Hipóteses e sistemas ecológicos podem ser descritos pelos mais variados tipos de modelos teóricos. Modelos teóricos por sua vez descrevem sistemas idealizados e podem ser construídos sob diferentes abordagens. A ecologia foi profundamente influenciada por modelos ou hipóteses verbais construídos em uma abordagem predominantemente indutiva. Apesar de inspiradoras, tais hipóteses podem apresentar previsões que são logicamente falhas, uma vez que sistemas ecológicos são altamente complexos cujas trajetórias são difíceis de se prever intuitivamente. Neste sentido modelos teóricos quantitativos podem ser usados como ferramentas para traduzir hipóteses e deduzir previsões que podem ser confrontadas com dados reais. Modelos matemáticos são a forma mais tradicional e aceita de abordagem quantitativa. Apesar das vantagens analíticas da aplicação de modelos matemáticos, eles apresentam limitações para tratar de sistemas mais complexos e em escalas mais basais. Além disso, eles podem se tornar rapidamente complicados não só em termos de tratamento matemático mas também de entendimento por parte de um público mais biológico e empírico. Essa dificuldade de entendimento pode estar impedindo que estudos empíricos sejam fortemente embasados em teoria. Neste sentido, modelos computacionais pode ser uma solução promissora. Modelos computacionais podem ser criados para descrever sistemas virtuais que além de ser mais fáceis de serem desenvolvidos e entendidos por biólogos, permitem a inclusão de vários processos, variáveis e interações. Neste trabalho desenvolvemos um modelo baseado em indivíduos (IBM) para descrever comunidades com estocasticidade demográfica, interações intra e inter-específicas e dispersão. Com essa composição de modelo é possível combinar de diferentes maneiras três dos quatro processos presentes em hipóteses e teorias em ecologia, a saber: deriva, seleção e dispersão. No primeiro capítulo descrevemos os detalhes do modelo e como foi sua concepção e implementação. Ainda no neste capítulo simulamos o modelo explorando um espaço de parâmetros arbitrário, i.e. sem especificar um grupo ou sistema de estudo e analisamos o comportamento do modelo em relação à proporção de espécies persistentes ao fim da simulação e comparamos com a previsão do modelo determinístico de competição sem dispersão. No segundo capítulo aplicamos o modelo em uma versão não espacializada para avaliar dentro das premissas do modelo a consistência lógica das previsões da Hipótese da perturbação intermediária (IDH). No terceiro capítulo simulamos o modelo explorando um espaço de parâmetros baseados em dados empíricos de aves e avaliamos quais características das espécies as tornavam mais ou menos suscetíveis à extinção em paisagens com destruição de habitat. Por fim, discutimos brevemente sobre como o modelo apresentado o modelo apresentado e explorado aqui pode ser usado para diferentes propósitos e responder diferentes perguntas dentro dos contextos teóricos de cada capítulo da tese. E concluímos com algumas considerações finais sobre quais foram as contribuições de se desenvolver um modelo computacional e aplicá-lo a diferentes contextos nesta tese para a formação da doutoranda. / Ecological systems and hypothesis can be described by many different kinds of theoretical models. Theoretical models, on the other hand, are idealized descriptions of real systems that can be constructed under different approaches. Ecology was deeply influenced by verbal models or hypothesis under a inductive approach. Although inspiring, such hypothesis can be logically flawed, since ecological systems are highly complex which trajectories are difficult to predict by intuition. Accordingly quantitative theoretical models can be used as tools to translate hypotheses and deduce predictions that can be confronted with empirical data. Mathematical models are most traditional and well-accepted quantitative approach. Despite of the analytical advantages of using mathematical models , they have limitations to address the complexity of biological systems in lower scales. Furthermore, they become rapidly complicated not only in terms of mathematical treatment but also in terms of comprehension by a biological and empirical audience. This difficulties might prevent that theoretical studies predictions play its role of ground empirical studies. In this sense, computer simulation models can be a promising solution. Computer simulation models are more flexible to include various processes, variables and interaction than mathematical models. Furthermore, they create virtual systems that are easier to be developed and understood by biologists. Here, we developed an individual based model (IBM) to describe communities with stochastic demography, intra and inter-specific interactions and dispersion. With this configuration we can build models combining of different manners three of the four processes present in hypotheses and theories in ecology: drift, selection and dispersal. In the first chapter we describe the model details of implementation and conceptions. We also simulated the model to explore a broad parameter space of competing systems, without specifying a group or system of study; we then analyze the model behavior regarding the proportion of persistent species in the end of the simulation and compared the results with the predictions of deterministic model with competition, without dispersion. In the second chapter we apply the model in a non spatialized version of it to assess the logical consistency of the predictions of the Intermediate disturbance hypothesis (IDH). In the third chapter we used the model to describe fragmented landscapes. We explored a parameter parameters based on empirical data of birds and we evaluate which characteristics of the species made them more or less susceptible to extinction in landscapes with habitat destruction. Finally, we discussed briefly how the model can be used for different purposes and some of the future directions within the theoretical contexts of each chapter of the thesis. We conclude the thesis with a reflexion on how the development and exploration of computer model in this thesis contributed to the student ecological background.

Conservation managers worldwide are increasingly faced with the challenges of managing and protecting fragmented landscapes, largely as a consequence of human activities. Over recent decades, ecological theory has made a significant contribution to the development of landscape-scale conservation and practice. However, recommendations accounting for what is practically achievable in the modern-day landscape are currently lacking, while criteria for conservation planning and prioritisation continue to neglect the role of habitat networks at the required spatial scale for the long-term persistence of biodiversity. In this thesis, I test and apply ideas surrounding the complexities of managing and conserving species in a landscape context, using a suite of bird species endemic to papyrus (Cyperus papyrus) swamps in East and Central Africa as a model system. In the face of large-scale habitat loss and degradation, practical measures that account for the fragmented nature of this system, the needs of multiple specialist species, and the reliance on this habitat by local people, are urgently required. I first review the concepts originating from reserve design theory to provide a decision-making framework for those involved in landscape-scale conservation amid 21st century challenges to biodiversity, highlighting the key principles to be considered for informed choices to be made. Second, I show that the needs of local people can be compatible with conservation planning in the tropics, and may play an important part in maintaining habitat quality for species residing in historically disturbed landscapes. Third, I develop a novel framework to make an explicit link between metapopulation dynamics and conservation planning. Despite differences in the patch-level dynamics of individual species, areas of habitat where populations of multiple species are resistant to extinction, and resilient because of high chances of (re)colonization can be identified, highlighting where resources could be invested to ensure species have the capacity to respond to future change. Finally, I simulate the metapopulation dynamics of the papyrus-endemic birds to demonstrate that the optimal conservation strategy for the long-term persistence of all species residing in a network depends on the characteristics of individual species, and the total area that can be protected. Overall, this thesis develops and tests the ecological theory used in spatial conservation planning, emphasising the importance of habitat disturbance and interspecific ecological differences for the effective management of habitat networks. The results increase the evidence base for the conservation of wetland birds in Africa, as well as for species residing in fragmented landscapes more generally.

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No. of bitstreams: 2 Dissertação - Suelem Martini Assmann - 2016.pdf: 3866760 bytes, checksum: ca76b11f1bc1b7e011b8779d07190fb7 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-04-07 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The Forest Code is a measure created in order to establish balance between nature exploitation and conservation. Since the first Brazilian Forest Codes (BFCs), the efficiency of the regulation has been discussed, for it established measures that preserved the minimum of each biome. Among the three BFCs which were created, the New Forest Code (NFC), Law no 12651, of May 25, 2012, is the one which least fulfills its role. The NFC has proved to be a result of needs of capital in a distorted perspective of the sustainability school of thought, which is dealt in this thesis. Regarding such a line of thought, one may understand the reasons for the controversial code amendments and which techniques determine them. In this thesis, we analyzed the NFC consequences in the Cerrado landscape by the means of a case study in the Paraíso creek sub-basin, in Jataí-GO, where several alterations were observed. Our results showed that the total area quantity, which was said to be protected by the forest code, decreased by 38% after the NFC. Areas of this study which suffered most from the code changes were: firstly, the wetlands PPAs (permanent preservation areas), which were decreased by 100%; secondly, the headwaters PPAs, which were decreased by 91%; and, thirdly, lake PPAs, which were decrease by 70% on their permanent area. It was also found, by means of other studies on Cerrado and on other biomes, that such landscape alterations can be noted in the entire ecosystem, causing complications to plants, insects, birds, reptiles, amphibians, fishes and mammals. Such alterations are caused mainly due to habitat changes, shortening a vast diversity of species into some merely generalist species. Besides that, the effects on quality and quantity of water in rivers and rainfall in the region, on physical, chemical and biological quality of the soil and on atmospheric temperature were also found. By using landscape projection maps, before and after the NFC, we were able to understand with this study that the code alterations are much greater to practice than the law alterations which were made. / O Código Florestal é a medida criada para estabelecer um equilíbrio entre a exploração e a preservação da natureza. Desde os primeiros Códigos Florestais Brasileiros (CFBs), já se discutia a eficiência da norma, pois estipulavam medidas que preservavam o mínimo de cada bioma. Entre os três CFBs criados, o Novo Código Florestal (NCF), lei nº 12.651 de 25 de maio de 2012, é o que menos cumpre seu papel. O NCF demonstra ser reflexo dos anseios do capital em uma ótica um tanto deturpada da corrente sustentabilista tratada neste trabalho. Perante este modelo de pensamento, percebe-se o porquê das polêmicas alterações deste código e quais práticas as definem. Neste trabalho, analisaram-se as consequências do NCF na paisagem do Cerrado por meio de um estudo de caso na sub-bacia do Ribeirão Paraíso, no município de Jataí-GO, onde se puderam constatar diversas alterações. Nos resultados, observou-se que a quantidade total de área, antes dita protegida pelo código florestal, diminuiu em 38% no NCF. As áreas deste estudo que mais sofreram com as alterações do código foram: em primeiro lugar, as APPs de alagados, que sofreram uma diminuição de 100%; em segundo lugar, as APPs de nascentes, sofrendo uma diminuição de 91%; e, em terceiro lugar, a APP de lago, sofrendo uma diminuição de 70% da área permanente. Observaram-se, por meio de outros estudos do Cerrado e em outros biomas, que essas alterações na paisagem refletem em todo o ecossistema, apresentando complicações para espécies de plantas, insetos, aves, répteis, anfíbios, peixes e mamíferos. Alterações estas dadas, principalmente, pela mudança de habitats, resumindo uma vasta diversidade de espécies em apenas algumas generalistas, além dos efeitos na qualidade e na quantidade da água de rios e da pluviosidade da região, na qualidade física, química e biológica dos solos. Através de mapas de projeção da paisagem de antes e depois do NCF, pôde-se compreender que as alterações do código são muito maiores na prática do que foi na lei.

This study investigated the utility to vertebrates of upland linear riparian rainforest fragments on the Atherton and Evelyn Tablelands in the Australian Wet Tropics region, north Queensland. Similar linear fragments were selected, that varied in forest age and their connectivity to large areas of continuous forest:- (connected primary (N=6), isolated primary (N=5), connected secondary (N=6) and isolated secondary (N=7)). Primary sites had either never been cleared or only subject to selective logging, while secondary forest had been completely cleared and allowed to regenerate for at least 30 years. These linear fragments were contrasted with riparian sites within continuous forest sites (N=6 to 7), which were situated in State Forest or National Parks, and sites within the cleared matrix (pasture, N=6). Vertebrates surveyed were birds, ground-dwelling mammals and reptiles, particularly leaf-litter skinks. All surveys were conducted between September and December in 2001 and/or 2000. Chapter 2 investigates the effects of forest age, isolation and structural vegetation features on bird assemblages within linear riparian fragments of rainforest. Bird surveys and structural vegetation assessments were conducted within connected and isolated primary and secondary linear fragments, and compared with those of continuous forest habitat (N=6) and pasture. There were strong effects of forest age; all three types of primary rainforest had higher values than secondary rainforest for most measured attributes of vegetation structure (including canopy height and cover; and frequency of large-diameter trees, lianes, epiphytes, strangler figs; and woody debris), but lower frequencies of tree ferns and thorny scramblers. Sites within primary rainforest also had a greater frequency of many bird species across different guilds of habitat, feeding and movement. Assemblages of rainforest-dependent birds showed an effect of isolation, although its strength was less than that of forest age. Isolated fragments of primary rainforest differed significantly from continuous primary rainforest in their rainforest-dependent bird species assemblages (and had lower species richness), and isolated fragments of secondary rainforest differed from those that were connected. There was a significant association between the species composition of rainforest birds and some measured vegetation parameters across all sites, but not within primary or secondary sites. Vegetation differences did not explain the lowered frequency of several species in isolated fragments. Limited dispersal seems unlikely to be a main cause, and causal processes probably vary among species. Specialist rainforest species endemic to the Wet Tropics region showed stronger responses to present-day rainforest age and fragmentation than those not endemic. Variation in nest depredation levels associated with rainforest fragmentation (edge effects) is examined in Chapter 3. Artificial nests were placed in the forest understorey at seven edge sites where continuous forest adjoined pasture, seven interiors (about one kilometre from the edge), and six primary linear riparian forest remnants (50-100 m wide) that were connected to continuous forest. Four nest types were compared, representing different combinations of two factors; height (ground, shrub) and shape (open, domed). At each site, four nests of each type, containing one quail egg and two model plasticine eggs, were interspersed about 15 m apart within a 160 m transect. Predators were identified from marks on the plasticine eggs. The overall depredation rate was 66.5% of 320 nests' contents damaged over a three-day period. Large rodents, especially the rat Uromys caudimaculatus, and birds, especially the spotted catbird Ailuroedus melanotis, were the main predators. Mammals comprised 56.5% and birds 31.0% of identified predators, with 12.5% of unknown identity. The depredation rate did not vary among site-types, or between open and domed nests, and there were no statistically significant interactions. Nest height strongly affected depredation rates by particular types of predator; depredation rates by mammals were highest at ground nests, whereas attacks by birds were most frequent at shrub nests. These effects counterbalanced so that overall there was little net effect of nest height. Mammals accounted for 78.4% of depredated ground nests and birds for at least 47.4% of shrub nests (and possibly up to 70.1%). The main predators were species characteristic of rainforest, rather than habitat generalists, open-country or edge specialists. For birds that nest in the tropical rainforest understorey of the study region, it is unlikely that edges and linear remnants presently function as ecological population sinks due to mortality associated with increased nest depredation. The use of linear riparian remnants by small ground-dwelling mammals and reptiles (mainly leaf litter skinks), is reported in Chapter 4. Site types were continuous rainforest, connected and isolated linear fragments of both uncleared primary rainforest and secondary regrowth rainforest. Mammals were also surveyed in pasture sites. Neither reptile species richness nor abundance varied significantly among site types. Although mammal species richness varied significantly between site types, with isolated primary sites containing highest species richness, overall mammal abundance did not differ significantly among site types. Pasture sites differed significantly from all rainforest sites in their mammal species composition, and were dominated by the introduced house mouse (Mus musculus). This species was absent from all rainforest sites, which were characterised by moderate abundances of bush rat/Cape York rat Rattus fuscipes/leucopus, fawn-footed melomys Melomys cervinipes and giant white-tailed rat Uromys caudimaculatus. None of these species varied significantly in abundance among site types, although the giant white-tailed rat showed a trend (P=0.09) for reduced abundance in isolated secondary sites. A single reptile species, the prickly forest skink Gnypetoscincus queenslandiae, occurred in sufficient numbers for individual analysis, and its abundance varied significantly among the forested site types, being less abundant in all linear fragments than in continuous forest sites. The utility of linear riparian rainforest for vertebrates appears to be species-specific and involves many factors. However, overall, species endemic to the Wet Tropics (which are hence of the highest conservation significance) appear to be the most sensitive to fragmentation. These species were most likely to show altered abundances or frequencies of occurrence due to isolation, forest age, and habitat linearity. The ecology of species within this group warrants further investigation within fragmented and non-fragmented regions of the Tablelands. For many other vertebrates examined in this study, there appears to be sufficient functional connectedness between remnants on the Tablelands to minimise the effects of fragmentation. Nevertheless, the lower density of many of these species in pasture may indicate that their long-term persistence within the fragmented rainforest areas could benefit from the maintenance or establishment of habitat linkages. Certainly, if the current rainforest vegetation cover were further reduced, or if the land use in the matrix became more intensive, the establishment of specific habitat linkages could become more important as existing dispersal routes could be lost. It also appears that nest depredation levels are unlikely to limit the value of linear rainforest remnants and other small rainforest remnants as breeding habitat for birds (at least for understorey-nesting species), relative to more intact rainforest, in the study region.

The local extinction of habitat patches and dispersal between the patches are important processes structuring animal populations in heterogeneous environments. Understanding these two processes is crucial for the conservation of wildlife populations in landscapes impacted by human land-use. Approximately 50% of the subtropical rainforest in South East Queensland, Australia has been lost to deforestation over the last 100 years. While large areas of rainforest are reserved, little is known about the distribution and population status of rainforest birds within smaller remnants in the region. The overall research problem for this thesis was to understand how deforestation and fragmentation of subtropical rainforest affects the occurrence of rainforest birds and the effective dispersal of a rainforest-restricted species, the logrunner (Orthonyx temminckii). Understanding why some bird species are lost from habitat patches while others remain will lead to improved conservation of extinction prone species in fragmented landscapes. Although the mechanisms underlying local extinctions are well established in temperate systems, the relative importance of local and regional processes on species occurrence in subtropical and tropical rainforests is poorly understood. Chapter 2 investigated the relative effects of life history and scale of habitat modification on avian site occupancy using observational data collected at 46 rainforest sites in South East Queensland. A probabilistic model for the joint site occupancy of 29 bird species was used to evaluate hypotheses for the effects of avian life history traits on the occurrence of multiple species. The single-species occurrence models incorporated habitat effects on detection, which may be especially important in rainforests because dense vegetation and idiosyncratic occurrence of species can interfere with sampling. Occupancy rates for each species were modelled to determine the relative influence of process operating at the stand, landscape and patch scales. The life history analysis indicated taxonomic Family, body mass, migratory strategy and feeding strata had large effects on avian site occupancy, whereas abundance traits such as mean density and extent of occurrence showed little predictive ability. After accounting for correlated extinction risk attributed to life history, the degradation of stand structure at the local scale was more important for species richness than habitat modification at landscape or patch scales. While individual species showed various responses to the different scales of habitat modification, the distribution of many species was limited by vegetation structure at the landscape scale. Maintaining stand basal area and restoring degraded rainforests at the local scale will increase the probability of occupancy for members of the rainforest bird community. However, revegetation and retention of forest cover at the landscape scale may be necessary for the successful colonisation of many species. Chapter 3 introduced a predictive hypothesis-driven approach for quantifying the relative contribution of historic and contemporary processes to genetic connectivity. Current analytic frameworks in population genetics have difficulty evaluating meaningful hypotheses about spatial processes in dynamic landscapes. Confronting genetic data with models of historic and contemporary landscapes allowed the identification of dispersal processes operating in naturally heterogeneous and human-altered systems. Two measures of indirect gene flow were estimated from microsatellite polymorphism among 11 logrunner populations. Of particular interest was how much information in the genetic data was attributable to processes occurring in a reconstructed historic landscape and a contemporary human-modified landscape. A linear mixed model was used to estimate appropriate sampling variance from non-independent data and information-theoretic model selection provided strength of evidence for alternate hypotheses. The historic and contemporary landscapes explained an equal proportion of variation in genetic differentiation and there was considerable evidence for a temporal shift in dispersal pattern. Migration rates estimated from genealogical information were primarily influenced by contemporary landscape change. Landscape heterogeneity appeared to facilitate gene flow prior to European settlement, but contemporary deforestation is rapidly becoming the most important barrier to logrunner dispersal. Understanding asymmetric dispersal is becoming an important consideration for the conservation metapopulations. Populations acting as net exporters of dispersing animals may be able to rescue local populations from extinction and allow metapopulations to persist in degraded landscapes impacted by habitat loss. In Chapter 4, I estimated bidirectional migration rates from genetic data to infer dispersal among 11 logrunner populations. The first question posed was, does logrunner dispersal correspond to the source-sink or balanced model of dispersal? The second question involved determining the strength of evidence for two hypotheses about how landscape structure has affected asymmetric dispersal. Hypothesis one proposed that asymmetric dispersal was primarily influenced by naturally occurring habitat heterogeneity. Hypothesis two asserted that asymmetric dispersal was predominantly influenced by anthropogenic landscape change. The data were confronted with the alternate hypotheses using linear mixed models and landscape covariates extracted from digital maps. The results showed the direction of asymmetric dispersal was consistent with source-sink population structure. I also discovered that the asymmetry in dispersal was influenced more by anthropogenic landscape change than by naturally occurring habitat heterogeneity. Intact landscapes were net exporters of dispersing logrunners while landscapes heavily impacted by rainforest clearing were net importers of individuals. Elevated immigration rates into landscapes impacted by rainforest clearing appeared to arrest population declines in accordance with the rescue effect. The primary conclusion emerging from the study of patch occupancy and dispersal was that logrunner populations in South East Queensland conformed to a mainland-island metapopulation. Asymmetric dispersal from the largest expanse of upland rainforest appeared to prevent fragmented rainforests in close proximity from going locally extinct. While the distribution of logrunners was limited by the spatial configuration of rainforest patches, other rainforest birds exhibited variable responses to scale of habitat modification. The most consistent pattern was several species dropping-out of the community in degraded stands affected by selective timber harvest. Deforestation at the landscape scale also played a role in the extremely low patch occupancy rates of Albert’s lyrebirds (Menura alberti) and green catbirds (Ailuroedus crassirostris).

The conversion of native forests to pastures and crops is one of the most extensive causes of deforestation worldwide. Concomitant with agricultural landscape modification are the processes of habitat loss and fragmentation, which are major causes of species’ extinctions, population declines and altered ecosystem functions. However, in many tropical, sub-tropical and temperate regions, abandoned agricultural lands are reverting to regrowth or secondary forest, which represents an important opportunity for passive landscape restoration. Regrowth may be particularly important in highly modified landscapes, where the area of mature forest may be insufficient to support viable plant and animal communities without some form of restoration. Some studies of fauna populations in regrowth forest have found recovery of species richness within several decades, although recovery of species composition may take at least 100 years and some species may be permanently lost. While these findings are encouraging, they generally fail to account for the landscape context in which regrowth occurs and focus mainly on tropical forests. The aim of this thesis was to advance the understanding of fauna recovery in regrowth forests on abandoned agricultural land by: i) comparing woodland bird communities in a replicated chronosequence of semi-arid sub-tropical regrowth forests; and ii) quantifying how the ecological values of regrowth habitat vary among stand-, patch- and landscape-levels of ecological organisation. A review of 68 studies of fauna recovery in regrowth forests, revealed that current knowledge is limited by the predominance of studies conducted: in tropical rainforests; with minimal replication of sites; in landscapes within proximity of large tracts of relatively undisturbed mature forests; and with limited consideration of the influence of the spatial context on fauna recovery in regrowth forest. This study makes a significant contribution to understanding fauna recovery in regrowth forests by quantifying the recovery of estimated bird species richness to levels similar to mature forest, within a period of 30-60 years, in highly modified semi-arid agricultural landscapes in sub-tropical Australia. An ordination of the similarity in species composition among forest types also suggested that after 30-60 years regrowth bird communities are more similar to mature brigalow forest than the younger regrowth. This is important for the recovery of brigalow ecosystems, an endangered ecological community where regrowth is currently given minimal protection from further clearing. Comparisons of the importance of habitat attributes using model averaging and hierarchical partitioning of generalised linear models of the species richness of woodland birds showed that bird species richness was positively associated with patch age, and that stand-level factors such as grazing disturbance and the abundance of mistletoes (Amyema spp.) were also important. The spatial context of vegetation patches (size, shape and isolation) was equally important for bird species richness, with more species of woodland dependent, nectar/frugivores and non-ground foraging insectivores occurring in less modified landscape contexts, and the converse for generalist species, ground foraging insectivores and granivores. While a number of woodland dependent bird species known to be in decline in temperate woodlands of southern Australia were absent or rare in regrowth forests, several species (e.g., eastern yellow robin) also occupied regrowth habitats. This finding suggests that these more sensitive species may respond positively to landscape restoration through targeted retention of brigalow regrowth. The landscape-level amount of forest varied in importance among regrowth age classes and bird groups. In general, the amount and number of mature forest patches in the landscape were of lower importance than local attributes. However, the amount of mature forest and old regrowth (> 30 years) in the landscape did have an important positive influence on the number of woodland bird species and species’ abundance; suggesting that regrowth is making an important contribution to landscape recovery in the study area. Mistletoe abundance was strongly dependent on particular species of frugivores for seed dispersal (e.g., mistletoebird, spiny-cheeked honeyeater and painted honeyeater), and varied considerably among three sub-regions of the study area. In general, mistletoe abundance increased in linear patches and more highly modified landscapes but was also dependent on the abundance of seed dispersers and brigalow stand condition. These findings suggest that narrow linear patches in brigalow landscapes can have important conservation values for woodland birds. The study outcomes have important implications for research and management of regrowth vegetation, both within Australia and internationally. From an international perspective, the study highlights the need for greater consideration of the importance of regrowth forest in a landscape context for conserving and restoring fauna communities. From an Australian perspective, the study provides important baseline information for the conservation and management of woodland bird habitat in fragmented brigalow landscapes. Prior to this research, very little was known on the spatial ecology of woodland birds in the region. The study highlights the important conservation values of small and often linear mature brigalow patches for woodland birds and the considerable potential for restoration of habitat for a diverse range of species through the retention of regrowth vegetation. In particular, the research outcomes suggest that targeting the retention of regrowth towards increasing the size and reducing the isolation of mature brigalow forests may be an effective strategy to maximise biodiversity benefits. Brigalow regrowth stands will need to be retained for at least 60 years and probably longer to maintain viable woodland bird communities. For this to happen on a regional-scale, brigalow regrowth needs to be given greater recognition for potential biodiversity benefits either within a legislative framework or by incentive schemes to promote the long term persistence of regrowth habitat within the landscape.

The conversion of native forests to pastures and crops is one of the most extensive causes of deforestation worldwide. Concomitant with agricultural landscape modification are the processes of habitat loss and fragmentation, which are major causes of species’ extinctions, population declines and altered ecosystem functions. However, in many tropical, sub-tropical and temperate regions, abandoned agricultural lands are reverting to regrowth or secondary forest, which represents an important opportunity for passive landscape restoration. Regrowth may be particularly important in highly modified landscapes, where the area of mature forest may be insufficient to support viable plant and animal communities without some form of restoration. Some studies of fauna populations in regrowth forest have found recovery of species richness within several decades, although recovery of species composition may take at least 100 years and some species may be permanently lost. While these findings are encouraging, they generally fail to account for the landscape context in which regrowth occurs and focus mainly on tropical forests. The aim of this thesis was to advance the understanding of fauna recovery in regrowth forests on abandoned agricultural land by: i) comparing woodland bird communities in a replicated chronosequence of semi-arid sub-tropical regrowth forests; and ii) quantifying how the ecological values of regrowth habitat vary among stand-, patch- and landscape-levels of ecological organisation. A review of 68 studies of fauna recovery in regrowth forests, revealed that current knowledge is limited by the predominance of studies conducted: in tropical rainforests; with minimal replication of sites; in landscapes within proximity of large tracts of relatively undisturbed mature forests; and with limited consideration of the influence of the spatial context on fauna recovery in regrowth forest. This study makes a significant contribution to understanding fauna recovery in regrowth forests by quantifying the recovery of estimated bird species richness to levels similar to mature forest, within a period of 30-60 years, in highly modified semi-arid agricultural landscapes in sub-tropical Australia. An ordination of the similarity in species composition among forest types also suggested that after 30-60 years regrowth bird communities are more similar to mature brigalow forest than the younger regrowth. This is important for the recovery of brigalow ecosystems, an endangered ecological community where regrowth is currently given minimal protection from further clearing. Comparisons of the importance of habitat attributes using model averaging and hierarchical partitioning of generalised linear models of the species richness of woodland birds showed that bird species richness was positively associated with patch age, and that stand-level factors such as grazing disturbance and the abundance of mistletoes (Amyema spp.) were also important. The spatial context of vegetation patches (size, shape and isolation) was equally important for bird species richness, with more species of woodland dependent, nectar/frugivores and non-ground foraging insectivores occurring in less modified landscape contexts, and the converse for generalist species, ground foraging insectivores and granivores. While a number of woodland dependent bird species known to be in decline in temperate woodlands of southern Australia were absent or rare in regrowth forests, several species (e.g., eastern yellow robin) also occupied regrowth habitats. This finding suggests that these more sensitive species may respond positively to landscape restoration through targeted retention of brigalow regrowth. The landscape-level amount of forest varied in importance among regrowth age classes and bird groups. In general, the amount and number of mature forest patches in the landscape were of lower importance than local attributes. However, the amount of mature forest and old regrowth (> 30 years) in the landscape did have an important positive influence on the number of woodland bird species and species’ abundance; suggesting that regrowth is making an important contribution to landscape recovery in the study area. Mistletoe abundance was strongly dependent on particular species of frugivores for seed dispersal (e.g., mistletoebird, spiny-cheeked honeyeater and painted honeyeater), and varied considerably among three sub-regions of the study area. In general, mistletoe abundance increased in linear patches and more highly modified landscapes but was also dependent on the abundance of seed dispersers and brigalow stand condition. These findings suggest that narrow linear patches in brigalow landscapes can have important conservation values for woodland birds. The study outcomes have important implications for research and management of regrowth vegetation, both within Australia and internationally. From an international perspective, the study highlights the need for greater consideration of the importance of regrowth forest in a landscape context for conserving and restoring fauna communities. From an Australian perspective, the study provides important baseline information for the conservation and management of woodland bird habitat in fragmented brigalow landscapes. Prior to this research, very little was known on the spatial ecology of woodland birds in the region. The study highlights the important conservation values of small and often linear mature brigalow patches for woodland birds and the considerable potential for restoration of habitat for a diverse range of species through the retention of regrowth vegetation. In particular, the research outcomes suggest that targeting the retention of regrowth towards increasing the size and reducing the isolation of mature brigalow forests may be an effective strategy to maximise biodiversity benefits. Brigalow regrowth stands will need to be retained for at least 60 years and probably longer to maintain viable woodland bird communities. For this to happen on a regional-scale, brigalow regrowth needs to be given greater recognition for potential biodiversity benefits either within a legislative framework or by incentive schemes to promote the long term persistence of regrowth habitat within the landscape.

The conversion of native forests to pastures and crops is one of the most extensive causes of deforestation worldwide. Concomitant with agricultural landscape modification are the processes of habitat loss and fragmentation, which are major causes of species’ extinctions, population declines and altered ecosystem functions. However, in many tropical, sub-tropical and temperate regions, abandoned agricultural lands are reverting to regrowth or secondary forest, which represents an important opportunity for passive landscape restoration. Regrowth may be particularly important in highly modified landscapes, where the area of mature forest may be insufficient to support viable plant and animal communities without some form of restoration. Some studies of fauna populations in regrowth forest have found recovery of species richness within several decades, although recovery of species composition may take at least 100 years and some species may be permanently lost. While these findings are encouraging, they generally fail to account for the landscape context in which regrowth occurs and focus mainly on tropical forests. The aim of this thesis was to advance the understanding of fauna recovery in regrowth forests on abandoned agricultural land by: i) comparing woodland bird communities in a replicated chronosequence of semi-arid sub-tropical regrowth forests; and ii) quantifying how the ecological values of regrowth habitat vary among stand-, patch- and landscape-levels of ecological organisation. A review of 68 studies of fauna recovery in regrowth forests, revealed that current knowledge is limited by the predominance of studies conducted: in tropical rainforests; with minimal replication of sites; in landscapes within proximity of large tracts of relatively undisturbed mature forests; and with limited consideration of the influence of the spatial context on fauna recovery in regrowth forest. This study makes a significant contribution to understanding fauna recovery in regrowth forests by quantifying the recovery of estimated bird species richness to levels similar to mature forest, within a period of 30-60 years, in highly modified semi-arid agricultural landscapes in sub-tropical Australia. An ordination of the similarity in species composition among forest types also suggested that after 30-60 years regrowth bird communities are more similar to mature brigalow forest than the younger regrowth. This is important for the recovery of brigalow ecosystems, an endangered ecological community where regrowth is currently given minimal protection from further clearing. Comparisons of the importance of habitat attributes using model averaging and hierarchical partitioning of generalised linear models of the species richness of woodland birds showed that bird species richness was positively associated with patch age, and that stand-level factors such as grazing disturbance and the abundance of mistletoes (Amyema spp.) were also important. The spatial context of vegetation patches (size, shape and isolation) was equally important for bird species richness, with more species of woodland dependent, nectar/frugivores and non-ground foraging insectivores occurring in less modified landscape contexts, and the converse for generalist species, ground foraging insectivores and granivores. While a number of woodland dependent bird species known to be in decline in temperate woodlands of southern Australia were absent or rare in regrowth forests, several species (e.g., eastern yellow robin) also occupied regrowth habitats. This finding suggests that these more sensitive species may respond positively to landscape restoration through targeted retention of brigalow regrowth. The landscape-level amount of forest varied in importance among regrowth age classes and bird groups. In general, the amount and number of mature forest patches in the landscape were of lower importance than local attributes. However, the amount of mature forest and old regrowth (> 30 years) in the landscape did have an important positive influence on the number of woodland bird species and species’ abundance; suggesting that regrowth is making an important contribution to landscape recovery in the study area. Mistletoe abundance was strongly dependent on particular species of frugivores for seed dispersal (e.g., mistletoebird, spiny-cheeked honeyeater and painted honeyeater), and varied considerably among three sub-regions of the study area. In general, mistletoe abundance increased in linear patches and more highly modified landscapes but was also dependent on the abundance of seed dispersers and brigalow stand condition. These findings suggest that narrow linear patches in brigalow landscapes can have important conservation values for woodland birds. The study outcomes have important implications for research and management of regrowth vegetation, both within Australia and internationally. From an international perspective, the study highlights the need for greater consideration of the importance of regrowth forest in a landscape context for conserving and restoring fauna communities. From an Australian perspective, the study provides important baseline information for the conservation and management of woodland bird habitat in fragmented brigalow landscapes. Prior to this research, very little was known on the spatial ecology of woodland birds in the region. The study highlights the important conservation values of small and often linear mature brigalow patches for woodland birds and the considerable potential for restoration of habitat for a diverse range of species through the retention of regrowth vegetation. In particular, the research outcomes suggest that targeting the retention of regrowth towards increasing the size and reducing the isolation of mature brigalow forests may be an effective strategy to maximise biodiversity benefits. Brigalow regrowth stands will need to be retained for at least 60 years and probably longer to maintain viable woodland bird communities. For this to happen on a regional-scale, brigalow regrowth needs to be given greater recognition for potential biodiversity benefits either within a legislative framework or by incentive schemes to promote the long term persistence of regrowth habitat within the landscape.

The local extinction of habitat patches and dispersal between the patches are important processes structuring animal populations in heterogeneous environments. Understanding these two processes is crucial for the conservation of wildlife populations in landscapes impacted by human land-use. Approximately 50% of the subtropical rainforest in South East Queensland, Australia has been lost to deforestation over the last 100 years. While large areas of rainforest are reserved, little is known about the distribution and population status of rainforest birds within smaller remnants in the region. The overall research problem for this thesis was to understand how deforestation and fragmentation of subtropical rainforest affects the occurrence of rainforest birds and the effective dispersal of a rainforest-restricted species, the logrunner (Orthonyx temminckii). Understanding why some bird species are lost from habitat patches while others remain will lead to improved conservation of extinction prone species in fragmented landscapes. Although the mechanisms underlying local extinctions are well established in temperate systems, the relative importance of local and regional processes on species occurrence in subtropical and tropical rainforests is poorly understood. Chapter 2 investigated the relative effects of life history and scale of habitat modification on avian site occupancy using observational data collected at 46 rainforest sites in South East Queensland. A probabilistic model for the joint site occupancy of 29 bird species was used to evaluate hypotheses for the effects of avian life history traits on the occurrence of multiple species. The single-species occurrence models incorporated habitat effects on detection, which may be especially important in rainforests because dense vegetation and idiosyncratic occurrence of species can interfere with sampling. Occupancy rates for each species were modelled to determine the relative influence of process operating at the stand, landscape and patch scales. The life history analysis indicated taxonomic Family, body mass, migratory strategy and feeding strata had large effects on avian site occupancy, whereas abundance traits such as mean density and extent of occurrence showed little predictive ability. After accounting for correlated extinction risk attributed to life history, the degradation of stand structure at the local scale was more important for species richness than habitat modification at landscape or patch scales. While individual species showed various responses to the different scales of habitat modification, the distribution of many species was limited by vegetation structure at the landscape scale. Maintaining stand basal area and restoring degraded rainforests at the local scale will increase the probability of occupancy for members of the rainforest bird community. However, revegetation and retention of forest cover at the landscape scale may be necessary for the successful colonisation of many species. Chapter 3 introduced a predictive hypothesis-driven approach for quantifying the relative contribution of historic and contemporary processes to genetic connectivity. Current analytic frameworks in population genetics have difficulty evaluating meaningful hypotheses about spatial processes in dynamic landscapes. Confronting genetic data with models of historic and contemporary landscapes allowed the identification of dispersal processes operating in naturally heterogeneous and human-altered systems. Two measures of indirect gene flow were estimated from microsatellite polymorphism among 11 logrunner populations. Of particular interest was how much information in the genetic data was attributable to processes occurring in a reconstructed historic landscape and a contemporary human-modified landscape. A linear mixed model was used to estimate appropriate sampling variance from non-independent data and information-theoretic model selection provided strength of evidence for alternate hypotheses. The historic and contemporary landscapes explained an equal proportion of variation in genetic differentiation and there was considerable evidence for a temporal shift in dispersal pattern. Migration rates estimated from genealogical information were primarily influenced by contemporary landscape change. Landscape heterogeneity appeared to facilitate gene flow prior to European settlement, but contemporary deforestation is rapidly becoming the most important barrier to logrunner dispersal. Understanding asymmetric dispersal is becoming an important consideration for the conservation metapopulations. Populations acting as net exporters of dispersing animals may be able to rescue local populations from extinction and allow metapopulations to persist in degraded landscapes impacted by habitat loss. In Chapter 4, I estimated bidirectional migration rates from genetic data to infer dispersal among 11 logrunner populations. The first question posed was, does logrunner dispersal correspond to the source-sink or balanced model of dispersal? The second question involved determining the strength of evidence for two hypotheses about how landscape structure has affected asymmetric dispersal. Hypothesis one proposed that asymmetric dispersal was primarily influenced by naturally occurring habitat heterogeneity. Hypothesis two asserted that asymmetric dispersal was predominantly influenced by anthropogenic landscape change. The data were confronted with the alternate hypotheses using linear mixed models and landscape covariates extracted from digital maps. The results showed the direction of asymmetric dispersal was consistent with source-sink population structure. I also discovered that the asymmetry in dispersal was influenced more by anthropogenic landscape change than by naturally occurring habitat heterogeneity. Intact landscapes were net exporters of dispersing logrunners while landscapes heavily impacted by rainforest clearing were net importers of individuals. Elevated immigration rates into landscapes impacted by rainforest clearing appeared to arrest population declines in accordance with the rescue effect. The primary conclusion emerging from the study of patch occupancy and dispersal was that logrunner populations in South East Queensland conformed to a mainland-island metapopulation. Asymmetric dispersal from the largest expanse of upland rainforest appeared to prevent fragmented rainforests in close proximity from going locally extinct. While the distribution of logrunners was limited by the spatial configuration of rainforest patches, other rainforest birds exhibited variable responses to scale of habitat modification. The most consistent pattern was several species dropping-out of the community in degraded stands affected by selective timber harvest. Deforestation at the landscape scale also played a role in the extremely low patch occupancy rates of Albert’s lyrebirds (Menura alberti) and green catbirds (Ailuroedus crassirostris).

The local extinction of habitat patches and dispersal between the patches are important processes structuring animal populations in heterogeneous environments. Understanding these two processes is crucial for the conservation of wildlife populations in landscapes impacted by human land-use. Approximately 50% of the subtropical rainforest in South East Queensland, Australia has been lost to deforestation over the last 100 years. While large areas of rainforest are reserved, little is known about the distribution and population status of rainforest birds within smaller remnants in the region. The overall research problem for this thesis was to understand how deforestation and fragmentation of subtropical rainforest affects the occurrence of rainforest birds and the effective dispersal of a rainforest-restricted species, the logrunner (Orthonyx temminckii). Understanding why some bird species are lost from habitat patches while others remain will lead to improved conservation of extinction prone species in fragmented landscapes. Although the mechanisms underlying local extinctions are well established in temperate systems, the relative importance of local and regional processes on species occurrence in subtropical and tropical rainforests is poorly understood. Chapter 2 investigated the relative effects of life history and scale of habitat modification on avian site occupancy using observational data collected at 46 rainforest sites in South East Queensland. A probabilistic model for the joint site occupancy of 29 bird species was used to evaluate hypotheses for the effects of avian life history traits on the occurrence of multiple species. The single-species occurrence models incorporated habitat effects on detection, which may be especially important in rainforests because dense vegetation and idiosyncratic occurrence of species can interfere with sampling. Occupancy rates for each species were modelled to determine the relative influence of process operating at the stand, landscape and patch scales. The life history analysis indicated taxonomic Family, body mass, migratory strategy and feeding strata had large effects on avian site occupancy, whereas abundance traits such as mean density and extent of occurrence showed little predictive ability. After accounting for correlated extinction risk attributed to life history, the degradation of stand structure at the local scale was more important for species richness than habitat modification at landscape or patch scales. While individual species showed various responses to the different scales of habitat modification, the distribution of many species was limited by vegetation structure at the landscape scale. Maintaining stand basal area and restoring degraded rainforests at the local scale will increase the probability of occupancy for members of the rainforest bird community. However, revegetation and retention of forest cover at the landscape scale may be necessary for the successful colonisation of many species. Chapter 3 introduced a predictive hypothesis-driven approach for quantifying the relative contribution of historic and contemporary processes to genetic connectivity. Current analytic frameworks in population genetics have difficulty evaluating meaningful hypotheses about spatial processes in dynamic landscapes. Confronting genetic data with models of historic and contemporary landscapes allowed the identification of dispersal processes operating in naturally heterogeneous and human-altered systems. Two measures of indirect gene flow were estimated from microsatellite polymorphism among 11 logrunner populations. Of particular interest was how much information in the genetic data was attributable to processes occurring in a reconstructed historic landscape and a contemporary human-modified landscape. A linear mixed model was used to estimate appropriate sampling variance from non-independent data and information-theoretic model selection provided strength of evidence for alternate hypotheses. The historic and contemporary landscapes explained an equal proportion of variation in genetic differentiation and there was considerable evidence for a temporal shift in dispersal pattern. Migration rates estimated from genealogical information were primarily influenced by contemporary landscape change. Landscape heterogeneity appeared to facilitate gene flow prior to European settlement, but contemporary deforestation is rapidly becoming the most important barrier to logrunner dispersal. Understanding asymmetric dispersal is becoming an important consideration for the conservation metapopulations. Populations acting as net exporters of dispersing animals may be able to rescue local populations from extinction and allow metapopulations to persist in degraded landscapes impacted by habitat loss. In Chapter 4, I estimated bidirectional migration rates from genetic data to infer dispersal among 11 logrunner populations. The first question posed was, does logrunner dispersal correspond to the source-sink or balanced model of dispersal? The second question involved determining the strength of evidence for two hypotheses about how landscape structure has affected asymmetric dispersal. Hypothesis one proposed that asymmetric dispersal was primarily influenced by naturally occurring habitat heterogeneity. Hypothesis two asserted that asymmetric dispersal was predominantly influenced by anthropogenic landscape change. The data were confronted with the alternate hypotheses using linear mixed models and landscape covariates extracted from digital maps. The results showed the direction of asymmetric dispersal was consistent with source-sink population structure. I also discovered that the asymmetry in dispersal was influenced more by anthropogenic landscape change than by naturally occurring habitat heterogeneity. Intact landscapes were net exporters of dispersing logrunners while landscapes heavily impacted by rainforest clearing were net importers of individuals. Elevated immigration rates into landscapes impacted by rainforest clearing appeared to arrest population declines in accordance with the rescue effect. The primary conclusion emerging from the study of patch occupancy and dispersal was that logrunner populations in South East Queensland conformed to a mainland-island metapopulation. Asymmetric dispersal from the largest expanse of upland rainforest appeared to prevent fragmented rainforests in close proximity from going locally extinct. While the distribution of logrunners was limited by the spatial configuration of rainforest patches, other rainforest birds exhibited variable responses to scale of habitat modification. The most consistent pattern was several species dropping-out of the community in degraded stands affected by selective timber harvest. Deforestation at the landscape scale also played a role in the extremely low patch occupancy rates of Albert’s lyrebirds (Menura alberti) and green catbirds (Ailuroedus crassirostris).