Avian patch occupancy and landscape genetics of logrunners (Orthonyx temminckii) in fragmented subtropical rainforests of South East Queensland

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).