Ditch the niche – is the niche a useful concept in ecology or species distribution modelling?

In this first of three papers we examine the use of niche concepts in ecology and especially in species distribution modelling (SDM). This paper deliberately focuses on the lack of clarity found in the term ‘niche’. Because its meanings are so diverse, the term niche tends to create confusion and requires constant qualification. The literature houses many idiosyncratic ideas of what the niche is, but few examples where niche is more explanatory than the terminologies of population and community ecology or the statistical methods used to implement SDM analyses. In many cases the original (and inspirational) concepts are not directly applicable to our modern applications (e.g. set theory). There are some conceptual limitations found in individual definitions of niche (e.g. the fundamental niche concept), so it is perhaps understandable why more neutral terminology is becoming popular in SDM. An examination of the literature reveals a wide range of uncritical use of niche terminology. Our findings in this paper do not necessarily support the position of niche as a universally useful concept.     

An ontology for landscapes

As ecological data increases in breadth, depth, and complexity, the discipline of ecology is increasingly influenced by information science. While this influence provides many opportunities for ecologists, it also necessitates a change in how we manage and share data, and perhaps more fundamentally, define concepts in ecology. Specifically, the information technology process of automated data integration entirely depends upon consistent concept definition. A common tool used in computer science and engineering to specify meanings, which is both novel and offers significant potential to ecology, is an ontology. An ontology is a formal representation of knowledge in which concepts are described by their meaning and their relationship to each other. Ontologies are a tool that can be used to ‘explicitly specify a concept’ (Gruber, 1993) and this approach is uncommon in ecology. In this paper, we develop an ontology for the concept of ‘landscape’ that captures the most general definitions and usages of this term. We selected the concept of landscape because it is often used in very different ways by investigators and hence generates linguistic uncertainty. A graphic theoretic (i.e., visual) model is provided which describes the set of structuring rules we used to define the relationships between ‘landscape’ and appropriately related terms. Based upon these rules, a landscape necessarily contains a spatial component (i.e., area), structure and function (i.e., ecosystems), and is scale independent. This approach provides the set of necessary conditions for landscape studies to reduce linguistic uncertainty, and facilitate interoperability of data, i.e., in a manner that promotes data linkages and quantitative synthesis particularly by automatic data synthesis programs that are likely to become an important part of ecology in the future. Simply put, we use an ontology, a technique novel to ecology but not other disciplines, to define ‘landscape,’ thereby clearly delineating one subset of its potential general usage. As such this ontology can serve as both a checklist for landscape studies and a blueprint for additional ecological ontologies.     

Commentary on Ditch,Stitch and Pitch: the niche is here to stay

A recent set of discussion papers in the Journal of Biogeography by McInerny and Etienne (henceforth M&E) questions the value of niche concepts in relation to a diverse group of practices collectively labelled species distribution modelling (SDM), and specifically the usefulness of the idea of a fundamental niche. In this Correspondence, I argue that certain types of SDM may indeed dispense with niche concepts, but that such is not the case for an important class of SDM‐based activities, including transferring predictions in space and time. Using a single term (SDM) to denote diverse objectives and practices does not help to clarify issues; I discuss this point. I also review several criticisms raised by M&E about the use of the concept of fundamental niche in the context of modelling species' distributions and their environments.     

生态位概念及其在昆虫生态学中的应用

生态位理论已成为现代生态学的重要内容。在生态位概念百年演变史中,“空间生态位”、“功能生态位”与“多维超体积生态位”最具代表性。生态位宽度和生态位重叠是描述物种内和物种间生态位关系最重要的2个指标。本文系统总结了生态位概念的演变历史及其主要测度公式在昆虫生态学中的应用概况;并就如何利用生态位理论,开展害虫综合治理提出了几点看法;最后就生态位理论在昆虫生态学中存在的问题及应用前景进行了分析和展望。合理利用生态位理论,将为切实制定有害生物综合治理策略和探讨外来入侵物种种群形成机理等方面提供理论指导。     

Using avatar species to model the potential distribution of emerging invaders

Aim Anticipating the potential distributions of emerging invasive species is complicated by the tendency for species distribution models to perform better when both native and invasive range data are available for model development. If invasive range data are lacking, species models are liable to under‐estimate distributions for emerging invaders, particularly for species that are not at equilibrium with their native range environment due to historical factors, dispersal limitation and/or ecological interactions. We demonstrate the potential to use well‐quantified niche shifts from established ‘avatar’ (i.e. the remote or virtual manifestation of an entity) invaders to develop plausible distributions for data‐poor emerging invaders contingent on niche shifts of similar magnitude or character. Location Global. Methods Using the globally invasive crayfishes Pacifastacus leniusculus and Procambarus clarkii as our avatar invaders, we quantify how niche position, size and structure differs between native and total ranges using Mahalanobis distance (a measure of multivariate similarity) and the climate predictors of annual minimum and maximum air temperature. We then generalize patterns of niche shift from these species to the emerging crayfish invader Cherax quadricarinatus. Results Some patterns of niche shifts were similar for Pacifastacus leniusculus and Procambarus clarkii, but niche shifts were of considerably greater magnitude for P. clarkii. When a native range model for C. quadricarinatus was modified with generalized niche shifts similar to Pacifastacus leniusculus and Procambarus clarkii, the potential global distribution for this species increased considerably, including many areas not identified by the native range model. Main conclusions We illustrate the potential to use avatar invaders to provide cautionary, niche shift‐assuming species distribution models for emerging invaders. Many theoretical and applied implications of the avatar species concept require additional investigation, including the development of frameworks to select appropriate avatar species and evaluate the performance of avatar‐derived models for emerging invaders. Despite these research needs, we believe this concept will have considerable utility for predicting vulnerability to invasion by data‐poor species; this is a critical management need because shifting pathways of introduction and climate change will produce many novel, emerging invasive species in the future.     

Can't see the colony for the bees: behavioural perspectives of biological individuality

The question ‘what is an individual’ does not often arise in studies within the field of behavioural ecology. Generally behavioural ecologists do not think about what makes an individual because they tend to use intuitive working concepts of individuality. Rarely do they explicitly mention how individuality affects their experimental design and interpretation of results. By contrast, the concept of individuality continues to intrigue philosophers of biology. It is interesting that while philosophers of biology debate definitions of individuality, biologists generally use the concept of individuality every day without much thought. Here we review the philosophical approaches to defining biological individuality, and illustrate how the biological individuality concepts used by biologists are affected by their study question and choice of organism. We clarify the behavioural perspective of biological individuality by introducing the concept of the behavioural individual. The notion of the behavioural individual is particularly interesting when explored in less‐conventional study organisms. By including less‐conventional organisms, it becomes clear why the concept of biological individuality is usually intuitive in behavioural ecology.     

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.     

Predicting phenology by integrating ecology,evolution and climate science

Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life‐history events. Phenology has well‐demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species’ reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.     

生态位模型的理论基础、发展方向与挑战

生态位模型是一个以生态位理论为基础的新兴研究领域.它通过采集研究对象的已知分布点及其相关的环境数据组成训练样本,利用数理统计或机器学习理论分析数据,构建特征函数表示物种在生态位空间的实际生态位.以生态位模型预测物种潜在分布地或计算物种间的生态位重叠等研究,在生态学、生物地理学和进化生物学研究中显得越来越重要.本文从生态位概念出发,详细解析了生态位模型的理论基础、相关的焦点争论、使用时的注意点以及可能的发展方向与面临的挑战,指出模型中要考虑人类活动对物种生态位的影响.希望本文所探讨的本领域最新的争论焦点能引起相关学者的关注与深入思考.     

A physiological analogy of the niche for projecting the potential distribution of plants

Aim  To develop a physiologically based model of the plant niche for use in species distribution modelling. Location  Europe. Methods  We link the Thornley transport resistance (TTR) model with functions which describe how the TTR’s model parameters are influenced by abiotic environmental factors. The TTR model considers how carbon and nutrient uptake, and the allocation of these assimilates, influence growth. We use indirect statistical methods to estimate the model parameters from a high resolution data set on tree distribution for 22 European tree species. Results  We infer, from distribution data and abiotic forcing data, the physiological niche dimensions of 22 European tree species. We found that the model fits were reasonable (AUC: 0.79–0.964). The projected distributions were characterized by a false positive rate of 0.19 and a false negative rate 0.12. The fitted models are used to generate projections of the environmental factors that limit the range boundaries of the study species. Main conclusions  We show that physiological models can be used to derive physiological niche dimensions from species distribution data. Future work should focus on including prior information on physiological rates into the parameter estimation process. Application of the TTR model to species distribution modelling suggests new avenues for establishing explicit links between distribution and physiology, and for generating hypotheses about how ecophysiological processes influence the distribution of plants.     

Determinants of resource use in lizard assemblages from the semiarid Caatinga,Brazil

Nonsessile animals could partition the use of resources in different axes, reducing the effects of competition and allowing coexistence. Here, we investigated the spatial and trophic niche dimensions in four lizard assemblages in the Neotropical semiarid Caatinga to investigate the determinants of resource use and the extent to which lizards partition their niches. We sampled each lizard assemblage once, for 10 days, in the dry season of 2017 and 2018. In two lizard assemblages, we detected nonrandom niche overlap patterns that were higher or lower than expected by chance. The high niche overlap patterns suggest that either there is intense current competition for available microhabitats or an abundance of microhabitats. The lower niche overlap may be influenced by the presence of species adapted to sandy habitats (psammophilous), suggesting that spatial partitioning detected has historical basis, which is supported by the pPCA results and by the lack of patterns in the realized niche distribution of species across niche space. We detected trophic niche partitioning in three lizard assemblages. In one assemblage, we discovered random spatial and trophic niche overlap patterns, revealing that competition is not a determining factor in the structure of that assemblage. In fact, phylogenetic effects were predominantly the main determinants of resource use in the four studied lizard assemblages. Arid and semiarid habitats cover about one third of land surface of the world. Comparisons between our findings and those from other regions of the world may aid identify general trends in the lizard ecology of dry environments.     

Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats

Human‐mediated habitat transformation is increasingly evident around the world. Yet, how this transformation influences species’ niche width and overlap remains unclear. On the one hand, human‐mediated habitat transformation promotes increased species similarity through trait‐based filtering, and an increased prevalence of generalist species with broad niches, resulting in functional homogenization. On the other hand, species that colonize transformed habitats could use empty niches, resulting in decreased species similarity and an expansion of assemblage‐level niche space. Here we explore these two alternatives in eight highly diverse passerine assembles in natural, rural and urban habitats in south and southwest China, a rapidly developing region of the world. Based on stable isotopes, we found that species’ niche width increased from natural to human‐made habitats, but there were no differences in niche overlap among habitats. Therefore, we found evidence for niche expansion, with generalists appearing to use empty niches created by human habitat modification, and with assemblages being comprised of complementary species. Further research is needed to determine whether increased between‐ or within‐individual niche variation is the main driver of niche expansion in transformed habitats.     

Does GARP really fail miserably? A response to Stockman et al. (2006)

Stockman et al. (2006 ) found that ecological niche models built using DesktopGARP ‘failed miserably’ to predict trapdoor spider (genus Promyrmekiaphila) distributions in California. This apparent failure of GARP (Genetic Algorithm for Rule‐Set Production) was actually a failure of the authors’ methods, that is, attempting to build ecological niche models using single data points. In this paper, we present a re‐analysis of their original data using standard methods with the data appropriately partitioned into training/testing subsets. This re‐evaluation generated accurate distributional predictions that we contrast with theirs. We address the consequences of model‐building using single data points and the need for a foundational understanding of the principles of ecological niche modelling.     

Behavioural ecology at the spatial–social interface

Spatial and social behaviour are fundamental aspects of an animal's biology, and their social and spatial environments are indelibly linked through mutual causes and shared consequences. We define the ‘spatial–social interface’ as intersection of social and spatial aspects of individuals' phenotypes and environments. Behavioural variation at the spatial–social interface has implications for ecological and evolutionary processes including pathogen transmission, population dynamics, and the evolution of social systems. We link spatial and social processes through a foundation of shared theory, vocabulary, and methods. We provide examples and future directions for the integration of spatial and social behaviour and environments. We introduce key concepts and approaches that either implicitly or explicitly integrate social and spatial processes, for example, graph theory, density-dependent habitat selection, and niche specialization. Finally, we discuss how movement ecology helps link the spatial–social interface. Our review integrates social and spatial behavioural ecology and identifies testable hypotheses at the spatial–social interface.     

Intragroup competition predicts individual foraging specialisation in a group‐living mammal

Individual foraging specialisation has important ecological implications, but its causes in group‐living species are unclear. One of the major consequences of group living is increased intragroup competition for resources. Foraging theory predicts that with increased competition, individuals should add new prey items to their diet, widening their foraging niche (‘optimal foraging hypothesis’). However, classic competition theory suggests the opposite: that increased competition leads to niche partitioning and greater individual foraging specialisation (‘niche partitioning hypothesis’). We tested these opposing predictions in wild, group‐living banded mongooses (Mungos mungo), using stable isotope analysis of banded mongoose whiskers to quantify individual and group foraging niche. Individual foraging niche size declined with increasing group size, despite all groups having a similar overall niche size. Our findings support the prediction that competition promotes niche partitioning within social groups and suggest that individual foraging specialisation may play an important role in the formation of stable social groupings.     

Unpacking the species conundrum: philosophy,practice and a way forward

The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as ‘individuals’ while the criteria for categorization treats them as ‘classes’. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an ‘inclusive’ probabilistic approach for understanding and delimiting species. Finally, we provide a Wallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and ‘inclusive’ probabilistic approaches may work best for delimitation.     

Tolerance niche expansion and potential distribution prediction during Asian openbill bird range expansion

It is prevalent to use ecological niche models in the analysis of species expansion and niche changes. However, it is difficult to estimate the niche when alien species fail to establish in exotic areas. Here, we applied the tolerance niche concept, which means that niche of species can live and grow but preclude a species from establishing self‐sustaining populations, in such fail‐to‐establish events. Taking the rapidly expanded bird, Asian openbill (Anastomus oscitans), as a model species, we investigated niche dynamics and its potential effects on the population by Niche A and ecospat, predicted potential distribution by biomod2. Results showed that niche expansion has occurred in two non‐native populations caused by the tolerance of colder and wetter environments, and potential distribution mainly concentrated on equatorial islands. Our study suggested that the expanded niche belongs to tolerance niche concept according to the populations'' dynamics and GPS tracking evidence. It is essential to consider source populations when we analyze the alien species. We recommended more consideration to the application of tolerance niche in alien species research, and there is still a need for standard measurement frameworks for analyzing the tolerance niche.