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.     

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.     

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。     

Nomenclatural benchmarking: the roles of digital typification and telemicroscopy

Nomenclatural benchmarking is the periodic realignment of species names with species theories and is necessary for the accurate and uniform use of Linnaean binominals in the face of changing species limits. Gaining access to types, often for little more than a cursory examination by an expert, is a major bottleneck in the advance and availability of biodiversity informatics. For the nearly two million described species it has been estimated that five to six million name-bearing type specimens exist, including those for synonymized binominals. Recognizing that examination of types in person will remain necessary in special cases, we propose a four-part strategy for opening access to types that relies heavily on digitization and that would eliminate much of the bottleneck: (1) modify codes of nomenclature to create registries of nomenclatural acts, such as the proposed ZooBank, that include a requirement for digital representations (e-types) for all newly described species to avoid adding to backlog; (2) an "r" strategy that would engineer and deploy a network of automated instruments capable of rapidly creating 3-D images of type specimens not requiring participation of taxon experts; (3) a "K" strategy using remotely operable microscopes to engage taxon experts in targeting and annotating informative characters of types to supplement and extend information content of rapidly acquired e-types, a process that can be done on an as-needed basis as in the normal course of revisionary taxonomy; and (4) creation of a global e-type archive associated with the commissions on nomenclature and species registries providing one-stop-shopping for e-types. We describe a first generation implementation of the "K" strategy that adapts current technology to create a network of Remotely Operable Benchmarkers Of Types (ROBOT) specifically engineered to handle the largest backlog of types, pinned insect specimens. The three initial instruments will be in the Smithsonian Institution(Washington, DC), Natural History Museum (London), and Museum National d'Histoire Naturelle (Paris), networking the three largest insect collections in the world with entomologists worldwide. These three instruments make possible remote examination, manipulation, and photography of types for more than 600,000 species. This is a cybertaxonomy demonstration project that we anticipate will lead to similar instruments for a wide range of museum specimens and objects as well as revolutionary changes in collaborative taxonomy and formal and public taxonomic education.     

GENERIC NAMES OF NORTHERN AND SOUTHERN FUR SEALS (MAMMALIA: OTARIIDAE)

We have resolved a nomenclatural problem discovered during research on the northern fur seal that concerns the correct generic name for this taxon and for fur seals of the Southern Hemisphere. The unfortunate practice by some 19th-century authors to use names in their Latinized form but to date them from their first appearance as French common names led to the use of Arctocepbalus for southern fur seals when the name correctly applies to the northern fur seal, known today as Callorbinus ursinus . However, Arctocepbalus and Callorbinus are antedated by Otoes G. Fischer, 1817, which is the earliest available generic name for the fur seal of the northern Pacific. The earliest available generic name for southern fur seals is Halarctus Gill, 1866. To avoid the confusion that would result from replacing the currently used generic names with those required by strict adherence to the Principle of Priority, we have petitioned the International Commission on Zoological Nomenclature to preserve Arctocepbalus and Callorbinus for the southern and northern fur seals, respectively.     

The List of Available Names (LAN): A new generation for stable taxonomic names in zoology?

The List of Available Names in Zoology (LAN) is an inventory of names with specific scope in time and content, presented and approved in parts, and constituted as a cumulative index of names available for use in zoological nomenclature. It was defined in Article 79 in the fourth edition of the International Code of Zoological Nomenclature. The LAN is likely to gain importance with the development of the online Official Registry for Zoological Nomenclature (ZooBank) as it is potentially a source of many nomenclaturally certified names. Article 79 describes the deliberative process for adding large numbers of names to the LAN simultaneously, detailing steps and chronology for submission of a candidate Part to the LAN and consideration of a candidate Part by the public and Commission, but it is largely mute about the contents of a candidate Part. It does make clear that a name within the scope of a Part but not on the LAN has no nomenclatural standing, even if it had previously been considered available, thereby preventing long-forgotten names from displacing accepted ones and the accumulation of nomina dubia. Thus, for taxa on the LAN, nomenclatural archaeology – the resurrecting of old unused names to replace by priority names in current usage – will not be worthwhile. Beyond that, it has been unclear if Article 79 is intended to document every available name known within the scope of the Part, or if its intention is to pare the inventory of available names within the scope of the Part. Consideration by the Commission and two committees to deal with the LAN have defined steps to implement Article 79 with the latter intent. Procedures for consideration of a candidate Part are defined in a manual, published as an appendix in this volume.     

中国菌物名录数据库在大型真菌红色名录编制中的作用

长期以来, 分类学的研究成果主要以平面的方式发表在各种纸质文献资料中。近年来, 随着计算机和人工智能等新兴技术的发展和应用, 平面资料信息的数字化成为一种趋势, 世界各国都非常重视本国生物资源信息的收集汇总, 构建了多种数据库, 为科学研究、政府决策、资源保护、合理利用和科学传播提供了重要的信息基础。本研究探索并建立从菌物学平面资料信息构建数据库的流程和方法, 并在中国菌物名录数据库和Index Fungorum所收集数据的基础上进行数据挖掘和分析。通过软件操作和程序设计, 在数据库中提取相关信息, 辅助完成了《中国生物多样性红色名录——大型真菌卷》的编制工作, 同时梳理和规范了菌物拉丁和汉语学名, 为菌物分类研究和资源评估与保护提供基础。     

Taxonomic revision of the genus Alternanthera (Amaranthaceae) in Italy

A taxonomic revision of the genus Alternanthera (Amaranthaceae) in Italy is here presented. Field surveys were carried out during the period 2007–2013. Thirty-six herbaria (both European and American) were consulted as well as extensive literature was analyzed. Four taxa are recognized, all of them to be considered aliens native to South America. Information about nomenclature (accepted names, main synonyms, and types), morphology, chromosome number, alien status (at national and regional levels), occurrence in Italy (at regional and provincial scale), ecology (preferential habitat, phenology, and elevation), taxonomical notes, and Italian vernacular names were provided for each taxon. A diagnostic key was given. For the nomenclatural purposes the generic name Alternanthera and its type was discussed, and the names A. paronychioides and A. pungens were studied and typified (lecto- and neotype, respectively) on specimens preserved at PH and P.     

The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research

The Zebrafish Information Network, ZFIN, is a WWW community resource of zebrafish genetic, genomic and developmental research information (http://zfin.org). ZFIN provides an anatomical atlas and dictionary, developmental staging criteria, research methods, pathology information and a link to the ZFIN relational database (http://zfin. org/ZFIN/). The database, built on a relational, object-oriented model, provides integrated information about mutants, genes, genetic markers, mapping panels, publications and contact information for the zebrafish research community. The database is populated with curated published data, user submitted data and large dataset uploads. A broad range of data types including text, images, graphical representations and genetic maps supports the data. ZFIN incorporates links to other genomic resources that provide sequence and ortholog data. Zebrafish nomenclature guidelines and an automated registration mechanism for new names are provided. Extensive usability testing has resulted in an easy to learn and use forms interface with complex searching capabilities.     

The development of a Biotic Pollution Index for the River Nile in Egypt

This article describes the development of a Nile Biotic Pollution Index (NBPI) for the River Nile in Egypt. Chemical data were collected from 30 locations along the Nile from Aswan to Cairo and 21 sites within the river delta, incorporating a range of conditions from unpolluted to grossly polluted. Seven chemical variables were used to calculate a Nile Chemical Pollution Index (NCPI) for each site. Biological data were collected primarily using Artificial Substrate Samplers (ASS). The UK developed, Biological Monitoring Working Party (BMWP) biotic index and the BMWP-ASPT were applied to the data. A Nile Biotic Pollution Index (NBPI) and the NBPI-ASPT were obtained by incorporating more of the Nile taxa. There were highly significant regressions (P < 0.001) for both the UK and the Nile Pollution Index scores with the NCPI for the whole river. The modification of the UK indices improved the Nile Indices increasing the number of taxa recorded from 29 to 43 and the total number of recorded taxon occurrences from 377 to 490. The Nile Indices provided better discrimination at both ends of the pollution spectrum. The NBPI-ASPT was best for the river as a whole, and particularly for the river from Aswan to Cairo. The NBPI was much better in the delta than from Aswan to Cairo. These differences in performance were attributed to the fact that the NBPI-ASPT excludes information on taxon diversity. In clean waters there was a wide range of NBPI score suggesting that the biodiversity of taxa is dependent on other aspects of habitat quality. Conversely in the polluted delta the high score of an individual taxon is critical for the NBPI-ASPT as it may have a distorting effect. As the NBPI-ASPT was the most consistent biotic index it is recommended as the regular biological assessment and regulatory tool for Egypt to meet the requirements of the Convention for Biodiversity. Handling editor: R. Norris     

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 tribute to Claude Shannon (1916–2001) and a plea for more rigorous use of species richness, species diversity and the 'Shannon–Wiener' Index

In the literature, the terms species richness and species diversity are sometimes used interchangeably. We suggest that at the very least, authors should define what they mean by either term. Of the many species diversity indices used in the literature, the Shannon Index is perhaps most commonly used. On some occasions it is called the Shannon–Wiener Index and on other occasions it is called the Shannon–Weaver Index. We suggest an explanation for this dual use of terms and in so doing we offer a tribute to the late Claude Shannon (who passed away on 24 February 2001).     

The taxonomic name resolution service: an online tool for automated standardization of plant names

Background

The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science.

Results

The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets.

Conclusions

We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/.     

Index to new names,combinations and emendation appearing in Mycoscience 52 (6)

Index

Index to new names, combinations and emendation appearing in Mycoscience 52 (6)     

Index to new names,combinations and emendation appearing in Mycoscience 52 (2)

Index

Index to new names, combinations and emendation appearing in Mycoscience 52 (2)