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.     

古北界在中国及其邻近国家的南部界线

论述了一种客观地划分生物地理区域界线的方法。根据物种分布范围和系统发生或生态渊源关系等概念,在过去所提出的分界线附近选择一些地点,确定在这些地区中是否有某个物种分布,从而确定这些物种可能所隶属的生物地理区。依此方法,作者在46°N,128°E和24°N,76°E之间选择了12个地点,通过兽类的区系成份分析,并结合植被特征,探讨了中国及其邻近国家的古北界南界。结果表明,古北界和东洋界兽类区系成份在各地区的分布（百分率）分别如下：东北部的吉林省(100、0)、东部的山东省（90、10）、江苏和安徽省（59、41）、浙江（54、46,沿海分别为44、56）、南部的海南岛（19、81）、四川邛崃山（87、13）、四川大雪山（79、21）、云南云岭（90、10）、缅甸东北部（52、48）、泰国（7、93）、尼泊尔、锡金和不丹以及中国的喜马拉雅山南麓（45、55）和巴基斯坦（63、37）。作者认为古北界和东洋界之间存在过渡区,过渡区东段在中国东部地区的中心约在30°N,南缘约在28°N,北缘约在33°N;中段山地的海拔高度在1500～2500m之间,过渡区中心的海拔高度为2000m;西段的印度河区作为东洋和古北两界的过渡区比作为东洋界向西的延伸更为合适。     

The community of an individual: implications for the community concept

The concept of the ecological community is examined from the perspective of its criteria and domain. The multiple definitions and uses of this concept indicate a variety of scales and approaches. In this paper, a core definition of the minimal criteria and domain is proposed. Using those criteria, a model of the ecological community is developed based on a focal individual and its interactions with other individuals. In order to increase the scale of the domain of this approach, additional criteria are required. This model is used to explore characteristics of the minimum domain and larger scales of the community concept. The structure that emerges emphasizes context dependency and the potential for indeterminacy for most types of interactions. A prominent historical argument, the nature of boundaries between communities, has no relevance in this model.     

A comment on testing for a decline in upper Cretaceous dinosaur diversity

A common problem in ecology is to determine whether the diversity of a biological community has changed over time or in response to a disturbance. This involves testing the null hypothesis that diversity is constant against the alternative hypothesis that it has changed. As the power of this test may be low, Fritsch and Hsu (1999, Biometrics 55, 1300-1305) proposed reversing the null and alternative hypothesis. Here, I return to the original formulation and point out that power can be improved by adopting a parametric model for relative abundances and by testing against an ordered alternative.     

Ecological communities: conceptual problems and definitions

Three major problems with respect to ecological communities are tackled. The first is the problem of ambiguity, i.e. the fact that the term “community” is being used for various kinds of objects at different levels of organisation. We argue that this problem can be resolved by restricting use of the term “community” to sets of co-occurring organisms belonging to a single taxonomic phylum or class (plants, birds, insects, etc.) and by using the term “biocoenosis” for sets of organisms belonging to multiple phyla or classes and comprising the biotic components of ecosystems. We also argue that interaction between organisms is neither a necessary nor a sufficient condition for community membership, or, in other words, that communities may consist of both interacting and non-interacting organisms. The second and third problems are the boundary problem and the problem of heterogeneity, i.e. the fact that communities, as currently defined, most often do not have discrete boundaries and are quite heterogeneous with respect to species composition. We argue that both problems result from the fact that communities are seen as groups of co-occurring populations of species, whereas actually populations of different species rarely if ever co-occur in exactly the same area. These problems can be resolved by redefining communities as particular sets of individuals occurring in the intersection of the areas occupied by different populations of species. In the final section we defend our definition against some potential objections, viz. (1) that it would lead to an excessive number of small communities, especially in species-rich situations, and (2) that, because population boundaries may change all the time, such communities would be very unstable.     

Autopoiesis 40 years Later. A Review and a Reformulation

The concept of autopoiesis was proposed 40 years ago as a definition of a living being, with the aim of providing a unifying concept for biology. The concept has also been extended to the theory of knowledge and to different areas of the social and behavioral sciences. Given some ambiguities of the original definitions of autopoiesis, the concept has been criticized and has been interpreted in diverse and even contradictory ways, which has prevented its integration into the biological sciences where it originated. Here I present a critical review and conceptual analysis of the definition of autopoiesis, and propose a new definition that is more precise, clear, and concise than the original ones. I argue that the difficulty in understanding the term lies in its refined conceptual subtlety and not, as has been claimed by some authors, because it is a vacuous, trivial or very complex concept. I also relate the concept of autopoiesis to the concepts of closed systems, boundaries, homeostasis, self-reproduction, causal circularity, organization and multicellularity. I show that under my proposed definition the concept of a molecular autopoietic system is a good demarcation criterion of a living being, allowing its general integration into the biological sciences and enhancing its interdisciplinary use.     

A Recipe for Unconventional Evenness Measures

The degree to which abundances are evenly divided among the species of a given community is a basic property of any biological community. Several evenness indices have thus far been proposed in ecological literature. However, despite their vast potential applicability in ecological research, none seems to be generally preferred. In this paper, I first summarize the basic requirements that evenness measures should meet to adequately behave in ecological studies. Then, I discuss the major drawbacks of these requirements and propose an alternative family of measures that are based on the notion of specificity used in fuzzy set theory for measuring the uncertainty associated with a fuzzy set.     

Ecological restoration should be redefined for the twenty‐first century

Forty years ago, ecological restoration was conceptualized through a natural science lens. Today, ecological restoration has evolved into a social and scientific concept. The duality of ecological restoration is acknowledged in guidance documents on the subject but is not apparent in its definition. Current definitions reflect our views about what ecological restoration does but not why we do it. This viewpoint does not give appropriate credit to contributions from social sciences, nor does it provide compelling goals for people with different motivating rationales to engage in or support restoration. In this study, I give a concise history of the conceptualization and definition of ecological restoration, and I propose an alternative definition and corresponding viewpoint on restoration goal‐setting to meet twenty‐first century scientific and public inquiry.     

Let the concept of trait be functional!

In its simplest definition, a trait is a surrogate of organismal performance, and this meaning of the term has been used by evolutionists for a long time. Over the last three decades, developments in community and ecosystem ecology have forced the concept of trait beyond these original boundaries, and trait-based approaches are now widely used in studies ranging from the level of organisms to that of ecosystems. Despite some attempts to fix the terminology, especially in plant ecology, there is currently a high degree of confusion in the use, not only of the term "trait" itself, but also in the underlying concepts it refers to. We therefore give an unambiguous definition of plant trait, with a particular emphasis on functional trait. A hierarchical perspective is proposed, extending the "performance paradigm" to plant ecology. "Functional traits" are defined as morpho-physio-phenological traits which impact fitness indirectly via their effects on growth, reproduction and survival, the three components of individual performance. We finally present an integrative framework explaining how changes in trait values due to environmental variations are translated into organismal performance, and how these changes may influence processes at higher organizational levels. We argue that this can be achieved by developing "integration functions" which can be grouped into functional response (community level) and effect (ecosystem level) algorithms.     

Temporal and spatial scales in epidemiological concepts.

Traditional concepts in epidemiology are reviewed from ecological, cultural, and logical perspectives. In zoological epidemiology (including the study of human and livestock diseases caused by pathogens), temporal and spatial scales are typically not used in definitions, by hypotheses, and theories concerning epidemic and endemic diseases. The same is true for botanical and theoretical epidemiology, although these two subdisciplines use a different definition of an epidemic than does zoological epidemiology. If hypotheses are to be tested and implemented, more precise concepts that include general temporal and spatial scales are needed. Criteria proposed here for identifying temporal and spatial scales are based on the need for consistency of observation and ecological validity. Consistency of observation depends upon the relative life cycles of the hosts and pathogens and upon the environmental effects that lead to stable or unstable population structures. Pathogens are classified as absent, sporadic, or persistent (endemic). Epidemics can occur in the latter two cases but require a separate evaluation. A definition of an epidemic based on temporal and spatial scales and statistics is proposed for use by all subdisciplines. An epidemic occurs when an indicator variable reaches a statistically unusually high value due to transmission of a pathogen in an ecologically proper space-time unit. Threshold theorems in botanical and theoretical epidemiology are also discussed. These proposals do not directly affect modeling, but changes to hypotheses may influence model analyses.     

Binding to δ and μ opioid receptors by deltorphin I/II analogues modified at the Phe and Asp/Glu side chains: a report of 32 new analogues and a QSAR study

The synthesis and binding affinities of 32 X³Gly⁴ dual-substitution analogues of the natural opioid heptapeptides deltorphin I and II are reported. A multiple regression QSAR analysis was performed using those results along with literature data for the X³Asp⁴ and Phe³X⁴ side chain analogues. Fitting to a three-term potential well model with hydrophobic and van der Waals attraction terms and a steric repulsion term indicates that the δ and μ receptor sites for binding the residue three side chain are similar, and that the binding interaction is primarily van der Waals and secondarily hydrophobic. Further analysis indicates that both sites are more constrained with respect to side chain length than width or thickness, and the μ site appears to be somewhat larger. A binding model consistent with these findings pictures the native third residues Phe ring laying on a step notched out of the receptor surface, pointing toward the back (riser) of the step, and sandwiched between the receptor and ligand. However, the binding sites for the residue four side chains are quite different on δ and μ receptors. Binding to the δ site appears to involve both electrostatic attraction (probably to a partial positive charge) and van der Waals attraction, but not necessarily hydrogen bonding, and more constraint with respect to side chain length than width or thickness. In contrast, there is no evidence for any kind of binding attraction between the side chain of residue four and the μ site, which acts more as steric repulsion site, as though the space that is a pocket on the δ receptor is filled in on the μ receptor. A regression model based only on steric repulsion by van der Waals bulk and/or the effective bulk of a hydration layer accounts for over 80% of the residue four related variation in μ affinity.

Abstract

Thirty-two new X³Gly⁴ analogues of deltrophin I/II opioid peptides are described. A QSAR study of the X³Gly⁴, X³Asp⁴, and Phe³X⁴ analogue series using a potential well model reveals the roles of hydrophobic, van der Waals, electrostatic, hydrogen bonding and steric interactions in δ and μ receptor binding of X³ and X⁴ side chains.     

Community ecological modelling as an alternative to physiographic classifications for marine conservation planning

Accurate mapping of marine species and habitats is an important yet challenging component of establishing networks of representative marine protected areas. Due to limited biological data, marine classifications based on abiotic data are often used as surrogates to represent biological patterns. We tested the surrogacy of an existing physiographic marine classification using non-metric multidimensional scaling and permutational analysis of variance to determine whether species composition was significantly different among physiographic units. We also present an alternative ecological classification that incorporates biological and environmental data in a community modeling approach. We use data on 174 species of demersal fish and benthic invertebrates to identify mesoscale biological assemblages in a 100,000 km² study area in the northeast Pacific Ocean. We identified assemblages using cluster analysis then used a random forest model with 12 environmental variables to delineate mesoscale ecological units. Our community modelling approach resulted in five geographically coherent ecological units that were best explained by changes in depth, temperature and salinity. Our model showed high predictive performance (AUC = 0.93) and the resulting ecological units represent more distinct species assemblages than those delineated by physiographic variables alone. A strength of our analysis is the ability to map model uncertainty to identify transition zones at unit boundaries. The output of this study provides a biotic driven classification that can be used to better achieve representativity in the MPA planning process.     

A species-based theory of insular zoogeography

• 1 I present an alternative to the equilibrium theory of island biogeography, one which is based on the premise that many of the more general patterns in insular community structure result from, not despite, nonrandom variation among species.
• 2 For the sake of simplicity, the model is limited to patterns and processes operating over scales of ecological space and time: evolution is not included in the current version of the model.
• 3 The model assumes, as did MacArthur and Wilson’s model, that insular community structure is dynamic in ecological time, but the model does not assume a balance, or equilibrium, of immigration and extinction.
• 4 The model presented here is hierarchical, phenomenological (it requires little parameterization beyond that which is directly derived from distributional data), graphical, and it includes potential feedback processes (including interspecific interactions).
• 5 The model offers an alternative explanation for a variety of patterns ranging from distributions of individual species, species–area and species–isolation relationships, to patterns of assembly of insular communities. The model also generates some new predictions and identifies some potentially important areas for future studies.

     

Organisms in evolution

Organisms constitute one of the most remarkable features of our living world. However, they have not yet received any accepted characterization within the framework of the evolutionary theory. The reasons for this contrast between the saliency of organisms in the biological landscape and their theoretical status are multiple and they are analyzed in the first part of this paper. Starting from this contrast, I argue for a theoretically grounded concept of organism within the framework of evolutionary theory itself. To this effect I argue that the theory of major transitions in evolution (Maynard Smith and Szathmáry 1995; Michod 1999) provides us with the theoretical basis for an understanding of the individuality of organisms and I propose a first characterization of organisms as evolutionary units structured by a division of reproductive labor among their parts. I also discuss one of the most important implications of this definition, namely that some colonial entities are to be counted as superorganisms. Finally, I show that though theoretically satisfying, this definition does not suffice in order fully to individuate the organisms and superorganisms in practice. To this end, physiology is needed, because it offers us some criteria for their individuation in ecological space. These criteria, however, are not immune to errors through misidentification and their shortcomings are discussed in the last section. In conclusion, I emphasize the positive implications of these criteria concerning the ecological significance of organisms.     

A simple and rapid microwave-assisted hematoxylin and eosin staining method using 1,1,1 trichloroethane as a dewaxing and a clearing agent

The use and practicability of microwave-assisted staining procedures in routine histopathology has been well established for more than 17 years. In the study reported here, we aimed to examine an alternative approach that would shorten the duration of dewaxing and clearing steps of hematoxylin and eosin (H & E) staining of paraffin sections by using a microwave oven. Although xylene is one of the most popular dewaxing and clearing agents, its flammability restricts its use in a microwave oven; thus we preferred 1,1,1 trichloroethane, which is not flammable, as the dewaxing and clearing agent in the present study. In Group I and Group II (control groups), intestine was processed with xylene and 1,1,1 trichloroethane, respectively. The sections were then stained with H & E according to the conventional staining protocol at room temperature and subdivided into two groups according to the duration of dewaxing and clearing in xylene. In Groups III and IV (experimental groups) similar tissues were processed with xylene and 1,1,1 trichloroethane, respectively; however, sections from these groups were divided into four subgroups to study the period required for dewaxing and clearing in 1,1,1 trichloroethane, then stained with H & E in the microwave oven at 360 W for 30 sec. Our conventional H & E staining procedure, which includes dewaxing, staining and clearing of sections, requires approximately 90 min, while our method using 1,1,1 trichloroethane and microwave heating required only 2 min. Our alternative method for H & E staining not only reduced the procedure time significantly, but also yielded staining quality equal or superior to those stained the conventional way. Our results suggest that 1,1,1 trichloroethane can be used effectively and safely as a dewaxing and clearing agent for H & E staining in a microwave oven.     

Protist taxonomy: an ecological perspective

This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.     

浅析物种概念的演变历史

本文是一篇关于物种概念演变的简述。生物学家用不同的方法或标准划分物种, 就形成了不同的物种概念, 如生物学物种、形态学物种、生态学物种、进化物种、系统发生或支序物种, 或它们的组合, 等等。它们都揭示了物种属性的特定侧面, 都是不同物种客观存在的真实反映, 但都无法令所有人满意。对真核生物来说, 无论它们在形态上的差别有多大, 生殖隔离(不能产生可育的后代)应该是两个群体能否真正分化成不同物种的关键, 这种隔离机制可以是地理的、行为的或其他方式; 而生殖隔离总会伴随着一些形态或遗传上的变化, 虽然这些特征可能与生殖隔离本身并无多大关系, 但往往成为分类学家或分子进化生物学家区分种的依据,对已经灭绝的化石物种来说, 生殖隔离的物种划分方式就无能为力了。如何准确定义一个物种依然充满着矛盾, 因为基于生殖隔离的物种概念不实用, 而实用的物种概念(如形态学物种)又被认为是人为的。     

Ecological thresholds: Concept,Methods and research outlooks

The concept of ecological thresholds was raised in the 1970s. However, it was subsequently given different definitions and interpretations depending on research fields or disciplines. For most scientists, ecological thresholds refer to the points or zones that link abrupt changes between alternative stable states of an ecosystem. The measurement and quantification of ecological thresholds have great theoretical and practical significance in ecological research for clarifying the structure and function of ecosystems, for planning sustainable development modes, and for delimiting ecological red lines in managing the ecosystems of a region. By reviewing the existing concepts and classifications of ecological thresholds, we propose a new concept and definition at two different levels: the ecological threshold points, i.e. the turning points of quantitative changes to qualitative changes, which can be considered as ecological red lines; the ecological threshold zones, i.e. the regime shifts of the quantitative changes among different stable states, which can be considered as the yellow and/or orange warning boundaries of the gradual ecological changes. The yellow thresholds mean that an ecosystem can return to a stable state by its self-adjustment, the orange thresholds indicate that the ecosystem will stay in the equilibrium state after interference factors being removed, whereas the red thresholds, as the critical threshold points, indicate that the ecosystem will undergo irreversible degradation or even collapse beyond those points. We also summarizes two types of popular Methods in determining ecological thresholds: statistical analysis and modeling based on data of field observations. The applications of ecological thresholds in ecosystem service, biodiversity conservation and ecosystem management research are also reviewed. Future research on ecological thresholds should focus on the following aspects: (1) methodological development for measurement and quantification of ecological thresholds; (2) emphasizing the scaling effect of ecological thresholds and establishment of national-scale observation system and network; and (3) implementation of ecological thresholds as early warning tools in ecosystem management and delimiting ecological red lines.