumption that we must classify to higher

Linnaean Ranks: Vestiges of a Bygone Era

We tend to think that there are different types of biological taxa: some taxa are species, others are genera, while others are families. Linnaeus gave us his ranks in 1731. Biological theory has changed since Linnaeus's time. Nevertheless, the vast majority of biologists still assign Linnaean ranks to taxa, even though that practice is at odds with evolutionary theory and even though it causes a number of practical problems. The Linnaean ranks should be abandoned and alternative methods for displaying the hierarchical relations of taxa should be adopted.

Species and phylogenetic nomenclature

TAXONVolume 51, Issue 3 p. 507-510 Points of ViewsFree Access Species and phylogenetic nomenclature Michael S. Y. Lee, Michael S. Y. Lee lee.mike@saugov.sa.gov.au Department of Palaeontology, The South Australian Museum and Department of Environmental Biology, University of Adelaide, North Terrace, Adelaide, SA5000 AustraliaSearch for more papers by this author Michael S. Y. Lee, Michael S. Y. Lee lee.mike@saugov.sa.gov.au Department of Palaeontology, The South Australian Museum and Department of Environmental Biology, University of Adelaide, North Terrace, Adelaide, SA5000 AustraliaSearch for more papers by this author First published: 01 August 2002 https://doi.org/10.2307/1554863Citations: 8AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume51, Issue3August 2002Pages 507-510 ReferencesRelatedInformation

Names, numbers and indentations: a guide to post-Linnaean taxonomy

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system.

Power spectra of extinction in the fossil record

Recent Fourier analyses of fossil extinction data have indicated that the power spectrum of extinction during the Phanerozoic may take the form of 1/f noise, a result which, it has been suggested, could be indicative of the presence of `critical dynamics' in the processes giving rise to extinction. In this paper we examine extinction power spectra in some detail, using family-level data from two widely available compilations. We find that although the average form of the power spectrum roughly obeys the 1/f law, the spectrum can be represented more accurately by dividing it into two regimes: a low-frequency one which is well fit by an exponential, and a high-frequency one in which it follows a power law with a 1/f2 form. We give explanations for the occurrence of each of these behaviours and for the position of the crossover between them.

Integrating phylogenetic analysis and classification in fungi

The central goal of taxonomic mycology is to create classifications that communicate understanding of fungal phylogeny. To insure that taxonomy reflects up-to-date phylogenetic hypotheses, there must be efficient mechanisms for translating phylogenetic trees into classifications. The current taxonomic system, which is based on the hierarchy of Linnaean ranks and the International Code of Botanical Nomenclature, is unsatisfactory for this purpose. One problem with the current taxonomic system is that a large number of ranks are necessary to classify complex phylogenetic trees. Rank proliferation creates a tension between the desire to name clades and the need to keep the number of ranks manageable. In addition, ranked classifications are quite sensitive to minor changes in tree topology, and are therefore unstable. The instability of ranked tree-based classifications encourages systematists to defer naming strongly supported clades if their internal structure or higher-level relationships are not well resolved. Thus, the current taxonomic system impedes progress toward a phylogenetic classification of fungi. As an alternative to the current taxonomic system, de Queiroz and Gauthier developed a system of “phylogenetic taxonomy,” which explicitly defines taxon names as designating clades, and which does not use taxonomic ranks. Eliminating the concept of rank promotes nomenclatural stability because the names of taxa are not sensitive to changes in their position in the tree relative to other taxa. As published fungal phylogenies grow in size and number, the problems of rank proliferation and nomenclatural instability caused by the current taxonomic system will become more severe. Serious consideration should be given to replacing the Code with a rankless system based on phylogenetic taxonomy. Although at this time there is no alternative to the Code, it is likely that detailed proposals for rankless codes of nomenclature will be developed in the next few years.

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool.39, 307–322; 1992: A. Rev. Ecol. Syst.23, 449–480; 1994: Trends Ecol. Evol.9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.