Spatially explicit estimates of length and biomass of Micromesistius poutassou (Blue Whiting) from acoustic and trawl surveys in the North-East Atlantic in May 2012

Acoustic estimates of herring and blue whiting abundance were obtained during the surveys using the Simrad ER60 scientific echosounder. The allocation of NASC-values to herring, blue whiting and other acoustic targets were based on the composition of the trawl catches and the appearance of echo recordings. To estimate the abundance, the allocated NASC -values were averaged for ICES-squares (0.5° latitude by 1° longitude). For each statistical square, the unit area density of fish (rA) in number per square nautical mile (N*nm-2) was calculated using standard equations (Foote et al., 1987; Toresen et al., 1998). To estimate the total abundance of fish, the unit area abundance for each statistical square was multiplied by the number of square nautical miles in each statistical square and then summed for all the statistical squares within defined subareas and over the total area. Biomass estimation was calculated by multiplying abundance in numbers by the average weight of the fish in each statistical square then summing all squares within defined subareas and over the total area. The Norwegian BEAM soft-ware (Totland and Godø 2001) was used to make estimates of total biomass.

Review of the ecology of Australian urban fauna: A focus on spatially explicit processes

Cities have a major impact on Australian landscapes, especially in coastal regions, to the detriment of native biodiversity. Areas suitable for urban development often coincide with those areas that support high levels of species diversity and endemism. However, there is a paucity of reliable information available to guide urban conservation planning and management, especially regarding the trade-off between investing in protecting and restoring habitat at the landscape level, and investing in programmes to maintain the condition of remnant vegetation at the local (site) level. We review the literature on Australian urban ecology, focusing on urban terrestrial and aquatic vertebrate and invertebrate fauna. We identify four main factors limiting our knowledge of urban fauna: (i) a lack of studies focusing at multiple ecological levels; (ii) a lack of multispecies studies; (iii) an almost total absence of long-term (temporal) studies; and (iv) a need for stronger integration of research outcomes into urban conservation planning and management. We present a set of key principles for the development of a spatially explicit, long-term approach to urban fauna research. This requires an understanding of the importance of local-level habitat quality and condition relative to the composition, configuration and connectivity of habitats within the larger urban landscape. These principles will ultimately strengthen urban fauna management and conservation planning by enabling us to prioritize and allocate limited financial resources to maximize the conservation return.

Spatially explicit estimates of stock size, structure and biomass of North Atlantic albacore tuna (Thunnus alalunga) in the North Atlantic for the period 1956-2010, compiled from the International Commission for the Conservation of Atlantic Tunas

The development of the ecosystem approach and models for the management of ocean marine resources requires easy access to standard validated datasets of historical catch data for the main exploited species. They are used to measure the impact of biomass removal by fisheries and to evaluate the models skills, while the use of standard dataset facilitates models inter-comparison. North Atlantic albacore tuna is exploited all year round by longline and in summer and autumn by surface fisheries and fishery statistics compiled by the International Commission for the Conservation of Atlantic Tunas (ICCAT). Catch and effort with geographical coordinates at monthly spatial resolution of 1° or 5° squares were extracted for this species with a careful definition of fisheries and data screening. In total, thirteen fisheries were defined for the period 1956-2010, with fishing gears longline, troll, mid-water trawl and bait fishing. However, the spatialized catch effort data available in ICCAT database represent a fraction of the entire total catch. Length frequencies of catch were also extracted according to the definition of fisheries above for the period 1956-2010 with a quarterly temporal resolution and spatial resolutions varying from 1°x 1° to 10°x 20°. The resolution used to measure the fish also varies with size-bins of 1, 2 or 5 cm (Fork Length). The screening of data allowed detecting inconsistencies with a relatively large number of samples larger than 150 cm while all studies on the growth of albacore suggest that fish rarely grow up over 130 cm. Therefore, a threshold value of 130 cm has been arbitrarily fixed and all length frequency data above this value removed from the original data set.

Treeline dynamics in Siberia under changing climates as inferred from an individual-based model for Larix, supplementary material

Siberian boreal forests are expected to expand northwards in the course of global warming. However, processes of the treeline ecotone transition, as well astiming and related climate feedbacks are still not understood. Here, we present 'Larix Vegetation Simulator' LAVESI, an individual-based spatially-explicit model that can simulate Larix gmelinii (RUPR.) RUPR. stand dynamics in an attempt to improve our understanding about past and future treeline movements under changing climates. The relevant processes (growth, seed production and dispersal, establishment and mortality) are incorporated and adjusted to observation data mainly gained from the literature. Results of a local sensitivity analysis support the robustness of the model's parameterization by giving relatively small sensitivity values. We tested the model by simulating tree stands under modern climate across the whole Taymyr Peninsula, north-central Siberia (c. 64-80° N; 92-119° E). We find tree densities similar to observed forests in the northern to mid-treeline areas, but densities are overestimated in the southern parts of the simulated region. Finally, from a temperature-forcing experiment, we detect that the responses of tree stands lag the hypothetical warming by several decades, until the end of 21st century. With our simulation experiments we demonstrate that the newly-developed model captures the dynamics of the Siberian latitudinal treeline.

Spatially explicit estimates of N2O emissions from croplands suggest climate mitigation opportunities from improved fertilizer management

Acknowledgements We are grateful to Stefan Seibert for advice on reconciling the Monfreda datasets of yield and area and the Portmann dataset for irrigated area of rice. We thank Deepak Ray and Jonathan Foley for helpful comments. Research support to J.G. K.C., N.M, and P.W. was primarily provided by the Gordon and Betty Moore Foundation and the Institute on Environment, with additional support from NSF Hydrologic Sciences grant 1521210 for N.M., and additional support to J.G. and P.W. whose efforts contribute to Belmont Forum/FACCE-JPI funded DEVIL project (NE/M021327/1). M.H. was supported by CSIRO's OCE Science Leaders Programme and the Agriculture Flagship. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

Temperature regulation of a pilot-scale batch reaction system via explicit model predictive control

In this paper, the temperature of a pilot-scale batch reaction system is modeled towards the design of a controller based on the explicit model predictive control (EMPC) strategy -- Some mathematical models are developed from experimental data to describe the system behavior -- The simplest, yet reliable, model obtained is a (1,1,1)-order ARX polynomial model for which the mentioned EMPC controller has been designed -- The resultant controller has a reduced mathematical complexity and, according to the successful results obtained in simulations, will be used directly on the real control system in a next stage of the entire experimental framework

Growth, mortality, and hatchdate distributions of larval and juvenile spotted seatrout (Cynoscion nebulosus) in Florida Bay, Everglades National Park

Life history aspects of larval and, mainly, juvenile spotted seatrout (Cynoscion nebulosus) were studied in Florida Bay, Everglades National Park, Florida. Collections were made in 1994−97, although the majority of juveniles were collected in 1995. The main objective was to obtain life history data to eventually develop a spatially explicit model and provide baseline data to understand how Everglades restoration plans (i.e. increased freshwater flows) could influence spotted seatrout vital rates. Growth of larvae and juveniles (<80 mm SL) was best described by the equation loge standard length = –1.31 + 1.2162 (loge age). Growth in length of juveniles (12–80 mm SL) was best described by the equation standard length = –7.50 + 0.8417 (age). Growth in wet weight of juveniles (15–69 mm SL) was best described by the equation loge wet-weight = –4.44 + 0.0748 (age). There were no significant differences in juvenile growth in length of spotted seatrout in 1995 between three geographical subdivisions of Florida Bay: central, western, and waters adjacent to the Gulf of Mexico. We found a significant difference in wet-weight for one of six cohorts categorized by month of hatchdate in 1995, and a significant difference in length for another cohort. Juveniles (i.e. survivors) used to calculate weekly hatchdate distributions during 1995 had estimated spawning times that were cyclical and protracted, and there was no correlation between spawning and moon phase. Temperature influenced otolith increment widths during certain growth periods in 1995. There was no evidence of a relationship between otolith growth rate and temperature for the first 21 increments. For increments 22–60, otolith growth rates decreased with increasing age and the extent of the decrease depended strongly in a quadratic fashion on the temperature to which the fish was exposed. For temperatures at the lower and higher range, increment growth rates were highest. We suggest that this quadratic relationship might be influenced by an environmental factor other than temperature. There was insufficient information to obtain reliable inferences on the relationship of increment growth rate to salinity.

Structure et dynamique des communautés multi-espèces : le rôle de l’espace

Cette thèse porte sur le rôle de l’espace dans l’organisation et dans la dynamique des communautés écologiques multi-espèces. Deux carences peuvent être identifiées dans les études théoriques actuelles portant sur la dimension spatiale des communautés écologiques : l’insuffisance de modèles multi-espèces représentant la dimension spatiale explicitement, et le manque d’attention portée aux interactions positives, tel le mutualisme, en dépit de la reconnaissance de leur ubiquité dans les systèmes écologiques. Cette thèse explore cette problématique propre à l’écologie des communautés, en utilisant une approche théorique s’inspirant de la théorie des systèmes complexes et de la mécanique statistique. Selon cette approche, les communautés d’espèces sont considérées comme des systèmes complexes dont les propriétés globales émergent des interactions locales entre les organismes qui les composent, et des interactions locales entre ces organismes et leur environnement. Le premier objectif de cette thèse est de développer un modèle de métacommunauté multi-espèces, explicitement spatial, orienté à l’échelle des individus et basé sur un réseau d’interactions interspécifiques générales comprenant à la fois des interactions d’exploitation, de compétition et de mutualisme. Dans ce modèle, les communautés locales sont formées par un processus d’assemblage des espèces à partir d’un réservoir régional. La croissance des populations est restreinte par une capacité limite et leur dynamique évolue suivant des mécanismes simples de reproduction et de dispersion des individus. Ces mécanismes sont dépendants des conditions biotiques et abiotiques des communautés locales et leur effet varie en fonction des espèces, du temps et de l’espace. Dans un deuxième temps, cette thèse a pour objectif de déterminer l’impact d’une connectivité spatiale croissante sur la dynamique spatiotemporelle et sur les propriétés structurelles et fonctionnelles de cette métacommunauté. Plus précisément, nous évaluons différentes propriétés des communautés en fonction du niveau de dispersion des espèces : i) la similarité dans la composition des communautés locales et ses patrons de corrélations spatiales; ii) la biodiversité locale et régionale, et la distribution locale de l’abondance des espèces; iii) la biomasse, la productivité et la stabilité dynamique aux échelles locale et régionale; et iv) la structure locale des interactions entre les espèces. Ces propriétés sont examinées selon deux schémas spatiaux. D’abord nous employons un environnement homogène et ensuite nous employons un environnement hétérogène où la capacité limite des communautés locales évoluent suivant un gradient. De façon générale, nos résultats révèlent que les communautés écologiques spatialement distribuées sont extrêmement sensibles aux modes et aux niveaux de dispersion des organismes. Leur dynamique spatiotemporelle et leurs propriétés structurelles et fonctionnelles peuvent subir des changements profonds sous forme de transitions significatives suivant une faible variation du niveau de dispersion. Ces changements apparaissent aussi par l’émergence de patrons spatiotemporels dans la distribution spatiale des populations qui sont typiques des transitions de phases observées généralement dans les systèmes physiques. La dynamique de la métacommunauté présente deux régimes. Dans le premier régime, correspondant aux niveaux faibles de dispersion des espèces, la dynamique d’assemblage favorise l’émergence de communautés stables, peu diverses et formées d’espèces abondantes et fortement mutualistes. La métacommunauté possède une forte diversité régionale puisque les communautés locales sont faiblement connectées et que leur composition demeure ainsi distincte. Par ailleurs dans le second régime, correspondant aux niveaux élevés de dispersion, la diversité régionale diminue au profit d’une augmentation de la diversité locale. Les communautés locales sont plus productives mais leur stabilité dynamique est réduite suite à la migration importante d’individus. Ce régime est aussi caractérisé par des assemblages incluant une plus grande diversité d’interactions interspécifiques. Ces résultats suggèrent qu’une augmentation du niveau de dispersion des organismes permet de coupler les communautés locales entre elles ce qui accroît la coexistence locale et favorise la formation de communautés écologiques plus riches et plus complexes. Finalement, notre étude suggère que le mutualisme est fondamentale à l’organisation et au maintient des communautés écologiques. Les espèces mutualistes dominent dans les habitats caractérisés par une capacité limite restreinte et servent d’ingénieurs écologiques en facilitant l’établissement de compétiteurs, prédateurs et opportunistes qui bénéficient de leur présence.

Late Pleistocene climate change and the global expansion of anatomically modern humans

The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317–1321]. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different approach to this problem; rather than relying on the appearance of fossils or archaeological evidence to determine arrival times in different parts of the world, we use patterns of genetic variation in modern human populations to determine the plausibility of past demographic parameters. We develop a spatially explicit model of the expansion of anatomically modern humans and use climate reconstructions over the past 120 ky based on the Hadley Centre global climate model HadCM3 to quantify the possible effects of climate on human demography. The combinations of demographic parameters compatible with the current genetic makeup of worldwide populations indicate a clear effect of climate on past population densities. Our estimates of this effect, based on population genetics, capture the observed relationship between current climate and population density in modern hunter–gatherers worldwide, providing supporting evidence for the realism of our approach. Furthermore, although we did not use any archaeological and anthropological data to inform the model, the arrival times in different continents predicted by our model are also broadly consistent with the fossil and archaeological records. Our framework provides the most accurate spatiotemporal reconstruction of human demographic history available at present and will allow for a greater integration of genetic and archaeological evidence.

Spatial prediction of rufous bristlebird habitat in a coastal heathland: a GIS-based approach

1. To develop a conservation management plan for a species, knowledge of its distribution and spatial arrangement of preferred habitat is essential. This is a difficult task, especially when the species of concern is in low   abundance. In south-western Victoria, Australia, populations of the rare rufous bristlebird Dasyornis broadbenti are threatened by fragmentation of suitable habitat. In order to improve the conservation status of this species, critical habitat requirements must be identified and a system of corridors must be established to link known populations. A predictive spatial model of rufous bristlebird habitat was developed in order to identify critical areas requiring preservation, such as corridors for dispersal.
2. Habitat models generated using generalized linear modelling techniques can assist in delineating the specific habitat requirements of a species. Coupled with geographic information system (GIS) technology, these models can be extrapolated to produce maps displaying the spatial configuration of suitable habitat.
3. Models were generated using logistic regression, with bristlebird presence or absence as the dependent variable and landscape variables, extracted from both GIS data layers and multispectral digital imagery, as the predictors. A multimodel inference approach based on Akaike’s information criterion was used and the resulting model was applied in a GIS to extrapolate predicted likelihood of occurrence across the entire area of concern. The predictive performance of the selected model was evaluated using the receiver operating characteristic (ROC) technique. A hierarchical partitioning protocol was used to identify the predictor variables most likely to influence variation in the dependent variable. Probability of species presence was used as an index of habitat suitability.
4. Negative associations between rufous bristlebird presence and  increasing elevation, 'distance to cree', 'distance to coast' and sun index were evident, suggesting a preference for areas relatively low in altitude, in close proximity to the coastal fringe and drainage lines, and receiving less direct sunlight. A positive association with increasing habitat complexity also suggested that this species prefers areas containing high vertical density of vegetation.
5. The predictive performance of the selected model was shown to be high (area under the curve 0·97), indicating a good fit of the model to the data. Hierarchical partitioning analysis showed that all the variables considered had significant  independent contributions towards explaining the variation in the dependent variable. The proportion of the total study area that was predicted as suitable habitat for the rufous bristlebird (using probability of occurrence at a ≥0·5 level ) was 16%.
6. Synthesis and applications. The spatial model clearly delineated areas predicted as highly suitable rufous bristlebird habitat, with evidence of potential corridors linking coastal and inland populations via gullies. Conservation of this species will depend on management actions that protect the critical habitats identified in the model. A multi-scale  approach to the modelling process is recommended whereby a spatially explicit model is first generated using landscape variables extracted from a GIS, and a second model at site level is developed using fine-scale habitat variables measured on the ground. Where there are constraints on the time and cost involved in measuring finer scale variables, the first step alone can be used for conservation planning.

A mathematical approach to simulate spatio-temporal patterns of an insect-pest, the corn rootworm Diabrotica speciosa (Coleoptera: Chrysomelidae) in intercropping systems

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Site Selection for Restoration Planning: A Protocol With Landscape and Legislation Based Alternatives

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.