冬虫夏草无性型研究概况*

文献调查结果表明与冬虫夏草有关的无性型菌种已报道有22个学名,涉及13个属。针对这些名称上存在的命名问题本文展开了讨论,并评述了不同名称与冬虫夏草的关系及其有关菌种的研究进展。在已报道的分离菌种中,作为新种正式描述的名称有8个,其中6个为合格发表,其余2个未能满足名称合格发表的条件;还有4个名称在文献中作为新种提到,但没有合格发表的出处,也有一例只提到名称而无其他要素;另有5个名称则只有属名,尚未鉴定到种的水平。中国被毛孢为多个独立的研究证明为冬虫夏草的无性型,还有3个无性型名称已被证明不可能是冬虫夏草的无性型。其他无性型名称与冬虫夏草的关系有待进一步验证。文中对与冬虫夏草有关的菌种定名、无性型分离和验证方法、复无性型现象,以及有关学名问题作了讨论。     

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.     

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.     

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

Let’s restart formally naming ‘larval’ trematodes

Arguably the most unique biological features of trematode parasites involve their clonal parthenitae and cercariae. These life stages are biologically fascinating, medically and scientifically important, and often studied for years, lacking knowledge of their corresponding sexual adult stages. But sexual adults are the focus of trematode species-level taxonomy, partially explaining the relative neglect of documenting the diversity of parthenitae and cercariae and why researchers who do describe them give them only provisional names. Provisional names are unregulated, unstable, often ambiguous, and, I argue, often unnecessary. I suggest that we recommence formally naming parthenitae and cercariae using an improved naming scheme. The scheme should permit us to reap the benefits of formal nomenclature and thereby enhance research involving these diverse and important parasites.     

A higher-level taxonomy for hummingbirds

In the context of a recently published phylogenetic estimate for 151 hummingbird species, we provide an expanded informal taxonomy, as well as a formal phylogenetic taxonomy for Trochilidae that follows the precepts of the PhyloCode, but remains consistent with the hierarchical nomenclature of the Linnaean system. We compare the recently published phylogenetic hypothesis with those of prior higher-level and more taxonomically circumscribed phylogenetic studies. We recommend the recognition of nine new clade names under the PhyloCode, eight of which are consistent with tribes and one with a subfamily under the Linnaean system.     

The creation of specific hominid names: Gloria in excelsis deo? or ego? or praxis?

The recent recommendation that it is preferable to recognize too many rather than too few species in the fossil record has led to a growing proliferation of specific names. Single specimens are being referred to different species by different authors, and new species are being proposed based on the juxtaposition of specimens from different sites and time levels representing different anatomical parts. In part this may represent the continuity of the Medieval assertion that a multitude of species is a better demonstration of the goodness of a divinely created world than a multitude of individuals in a single species. This has apparently accompanied the resurgence of the Medieval faith that species relationship are best demonstrated by the application of hierarchical Aristotelean logic. On the other hand, the suspicion remains that the vanity of the namer is frequently involved in the creation of new nomina. In general, anthropologists do not exhibit the “wide experience” and consequent “sound judgment” that Darwin recommended as necessary for those giving specific names. If the same criteria used to assign specific fossil names were applied to modern Homo sapiens, the different regional human populations would have to be recognized as specifically distinct. In opposition to the recommendation that we should recognize ever more specific names, there should be a moratorium called and no new species names should be proposed at all. The continuation of patterns of trivial trait configurations associated with the various inhabited regions of the world clearly indicates genetic continuity through time but, unless it can be shown that there is no reproductive continuity between one region and another, these differences do not warrant taxonomic recognition. Major adaptive changes such as significant increases in relative brain size do warrant formal named recognition.     

SCoP: An interactive simulation control program for micro- and minicomputers

A nes software system is described for building simulation programs on micro- and minicomputers. Model equations are written as C subroutines, compiled and linked to the SCoP package to produce a menu-driven, interactive program. The system maintains a database of names, values, and units for all model parameters and variables. Run-time options include several methods for interactive parameter modification and both graphic and tabular outputs, with output values presented as they are calculated. Simulation output values can be compared with experimental data graphically and a companion program SCoPFit is provided for formal optimization of parameter values.     

The kingdom Protista and its 45 phyla

Because most recent treatments of the protists ('lower' eukaryotes comprising the kingdom PROTISTA Haeckel, 1866) have been preoccupied with either a 'phylogenetic-tree' approach or a discussion of the impact of possible endosymbiotic origins of major intracellular organelles, the overall systematics of the group, from taxonomic and nomenclatural points of view, has been almost totally neglected. As a result, confusion over contained phyla, their places in a classification scheme, and even their names (and authorships) is growing; the situation could become chaotic. The principal objective of the present paper is to recognize the taxonomic interrelationships among all protist groups; and it includes the specific proposal that some 45 phyla, defined and characterized, be assigned to 18 supraphyletic assemblages within the kingdom PROTISTA (itself redefined and contrasted with the other eukaryotic kingdoms recognized here: ANIMALIA, PLANTAE and FUNGI). Vernacular terms are employed for identification of the 18 assemblages, but defensible formal names are proposed at the level of phylum. None is presented as new: authorship-and-date credits are given to preceding workers on the taxonomy of the many groups involved. By presenting taxonomic characterizations as well as relevant nomenclatural data for each taxon described, a comprehensive scheme of overall higher-level classification within the kingdom emerges that may be considered to serve as a solid base or 'taking-off point' for future discussions. The 18 supraphyletic groups and their phyla (in parentheses and including authorships and dates of their formal names) are as follows: I. The rhizopods (phyla Karyoblastea Margulis, 1974; Amoebozoa Lühe, 1913; Acrasia Van Tieghem, 1880; Eumycetozoa Zopf, 1885; Plasmodiophorea Zopf, 1885; Granuloreticulosa De Saedeleer, 1934; incertae sedis Xenophyophora Schulze, 1904). II. The mastigomycetes (Hypochytridiomycota Sparrow, 1959; Oomycota Winter, 1897; incert. sed. Chytridiomycota Sparrow, 1959). III. The chlorobionts (Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa (Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes (Rhodophyta Rabenhorst, 1863). VI. The cryptomonads (Cryptophyta Pascher, 1914). VII. The choanoflagellates (Choanoflagellata Kent, 1880).(ABSTRACT TRUNCATED AT 400 WORDS)     

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     

Phylogeny and taxonomy of thegenera of south-western North American Euctenizinae trapdoor spidersand their relatives (Araneae: Mygalomorphae, Cyrtaucheniidae)

The primary focus of this paper is to evaluate the monophylyand intergeneric relationships of the cyrtaucheniid subfamily Euctenizinaeand to a lesser degree the monophyly of Cyrtaucheniidae. Using 71morphological characters scored for 29 mygalomorph taxa our cladisticanalysis shows that Cyrtaucheniidae is likely paraphyletic withrespect to the Domiothelina, the clade that comprises the Migidae,Actinopodidae, Ctenizidae, and Idiopidae. Together, the Domiothelinaand Cyrtaucheniidae have been treated as the Rastelloidina clade.A strict interpretation of rastelloid classification based on ourcladogram would require the establishment of four additional spiderfamilies. However, we choose to use informal names for these cladesso that these taxa can be validated by subsequent studies of mygalomorphphylogeny before formal names are introduced. The phylogenetic analysisalso serves as a vehicle for examining the patterns of homoplasyobserved in mygalomorphs. The secondary focus of this paper is ataxonomic revision of Euctenizinae genera from the south-westernUnited States that includes a key to its genera. The cyrtaucheniid genera Enrico and Astrosoga areconsidered junior synonyms of Eucteniza. Actinoxia and Nemesoides arejunior ­synonyms of Aptostichus . At present theNorth American Euctenizinae comprises these seven nominal genera: Eucteniza, Neoapachella gen.nov. ( Neoapachella rothi sp. nov. ), Myrmekiaphila,Entychides, Promyrmekiaphila, Apomastus gen. nov. ( Apomastusschlingeri sp. nov. ), and Aptostichus .  © 2002The Linnean Society of London . Zoological Journal of the LinneanSociety, 2002, 136 , 487−534     

化石植物中文名的现状、问题与建议

化石植物的中文名,即化石植物学名的中文译名,在古植物学、植物演化生物学专业领域和科学普及等方面起着重要的作用。然而,长期以来对化石植物中文名重视程度不够且拟订时缺乏统一的标准,导致各种文本中化石植物的中文名比较混乱,不利于古植物学知识的传播及科学普及。本文通过统计中文古植物学综合性文献和教材中的化石植物中文名,梳理出化石植物中文名拟订方面出现的一些包括同物异中文名、中文名重名、音译拗口和存在生僻字的使用等常见问题。针对这些问题,本文提出应尽快制定出一套规范统一的化石植物中文名拟定方案,编写和出版化石植物拉汉词典及相应网络查询系统等,从而统一和规范化石植物的中文名,同时也可为化石动物中文名的拟订方案提供相关参考。     

Are species names proper names?

The nature of species names has been a source of controversy, and has played a role in developing ideas about the status of species, such as the species‐as‐individuals hypothesis. Some argue that species names are Millian proper names: names that have no meaning. Others have countered that species names are Millian general names that have stipulative definitions. Here I argue that species names belong to neither category. In particular, unlike Millian proper names, species names have unique referents and are connotative. Further, species names are names of intension that, unlike Millian general names, refer to specific collective entities. Because species names have unique properties not associated with Millian general or proper names, but recognizing the similarity to proper names in most respects, I propose that they be categorized as extra‐proper names.
     

多道检索表的研究进展

在没有利用计算机技术之前,多道检索表停留在“穿孔卡”检索表形式,目前,在计算机辅助下的多道检索表已很快发展出多种检索系统,如DELTA、Lucid和NaviKey等。本文主要比较了在国内外影响较大的6种多道检索系统在体系结构、用户界面、数据库和检索策略等方面的异同,并从性状选取自由、容错度、模糊表达、数值型性状、最佳检索性状、保留性状未知的分类群以及检索特征等7个方面对检索策略进行了深入分析。鉴于多道检索表存在多种异名,不便于研究交流,我们建议使用“Multi access keys”作为正式名称。最后本文就多道检索表的发展趋势提出了展望。     

Electrophysiological Correlation of the Degree of Self-Reference Effect

The present study investigated neural correlations underlying the psychological processing of stimuli with various degrees of self-relevance. Event-related potentials were recorded for names that differ in their extent of relevance to the study participant. Participants performed a three-stimulus oddball task. ERP results showed larger P2 averaged amplitudes for highly self-relevant names than for moderately self-relevant, minimally self-relevant, and non-self-relevant names. N2 averaged amplitudes were larger for the highly self-relevant names than for the moderately self-relevant, minimally self-relevant, and non-self-relevant names. Highly self-relevant names elicited larger P3 averaged amplitudes than the moderately self-relevant names which, in turn, had larger P3 values than for minimally self-relevant names. Minimally self-relevant stimuli elicited larger P3 averaged amplitudes than non-self-relevant stimuli. These results demonstrate a degree effect of self-reference, which was indexed using electrophysiological activity.     

多道检索表的研究进展

在没有利用计算机技术之前, 多道检索表停留在“穿孔卡”检索表形式, 目前, 在计算机辅助下的多道检索表已很快发展出多种检索系统, 如DELTA、Lucid和NaviKey等。本文主要比较了在国内外影响较大的6种多道检索系统在体系结构、用户界面、数据库和检索策略等方面的异同, 并从性状选取自由、容错度、模糊表达、数值型性状、最佳检索性状、保留性状未知的分类群以及检索特征等7个方面对检索策略进行了深入分析。鉴于多道检索表存在多种异名, 不便于研究交流, 我们建议使用“Multi-access keys”作为正式名称。最后本文就多道检索表的发展趋势提出了展望。