Pitch the niche – taking responsibility for the concepts we use in ecology and species distribution modelling

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an ‘ultimate goal of the niche’ by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word ‘niche’. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling.     

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.     

Neutral theory and the species abundance distribution: recent developments and prospects for unifying niche and neutral perspectives

Published in 2001, The Unified Neutral Theory of Biodiversity and Biogeography (UNTB) emphasizes the importance of stochastic processes in ecological community structure, and has challenged the traditional niche‐based view of ecology. While neutral models have since been applied to a broad range of ecological and macroecological phenomena, the majority of research relating to neutral theory has focused exclusively on the species abundance distribution (SAD). Here, we synthesize the large body of work on neutral theory in the context of the species abundance distribution, with a particular focus on integrating ideas from neutral theory with traditional niche theory. First, we summarize the basic tenets of neutral theory; both in general and in the context of SADs. Second, we explore the issues associated with neutral theory and the SAD, such as complications with fitting and model comparison, the underlying assumptions of neutral models, and the difficultly of linking pattern to process. Third, we highlight the advances in understanding of SADs that have resulted from neutral theory and models. Finally, we focus consideration on recent developments aimed at unifying neutral‐ and niche‐based approaches to ecology, with a particular emphasis on what this means for SAD theory, embracing, for instance, ideas of emergent neutrality and stochastic niche theory. We put forward the argument that the prospect of the unification of niche and neutral perspectives represents one of the most promising future avenues of neutral theory research.     

Nest site availability and niche differentiation between two cavity‐nesting birds in time and space

Niche differentiation is a key concept in the field of ecology and refers to the process by which competing species within an ecological community partition utilization of environmental resources to achieve coexistence. The existence of niche differentiation is uniquely difficult to prove on account of the fact that historical interaction among species, which plays a key role in elucidating the current state of coexistence among species, is not well known. We created continuous niche gradients in nest‐site resources between two sympatric secondary cavity‐nesting birds, the green‐backed tit (Parus monticolus) and the russet sparrow (Passer cinnamomeus), and investigated whether nesting site is a factor contributing to limiting breeding overlap by regular inspection and 388,160 min of film recording. Our results indicate that although we manipulated nest site availability to be uniformly high along the habitat gradient, the two bird species have little overlap in nest sites and rarely compete for them. Furthermore, the green‐backed tit possessed a wide range of fundamental niche that covered that of the russet sparrow, while their reproductive time was largely segregated. The sparrow was more aggressive and outcompeted the tit in their overlapped range. These results suggest that even though nesting sites are crucial to the reproduction of cavity‐nesting birds, some other factor plays a more important role in limiting niche overlap between sparrows and tits in space and time. Given that these two cavity‐nesting birds continued to use different habitats and breed in segregated time after our manipulation, their relationship is better explained by the ghost of competition past theory.     

The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long‐toed salamander (Ambystoma macrodactylum Baird)

The relative importance of ecological vs. nonecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages – such as the distinct genetic groups that make up the ranges of many northern species – represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long‐toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long‐toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non‐ecological factors to play a more important role in the maintenance of northern taxa.     

Ecological niche models display nonlinear relationships with abundance and demographic performance across the latitudinal distribution of Astragalus utahensis (Fabaceae)

The potential for ecological niche models (ENMs) to accurately predict species' abundance and demographic performance throughout their geographic distributions remains a topic of substantial debate in ecology and biogeography. Few studies simultaneously examine the relationship between ENM predictions of environmental suitability and both a species' abundance and its demographic performance, particularly across its entire geographic distribution. Yet, studies of this type are essential for understanding the extent to which ENMs are a viable tool for identifying areas that may promote high abundance or performance of a species or how species might respond to future climate conditions. In this study, we used an ensemble ecological niche model to predict climatic suitability for the perennial forb Astragalus utahensis across its geographic distribution. We then examined relationships between projected climatic suitability and field‐based measures of abundance, demographic performance, and forecasted stochastic population growth (λ_s). Predicted climatic suitability showed a J‐shaped relationship with A. utahensis abundance, where low‐abundance populations were associated with low‐to‐intermediate suitability scores and abundance increased sharply in areas of high predicted climatic suitability. A similar relationship existed between climatic suitability and λ_s from the center to the northern edge of the latitudinal distribution. Patterns such as these, where density or demographic performance only increases appreciably beyond some threshold of climatic suitability, support the contention that ENM‐predicted climatic suitability does not necessarily represent a reliable predictor of abundance or performance across large geographic regions.     

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.     

Morphological and niche divergence of pinyon pines

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.     

舟山长白海域主要游泳动物生态位及其分化研究

基于2016年10月（秋季）和2017年4月（春季）舟山长白海域的渔业资源调查数据,运用生态位宽度、生态位重叠及冗余分析等方法,研究了主要游泳动物的生态位,种间生态关系及生态位分化。结果显示：春、秋季主要游泳动物分别11种与8种,两季生态位宽度值差异均较大,其中春季广生态位种、中生态位种均为3种,而秋季均为2种,窄生态位种分别为5种与4种。相对重要性指数（IRI）与生态位宽度值（B_i）之间呈显著正相关。生态位重叠程度不均衡,秋季主要游泳动物的生态位重叠程度较高,O_ik > 0.6的种对数占总种对数的42.86%;春季的重叠程度较低,仅占总种对数的21.82%。RDA分析得出温度、盐度为影响主要游泳动物分布的直接因素,而溶解氧、悬浮物和pH等则为重要因素,主要游泳动物在这些资源维上存在生态分化现象。综上,分布在毗邻杭州湾口且位于著名的岱衢洋的主要游泳动物种类总体营养级较低却生态宽度值较大,大黄鱼（Larimichthys crocea）、黄姑鱼（Nibea albiflora）等一些传统的高营养级、典型特色经济种类却沦为生态位宽度极小的一般种或少有种,群落种类显著减少,资源量下降,群落结构与功能退化,稳定性下降。因此,加强游泳动物资源修复、保护与管理十分迫切且具有重要意义。     

Ecological niche conservation and differentiation in the wood-feeding cockroaches, Cryptocercus, in the United States

The distribution of a species is determined by a set of ecological correlates (biotic and abiotic factors) and historical phenomena that define and constrain its ecological niche. By examining the geographical projection of the ecological niche, it is possible to identify areas that are suitable for the species ecologically but that are not actually inhabited. Previous studies have used such discords to anticipate the existence of undescribed species; the absence of species may also result from historical barriers that have prevented colonization of the area. Thus, discords between potential and realized niches of a species may result from aspects of the species’s biology (e.g. lack of dispersal ability, specific habitat requirements) or from barriers to dispersal. In this study, we developed ecological niche models of the five Nearctic species of wood‐feeding cockroaches in the genus Cryptocercus. One species, C. clevelandi, occurs in the western USA and four (C. darwini, C. garciai, C. punctulatus, C. wrighti) are distributed in the Appalachian Mountains in the eastern USA. In general, modelled niches for all species showed ecological restriction relative to the total range of available conditions. Niche models for the eastern USA species predicted the geographical distributions of the other eastern USA species, with the exception of C. garciai, suggesting general overall conservatism in ecological characteristics. Some interspecific differences in modelled niches were also apparent. In general, C. clevelandi was predicted to occupy cooler and drier areas relative to the eastern USA species; among the eastern USA species, C. darwini and C. garciai were predicted to inhabit warmer areas relative to C. punctulatus and C. wrighti. Interspecific differences and similarities were consistent with the phylogenetic relationships among Cryptocercus species previously reported. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 457–466.     

Defining and measuring ecological specialization

1.  Ecological specialization is one of the main concepts in ecology and conservation. However, this concept has become highly context-dependent and is now obscured by the great variability of existing definitions and methods used to characterize ecological specialization.
2.  In this study, we clarify this concept by reviewing the strengths and limitations of different approaches commonly used to define and measure ecological specialization. We first show that ecological specialization can either be considered as reflecting species' requirements or species' impacts. We then explain how specialization depends on species-specific characteristics and on local and contingent environmental constraints. We further show why and how ecological specialization should be scaled across spatial and temporal scales, and from individuals to communities.
3.  We then illustrate how this review can be used as a practical toolbox to classify widely used metrics of ecological specialization in applied ecology, depending on the question being addressed, the method used, and the data available.
4.   Synthesis and applications . Clarifying ecological specialization is useful to make explicit connections between several fields of ecology using the niche concept. Defining this concept and its practical metrics is also a crucial step to better formulate predictions of scientific interest in ecology and conservation. Finally, understanding the different facets of ecological specialization should facilitate to investigate the causes and consequences of biotic homogenization and to derive relevant indicators of biodiversity responses to land-use changes.     

Metagenomics and the niche concept

The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space. Diana Marco is a member of the Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET).     

Human behavioral ecology and niche construction

We examine the relationship between niche construction theory (NCT) and human behavioral ecology (HBE), two branches of evolutionary science that are important sources of theory in archeology. We distinguish between formal models of niche construction as an evolutionary process, and uses of niche construction to refer to a kind of human behavior. Formal models from NCT examine how environmental modification can change the selection pressures that organisms face. In contrast, formal models from HBE predict behavior assuming people behave adaptively in their local setting, and can be used to predict when and why people engage in niche construction. We emphasize that HBE as a field is much broader than foraging theory and can incorporate social and cultural influences on decision‐making. We demonstrate how these approaches can be formally incorporated in a multi‐inheritance framework for evolutionary research, and argue that archeologists can best contribute to evolutionary theory by building and testing models that flexibly incorporate HBE and NCT elements.     

Within-genotype epigenetic variation enables broad niche width in a flower living yeast

Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species niche as all of the factors that effect the persistence of the species as well as the impact of the species in a given location ( Hutchinson 1957 ; Chase 2011 ). Many studies have argued that phenotypic plasticity enhances niche width because plastic responses allow organisms to express advantageous phenotypes in a broader range of environments ( Bradshaw 1965 ; Van Valen 1965 ; Sultan 2001 ). Further, species that exploit habitats with fine‐grained variation, or that form metapopulations, are expected to develop broad niche widths through phenotypic plasticity ( Sultan & Spencer 2002 ; Baythavong 2011 ). Although a long history of laboratory, greenhouse and reciprocal transplant experiments have provided insight into how plasticity contributes to niche width ( Pigliucci 2001 ), recent advances in molecular approaches allow for a mechanistic understanding of plasticity at the molecular level ( Nicotra et al. 2010 ). In particular, variation in epigenetic effects is a potential source of the within‐genotype variation that underlies the phenotypic plasticity associated with broad niche widths. Epigenetic mechanisms can alter gene expression and function without altering DNA sequence ( Richards 2006 ) and may be stably transmitted across generations ( Jablonka & Raz 2009 ; Verhoeven et al. 2010 ). Also, epigenetic mechanisms may be an important component of an individual’s response to the environment ( Verhoeven et al. 2010 ). While these ideas are intriguing, few studies have made a clear connection between genome‐wide DNA methylation patterns and phenotypic plasticity (e.g. Bossdorf et al. 2010 ). In this issue of Molecular Ecology, Herrera et al. (2012) present a study that demonstrates epigenetic changes in genome‐wide DNA methylation are causally active in a species’ ability to exploit resources from a broad range of environments and are particularly important in harsh environments.     

Towards a trait-based quantification of species niche

Aims Although the niche concept is of prime importance in ecology, the quantification of plant species' niches remains difficult. Here we propose that plant functional traits, as determinants of species performance, may be useful tools for quantifying species niche parameters over environmental gradients.Important findings Under this framework, the mean trait values of a species determine its niche position along gradients, and intraspecific trait variability determines its niche breadth. This trait-based approach can provide an operational assessment of niche for a potentially large number of species, making it possible to understand and predict species niche shifts under environmental changes. We further advocate a promising method that recently appeared in the literature, which partitions trait diversity into among- and within-community components as a way to quantify the species niche in units of traits instead of environmental parameters. This approach allows the switch of the focus from ecological niches to trait niches, facilitating the examination of species coexistence along undefined environmental gradients. Altogether, the trait-based approach provides a promising toolkit for quantifying the species ecological niche and for understanding the evolution of species niche and traits.     

Stable isotopes are quantitative indicators of trophic niche

Hette‐Tronquart (2019, Ecol. Lett.) raises three concerns about our interpretation of stable isotope data in Sheppard et al. (2018, Ecol. Lett., 21, 665). We feel that these concerns are based on comparisons that are unreasonable or ignore the ecological context from which the data were collected. Stable isotope ratios provide a quantitative indication of, rather than being exactly equivalent to, trophic niche.     

Cryptic niche conservatism among evolutionary lineages of an invasive lizard

Aim There is increasing evidence that the quality and breadth of ecological niches vary among individuals, populations, evolutionary lineages and therefore also across the range of a species. Sufficient knowledge about niche divergence among clades might thus be crucial for predicting the invasion potential of species. We tested for the first time whether evolutionary lineages of an invasive species vary in their climate niches and invasive potential. Furthermore, we tested whether lineage‐specific models show a better performance than combined models. Location Europe. Methods We used species distribution models (SDMs) based on climatic information at native and invasive ranges to test for intra‐specific niche divergence among mitochondrial DNA (mtDNA) clades of the invasive wall lizard Podarcis muralis. Using DNA barcoding, we assigned 77 invasive populations in Central Europe to eight geographically distinct evolutionary lineages. Niche similarity among lineages was assessed and the predictive power of a combination of clade‐specific SDMs was compared with a combined SDM using the pooled records of all lineages. Results We recorded eight different invasive mtDNA clades in Central Europe. The analysed clades had rather similar realized niches in their native and invasive ranges, whereas inter‐clade niche differentiation was comparatively strong. However, we found only a weak correlation between geographic origin (i.e. mtDNA clade) and invasive occurrences. Clades with narrow realized niches still became successful invaders far outside their native range, most probably due to broader fundamental niches. The combined model using data for all invasive lineages achieved a much better prediction of the invasive potential. Conclusions Our results indicate that the observed niche differentiation among evolutionary lineages is mainly driven by niche realization and not by differences in the fundamental niches. Such cryptic niche conservatism might hamper the success of clade‐specific niche modelling. Cryptic niche conservatism may in general explain the invasion success of species in areas with apparently unsuitable climate.     

Beyond ecological opportunity: Prey diversity rather than abundance shapes predator niche variation

1. Ecological opportunity (i.e. the diversity of available resources) has a pivotal role in shaping niche variation and trophic specialisation of animals. However, ecological opportunity can be described with regard to both diversity and abundance of resources. The degree to which these two components contribute to niche variation remains unexplored.
2. To address this, we used an extensive dataset on fish diet and benthic invertebrate diversity and density from 73 sampling events in three Norwegian rivers in order to explore realised trophic niches and the response of dietary niche variation along gradients of resource diversity (potential trophic niches), resource density (as a proxy of resource abundance) and fish density (as a proxy of inter‐ and intra‐specific competition) in a freshwater top predator (the brown trout, Salmo trutta L.).
3. Linear models indicated that individual and population niche variation increased with increasing ecological opportunity in terms of prey diversity. However, no simple cause‐and‐effect associations between niche indices and prey abundance were found. Our multiple regression analyses indicated that the abundance of certain resources (e.g. Chironomidae) can interact with prey diversity to determine individual and population realised trophic niches. Niche variation (within‐individual component and inter‐individual diet variation) decreased with increasing inter‐ and intra‐specific competition.
4. This study extends prevailing trophic ecology theory by identifying diversity, rather than density, of available prey resources as a primary driver of niche variation in fish of temperate riverine systems with no extensive resource limitation. The study also shows that ecological opportunity may mask the direction of the effect (compression or expansion) of competition on niche variation when food resources are diverse.
5. Our study provides novel empirical insight to the driving forces behind niche variation and reveals that diversity, rather than density, of available prey resources may be a primary driver of niche variation in freshwater fish. Our study supports the view that a broader potential trophic niche promotes broader realised trophic niche variation by individuals, which leads to individual niche diversification by opening access to alternatives resources, resulting in a concomitant rise in the realised trophic niche width of the population.