Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.

The homeostatic psyche: Freudian theory and somatic markers.

After years of reciprocal lack of interest, if not opposition, neuroscience and psychoanalysis are poised for a renewed dialogue. This article discusses some aspects of the Freudian metapsychology and its link with specific biological mechanisms. It highlights in particular how the physiological concept of homeostasis resonates with certain fundamental concepts of psychoanalysis. Similarly, the authors underline how the Freud and Damasio theories of brain functioning display remarkable complementarities, especially through their common reference to Meynert and James. Furthermore, the Freudian theory of drives is discussed in the light of current neurobiological evidences of neural plasticity and trace formation and of their relationships with the processes of homeostasis. The ensuing dynamics between traces and homeostasis opens novel avenues to consider inner life in reference to the establishment of fantasies unique to each subject. The lack of determinism, within a context of determinism, implied by plasticity and reconsolidation participates in the emergence of singularity, the creation of uniqueness and the unpredictable future of the subject. There is a gap in determinism inherent to biology itself. Uniqueness and discontinuity: this should today be the focus of the questions raised in neuroscience. Neuroscience needs to establish the new bases of a "discontinuous" biology. Psychoanalysis can offer to neuroscience the possibility to think of discontinuity. Neuroscience and psychoanalysis meet thus in an unexpected way with regard to discontinuity and this is a new point of convergence between them.

The Implied Book and the Narrative Text. On a Blind Spot in Narratological Theory - from a Media Studies Perspective

The article is concerned with the formal definition of a largely unnoticed factor in narrative structure. Based on the assumptions that (1) the semantics of a written text depend, among other factors, directly on its visual alignment in space, that (2) the formal structure of a text has to meet that of its spatial presentation and that (3) these assumptions hold true also for narrative texts (which, however, in modern times typically conceal their spatial dimensions by a low-key linear layout), it is argued that, how ever low-key, the expected material shape of a given narrative determines the configuration of its plot by its author. The ,implied book' thus denotes an author's historically assumable, not necessarily conscious idea of how his text, which is still in the process of creation, will be dimensionally presented and under these circumstances visually absorbed. Assuming that an author's knowledge of this later (potentially) substantiated material form influences the composition, the implied book is to be understood as a text-genetically determined, structuring moment of the text. Historically reconstructed, it thus serves the methodical analysis of structural characteristics of a completed text.

Debating the centre : the theory of principal qualificand (mukhyavisesya) in classical Indian philosophy

The theory of language has occupied a special place in the history of Indian thought. Indian philosophers give particular attention to the analysis of the cognition obtained from language, known under the generic name of śābdabodha. This term is used to denote, among other things, the cognition episode of the hearer, the content of which is described in the form of a paraphrase of a sentence represented as a hierarchical structure. Philosophers submit the meaning of the component items of a sentence and their relationship to a thorough examination, and represent the content of the resulting cognition as a paraphrase centred on a meaning element, that is taken as principal qualificand (mukhyaviśesya) which is qualified by the other meaning elements. This analysis is the object of continuous debate over a period of more than a thousand years between the philosophers of the schools of Mimāmsā, Nyāya (mainly in its Navya form) and Vyākarana. While these philosophers are in complete agreement on the idea that the cognition of sentence meaning has a hierarchical structure and share the concept of a single principal qualificand (qualified by other meaning elements), they strongly disagree on the question which meaning element has this role and by which morphological item it is expressed. This disagreement is the central point of their debate and gives rise to competing versions of this theory. The Mïmāmsakas argue that the principal qualificand is what they call bhāvanā ̒bringing into being̒, ̒efficient force̒ or ̒productive operation̒, expressed by the verbal affix, and distinct from the specific procedures signified by the verbal root; the Naiyāyikas generally take it to be the meaning of the word with the first case ending, while the Vaiyākaranas take it to be the operation expressed by the verbal root. All the participants rely on the Pāninian grammar, insofar as the Mimāmsakas and Naiyāyikas do not compose a new grammar of Sanskrit, but use different interpretive strategies in order to justify their views, that are often in overt contradiction with the interpretation of the Pāninian rules accepted by the Vaiyākaranas. In each of the three positions, weakness in one area is compensated by strength in another, and the cumulative force of the total argumentation shows that no position can be declared as correct or overall superior to the others. This book is an attempt to understand this debate, and to show that, to make full sense of the irreconcilable positions of the three schools, one must go beyond linguistic factors and consider the very beginnings of each school's concern with the issue under scrutiny. The texts, and particularly the late texts of each school present very complex versions of the theory, yet the key to understanding why these positions remain irreconcilable seems to lie elsewhere, this in spite of extensive argumentation involving a great deal of linguistic and logical technicalities. Historically, this theory arises in Mimāmsā (with Sabara and Kumārila), then in Nyāya (with Udayana), in a doctrinal and theological context, as a byproduct of the debate over Vedic authority. The Navya-Vaiyākaranas enter this debate last (with Bhattoji Dïksita and Kaunda Bhatta), with the declared aim of refuting the arguments of the Mïmāmsakas and Naiyāyikas by bringing to light the shortcomings in their understanding of Pāninian grammar. The central argument has focused on the capacity of the initial contexts, with the network of issues to which the principal qualificand theory is connected, to render intelligible the presuppositions and aims behind the complex linguistic justification of the classical and late stages of this debate. Reading the debate in this light not only reveals the rationality and internal coherence of each position beyond the linguistic arguments, but makes it possible to understand why the thinkers of the three schools have continued to hold on to three mutually exclusive positions. They are defending not only their version of the principal qualificand theory, but (though not openly acknowledged) the entire network of arguments, linguistic and/or extra-linguistic, to which this theory is connected, as well as the presuppositions and aims underlying these arguments.

On the evolution of harming and recognition in finite panmictic and infinite structured populations.

Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. Although social evolutionary theory has mainly dealt with helping behaviors, competition for limited resources creates ecological conditions in which an actor may benefit from expressing behaviors that reduce the vital rates of neighbors. This may occur if the reduction in vital rates decreases the intensity of competition experienced by the actor or that experienced by its offspring. Here, we explore the joint evolution of neutral recognition markers and marker-based costly conditional harming whereby actors express harming, conditional on actor and recipient bearing different conspicuous markers. We do so for two complementary demographic scenarios: finite panmictic and infinite structured populations. We find that marker-based conditional harming can evolve under a large range of recombination rates and group sizes under both finite panmictic and infinite structured populations. A direct comparison with results for the evolution of marker-based conditional helping reveals that, if everything else is equal, marker-based conditional harming is often more likely to evolve than marker-based conditional helping.

Ecological-niche factor analysis: how to compute habitat-suitability maps without absence data?

We propose a multivariate approach to the study of geographic species distribution which does not require absence data. Building on Hutchinson's concept of the ecological niche, this factor analysis compares, in the multidimensional space of ecological variables, the distribution of the localities where the focal species was observed to a reference set describing the whole study area. The first factor extracted maximizes the marginality of the focal species, defined as the ecological distance between the species optimum and the mean habitat within the reference area. The other factors maximize the specialization of this focal species, defined as the ratio of the ecological variance in mean habitat to that observed for the focal species. Eigenvectors and eigenvalues are readily interpreted and can be used to build habitat-suitability maps. This approach is recommended in Situations where absence data are not available (many data banks), unreliable (most cryptic or rare species), or meaningless (invaders). We provide an illustration and validation of the method for the alpine ibex, a species reintroduced in Switzerland which presumably has not yet recolonized its entire range.

Effect of spatial processes on the evolution of ecological niches and dispersal in metacommunity systems

RésuméLa coexistence de nombreuses espèces différentes a de tout temps intrigué les biologistes. La diversité et la composition des communautés sont influencées par les perturbations et l'hétérogénéité des conditions environnementales. Bien que dans la nature la distribution spatiale des conditions environnementales soit généralement autocorrélée, cet aspect est rarement pris en compte dans les modèles étudiant la coexistence des espèces. Dans ce travail, nous avons donc abordé, à l'aide de simulations numériques, la coexistence des espèces ainsi que leurs caractéristiques au sein d'un environnement autocorrélé.Afin de prendre en compte cet élément spatial, nous avons développé un modèle de métacommunauté (un ensemble de communautés reliées par la dispersion des espèces) spatialement explicite. Dans ce modèle, les espèces sont en compétition les unes avec les autres pour s'établir dans un nombre de places limité, dans un environnement hétérogène. Les espèces sont caractérisées par six traits: optimum de niche, largeur de niche, capacité de dispersion, compétitivité, investissement dans la reproduction et taux de survie. Nous nous sommes particulièrement intéressés à l'influence de l'autocorrélation spatiale et des perturbations sur la diversité des espèces et sur les traits favorisés dans la métacommunauté. Nous avons montré que l'autocorrélation spatiale peut avoir des effets antagonistes sur la diversité, en fonction du taux de perturbations considéré. L'influence de l'autocorrélation spatiale sur la capacité de dispersion moyenne dans la métacommunauté dépend également des taux de perturbations et survie. Nos résultats ont aussi révélé que de nombreuses espèces avec différents degrés de spécialisation (i.e. différentes largeurs de niche) peuvent coexister. Toutefois, les espèces spécialistes sont favorisées en absence de perturbations et quand la dispersion est illimitée. A l'opposé, un taux élevé de perturbations sélectionne des espèces plus généralistes, associées avec une faible compétitivité.L'autocorrélation spatiale de l'environnement, en interaction avec l'intensité des perturbations, influence donc de manière considérable la coexistence ainsi que les caractéristiques des espèces. Ces caractéristiques sont à leur tour souvent impliquées dans d'importants processus, comme le fonctionnement des écosystèmes, la capacité des espèces à réagir aux invasions, à la fragmentation de l'habitat ou aux changements climatiques. Ce travail a permis une meilleure compréhension des mécanismes responsables de la coexistence et des caractéristiques des espèces, ce qui est crucial afin de prédire le devenir des communautés naturelles dans un environnement changeant.AbstractUnderstanding how so many different species can coexist in nature is a fundamental and long-standing question in ecology. Community diversity and composition are known to be influenced by heterogeneity in environmental conditions and disturbance. Though in nature the spatial distribution of environmental conditions is frequently autocorrelated, this aspect is seldom considered in models investigating species coexistence. In this work, we thus addressed several questions pertaining to species coexistence and composition in spatially autocorrelated environments, with a numerical simulations approach.To take into account this spatial aspect, we developed a spatially explicit model of metacommunity (a set of communities linked by dispersal of species). In this model, species are trophically equivalent, and compete for space in a heterogeneous environment. Species are characterized by six life-history traits: niche optimum, niche breadth, dispersal, competitiveness, reproductive investment and survival rate. We were particularly interested in the influence of environmental spatial autocorrelation and disturbance on species diversity and on the traits of the species favoured in the metacommunity. We showed that spatial autocorrelation can have antagonistic effects on diversity depending on disturbance rate. Similarly, spatial autocorrelation interacted with disturbance rate and survival rate to shape the mean dispersal ability observed in the metacommunity. Our results also revealed that many species with various degrees of specialization (i.e. different niche breadths) can coexist together. However specialist species were favoured in the absence of disturbance, and when dispersal was unlimited. In contrast, high disturbance rate selected for more generalist species, associated with low competitive ability.The spatial structure of the environment, together with disturbance and species traits, thus strongly impacts species diversity and, more importantly, species composition. Species composition is known to affect several important metacommunity properties such as ecosystem functioning, resistance and reaction to invasion, to habitat fragmentation and to climate changes. This work allowed a better understanding of the mechanisms responsible for species composition, which is of crucial importance to predict the fate of natural metacommunities in changing environments

The evolution of trans-generational altruism: kin selection meets niche construction.

A cornerstone result of sociobiology states that limited dispersal can induce kin competition to offset the kin selected benefits of altruism. Several mechanisms have been proposed to circumvent this dilemma but all assume that actors and recipients of altruism interact during the same time period. Here, this assumption is relaxed and a model is developed where individuals express an altruistic act, which results in posthumously helping relatives living in the future. The analysis of this model suggests that kin selected benefits can then feedback on the evolution of the trait in a way that promotes altruistic helping at high rates under limited dispersal. The decoupling of kin competition and kin selected benefits results from the fact that by helping relatives living in the future, an actor is helping individuals that are not in direct competition with itself. A direct consequence is that behaviours which actors gain by reducing the common good of present and future generations can be opposed by kin selection. The present model integrates niche-constructing traits with kin selection theory and delineates demographic and ecological conditions under which altruism can be selected for; and conditions where the 'tragedy of the commons' can be reduced.