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.

Développement d’un modèle centré sur l’individu des déplacements du caribou, du loup et de l’orignal, et de leurs interactions, en forêt boréale aménagée

Le caribou forestier est une espèce menacée au Canada, la principale hypothèse au déclin des populations étant l’intensification de la prédation provoquée par les perturbations anthropiques du paysage. Afin de faire face à cette situation, il est nécessaire d’étudier et comprendre l’impact de l’environnement sur les interactions prédateur-proies entre le caribou et le loup, ainsi qu’avec l’orignal, qui est sa principale proie alternative. Pour cela, cette thèse présente la conception d’un modèle centré sur l’individu des déplacements de ces trois espèces en fonction de leur environnement, dont résulteront les interactions prédateur-proies. Afin de permettre l’application de ce modèle sur de longues périodes, et donc pour un environnement changeant, une méthodologie a été développée, qui s’articule atour de deux aspects principaux. Tout d’abord, la notion de niveaux d’émergence est introduite, permettant d’ordonner les comportements observables du système selon leurs interdépendances, afin de choisir comme trait du modèle un com- portement correspondant au domaine d’applicabilité visé. Ordonner les comportements selon leurs niveaux d’émergence permet également d’identifier la redondance entre les patrons, qui peut être à l’origine d’un phénomène de sur-apprentissage lorsqu’ils sont utilisés lors de la calibration. Dans un second temps, un nouveau protocole pour la calibration et la validation du ou des traits choisis à l’aide des niveaux d’émergence, nommé réplication de système basé sur l’individu (Individual Based System Replication - IBSRtion) est également présenté. Ce protocole met l’emphase sur la modélisation directe, contrairement au principal protocole existant, la modélisation orientée patrons (Pattern Oriented Modelling - POM), et permet une approche empirique en générant artificiellement des données non disponibles ou ne pouvant être récoltées par des études de terrains. IBSRtion a également l’avantage de pouvoir être intégrée dans POM, afin de contribuer à la création d’une méthodologie universelle pour la conception de modèles centrés sur l’individu. Le processus de conception de ce modèle aura entre autre permis de faire une synthèse des connaissances et d’identifier certaines lacunes. Une étude visant à palier le manque de connaissances satisfaisantes sur les réponses comportementales à court-terme des proies face au risque de prédation a notamment permis d’observer que celles-ci sont une combinaison de comportements chroniques et éphémères, et que les mécanismes qui en sont à l’origine sont complexes et non-linéaires. Le résultat de ce travail est un modèle complexe utilisant de nombreux sous-modèles, et calibré de façon empirique, applicable à une grande variété d’environnements. Ce modèle a permis de tester l’impact de l’enfeuillement sur les relations prédateur-proies. Des simulations ont été effectuées pour différentes quantités d’enfeuillement, suivant deux configurations spatiales différentes. Les résultats de simulation suggèrent que des plans d’aménagement considérant également l’habitat de l’orignal pourraient être bénéfiques pour le caribou forestier, car ils permettraient d’améliorer la ségrégation spatiale entre les deux espèces, et donc entre le caribou et le loup. En le couplant avec un module de naissances et de morts naturelles ainsi qu’un modèle d’évolution du paysage, ce modèle permettra par la suite d’évaluer l’impact de plans d’aménagement forestier sur la viabilité des populations de caribou forestier.

Modélisation de l'influence de la fragmentation des habitats sur le risque de prédation chez le caribou forestier

Les populations du caribou forestier (Rangifer tarandus caribou) sont en déclin sur l’ensemble de leur aire de répartition en Amérique du Nord. Il s’avère que la prédation, amplifiée par l’exploitation forestière, en est la principale cause. Ce projet consiste à mettre en place un outil d'aide à la décision, permettant de modéliser les changements du risque de prédation chez le caribou forestier durant la succession forestière, et ce, selon différents scénarios d'aménagement forestier simulés sur la Côte-Nord du Québec, Canada. Ces scénarios, simulés de 2000 à 2150, sont caractérisés par (i) des coupes limitées aux blocs de protection et de remplacement, (ii) des coupes étendues sur le paysage, et finalement (iii) par l'absence de coupe dès 2000. Un modèle basé sur l'individu (MBI) permet de modéliser les déplacements simultanés du caribou forestier, de l'orignal (Alces alces) et du loup gris (Canis lupus) afin d'évaluer le risque de prédation selon les scénarios. En général, le risque de prédation est plus important lorsque les coupes sont limitées aux blocs de protection et de remplacement. En effet, il semble que ces blocs augmentent les probabilités de rencontre entre les proies et leurs prédateurs. Toutefois, certains résultats ne reflètent pas la littérature, ce qui montre la nécessité d'améliorer le MBI. Certaines recommandations visent finalement à bonifier ce MBI pour permettre l'analyse de la viabilité à long terme du caribou forestier en fonction de différents scénarios d'aménagement forestier.

Modélisation de répartition d’espèces aviaires et de feux en forêt boréale du Québec dans un contexte de changement climatique

Les changements climatiques prennent une importance grandissante dans l’étude des phénomènes spatiaux à grande échelle. Plusieurs experts affirment que les changements climatiques seront un des principaux moteurs de changement écologique dans les prochaines décennies et que leurs conséquences seront inévitables. Ces changements se manifesteront sur le milieu physique par la fonte des calottes glaciaires, le dégel du pergélisol, l’instabilité des versants montagneux en zone de pergélisol, l’augmentation de l’intensité, de la sévérité et de la fréquence des événements climatiques extrêmes tels les feux de forêt. Les changements climatiques se manifesteront aussi sur le milieu biologique, tel la modification de la durée de la saison végétative, l’augmentation des espèces exotiques invasives et les changements dans la distribution en espèces vivantes. Deux aspects sont couverts par cette étude : 1) les changements dans la répartition spatiale de 39 espèces d’oiseaux et 2) les modifications dans les patrons spatiaux des feux, en forêt boréale québécoise, tous deux dans l’horizon climatique de 2100. Une approche de modélisation statistique démontre que la répartition spatiale des oiseaux de la forêt boréale est fortement liée à des variables bioclimatiques (R2adj = 0.53). Ces résultats permettent d’effectuer des modélisations bioclimatiques pour le gros-bec errant et la mésange à tête noire quivoient une augmentation de la limite nordique de distribution de l’espèce suivant l’intensité du réchauffement climatique. Finalement, une modélisation spatialement explicite par automate cellulaire permet de démontrer comment les changements climatiques induiront une augmentation dans la fréquence de feux de forêt et dans la superficie brûlée en forêt boréale du Québec.

The impact of buffer zone size and management on illegal extraction, park protection and enforcement

Many protected areas or parks in developing countries have buffer zones at their boundaries to achieve the dual goals of protecting park resources and providing resource benefits to neighbouring people. Despite the prevalence of these zoning policies, few behavioural models of people’s buffer zone use inform the sizing and management of those zones. This paper uses a spatially explicit resource extraction model to examine the impact of buffer zone size and management on extraction by local people, both legal and illegal, and the impact of that extraction on forest quality in the park’s core and buffer zone. The results demonstrate trade-offs between the level of enforcement, the size of a buffer zone, and the amount of illegal extraction in the park; and describe implications for “enrichment” of buffer zones and evaluating patterns of forest degradation.

Effects of noise and by-catch on a Danish harbour porpoise population

Ships and wind turbines generate noise, which can have a negative impact on marine mammal populations by scaring animals away. Effective modelling of how this affects the populations has to take account of the location and timing of disturbances. Here we construct an individual-based model of harbour porpoises in the Inner Danish Waters. Individuals have their own energy budgets constructed using established principles of physiological ecology. Data are lacking on the spatial distribution of food which is instead inferred from knowledge of time-varying porpoise distributions. The model produces plausible patterns of population dynamics and matches well the age distribution of porpoises caught in by-catch. It estimates the effect of existing wind farms as a 10% reduction in population size when food recovers fast (after two days). Proposed new wind farms and ships do not result in further population declines. The population is however sensitive to variations in mortality resulting from by-catch and to the speed at which food recovers after being depleted. If food recovers slowly the effect of wind turbines becomes negligible, whereas ships are estimated to have a significant negative impact on the population. Annual by-catch rates ≥10% lead to monotonously decreasing populations and to extinction, and even the estimated by-catch rate from the adjacent area (approximately 4.1%) has a strong impact on the population. This suggests that conservation efforts should be more focused on reducing by-catch in commercial gillnet fisheries than on limiting the amount of anthropogenic noise. Individual-based models are unique in their ability to take account of the location and timing of disturbances and to show their likely effects on populations. The models also identify deficiencies in the existing database and can be used to set priorities for future field research.

Fragmentation drives tropical forest fragments to early successional states: A modelling study for Brazilian Atlantic forests

Land use leads to massive habitat destruction and fragmentation in tropical forests. Despite its global dimensions the effects of fragmentation on ecosystem dynamics are not well understood due to the complexity of the problem. We present a simulation analysis performed by the individual-based model FORMIND. The model was applied to the Brazilian Atlantic Forest, one of the world`s biodiversity hot spots, at the Plateau of Sao Paulo. This study investigates the long-term effects of fragmentation processes on structure and dynamics of different sized remnant tropical forest fragments (1-100 ha) at community and plant functional type (PFT) level. We disentangle the interplay of single effects of different key fragmentation processes (edge mortality, increased mortality of large trees, local seed loss and external seed rain) using simulation experiments in a full factorial design. Our analysis reveals that particularly small forest fragments below 25 ha suffer substantial structural changes, biomass and biodiversity loss in the long term. At community level biomass is reduced up to 60%. Two thirds of the mid- and late-successional species groups, especially shade-tolerant (late successional climax) species groups are prone of extinction in small fragments. The shade-tolerant species groups were most strongly affected; its tree number was reduced more than 60% mainly by increased edge mortality. This process proved to be the most powerful of those investigated, explaining alone more than 80% of the changes observed for this group. External seed rain was able to compensate approximately 30% of the observed fragmentation effects for shade-tolerant species. Our results suggest that tropical forest fragments will suffer strong structural changes in the long term, leading to tree species impoverishment. They may reach a new equilibrium with a substantially reduced subset of the initial species pool, and are driven towards an earlier successional state. The natural regeneration potential of a landscape scattered with forest fragments appears to be limited, as external seed rain is not able to fully compensate for the observed fragmentation-induced changes. Our findings suggest basic recommendations for the management of fragmented tropical forest landscapes. (C) 2011 Elsevier B.V. All rights reserved.

Formação de teias tróficas e sua resistência à introdução e exclusão de espécies: propriedades resultantes de um modelo computacional baseado no indivíduo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Convergence results for stochastic particle systems with social interaction

We consider stochastic individual-based models for social behaviour of groups of animals. In these models the trajectory of each animal is given by a stochastic differential equation with interaction. The social interaction is contained in the drift term of the SDE. We consider a global aggregation force and a short-range repulsion force. The repulsion range and strength gets rescaled with the number of animals N. We show that for N tending to infinity stochastic fluctuations disappear and a smoothed version of the empirical process converges uniformly towards the solution of a nonlinear, nonlocal partial differential equation of advection-reaction-diffusion type. The rescaling of the repulsion in the individual-based model implies that the corresponding term in the limit equation is local while the aggregation term is non-local. Moreover, we discuss the effect of a predator on the system and derive an analogous convergence result. The predator acts as an repulsive force. Different laws of motion for the predator are considered.

Can we infer plant facilitation from remote sensing? a test across global drylands

Facilitation is a major force shaping the structure and diversity of plant communities in terrestrial ecosystems. Detecting positive plant–plant interactions relies on the combination of field experimentation and the demonstration of spatial association between neighboring plants. This has often restricted the study of facilitation to particular sites, limiting the development of systematic assessments of facilitation over regional and global scales. Here we explore whether the frequency of plant spatial associations detected from high-resolution remotely sensed images can be used to infer plant facilitation at the community level in drylands around the globe. We correlated the information from remotely sensed images freely available through Google Earth with detailed field assessments, and used a simple individual-based model to generate patch-size distributions using different assumptions about the type and strength of plant–plant interactions. Most of the patterns found from the remotely sensed images were more right skewed than the patterns from the null model simulating a random distribution. This suggests that the plants in the studied drylands show stronger spatial clustering than expected by chance. We found that positive plant co-occurrence, as measured in the field, was significantly related to the skewness of vegetation patch-size distribution measured using Google Earth images. Our findings suggest that the relative frequency of facilitation may be inferred from spatial pattern signals measured from remotely sensed images, since facilitation often determines positive co-occurrence among neighboring plants. They pave the road for a systematic global assessment of the role of facilitation in terrestrial ecosystems. Read More: http://www.esajournals.org/doi/10.1890/14-2358.1

Modelling the impact of deferring HCV treatment on liver-related complications in HIV coinfected men who have sex with men

BACKGROUND AND AIMS Hepatitis C (HCV) is a leading cause of morbidity and mortality in people who live with HIV. In many countries, access to direct acting antiviral agents to treat HCV is restricted to individuals with advanced liver disease (METAVIR stage F3 or F4). Our goal was to estimate the long term impact of deferring HCV treatment for men who have sex with men (MSM) who are coinfected with HIV and often have multiple risk factors for liver disease progression. METHODS We developed an individual-based model of liver disease progression in HIV/HCV coinfected men who have sex with men. We estimated liver-related morbidity and mortality as well as the median time spent with replicating HCV infection when individuals were treated in liver fibrosis stages F0, F1, F2, F3 or F4 on the METAVIR scale. RESULTS The percentage of individuals who died of liver-related complications was 2% if treatment was initiated in F0 or F1. It increased to 3% if treatment was deferred until F2, 7% if it was deferred until F3 and 22% if deferred until F4. The median time individuals spent with replicating HCV increased from 5 years if treatment was initiated in F2 to almost 15 years if it was deferred until F4. CONCLUSIONS Deferring HCV therapy until advanced liver fibrosis is established could increase liver-related morbidity and mortality in HIV/HCV coinfected individuals, and substantially prolong the time individuals spend with replicating HCV infection.

Conservation of freshwater thermal habitats for Pacific salmon in a changing climate

Thesis (Ph.D.)--University of Washington, 2016-06

Do harvest refuges buffer kangaroos against evolutionary responses to selective harvesting?

There is a wealth of literature documenting a directional change of body size in heavily harvested populations. Most of this work concentrates on aquatic systems, but terrestrial populations are equally at risk. This paper explores the capacity of harvest refuges to counteract potential effects of size-selective harvesting on the allele frequency,of populations. We constructed a stochastic, individual-based model parameterized with data on red kangaroos. Because we do not know which part of individual growth would change in the course of natural selection, we explored the effects of two alternative models of individual growth in which alleles affect either the growth rate or the maximum size. The model results show that size-selective harvesting can result in significantly smaller kangaroos for a given age when the entire population is subject to harvesting. In contrast, in scenarios that include dispersal from harvest refuges, the initial allele frequency remains virtually unchanged.

Intake rates and the functional response in shorebirds (Charadriiformes) eating macro-invertebrates

As field determinations take much effort, it would be useful to be able to predict easily the coefficients describing the functional response of free-living predators, the function relating food intake rate to the abundance of food organisms in the environment. As a means easily to parameterise an individual-based model of shorebird Charadriiformes populations, we attempted this for shorebirds eating macro-invertebrates. Intake rate is measured as the ash-free dry mass (AFDM) per second of active foraging; i.e. excluding time spent on digestive pauses and other activities, such as preening. The present and previous studies show that the general shape of the functional response in shorebirds eating approximately the same size of prey across the full range of prey density is a decelerating rise to a plateau, thus approximating the Holling type 11 ('disc equation') formulation. But field studies confirmed that the asymptote was not set by handling time, as assumed by the disc equation, because only about half the foraging time was spent in successfully or unsuccessfully attacking and handling prey, the rest being devoted to searching. A review of 30 functional responses showed that intake rate in free-living shorebirds varied independently of prey density over a wide range, with the asymptote being reached at very low prey densities (< 150/m(-2)). Accordingly, most of the many studies of shorebird intake rate have probably been conducted at or near the asymptote of the functional response, suggesting that equations that predict intake rate should also predict the asymptote. A multivariate analysis of 468 'spot' estimates of intake rates from 26 shorebirds identified ten variables, representing prey and shorebird characteristics, that accounted for 81 % of the variance in logarithm-transformed intake rate. But four-variables accounted for almost as much (77.3 %), these being bird size, prey size, whether the bird was an oystercatcher Haematopus ostralegus eating mussels Mytilus edulis, or breeding. The four variable equation under-predicted, on average, the observed 30 estimates of the asymptote by 11.6%, but this discrepancy was reduced to 0.2% when two suspect estimates from one early study in the 1960s were removed. The equation therefore predicted the observed asymptote very successfully in 93 % of cases. We conclude that the asymptote can be reliably predicted from just four easily measured variables. Indeed, if the birds are not breeding and are not oystercatchers eating mussels, reliable predictions can be obtained using just two variables, bird and prey sizes. A multivariate analysis of 23 estimates of the half-asymptote constant suggested they were smaller when prey were small but greater when the birds were large, especially in oystercatchers. The resulting equation could be used to predict the half-asymptote constant, but its predictive power has yet to be tested. As well as predicting the asymptote of the functional response, the equations will enable research workers engaged in many areas of shorebird ecology and behaviour to estimate intake rate without the need for conventional time-consuming field studies, including species for which it has not yet proved possible to measure intake rate in the field.

Accounting for management costs in sensitivity analyses of matrix population models

Traditional sensitivity and elasticity analyses of matrix population models have been used to p inform management decisions, but they ignore the economic costs of manipulating vital rates. For exam le, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously, These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency.