THE ENGLISH NAMES OF THE AFROTROPICAL NIGHTJARS (CAPRIMULGIDAE)

Jackson, H. D. 1993. The English names of the Afrotropical nightjars (Caprimulgidae). Ostrich 64: 148–159.

At least 172 different English names have been used on the nightjars of Africa and its related islands, including Madagascar. A review of the literature chronicles the name changes within each species. Problems created by some duplication and transposition of names between species are discussed. A key to all the names is provided by an alphabetical list cross referenced to the species concerned. The orthography of names is discussed and it is recommended that all animal names be capitalized and freed of unnecessary hyphens. The nightjar names used in The Birds of Africa are accepted as the standard to be followed subject to a few changes.     

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.     

Current usage of nomenclature for parasitic diseases, with special reference to those involving arthropods

Terminological confusion has been aggravated by efforts to develop a standardized nomenclature for parasitic diseases (SNOPAD) arising from the proposal by Kassai et al., 1988) for a standardized nomenclature of animal diseases (SNOAPAD). To restabilize international nomenclature of parasitic diseases it is recommended that, whenever appropriate, names should follow the 'International Nomenclature of Diseases' (IND) compiled by the Council for International Organizations for Medical Sciences (CIOMS/WHO, 1987). For diseases not included in IND, familiarity should guide the choice of name: traditional English language names of diseases should be preferred, e.g. 'malaria', 'scabies' or, for parasitic diseases having no traditional name, the taxonomic name of the causative organism should be applied, e.g. 'Brugia timori microfilaraemia'; 'Plasmodium malariae infection'; 'Simulium allergy'--instead of the generic derivatives proposed by SNOPAD, i.e. brugiosis, plasmodiosis and simuliidosis, respectively. For names of new diseases or those rarely mentioned, the suffix -osis would normally take precedence. Generally, the name of choice for any disease in any language should be the vernacular term, with commonest English usage preferred for international communication, and publications should include synonyms in the list of keywords.     

Back from the dead: Thyreophora cynophila (Panzer, 1798) (Diptera: Piophilidae) ‘globally extinct’ fugitive in Spain

We report on a sensational find in central Spain of six specimens of Thyreophora cynophila ( Panzer, 1798 ), a colourful, strange‐looking piophilid fly living on carcasses of big mammals in advanced stages of decay. Published data suggest that the species is known exclusively from central western Europe (Germany, Austria and France), and was observed last near Paris, France, in the late 1840s, i.e. more than 160 years ago. Accordingly, T. cynophila was placed in 2007 as the only dipteran on a list of recent European animals considered to be globally extinct. Collection‐based data from all 16 known extant specimens found in seven European natural history museums revealed a specimen without date of T. cynophila from Algiers, Algeria. The status of the three thyreophorine piophilids known from Europe is summarized. For the smallest species we reinstate the name Centrophlebomyia anthropophaga ( Robineau‐Desvoidy, 1830 ) with Centrophlebomyia orientalis Hendel, 1907 as a subjective junior synonym ( syn.n. ). We speculate as to why thyreophorines, and T. cynophila in particular, have evaded detection for so long.     

The anArchive taxonomic Checklist for Italian botanical data banking and vegetation analysis: Theoretical basis and advantages

In recent years, research in botany was increasingly related with the use of large data-sets and data banks, in order to address emerging issues such as the severe risk of species, habitats and biodiversity loss. In this frame, the anArchive taxonomic Checklist, an online synonymized list of botanical species names, developed to support the botanical data banking and vegetation analysis, is presented and discussed here. The benefits deriving from such a supervised and referenced tool are emphasized. They include the possibility to keep track of old and new species names, pointing out the latest reviewed accepted scientific name and its synonyms, and harmonizing different taxonomic points of view. Furthermore, the list is open access and expert qualified customers can collaborate to its improvement. The basic unit of the taxonomic Checklist is an object including the taxon name at specific or, when present, infraspecific level; the taxonomic frame stops at the level of family and ranks higher than genus are not treated hierarchically. Some technical features, the main taxonomic references and the current state of the art are reported.     

Ravens (Corvus corax corax L.) in the British landscape: a thousand years of ecological biogeography in place-names

Abstract Aim To investigate the information content of place‐names regarding the habits, habitat and biogeography of ravens in Britain over the past millennium. Location England, Scotland and Wales. Methods Linguistic and ecological analysis of over 400 British place‐names that have a putative ‘raven’ derivation. Results Most of the ‘raven’ place‐names are Old English in origin. Some of these (a minority), however, derive from personal names. The derivations of most names reflect landscape rather than man‐made features; the majority relating to high, craggy ground or coastal features, a minority to wooded situations or human habitations. In lowland Scotland and the Scottish borders the colloquial name corbie dominates ‘raven’ place‐names, perhaps reflecting French influence. In the Highlands and the Western Isles the Gaelic fitheach and its derivatives are predominant. Relatively fewer place‐names that have ‘raven’ roots have been educed in other parts of the Celtic West, i.e. Wales and Cornwall (only one traced in the latter). Main conclusions Comparison of the geographical distribution of ‘raven’‐derived place‐names with the present‐day distribution of the species in Britain reveals the extent of the contraction in the raven's range to the West over historical time, most notably during theprevious two centuries, associated with changed land‐management practices in particular.     

Chelodesmid studies. XIII. A synopsis of the Brasilian tribe Strongylomorphini

The new diplopod tribe Strongylomorphini (fam. Chelodesmidae) is proposed for the two Brasilian genera Strongylomorpha and Brasilodesmus, characterized by the distal torsion of the solenomerite and form of the apical end of the prefemoral process, of the male gonopod. Strongylomorpha has been of uncertain status since 1897, but study of its type species shows the name to be a senior synonym of Erythrodesmus Silvestri, 1902, Neocamptomorpha Schubart, 1954, and Camptomorphoides Schubart 1962. Drawings of the gonopods are given for several old species, made from Iectotype specimens, and a list of the names considered referable to Strongylomorpha. The new species Brasilodesmus austrocrucis is described from Santa Catarina, Brasil.     

Index nominum familiarum plantarum vascularium

A list of 2510 vascular plant family names is provided, valid and not validly published as well as legitimate and not legitimate. Each entry has a full bibliographic reference, nomenclatural status, generic type (when based on a generic name), means of validation, original place of publication for pre-1789 works, isonyms, invalid names proposed prior to a name’s validation, first use of correct orthography (if not given in the original publication), first uses of other orthographic variations, divisional placements of typified names, indication of acceptance in the botanical literature after 1960, and a four-letter abbreviation for the legitimate family name. In addition, nomenclaturally correct, typified names are listed for the ranks of order, superorder, subclass, class, subdivision, division/phylum, and subkingdom (for a total of 753 names), with full bibliographic citations. A similar list of 1569 currently available extant vascular plant family names is also given, of which 960 are considered to be in “current use.” A starting date for all names is assumed to be 4 August 1789 (Jussieu,Generaplantarum). Current difficulties with family nomenclature, and potential changes to bibliographic citations as a result of recently proposed changes to theInternational Code of Botanical Nomenclature, are noted.     

Taxamatch,an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.     

Ethnobotany of the Jicaque of Honduras

An ethnobotanical study was conducted among the Jicaque Indians of the Montana de la Flor reservation in central Honduras to collect information regarding their plant-use practices. The data, including vernacular names, ecological settings, and uses, were recorded during collecting forays with Jicaque informants. Scientific and Jicaque names have been provided for 23 plant species used for food, 11 used for medicine, 4 used for beverages, 3 used as sources of wood, 5 in artifact manufacturing, and 3 used in other ways. Also, a list of 43 species is included for which the Jicaques have a name but no known use.     

Equipped to cope with climate change: traits associated with range filling across European taxa

In order to understand the ecological effects of climate change it is essential to forecast suitable areas for species in the future. However, species’ ability to reach potentially suitable areas is also critical for species survival. These ‘range‐shift’ abilities can be studied using life‐history traits related to four range‐shift stages: emigration, movement, establishment, and proliferation. Here, we use the extent to which species’ ranges fill the climatically suitable area available (‘range filling’) as a proxy for the ability of European mammals and birds to shift their ranges under climate change. We detect which traits associate most closely with range filling. Drawing comparisons with a recent analysis for plants, we ask whether the latitudinal position of species’ ranges supports the assertion that post‐glacial range‐shift limitations cause disequilibrium between ranges and climate. We also disentangle which of the three taxonomic groups has greatest range filling. For mammals, generalists and early‐reproducing species have the greatest range filling. For birds, generalist species with high annual fecundity, which live longer than expected based on body size, have the greatest range filling. Although we consider traits related to the four range‐shift stages, only traits related to establishment and proliferation ability significantly influence range filling of mammals and birds. Species with the greatest range filling are those whose range centroid falls in the latitudinal centre of Europe, suggesting that post‐glacial range expansion is a leading cause of disequilibrium with climate, although other explanations are also possible. Range filling of plants is lower than that of mammals or birds, suggesting that plants are more range‐limited by non‐climatic factors. Therefore, plants might be face greater non‐climatic restraints on range shifts than mammals or birds.     

Species names and metaphyly: a case study in Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina)

Dayrat, B. & Gosliner, T. M. (2005). Species names and metaphyly: a case study in Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) —Zoologica Scripta, **, ***–***. Absence of resolution in phylogenetic trees, or metaphyly, is a common phenomenon. It mainly results from the fact that each data set has its own limit and can hardly be expected to reconstruct alone an entire hierarchy. Because metaphyly helps point out which regions of a tree merit further investigation, one should not avoid metaphyly but rather should try to detect it by addressing carefully node reliability. In this paper we explore the implication of metaphyly for species names. We present a phylogenetic analysis of Discodorididae (Mollusca, Gastropoda, Nudibranchia, Doridina), with an emphasis on relationships among species of Discodoris and its traditionally close ‘allies’ such as Peltodoris and Anisodoris. We demonstrate that some species must be transferred to different discodoridid subclades with which they share synapomorphies, but that many species form a metaphyletic group at the base of Discodorididae, and therefore cannot be placed in any taxon of genus level. We demonstrate that the current International Code of Zoological Nomenclature does not allow taxonomists to handle this situation because it requires selecting a taxon name of genus rank for every species binomial. Then we evaluate the results provided by new forms of species names, both in a rank‐based system, such as the current nomenclature, and a rank‐free system. All solutions considered would cause radical changes to the ‘spirit’ of the current ICZN (and, by extension, to the other current codes). In a rank‐free system of nomenclature, such as the PhyloCode, the best result is obtained with an epithet‐based form that does not mention supra‐specific relationships. Under this method, official species names would take the form ‘boholiensis Bergh, 1877’, although page numbers and letters can be added for uniqueness purposes. Taxonomists would then be free to add supra‐specific taxon names in ‘common’ species names, such as Discodorididae boholiensis Bergh, 1877 or simply Discodorididae boholiensis. Here we wish to stimulate discussion of a problem that we believe merits wide debate: absence of resolution in phylogenetic reconstruction and its impact on species nomenclature.     

Assessment of the Diversity of African Primates

This account of the systematics of African primates is the consensus view of a group of authors who attended the Workshop of the IUCN/SSC Primate Specialist Group held at Orlando, Florida, in February 2000. We list all species and subspecies that we consider to be valid, together with a selected synonymy for all names that have been controversial in recent years or that have been considered to be valid by other authors in recent publications. For genera, species-groups or species, we tabulate and discuss different published systematic interpretations, with emphasis on more recent publications. We explain why we have adopted our taxonomic treatment and give particular attention to cases where more research is urgently required and in which systematic changes are most likely to be made. For all taxa, from suborder to subspecies, we provide English names.     

A note on some adulatory botanical plates distributed by Sir Joseph Banks

An explanation for the attribution to Joseph Banks of two species names, the only two (besides one genus name) so attributable to him alone, is provided: currently the species concerned are correctly referred to as Phaius tankervilleae (Banks) Blume (Orchidaceae) and Strelitzia reginae Banks (Strelitziaceae).     

914. CENTAUREA AFRICANA

Centaurea africana L. (Compositae: Cardueae: Centaureinae) is illustrated and described. The species has a long history of cultivation that probably exceeds 350 years, although it is apparently rarely available from commercial sources as seed or plant material. Other than the tribal name to use when placing this species, its more recent recognition as a species of Rhaponticoides Vaill. is not accepted; the issue of Vaillant names is once again raised. The capitula of C. africana are considered heterogamous and disciform, not radiant, with the few marginal florets possessing equal length, certainly non‐showy, corolla lobes, and usually containing staminodes. A number of synonyms, appearing in a couple of well‐known databases, are excluded; one belongs to a purple‐flowered species endemic to northern Morocco, the other to a yellow‐flowered, pinnatisect‐leaved plant of northern Spain. A potentially exciting use of one flavonoid extracted from flowering parts of the plant, algerianin, in combatting human myeloid leukaemia, is highlighted.     

Morphology‐based phylogenetic binning to assess a taxonomic challenge: a case study in Graphidaceae (Ascomycota) requires a new generic name for the widespread Leptotrema wightii

Molecular phylogenetic analysis presents two challenges when it is transformed into formal classifications: the taxonomic challenge (whether and how to distinguish monophyletic sister clades or how to deal with paraphyletic grades) and the nomenclatural challenge (naming clades, i.e. placing name‐giving types accurately on a tree). One approach to the latter is morphology‐based phylogenetic binning, which places specimens based on phenotypic features on a molecular tree and assigns uncertainty values to alternative placement options. Here, we use the example of the lichenized fungal genus Leptotrema to demonstrate how morphology‐based phylogenetic binning can help to clarify taxonomic and nomenclatural issues when naming phylogenetically defined entities. Leptotrema is known for a common and widespread species, L. wightii, and phylogenetic analyses have been based exclusively on this species, including the recognition of a separate tribe, Leptotremateae. However, the genus name Leptotrema and the tribal name Leptotremateae are based on the name L. zollingeri, which was initially considered to be a synonym of L. wightii, but has recently been shown to represent a distinct species. As L. zollingeri differs considerably in phenotypic features from L. wightii, it can be questioned whether the two are at all related or whether L. zollingeri is actually closer to the genera Myriotrema and Ocellularia in tribe Ocellularieae. The solution to this problem is not trivial, as it affects the correct use of the names Leptotrema and Leptotremateae. Morphology‐based phylogenetic binning indeed demonstrated that L. zollingeri clusters with the Myriotrema album group in tribe Ocellularieae with high support. Hence, in contrast with current use, the name Leptotrema becomes available for the M. album group and Leptotremateae becomes a synonym of Ocellularieae. As a consequence, the new names Sanguinotrema and Sanguinotremateae are introduced to accommodate L. wightii and the tribe including this species and the genus Reimnitzia. Although the studied case is specific to lichen fungi, the approach can be used in a much broader context with any kind of taxon or organism. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 436–443.     

Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges

Aim The goal of this study was to determine the extent of suitable habitats across the basins and ranges of the Great Basin for 13 montane mammals in the present and during the Last Glacial Maximum (LGM). For all these mammal species, we test whether: (1) more suitable habitat was available in basin areas during the LGM; (2) suitable habitat shifted upwards in elevation between the LGM and the present; (3) more ranges have suitable habitat than are currently occupied; and (4) these species are currently restricted to suitable habitats at higher‐elevation range areas. We also examine whether and how much distributional response varies among these montane mammal species. Location The Great Basin of western North America. Methods We re‐examine the past and present distributions of 13 Great Basin montane mammals using ecological niche modelling techniques that utilize now widely available species occurrence data and new, fine‐scale past climatological GIS layers in the present and at the LGM. These methods provide an objective, repeatable means for visual comparison of past and present modelled distributions for species examined in previous biogeographical studies. Results Our results indicate greater areal and lower elevational suitable habitat in the LGM than at present for nearly all montane mammals, and that there is more suitable habitat at present than is currently occupied. Our results also show that lowland areas provide suitable dispersal routes between ranges for most of the montane mammals both at the LGM and at present. However, three of the 13 species have little to no predicted suitable habitat in the LGM near currently occupied ranges, in contrast to the pattern for the other 10. For these species, the model results support more recent long‐distance colonization. Main conclusions Our finding of suitable lowland dispersal routes in the present for most species supports and greatly extends similar findings from single‐species studies. Our results also provide a visually striking confirmation that changes in species distribution and colonization histories of Great Basin montane mammals vary in a fashion related to the tolerances and requirements of each of these species; this has previously been hypothesized but not rigorously tested for multiple montane mammals in the region.     

Gene name ambiguity of eukaryotic nomenclatures

MOTIVATION: With more and more scientific literature published online, the effective management and reuse of this knowledge has become problematic. Natural language processing (NLP) may be a potential solution by extracting, structuring and organizing biomedical information in online literature in a timely manner. One essential task is to recognize and identify genomic entities in text. 'Recognition' can be accomplished using pattern matching and machine learning. But for 'identification' these techniques are not adequate. In order to identify genomic entities, NLP needs a comprehensive resource that specifies and classifies genomic entities as they occur in text and that associates them with normalized terms and also unique identifiers so that the extracted entities are well defined. Online organism databases are an excellent resource to create such a lexical resource. However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it. RESULTS: We obtained gene information from 21 organisms and quantified naming ambiguities within species, across species, with English words and with medical terms. When the case (of letters) was retained, official symbols displayed negligible intra-species ambiguity (0.02%) and modest ambiguities with general English words (0.57%) and medical terms (1.01%). In contrast, the across-species ambiguity was high (14.20%). The inclusion of gene synonyms increased intra-species ambiguity substantially and full names contributed greatly to gene-medical-term ambiguity. A comprehensive lexical resource that covers gene information for the 21 organisms was then created and used to identify gene names by using a straightforward string matching program to process 45,000 abstracts associated with the mouse model organism while ignoring case and gene names that were also English words. We found that 85.1% of correctly retrieved mouse genes were ambiguous with other gene names. When gene names that were also English words were included, 233% additional 'gene' instances were retrieved, most of which were false positives. We also found that authors prefer to use synonyms (74.7%) to official symbols (17.7%) or full names (7.6%) in their publications. CONTACT: lifeng.chen@dbmi.columbia.edu