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.     

Effects of trophic similarity on community composition

Understanding how ecological processes determine patterns among species coexisting within ecosystems is central to ecology. Here, we explore relationships between species’ local coexistence and their trophic niches in terms of their feeding relationships both as consumers and as resources. We build on recent concepts and methods from community phylogenetics to develop a framework for analysing mechanisms responsible for community composition using trophic similarity among species and null models of community assembly. We apply this framework to 50 food webs found in 50 Adirondack lakes and find that species composition in these communities appears to be driven by both bottom‐up effects by which the presence of prey species selects for predators of those prey, and top‐down effects by which prey more tolerant of predation out‐compete less tolerant prey of the same predators. This approach to community food webs is broadly applicable and shows how species interaction networks can inform an increasingly large array of theory central to community ecology.     

Species concepts and species reality: salvaging a Linnaean rank

The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.     

Life With or Without Names

The terms ‘life’, ‘species’ and ‘individuals’ are key concepts in biology. However, theoretical and practical concerns are directly associated with definitions of these terms and their use in researchers’ work. Although the practical implications of employing definition of ‘species’ and ‘individuals’ are often clear, it is surprising how most biologists work in their field of study without adhering to a specific definition of life. In everyday scientific practice, biologists rarely define life. This is somewhat understandable: the majority of biologists accept the standard definition of life without exploring it, but this represents a bad attitude. In this essay, we update the concepts of life, species, and individuals in the light of the new techniques for massive DNA sequencing collectively known as high throughput DNA sequencing (HTS). A re-evaluation of the newest approaches and traditional concepts is required, because in many scientific publications, HTS users apply concepts ambiguously (in particular that of species). However, the absence of clarity is understandable. For most of the last 250 years, from Linnaeus to the most recent researches, identification and classification have been performed applying the same process. On the contrary, through HTS, biologists have become simply identifiers, who construct boundaries around the biological entities and do not examine the taxa at length, resulting in uncertainty in most readers and displeasure in traditional taxonomists. We organised our essay to answer a basic question: can we develop new means to observe living organisms?     

Resource quality or competition: why increase resource acceptance in the presence of conspecifics?

Some animal species increase resource acceptance rates in the presence of conspecifics. Such responses may be adaptive if the presence of conspecifics is a reliable indicator of resource quality. Similarly, these responses could represent an adaptive reduction in choosiness under high levels of scramble competition. Although high resource quality and high levels of scramble competition should both favor increased resource acceptance, the contexts in which the increase occurs should differ. In this paper, we tested the effect of social environment on egg-laying and aggressive behavior in the walnut fly, Rhagoletis juglandis, in multiple contexts to determine whether increased resource acceptance in the presence of conspecifics was better viewed as a response to increased host quality or increased competition. We found that grouped females oviposit more readily than isolated females when provided small (low-quality) artificial hosts but not when provided large (high-quality) artificial hosts, indicating that conspecific presence reduces choosiness. Increased resource acceptance was observed even when exposure to conspecifics was temporally or spatially separate from exposure to the resource. Finally, we found that individuals showed reduced aggression after being housed in groups, as expected under high levels of scramble competition. These results indicate that the pattern of resource acceptance in the presence of conspecifics may be better viewed as a response to increased scramble competition rather than as a response to public information about resource quality.     

Fish species – how and why

It is argued, with selected examples from freshwaterfish systematics, that species should be viewed as anexpression of self-perpetuated clustered variation innature, conforming to the phylogenetic speciesconcept. The importance of species lies in thefunctional and structural significance of theirdiagnostic characters. Species can be nested by theircharacters into a tree diagram (phylogeny) orhierarchical alignment structure (classification) ofcharacter distribution, which may be taken to reflectevolution, the unifying theory of organismaldiversification. The phylogenetic species concept,which emphasizes recognition of a pattern ofvariation, describes better than any other proposedconcept the units called species by systematists.Other concepts are based on processes and normally donot permit recognition of particular taxa. Specieshave unique histories, and speciation may proceed bydifferent mechanisms. Whereas it may be postulatedthat speciation entails an irreversible change in thegenetic structure of taxa, recognized by phenotypicexpression and apparently also maintained to a largeextent by selection for a particular phenotype,species recognition must remain independent ofassumptions about species history and spatialdistribution. Species are monophyletic taxa and thespecies category does not differ significantly inphylogenetic regard from other systematic categories.Species as such are not necessarily evolutionaryunits. It is recommended to apply species names withreference to the diagnostic characters of the speciesand to abandon the type specimen described by theInternational Code of Zoological Nomenclature as anomenclatural reference unit.     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

The cladistic solution to the species problem

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept.     

Body size and elevation: do Bergmann's and Rensch's rule apply in the polytypic bushcricket Poecilimon veluchianus?

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Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.     

De-extinction and the conception of species

Developments in genetic engineering may soon allow biologists to clone organisms from extinct species. The process, dubbed “de-extinction,” has been publicized as a means to bring extinct species back to life. For theorists and philosophers of biology, the process also suggests a thought experiment for the ongoing “species problem”: given a species concept, would a clone be classified in the extinct species? Previous analyses have answered this question in the context of specific de-extinction technologies or particular species concepts. The thought experiment is given more comprehensive treatment here. Given the products of three de-extinction technologies, twenty-two species concepts are “tested” to see which are consistent with the idea that species may be resurrected. The ensuing discussion considers whether or not de-extinction is a conceptually coherent research program and, if so, whether or not its development may contribute to a resolution of the species problem. Ultimately, theorists must face a choice: they may revise their commitments to species concepts (if those concepts are inconsistent with de-extinction) or they may recognize de-extinction as a means to make progress in the species problem.     

What is an individual organism? A multilevel selection perspective

Most biologists implicitly define an individual organism as "one genome in one body." This definition is based on physiological and genetic criteria, but it is problematic for colonial organisms. We propose a definition based instead on the evolutionary criteria of alignment of fitness, export of fitness by germ-soma specialization, and adaptive functional organization. We consider how these concepts apply to various putative individual organisms. We conclude that complex multicellular organisms and colonies of eusocial insects satisfy these three criteria, but that, in most cases (with at least one notable exception), colonies of modular organisms and genetic chimeras do not. While species do not meet these criteria, they may meet the criteria for a broader concept--that of an evolutionary individual--and sexual reproduction may be a species-level exaptation for enhancing evolvability. We also review the costs and benefits of internal genetic heterogeneity within putative individuals, demonstrating that high relatedness is neither a necessary nor a sufficient condition for individuality, and that, in some cases, genetic variability may have adaptive benefits at the level of the whole.     

Foraging sequence,energy intake and torpor: an individual‐based field study of energy balancing in desert golden spiny mice

We studied the relationship between sequence of foraging, energy acquired and use of torpor as an energy‐balancing strategy in diurnally active desert golden spiny mice. We hypothesised that individuals that arrive earlier to forage will get higher returns and consequently spend less time torpid. If that is the case, then early foragers can be viewed as more successful; if the same individuals arrive repeatedly early, they are likely to have higher fitness under conditions of resource limitation. For the first time, we show a relationship between foraging sequence and amount of resources removed, with individuals that arrive later to a foraging patch tending to receive lower energetic returns and to spend more time torpid. Torpor bears not only benefits but also significant costs, so these individuals pay a price both in lower energy intake and in extended periods of torpor, in what may well be a positive feedback loop.     

A Novel Analytical Framework for Dissecting the Genetic Architecture of Behavioral Symptoms in Neuropsychiatric Disorders

Background

For diagnosis of neuropsychiatric disorders, a categorical classification system is often utilized as a simple way for conceptualizing an often complex clinical picture. This approach provides an unsatisfactory model of mental illness, since in practice patients do not conform to these prototypical diagnostic categories. Family studies show notable familial co-aggregation between schizophrenia and bipolar illness and between schizoaffective disorders and both bipolar disorder and schizophrenia, revealing that mental illness does not conform to such categorical models and is likely to follow a continuum encompassing a spectrum of behavioral symptoms.

Results and Methodology

We introduce an analytic framework to dissect the phenotypic heterogeneity present in complex psychiatric disorders based on the conceptual paradigm of a continuum of psychosis. The approach identifies subgroups of behavioral symptoms that are likely to be phenotypically and genetically homogenous. We have evaluated this approach through analysis of simulated data with simulated behavioral traits and predisposing genetic factors. We also apply this approach to a psychiatric dataset of a genome scan for schizophrenia for which extensive behavioral information was collected for each individual patient and their families. With this approach, we identified significant evidence for linkage among depressed individuals with two distinct symptom profiles, that is individuals with sleep disturbance symptoms with linkage on chromosome 2q13 and also a mutually exclusive group of individuals with symptoms of concentration problems with linkage on chromosome 2q35. In addition we identified a subset of individuals with schizophrenia defined by language disturbances with linkage to chromosome 2p25.1 and a group of patients with a phenotype intermediate between those of schizophrenia and schizoaffective disorder with linkage to chromosome 2p21.

Conclusions

The findings presented are novel and demonstrate the efficacy of this approach in detection of genes underlying such complex human disorders as schizophrenia and depression.     

Categorical judgments do not modify sensory representations in working memory

Categorical judgments can systematically bias the perceptual interpretation of stimulus features. However, it remained unclear whether categorical judgments directly modify working memory representations or, alternatively, generate these biases via an inference process down-stream from working memory. To address this question we ran two novel psychophysical experiments in which human subjects had to reverse their categorical judgments about a stimulus feature, if incorrect, before providing an estimate of the feature. If categorical judgments indeed directly altered sensory representations in working memory, subjects’ estimates should reflect some aspects of their initial (incorrect) categorical judgment in those trials. We found no traces of the initial categorical judgment. Rather, subjects seemed to be able to flexibly switch their categorical judgment if needed and use the correct corresponding categorical prior to properly perform feature inference. A cross-validated model comparison also revealed that feedback may lead to selective memory recall such that only memory samples that are consistent with the categorical judgment are accepted for the inference process. Our results suggest that categorical judgments do not modify sensory information in working memory but rather act as top-down expectations in the subsequent sensory recall and inference process.     

Origins, taxa, names and meanings

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Do larvae of species in macrolepidopteran assemblages share traits that influence susceptibility to parasitism?

Research on how morphology, behavior, and life histories of insects determine their susceptibility to parasitism has primarily focused on the traits of single host species. Very little research has been conducted attempting to determine if similarities or differences in the traits of co-occurring species, on a single plant or in a habitat, influence levels of parasitism imposed on any member of an assemblage. In this study, we use categorical and regression tree analyses to determine which traits of the larvae of macrolepidopteran species are associated with highest levels of parasitism. Of a variety of morphological, behavioral, and ecological traits of 72 species (representing eight families), caterpillar color was the trait that had the greatest influence on susceptibility to parasitism. The highest levels of parasitism were associated primarily with green larvae. These results suggest that the herbivore species composition and, specifically, the traits possessed by the species may influence community or assemblagewide patterns of parasitism. That is, sharing of traits that enhance host finding and successful parasitism may result in associational susceptibility to parasitism, whereas co-occurrence with species that differ morphologically, behaviorally, or ecologically may reduce the likelihood of parasitism and thus result in associational resistance. The concepts of associational resistance and susceptibility have historically been restricted to plant-plant interactions. The extension of these concepts to herbivores is novel. If found to be widespread, these interactions can have significant impacts on our expectations of the effectiveness of biological control agents.     

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。     

Antisense therapeutics in oncology: points to consider in their clinical evaluation

Novel therapeutics in oncology stem from a rational design of drugs targeting selective pathways that stimulate and maintain tumor cell growth. Many of these agents are cytostatic in action and also have a limited toxicity profile. However, some can be cytotoxic if they successfully modulate molecular pathways of apoptosis, such as bcl-2. This article discusses points to consider in the design of one class of cytostatic agents, antisense therapy. Our purpose is to stimulate designs that answer the question specifically with regard to proof-of-concept, and the concepts proposed should be viewed as ideas in development rather than firm recommendations.