Organism-substrate relations: terminology for ecology and palaeoecology

Terms for indicating the relationship between organisms and their substrates are necessary for effective communication in ecology and palaeoecology. Usage of terms denoting these relationships are discussed and suggestions for more meaningful usage given. Suggested/recommended usage attempts to adhere as closely as possible to the meanings of the terms as originally proposed (e.g. symbiosis). Distinction between substrate and medium is important. Although substrate is categorized as firm and loose, detailed petrographical and/or sedimentological analyses of substrates are needed in both ecology and palaeoecology. A symmetrical classification of organism-substrate relations defining recommended terms which cover broad categories provides a terminology which hopefully is flexible and serves a useful function.     

Mobilizing metaphors: the popular use of keystone,flagship and umbrella species concepts

Misrepresentation of terminology is a major impediment for attempts at enhancing public conservation literacy. Despite being critically important for improving conservation practice, there have been few systematic analyses of the popular use of conservation terminology. This paper draws from science communication studies and metaphor analysis, to examine how keystone, flagship and umbrella species concepts are used and represented in non-academic contexts. 557 news articles containing these terms were systematically analyzed. Mammals featured in 60% of articles on keystones, 55% on flagships and 63% on umbrella species. Number of articles explaining the terms keystone (35%) and flagship (31%) was low, and keystones were the most misrepresented term. Keystones were metaphorically linked with balance, flagships with representation and umbrella species with protection. These metaphors influenced public interpretation of scientific terminology, oriented actions towards select species, and led to a valuation of such actions. Together, the findings highlight three important aspects of popular use of conservation terminology: (1) communication is largely biased towards mammals, (2) everyday language plays a vital role in the interpretation of concepts, and (3) metaphors influence peoples’ actions and understanding. Conservation biologists need to engage with issues of language if public conservation literacy is to be improved. Further evaluations of concepts with high public and policy relevance, systematic identification of communication shortfalls, and linguistic assessments prior to promoting new terms are potential ways of achieving this.     

Les Mollusques Céphalopodes dans les Annales de Paléontologie

About more than forty papers on cephalopods have been published in the ninety one issues of the “Annales” during one century. Most are monographs contributing to enlarge our knowledge on the biodiversity of these Molluscs which play an important part in the fossil record. Jurassic and Cretaceous ammonites are well illustrated; Palaeozoic and Triassic ones, Orthoceratoidea, Nautiloidea and Dibranchiata are seldom studied. As successive issues are published, hypothesis concerning palaeontological and geological applications are proposed by authors: systematics, phylogeny, biostratigraphy, palaeoecology, palaeobiogeography. However, these ones cannot be argued every time because of incomplete knowledge or adapted concepts. Several years or decades later, these hypothesis, reconsidered in a different context and other scientific publications, are the starting point of new ideas, at once developed and then accepted. From this point of view and by their contents, the “Annales” have answered to there vocation of publishing data, carried on year by year and enriched with the discoveries of each new palaeontologists generation.     

On the changing concept of evolutionary population stability as a reflection of a changing point of view in the quantitative theory of evolution

 Eighteen different terms, currently employed to define various concepts of evolutionary stability in population dynamics are mentioned in this paper. Most of these terms are used in different connotations and even different meanings by different authors. On the other hand, different terms are often employed by different authors to define quite the same concept. Twenty-five years ago there was only one, well-defined, concept of stability, universally recognized in the field. In this paper I will try to relate the recent confusion, concerning concepts of population stability, with a more serious, though not that well-recognized, confusion in the modern analytic approach to population dynamics and quantitative evolution. Concepts of population stability will be examined in relation to each other on the one hand and, on the other hand, in relation to two dichotomies regarding the dynamic processes to which they correspond: Short-term versus long-term processes and processes concerning phenotypic changes versus process concerning genotypic changes. A hopefully more consistent use of the current terminology is suggested. Received 15 August 1993; received in revised form 15 September 1994     

On the Numerous Concepts in Invasion Biology

The study of biological invasions has triggered the production of a diversity of concepts. The terminology has, however, often been applied inconsistently and inaccurately. This article lists and assesses the most commonly used terms and concepts in invasion ecology. In each case the most coherent definition and use is suggested.     

Terminology and quantification of environmental heterogeneity in species‐richness research

Spatial environmental heterogeneity (EH) is an important driver of species diversity, and its influence on species richness has been analysed for numerous taxa, in diverse ecological settings, and over a large range of spatial scales. The variety and ambiguity of concepts and terminology, however, have hampered comparisons among studies. Based on a systematic literature survey of 192 studies including 1148 data points, we provide an overview of terms and measures related to EH, and the mechanisms that relate EH to species richness of plants and animals in terrestrial systems. We identify 165 different measures used to quantify EH, referred to by more than 350 measure names. We classify these measures according to their calculation method and subject area, finding that most studies have analysed heterogeneity in land cover, topography, and vegetation, whereas comparatively few studies have focused on climatic or soil EH. Overall, elevation range emerged as the most frequent measure in our dataset. We find that there is no consensus in the literature about terms (such as ‘habitat diversity’ or ‘habitat complexity’), their meanings and associated quantification methods. More than 100 different terms have been used to denote EH, with largely imprecise delimitations. We reveal trends in use of terms and quantification with respect to spatial scales, study taxa, and locations. Finally, we discuss mechanisms involved in EH–richness relationships, differentiating between effects on species coexistence, persistence, and diversification. This review aims at guiding researchers in their selection of heterogeneity measures. At the same time, it shows the need for precise terminology and avoidance of ambiguous synonyms to enhance understanding and foster among‐study comparisons and synthesis.     

灵长类学术语的规范化表述:以α-雄性更替为例

术语是科学概念的约定性语言符号,是科技信息交流的工具。中国的灵长类学研究虽然起步较晚,但发展迅速。在研究过程中,学者们广泛参阅、借鉴国际同行的研究成果,并引入了一些灵长类学专业术语。科学、规范、准确、明晰的表达理应成为学者们的共识,而这对信息的沟通与交流至关重要。本文阐述了科学研究术语规范化表述的重要性,并基于文献梳理,介绍了非人灵长类社会中α-雄性更替（α-male replacement）的主要类型之术语及其含义,建议国内研究者使用：（1）取代（Takeover）;（2）等级反转（Rank reversal）;（3）继承（Succession）;（4）补缺（Waltz-in）;（5）分群（Fission）。文中还讨论了影响α-雄性更替的主要因素。     

Who thinks clearly--writes in plain terms...(about the problems of the terminology in epidemiology)

The work deals with the tendency of introducing superfluous terms in epidemiology and other medical sciences. Four groups of foreign terminology, occurring in scientific literature on different problems of epidemiology, are presented. Examples of publications containing terms and notions whose interpretation is absent in dictionaries are given.     

The value of stress and limitation in an imperfect world: A reply to Körner

A recent perspective paper offered by Körner essentially argued that ‘limitation’ and ‘stress’ are functionally useless terms for ecology except perhaps within limited contexts such as plant physiology or agriculture. We strongly disagree, and to this end argue that, although stress is not as precise as other concepts in ecology and is probably more difficult to apply to communities than to individuals, if ecologists want to communicate in a meaningful and interesting way about the distribution and abundance of species, we have to use multi‐purpose terminology that allows us to scale from reductionistic, strictly quantifiable levels of analysis to more general conceptual levels. Here, we revisit the main arguments presented against these concepts and use three lines of counter‐argument to support our conclusion that limitation and stress are necessary concepts for organizing and integrating general ecological inquiry. We discuss (1) the role of interactions between individuals in changing the limitation experienced by a species, (2) the importance of delineating whether stress is being applied to individuals or to the community, and (3) the evolutionary argument that fitness is never perfect since even adapted species are likely limited to some degree by the environment.     

A consistent terminology for quantifying species diversity?

There is a genuine need for consensus on a clear terminology in the study of species diversity given that the nature of the components of diversity is the subject of an ongoing debate and may be the key to understanding changes in ecosystem processes. A recent and thought-provoking paper (Jurasinski et al. Oecologia 159:15–26, 2009) draws attention to the lack of precision with which the terms alpha, beta, and gamma diversity are used and proposes three new terms in their place. While this valuable effort may improve our understanding of the different facets of species diversity, it still leaves us far from achieving a consistent terminology. As such, the conceptual contribution of these authors is limited and does little to elucidate the facets of species diversity. It is, however, a good starting point for an in-depth review of the available concepts and methods.     

Problems of terminology in the teaching of plant water relations

The considerable variation and confusion in terminology used in the teaching of plant water relations is discussed. The concept of water potential is described briefly and compared with the older concepts of diffusion pressure deficit and suction pressure. The advantages of using water potential terminology are considered. Reference is made to some well-known student texts to illustrate the conflicting meanings of osmotic terms and symbols, and attention is drawn to the problems which arise when authors mix old and new terms. It is recommended that the new terminology should be incorporated into school examination syllabuses and textbooks as soon as possible.     

Nomina dubia der Hippocardioidea (Mollusca; Rostroconchia)

During the course of our revision of rostroconch molluscs quite some more taxa were studied with respect to nomenclatural validity and systematic position than those we redefined, reassigned and introduced. Nomenclatural difficulties as well as untraced, destroyed or simply inadequate type material led to a comprehensive list of invalid taxa or useless species concepts. To enable systematic stability and equal taxonomic concepts we here present 53 species which are very likely members of the superfamily HippocardioideaPojeta & Runnegar, 1976, but judged as nomina dubia for various reasons explained in the text. We strongly recommend no further use of these taxa at least until better preserved material makes redefinition of these species possible.     

Palaeoniches get stitches: analyses of niches informing macroevolutionary theory

The concept of the niche is fundamental to ecology and palaeoecology, and an extensive body of scientific literature exists on the subject Here we discuss how recent palaeontological studies, particularly those focusing on species’ niche dynamics through time, continue to integrate palaeoecology with macroevolutionary theory.     

Lethal interactions among vertebrate top predators: a review of concepts,assumptions and terminology

Lethal interactions among large vertebrate predators have long interested researchers because of ecological and conservation issues. Research focusing on lethal interactions among vertebrate top predators has used several terms with a broad sense, and also introduced new terminology. We analysed the published literature with reference to the main underlying concepts and the use of terminology and its ecological context. The most frequently used terms in the literature were ‘predation’, ‘intraguild predation’, ‘interference competition’, and ‘interspecific killing’. Most studies presented evidence of the killing of the victim (77%), but information regarding its consumption was not given in 48% of cases. More than half of the analysed studies (56%) had no solid information on the degree of competition between interacting species. By reviewing definitions and their underlying assumptions, we demonstrate that lethal interactions among large vertebrate predators could be designated using four terms—‘predation’, ‘intraguild predation’, ‘interspecific competitive killing’, and ‘superpredation’—without the need to employ additional terminology that may increase confusion and misuse. For a correct framework of these lethal interactions it is critical to assess if the kill is consumed, if the victim is indeed a competitor of the killer, and if the prey is a high‐order predator. However, these elements of the framework are simultaneously the most common constraints to studies of lethal interactions, since they often require a great effort to obtain. The proper use of terms and concepts is fundamental to understanding the causes behind lethal interactions and, ultimately, what is actually happening in these complex interactions.     

Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text

Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. However, a limited scope of proteins is annotated due to the amount of human resources required to fully annotate each individual gene product from the literature. We introduce a novel method for automatic identification of GO terms in natural language text. The method takes into consideration several features: (1) the evidence for a GO term given by the words occurring in text, (2) the proximity between the words, and (3) the specificity of the GO terms based on their information content. The method has been evaluated on the BioCreAtIvE corpus and has been compared to current state of the art methods. The precision reached 0.34 at a recall of 0.34 for the identified terms at rank 1. In our analysis, we observe that the identification of GO terms in the _cellular component_ subbranch of GO is more accurate than for terms from the other two subbranches. This observation is explained by the average number of words forming the terminology over the different subbranches.     

DEFINING DYSKARYOSIS – THE BSCC CLASSIFICATION IN 2006

The terminology used for reporting cervical samples in the UK is the BSCC classification, which has evolved over many years. In 2002 the BSCC held a consensus conference to review the BSCC classification, with the intention of providing clearer results for women, improving concordance with other terminologies and facilitating consistency with new scientific developments and technologies. The consensus conference was well attended and robust. In the intervening years there have also been other further advances on morphometry, data on outcomes, data from EQA and other sources. Liquid Based cytology (LBC) has been implemented by the NHS CSP. All of these developments have impacted on the proposed classification, which will be presented in full. The term 'dyskaryosis' will be retained and several of the current reporting categories will be relatively unchanged, though additional information on LBC will be provided.
The major proposed changes are:
(1) A move to a single category of 'High Grade Dyskaryosis' to replace the existing categories of moderate and severe dyskaryosis.
(2) Sub-division of Borderline change into three categories.
Borderline change in glandular cells
Borderline change ?high grade
Borderline change, NOS
(3) The current grades of Mild Dyskaryosis and Borderline change with Koilocytosis to be merged.
Details of these proposals, together with illustrations and the evidence base for change will be presented.