Cladistic analyses of the animal kingdom

A recently published book on the phylogeny of the animal kingdom, written by the first author, provided a classification based on a 'manual' cladistic analysis at the phylum level. We have extracted a data matrix consisting of 61 characters for 32 phyla from this book and treated it in more formal analyses using three different parsimony programs. Following a posteriori weighting, one cladogram emerged as the most parsimonious explanation of the data. This cladogram is compared to those in recent publications. Congruence is greatest with the phylogeny published by the first author, as the monophyly of 18 of the 21 supraphyletic categories proposed therein are supported in our cladogram. The exceptions are Aschelminthes, Frotornaeozoa and Neorenalia, but the latter group does emerge as a monophyletic taxon in a number of equally parsimonious, equally weighted trees. Comparisons with other recent phytogenies show varying degrees of divergence, especially concerning the monophyly of Spiralia and Aiticulata, both of which are advocated in the present paper. Significant characters of most of the supraphyletic taxa proposed by the first author are discussed. C1996 The Linnean Society of London     

The genus Goniothalamus (Annonaceae) in Sumatra

A comprehensive taxonomic revision of the species of Goniothalamus (Blume) Hook. f. & Thomson (Annonaceae) occurring in Sumatra and adjacent islands is presented for the first time. Fourteen species are recognized, including six endemics that are described as new to science ( G. acehensis, G. alatus, G. dewildei, G. loerzingii, G. longistaminus and G. miquelianus ). In addition, two species are newly recorded from Sumatra, viz. G. parallelivenius Ridl. (previously reported from Borneo), and G. wrayi King (previously reported from Peninsular Malaysia). The extensive nomenclatural confusion regarding the application of the names G. costulatus Miq. and G. opacus Bakh. f. is clarified: the names are shown to be synonymous, with the former having nomenclatural priority. The utility of specific taxonomic characters are also discussed, with particular emphasis on petal indumentum, staminal connective shape, ovary indumentum, stigma shape, monocarp size and shape, and seed indumentum. Biogeographical relationships in the genus are discussed, and the significance of the Barisan mountain range and the Quaternary volcanic tuffs around Lake Toba are highlighted as potential ecological barriers limiting dispersal.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 225–254.     

Should there be a separate code of nomenclature for the protists?

The present Botanical and Zoological Codes of Nomenclature are often inadequate for resolution of all the peculiar problems caused by the very nature of the numerous and diverse groups of the so-called 'lower' eukaryotic organisms known as protists. Whether or not a separate code should therefore be created for these species--many but not all of which are unicellular in structure and microscopic in size--is complicated by several factors. The principal one is related to the wide dispersal of protists throughout many taxonomic classes and phyla/divisions; sometimes even multiple kingdoms are involved. If recognition of a single kingdom Protista is no longer tenable, then even the concept of one code per kingdom is not applicable. Other difficulties arise primarily from long-standing differences in major provisions of present Botanical and Zoological Codes. Numerous 'ambiregnal' forms exist, species currently under dual code jurisdiction. The matter of names for suprafamilial taxa of protists, irrespective of their ultimate kingdom assignment, poses another set of concerns not yet resolved. A plea is made to recognize the legitimacy of having distinct high-level ranks for protist species that seem to be widely separated phylogenetically from fellow protists or from other eukaryotic assemblages.     

Catalog of the adelgids of the world (Hemiptera,Adelgidae)

A taxonomic and nomenclatural Catalogue of the adelgids (Hemiptera: Adelgidae) is presented. Six family-group names are listed, five being synonyms of Adelgidae. Twenty-two genus-group names, of which nine are subjectively valid and in use, are presented with their type species, etymology, and grammatical gender. One hundred and six species-group names are listed, of which 70 are considered subjectively valid.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Prokaryotic taxonomy and nomenclature in the age of big sequence data

The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.Subject terms: Archaea, Bacteria     

Subspecies names from Berher,La flore des Vosges (1887)

Subspecies names have been studied from the nomenclaturally omitted bookBerher, La flore des vosges, 1887. A commented enumeration containing 107 names published in that book has been comiled. 41 subspecies names have been examined in more detail. Thirteen ofBerher's subspecific combinations may be employed in present taxonomic classifications. Nine ofBerher's names determine priority of the relevant subspecific epithets (parabasionyms). Two new nomenclatural combinations are proposed:Acetosa alpina subsp.amplexicaulis andBetula alba subsp.glutinosa. More detailed attention has been paid to the problems of names in the group ofRumex arifolius.     

Was high grouse hag in early 20th century Norway due to a program for extermination of small game predators?

A Norwegian program for extermination of (small game) predators (NPEP) was run during 1900‐ 1914, This initiative is believed to have caused larger small game stocks and more regional synchrony in rodents. To investigate the effectiveness of the NPEP time series of predators bountied (1885–1914), rodent dynamics (1885–1914), ptarmigan hunting index (1885–1914 and 1900/1‐1914), and willow ptarmigan and berry export statistics (1885–1914) were analyzed for three different regions: south, east and central Norway. In south and east Norway there were higher ptarmigan export in the period 1907–1914 than the years before, but not in central Norway. There was not bountied higher number of red fox. eagle or goshawk in any of the three regions when comparing years a) before and after 1900. and b) when comparing the periods 1900–1906 and 1907–1914. This suggests that predator removal was not the cause of increased ptarmigan export. The ptarmigan hunting index and rodent index for south and east Norway were correlated in the period 1885 1914, while the ptarmigan export from east Norway was correlated with berry export from the year before. However, for central Norway the rodent index was not correlated with the hunting index. There were cross correlation between berry and ptarmigan export with lag from minus one to nine years for south and east Norway, The NAO (North Atlantic Oscillation) ‐ an indication of the winter weather variation ‐ had higher values during 1900–1914 than 1885–1899, indicating moister and warmer winters in the last period. This analysis indicates that NPEP generally did not increase predator removal. The results suggest, however, that it was a series of years with high rodent density, that caused the increase in ptarmigan populations In south and cast Norway, which, in turn, may have been caused by favourable weather conditions leading to among others good berry crops. Conclusions based on old data series must, however, be drawn with caution.     

Thermotolerant fungi erroneously reported in applied research work as possessing thermophilic attributes

In applied research work dealing with heat-tolerant fungi, currently classified into two groups: namely thermotolerants and thermophiles, information on levels of thermotolerance is generally scant. Cited binomials are often referred to as representatives of thermophilic taxa. The present contribution attempts to specify proper heat-tolerance levels of species cited in biotechnological papers of academic and applied research types published in the last four decades. This assessment integrates relevant available information concerning well defined thermotolerant taxa. Distinction between both groups of heat-tolerant fungi is a mean to optimize investigations of temperature-dependent physiological processes. The nomenclatural status of the binomials retrieved was also re-appraised following the International Code of Botanical Nomenclature. Articles of the code govern the legal validity of fungal names. The goal is to deter `ghost names' that have no status of any kind. Their use in the literature is not only a source of confusion but also hinders the preparation of sound reviews and reference documents. The intention was also to detect names which do not fulfill all criteria for a valid legal publication. Their status could then be validated if the taxonomic position of the fungus justifies this procedure. The taxonomic status of these thermotolerants was also re-examined following present-day knowledge of their respective genera. Integration of warranted taxonomic decisions in the literature of applied research is crucial. These decisions consider the status of a fungus as a valid species (proposed synonymies) or the nature of its generic affinities (name change). Strict application of these decisions severly reduces levels of heterogeneity regarding names used for the same organism. It also clarifies its generic affinities with other thermotolerant fungi. The present note is not an exhaustive assessment on the nomenclatural and taxonomic positions of known thermotolerant fungi, an ecological group for which a global document remains to be produced. It only deals with those taxa most commonly cited in the literature examined. Over 130 fungi are here considered. The group manifests a diversity of taxonomic characters since it includes members of the following systematic groupings: Oomycetes, Zygomycetes, Ascomycetes, anamorphic fungi and Holobasidiomycetes. Few new taxonomic synonyms and invalid binomials are introduced in the present contribution. The former concern the following taxa: Gilmaniella thermophila, Mucor thermoaerospora, Sporotrichum lignicola and Zalerion thermophylii. Three binomials proved to have no taxonomic status of any sort: Acremonium cellulophilum, Nodulisporium microsporum and N. thermoroseum. This revised version was published online in November 2006 with corrections to the Cover Date.     

Annotated checklist of the recent and extinct pythons (Serpentes, Pythonidae), with notes on nomenclature, taxonomy, and distribution

McDiarmid et al. (1999) published the first part of their planned taxonomic catalog of the snakes of the world. Since then, several new python taxa have been described in both the scientific literature and non-peer-reviewed publications. This checklist evaluates the nomenclatural status of the names and discusses the taxonomic status of the new taxa, and aims to continue the work of McDiarmid et al. (1999) for the family Pythonidae, covering the period 1999 to 2010. Numerous new taxa are listed, and where appropriate recent synonymies are included and annotations are made. A checklist and a taxonomic identification key of valid taxa are provided.     

Lectotypifications and notes on the application of names of Hieracium sect. Hieracium, sect. Bifida and sect. Vulgata (Asteraceae) based on material from the province of Dalarna, central Sweden

Lectotypes are designated for 174 names of taxa described based on material from the Swedish province of Dalarna and accepted to belong to Hieracium sect. Hieracium , sect. Bifida and sect. Vulgata . The taxonomic and nomenclatural implications, i.e. taxonomic synonyms and infraspecific taxa not worthy of taxonomic recognition, of the lectotypifications are discussed. Three new combinations, H. mundulifolium (Johanss.) T. Tyler, H. oligasterum (Johanss. & Sam.) T. Tyler and H. transtrandense T. Tyler, are proposed to accommodate the infraspecific taxa H. gilvocaniceps Johanss. var. mundulifolium Johanss., H. expallidiforme (Dahlst. ex. Stenstr.) Dahlst. var. oligasterum Johanss. & Sam. and H. insuccatum Johanss. var. occidentale Johanss. & Sam. respectively, when treated at the rank of species.     

The Linnaean system and its 250-year persistence

The Linnaean system of nomenclature has been used and adapted by biologists over a period of almost 250 years. Under the current system of codes, it is now applied to more than 2 million species of organisms. Inherent in the Linnaean system is the indication of hierarchical relationships. The Linnaean system has been justified primarily on the basis of stability. Stability can be assessed on at least two grounds: the absolute stability of names, irrespective of taxonomic concept; and the stability of names under changing concepts. Recent arguments have invoked conformity to phylogenetic methods as the primary basis for choice of nomenclatural systems, but even here stability of names as they relate to monophyletic groups is stated as the ultimate objective. The idea of absolute stability as the primary justification for nomenclatural methods was wrong from the start. The reasons are several. First, taxa are concepts, no matter the frequency of assertions to the contrary; as such, they are subject to change at all levels and always will be, with the consequence that to some degree the names we use to refer to them will also be subject to change. Second, even if the true nature of all taxa could be agreed upon, the goal would require that we discover them all and correctly recognize them for what they are. Much of biology is far from that goal at the species level and even further for supraspecific taxa. Nomenclature serves as a tool for biology. Absolute stability of taxonomic concepts—and nomenclature—would hinder scientific progress rather than promote it. It can been demonstrated that the scientific goals of systematists are far from achieved. Thus, the goal of absolute nomenclatural stability is illusory and misguided. The primary strength of the Linnaean system is its ability to portray hierarchical relationships; stability is secondary. No single system of nomenclature can ever possess all desirable attributes: i.e., convey information on hierarchical relationships, provide absolute stability in the names portraying those relationships, and provide simplicity and continuity in communicating the identities of the taxa and their relationships. Aside from myriad practical problems involved in its implementation, it must be concluded that “phylogenetic nomenclature” would not provide a more stable and effective system for communicating information on biological classifications than does the Linnaean system.     

Ostrich,Southern Ostrich or Common Ostrich? The ‘eternal vexed question’ of English bird names and name changes in southern Africa through eight editions of Roberts field guides, 1940–2016

A set of stable simple common bird names helps non-ornithologist birders, who contribute to conservation by visiting protected areas and participating in citizen science projects. Changes in English bird names have caused discomfort in the local birding community, especially those that followed international standardisation of common bird names between 2000 and 2005. To understand the extent and nature of English bird name changes, an analysis was done of all southern African bird names through the eight editions of Roberts Birds of South/Southern Africa field guides published from 1940 to 2016. Of 813 species listed in both the first and the latest of the field guides, 453 (55.7%) had their names changed, among which 108 (13.3%) had changes in both the group name and the species epithet. The greatest single wave of changes (31.4%) occurred in the first ‘Roberts bird guide’ (the seventh field guide) in 2007, following international standardisation. Mean word and syllable counts of bird names also increased significantly in that edition. Name changes were associated with new authorships, taxonomic changes and use of geographic species epithets. There was a trend towards name stability for southern African endemic species. Further name changes should be kept to a minimum, shortening and simplifying wherever possible.     

Invalidly published names inJanchen's “Catalogus florae Austriae”: Survey,analysis, and notes

Names of species and subspecies fromJanchen's Catalogus were revised with regard to their validity; invalidly published names were compiled in a commented list of 120 names. About sixty of them were analyzed at length from nomenclatural and taxonomical viewpoints. The cause of the invalidity of these names were discussed; omission of citations of basionyms to proposals of new nomenclatural combinations is the main reason for the invalidity ofJanchen's names. Taxonomic reclassifications and nomenclatural revisions resulted in 23 new nomenclatural combinations, five of these proposals representing direct validations ofJanchen's invalidly published names. Some more general problems of nomenclature are discussed: indirect validation of invalidly published names; omission of infraspecific homonymy; the correctness and necessity to attach neglected authors' names to the names of plants based on those names distinctly taken over from such authors; problems of autonyms in the ICBN Code. The use of the category “convarietas” in cultivated plants (instead of subspecies) is emphasized. Names validated byJanchen himself in his paper of 1959 should be used with this publication place instead of their invalid publication in the Catalogus. Some propositions for future research by other authors are also added.     

HOW MANY SPECIES OF ALGAE ARE THERE?

Algae have been estimated to include anything from 30,000 to more than 1 million species. An attempt is made here to arrive at a more accurate estimate using species numbers in phyla and classes included in the on‐line taxonomic database AlgaeBase ( http://www.algaebase.org ). Despite uncertainties regarding what organisms should be included as algae and what a species is in the context of the various algal phyla and classes, a conservative approach results in an estimate of 72,500 algal species, names for 44,000 of which have probably been published, and 33,248 names have been processed by AlgaeBase to date (June 2012). Some published estimates of diatom numbers are of over 200,000 species, which would result in four to five diatom species for every other algal species. Concern is expressed at the decline and potential extinction of taxonomists worldwide capable of improving and completing the necessary systematic studies.     

Flat-faced longhorn beetles (Coleoptera: Cerambycidae: Lamiinae) from the Neotropical region: new species from Ecuador,nomenclatural changes and notes

Summary

The differences between Anisopodus White, 1853 and Hyperplatys Haldeman, 1847 are discussed and the gender of the latter is corrected. Notes on Hyperplatys pusillus (Bates, 1863) are provided. Hyperplatys nigrisparsus is considered a new rank for H. pusillus nigrisparsus (Bates, 1885). This species is newly recorded from Brazil (Amazonas). Alcidion laetulum Bates, 1880 (currently Nealcidion laetulum), Alcidion costatum Monné & Martins, 1976 (currently Nealcidion costatum), and Nealcidion murinum Monné, 1998, are synonymized with Alcidion bispinum Bates, 1863 (currently Nealcidion bispinum). Anisopodus melzeri Gilmour, 1965 is transferred to Hyperplatys with a new record from the Brazilian state of Mato Grosso do Sul. Notes on a second specimen of Confluentia colombiana (Gilmour, 1950) are provided. Three new species are described from Ecuador: Nealcidion kayi n. sp. (Acanthocinini), Hyperplatys pichinchensis n. sp. (Acanthocinini) and Confluentia quijos n. sp. (Colobotheini).