Evaluation of three methods for sampling ground-dwelling Ants in the Brazilian Cerrado

Few studies have evaluated the efficiency of methods for sampling ants, especially in regions with highly variable vegetation physiognomies such as the Cerrado region of central Brazil. Here we compared three methods to collect ground-dwelling ants: pitfall traps, sardine baits, and the Winkler litter extractor. Our aim was to determine which method would be most appropriate to characterize the ant assemblages inhabiting different vegetation types. More species were collected with pitfall traps and with the Winkler extractor than with sardine baits. Pitfall traps collected more species in the cerrado (savanna) physiognomies, particularly in those with a poor litter cover, whereas the Winlker extractor was more efficient in the forest physiognomies, except the one subject to periodic inundations. There was a low similarity in species composition between forest and cerrado physiognomies, and this pattern was detected regardless of the method used to sampling ants. Therefore, even the use of a single, relatively selective method of collection can be enough for studies comparing highly distinct habitats and/or conditions. However, if the purpose of the sampling is to produce a more thoroughly inventory of the ant fauna, we suggest the use of a combination of methods, particularly pitfall traps and the Winkler extractor. Therefore, the Ants of the Leaf-Litter (ALL) Sampling Protocol appear to be an adequate protocol for sampling ants in the highly-threatened Brazilian cerrado biome.     

International Code of Area Nomenclature

Biogeography needs a standard, coherent nomenclature. Currently, in biogeography, the same name is used for different areas of biological endemism, and one area of endemism is known by more than one name, which leads to conflict and confusion. The name 'Mediterranean', for example, may mean different things to different people – all or part of the sea, or the land in and around it. This results in ambiguity concerning the meaning of names and, more importantly, may lead to conflicts between inferences based on different aspects of a given name. We propose the International Code of Area Nomenclature (ICAN), a naming system that can be used to classify newly coined or existing names based on a standard. When fully implemented, the ICAN will improve communication among biogeographers, systematists, ecologists and conservation biologists.     

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.     

Plant names in vegetation databases – a neglected source of bias

Problem: The increasing availability of large vegetation databases holds great potential in ecological research and biodiversity informatics, However, inconsistent application of plant names compromises the usefulness of these databases. This problem has been acknowledged in recent years, and solutions have been proposed, such as the concept of “potential taxa” or “taxon views”. Unfortunately, awareness of the problem remains low among vegetation scientists. Methods: We demonstrate how misleading interpretations caused by inconsistent use of plant names might occur through the course of vegetation analysis, from relevés upward through databases, and then to the final analyses. We discuss how these problems might be minimized. Results: We highlight the importance of taxonomic reference lists for standardizing plant names and outline standards they should fulfill to be useful for vegetation databases. Additionally, we present the R package vegdata, which is designed to solve name‐related problems that arise when analysing vegetation databases. Conclusions: We conclude that by giving more consideration to the appropriate application of plant names, vegetation scientists might enhance the reliability of analyses obtained from large vegetation databases.     

Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names

A phylogenetic definition of a taxon name associates that name with a clade through its reference to a particular ancestor and all of its descendants. Depending on one's perspective, phylogenetic definitions name either clades on the one true, but unknown, phylogeny, or components on cladograms (clades on hypotheses regarding the true phylogeny). Phylogenetic definitions do not contain enough information to identify components without a reference cladogram. As a result, (1) if clades are equated with components on cladograms, a phylogenetic definition may associate a taxon name with different clades on different cladograms, and (2) the inclusiveness, diagnostic synapomorphies, and distribution in time and space of the clade with a particular name can differ markedly depending on the phylogenetic hypothesis one chooses to adopt. This potentially unacceptable lability in the clade to which a name refers can be avoided by using a taxon name in conjunction with only phylogenetic hypotheses on which specific taxa are related in a particular fashion. This designated phylogenetic context can be described in an n-taxon statement that would be appended to the phylogenetic definition. Use of the taxon name would be considered inappropriate in conjunction with cladograms on which the relationships contradict those in the n-taxon statement. Whereas phylogenetic definitions stabilize the meaning of taxon names, designated phylogenetic contexts would stabilize the usage of those names.     

The importance of designating type material for uncultured taxa

Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single amplified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.     

中国外来入侵植物的学名考证 (3)

基于中国外来入侵植物的相关报道与文献,发现一些入侵植物的学名使用比较混乱：不同时期、不同地区、不同作者在报道同一外来物种时使用不同的学名,或因中文名相近,而将其他植物作为外来入侵植物报道。依据最新资料,对国内报道的16种外来入侵植物学名进行了考证,包括中文名、英文名、异名、原产地及其在国内外的分布情况。     

被子植物非国产科汉名的初步拟订

报道了中国产12种苔藓植物染色体数目,结果为:壶苞苔Blasia pusilla,n=9;艳 绿光苔Cyathodium smaragdinum,n=9;紫背苔Plagiochasma rupestre,n=9;石地钱Rebou lia hemisphaerica,n=9;宽片叶苔Riccardia latifrons,n=10;尖叶美喙藓Eurhynchium eustegium,n=11;东亚沼羽藓Helodium sachalinense,n=11;白齿藓Leucodon sciuroides,     

中国外来入侵植物的学名考证

基于中国外来入侵植物的相关报道和文献,发现一些入侵植物的学名使用比较混乱,一个物种存在两个或两个以上的名称。依据最新植物志资料,对国内30种外来人侵植物学名进行了考证,包括中名、基名（若存在）、异名、原产地以及在中国的分布等。     

Land Tenure and Naming Systems in Aboriginal Australia

Naming systems play a prominent role in discussions of land tenure by Aboriginal people. Reference to one area of land and its owners is most commonly in terms of name ‘X’, whereas reference to another area of land and its owners is most commonly made in terms of name ‘Y’. Much of the analytical literature examines how these names refer to groups of people. There is considerable dispute as to whether the reference of these names suffices to determine disjoint groupings of owners that can be described by the term ‘clan’. This paper proposes that the analysis of linkages between names and areas of land should have priority over the analysis of linkages between names and groups of people. The evidence shows that the attachment of names to areas of land is more stable and consistent than their attachment to groups of people. There are differences in the ways that names attach to the landscape, and these differences are significant—they determine whether or not more than one name from the same system may be attached to an area of land. This paper focuses on two areas of Australia: the northern Kakadu‐Oenpelli area and the Timber Creek area (both in the Northern Territory). It shows that naming systems identify disjunctive areas of land as the targets for claims of primary ownership in both areas. These disjunctive areas may reasonably be described with the translation term ‘estates’. In the northern Kakadu‐Oenpelli area, corresponding to these estates, there are disjunctive groupings of owners, which may be termed ‘clans’. However, groupings of owners are not clearly disjunctive in the Timber Creek area, and there is little motivation for using the term ‘clan’. This paper proposes that this difference reflects a general pattern in Aboriginal Australia, with naming systems stably and consistently identifying ‘estates’ across much of the continent. They do not identify ‘clans’ with equivalent stability and consistency.     

Traditional knowledge among Zapotecs of Sierra Madre Del Sur, Oaxaca. Does it represent a base for plant resources management and conservation?

ABSTRACT: Traditional classification systems represent cognitive processes of human cultures in the world. It synthesizes specific conceptions of nature, as well as cumulative learning, beliefs and customs that are part of a particular human community or society. Traditional knowledge has been analyzed from different viewpoints, one of which corresponds to the analysis of ethnoclassifications. In this work, a brief analysis of the botanical traditional knowledge among Zapotecs of the municipality of San Agustin Loxicha, Oaxaca was conducted. The purposes of this study were: a) to analyze the traditional ecological knowledge of local plant resources through the folk classification of both landscapes and plants and b) to determine the role that this knowledge has played in plant resource management and conservation. The study was developed in five communities of San Agustin Loxicha. From field trips, plant specimens were collected and showed to local people in order to get the Spanish or Zapotec names; through interviews with local people, we obtained names and identified classification categories of plants, vegetation units, and soil types. We found a logic structure in Zapotec plant names, based on linguistic terms, as well as morphological and ecological caracteristics. We followed the classification principles proposed by Berlin [6] in order to build a hierarchical structure of life forms, names and other characteristics mentioned by people. We recorded 757 plant names. Most of them (67%) have an equivalent Zapotec name and the remaining 33% had mixed names with Zapotec and Spanish terms. Plants were categorized as native plants, plants introduced in pre-Hispanic times, or plants introduced later. All of them are grouped in a hierarchical classification, which include life form, generic, specific, and varietal categories. Monotypic and polytypic names are used to further classify plants. This holistic classification system plays an important role for local people in many aspects: it helps to organize and make sense of the diversity, to understand the interrelation among plants-soil-vegetation and to classify their physical space since they relate plants with a particular vegetation unit and a kind of soil. The locals also make a rational use of these elements, because they know which crops can grow in any vegetation unit, or which places are indicated to recollect plants. These aspects are interconnected and could be fundamental for a rational use and management of plant resources.     

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.     

Phylogenetic classification and the definition of taxon names

Taxon names should be founded on phylogenetic relationships. and the names defined on the basis of common ancestry. Definitions based on evolutionary relationships relate the names to a phylogeny, and while the inclusiveness of the name may change with changing hypotheses of monophyly, the actual name remains unaltered. The limits of the name arc fixed by pointing to a monophyletic clade, where group membership is determined by the relationship to this clade. and not to subjective decisions of taxon delineations. Since phylogenetic definitions unambiguously connect the name to a specified clade, and not to a type, the conventional type concept becomes superfluous. We furthermore consider the Linnean categories poorly suited to convey the information in evolutionary trees, and suggest that these categories are abandoned.     

Nomenclature for enkephalin degrading peptidases

The use of trivial names for enkephalin degrading peptidases such as "aminoenkephalinase" and "carboxyenkephalinase" imply a specificity and cellular localization which is not inherent in any of the peptidases implicated in the degradation of endogenous enkephalins. Rather than name these enzymes on the basis of one of their many substrates, it is proposed that they be named according to their general reaction type. Such a nomenclature has already been proposed for the enkephalin degrading endopeptidase 24.11 given the trivial name "enkephalinase".     

Nutrient and water dynamics of Amazonian <Emphasis Type="Italic">canga</Emphasis> vegetation differ among physiognomies and from those of other neotropical ecosystems

Ferriferous savannas, also known as cangas in Brazil, are nutrient-impoverished ecosystems adapted to seasonal droughts. These ecosystems support distinctive vegetation physiognomies and high plant diversity, although little is known about how nutrient and water availability shape these ecosystems. Our study was carried out in the cangas from Carajás, eastern Amazonia, Brazil. To investigate the N cycling and drought adaptations of different canga physiognomies and compare the findings with those from other ecosystems, we analyzed nutrient concentrations and isotope ratios (δ¹³C and δ¹⁵N) of plants, litter, and soils from 36 plots distributed in three physiognomies: typical scrubland (SB), Vellozia scrubland (VL), and woodland (WD). Foliar δ¹⁵N values in cangas were higher than those in savannas but lower than those in tropical forests, indicating more conservative N cycles in Amazonian cangas than in forests. The lower δ¹⁵N in savanna formations may be due to a higher importance of mycorrhizal species in savanna vegetation than in canga vegetation. Elevated δ¹³C values indicate higher water shortage in canga ecosystems than in forests. Foliar and litter nutrient concentrations vary among canga physiognomies, indicating differences in nutrient dynamics. Lower nutrient availability, higher C:N ratios, and lower δ¹⁵N values characterize VL, whereas WD is delineated by lower δ¹³C values and higher soil P. These results suggest lower water restriction and lower P limitation in WD, whereas VL shows more conserved N cycles due to lower nutrient availability. Differences in nutrient and water dynamics among physiognomies indicate different ecological processes; thus, the conservation of all physiognomies is required to ensure the maintenance of functional diversity in this unique ecosystem.     

Parents Accidentally Substitute Similar Sounding Sibling Names More Often than Dissimilar Names

When parents select similar sounding names for their children, do they set themselves up for more speech errors in the future? Questionnaire data from 334 respondents suggest that they do. Respondents whose names shared initial or final sounds with a sibling’s reported that their parents accidentally called them by the sibling’s name more often than those without such name overlap. Having a sibling of the same gender, similar appearance, or similar age was also associated with more frequent name substitutions. Almost all other name substitutions by parents involved other family members and over 5% of respondents reported a parent substituting the name of a pet, which suggests a strong role for social and situational cues in retrieving personal names for direct address. To the extent that retrieval cues are shared with other people or animals, other names become available and may substitute for the intended name, particularly when names sound similar.     

Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication

Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are “node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.     

North-American Norms for Name Disagreement: Pictorial Stimuli Naming Discrepancies

Pictorial stimuli are commonly used by scientists to explore central processes; including memory, attention, and language. Pictures that have been collected and put into sets for these purposes often contain visual ambiguities that lead to name disagreement amongst subjects. In the present work, we propose new norms which reflect these sources of name disagreement, and we apply this method to two sets of pictures: the Snodgrass and Vanderwart (S&V) set and the Bank of Standardized Stimuli (BOSS). Naming responses of the presented pictures were classified within response categories based on whether they were correct, incorrect, or equivocal. To characterize the naming strategy where an alternative name was being used, responses were further divided into different sub-categories that reflected various sources of name disagreement. Naming strategies were also compared across the two sets of stimuli. Results showed that the pictures of the S&V set and the BOSS were more likely to elicit alternative specific and equivocal names, respectively. It was also found that the use of incorrect names was not significantly different across stimulus sets but that errors were more likely caused by visual ambiguity in the S&V set and by a misuse of names in the BOSS. Norms for name disagreement presented in this paper are useful for subsequent research for their categorization and elucidation of name disagreement that occurs when choosing visual stimuli from one or both stimulus sets. The sources of disagreement should be examined carefully as they help to provide an explanation of errors and inconsistencies of many concepts during picture naming tasks.