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Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2−, ER− HER2−, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2− and ER− HER2− primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG , and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2− and ER− HER2− patients, showing that these events were truly subtype specific.

Controlling problem species for conservation can be fraught, particularly when native species are subject to lethal control. The noisy miner (Manorina melanocephala), has been the target of numerous lethal control efforts. Outcomes of these noisy miner removals have varied substantially, so identifying the circumstances under which they are effective is essential for ethical and effective management. We compiled data for all identified noisy miner removals (n = 45), including both permit‐based and unofficial removals. We investigated whether methodological and ecological factors explained the effectiveness of removals in reducing noisy miner density or increasing woodland bird richness and abundance. The only predictor of any measure of success was time between first and final culls which was positively related to reduction in noisy miner density. Surprisingly, despite removals mainly failing to reduce noisy miner density to below a threshold above which noisy miners impact smaller birds, woodland birds usually still increased. Disrupted social structure as noisy miners recolonized may have led to less effective aggressive exclusion of small birds. Further removals may not need to reduce noisy miner density to below this threshold to benefit woodland birds, but consistent monitoring and reporting would support better evaluation of effectiveness and correlates of success. The outcomes of noisy miner removal initiatives to conserve woodland birds have varied substantially, thus identifying the circumstances under which they are effective is essential for ethical management of this native problematic species. We collected and analyzed data for all known permit‐based and unofficial noisy miner removals to identify whether methodological and ecological factors explained the effectiveness of removals in reducing population sizes and improving richness and abundance of small woodland birds. To benefit small woodland birds, noisy miner density may not need to be reduced to below the threshold at which assemblages are disrupted in unmanaged situations.

Considerable resources are spent on habitat restoration across the globe to counter the impacts of habitat loss and degradation on wildlife populations. But, because of time and resourcing constraints on many conservation programs, the effectiveness of these habitat restoration programs in achieving their long-term goals of improving the population viability of particular wildlife species is rarely assessed and many restoration programs cannot demonstrate their effectiveness. Without such demonstration, and in particular demonstrating the causal relationships between habitat restoration actions and demographic responses of the target species, investments in restoration to achieve population outcomes are of uncertain value. Here, we describe an approach that builds on population data collected for a threatened Australian bird - the Grey-crowned Babbler Pomatostomus temporalis - to evaluate how effectively targeted habitat restoration work improves its viability. We built upon an extensive historical survey by conducting surveys 13 years later at 117 sites stratified by presence/absence of restoration works and by detection or not of birds in the first survey. Our performance metric was the number of individuals in a social group, which is both a measure of local abundance and directly related to breeding success. We employed an occupancy model to estimate the response of Grey-crowned Babbler social group size to the effects of time, restoration works, local habitat as measured by the density of large trees, and distance to the nearest other known group of babblers. Babbler group size decreased over the survey period at sites without restoration works, but restoration works were effective in stemming declines where they were done. Restoration was responsible for a difference of about one bird per group of 3-5 individuals; this is an important effect on the reproductive success of the social group. Effectiveness of restoration works targeted at the Grey-crowned Babbler was only demonstrable by sampling through time and including control sites without restoration works. This work demonstrates that while calls for better monitoring of restoration are valid, scope exists to recover a signal of effectiveness from opportunistic retrospective analyses.

Understanding the impact of management interventions on the environment over decadal and longer timeframes is urgently required. Longitudinal or large-scale studies with consistent methods are best practice, but more commonly, small datasets with differing methods are used to achieve larger coverage. Changes in methods and interpretation affect our ability to understand data trends through time or across space, so an ability to understand and adjust for such discrepancies between datasets is important for applied ecologists. Calibration or double sampling is the key to unlocking the value from disparate datasets, allowing us to account for the differences between datasets while acknowledging the uncertainties. We use a case study of livestock grazing impacts on riparian vegetation in southeastern Australia to develop a flexible and powerful approach to this problem. Using double sampling, we estimated changes in vegetation attributes over a 12-year period using a pseudo-quantitative visual method as the starting point, and the same technique plus point-intercept survey for the second round. The disparate nature of the datasets produced uncertain estimates of change over time, but accounting for this uncertainty explicitly is precisely the objective and highlights the need to look more closely at this very common problem in environmental management, as well as the potential benefits of the double sampling approach.

Aim Holistic measurement of the response of fauna communities to interventions requires suitable community condition metrics. However, the development of such metrics is hindered by the absence of broad‐scale typologies at suitable spatial and ecological resolutions. We aimed to derive a preliminary typology of terrestrial bird communities for Australia, based on bird co‐occurrence data, and describe and map the likely distribution of each community type across the continent. Location Mainland Australia, continental islands. Time Period 1973–2022. Major Taxa Studied Aves. Methods We used fine‐scale co‐occurrence data from standard 2‐ha surveys in BirdLife Australia's citizen‐science database. After filtering to reduce bias, we used hierarchical clustering followed by iterative consultation with experts to identify reliably distinct and recognisable terrestrial bird communities across Australia. We used Maxent to model the likely distributions of each community and developed community descriptions based on each community's composition and distribution. Results The resultant typology included 29 reliably distinct and recognisable bird communities with major clusters corresponding with seven broad geographical regions. The distributions of bird communities did not correspond tightly to the boundaries of major vegetation groups, with most communities occurring across multiple vegetation types. Main Conclusions Our preliminary typology of bird communities provides a standard classification at a continental scale. It newly defines distinct bird communities as entities for which condition benchmarks can be established to allow assessment of their conservation status and monitoring of change over time. Refinement will enable cryptic communities in areas with sparse data to be identified. The method could be translated to other regions where adequate coverage of data in the form of standardised surveys of fauna is available. Vast biodiversity datasets delivered through citizen science programs provide the opportunity to develop such typologies for fauna communities, as a precursor to developing targeted and informative community condition metrics.

Many objectives motivate ecological restoration, including improving vegetation condition, increasing the range and abundance of threatened species, and improving species richness and diversity. Although models have been used to examine the outcomes of ecological restoration, few researchers have attempted to develop models to account for multiple, potentially competing objectives. We developed a combined state-and-transition, species-distribution model to predict the effects of restoration actions on vegetation condition and extent, bird diversity, and the distribution of several bird species in southeastern Australian woodlands. The actions reflected several management objectives. We then validated the models against an independent data set and investigated how the best management decision might change when objectives were valued differently. We also used model results to identify effective restoration options for vegetation and bird species under a constrained budget. In the examples we evaluated, no one action (improving vegetation condition and extent, increasing bird diversity, or increasing the probability of occurrence for threatened species) provided the best outcome across all objectives. In agricultural lands, the optimal management actions for promoting the occurrence of the Brown Treecreeper (Climacteris picumnus), an iconic threatened species, resulted in little improvement in the extent of the vegetation and a high probability of decreased vegetation condition. This result highlights that the best management action in any situation depends on how much the different objectives are valued. In our example scenario, no management or weed control were most likely to be the best management options to satisfy multiple restoration objectives. Our approach to exploring trade-offs in management outcomes through integrated modeling and structured decision-support approaches has wide application for situations in which trade-offs exist between competing conservation objectives. Muchos objetivos motivan la restauración ecológica, incluyendo la mejora de la condición de la vegetación, el incremento de la extensión y abundancia de las especies amenazadas, y la mejora de la riqueza de especies y la diversidad. Aunque se han utilizado modelos para examinar los resultados de la restauración ecológica, pocos investigadores han intentado desarrollar modelos que consideren objetivos múltiples, potencialmente competitivos. Desarrollamos un modelo combinado de estado y transición y distribución de especies para predecir los efectos de las acetones de restauración sobre la condición y extensión de la vegetación, la diversidad de aves, y la distribución de varias especies de aves en los bosques del sureste de Australia. Las acciones reflejaron varios objetivos de manejo. Después validamos los modelos ante un conjunto independiente de datos e investigamos cómo las mejores decisiones de manejo podrían cambiar cuando los objetivos fueran valorados de forma diferente. También utilizamos resultados de modelos para identificar las opciones efectivas de restauración para la vegetación y las especies de aves bajo un presupuesto restringido. En los ejemplos que evaluamos ninguna acción única (la mejora de la extensión y condición de la vegetación, el incremento de la diversidad de aves, o el incremento de la probabilidad de presencia de las especies amenazadas) proporcionó el mejor resultado en todos los objetivos. En las tierras agricolas, las acciones de manejo óptimo para promover la presencia del trepatroncos café (Climacteris picumnus), una especie amenazada icónica, resultó en una pequeña mejora en la extensión de la vegetación y una alta probabilidad de una condición vegetal disminuida. Este resultado resalta que la mejor acción de manejo en cualquier situación depende de cuánto se valoren los diferentes objetivos. En nuestro escenario de ejemplo, el control de hierbas ningún manejo tuvieron la probabilidad de ser las mejores opeiones de manejo para satisfacer los múltiples objetivos de restauración. Nuestra estrategia para explorar las compensaciones en los resultados de manejo por medio de un modelado integrado y estrategias apoyadas por decisiones estructuradas tiene una aplicación amplia para situaciones en las que existen compensaciones entre los objetivos de conservación en competencia.

Aim Strongly interacting species have disproportionately large ecological effects relative to their abundances or biomass. We previously developed two conceptual models that described how one such strong interactor, the Australian bird the noisy miner Manorina melanocephala: (1) establishes resident high-density and hyperaggressive colonies and (2) in doing so, affects other biota and ecosystem processes. Here, we evaluate parts of those models relating to noisy miner habitat preferences and effects on bird assemblages using data from across the geographical range of the miner. Location Eastern Australia. Methods Avian-assemblage data were compiled for 2 128 survey transects (distributed over > 1.3 × 106 km2) and were linked to variables reflecting productivity, local habitat structure and landscape context. Predictors were chosen based on the models, although detailed data for some variables were unavailable at such large scales. We used hierarchical Bayesian models that included observation models to account for different survey effort coupled with potentially nonlinear, spatially-explicit process models. Conclusions Noisy miner densities increased with proximity to forest edges (higher densities on forest edges and open sites), in low rainfall areas, and in vegetation dominated by trees with blade-shaped rather than needle-shaped leaves. The presence of noisy miners at even relatively small densities (> 0.6 individuals ha–1) depressed both species richness and the abundances of smaller (< 63 g) bird species, by 50% on average. There were positive associations between densities of noisy miners and the abundance and richness of larger-bodied (> 63 g) bird species. In areas with higher mean rainfall, the associations between noisy miners and small- and large-bird species were more negative and less positive, respectively.