Environmental Niche

In this chapter, we first trace the history of the concept of ecological niche and see how its meanings varied with the search for a theory of ecology. The niche concept has its roots in the Darwinian view of ecosystems that are structured by struggle for survival and, originally, the niche was perceived as an invariant place within the ecosystem, that would preexist the assembly of the ecosystem. The concept then slipped towards a sense in which the niche, no longer a pre-existing ecosystem structure, eventually became a variable that would in turn have to be explained by the competitive exclusion principle and the coevolution of species. The niche concept used at that time, while more operational from an empirical point of view than the previous one, suffered however from an ill-founded definition. A recent refoundation by Chase & Leibold enabled to overcome some of the definitional difficulties.
We then present how, in contemporary ecology, the niche concept is recruited to explain biodiversity and species coexistence patterns. We show how, in parallel, neutralist models, by succeedingly explaining some ecological patterns without resorting to explanations in terms of niche, have questioned the explanatory virtues of the niche concept.
In conclusion, it seems that the forunes and misfortunes of the niche concept can be seen as a reflection of the difficulties of ecology to give birth to a theory that would be both predictive and explanatory.

M. Niedziałkowska - K. Doan - M. Sykut - M. Górny - K. Stefaniak - N. Piotrowska - B. Jędrzejewska - B. Ridusch - S. Pawełczyk - F. Zachos - P. Mackiewicz - U. Schmölcke - P. Kosintsev - D. Makowiecki - M. Charniauski - R. Smith - D. Krasnodębski - U. Saarma - M. Arakelyan - N. Manaseryan - V. Titov - P. Hulva - A. Balasescu - R. Fyfe - J. Woodbridge - K. Trantalidou - A. Pisarenko - V. Dimitrijevic - J. Wilczyński - I. Foronova - G. Lipecki - A. Arabey - A. Stankovic Aim: The Expansion-Contraction model has been used to explain the responses of species to climatic changes. During periods of unfavourable climatic conditions, species retreat to refugia from where they may later expand. This paper focuses on the palaeoecology of red deer over the past 54 ka across Europe and the Urals, to reveal patterns of change in their range and explore the role of environmental conditions in determining their distribution. Location: Europe and western Asia to 63°E. Taxon: Red deer (Cervus elaphus). Methods: We collected 984 records of radiocarbon-dated red deer subfossils from the Late Pleistocene and the Holocene, including 93 original dates. For each deer sample we compiled climatic and biome type data for the corresponding time intervals. Results: During the last 54 ka changes in red deer range in Europe and the Urals were asynchronous and differed between western and eastern Europe and western Asia due to different environmental conditions in those regions. The range of suitable areas for deer during the Last Glacial Maximum (LGM) was larger than previously thought and covered vast regions not only in southern but also in western and eastern Europe. Throughout the period investigated the majority of specimens inhabited forests in the temperate climatic zone. The contribution of forests in deer localities significantly decreased during the last 4 ka, due to deforestation of Europe caused by humans. Mean January temperature was the main limiting factor for species distribution. Over 90% of the samples were found in areas where mean January temperature was above −10°C. Main conclusions: Red deer response to climatic oscillations are in agreement with the Expansion-Contraction model but in contradiction to the statement of only the southernmost LGM refugia of the species. During the last 54 ka red deer occurred mostly in forests of the temperate climatic zone. K E Y W O R D S environmental niche modelling, expansion-contraction model, forest habitat, Holocene, January temperature, Last Glacial Maximum refugia, palaeoecology, radiocarbon dating, temperate climatic zone, ungulates

1. In the last decade, an increasing number of papers testifies a renewed interest in the topic of individual specialization in resource use and its implication at higher levels of ecological organization. 2. We present the package R Individual Specialization (RInSp) for the free open-source statistical software R. RInSp provides a comprehensive set of classical and recently proposed indices for quantifying the degree of individual specialization using both categorical and continuous resource use data. The package also includes tools for ad hoc Monte Carlo and jackknife resampling procedures for significance testing, plotting and input/output data manipulation. 3. The use of RInSp is demonstrated by two examples. In addition, the potential of the package to be implemented beyond its original scope for multi-level quantitative analyses of individual trait variance in natural communities is illustrated.

Species distribution modeling (SDM) is a booming area of research that has had an exponential increase in use and development in recent years. We performed a search of scientific literature and found 5,533 documents published from 1993 to 2018 using SDM, representing a global network of 4,329 collaborating institutions from 155 countries, with Brazil and Mexico being in the top 10 of the most prolific countries globally. National Autonomous University of Mexico, Chinese Academy of Sciences, University of Kansas, and U.S. Geological Survey are the most prolific institutions worldwide. Latin American institutions ( n = 556) participated in 1,000 (18% of global productivity) documents published in collaboration with 591 institutions outside Latin American countries, from which the National Autonomous University of Mexico, Federal University of Goiás, Institute of Ecology A.C., National Scientific and Technical Research Council in Argentina, University of São Paulo, and University of Br...

Climate change threatens Earth's biodiversity, although its impacts are variable and depend on the capacity of species and ecosystems to cope with the magnitude and speed of change. Natural protected areas (NPAs) constitute potential refugia for species' persistence and for sustaining the provisioning of ecosystem services. Biosphere reserves are NPAs that are less altered by human actions and provide habitat to endemic, threatened or endangered species. Here, we aim to evaluate the threat imposed by climate change on the network of biosphere reserves in Mexico. Focusing on five bioclimatic variables, we computed the climatic spacemeasured as an n-dimensional hypervolume-of 40 NPAs. Increases in temperature are predicted for all NPAs by 2050, whereas decreases in annual rainfall are predicted for 30 NPAs. By 2050, 31 NPAs that provide habitat to 22,866 recorded species are predicted to lose 100% of their baseline climatic space, shifting to completely novel climates. On average, the other nine NPAs are predicted to lose 55.7% (SD = 26.7%) of their baseline climatic space, while 54.5% (SD = 32.5%) of the future climatic space will be novel. Seventeen NPAs may lose climate variability (homogenization), decreasing species' niches. The extent to which non-analogue conditions will remain within the tolerance of species and ecosystems is currently unknown. Finally, we propose a vulnerability index to categorise NPAs based on their loss of existing climatic space, total geographic area, species richness, and uniqueness of species composition, finding los Tuxtlas and Tiburon Ballena as the most and least vulnerable NPAs, respectively.

Species distribution modeling (SDM) is a booming area of research that has had an exponential increase in use and development in recent years. We performed a search of scientific literature and found 5,533 documents published from 1993 to 2018 using SDM, representing a global network of 4,329 collaborating institutions from 155 countries, with Brazil and Mexico being in the top 10 of the most prolific countries globally. National Autonomous University of Mexico, Chinese Academy of Sciences, University of Kansas, and U.S. Geological Survey are the most prolific institutions worldwide. Latin American institutions ( n = 556) participated in 1,000 (18% of global productivity) documents published in collaboration with 591 institutions outside Latin American countries, from which the National Autonomous University of Mexico, Federal University of Goiás, Institute of Ecology A.C., National Scientific and Technical Research Council in Argentina, University of São Paulo, and University of Br...

The potential impact of climate change on biodiversity is well documented. A well developed range of statistical methods currently exists that projects the possible future habitat of a species directly from the current climate and a species distribution. However, studies incorporating ecological and evolutionary processes remain limited. Here, we focus on the potential role that local adaptation to climate may play in driving the range dynamics of sessile organisms. Incorporating environmental adaptation into a stochastic simulation yields several new insights. Counter-intuitively, our simulation results suggest that species with broader ranges are not necessarily more robust to climate change. Instead, species with broader ranges can be more susceptible to extinction as locally adapted genotypes are often blocked from range shifting by the presence of cooler adapted genotypes that persist even when their optimum climate has left them behind. Interestingly, our results also suggest that it will not always be the cold-adapted phenotypes that drive polewards range expansion. Instead, range shifts may be driven by phenotypes conferring adaptation to conditions prevalent towards the centre of a species' equilibrium distribution. This may have important consequences for the conservation method termed predictive provenancing. These initial results highlight the potential importance of local adaptation in determining how species will respond to climate change and we argue that this is an area requiring urgent theoretical and empirical attention.

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains.

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types-for example in genotypes, phenotypes, and environment types-in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes.

Climate change threatens Earth's biodiversity, although its impacts are variable and depend on the capacity of species and ecosystems to cope with the magnitude and speed of change. Natural protected areas (NPAs) constitute potential refugia for species' persistence and for sustaining the provisioning of ecosystem services. Biosphere reserves are NPAs that are less altered by human actions and provide habitat to endemic, threatened or endangered species. Here, we aim to evaluate the threat imposed by climate change on the network of biosphere reserves in Mexico. Focusing on five bioclimatic variables, we computed the climatic spacemeasured as an n-dimensional hypervolume-of 40 NPAs. Increases in temperature are predicted for all NPAs by 2050, whereas decreases in annual rainfall are predicted for 30 NPAs. By 2050, 31 NPAs that provide habitat to 22,866 recorded species are predicted to lose 100% of their baseline climatic space, shifting to completely novel climates. On average, the other nine NPAs are predicted to lose 55.7% (SD = 26.7%) of their baseline climatic space, while 54.5% (SD = 32.5%) of the future climatic space will be novel. Seventeen NPAs may lose climate variability (homogenization), decreasing species' niches. The extent to which non-analogue conditions will remain within the tolerance of species and ecosystems is currently unknown. Finally, we propose a vulnerability index to categorise NPAs based on their loss of existing climatic space, total geographic area, species richness, and uniqueness of species composition, finding los Tuxtlas and Tiburon Ballena as the most and least vulnerable NPAs, respectively.

Community diversity is expected to reflect variations in local conditions but, recently, ecologists have started to realize that local diversity is also under pressure from global processes. As a result, the traditional view of community structure based on local interspecific interactions was replaced by the idea that community structure is a result of multiple processes acting in different spatial scales. This study is aimed at quantifying the relative importance of spatial, environmental and spatially structured processes on Ephemeroptera community in Cerrado streams in Brazil. Thirty-four rivers and streams in the Brazilian state Mato Grosso were sampled. Ephemeroptera species composition, based on abundance and presence data, was evaluated in relation to niche and neutral predictors by using a partial redundancy analysis (pRDA). Results obtained through the pRDA indicated that both environmental and spatial processes influenced Ephemeroptera abundance. On the other hand, only environmental processes showed effects on community patterns when using species presence data from preserved, altered and large streams and also when looking only at the preserved sites. When streams larger than 20 m were excluded from analysis, both environmental and spatially processes showed influence on Ephemeroptera composition. Adjusted R 2 values were higher for environmental than for spatial processes in all analyses. The relatively high influence of both environmental processes and stream width in the analyses highlights the sensitivity of mayflies assemblies to environmental variation, and emphasizes the importance of local processes, as predicted by niche theory, while neutral processes act to a lesser extent on the structure of the studied communities.

Cave shrimps of the Typhlatya genus are common and widespread in fresh, brackish and marine groundwater throughout the Yucatan Peninsula (Mexico). These species are ideal models to test niche partitioning within sympatric species in oligotrophic systems. Nevertheless, their food sources remain unidentified, and despite their frequency and functional importance, distribution and abundance patterns of these species within caves have not been fully recognized. Here, we describe the abundance of three Typhlatya species in different temporal and spatial scales, investigate changes in water conditions, and potential sources of carbon as an indication of food origin. Species composition and abundance varied markedly in space and time revealing patterns that differed from one system to another and in relation to environmental parameters. Isotope analysis showed that each species reflects a particular δ13C and Δ14C fingerprint, suggesting they feed in different proportions from the available...

Didelphis albiventris and D. aurita are Neotropical marsupials that share a unique evolutionary history and both are largely distributed throughout South America, being primarily allo-patric throughout their ranges. In the Araucaria moist forest of Southern Brazil these species are sympatric and they might potentially compete having similar ecology. For this reason, they are ideal biological models to address questions about ecological character displacement and how closely related species might share their geographic space. Little is known about how two morphologically similar species of marsupials may affect each other through competition, if by competitive exclusion and competitive release. We combined ecological niche modeling and geometric morphometrics to explore the possible effects of competition on their distributional ranges and skull morphology. Ecological niche modeling was used to predict their potential distribution and this method enabled us to identify a case of biotic exclusion where the habit generalist D. albiventris is excluded by the presence of the specialist D. aurita. The morphometric analyses show that a degree of shape discrimination occurs between the species, strengthened by allometric differences, which possibly allowed them to occupy marginally different feeding niches supplemented by behavioral shift in contact areas. Overlap in skull morphology is shown between sympatric and allopat-ric specimens and a significant, but weak, shift in shape occurs only in D. aurita in sympatric areas. This could be a residual evidence of a higher past competition between both species, when contact zones were possibly larger than today. Therefore, the specialist D. aurita acts a biotic barrier to D. albiventris when niche diversity is not available for coexistence. On the PLOS ONE |

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types-for example in genotypes, phenotypes, and environment types-in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes.

This paper presents the outline of a formal ontology of contexts. More specifically, it deals with the ontology of ecological contexts (niches, habitats, environments, ambients) and of the relations between organisms, niches, and the spatial regions they occupy. The first part sets out the basic conceptual background. The second part outlines a semi-formal theory which builds upon notions and principles of mereology, topology, and the theory of spatial location.

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche.