Modeling Habitat Split: Landscape and Life History Traits Determine Amphibian Extinction Thresholds

Habitat split is a major force behind the worldwide decline of amphibian populations, causing community change in richness and species composition. In fragmented landscapes, natural remnants, the terrestrial habitat of the adults, are frequently separated from streams, the aquatic habitat of the larvae. An important question is how this landscape configuration affects population levels and if it can drive species to extinction locally. Here, we put forward the first theoretical model on habitat split which is particularly concerned on how split distance - the distance between the two required habitats - affects population size and persistence in isolated fragments. Our diffusive model shows that habitat split alone is able to generate extinction thresholds. Fragments occurring between the aquatic habitat and a given critical split distance are expected to hold viable populations, while fragments located farther away are expected to be unoccupied. Species with higher reproductive success and higher diffusion rate of post-metamorphic youngs are expected to have farther critical split distances. Furthermore, the model indicates that negative effects of habitat split are poorly compensated by positive effects of fragment size. The habitat split model improves our understanding about spatially structured populations and has relevant implications for landscape design for conservation. It puts on a firm theoretical basis the relation between habitat split and the decline of amphibian populations. © 2013 Fonseca et al.

Modelling the human accommodation system using finite element analysis

The human accommodation system has been extensively examined for over a century, with a particular focus on trying to understand the mechanisms that lead to the loss of accommodative ability with age (Presbyopia). The accommodative process, along with the potential causes of presbyopia, are disputed; hindering efforts to develop methods of restoring accommodation in the presbyopic eye. One method that can be used to provide insight into this complex area is Finite Element Analysis (FEA). The effectiveness of FEA in modelling the accommodative process has been illustrated by a number of accommodative FEA models developed to date. However, there have been limitations to these previous models; principally due to the variation in data on the geometry of the accommodative components, combined with sparse measurements of their material properties. Despite advances in available data, continued oversimplification has occurred in the modelling of the crystalline lens structure and the zonular fibres that surround the lens. A new accommodation model was proposed by the author that aims to eliminate these limitations. A novel representation of the zonular structure was developed, combined with updated lens and capsule modelling methods. The model has been designed to be adaptable so that a range of different age accommodation systems can be modelled, allowing the age related changes that occur to be simulated. The new modelling methods were validated by comparing the changes induced within the model to available in vivo data, leading to the definition of three different age models. These were used in an extended sensitivity study on age related changes, where individual parameters were altered to investigate their effect on the accommodative process. The material properties were found to have the largest impact on the decline in accommodative ability, in particular compared to changes in ciliary body movement or zonular structure. Novel data on the importance of the capsule stiffness and thickness was also established. The new model detailed within this thesis provides further insight into the accommodation mechanism, as well as a foundation for future, more detailed investigations into accommodation, presbyopia and accommodative restoration techniques.

A succession of theories : purging redundancy from disturbance theory

The topics of succession and post-disturbance ecosystem recovery have a long and convoluted history. There is extensive redundancy within this body of theory, which has resulted in confusion, and the links among theories have not been adequately drawn. This review aims to distil the unique ideas from the array of theory related to ecosystem change in response to disturbance. This will help to reduce redundancy, and improve communication and understanding between researchers. We first outline the broad range of concepts that have developed over the past century to describe community change in response to disturbance. The body of work spans overlapping succession concepts presented by Clements in 1916, Egler in 1954, and Connell and Slatyer in 1977. Other theories describing community change include state and transition models, biological legacy theory, and the application of functional traits to predict responses to disturbance. Second, we identify areas of overlap of these theories, in addition to highlighting the conceptual and taxonomic limitations of each. In aligning each of these theories with one another, the limited scope and relative inflexibility of some theories becomes apparent, and redundancy becomes explicit. We identify a set of unique concepts to describe the range of mechanisms driving ecosystem responses to disturbance. We present a schematic model of our proposed synthesis which brings together the range of unique mechanisms that were identified in our review. The model describes five main mechanisms of transition away from a post-disturbance community: (i) pulse events with rapid state shifts; (ii) stochastic community drift; (iii) facilitation; (iv) competition; and (v) the influence of the initial composition of a post-disturbance community. In addition, stabilising processes such as biological legacies, inhibition or continuing disturbance may prevent a transition between community types. Integrating these six mechanisms with the functional trait approach is likely to improve the predictive capacity of disturbance theory. Finally, we complement our discussion of theory with a case study which emphasises that many post-disturbance theories apply simultaneously to the same ecosystem. Using the well-studied mountain ash (Eucalyptus regnans) forests of south-eastern Australia, we illustrate phenomena that align with six of the theories described in our model of rationalised disturbance theory. We encourage further work to improve our schematic model, increase coverage of disturbance-related theory, and to show how the model may link to, or integrate with, other domains of ecological theory.

Reptile responses to fire and the risk of post-disturbance sampling bias

Altered fire regimes are a driver of biodiversity decline. To plan effective management, we need to know how species are influenced by fire and to develop theory describing fire responses. Animal responses to fire are usually measured using methods that rely on animal activity, but animal activity may vary with time since fire, potentially biasing results. Using a novel approach for detecting bias in the pit-fall trap method, we found that leaf-litter dependent reptiles were more active up to 6 weeks after fire, giving a misleading impression of abundance. This effect was not discovered when modelling detectability with zero-inflated binomial models. Two species without detection bias showed early-successional responses to time since fire, consistent with a habitat-accommodation succession model. However, a habitat specialist did not have the predicted low abundance after fire due to increased post-fire movement and non-linear recovery of a key habitat component. Interactions between fire and other processes therefore must be better understood to predict reptile responses to changing fire-regimes. We conclude that there is substantial bias when trapping reptiles after fire, with species that are otherwise hard to detect appearing to be abundant. Studies that use a survey method based on animal activity such as bird calls or animal movements, likely face a similar risk of bias when comparing recently-disturbed with control sites.

A surveillance strategy for invasive species of concern in deepwater habitats of the Northwestern Hawaiian Islands

This report describes a surveillance strategy to detect deepwater invasive species in the Northwestern Hawaiian Islands. A need for this strategy was identified in the Papahānaumokuākea Marine National Monument Management Plan and the Monument’s Draft Natural Resources Science Plan. This strategy focuses on detecting two species of concern, the octocoral Carijoa riisei and the red alga Hypnea musciformis. Most research on invasive species in the Hawaiian archipelago has focused on shallow water habitats within the limits of conventional SCUBA (0-30 m). Deeper habitats such as mesophotic reefs are much more difficult to access and consequently little is known about the distribution of deepwater invasive species or their impacts. Recent deepwater (>30 m) sightings of H. musciformis and C. riisei, in and near NWHI, respectively, have prompted a call for further research and surveillance of invasive species in deepwater habitats. This report compiles the most up to date information about these two species of concern in deepwater habitats. A literature search and conversations with subject matter experts was used to identify their current distribution, preferred habitat types, optimal detection methods and ways to efficiently sample the vast extent of NWHI. The proposed sampling strategy prioritizes survey effort where C. riisei and H. musciformis are most likely to be found. At coarse spatial scales (tens to hundreds of kilometers), opportunistic observations and distance from the Main Hawaiian Islands, a principal propagule source, are used to identify high-risk islands and banks. At fine spatial scales (meters to tens of kilometers) a habitat suitability model was developed to identify high-risk habitats. The habitat suitability model focused on habitat preferences of C. riisei, since the species is well studied and adequate data exists to map habitats. There was insufficient information to identify suitable habitat for H. muscifomis. Habitat preferences for the algae are poorly understood and there is a lack of data at relevant spatial scales to map those preferences which are known. The principal habitats identified by the habitat suitability model were ledges and the edges of rugose coral reefs, where the shade loving octocoral would likely be found. Habitat suitability maps were developed for seven atolls and banks to aid in survey site selection. The protocol relied on technical divers to conduct visual surveys of benthic habitats. It was developed to increase the efficiency of surveys, maximize the probability of detection, identify important information relevant to future surveys and standardize results. The strategy, model and protocol were tested during a field mission in 2009 at several atolls and islands in NWHI. The field mission did not detect any invasive species among deepwater habitats and much was learned to improve future surveys. Data gaps and improvements are discussed.

溪流大型底栖动物栖息地适合度模型的构建与河道内环境流量研究——以三峡库区香溪河为例

基于对香溪河河流生态系统的多年研究,以该流域河流大型底栖动物最优势类群四节蜉为指示生物,建立了我国大陆地区第一个基于长期的连续的野外现场实测数据的水生生物栖息地适合度模型(habitat suitability model,HSM).为保护河流生态系统结构和功能的完整性,文中将河道内环境流量分为3个层次,即河道内最小需水量、最小环境流量和适宜环境流量,并利用水文法和加权可利用面积法(weighted usable area,WUA)分别构建了这3个层次的河道内环境流量的计算模型.结果表明:香溪河的最小需水

Applying species distribution modelling to identify areas of high conservation value for endangered species: A case study using Margaritifera margaritifera (L.)

The development and implementation of a population supplementation and restoration plan for any endangered species should involve an understanding of the species’ habitat requirements prior to the release of any captive bred individuals. The freshwater pearl mussel, Margaritifera margaritifera, has undergone dramatic declines over the last century and is now globally endangered. In Northern Ireland, the release of captive bred individuals is being used to support wild populations and repatriate the species in areas where it once existed. We employed a combination of maximum entropy modelling (MAXENT) and Generalized Linear Mixed Models (GLMM) to identify ecological parameters necessary to support wild populations using GIS-based landscape scale and ground-truthed habitat scale environmental parameters. The GIS-based landscape scale model suggested that mussel occurrence was associated with altitude and soil characteristics including the carbon, clay, sand, and silt content. Notably, mussels were associated with a relatively narrow band of variance indicating that M. margaritifera has a highly specific landscape niche. The ground-truthed habitat scale model suggested that mussel occurrence was associated with stable consolidated substrates, the extent of bankside trees, presence of indicative macrophyte species and fast flowing water. We propose a three phase conservation strategy for M. margaritifera identifying suitable areas within rivers that (i) have a high conservation value yet needing habitat restoration at a local level, (ii) sites for population supplementation of existing populations and (iii) sites for species reintroduction to rivers where the mussel historically occurred but is now locally extinct. A combined analytical approach including GIS-based landscape scale and ground-truthed habitat scale models provides a robust method by which suitable release sites can be identified for the population supplementation and restoration of an endangered species. Our results will be highly influential in the future management of M. margaritifera in Northern Ireland.

Sei whale (Balaenoptera borealis) ecology and management in the North Atlantic

Tese de Doutoramento em Ciências do Mar, especialidade em Ecologia Marinha.

Échantillonnage et modélisation de l’habitat des communautés de poissons de rivière des basses Laurentides

Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices.

Effectiveness of the development of internal auditing in the Victorian Public Service (1982-1987)

The selection of an inappropriate regime by policy makers can thwart the effective implementation of public policy and lead to implementation failure. Competing values in the implementation process have a significant impact on the results of implementation, and the regime selected for implementation implies the choice of one value over another. Stoker has argued that on the one hand central leadership is valued for consistency, benefits of scale, co-ordination and cost sharing (instrumental model); and on the other, diffuse authority is valued as knowledge is particular and situational, and the task of analysis is to understand the problems, perspectives and interactions of implementation participants at the contact point between public programs and their clients (accommodation model). This study examines the implementation regime chosen by the Victorian Government for the introduction of a modern internal auditing function into the Victorian Public Service, using the Bureau of Internal Audit within its Department of Management and Budget. The selection of the Department of Management and Budget for the introduction of Internal Audit as a managerial accountability mechanism indicates that the instrumental model was held by the Victorian Government to be the most important in implementation. It is argued that use of a top-down central agency leadership approach resulted in implementation failure. Three propositions suggesting the mechanisms by which this result is brought about are examined: that lack of co-ordinated planning at the outset will result in inadequate definition of client needs as part of policy formulation; that intraorganisational conflict during the implementation success, as individual participants are likely to exercise their veto; and the increasing the number of participants contributes to complexity, so that they should only be involved in implementation when their presence is absolutely required. It is argued that the essential task of implementation is to create an environment where participants are likely to co-operate to achieve predetermined public policy goals; and that the introduction of a modern internal auditing approach into the Victorian Public Service required a more participatory implementation regime in order to facilitate policy outcomes and prevent implementation failure. It is also argued that the dominance of economic reform over accountability in Victoria restricted the ability of the Bureau of Internal Audit to implement change to internal audit practices within Victorian Government departments. The selection of an instrumental model of implementation by the Department of Management and Budget is examined in the context of the environment that existed in Victoria between 1982-1987; and while some of the values which Stoker associates with the top-down approach to policy making were observed, an alternative view to the development of internal auditing in the Victorian Public Service can be sustained.

Repeatable sediment associations of burrowing bivalves across six European tidal flat systems

Burrowing bivalves are associated with particular sediment types within sedimentary systems. The degree to which bivalve sediment associations are repeatable across systems has seldom been investigated. To investigate whether such repeatability exists across tidal flats, we compared adult and juvenile distributions of 3 bivalve species (Cerastoderma edule, Scrobicularia plana, Macoma balthica) across 6 European tidal flats. Across systems, the adult bivalves showed fairly repeatable distributions, with C. edule occurring in sandy sediments and M. balthica and S. plana occurring in muddy sediments. Exceptions were observed in systems composed primarily of muddy sediments (Aiguillon Bay and Marennes-Oléron Bay) and the Dutch Wadden Sea. Interestingly, juveniles and adults of C. edule and S. plana showed similar distributions across systems. M. balthica juveniles and adults showed habitat separation in 3 of the 6 studied systems; in 2 of these, it has been shown previously that juvenile M. balthica settle in mud at high tidal levels and migrate to lower sandier flats later in life. The high occurrence of juvenile M. balthica towards high sandy flats in Mont Saint-Michel Bay suggests that juveniles might choose high tidal flats rather than muddy sediments per se. A repeatable association in adults and juveniles with respect to sediment could suggest that juveniles actively settle in the proximity of the adults and/or that juveniles settling away from the adults incur a higher mortality due to either predation, physiological stress, or other factors.

Testing the influence of survey method for building species distribution models of marine fishes

Accurate estimates of fish species occurrence are important to any species’ assessments and habitat suitability model. However, surveys of marine fishes are often biased by method. Surveys of marine fishes are often biased by method. Such bias could influence the interpretation of any habitat suitability model. With increasing emphasis on non-destructive sampling, underwater video techniques are commonly used without a thorough understanding of their advantages and disadvantages. This study compared data collected from baited remote underwater stereo-video systems and towed-video systems to provide occurrence data to develop habitat suitability models of nine temperate marine fishes. While numerous studies have compared modelling approaches in terms of model performance (i.e. via AUC or Kappa) the point of this paper was to highlight how very sensiblelooking, well-performing (based on AUC) models can provide different predictions of habitat suitability depending on which dataset is used.

Predicting avian distributions to evaluate spatiotemporal overlap with locust control operations in eastern Australia.

Locusts and grasshoppers cause considerable economic damage to agriculture worldwide. The Australian Plague Locust Commission uses multiple pesticides to control locusts in eastern Australia. Avian exposure to agricultural pesticides is of conservation concern, especially in the case of rare and threatened species. The aim of this study was to evaluate the probability of pesticide exposure of native avian species during operational locust control based on knowledge of species occurrence in areas and times of application. Using presence-absence data provided by the Birds Australia Atlas for 1998 to 2002, we developed a series of generalized linear models to predict avian occurrences on a monthly basis in 0.5 degrees grid cells for 280 species over 2 million km2 in eastern Australia. We constructed species-specific models relating occupancy patterns to survey date and location, rainfall, and derived habitat preference. Model complexity depended on the number of observations available. Model output was the probability of occurrence for each species at times and locations of past locust control operations within the 5-year study period. Given the high spatiotemporal variability of locust control events, the variability in predicted bird species presence was high, with 108 of the total 280 species being included at least once in the top 20 predicted species for individual space-time events. The models were evaluated using field surveys collected between 2000 and 2005, at sites with and without locust outbreaks. Model strength varied among species. Some species were under- or over-predicted as times and locations of interest typically did not correspond to those in the prediction data set and certain species were likely attracted to locusts as a food source. Field surveys demonstrated the utility of the spatially explicit species lists derived from the models but also identified the presence of a number of previously unanticipated species. These results also emphasize the need for special consideration of rare and threatened species that are poorly predicted by presence-absence models. This modeling exercise was a useful a priori approach in species risk assessments to identify species present at times and locations of locust control applications, and to discover gaps in our knowledge and need for further focused data collection.

Feasibility of the Reintroduction of Wolves in Maine: a GIS Study

The eastern timber wolf (Canis lupus lycaon) once inhabited Maine, as well as the rest of the eastern United States and southern Canada. As a result of human land use and widespread extermination campaigns, wolf numbers dramatically decreased, and by the early twentieth century, no wolves remained in Maine. As large carnivorous and territorial mammals, wolves require contiguous undeveloped areas with abundant prey. This project is a feasibility study that identifies the areas in Maine that are suitable for the reintroduction of wolves. We used GIS modeling to identify contiguous forested areas over 1,000 km2, calculate road and population density, and map the presence or absence of prey throughout the state. These variables were combined in a habitat suitability model to determine the location and amount of suitable wolf habitat in Maine. The northwestern part of the state appears most suitable for wolf reintroduction as it is relatively undeveloped with low road and population densities. There is also a smaller isolated area in Washington County that might be suitable, but further investigation is required.