Spatial and temporal variation of house prices

This thesis originally developed a spatial and temporal analysis approach. This approach was applied to investigate the variation of house prices in Australia. The findings discovered the behaviours of house prices and the interconnections between them across the Australian cities.

Climate-related spatial and temporal variation in bill morphology over the past century in Australian parrots

Aim: Allen's rule posits that the appendages of endothermic organisms will be larger in warmer climates to allow for dumping of heat loads. Given a link between appendage size and climate, we tested the prediction that climate change has driven the evolution of larger bills in birds, resulting in measurable changes over the recent past. Location: Australia. Methods: We explored geographical and temporal variation in bill surface area of five Australian parrot species to determine whether individuals from warmer climates have larger bills, and whether there have been increases in bill surface area over time, consistent with climatic warming. Measurements were obtained from museum specimens dating from 1871 to 2008. These data were then related to geographical location, collection date and locality-specific climate data, in order to construct and compare models of spatio-temporal and climate-related variation in bill morphology. Results: There have been increases in bill surface area in mulga parrots (Psephotus varius), gang-gang cockatoos (Callocephalon fimbriatum), red-rumped parrots (Psephotus haematonotus) and male crimson rosellas (Platycercus elegans), equating to a c. 4-10% increase in bill surface area since 1871. Average maximum summer temperature in the 5 years prior to specimen collection also positively predicted bill surface area in mulga parrots, red-rumped parrots and crimson rosellas, consistent with Allen's rule. With the exception of red-rumped parrots, however, models with geographical location and year of collection were still better predictors of bill surface area than local climate at the date of collection. Main conclusions: Our analysis provides evidence that four species of parrot have exhibited adaptive change in bills over the past century potentially mitigating the thermal stress caused by climatic warming. Although consistent with the predicted effects of climate change, the temporal patterns we observe may have additional causes, however, such as changes in primary productivity, habitat or food availability.

Spatial prediction of rufous bristlebird habitat in a coastal heathland: a GIS-based approach

1. To develop a conservation management plan for a species, knowledge of its distribution and spatial arrangement of preferred habitat is essential. This is a difficult task, especially when the species of concern is in low   abundance. In south-western Victoria, Australia, populations of the rare rufous bristlebird Dasyornis broadbenti are threatened by fragmentation of suitable habitat. In order to improve the conservation status of this species, critical habitat requirements must be identified and a system of corridors must be established to link known populations. A predictive spatial model of rufous bristlebird habitat was developed in order to identify critical areas requiring preservation, such as corridors for dispersal.
2. Habitat models generated using generalized linear modelling techniques can assist in delineating the specific habitat requirements of a species. Coupled with geographic information system (GIS) technology, these models can be extrapolated to produce maps displaying the spatial configuration of suitable habitat.
3. Models were generated using logistic regression, with bristlebird presence or absence as the dependent variable and landscape variables, extracted from both GIS data layers and multispectral digital imagery, as the predictors. A multimodel inference approach based on Akaike’s information criterion was used and the resulting model was applied in a GIS to extrapolate predicted likelihood of occurrence across the entire area of concern. The predictive performance of the selected model was evaluated using the receiver operating characteristic (ROC) technique. A hierarchical partitioning protocol was used to identify the predictor variables most likely to influence variation in the dependent variable. Probability of species presence was used as an index of habitat suitability.
4. Negative associations between rufous bristlebird presence and  increasing elevation, 'distance to cree', 'distance to coast' and sun index were evident, suggesting a preference for areas relatively low in altitude, in close proximity to the coastal fringe and drainage lines, and receiving less direct sunlight. A positive association with increasing habitat complexity also suggested that this species prefers areas containing high vertical density of vegetation.
5. The predictive performance of the selected model was shown to be high (area under the curve 0·97), indicating a good fit of the model to the data. Hierarchical partitioning analysis showed that all the variables considered had significant  independent contributions towards explaining the variation in the dependent variable. The proportion of the total study area that was predicted as suitable habitat for the rufous bristlebird (using probability of occurrence at a ≥0·5 level ) was 16%.
6. Synthesis and applications. The spatial model clearly delineated areas predicted as highly suitable rufous bristlebird habitat, with evidence of potential corridors linking coastal and inland populations via gullies. Conservation of this species will depend on management actions that protect the critical habitats identified in the model. A multi-scale  approach to the modelling process is recommended whereby a spatially explicit model is first generated using landscape variables extracted from a GIS, and a second model at site level is developed using fine-scale habitat variables measured on the ground. Where there are constraints on the time and cost involved in measuring finer scale variables, the first step alone can be used for conservation planning.

Bayesian classification of catchments using spatial data: a first step to improved modelling of catchment effects on stream ecological condition

A major challenge facing freshwater ecologists and managers is the development of models that link stream ecological condition to catchment scale effects, such as land use. Previous attempts to make such models have followed two general approaches. The bottom-up approach employs mechanistic models, which can quickly become too complex to be useful. The top-down approach employs empirical models derived from large data sets, and has often suffered from large amounts of unexplained variation in stream condition.

We believe that the lack of success of both modelling approaches may be at least partly explained by scientists considering too wide a breadth of catchment type. Thus, we believe that by stratifying large sets of catchments into groups of similar types prior to modelling, both types of models may be improved. This paper describes preliminary work using a Bayesian classification software package, ‘Autoclass’ (Cheeseman and Stutz 1996) to create classes of catchments within the Murray Darling Basin based on physiographic data.

Autoclass uses a model-based classification method that employs finite mixture modelling and trades off model fit versus complexity, leading to a parsimonious solution. The software provides information on the posterior probability that the classification is ‘correct’ and also probabilities for alternative classifications. The importance of each attribute in defining the individual classes is calculated and presented, assisting description of the classes. Each case is ‘assigned’ to a class based on membership probability, but the probability of membership of other classes is also provided. This feature deals very well with cases that do not fit neatly into a larger class. Lastly, Autoclass requires the user to specify the measurement error of continuous variables.

Catchments were derived from the Australian digital elevation model. Physiographic data werederived from national spatial data sets. There was very little information on measurement errors for the spatial data, and so a conservative error of 5% of data range was adopted for all continuous attributes. The incorporation of uncertainty into spatial data sets remains a research challenge.

The results of the classification were very encouraging. The software found nine classes of catchments in the Murray Darling Basin. The classes grouped together geographically, and followed altitude and latitude gradients, despite the fact that these variables were not included in the classification. Descriptions of the classes reveal very different physiographic environments, ranging from dry and flat catchments (i.e. lowlands), through to wet and hilly catchments (i.e. mountainous areas). Rainfall and slope were two important discriminators between classes. These two attributes, in particular, will affect the ways in which the stream interacts with the catchment, and can thus be expected to modify the effects of land use change on ecological condition. Thus, realistic models of the effects of land use change on streams would differ between the different types of catchments, and sound management practices will differ.

A small number of catchments were assigned to their primary class with relatively low probability. These catchments lie on the boundaries of groups of catchments, with the second most likely class being an adjacent group. The locations of these ‘uncertain’ catchments show that the Bayesian classification dealt well with cases that do not fit neatly into larger classes.

Although the results are intuitive, we cannot yet assess whether the classifications described in this paper would assist the modelling of catchment scale effects on stream ecological condition. It is most likely that catchment classification and modelling will be an iterative process, where the needs of the model are used to guide classification, and the results of classifications used to suggest further refinements to models.

Variation in gametophyte dominance in populations of Chondrus verrucosus (Gigartinaceae, Rhodophyta)

We describe the abundance, including spatial and temporal variability, of phases of the isomorphic Chondrus verrucosus Mikami from Japan. Chondrus verrucosus occurred in a dense (∼90% cover) and temporally stable bed on a small, isolated rocky outcrop (Oyakoiwa) in Shizuoka Prefecture. Small vegetative fronds were always much more abundant than large vegetative and fertile fronds over the spring to late summer periods in 1999 and 2000. Over the same period, fertile carposporophytic fronds were generally more abundant than fertile tetrasporophytic fronds, and fertile male fronds appeared infrequently at low densities. Using the resorcinol-acetal test, we determined the proportion of gametophytes and tetrasporophytes in three populations of C. verrucosus: Oyakoiwa and Noroshi (Shizuoka) in the summers of 1999 and 2000 and Kamehana Point (Miyagi) in autumn 2000. All populations had a significantly higher proportion of gametophytes than tetrasporophytes in both years, although gametophytic proportions were lower at Noroshi (∼70%) than at Oyakoiwa (∼80%) and Kamehana Point (∼97%). However, examination of all isolated individuals sampled on Noroshi showed equal proportions of each phase in 1999, but gametophyte dominance (74%) in 2000. Differences in dispersal and spore production between phases are discussed as mechanisms potentially contributing to variation in gametophyte dominance.

The spatial pattern of natural selection when selection depends upon experience

Apostatic (frequency‐ or density‐dependent) selection, aposematic signals, and mate choice behavior generally require that the mean prey or potential mate density m value be high enough (above a threshold T) to result in sufficient encounter rates for the searcher to learn or retain the association between conspicuous signals and prey unprofitability, to forage apostatically, or to choose among mates. This assumes that all searchers experience , which implicitly assumes an even dispersion of targets among searcher territories. Uneven dispersion generates new phenomena. If , then only territories with local density x values that are greater than T favor experience‐based behavior, leading to spatially variable frequency‐ or density‐dependent selection intensity. As aggregation increases, the increase in percentage of targets in favorable territories ( ) is greater than the increase in the percentage of territories that are favorable. The relationship is reversed when . In both cases, because as few as 10% of the territories can contain 80% of the targets, only a few territory holders may account for most of the selection on most of the target population; accidents of experience in only a few searchers can have unexpectedly large effects on the target population. This also provides an explanation for high searcher behavior variation (personalities) : individuals from favorable territories will behave differently in behavioral experiments than those from unfavorable territories, at least with respect to similar kinds of targets. These effects will generate spatial heterogeneity in natural and sexual selection in what are otherwise uniform environments.

Environmental variation and the maintenance of polymorphism : the effect of ambient light spectrum on mating behaviour and sexual selection in guppies

The intensity of sexual selection is influenced by environmental conditions because these conditions influence signal propagation and the risks of the signal being exploited by predators and parasites. We explore the possibility that spatial or temporal heterogeneity in environmental signalling conditions (in this case light spectrum) may induce fluctuating sexual selection on male behaviour and ornamentation in guppies. We used shade cloth and filters to experimentally manipulate light spectrum, mimicking conditions found naturally: early morning/late afternoon light (SC treatment), midday forest shade (F89 filter treatment) and midday woodland shade (F55 filter treatment). Females were more responsive to male courtship and males were less likely to attempt sneak copulations under F55 light than the other two treatments. By contrast, male display rate was not influenced by treatment. Females tended to prefer the same males under SC and F55 light, but attractiveness in these treatments was unrelated to attractiveness under F89 light. There were similarities among treatments in the traits that females preferred: females preferred males with larger areas of orange in all three treatments. There were, however, also some differences, including preference for larger males under F89 light and for smaller males under the other treatments. Overall, the influence of ambient light spectrum on the relative importance of mate choice and male sneak copulation may have important implications for the mode and strength of sexual selection in different environments. The findings on attractiveness and preference functions, however, suggest that light spectrum only weakly affects the direction of sexual selection by female choice.

Explanations for variation in cognitive ability : behavioural ecology meets comparative cognition

Sara Shettleworth has played a defining role in the development of animal cognition and its integration into other parts of biology, especially behavioural ecology. Here we chart some of that progress in understanding the causes and importance of variation in cognitive ability and highlight how Tinbergen's levels of explanation provide a useful framework for this field. We also review how experimental design is crucial in investigating cognition and stress the need for naturalistic experiments and field studies. We focus particularly on the example of the relationship among food hoarding, spatial cognition and hippocampal structure, and review the conflicting evidence for sex differences in spatial cognition. We finish with speculation that a combination of Tinbergen and Shettleworth-style approaches would be the way to grapple with the as-yet unanswered questions of why birds mimic heterospecifics.

Large-herbivore distribution and abundance : intra-and interspecific niche variation in the tropics

Determining the biological and environmental factors that limit the distribution and abundance of organisms is central to our understanding of the niche concept and crucial for predicting how species may respond to large-scale environmental change, such as global warming. However, detailed ecological information for the majority of species has been collected only at a local scale, and insufficient consideration has been given to geographical variation in intraspecific niche requirements. To evaluate the influence of environmental and biological factors on patterns of species distribution and abundance, we conducted a detailed, broadscale study across the tropical savannas of northern Australia on the ecology of three large, sympatric marsupial herbivores (family Macropodidae): the antilopine wallaroo (Macropus antilopinus), common wallaroo (M. robustus), and eastern grey kangaroo (M. giganteus). Using information on species abundance, climate, fire history, habitat, and resource availability, we constructed species' habitat models varying from the level of the complete distribution to smaller regional areas. Multiple factors affected macropod abundance, and the importance of these factors was dependent on the spatial scale of analyses. Fire regimes, water availability, geology, and soil type and climate were most important at the large scale, whereas aspects of habitat structure and interspecific species abundance were important at smaller scales. The distribution and abundance of eastern grey kangaroos and common wallaroos were strongly influenced by climate. Our results suggest that interspecific competition between antilopine wallaroos and eastern grey kangaroos may occur. The antilopine wallaroo and eastern grey kangaroo (grazers) preferred more nutrient-rich soils than the common wallaroo (grazer/browser), which we relate to differences in feeding modes. The abundance of antilopine wallaroos was higher on sites that were burned, whereas the abundance of common wallaroos was higher on unburned sites. Future climate change predicted for Australia has the capacity to seriously affect the abundance and conservation of macropod species in tropical savannas. The results of our models suggest that, in particular, the effects of changing climatic conditions on fire regimes, habitat structure, and water availability may lead to species declines and marked changes in macropod communities.

Temporal and spatial variability of breeding in Australian birds and the potential implications of climate change

Climate change has profound implications for biodiversity worldwide. To understand its effects on Australia's avifauna, we need to evaluate the effects of annual climatic variability and geographical climate gradients. Here, we use national datasets to examine variation in breeding of 16 species of common and widespread Australian landbirds, in relation to four variables: altitude, latitude, year and the Southern Oscillation Index. Analysis of 30 years of nesting records confirmed that breeding was generally later in colder altitudes and latitudes (geographic variation), but was not consistently related to year or the Southern Oscillation Index (temporal variation). However, power to detect expected temporal effects was low. The timing of breeding became significantly earlier with year only in south-eastern Australia. In contrast, an index of breeding activity (the proportion of atlas records for a species for which breeding was reported) increased with increasing winter values of the Southern Oscillation Index (generally wetter conditions) for all 16 species across Australia. This suggests that annual fluctuations in rainfall can have dramatic and immediate effects on breeding, even for largely sedentary, seasonally breeding species. If, as expected, climate change creates drier conditions over much of Australia, we predict a marked negative effect on bird breeding.

Threshold dynamic time warping for spatial activity recognition

Non-invasive spatial activity recognition is a difficult task, complicated by variation in how the same activities are conducted and furthermore by noise introduced by video tracking procedures. In this paper we propose an algorithm based on dynamic time warping (DTW) as a viable method with which to quantify segmented spatial activity sequences from a video tracking system. DTW is a widely used technique for optimally aligning or warping temporal sequences through minimisation of the distance between their components. The proposed algorithm threshold DTW (TDTW) is capable of accurate spatial sequence distance quantification and is shown using a three class spatial data set to be more robust and accurate than DTW and the discrete hidden markov model (HMM). We also evaluate the application of a band dynamic programming (DP) constraint to TDTW in order to reduce extraneous warping between sequences and to reduce the computation complexity of the approach. Results show that application of a band DP constraint to TDTW improves runtime performance significantly, whilst still maintaining a high precision and recall.

Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ~16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

Spatial and temporal drivers of small mammal distributions in a semi-arid environment : the role of rainfall, vegetation and life-history

A key task in ecology is to understand the drivers of animal distributions. In arid and semi-arid environments, this is challenging because animal populations show considerable spatial and temporal variation. An effective approach in such systems is to examine both broad-scale and long-term data. We used this approach to investigate the distribution of small mammal species in semi-arid ‘mallee’ vegetation in south-eastern Australia. First, we examined broad-scale data collected at 280 sites across the Murray Mallee region. We used generalized additive mixed models (GAMMs) to examine four hypotheses concerning factors that influence the distribution of individual mammal species at this scale: vegetation structure, floristic diversity, topography and recent rainfall. Second, we used long-term data from a single conservation reserve (surveyed from 1997 to 2012) to examine small mammal responses to rainfall over a period spanning a broad range of climatic conditions, including record high rainfall in 2011. Small mammal distributions were strongly associated with vegetation structure and rainfall patterns, but the relative importance of these drivers was species-specific. The distribution of the mallee ningaui Ningaui yvonneae, for example, was largely determined by the cover of hummock grass; whereas the occurrence of the western pygmy possum Cercartetus concinnus was most strongly associated with above-average rainfall. Further, the combination of both broad-scale and long-term data provided valuable insights. Bolam's mouse Pseudomys bolami was uncommon during the broad-scale survey, but long-term surveys showed that it responds positively to above-average rainfall. Conceptual models developed for small mammals in temperate and central arid Australia, respectively, were not, on their own, adequate to account for the distributional patterns of species in this semi-arid ecosystem. Species-specific variation in the relative importance of different drivers was more effectively explained by qualitative differences in life-history attributes among species.