Landscape characteristics associated with species richness and occurrence of small native mammals inhabiting a coastal heathland: a spatial modelling approach

In the coastal region of south-western Victoria, Australia, populations of native small mammal species are restricted to patches of suitable habitat in a highly fragmented landscape. The size and spatial arrangement of these patches is likely to influence both the occupancy and richness of species at a location. Geographic Information System (GIS)-based habitat models of the species richness of native small mammals, and individual species  occurrences, were developed to produce maps displaying the spatial  configuration of suitable habitat. Models were generated using either generalised linear Poisson regression (for species richness) or logistic regression (for species occurrences) with species richness or  presence/absence as the dependent variable and landscape variables, extracted from both GIS data layers and multi-spectral digital imagery, as the predictor variables. A multi-model inference approach based on the Akaike Information Criterion was used and the resulting model was applied in a GIS framework to extrapolate predicted richness/likelihood of occurrence across the entire area of the study. A negative association between species  richness and elevation, habitat complexity and sun index indicated that richness within the study area decreases with increasing altitude, vertical vegetation structure and exposure to solar radiation. Landform  characteristics were important (to varying degrees) in determining habitat occupancy for all of the species examined, while the influence of habitat complexity was important for only one of the species. Performance of all but one of the models generated using presence/absence data was high, as indicated by the area under the curve of a receiver-operating characteristic plot. The effective conservation of the small mammal species in the area of concern is likely to depend on management actions that promote the protection of the critical habitats identified in the models.

Geographical variation in bill size across bird species provides evidence for Allen's rule

Allen’s rule proposes that the appendages of endotherms are smaller, relative to body size, in colder climates, in order to reduce heat loss. Empirical support for Allen’s rule is mainly derived from occasional reports of geographical clines in extremity size of individual species. Interspecific evidence is restricted to two studies of leg proportions in seabirds and shorebirds. We used phylogenetic comparative analyses of 214 bird species to examine whether bird bills, significant sites of heat exchange, conform to Allen’s rule. The species comprised eight diverse taxonomic groups—toucans, African barbets, Australian parrots, estrildid finches, Canadian galliforms, penguins, gulls, and terns. Across all species, there were strongly significant relationships between bill length and both latitude and environmental temperature, with species in colder climates having significantly shorter bills. Patterns supporting Allen’s rule in relation to latitudinal or altitudinal distribution held within all groups except the finches. Evidence for a direct association with temperature was found within four groups (parrots, galliforms, penguins, and gulls). Support for Allen’s rule in leg elements was weaker, suggesting that bird bills may be more susceptible to thermoregulatory constraints generally. Our results provide the strongest comparative support yet published for Allen’s rule and demonstrate that thermoregulation has been an important factor in shaping the evolution of bird bills.

Prioritizing climate change adaptation options for iconic marine species

© 2015, Springer Science+Business Media Dordrecht. Adaptation options in response to climate impact scenarios for marine mammals and seabirds were developed based on the IPCC vulnerability framework. Under this framework, vulnerability to the physical effects of climate change can be reduced by adaptation options that reduce exposure of individuals, reduce the sensitivity of individuals, and increase the adaptive capacity of individual/species to cope with climate change. We evaluated options in each vulnerability category with three screening tools collectively forming an approach we term sequential adaptation prioritization for species. These tools were designed to evaluate (i) technical aspects (cost-benefit-risk, CBR), (ii) institutional barriers, and (iii) potential social acceptability. The CBR tool identified which adaptation options were high cost and low benefit, might be discarded, and which were high benefit and low cost, might be rapidly implemented (depending on risk). Low cost and low benefit options might not be pursued, while those that are high cost, but high benefit deserve further attention. Even with technical merit, adaptation options can fail because of institutional problems with implementation. The second evaluation tool, based on the conceptual framework on barriers to effective climate adaptation, identifies where barriers may exist, and leads to strategies for overcoming them. Finally, adaptation options may not be acceptable to society at large, or resisted by vocal opponents or groups. The social acceptability tool identifies potentially contested options, which may be useful to managers charged with implementing adaptation options. Social acceptability, as scored by experts, differed from acceptability scored by the public, indicating the need to involve the public in assessing this aspect. Scores from each tool for each scenario can be combined to rank the suite of adaptation options. This approach provides useful tools to assist conservation managers in selecting from a wide range of adaptation strategies; the methodology is also applicable to other conservation sectors.

Can the intermediate disturbance hypothesis and information on species traits predict anuran responses to fire?

Fire is a common form of recurrent disturbance in many ecosystems, but ecological theory has a poor record of predicting animal responses to fire, at both species and assemblage levels. As a consequence, there is limited information to guide fire regime management for biodiversity conservation. We investigated a key research gap in the fire ecology literature; that is, the response of an anuran assemblage to variation in the fire return interval. We tested two hypotheses using a spatially-explicit fire database collected over a 40 year period: 1) species richness would peak at intermediate levels of disturbance. 2) Species with traits which enabled them to escape fire - burrowing or canopy dwelling - would be better able to survive fires, resulting in higher levels of occurrence in frequently burned sites. We found no evidence for either a reduction in species richness at locations with short fire return intervals, or a peak in species richness at intermediate levels of disturbance. Although we found some support for individual species responses to fire return intervals, these were inconsistent with the interpretation of burrowing or climbing being functional traits for fire-avoidance. Instead burrowing and climbing species may be more likely to be disadvantaged by frequent fire than surface dwelling frogs. More generally, our results show that many species in our study system have persisted despite a range of fire frequencies, and therefore that active management of fire regimes for anuran persistence may be unnecessary. The responses of anurans to fire in this location are unlikely to be predictable using simple life-history traits. Future work should focus on understanding the mechanistic underpinnings of fire responses, by integrating information on animal behavior and species' ecological requirements.

Foraging ecology of ground-feeding woodland birds in temperate woodlands of Southern Australia

Ground-foraging birds of temperate woodlands of southern Australia are prominent among bird species considered to be susceptible to population decline. We examined the foraging ecology, including foraging substrates, actions and heights, of 13 ground-foraging species at four woodland sites in northern Victoria. Nine species are regarded as declining in southern Australia and four are considered common. Ten foraging substrates were identified, of which leaf-litter (54% of observations) and bare ground (17%) were most frequently used. In all woodland sites, litter was used more frequently than expected from its proportional cover. Bare ground was frequently used as a substrate by individual species, and fallen timber and grass were important for some species. Most species were generalists in their use of substrates. Six foraging actions were observed, of which gleaning and pouncing were most frequently recorded. All species foraged close to the ground and four foraged almost entirely at ground level. For pouncing birds, dead branches and fallen timber were the most important launch substrates from which pouncing actions were initiated. Eight of the 13 species differed in some aspect of their foraging ecology between woodland sites, especially in relation to the use of substrates (seven species). Fewer species (four) displayed differences in foraging ecology between seasons, with the greatest seasonal variation being in use of foraging substrates (three species). Overall, no significant differences were evident in the foraging ecologies of common and declining species. Species in both groups encompassed a wide range of foraging behaviours. Owing to this range in foraging ecology, the conservation of diverse assemblages of ground-foraging birds requires the maintenance of heterogeneous ground layers and careful management of disturbance processes.

'Green' treatment of acid mine drainage - a step towards sustainability

Sustainability is becoming increasingly important in the mining and mineral processing industries and must incorporate the associated waste products. Acid mine drainage (AMD) is one such by-product and is one of the most serious environmental problems facing the minerals industry today. The oxidation of sulphidic mine wastes often continues for a substantial period of time after mine closure, resulting in difficult and costly remediation and rehabilitation works. Mining companies are often reluctant to spend increasing amounts of money on waste treatment when the mine life is limited or even finished. Hence a simple, low maintenance and low-cost method of treating AMD is required. Whilst this paper does not address the issue of AMD, it does propose methods for removal of individual species from AMD with potential benefits, including raising AMD pH.

A novel concept of using biosolids as a biological adsorbent, or ‘biosorbent’, of metals from AMD is being investigated at a laboratory/pilot scale level. Biosolids are a by-product resulting from the biological treatment of wastewater, and have been previously shown to adsorb metals from aqueous solutions. This could lead to an environmentally sustainable or ‘green’ method for treating both AMD discharges and disposing/reusing the biosolids.

The result of a laboratory-scale study of the biosorption of Zn(II) is presented in this paper. Physical parameters including reaction kinetics, mixing speed and solution pH were investigated. Solution pH also rose an average of 2 pH units over the 24 hour equilibrium time – a valuable side effect when treating acid mine drainage. The outcome of the study highlights the usefulness of biosolids as a biosorbent for the removal/recovery of metal ions from acid mine drainage. A simple, low-cost treatment technology requiring low maintenance would be beneficial to the mining industry to address some issues relating to AMD and would help integrate environmental and economic considerations into sustainable environmental management.

Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Occurrence of small mammals in a fragmented landscape: the role of vegetation heterogeneity

Most studies of habitat use by small mammals rely on data from trapping grids. Such studies pertain to habitat use by individuals, which may not reflect population-level requirements. To meet the challenge of landscape change, it is important to understand habitat use by populations across large geographic areas. We surveyed small mammals in 48 forest remnants across a 300 km2 study area, to investigate the influence of vegetation heterogeneity on regional distributions. Information-theoretic techniques were used to evaluate models of vegetation associations. Richness of native mammals was influenced by vegetation condition: disturbed sites supported fewer species. Models for individual species showed the agile antechinus, Antechinus agilis, to prefer structurally diverse forest vegetation, the long-nosed potoroo, Potorous tridactylus, to favour mesic shrub communities, the bush rat, Rattus fuscipes, to prefer complex low cover regardless of composition, the swamp rat, Rattus lutreolus, to favour reduced canopy cover, and the house mouse, Mus domesticus, to prefer disturbed vegetation. To satisfy the needs of all native species, a mosaic of natural vegetation is required. Degradation and simplification of forest vegetation have detrimental consequences. These results highlight the need to consider habitat quality, together with more traditional biogeographic variables, when investigating factors influencing patch occupancy by native fauna in modified landscapes.

Defining plant resistance against Phytophthora Cinnamomi and application of resistance to revegetation

Phytophthora cinnamomi is a soil borne plant pathogen that causes devastating disease in many Australian ecosystems and threatens the survival of native flora. Compared with the number of plant species that are susceptible to P. cinnamomi, only a few species are known to be resistant and control of this pathogen by chemicals is difficult and undesirable in natural systems. The major aim of our research is therefore to characterise natural resistance and determine which signalling pathways and defence responses are involved. Our examination of resistance is being approached at several levels, one of which is through the use of the model plant, Arabidopsis. Previously, Arabidopsis had been shown to display ecotypic variation in responses to P. cinnamomi and we are exploring this further in conjunction with the analysis of a bank of Arabidopsis defence pathway mutants for their responses to the pathogen. These experiments will provide a fundamental basis for further analysis of the defence responses of native plants. Native species (susceptible and resistant) are being assessed for their responses to P. cinnamomi at morphological, biochemical and molecular levels. This research also involves field-based studies of plants under challenge at various sites throughout Victoria, Australia. The focus of this field-based research is to assess the responses of individual species to P. cinnamomi in the natural environment with the goal of identifying individuals within susceptible species that display 'resistance'. Understanding how plants are able to resist this pathogen will enable strategies to be developed to enhance species survival and to restore structure and biodiversity to the ecosystems under threat.

Maximising trapping efficiency in reptile surveys : the role of seasonality, weather conditions and moon phase on capture success

Context : Designing an appropriate survey protocol requires understanding of how capture rates of target species may be influenced by factors other than on-ground abundance, such as weather conditions or seasonality. This is particularly relevant for ectotherms such as reptiles, as activity can be affected by environmental conditions such as ambient temperature.
Aims : The present study examines factors affecting capture success of reptiles in semi-arid environments of southern Australia, and addresses the following two main questions: (1) what is the influence of weather and seasonal factors on capture rates of reptiles, and (2) what are the implications for developing an effective protocol for reptile surveys?
Methods : We surveyed reptiles using pitfall traps in spring and summer of 2006/07 and 2007/08 at sites (n = 280) throughout the Murray Mallee region of south-eastern Australia. We used mixed-effect regression models to investigate the influence of seasonal and weather-related variables on species’ capture success.
Key results : Total captures of reptiles, and the likelihood of capture of 15 reptile species, increased with rising daily temperature. Greater numbers of individual species were captured during spring than in summer, even though temperatures were cooler. This probably reflects greater levels of activity associated with breeding. Several species were more likely to be captured when maximum or minimum daily temperatures exceeded a certain level (e.g. Lerista labialis, Delma australis, Nephrurus levis). Other factors, such as rainfall and moon phase, also influenced capture success of some species.
Conclusions : Surveys for reptiles in semi-arid environments are likely to capture the greatest diversity of species on warm days in late spring months, although surveys on hot days in summer will enhance detection of particular species (e.g. Morethia boulengeri, Varanus gouldii). We recommend trapping during periods with maximum temperatures exceeding 25–30C and minimum overnight temperatures of 15C. Finally, trapping during rainfall and full-moon events will maximise chances of encountering species sensitive to these variables (blind snakes and geckoes).
Implications : Selecting the most favourable seasonal and weather conditions will help ensure that reptile surveys maximise the likelihood of capturing the greatest diversity of reptiles, while minimising trap-effort required.

Managing fire mosaics for small mammal conservation : a landscape perspective

1.Fire is a major driver of ecosystem structure and function worldwide. It is also widely used as a management tool to achieve conservation goals. A common objective is the maintenance of 'fire mosaics' comprising spatially heterogeneous patches of differing fire history. However, it is unclear what properties of fire mosaics most enhance conservation efforts. Here we focus on the spatial and temporal properties of fire-prone landscapes that influence the distribution of small mammals.

2.We surveyed small mammals in 28 landscapes (each 12·6km²) representing a range of fire histories in the Murray Mallee region (104 000km²) of semi-arid Australia. Generalised linear mixed models were used to examine the influence of five landscape properties on the capture rate of individual species and the species richness of native small mammals. We investigated the influence of the proportional extent of fire age-classes, the diversity of fire age-classes, the extent of the dominant vegetation type, rainfall history and biogeographic context.

3.Three of four study species were associated with the spatial extent of fire age-classes. Older vegetation was found to provide important habitat for native small mammals. Overall, however, rainfall history and biogeographic context were dominant influences: for example, the species richness of native mammals was positively associated with above-average rainfall. There was little evidence that the diversity of fire age-classes influenced either the capture rate of individual species or species richness.

4.Synthesis and applications. In fire-prone environments, habitat availability can change markedly over short time-scales. Sufficient habitat at a suitable seral stage within the landscape is a key requirement for species conservation. In mallee ecosystems, the retention of older vegetation is recommended to create more desirable fire mosaics for native small mammals. In addition to such spatial properties of mosaics that are amenable to manipulation, an understanding of how ecological processes affect the biota (such as variation in rainfall-driven productivity) is also essential for informed conservation management.

Spatial patterns, landscape genetics and post virus recovery of blacklip abalone, Haliotis rubra (Leach), in the western commercial fishing zone of Victoria

Historically, collecting nearshore habitat information has been problematic. Existing methods, such as aerial and satellite image interpretation are limited due to the attenuation of light in the water column obscuring the seabed structure. The advent of airborne bathymetric LiDAR (Light Detection and Ranging) systems (laser scanning of the seabed) now provides high-resolution seabed ‘images’ in areas that were previously difficult to survey. LiDAR imagery is available for the entire coastline of Victoria, Australia to depths of around 25 m, after being initially collected for climate change modelling by the Future Coasts Program (http://www.climatechange.vic.gov.au/adapting-to-climate-change/future-coasts). This dataset has provided the opportunity to test its applicability to inform fisheries management. Detailed geophysical information combined with spatially explicit AbTrack GPS located fisheries records and targeted genetic sampling is used in this study to provide a better understanding of the extent of available fishing grounds, direction of fishing effort and stock population structure within the Victorian western zone abalone fishery.
The species distribution modelling technique MaxEnt was used to produce a potential habitat suitability map for abalone in an attempt to capture the effective footprint of the  fishery. Also, by interrogating the spatially defined effort localities, we demonstrate an approach that may be used to identify areas where fishing effort is concentrated, and how this parameter changes temporally.
Despite barriers to adult dispersal (soft sediment barriers between reef patches), the genetic study indicates that larval movement is able to homogenize the gene pool over  large geographic distances. The western, central and eastern zone abalone stocks in Victoria were found to be a single large panmictic unit. This indicates high levels of stock connectivity and no obvious impacts of Abalone Viral Ganglioneuritis (AVG) on the genetic health of western zone stocks. We used detailed seafloor structure information interpreted from LiDAR to inform a replicated hierarchical fine scale genetic sampling design. We demonstrated that there may be extensive migration among abalone stocks across the Victorian abalone fishery.
This is contrary to previous studies that suggest recruitment is highly localised. In combination, these findings provide a valuable insight into the biology of H. rubra and immediate benefits for fisheries management. We discuss these results in the context of predicting resilience and adaptive potential of H. rubra stocks to environmental pressures and the spread of heritable diseases.
Adoption pathways are also provided to benefit future stock augmentation activities to catalyse the recovery of AVG affected reef codes. As larval dispersal is likely to be spatially and temporally variable, some AVG affected stocks are likely to recover through natural recruitment, while others will benefit from augmentation activities to ‘kick-start’ stock recovery. Evidence of neutral genetic homogeneity across Victorian reef codes suggests that the relocation of animals is unlikely to have significant genetic risks; however the potential for locally adaptive genetic differences may exist, and should be taken into consideration in future stock augmentation planning.
When combined, the spatial and genetic analyses provide valuable insights into stock productivity within the western zone fishery. Reefs appear to be expansive and support much available habitat, and the movement of larvae among reef structures is likely to be extensive in this region. Consequently, we propose that colonisation success and productivity is likely to be driven by ecological factors such as resources and/or competition, or physical factors such as wave exposure.

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Tropical savannas cover 20-30% of the world's land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australia's dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species' biologies have resulted in less predictable and idiosyncratic responses.

Establishing IUCN red list criteria for threatened ecosystems

The potential for conservation of individual species has been greatly advanced by the International Union for Conservation of Nature's (IUCN) development of objective, repeatable, and transparent criteria for assessing extinction risk that explicitly separate risk assessment from priority setting. At the IV World Conservation Congress in 2008, the process began to develop and implement comparable global standards for ecosystems. A working group established by the IUCN has begun formulating a system of quantitative categories and criteria, analogous to those used for species, for assigning levels of threat to ecosystems at local, regional, and global levels. A final system will require definitions of ecosystems; quantification of ecosystem status; identification of the stages of degradation and loss of ecosystems; proxy measures of risk (criteria); classification thresholds for these criteria; and standardized methods for performing assessments. The system will need to reflect the degree and rate of change in an ecosystem's extent, composition, structure, and function, and have its conceptual roots in ecological theory and empirical research. On the basis of these requirements and the hypothesis that ecosystem risk is a function of the risk of its component species, we propose a set of four criteria: recent declines in distribution or ecological function, historical total loss in distribution or ecological function, small distribution combined with decline, or very small distribution. Most work has focused on terrestrial ecosystems, but comparable thresholds and criteria for freshwater and marine ecosystems are also needed. These are the first steps in an international consultation process that will lead to a unified proposal to be presented at the next World Conservation Congress in 2012.

Urbanization impacts on mammals across urban-forest edges and a predictive model of edge effects

With accelerating rates of urbanization worldwide, a better understanding of ecological processes at the wildland-urban interface is critical to conserve biodiversity. We explored the effects of high and low-density housing developments on forest-dwelling mammals. Based on habitat characteristics, we expected a gradual decline in species abundance across forest-urban edges and an increased decline rate in higher contrast edges. We surveyed arboreal mammals in sites of high and low housing density along 600 m transects that spanned urban areas and areas turn on adjacent native forest. We also surveyed forest controls to test whether edge effects extended beyond our edge transects. We fitted models describing richness, total abundance and individual species abundance. Low-density housing developments provided suitable habitat for most arboreal mammals. In contrast, high-density housing developments had lower species richness, total abundance and individual species abundance, but supported the highest abundances of an urban adapter (Trichosurus vulpecula). We did not find the predicted gradual decline in species abundance. Of four species analysed, three exhibited no response to the proximity of urban boundaries, but spilled over into adjacent urban habitat to differing extents. One species (Petaurus australis) had an extended negative response to urban boundaries, suggesting that urban development has impacts beyond 300 m into adjacent forest. Our empirical work demonstrates that high-density housing developments have negative effects on both community and species level responses, except for one urban adapter. We developed a new predictive model of edge effects based on our results and the literature. To predict animal responses across edges, our framework integrates for first time: (1) habitat quality/preference, (2) species response with the proximity to the adjacent habitat, and (3) spillover extent/sensitivity to adjacent habitat boundaries. This framework will allow scientists, managers and planners better understand and predict both species responses across edges and impacts of development in mosaic landscapes.