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.

Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology.

BACKGROUND: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years. SCOPE: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants. CONCLUSIONS: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.

Height distributions of Scots pine sapling stands affected by retained tree and edge stand competition

Abstract

Benefits from ecological study methods to taxonomy of enchytraeids in southern Mata Atlântica

The objective of this work was to determine how taxonomy benefited from the ecological quantitative and site-based sampling methods in enchytraeids studies. Enchytraeids (small relatives of earthworms) were sampled in different phases of rain forest regeneration in the southern Mata Atlântica in Paraná, Brazil. The research combined ecological and taxonomic work, because enchytraeids are poorly studied and difficult to identify, and many new species were expected. The provision of large numbers of specimens enabled the test of species diagnoses by investigating the ranges of character variations in a larger series of specimens. Simplified species diagnoses adapted to the local conditions that allowed the identification of all specimens, juveniles included, were developed. Key characters and character states are presented for the three genera: Achaeta, Hemienchytraeus and Guaranidrilus. Among several new species, a rare species, possibly a remnant of the autochthonous forest fauna, was found and described.

Towards an ecological index for tropical soil quality based on soil macrofauna

The objective of this work was to construct a simple index based on the presence/absence of different groups of soil macrofauna to determine the ecological quality of soils. The index was tested with data from 20 sites in South and Central Tabasco, Mexico, and a positive relation between the model and the field observations was detected. The index showed that diverse agroforestry systems had the highest soil quality index (1.00), and monocrops without trees, such as pineapple, showed the lowest soil quality index (0.08). Further research is required to improve this model for natural systems that have very low earthworm biomass (<10 g m-2) and a high number of earthworm species (5-7), as it is in the tropical rain forest, whose soil quality index was medium (0.5). The application of this index will require an illustrated guide for its users. Further studies are required in order to test the use of this index by farmers.

Spatial polarization of the ecological footprint distribution

The international allocation of natural resources is determined, not by any ethical or ecological criteria, but by the dominance of market mechanisms. From a core-periphery perspective, this allocation may even be driven by historically determined structural patterns, with a core group of countries whose consumption appropriates most available natural resources, and another group, having low natural resource consumption, which plays a peripheral role. This article consists of an empirical distributional analysis of natural resource consumption (as measured by Ecological Footprints) whose purpose is to assess the extent to which the distribution of consumption responds to polarization (as opposed to mere inequality). To assess this, we estimate and decompose different polarization indices for a balanced sample of 119 countries over the period 1961 to 2007. Our results points toward a polarized distribution which is consistent with a core-periphery framework. Keywords: Polarization, Core-Periphery, Ecological Footprint

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.

Transcriptome analysis of intraspecific competition in Arabidopsis thaliana reveals organ-specific signatures related to nutrient acquisition and general stress response pathways.

ABSTRACT: BACKGROUND: Plants are sessile and therefore have to perceive and adjust to changes in their environment. The presence of neighbours leads to a competitive situation where resources and space will be limited. Complex adaptive responses to such situation are poorly understood at the molecular level. RESULTS: Using microarrays, we analysed whole-genome expression changes in Arabidopsis thaliana plants subjected to intraspecific competition. The leaf and root transcriptome was strongly altered by competition. Differentially expressed genes were enriched in genes involved in nutrient deficiency (mainly N, P, K), perception of light quality, and responses to abiotic and biotic stresses. Interestingly, performance of the generalist insect Spodoptera littoralis on densely grown plants was significantly reduced, suggesting that plants under competition display enhanced resistance to herbivory. CONCLUSIONS: This study provides a comprehensive list of genes whose expression is affected by intraspecific competition in Arabidopsis. The outcome is a unique response that involves genes related to light, nutrient deficiency, abiotic stress, and defence responses.

The establishment of communication systems depends on the scale of competition

How communication systems emerge and remain stable is an important question in both cognitive science and evolutionary biology. For communication to arise, not only must individuals cooperate by signaling reliable information, but they must also coordinate and perpetuate signals. Most studies on the emergence of communication in humans typically consider scenarios where individuals implicitly share the same interests. Likewise, most studies on human cooperation consider scenarios where shared conventions of signals and meanings cannot be developed de novo. Here, we combined both approaches with an economic experiment where participants could develop a common language, but under different conditions fostering or hindering cooperation. Participants endeavored to acquire a resource through a learning task in a computer-based environment. After this task, participants had the option to transmit a signal (a color) to a fellow group member, who would subsequently play the same learning task. We varied the way participants competed with each other (either global scale or local scale) and the cost of transmitting a signal (either costly or noncostly) and tracked the way in which signals were used as communication among players. Under global competition, players signaled more often and more consistently, scored higher individual payoffs, and established shared associations of signals and meanings. In addition, costly signals were also more likely to be used under global competition; whereas under local competition, fewer signals were sent and no effective communication system was developed. Our results demonstrate that communication involves both a coordination and a cooperative dilemma and show the importance of studying language evolution under different conditions influencing human cooperation.

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

Efficiency and significance of multiple vocal signals in sibling competition

Animals can compete for resources by displaying various acoustic signals that may differentially affect the outcome of competition. We propose the hypothesis that the most efficient signal to deter opponents should be the one that most honestly reveals motivation to compete. We tested this hypothesis in the barn owl (Tyto alba) in which nestlings produce more calls of longer duration than siblings to compete for priority access to the indivisible prey item their parents will deliver next. Because nestlings increase call rate to a larger extent than call duration when they become hungrier, call rate would signal more accurately hunger level. This leads us to propose three predictions. First, a high number of calls should be more efficient in deterring siblings to compete than long calls. Second, the rate at which an individual calls should be more sensitive to variation in the intensity of the sibling vocal competition than the duration of its calls. Third, call rate should influence competitors' vocalization for a longer period of time than call duration. To test these three predictions we performed playback experiments by broadcasting to singleton nestlings calls of varying durations and at different rates. According to the first prediction, singleton nestlings became less vocal to a larger extent when we broadcasted more calls compared to longer calls. In line with the second prediction, nestlings reduced vocalization rate to a larger extent than call duration when we broadcasted more or longer calls. Finally, call rate had a longer influence on opponent's vocal behavior than call duration. Young animals thus actively and differentially use multiple signaling components to compete with their siblings over parental resources.