Zoological nomenclature in the digital era

Creation and use of the scientific names of animals are ruled by the International Code of Zoological Nomenclature. Until recently, publication of new names in a work produced with ink on paper was required for their availability. A long awaited amendment to the Code issued in September 2012 by the International Commission on Zoological Nomenclature now allows publication of new names in online-only works, provided that the latter are registered with ZooBank, the Official Register of Animal Names. With this amendment, the rules of zoological nomenclature have been aligned with the opportunities (and needs) of our digital era. However, possible causes for nomenclatural instability remain. These could be completely removed if the Code-compliant publication of new names will be identified with their online registration, under suitable technological and formal (legal) conditions. Future developments of the ZooBank may provide the tool required to make this definitive leap ahead in zoological nomenclature.     

Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication

The International Commission on Zoological Nomenclature has voted in favour of a revised version of the amendment to the International Code of Zoological Nomenclature that was proposed in 2008. The purpose of the amendment is to expand and refine the methods of publication allowed by the Code, particularly in relation to electronic publication. The amendment establishes an Official Register of Zoological Nomenclature (with ZooBank as its online version), allows electronic publication after 2011 under certain conditions, and disallows publication on optical discs after 2012. The requirements for electronic publications are that the work be registered in ZooBank before it is published, that the work itself state the date of publication and contain evidence that registration has occurred, and that the ZooBank registration state both the name of an electronic archive intended to preserve the work and the ISSN or ISBN associated with the work. Registration of new scientific names and nomenclatural acts is not required. The Commission has confirmed that ZooBank is ready to handle the requirements of the amendment.     

种级异物同名处理及属名变动影响分析

讨论《国际动物命名法规》(简称《法规》)关于种级单元异物同名的处理及相关规定。以斧须隐翅虫亚科Oxyporinae的同名问题为例,笔者分析了属级单元名称变动对种级单元同名关系的影响。一些古老的属级单元有很长且比较复杂的分类历史,深入分析可将各类变化归纳为六类,其中三类与原同名有关,二类与后同名有关,余一类不再影响种级同名关系。文中讨论了第4版《法规》中与种级同名关系有关的若干重要变动,通过分析比较,说明《法规》的这类变动如何影响动物分类名称的稳定性与正确性。这些分析,可望有助于避免产生新的次同名,也有助于正确恰当地解决已有的同名问题。     

Taxonomy and species delimitation in Cryptosporidium

Amphibians, reptiles, birds and mammals serve as hosts for 19 species of Cryptosporidium. All 19 species have been confirmed by morphological, biological, and molecular data. Fish serve as hosts for three additional species, all of which lack supporting molecular data. In addition to the named species, gene sequence data from more than 40 isolates from various vertebrate hosts are reported in the scientific literature or are listed in GenBank. These isolates lack taxonomic status and are referred to as genotypes based on the host of origin. Undoubtedly, some will eventually be recognized as species. For them to receive taxonomic status sufficient morphological, biological, and molecular data are required and names must comply with the rules of the International Code for Zoological Nomenclature (ICZN). Because the ICZN rules may be interpreted differently by persons proposing names, original names might be improperly assigned, original literature might be overlooked, or new scientific methods might be applicable to determining taxonomic status, the names of species and higher taxa are not immutable. The rapidly evolving taxonomic status of Cryptosporidium sp. reflects these considerations.     

New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature

The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and informative nomina for non-specialist users, and is more economic in terms of number of nomina needed to account for a given hierarchy. These ideas are exemplified by a comparative study of three possible nomenclatures for the taxonomy recently proposed by Hillis and Wilcox (2005) for American frogs traditionally referred to the genus Rana.     

The taxonomist - an endangered race. A practical proposal for its survival

Background

Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based.

Discussion

Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISI^SM.

Summary

The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty.     

红菇科可食真菌的若干分类问题

红菇科Russulaceae包含大量全球广泛采食的野生食用菌,同时也有一定数目的毒菌。该科特别是红菇属的分类是大型真菌分类的难点。近年来DNA数据大量应用于红菇科的分类,更新了属的界定和概念,发现了大量新物种,为食用菌和毒菌的识别和鉴定带来了可用的名称。然而,DNA证据并不总是与形态证据吻合,这又为食用菌和毒菌的识别和名称的使用带来了困扰和不便。本文针对乳菇属、多汁乳菇属和红菇属中的重要食用菌类群,回顾了近年来的分类研究进展,分析了研究背后的数据实情和存在的分类问题。认为：在食用菌和毒菌的确定上,依靠物种复合群共有的形态特征更具有可操作性;依据DNA序列进行的劈分式分类和依靠少数样品的特征及DNA序列上的少量差异发表新种的做法可能产生不便于使用的后果;在乳菇属和红菇属中,“BLAST相似度低的即为新种”的分类实践存在错误风险;充分结合历史资料和各个类群的特点,确定物种划分的阈值,才能有望解决红菇科真菌的分类问题。     

在线植物志: 网络时代分类学的方法和实践

全球气候变化、环境污染、资源被过度利用、外来物种入侵和生境丧失威胁着地球上物种的生存。分类学研究的主要任务就是在这些物种即将消失之前去发现、记录和认知它们。社会公众、政府决策部门和科学发展本身都对分类学提出了诸多需求。然而, 当前分类学所面临的困境包括认识上的误区、不科学的评价机制、研究队伍的萎缩以及陈旧的知识管理和发布模式等, 这些因素不仅阻碍了分类学的学科发展, 而且也制约了分类学家履行社会责任。利用现代的网络信息技术, 构建一个覆盖分类学研究工作流程、整合已有在线数据资源、满足分类学研究群体、项目和研究机构共同需求的分类学社区网络, 并最终实现分类学的终极目标--在线植物志, 将会极大地改善分类学的知识产出和应用环境, 提升它在当今科学技术发展条件下的竞争力, 使其真正成为一门21世纪的科学。     

Unavailable names in the Myotis nattereri species complex

The discovery of new species of mammals in Europe is a rare event, but owing to recent progress in genetic methods used to survey current biodiversity, such discoveries have been accumulating during the last decades. The naming of these new taxa has important bearings in conservation, as this is the first step needed for them to be recognised by the scientific community but also legally. The naming of new animal species, however, needs to follow the strict rules of the International Code of Zoological Nomenclature in order to be available and to provide a stable basis for further taxonomic research. We report here a case where new names have been improperly proposed to designate distinctive lineages in the Natterer's bat species complex. As these new names do not follow several mandatory rules imposed by the Code, they are declared unavailable and are not to be used for further taxonomy studies.     

An investigation of human-animal interactions and empathy as related to pet preference,ownership, attachment,and attitudes in children

ABSTRACT

Osgood's Semantic Differential technique was used with a sample of 12 animal names to see if they elicited responses that were distinctively characteristic, and therefore useful in uncovering connotative meaning. The 100 survey participants responded with unanimity to some species, whereas their responses to others were highly variable. Results disclosed a taxonomy of grouping animal names that differed from the normal zoological taxonomy. This suggests that the technique may be useful for discovering the connotations that animals have, and what various animal species may mean to people.     

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.     

我国进境检疫性菌物名录亟待修订完善

中华人民共和国现行进境检疫性菌物名录中共有130种。近年来由于菌物分类研究的快速发展,许多检疫性菌物的分类地位已经发生变化。本文对我国进境检疫性菌物名录中的名称与国际公认的分类体系和现用名进行了初步的比较和分析,进一步以茎点霉属和轮枝菌属为例说明分类系统的变化对菌物名称的影响。另外,名录中很多汉语学名的使用也不符合规范。我国进境检疫性菌物名录亟需修订。     

Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

The need for a more effective biological nomenclature for the 21st century

HAWKSWORTH, D. L., 1992. The need for a more effective biological nomenclature for the 21st century. The procedures of biological nomenclature are now under immense pressure to change. Users are frustrated by the instability of names and lack of consensus, and increasingly undertake work previously the province of taxonomists; data are presented to show they tend to ignore unwelcome changes. Taxonomists themselves are deflected from both systematic and phylogenetic investigations, and documenting the world's biodiversity, by nomenclatural matters. A survey of 60 U.K. botanical taxonomists revealed that about half spent 10–75% of their research time on nomenclatural matters; extrapolated to the U.K. as a whole, botanical nomenclature could occupy up to 52 full-time posts at a cost of £ 1.3 million. Further, an analysis of 15 monographs of fungal genera showed that overall 85% of the names investigated were not accepted. The major problems to confront relate to concepts of priority, effective and valid publication, illegitimacy, types, ambiregnal organisms and the decision-making bodies. While most of these issues have been overcome by bacteriologists, only now are those concerned with botanical and zoological nomenclature starting to tackle them in earnest. A more effective biological nomenclature could be produced by extending the concept of lists of nomenclaturally protected names. This would resolve questions of effective and valid publication, priority, and application. Such lists would primarily assist taxonomists by dealing with much of the nomenclatural ‘noise’ of the past. Registration procedures are needed to complement such lists for names introduced in the future. The need for standard names and classifications fixed for limited periods is increasingly being met by specialist user groups and also concerns some taxonomists, but is best handled outside formal systems by appropriate specialist bodies. Increased harmonization of the Codes is possible when facing common problems and essential to resolve the difficulties posed by ambiregnal organisms. The image of taxonomy is adversely affected by unsatisfactory nomenclatural systems. Taxonomists should be responsible and refrain from changing names only for nomenclatural reasons while these matters are in discussion. Users and taxonomists need to work with nomenclaturalists to improve the effectiveness of biological nomenclature, if they are to ensure that it will fulfil both their requirements in the 21st century. The prospects for systematics are bleak if it fails to consummate the dual responsibilities of scientific endeavour and user requirements