Climate change refugia for terrestrial biodiversity

AbstractWe are currently facing the likelihood of severe climate change before the close of the century. In the face of such a global driver of species loss, we urgently need to identify refugia that will shelter species from the worst impacts of climate change. This  will be  a critical component of successful conservation and management of our biodiversity. Despite this, little is known about how best to identify refugia in the landscape, and the practical strategies needed to identify, protect and expand refugia are just beginning to be developed. Identifying refugia that will protect most species, or large numbers of species, remains a complex and daunting endeavour due to the large variations in climatic and biotic requirements of species. A first step to identifying refugia for biodiversity across Australia is to locate the areas which show the least change into the future (i.e. the most environmentally stable), particularly along axes of temperature and precipitation. The second and crucial step is to identify the areas that will retain most of their biodiversity and provide opportunities for additional species to relocate to into the future. Using these approaches in this project, we take the first steps to identify refugial areas across the Australian continent under contemporary climate change scenarios. We find that the southern and eastern parts of the continent contain refugia that many species will retreat to over the next 75 years, but that the current reserve system may be inadequate to allow species to shift to and persist in these areas. Disturbingly, we also find that there is a large portion of the Australian vertebrate community for which adequate natural refugia do not appear to exist. Fine-scaled regional analyses will be required to clarify these broad findings, and we examine a number of case studies demonstrating how these regional analyses might best proceed. Lessons learnt across the multiple techniques employed in this study include:1. High elevation areas are important refugia.2. Tasmania and the east coast of mainland Australia contain most of the key areas for refugia into the future.3. Results are dependent on which objectives, techniques, taxonomic groups and climate scenarios are used.Please cite this report as:Reside, AE, VanDerWal, J, Phillips, B, Shoo, LP, Rosauer, DF, Anderson, BA, Welbergen, J, Moritz, C, Ferrier, S, Harwood, TD, Williams, KJ, Mackey, B, Hugh, S, Williams, SE 2013 Climate change refugia for terrestrial biodiversity: Defining areas that promote species persistence and ecosystem resilience in the face of global climate change, National Climate Change Adaptation Research Facility, Gold Coast, pp. 216We are currently facing the likelihood of severe climate change before the close of the century. In the face of such a global driver of species loss, we urgently need to identify refugia that will shelter species from the worst impacts of climate change. This  will be  a critical component of successful conservation and management of our biodiversity. Despite this, little is known about how best to identify refugia in the landscape, and the practical strategies needed to identify, protect and expand refugia are just beginning to be developed. Identifying refugia that will protect most species, or large numbers of species, remains a complex and daunting endeavour due to the large variations in climatic and biotic requirements of species. A first step to identifying refugia for biodiversity across Australia is to locate the areas which show the least change into the future (i.e. the most environmentally stable), particularly along axes of temperature and precipitation. The second and crucial step is to identify the areas that will retain most of their biodiversity and provide opportunities for additional species to relocate to into the future. Using these approaches in this project, we take the first steps to identify refugial areas across the Australian continent under contemporary climate change scenarios. We find that the southern and eastern parts of the continent contain refugia that many species will retreat to over the next 75 years, but that the current reserve system may be inadequate to allow species to shift to and persist in these areas. Disturbingly, we also find that there is a large portion of the Australian vertebrate community for which adequate natural refugia do not appear to exist. Fine-scaled regional analyses will be required to clarify these broad findings, and we examine a number of case studies demonstrating how these regional analyses might best proceed. Lessons learnt across the multiple techniques employed in this study include:High elevation areas are important refugia.Tasmania and the east coast of mainland Australia contain most of the key areas for refugia into the future.Results are dependent on which objectives, techniques, taxonomic groups and climate scenarios are used

Scaling the benefits of agri-environment schemes for biodiversity conservation in agricultural landscapes

Agricultural expansion and intensification are major causes of biodiversity loss. To mitigate this, billions of dollars are committed by governments annually to agri-environment conservation schemes aiming to engage landholders, often at large (continental) scales, in sustainable farming practices. While some schemes have been successful in addressing the social and policy elements of farmland conservation, assessments of their effectiveness for conserving biodiversity in farming systems is lacking. Recent studies have demonstrated that the effectiveness of programs is influenced by a number of scale-dependent factors that may influence biodiversity response but remain poorly understood. Specifically, local- and landscape-scale management actions can influence biodiversity response, and hence the effectiveness of programs, but this aspect has been little explored. My research aimed to identify ways to enhance the effectiveness of agri-environmental schemes through a better understanding of scale-related management effects on herpetofauna (reptiles and amphibians); a critical and declining vertebrate group severely threatened by agricultural development. First, I summarise current knowledge of local- and landscape-scale factors influencing agri-environment scheme effectiveness for biodiversity, highlighting novel research priorities relevant to practitioners (Paper #1). I then conducted baseline herpetofaunal surveys at 325 treatment/control sites within a critically endangered remnant woodland targeted under a large-scale (>1000 km; 172,000 km2) agri-environment scheme; the Australian Government Environmental Stewardship Programme (Paper #2). This is the most extensive xii herpetofaunal survey conducted to date throughout this woodland ecosystem. I found high levels of spatial variation in species detected across the study area; with large differences in species richness between biogeographic regions but not between treatment and control sites. Second, I conducted multi-season vegetation, habitat structural and herpetofaunal surveys at each of the 325 sites to identify key habitat variables (Paper #3) and management activities (livestock grazing; Paper #4) at local levels. I found that habitat use varied over biogeographically distinct regions, suggesting schemes that consider regional differences in local habitat preferences may be more effective than schemes that ignore such variation. Furthermore, past and present livestock grazing influenced herpetofaunal populations, but in complex and varied ways that have previously been overlooked. Finally, I collected data on land-use surrounding the remnant woodland sites and its influence on reptile movement to quantify the impact of landscape modification on community structure (Paper #5) and habitat connectivity (Paper #6). Landscape modification resulted in a change in community composition and a loss of species co-occurrence, but not a loss of species. Importantly, changes in co-occurrence pattern were complex and allowed for a novel classification of species susceptibility to the threat of land modification. Additionally, I found that pasture height and crop-sowing direction influenced reptile movements within the agricultural matrix, and hence must be considered where connectivity is a goal of agri-environment investment (Paper #6). xiii Collectively, my research identifies several outcomes that strengthen the theoretical and applied opportunities for enhancing effectiveness of agri-environment schemes. These include: (1) An improved knowledge of the environmental and anthropogenic drivers of the distributions of herpetofauna (2) Incorporating ecological effects operating at different scales can help agri-environment schemes to become more effective (3) A range of management actions is required to meet the conservation requirements for herpetofauna (4) Large occupancy datasets should be collected to extend observations of ecological patterns to identify underlying ecological processes (5) Management recommendations can be adaptively integrated into existing agri-environment schemes; as well as in new schemes. Such considerations are of broad relevance for the design of large-scale conservation strategies targeting the conservation of biodiversity across agricultural landscapes

INTEGRATED MODELING OF LAND USE AND CLIMATE CHANGE IMPACTS ON MULTISCALE ECOSYSTEMS OF CENTRAL AFRICAN WATERSHEDS

Assessment and management of ecosystem services demands diverse knowledge of the system components. Land use change occurring mainly through deforestation, expansion of agriculture and unregulated extraction of natural resources are the greatest challenges of the Congo basin and yet is central to supporting over 100 million people. This study undertook to implement an integrated modeling of multiscale ecosystems of central African watersheds and model the impact of anthropogenic factors on elephant population in Greater Virunga landscape. The study was conducted at varied scales, regional, landscape, and community. Regional study included watershed analysis and hydrological assessment using remotely sensed data implemented in Geographical information System. Species distribution modeling using generalized linear models using presence only and pseudo absence data was also done at regional scale. The major findings were that ecosystem services for the Congo basin are spatially varied and there are significant differences in their distribution of ecosystem services at a subwatershed level three and six and the distribution of endangered and threatened species is more concentrated in the central part of the basin and most of these species occur mainly inside protected areas. Poaching and sustained civil wars were the biggest threat to elephant conservation in the region. Improvement in law enforcement, monitoring, and increasing household incomes for communities living adjacent to protected areas would help to reduce the impact of poaching on elephant population dynamics. Climate change did not show immediate direct impacts on the elephant population, but thermal and latent heat effects could be occurring. A change in habitat, however, showed resulted in an upward trend in elephant population for all age classes. The local communities heavily depend on these ecosystem services for their livelihoods. It is therefore recommended that reasonable financing to strengthen law enforcement and monitoring is done, multiple policy options should be considered in order to maximize ecosystem benefits. Creation of partnerships and research networks need to be promoted. Existing transboundary collaboration initiatives should continue and be supported by the donor community in order to build peace and dram support for wildlife and wild habitat protection

The conservation and landscape genetics of the sand lizard Lacerta agilis

Lacerta agilis is a widespread lizard which reaches the western edge of its range in Britain where it is restricted to three geographically separated areas. Recent habitat loss and fragmentation have resulted in a significant decline and it is now a UK conservation priority. Sand lizards from across the Britain were genotyped at 15 microsatellite loci and the resulting dataset used to address questions regarding the conservation genetics, phylogeography and influence of landscape on patterns of genetic diversity. Genetic diversity of Dorset populations compared favourably to European examples. However, diversity was significantly lower in Surrey and Merseyside. Significant genetic structuring occurred across small geographical distances even in relatively unfragmented landscapes. Lacerta agilis colonised Britain via a land bridge across the North Sea and reached the limits of its current distribution approximately 5,000 years BP. Subsequent climate cooling has resulted in a range contraction to areas where the habitat is suitable for the successful incubation of eggs. A resistance surface was used to investigate the effect of landscape configuration on patterns of genetic diversity at multiple scales in Dorset. At a local scale, habitat type and rivers were the best predictors of genetic diversity. At a regional scale, rivers were most important, whereas habitat type and artificial barriers were less important. Artificial barriers may be more significant than the results suggest as their true effect has not yet been realised due to a genetic time-lag. Male lizards from Merseyside exhibited significant differences in colour and pattern to the Dorset and Surrey populations. However, despite difference in colour, all populations were equally green, which is in keeping with the importance of ‘greenness’ as a sexual signal. The implications of these findings for the conservation of L. agilis are discussed in the context of current challenges and predicted future global climate change

Etude de l’hybridation inter-spécifique entre espèces du genre Coffea en Nouvelle-Calédonie : distribution des niches favorables et structuration de la diversité

Coffee trees are originated from inter-tropical forests of Africa and Madagascar and their diversification origin areas are highly threatened. Among the 103 species of the Coffea genus, only three are cultivated: C. arabica, C. canephora and C. liberica. C. canephora has the widest natural distribution in tropical African forests, and its genetic diversity is structured in five distinct groups. The study of the genetic diversity structuring has revealed a particular importance of the Dahomey gap floristic breaking as biogeographic barrier, as well as the past climatic variations on the diversity structuring (model to study the “refuge theory”). A core set of both wild and cultivated (represented in majority by inter-group hybrids) accessions was selected to characterize the introduced diversity in New-Caledonia (since 1856). On introduced New-Caledonian sample, high levels of genetic diversity have been revealed for C. canephora and C. liberica while as expected, low level of diversity has been revealed for C. arabica. These three species (C. liberica to a lesser extent) have been introduced in different regions of New Caledonia for their culture. Because of economical reasons, a lot of traditional coffee plantations have been abandoned during the Second World War, leaving the cultivars to evolve in natural conditions. Inter-specific hybridizations are occurring between coffee species (at a level of 3% according to the study of a tri-specific population) thanks to a removal of reproductive barriers facilitated by particular environmental conditions. An environmental expertise based on the comparisons of environmental conditions between Sarramea region and African origin regions of the three species has underlined the favorable environmental combinations to sympatry and inter-specific hybridizations. Equilibrium between draining and humidity, precipitations sequences and the forest cover are important parameters maintaining a favorable microclimate. The canopy forest study by remote sensing tools has reinforced the predicting distribution model of favorable niches to inter-specific hybridization thanks to the information brought on canopy heterogeneity and large tree crowns and to the spatial resolution improving the detection of micro-habitats. Favorable niches are micro-environments distributed throughout the study area. The question is to underline the preservation of such de novo adapted coffee genetic resources.Les caféiers sont des arbres ou arbustes natifs des forêts intertropicales d'Afrique, de Madagascar, des Mascareignes et des Comores et leurs aires d'origine ou de diversification sont en forte régression. Parmi les 103 espèces du genre Coffea seules trois sont cultivées : C. arabica, C. canephora et C. liberica. L‟espèce C. canephora est celle du genre qui a la plus grande distribution dans les forêts tropicales africaines, et sa diversité génétique est structurée en cinq groupes bien distincts. L‟étude fine de la structuration de sa diversité génétique a révélé une importance particulière de la rupture floristique du Dahomey gap en tant que barrière biogéographique, ainsi que des variations climatiques du passé sur la structuration de la diversité (modèle d'étude des refuges forestiers du Quaternaire). Une collection de référence (core-collection) de la diversité sauvage et cultivée (représentée par une majorité d'hybrides inter-groupes) a été mise en place pour caractériser la diversité introduite en Nouvelle-Calédonie (depuis 1856). Cette diversité s'est révélée être élevée pour C. canephora et C. liberica et comme attendu, faible pour C. arabica. C. canephora et C. arabica (C. liberica de manière plus anecdotique) ont été introduites un peu partout en Nouvelle-Calédonie pour leur culture. Pour des raisons économiques, beaucoup de plantations traditionnelles ont été abandonnées au moment de la deuxième guerre mondiale, laissant les arbres de caféiers évoluer de manière naturelle. Des hybridations inter-spécifiques se produisent entre ces trois espèces (à hauteur de 3% dans une population tri-spécifique) grâce à une levée de barrières à la reproduction, permise par une conjoncture environnementale particulière. Une expertise environnementale fine, basée sur la comparaison des conditions environnementales entre la région de Sarraméa et les régions d'origine des trois espèces en Afrique, a permis de mettre en exergue les combinaisons environnementales favorables à la cohabitation des espèces et à leur hybridation inter-spécifique. L'équilibre entre drainage et humidité, un régime pluviométrique particulier et la présence d'un couvert forestier, sont des paramètres environnementaux importants qui maintiennent un microclimat favorable. L'étude du couvert forestier par télédétection a permis de renforcer le modèle de prédiction des niches favorables aux hybridations inter-spécifiques grâce à l‟information apportée quant à l'hétérogénéité et la présence de gros arbres dans la canopée ainsi que à l'amélioration de la résolution spatiale qui permet la détection fine de micro-habitats. Les niches favorables sont des micro-environnements répartis dans la région d'étude. Il s‟agit de mettre l‟accent sur la conservation d‟une telle néo-diversité adaptée et de valoriser ce patrimoine naturel

O uso por lacertídeos de elementos biofísicos da paisagem de montado

O objetivo geral deste estudo foi determinar o uso espacial dos principais elementos biofísicos presentes no sistema agro-silvo-pastoril (árvores e arbustos, troncos e ramos caídos, afloramentos rochosos e amontoados de pedras/muros) por parte de três espécies de lacertídeos: Acanthodactylus erythrurus, Podarcis virescens e Psammodromus algirus. Todavia nas dez parcelas estudadas não se encontrou A. erythrurus. Para as restantes duas espécies os testes de hipóteses mostraram que existem diferenças no número de indivíduos quando se comparam as cinco parcelas com pastoreio com as cinco parcelas sem pastoreio dentro da paisagem do montado. Onde há afloramentos rochosos predomina P. virescens (sobretudo em zonas com pastoreio), enquanto Ps. algirus ocorre mais nas zonas sem pastoreio. Ao mesmo tempo, também existem diferenças nos elementos usados como poleiro e como refúgio entre as duas lagartixas. Este tipo de trabalho auxilia à criação de planos de gestão por parte de agricultores e proprietários/decisores, com vista a uma conservação eficiente dos répteis; ABSTRACT: The use by lacertids of some biophysical elements of the montado's landscape The aim of this study was to determine the spatial use of the main biophysical elements present in the agro-silvo-pastoral system (trees and shrubs, fallen trunks and branches, rocky outcrops and piles of stones/walls) by three lizard speciess: Acanthodactylus erythrurus, Podarcis virescens and Psammodromus algirus. However, A. erythrurus was not found in the ten plots studied. For the remaining two species, the hypothesis tests showed that there are differences in the number of individuals when comparing the five plots with grazing with the five plots without grazing, within the montado landscape. Where there are rocky outcrops, P. virescens predominates (especially in grazing areas), while Ps. algirus mainly occurs in areas without grazing. At the same time, there are also differences in the elements used as a perch and as a refuge between the two lizards. This type of work helps the creation of management plans by farmers and owners / decision makers, towards an efficient conservation of reptiles

Toward the development of predictive systems ecology modeling: MetaConnect and its use as an innovative modeling platform in theoretical and applied fields of ecological research

Dans un contexte de changements globaux, les scientifiques et les législateurs requièrent des outils leur permettant de traiter la question de la perte de biodiversité. L'analyse de viabilité de population (PVA) est l'outil principal pour traiter le problème. Cependant, les outils développés dans les années 90 n'intègrent que très peu les récents progrès réalisés en génétic du paysage et sur la compréhension de la dipsersion. Ici, j'ai développé une plateforme de modélisation flexible et modulaire pour réaliser des PVA qui palie à la plupart des limitations des logiciels existants et répondant de ce fait à l'appel fait par Evans et al. (2013) pour développer des modèles prédictifs des systèmes écologiques. MetaConnect est un modèle individu centré, basé sur le déroulement des processus biologiques et principalement basé sur la réalisation d'analyses de viabilités qui peut être utlisé à la fois comme un outil de recherche ou d'aide à la décision. Dans ma thèse, je présente le module central de MetaConnect et sa validation puis présente différentes application de cette plateforme à des fins théoriques et appliquées.In a context of global change, scientists and policy-makers require tools to address the issue of biodiversity loss. Population viability analysis (PVA) has been the main tool to understand and plan for this problem. However, the tools developed during the 90s poorly integrate recent scientific advances in landscape genetics and dispersal. Here, I developed a flexible and modular modeling platform for PVA that addresses many of the limitations of existing software and in this way answer the call made by Evans et al. (2013) for predictive systems ecology models. MetaConnect is an individual-based, process-based and PVA-based modeling platform which could be used as a research or a decision-making tool. In my thesis, I present the modeling base core of MetaConnect and its validation and then present different uses of this platform in theoretical and applied ecology

Ecology of feral cats Felis catus and their prey in relation to shrubland fire regimes

Invasive predators are major drivers of global biodiversity loss and their impacts may be worsened by other disturbances such as fire. I examined how the fire history of shrublands influences the ecology of feral cats Felis catus, dingoes Canis dingo and their prey species in Western Australia’s northern Wheatbelt region. A review of the literature revealed that feral cats inhabit a diverse range of ecosystems worldwide, but are generally recorded most often in habitat types characterised by a mixture of plant growth forms close to ground level. Cat habitat use is influenced by predation/competition, prey availability, shelter availability and anthropogenic resource subsidies. Relatively few studies were available for review and the strength of evidence contained within them was generally low, which highlighted the need for more rigorous field studies. I examined overlap in resource use between cats and dingoes using remote camera surveys and dietary analysis of scats. Both carnivores were recorded in all four major habitat types: recently burnt shrublands (10 to 14 years since last fire), long unburnt shrublands (34 to ~49 years), very long unburnt shrublands (\u3e 50 years), and woodlands. Dingoes and cats preferred woodlands and very long unburnt shrublands respectively, but spatial overlap between the two species was still common. Mean diurnal activity time for feral cats was two and a half hours later than that of dingoes. The diet of feral cats was more diverse than that of dingoes and dietary overlap between the two carnivores was relatively low. Rabbit remains did occur relatively frequently in both cat and dingo scats, but small mammals, reptiles and birds were also common in cat scats, and macropods in dingo scats. Nine of the 15 prey species studied showed a preference for either recently burnt or long unburnt shrublands. Two small mammals and three reptiles were most abundant in recently burnt areas, while the abundance of one small mammal and three reptiles was highest in long unburnt areas. Using giving up density experiments, I showed that rodents exhibited differential foraging behaviour in the two vegetation fire ages. The rodents foraged for longer in sheltered compared to open microhabitats, but this pattern only occurred in recently burnt, not long unburnt shrublands, probably because the higher density of understorey vegetation in recently burnt areas provided the rodents with extra cover to hide and escape from predators. I also developed a new framework for conceptualising interactions between invasive predators and other ecological disturbances, such as fire, habitat fragmentation, and top -predator decline. The impacts of invasive predators can be classified as either functional (density -independent) or numerical (density -dependent), and they interact with other threats through both habitat -mediated (fire, grazing, land clearing) and community -mediated (top -predator decline, altered prey populations, anthropogenic resource subsidies) interaction pathways. The key findings of this thesis show that both old and young shrublands can be suitable habitat for feral cats; predator -prey dynamics are influenced by successional habitat stages; small mammals show behavioural, as well as population -level responses to fire; and that invasive predator management is likely to benefit from addressing multiple threats in unison