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.

Mineral zoning and geochemistry of epithermal polymetallic Zn-Pb-Ag-Cu-Bi mineralization at Cerro de Pasco, Peru

The large Cerro de Pasco Cordilleran base metal deposit in central Peru is located on the eastern margin of a middle Miocene diatreme-dome complex and comprises two mineralization stages. The first stage consists of a large pyrite-quartz body replacing Lower Mesozoic Pucara carbonate rocks and, to a lesser extent, diatreme breccia. This body is composed of pyrite with pyrrhotite inclusions, quartz, and black and red chalcedony (containing hypogene hematite). At the contact with the pyrite-quartz body, the diatreme breccia is altered to pyrite-quartz-sericite-pyrite. This body was, in part, replaced by pipelike pyrrhotite bodies zoned outward to carbonate-replacement Zn-Pb ores hearing Fe-rich sphalerite (up to 24 mol % Fes). The second mineralization stage is partly superimposed on the first and consists of zoned east-west-trending Cu-Ag-(Au-Zn-Pb) enargite-pyrite veins hosted in the diatreme breccia in the western part of the deposit and well-zoned Zn-Pb-(Bi-Ag-Cu) carbonate-replacement orebodies; in both cases, sphalerite is Fe poor and the inner parts of the orebodies show typically advanced argillic alteration assemblages, including aluminum phosphate Sulfate (APS) minerals. The zoned enargite-pyrite veins display mineral zoning, from a core of enargite-pyrite +/- alunite with traces of Au, through an intermediate zone of tennantite, chalcopyrite, and Bi minerals to a poorly developed Outer zone hearing sphalerite-galena +/- kaolinite. The carbonate-hosted replacement ores are controlled along N 35 degrees E, N 90 degrees E, N 120 degrees E, and N 170 degrees E faults. They form well-zoned upward-flaring pipelike orebodies with a core of famatinite-pyrite and alunite, an intermediate zone with tetrahedrite-pyrite, chalcopyrite, matildite, cuprobismutite, emplectite, and other Bi minerals accompanied by APS minerals, kaolinite, and dickite, and an outer zone composed of Fe-poor sphalerite (in the range of 0.05-3.5 mol % Fes) and galena. The outermost zone consists of hematite, magnetite, and Fe-Mn-Zn-Ca-Mg carbonates. Most of the second-stage carbonate-replacement orebodies plunge between 25 degrees and 60 degrees to the west, suggesting that the hydrothermal fluids ascended from deeper levels and that no lateral feeding from the veins to the carbonate-replacement orebodies took place. In the Venencocha and Santa Rosa areas, located 2.5 km northwest of the Cerro de Pasco open pit and in the southern part of the deposit, respectively, advanced argillic altered dacitic domes and oxidized veins with advanced argillic alteration halos occur. The latter veins are possibly the oxidized equivalent of the second-stage enargite-pyrite veins located in the western part of the deposit. The alteration assemblage quartz-muscovite-pyrite associated with the pyrite-quartz body suggests that the first stage precipitated at slightly, acidic fin. The sulfide mineral assemblages define an evolutionary path close to the pyrite-pyrrhotite boundary and are characteristic of low-sulfidation states; they suggest that the oxidizing slightly acidic hydrothermal fluid was buffered by phyllite, shale, and carbonate host rock. However, the presence in the pyrite-quartz body of hematite within quartz suggests that, locally, the fluids were less buffered by the host rock. The mineral assemblages of the second mineralization stage are characteristic of high- to intermediate-sulfidation states. High-sulfidation states and oxidizing conditions were achieved and maintained in the cores of the second-stage orebodies, even in those replacing carbonate rocks. The observation that, in places, second-stage mineral assemblages are found in the inner and outer zones is explained in terms of the hydrothermal fluid advancing and waning. Microthermometric data from fluid inclusions in quartz indicate that the different ores of the first mineralization stage formed at similar temperatures and moderate salinities (200 degrees-275 degrees C and 0.2-6.8 wt % NaCl equiv in the pyrite-quartz body; 192 degrees-250 degrees C and 1.1-4.3 wt % NaCl equiv in the pyrrhotite bodies; and 183 degrees-212 degrees C and 3.2-4.0 wt % NaCl equiv in the Zn-Pb ores). These values are similar to those obtained for fluid inclusions in quartz and sphalerite from the second-stage ores (187 degrees-293 degrees C and 0.2-5.2 wt % NaCl equiv in the enargite-pyrite veins: 178 degrees-265 degrees C and 0.2-7.5 wt % NaCl equiv in quartz of carbonate-replacement orebodies; 168 degrees-999 degrees C and 3-11.8 wt % NaCl equiv in sphalerite of carbonate-replacement orebodies; and 245 degrees-261 degrees C and 3.2-7.7 wt % NaCl equiv in quartz from Venencocha). Oxygen and hydrogen isotope compositions oil kaolinite from carbonate-replacement orebodies (delta(18)O = 5.3-11.5%o, delta D = -82 to -114%o) and on alunite from the Venencocha and Santa Rosa areas (delta(18)O = 1.9-6.9%o, delta D = -56 to -73%o). Oxygen isotope compositions of quartz from the first and second stages have 6180 values from 9.1 to 1.7.8 per mil. Calculated fluids in equilibrium with kaolinite have delta(18)O values of 2.0 to 8.2 and delta D values of -69 to -97 per mil; values in equilibrium with alunite are -1.4 to -6.4 and -62 to -79 per mil. Sulfur isotope compositions of sulfides from both stages have a narrow range of delta(34)S values, between -3.7 and +4.2 per mil; values for sulfates from the second stage are between 4.2 and 31.2 per mil. These results define two mixing trends for the ore-forming fluids. The first trend reflects mixing between a moderately saline (similar to 10 wt % NaCl equiv) magmatic end member that had degassed (as indicated by the low delta D values) and meteoric water. The second mixing indicates condensation of magmatic vapor with HCl and SO(2) into meteoric water, which formed alunite. The hydrothermal system at Cerro de Pasco was emplaced at a shallow depth (similar to 500 m) in the epithermal and upper part of a porphyry environment. The similar temperatures and salinities obtained for the first stage and second stages, together with the stable isotope data, indicate that both stages are linked and represent successive stages of epithermal polymetallic mineralization in the upper part of a porphyry system.

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

Defining ecological strategies in neuroprosthetics.

Neurological disorders disrupt the equilibrium within the brain and spinal cord ecosystems. Ecology reuses, recycles, and reduces to help maintain the balance across ecosystems. Likewise, neuroprosthetics can help the brain help itself with ecoprosthetic designs that integrate the principles of the "three 'R's."

Morphological, hydrological, biogeochemical and ecological changes and challenges in river restoration - the Thur River case study

River restoration can enhance river dynamics, environmental heterogeneity and biodiversity, but the underlying processes governing the dynamic changes need to be understood to ensure that restoration projects meet their goals, and adverse effects are prevented. In particular, we need to comprehend how hydromorphological variability quantitatively relates to ecosystem functioning and services, biodiversity as well as ground-and surface water quality in restored river corridors. This involves (i) physical processes and structural properties, determining erosion and sedimentation, as well as solute and heat transport behavior in surface water and within the subsurface; (ii) biogeochemical processes and characteristics, including the turnover of nutrients and natural water constituents; and (iii) ecological processes and indicators related to biodiversity and ecological functioning. All these aspects are interlinked, requiring an interdisciplinary investigation approach. Here, we present an overview of the recently completed RECORD (REstored CORridor Dynamics) project in which we combined physical, chemical, and biological observations with modeling at a restored river corridor of the perialpine Thur River in Switzerland. Our results show that river restoration, beyond inducing morphologic changes that reshape the river bed and banks, triggered complex spatial patterns of bank infiltration, and affected habitat type, biotic communities and biogeochemical processes. We adopted an interdisciplinary approach of monitoring the continuing changes due to restoration measures to address the following questions: How stable is the morphological variability established by restoration? Does morphological variability guarantee an improvement in biodiversity? How does morphological variability affect biogeochemical transformations in the river corridor? What are some potential adverse effects of river restoration? How is river restoration influenced by catchment-scale hydraulics [GRAPHICS] and which feedbacks exist on the large scale? Beyond summarizing the major results of individual studies within the project, we show that these overarching questions could only be addressed in an interdisciplinary framework.

Selection on a genetic polymorphism counteracts ecological speciation in a stick insect.

The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation [1-3]. Despite accumulating evidence that speciation can progress to "intermediate" stages-with populations evolving only partial reproductive isolation-studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism [4, 5]. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.

A macro-ecological perspective on crassulacean acid metabolism (CAM) photosynthesis evolution in Afro-Madagascan drylands: Eulophiinae orchids as a case study.

Crassulacean acid metabolism (CAM) photosynthesis is an adaptation to water and atmospheric CO2 deficits that has been linked to diversification in dry-adapted plants. We investigated whether CAM evolution can be associated with the availability of new or alternative niches, using Eulophiinae orchids as a case study. Carbon isotope ratios, geographical and climate data, fossil records and DNA sequences were used to: assess the prevalence of CAM in Eulophiinae orchids; characterize the ecological niche of extant taxa; infer divergence times; and estimate whether CAM is associated with niche shifts. CAM evolved in four terrestrial lineages during the late Miocene/Pliocene, which have uneven diversification patterns. These lineages originated in humid habitats and colonized dry/seasonally dry environments in Africa and Madagascar. Additional key features (variegation, heterophylly) evolved in the most species-rich CAM lineages. Dry habitats were also colonized by a lineage that includes putative mycoheterotrophic taxa. These findings indicate that the switch to CAM is associated with environmental change. With its suite of adaptive traits, this group of orchids represents a unique opportunity to study the adaptations to dry environments, especially in the face of projected global aridification.

The Association of H1N1 Pandemic Influenza with Congenital Anomaly Prevalence in Europe: An Ecological Time Series Study.

BACKGROUND: In the context of the European Surveillance of Congenital Anomalies (EUROCAT) surveillance response to the 2009 influenza pandemic, we sought to establish whether there was a detectable increase of congenital anomaly prevalence among pregnancies exposed to influenza seasons in general, and whether any increase was greater during the 2009 pandemic than during other seasons. METHODS: We performed an ecologic time series analysis based on 26,967 pregnancies with nonchromosomal congenital anomaly conceived from January 2007 to March 2011, reported by 15 EUROCAT registries. Analysis was performed for EUROCAT-defined anomaly subgroups, divided by whether there was a prior hypothesis of association with influenza. Influenza season exposure was based on World Health Organization data. Prevalence rate ratios were calculated comparing pregnancies exposed to influenza season during the congenital anomaly-specific critical period for embryo-fetal development to nonexposed pregnancies. RESULTS: There was no evidence for an increased overall prevalence of congenital anomalies among pregnancies exposed to influenza season. We detected an increased prevalence of ventricular septal defect and tricuspid atresia and stenosis during pandemic influenza season 2009, but not during 2007-2011 influenza seasons. For congenital anomalies, where there was no prior hypothesis, the prevalence of tetralogy of Fallot was strongly reduced during influenza seasons. CONCLUSIONS: Our data do not suggest an overall association of pandemic or seasonal influenza with congenital anomaly prevalence. One interpretation is that apparent influenza effects found in previous individual-based studies were confounded by or interacting with other risk factors. The associations of heart anomalies with pandemic influenza could be strain specific.

Ecological change predicts population dynamics and genetic diversity over 120 000 years.

While ecological effects on short-term population dynamics are well understood, their effects over millennia are difficult to demonstrate and convincing evidence is scant. Using coalescent methods, we analysed past population dynamics of three lizard species (Psammodromus hispanicus, P. edwardsianus, P. occidentalis) and linked the results with climate change data covering the same temporal horizon (120 000 years). An increase in population size over time was observed in two species, and in P. occidentalis, no change was observed. Temporal changes in temperature seasonality and the maximum temperature of the warmest month were congruent with changes in population dynamics observed for the three species and both variables affected population density, either directly or indirectly (via a life-history trait). These results constitute the first solid link between ecological change and long-term population dynamics. The results moreover suggest that ecological change leaves genetic signatures that can be retrospectively traced, providing evidence that ecological change is a crucial driver of genetic diversity and speciation.