The diet of Pacific gulls (Larus pacificus) breeding at Seal Island in northern Bass Strait

The endemic Pacific gull (Larus pacificus) is Australia's largest larid, and though little is currently known of its foraging ecology, its size and wide distribution suggest that it may play an important role within the marine environment. In the present study, regurgitate pellets collected from Seal Island in northern Bass Strait were used to compare intra- and interannual trends in diet composition. The main taxa identified in pellets were the common diving-petrel (Pelecanoides urinatrix), leatherjacket species (Family Monacanthidae), short-tailed shearwater (Puffinus tenuirostris) and mirror bush (Coprosma repens). Analysis of similarity (ANOSIM) identified no significant differences in numerical abundance of the dominant prey species between years, suggesting that the prey base in this region is temporally consistent or that the gulls consume low enough numbers to be unaffected by fluctuation in prey populations. Diving-petrels were consumed in consistently high numbers, suggesting the gulls may be an important predator of this species, or that the gulls are particularly skilled at foraging for them. © CSIRO 2014.

Stable feature selection for clinical prediction: Exploiting ICD tree structure using Tree-Lasso

Modern healthcare is getting reshaped by growing Electronic Medical Records (EMR). Recently, these records have been shown of great value towards building clinical prediction models. In EMR data, patients' diseases and hospital interventions are captured through a set of diagnoses and procedures codes. These codes are usually represented in a tree form (e.g. ICD-10 tree) and the codes within a tree branch may be highly correlated. These codes can be used as features to build a prediction model and an appropriate feature selection can inform a clinician about important risk factors for a disease. Traditional feature selection methods (e.g. Information Gain, T-test, etc.) consider each variable independently and usually end up having a long feature list. Recently, Lasso and related l1-penalty based feature selection methods have become popular due to their joint feature selection property. However, Lasso is known to have problems of selecting one feature of many correlated features randomly. This hinders the clinicians to arrive at a stable feature set, which is crucial for clinical decision making process. In this paper, we solve this problem by using a recently proposed Tree-Lasso model. Since, the stability behavior of Tree-Lasso is not well understood, we study the stability behavior of Tree-Lasso and compare it with other feature selection methods. Using a synthetic and two real-world datasets (Cancer and Acute Myocardial Infarction), we show that Tree-Lasso based feature selection is significantly more stable than Lasso and comparable to other methods e.g. Information Gain, ReliefF and T-test. We further show that, using different types of classifiers such as logistic regression, naive Bayes, support vector machines, decision trees and Random Forest, the classification performance of Tree-Lasso is comparable to Lasso and better than other methods. Our result has implications in identifying stable risk factors for many healthcare problems and therefore can potentially assist clinical decision making for accurate medical prognosis.

Natural selection for earlier male arrival to breeding grounds through direct and indirect effects in a migratory songbird

For migratory birds, the earlier arrival of males to breeding grounds is often expected to have fitness benefits. However, the selection differential on male arrival time has rarely been decomposed into the direct effect of male arrival and potential indirect effects through female traits. We measured the directional selection differential on male arrival time in the pied flycatcher (Ficedula hypoleuca) using data from 6 years and annual number of fledglings as the fitness proxy. Using structural equation modeling, we were able to take into account the temporal structure of the breeding cycle and the hierarchy between the examined traits. We found directional selection differentials for earlier male arrival date and earlier female laying date, as well as strong selection differential for larger clutch size. These selection differentials were due to direct selection only as indirect selection for these traits was nonsignificant. When decomposing the direct selection for earlier male arrival into direct and indirect effects, we discovered that it was almost exclusively due to the direct effect of male arrival date on fitness and not due to its indirect effects via female traits. In other words, we showed for the first time that there is a direct effect of male arrival date on fitness while accounting for those effects that are mediated by effects of the social partner. Our study thus indicates that natural selection directly favored earlier male arrival in this flycatcher population.

An assessment of riparian restoration outcomes in two rural catchments in south-western Victoria: Focusing on tree and shrub species richness, structure and recruitment characteristics

Riparian ecosystems are among the most degraded systems in the landscape,and there has been substantial investment in their restoration. Consequently, monitoring restoration interventions offers opportunities to further develop the science of riparian restoration, particularly how to move from small-scale implementation to a broader landscape scale. Here, we report on a broad range of riparian revegetation projects in two regions of south-western Victoria, the Corangamite and Glenelg-Hopkins Catchment Management Areas. The objectives of restoration interventions in these regions have been stated quite broadly, for example, to reinstate terrestrial habitat and biodiversity, control erosion and improve water quality. This study reports on tree and shrub composition, structure and recruitment after restoration works compared with remnant vegetation found regionally. Within each catchment, a total of 57 sites from six subcatchments were identified, representing three age-classes: <4, 4–8 and >8–12 years after treatment, as well as untreated (control) sites. Treatments comprised fencing to exclude stock, spraying or slashing to reduce weed cover, followed by planting with tube stock. Across the six subcatchments, 12 reference (remnant) sites were used to provide a benchmark for species richness, structural and recruitment characteristics and to aid interpretation of the effects of the restoration intervention. Vegetation structure was well developed in the treated sites by 4–8 years after treatment. However, structural complexity was higher at remnant sites than at treated or untreated sites due to a higher richness of small shrubs. Tree and shrub recruitment occurred in all remnant sites and at 64% of sites treated >4 years ago. Most seedling recruitment at treatment sites was by Acacia spp. This assessment provides data on species richness, structure and recruitment characteristics following restoration interventions. Data from this study will contribute to longitudinal studies of vegetation processes in riparian landscapes of south-western Victoria.

Employing sea-level rise scenarios to strategically select sea turtle nesting habitat important for long-term management at a temperate breeding area

Management strategies to protect endangered species primarily focus on safeguarding habitats currently perceived as important (due to high-density use, rarity or contribution to the biological cycle), rather than sites of future ecological importance. This discrepancy is particularly relevant for species inhabiting beaches and coastal areas that may be lost due to sea-level rise over the next 100 years through climate change. Here, we modelled four sea-level rise (SLR) scenarios (0.2, 0.6, 0.9 and 1.3 m) to determine the future vulnerability and viability of nesting habitat (six distinct nesting beaches totalling about 6 km in length) at a key loggerhead sea turtle (Caretta caretta) rookery (Zakynthos, Greece) in the Mediterranean. For each of the six nesting beaches, we identified (1) the area of beach currently used by turtles, (2) the area of the beach anticipated to become inundated under each SLR, (3) the area of beach anticipated to become unsuitable for nesting under each SLR, (4) the potential for habitat loss under the examined SLR, and (5) the extent to which the beaches may shift in relation to natural (i.e. cliffs) and artificial (i.e. beach front development) physical barriers. Even under the most conservative 0.2 m SLR scenario, about 38% (range: 31–48%) total nesting beach area would be lost, while an average 13% (range: 7–17%) current nesting beach area would be lost. About 4 km length of nesting habitat (representing 85% of nesting activity) would be lost under the 0.9 m scenario, because cliffs prevent landward beach migration. In comparison, while the other 2 km of beach (representing 15% nests) is also at high risk, it has the capacity for landward migration, because of an adjoining sand-dune system. Therefore, managers should strengthen actions on this latter area, as a climatically critical safeguard for future sea turtle nesting activity, in parallel to regularly assessing and revising measures on the current high-use nesting habitats of this important Mediterranean loggerhead population.

Tree-based iterated local search for Markov random fields with applications in image analysis

The maximum a posteriori assignment for general structure Markov random fields is computationally intractable. In this paper, we exploit tree-based methods to efficiently address this problem. Our novel method, named Tree-based Iterated Local Search (T-ILS), takes advantage of the tractability of tree-structures embedded within MRFs to derive strong local search in an ILS framework. The method efficiently explores exponentially large neighborhoods using a limited memory without any requirement on the cost functions. We evaluate the T-ILS on a simulated Ising model and two real-world vision problems: stereo matching and image denoising. Experimental results demonstrate that our methods are competitive against state-of-the-art rivals with significant computational gain.

Regulation of HbPIP2;3, a latex-abundant water transporter, is associated with latex dilution and yield in the rubber tree (Hevea brasiliensis Muell. Arg.)

Rubber tree (Hevea brasiliensis) latex, the source of natural rubber, is synthesised in the cytoplasm of laticifers. Efficient water inflow into laticifers is crucial for latex flow and production since it is the determinant of the total solid content of latex and its fluidity after tapping. As the mature laticifer vessel rings are devoid of plasmodesmata, water exchange between laticifers and surrounding cells is believed to be governed by plasma membrane intrinsic proteins (PIPs). To identify the most important PIP aquaporin in the water balance of laticifers, the transcriptional profiles of ten-latex-expressed PIPs were analysed. One of the most abundant transcripts, designated HbPIP2;3, was characterised in this study. When tested in Xenopus laevis oocytes HbPIP2;3 showed a high efficiency in increasing plasmalemma water conductance. Expression analysis indicated that the HbPIP2;3 gene was preferentially expressed in latex, and the transcripts were up-regulated by both wounding and exogenously applied Ethrel (a commonly-used ethylene releaser). Although regular tapping up-regulated the expression of HbPIP2;3 during the first few tappings of the virginal rubber trees, the transcriptional kinetics of HbPIP2;3 to Ethrel stimulation in the regularly tapped tree exhibited a similar pattern to that of the previously reported HbPIP2;1 in the virginal rubber trees. Furthermore, the mRNA level of HbPIP2;3 was associated with clonal yield potential and the Ethrel stimulation response. Together, these results have revealed the central regulatory role of HbPIP2;3 in laticifer water balance and ethylene stimulation of latex production in Hevea.

Clustering and visualization of failure modes using an evolving tree

Despite the popularity of Failure Mode and Effect Analysis (FMEA) in a wide range of industries, two well-known shortcomings are the complexity of the FMEA worksheet and its intricacy of use. To the best of our knowledge, the use of computation techniques for solving the aforementioned shortcomings is limited. As such, the idea of clustering and visualization pertaining to the failure modes in FMEA is proposed in this paper. A neural network visualization model with an incremental learning feature, i.e., the evolving tree (ETree), is adopted to allow the failure modes in FMEA to be clustered and visualized as a tree structure. In addition, the ideas of risk interval and risk ordering for different groups of failure modes are proposed to allow the failure modes to be ordered, analyzed, and evaluated in groups. The main advantages of the proposed method lie in its ability to transform failure modes in a complex FMEA worksheet to a tree structure for better visualization, while maintaining the risk evaluation and ordering features. It can be applied to the conventional FMEA methodology without requiring additional information or data. A real world case study in the edible bird nest industry in Sarawak (Borneo Island) is used to evaluate the usefulness of the proposed method. The experiments show that the failure modes in FMEA can be effectively visualized through the tree structure. A discussion with FMEA users engaged in the case study indicates that such visualization is helpful in comprehending and analyzing the respective failure modes, as compared with those in an FMEA table. The resulting tree structure, together with risk interval and risk ordering, provides a quick and easily understandable framework to elucidate important information from complex FMEA forms; therefore facilitating the decision-making tasks by FMEA users. The significance of this study is twofold, viz., the use of a computational visualization approach to tackling two well-known shortcomings of FMEA; and the use of ETree as an effective neural network learning paradigm to facilitate FMEA implementations. These findings aim to spearhead the potential adoption of FMEA as a useful and usable risk evaluation and management tool by the wider community.

Fathers with highly demanding partners and offspring in a semidesert environment: energetic aspects of the breeding system of Monteiro's Hornbills (Tockus monteiri) in Namibia

Molting females of Monteiro's Hornbills (Tockus monteiri) seal themselves in nest cavities to breed until chicks are about half grown. To gain insight into the chronology of energy requirements of the Monteiro's Hornbill family unit in relation to this peculiar breeding strategy, we measured a number of ecological, physiological, and environmental variables during the Monteiro's Hornbill's breeding season. Those measurements included rates of energy expenditure of female Monteiro's Hornbills while in the nest cavity, characterizing their thermal environment, timing of egg laying, molt, hatching and fledging of chicks, as well as measuring clutch size and chick growth. Temperatures within the nest box varied between 12 and 39°C and did not affect the female energy expenditure. Female body mass and energy expenditure averaged 319 g and 5 W, respectively, at the start of concealment and decreased by on average 1.1 g day -1 and 0.05 W day -1 during at least the first 30 days of the 52-58 day concealment period. Clutch size varied between 1 and 8 and averaged 4.1 eggs, with eggs averaging only 66% of the mass predicted for a bird of this size. Over the range of chick ages at which the female might leave the nest, the predicted energy requirements for maintenance and tissue growth for a Monteiro's Hornbill chick increase sharply from 1.2 W at age 8 to 3.0 W at age 25. Reduction of the female energy requirement with time, the relatively low growth rate and therewith low energy requirements of Monteiro's Hornbill chicks, and an appropriate timing of the female's exodus from the nest cavity all aid in containing peak energy demands to levels that are sustainable for the food provisioning male.

Breeding short-tailed shearwaters buffer local environmental variability in south-eastern Australia by foraging in Antarctic waters

BACKGROUND: Establishing patterns of movements of free-ranging animals in marine ecosystems is crucial for a better understanding of their feeding ecology, life history traits and conservation. As central place foragers, the habitat use of nesting seabirds is heavily influenced by the resources available within their foraging range. We tested the prediction that during years with lower resource availability, short-tailed shearwaters (Puffinus tenuirostris) provisioning chicks should increase their foraging effort, by extending their foraging range and/or duration, both when foraging in neritic (short trips) and distant oceanic waters (long trips). Using both GPS and geolocation data-loggers, at-sea movements and habitat use were investigated over three breeding seasons (2012-14) at two colonies in southeastern Australia. RESULTS: Most individuals performed daily short foraging trips over the study period and inter-annual variations observed in foraging parameters where mainly due to few individuals from Griffith Island, performing 2-day trips in 2014. When performing long foraging trips, this study showed that individuals from both colonies exploited similar zones in the Southern Ocean. The results of this study suggest that individuals could increase their foraging range while exploiting distant feeding zones, which could indicate that short-tailed shearwaters forage in Antarctic waters not only to maintain their body condition but may also do so to buffer against local environmental stochasticity. Lower breeding performances were associated with longer foraging trips to distant oceanic waters in 2013 and 2014 indicating they could mediate reductions in food availability around the breeding colonies by extending their foraging range in the Southern Ocean. CONCLUSIONS: This study highlights the importance of foraging flexibility as a fundamental aspect of life history in coastal/pelagic marine central place foragers living in highly variable environments and how these foraging strategies are use to buffer this variability.

Breeding habitat selection in an obligate beach bird: a test of the food resource hypothesis

The food resource hypothesis of breeding habitat selection in beach-nesting birds suggests that birds breed at sites with more prey to meet the increased energetic requirements associated with breeding. We compare prey resources using pitfall traps and core samples at breeding sites and absence sites of the eastern population of hooded plover, Thinornis rubricollis rubricollis, which, in this part of its range, is a threatened obligate beach bird. Breeding sites had higher abundances, equivalent species richness, and different assemblages of invertebrate prey compared with absence sites. Assemblages at breeding sites were characterised by more isopods, and fewer beetles of the family Phycosecidae. Breeding habitat selection by plovers appears to be associated with selection for sites with more food, and any process that degrades food resources at a site (e.g. kelp harvesting or marine pollution events) may reduce the likelihood of occupancy of that site by breeding birds.

Corvids congregate to breeding colonies of a burrow-nesting seabird

Egg predation is a major cause of reproductive failure among birds, and can compromise the viability of affected populations. Some egg predators aggregate near colonially breeding birds to exploit the seasonal increase of prey resources. We investigated spatial and temporal variations in the abundance of an egg predator (little raven Corvus mellori; Corvidae) to identify whether ravens aggregate spatially or temporally to coincide with any of three potential prey species: burrow-nesting little penguin (Eudyptula minor; Spheniscidae), short-tailed shearwater (Ardenna tenuirostris; Procellariidae), and surface-nesting silver gull (Chroicocephalus novaehollandiae; Laridae). We derived spatially explicit density estimates of little ravens using distance sampling along line transects throughout a calendar year, which encompassed little penguin, short-tailed shearwater and silver gull breeding and non-breeding seasons. High raven abundance coincided temporally with penguin and gull egg laying periods but not with that of shearwaters. The spatial distribution of raven density corresponded with the little penguin colony but not with shearwater or gull colonies. Thus, the presence of little penguin eggs in burrows correlated strongly with little raven activity, and this implies that little ravens may have learnt to exploit the plentiful subsurface food resource of little penguin eggs. Corvid management may be required to maintain the viability of this socially and economically important penguin colony.

Loss of periodicity in breeding success of waders links to changes in lemming cycles in Arctic ecosystems

Lemming population cycles in the Arctic have an important impact on the Arctic food web, indirectly also affecting breeding success in Arctic-nesting birds through shared predators. Over the last two decades lemming cycles have changed in amplitude and even disappeared in parts of the Arctic. To examine the large scale effect of these recent changes we re-analysed published data from the East Atlantic Flyway (EAF), where a relationship between lemming cycles and wader breeding success was earlier found, and new data on breeding success of waders in the East Asian-Australasian Flyway (EAAF). We found that 1) any long-term periodicities in wader breeding success existed only until the year 2000 in the EAAF and until the 1980s in the EAF; 2) studying these patterns at a smaller spatial scale, where the Siberian-Alaskan breeding grounds were divided into five geographical units largely based on landscape features, breeding success of waders from the EAAF was not correlated to an index of predation pressure, but positively correlated to Arctic summer temperatures in some species. We argue that fading out of lemming cycles in some parts of the Arctic is responsible for faltering periodicity in wader breeding success along both flyways. These changed conditions have not yet resulted in any marked changing trends in breeding success across years, and declining numbers of waders along the EAAF are therefore more likely a result of changing conditions at stop-over and wintering sites.