The traits of “trait ecologists”: An analysis of the use of trait and functional trait terminology

Trait and functional trait approaches have revolutionized ecology improving our understanding of community assembly, species coexistence, and biodiversity loss. Focusing on traits promotes comparability across spatial and organizational scales, but terms must be used consistently. While several papers have offered definitions, it remains unclear how ecologists operationalize “trait” and “functional trait” terms. Here, we evaluate how researchers and the published literatures use these terms and explore differences among subdisciplines and study systems (taxa and biome). By conducting both a survey and a literature review, we test the hypothesis that ecologists’ working definition of “trait” is adapted or altered when confronting the realities of collecting, analyzing and presenting data. From 486 survey responses and 712 reviewed papers, we identified inconsistencies in the understanding and use of terminology among researchers, but also limited inclusion of definitions within the published literature. Discrepancies were not explained by subdiscipline, system of study, or respondent characteristics, suggesting there could be an inconsistent understanding even among those working in related topics. Consistencies among survey responses included the use of morphological, phonological, and physiological traits. Previous studies have called for unification of terminology; yet, our study shows that proposed definitions are not consistently used or accepted. Sources of disagreement include trait heritability, defining and interpreting function, and dealing with organisms in which individuals are not clearly recognizable. We discuss and offer guidelines for overcoming these disagreements. The diversity of life on Earth means traits can represent different features that can be measured and reported in different ways, and thus, narrow definitions that work for one system will fail in others. We recommend ecologists embrace the breadth of biodiversity using a simplified definition of “trait” more consistent with its common use. Trait‐based approaches will be most powerful if we accept that traits are at least as diverse as trait ecologists.     

Adipose Tissue Quantification by Imaging Methods: A Proposed Classification

Recent advances in imaging techniques and understanding of differences in the molecular biology of adipose tissue has rendered classical anatomy obsolete, requiring a new classification of the topography of adipose tissue. Adipose tissue is one of the largest body compartments, yet a classification that defines specific adipose tissue depots based on their anatomic location and related functions is lacking. The absence of an accepted taxonomy poses problems for investigators studying adipose tissue topography and its functional correlates. The aim of this review was to critically examine the literature on imaging of whole body and regional adipose tissue and to create the first systematic classification of adipose tissue topography. Adipose tissue terminology was examined in over 100 original publications. Our analysis revealed inconsistencies in the use of specific definitions, especially for the compartment termed “visceral” adipose tissue. This analysis leads us to propose an updated classification of total body and regional adipose tissue, providing a well‐defined basis for correlating imaging studies of specific adipose tissue depots with molecular processes.     

COGA phenotypes and linkages on chromosome 2

An initial linkage analysis of the alcoholism phenotype as defined by DSM-III-R criteria and alcoholism defined by DSM-IV criteria showed many, sometimes striking, inconsistencies. These inconsistencies are greatly reduced by making the definition of alcoholism more specific. We defined new phenotypes combining the alcoholism definitions and the latent variables, defining an individual as affected if that individual is alcoholic under one of the definitions (either DSM-III-R or DSM-IV), and indicated having a symptom defined by one of the latent variables. This was done for each of the two alcoholism definitions and five latent variables, selected from a canonical discriminant analyses indicating they formed significant groupings using the electrophysiological variables. We found that linkage analyses utilizing these latent variables were much more robust and consistent than the linkage results based on DSM-III-R or DSM-IV criteria for definition of alcoholism. We also performed linkage analyses on two first principal components derived phenotypes, one derived from the electrophysiological variables, and the other derived from the latent variables. A region on chromosome 2 at 250 cM was found to be linked to both of these derived phenotypes. Further examination of the SNPs in this region identified several haplotypes strongly associated with these derived phenotypes.     

Endogamy in settlement populations of semai senoi: Potential mate pool analysis and simulation

Abstract

Two methods have been used to evaluate potential endogamy in three settlement populations of a swidden farming group, the Semai Senoi of Malaysia. One method involved determining the number of potential mates available to individuals in each population based on demographic structure and cultural rules concerning appropriate mates. A Monte Carlo simulation of Semai settlement populations was also carried out under two different regimes of mate choice. Both procedures suggest that individuals in the largest Semai settlements are potentially able to marry endogamously but that in smaller groups few potential mates are available and many persons must marry exogamously or remain unmarried. The relatively high rate of marital migration required among small settlement populations implies that newly founded small groups would be unlikely to become sufficiently isolated to form distinct breeding populations.     

Blood Drunkenness and the Bloodthirsty Semai: Unmaking Another Anthropological Myth

The Senoi Semai of Malaysia have frequently been cited as examples in the debates over the wellsprings of human violence. Numerous writers have employed selected Semai ethnographic material to support assertions that, their apparent peacefulness notwithstanding, Semai are in reality bloodthirsty killers. This assertion has in turn been used as evidence in support of a variety of approaches whose common thread is a view of aggressiveness and violence as somehow innate in human beings. The authors of this article, whose publications form the basis of most anthropological knowledge of Semai life and culture, draw on their own published and unpublished work as well as on documentation from other sources to refute these interpretations. We hold that Semai life is, as first-hand observers have described it, notably free of interpersonal violence, and we argue that misrepresentations rooted in particular theoretical or philosophical a priori assumptions are scientifically untenable and culturally slanderous.     

Some thoughts on taxonomic terminology

There are gaps and inconsistencies in current taxonomic vocabulary which might benefit from some attention. To address these issues, some terminological standards are proposed and explained herein. The validity of terminology derived from clear grammatical patterns is not necessarily precluded by an absence of previous use. It is still, however, a worthwhile exercise to include such potential terms in a body of text that can serve as a reference to anyone wishing to employ terminology of this nature, with the secondary benefit that it may encourage more widespread use of these terms for a more consistent use of taxonomic terminology.     

Ecological units: definitions and application

Concepts of ecological units, such as population, community, and ecosystem, are at the basis of ecological theory and research and have increasingly become the focus of conservation strategies. Concepts of these units still suffer from inconsistencies and confusions over terminology. The different concepts are treated here together as a common "conceptual cluster," with similar ecological functions (roles) and similar problems in their definition and use. An analysis of the multitude of existing terms and concepts that have been developed for these units reveals that they differ with respect to at least four basic criteria: (i) the questions as to whether they are defined statistically or via a network of interactions; (ii) if their boundaries are drawn by topographical or process-related criteria; (iii) how high the required internal relationships are; and (iv) if they are perceived as "real" entities or abstractions by an observer The various definitions cannot be easily sorted into just a few types, but they can be characterized by several independent criteria. I argue that serious problems arise if the different possibilities of defining ecological units are not recognized and if the concepts are perceived as self-evident. The different concepts of ecological units should be defined and used in a philosophically informed manner I propose a dual approach to the use of ecological units. Generic meanings of the main concepts (especially population, community, and ecosystem) should be retained only as heuristically useful perspectives, while specific and "operational" definitions of the concepts as units should be developed, depending on specific purposes of their use. Some thoughts on the basic requirements for such definitions and the domains of their uses are briefly explained.     

Adenosine deaminase polymorphism among the Semai, Temuan, Semelai, and Jakun groups of West Malaysian Orang Asli

812 West Malaysian Orang Asli belonging to four ethnic groups were surveyed for adenosine deaminase (ADA; EC 3.5.4.4) using starch gel electrophoresis. Only the common ADA1 and ADA2 alleles were found, with the frequencies of the latter being 0.025, 0.103, 0.115 and 0.028 in the Semai, Semelai, Temuan, and Jakun groups, respectively. A new 'breeding genetic distance' was applied to these gene frequencies and the Semelai and Temuan were found to be more closely related to each other, and to have considerably more evolutionary flexibility on this scale of 'micro-evolution' than the other two groups. The Semai and Jakun were more similar to each other on the basis of these ADA gene frequencies.     

Resource limited and equilibrium models of populations

Summary The logistic equation has been used as the basis of two distinct models of population dynamics, a resource limited model and an equilibrium model. It is argued that although the two models are very different, the distinction between them has been obscured by the use of the same terminology for the parameters of both. It is further argued that the simple equilibrium model developed from the logistic equation has inconsistencies which make it untenable as a population model.     

Fission-fusion and lineal effect: aspects of the population structure of the Semai Senoi of Malaysia.

Analysis of histories and genealogies from seven relatively unacculturated, swidden-farming Semai settlements shows that the composition of local groups fluctuates through time. This instability is similar to a pattern which Neel and his colleagues have suggested is typical of primitive society, the fission-fusion model. In addition, the individuals comprising Semai fission groups are kinsmen which implies that the number of independent genomes represented is markedly less than the number of individual migrants (the lineal effect). Fission groups may form new villages or fuse with an established settlement. In either case, the genetic effects of such migration are more pronounced than would be expected on the basis of founder effect or random migration. Despite several conspicuous differences in social organization between the Semai and the South American Indians (e.g., bilateral vs. unilineal descent) whose population structure provided the empirical basis for the fission-fusion, lineal effect model, the basic similarities are striking. The Semai case thus lends support to the proposition that this pattern may be of some generality in technologically primitive populations.     

Consensus for experimental design in electromyography (CEDE) project: Terminology matrix

Consensus on the definition of common terms in electromyography (EMG) research promotes consistency in the EMG literature and facilitates the integration of research across the field. This paper presents a matrix developed within the Consensus for Experimental Design in Electromyography (CEDE) project, providing definitions for terms used in the EMG literature. The definitions for physiological and technical terms that are common in EMG research are included in two tables, with key information on each definition provided in a comment section. A brief outline of some basic principles for recording and analyzing EMG is included in an appendix, to provide researchers new to EMG with background and context for understanding the definitions of physiological and technical terms. This terminology matrix can be used as a reference to aid researchers new to EMG in reviewing the EMG literature.     

Genetic microdifferentiation in the Semai Senoi of Malaysia.

Blood samples, demographic and cultural data were collected from seven settlements of Semai Senoi, a swidden farming ethnic group of Malaysia. Three genetic loci (ABO blood group, hereditary ovalcytosis, and hemoglobin) were analyzed in a total sample of 546 individuals. These data indicate a considerable degree of genetic microdifferentiation in this area of the Semai distribution. Parent-offspring birthplace data (analyzed by means of a migration matrix) and settlement histories show that settlements are not strongly isolated. Genetic differences in the study area demonstrate a reasonable correspondence with migration and the history of the settlements. Genetic convergence also occurs through the addition of migrant groups to established populations leading to new patterns of marriage between donor and recipient groups. The genetic structure of the total Semai population through time thus comprises a mosaic of shifiting allele frequencies in a series of semi-isolated local populations.     

Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticians

Bioinformatics is the field where computational methods from various domains have come together for analysis of biological data. Each domain has introduced its own specific jargon. However, in closely related domains, e.g. machine learning and statistics, concordant and discordant terminology occurs, the later can lead to confusion. This article aims to help solve the confusion of tongues arising from these two closely related domains, which are frequently used in bioinformatics. We provide a short summary of the most commonly applied machine learning and statistical approaches to data analysis in bioinformatics, i.e. classification and statistical hypothesis testing. We explain differences and similarities in common terminology used in various domains, such as precision, recall, sensitivity and true positive rate. This primer can serve as a guide to the terminology used in these fields.     

Homology a personal view on some of the problems

There are many problems relating to defining the terminology used to describe various biological relationships and getting agreement on which definitions are best. Here, I examine 15 terminological problems, all of which are current, and all of which relate to the usage of homology and its associated terms. I suggest a set of definitions that are intended to be totally consistent among themselves and also as consistent as possible with most current usage.     

Changing sex ratio of mortality in the Semai Senoi, 1969-1987

An excess of male over female deaths is characteristic of modern national populations, whereas in some high-mortality societies female mortality exceeds that of males. Among the Semai Senoi, a Malaysian Orang Asli ("aboriginal") population, women experienced higher mortality than males in the decades before 1969. This differential occurred in all age classes older than 15 years so that the sex ratio progressively increased with age. A recent (1987) restudy of the Semai population found that sex-specific differential mortality is much reduced. A comparison of the 1969 and 1987 life tables shows a sharp shift in the sex ratios of mortality for the post-15-year-old age classes (the geometric means of age classes 15-44 were 0.768 in 1969 and 0.997 in 1987) so that male and female expectations of further life at age 15 are now nearly identical. In contrast to the best-known cases of high female mortality (mostly in South Asia), Semai sex differential mortality does not include the childhood ages. The Semai have traditionally been relatively sexually egalitarian, and sex bias in care has not occurred. Analysis of sex-specific causes of death for the pre-1969 population suggests that maternal mortality is the major cause of the excess female deaths. The reduced number of maternal deaths seems largely due to better health care, particularly the availability of hospital services. Interestingly, the reduction in female mortality has occurred simultaneously with increased fertility, and overall mortality has continued at relatively high levels (eO less than 36). Thus, rather than forming a component of a unitary demographic transition, declining sex differences in mortality can be accounted for by a specific factor, better maternal care.     

Rapid global change: implications for defining natives and aliens

The ability to ascribe native or alien status to species in a rapidly changing world underpins diverse research fields that overlap with global change and biological invasions via biodiversity. Current definitions generally link alien status to anthropogenic dispersal events, but this can create conflicts for active management and global change adaptation strategies, such as managed relocation and restoration ecology. Here we propose a unifying approach that allows for the incorporation of rapid global change into biological invasion terminology. We introduce the concept of a projected dispersal envelope (PDE) to define the region where a species is or could be native, irrespective of human involvement. The PDE integrates biogeography and niche theory with existing invasion terminology to place a spatial and temporal context on species movements. We draw on a diverse suite of topical organism movements to illustrate these concepts. Our restructured definitions allow for native species to move into or with rapidly shifting climatic regions, as well as identifying the inappropriate introduction of alien species to new areas. Moreover, our definitions framework forms a timely and essential component of adaptation policies and responses for invasive species management and the enhancement of biodiversity in a rapidly changing world.     

A bottom-up ontology-based approach to monitor circular economy: Aligning user expectations,tools, data and theory

With circular economy being high on governmental agendas, there is an increasing request from governing bodies for circularity measurements. Yet, currently existing macro-level monitoring frameworks are widely criticized for not being able to inform the decision-making. The criticism includes, among others, a lack of consensus on terminologies and definitions among scholars, politicians, and practitioners, a lack of supporting data and tools and, consequently, a lack of transparency and trustworthiness. To address those needs, a bottom-up approach to build a shared terminology is suggested as a starting point for monitoring development. The government, data providers, and tool developers are involved in the process of formal ontology development and alignment. The experiment builds upon a use case of the Amsterdam Circular Economy Monitor (2020). First, four ontology development approaches are used to create a theory-centered, a user-centered, a tool-centered, and a data-centered ontology. The ontologies are later compared, merged, and aligned to arrive at one single ontology which forms the basis of the circular economy monitor. The notes taken during the process have revealed that next to a material flow model, typical of socioeconomic metabolism analysis, policy makers are concerned with actors (i.e., institutions, companies, or groups of people) who participate in the analyzed processes and services. Furthermore, a number of terms used by the decision-makers lack clear definitions and references to be directly associated with the available data. Finally, a structured terminology alignment process between monitor users, developers, and data providers helps in exposing terminology conflicts and ambiguities.     

Ecosystem services classification: A systems ecology perspective of the cascade framework

Ecosystem services research faces several challenges stemming from the plurality of interpretations of classifications and terminologies. In this paper we identify two main challenges with current ecosystem services classification systems: i) the inconsistency across concepts, terminology and definitions, and; ii) the mix up of processes and end-state benefits, or flows and assets. Although different ecosystem service definitions and interpretations can be valuable for enriching the research landscape, it is necessary to address the existing ambiguity to improve comparability among ecosystem-service-based approaches. Using the cascade framework as a reference, and Systems Ecology as a theoretical underpinning, we aim to address the ambiguity across typologies. The cascade framework links ecological processes with elements of human well-being following a pattern similar to a production chain. Systems Ecology is a long-established discipline which provides insight into complex relationships between people and the environment. We present a refreshed conceptualization of ecosystem services which can support ecosystem service assessment techniques and measurement. We combine the notions of biomass, information and interaction from system ecology, with the ecosystem services conceptualization to improve definitions and clarify terminology. We argue that ecosystem services should be defined as the interactions (i.e. processes) of the ecosystem that produce a change in human well-being, while ecosystem components or goods, i.e. countable as biomass units, are only proxies in the assessment of such changes. Furthermore, Systems Ecology can support a re-interpretation of the ecosystem services conceptualization and related applied research, where more emphasis is needed on the underpinning complexity of the ecological system.