Research Publications and Outputs

Resilience and adaptation of COTS larvae to development in oligotrophic tropical waters: maternal provisioning and larval cloning

Tue, 19 May 2026 00:00:00 GMT

Resilience and adaptation of COTS larvae to development in oligotrophic tropical waters: maternal provisioning and larval cloning Byrne, Maria; McLaren, Emily; Hill, Ronan Explanations of crown-of-thorns sea star (COTS, Acanthaster) outbreaks have focussed on the larval stage and the terrestrial runoff – larval starvation hypothesis – whereby eutrophic runoff from floods generate plankton blooms increasing larval food and success. In contrast to this notion, we found that the larvae of COTS are highly resilient to food scarcity. This is likely an adaption to life in oligotrophic (low nutrient) tropical seas as well as due to the extensive energetic reserves provided by their unusually large eggs. We reared eight populations of COTS larvae all from different parents in course filtered lagoon water (60 µm FSW) to remove potential predators but retain nutrients typical of reef waters. Over 21-25 days the larvae grew to the advanced larval stage. The energetic buffer provided by the eggs allowed for an extended period when the larvae developed in the absence of food augmentation but in parallel would be competent to avail of patches of phytoplankton as they may encounter in nature. This is the longest facultative feeding period for any sea star species with a feeding larva. There was some difference in the larval populations in how long they lasted as well as in the propensity of larval cloning – where the larvae fragment and regenerate to make more of themselves. Although the larvae achieved an advanced stage in the absence of exogenous food it was clear that an algal food source is needed to achieve the final settlement stage. Our findings reinforce the resilience of the larvae of COTS to food scarcity and show that they do not require nutrient augmentation generated by runoff to reach the advanced larval stage.

Climate-change resilience and positive scope for growth in wild adult Sydney rock oysters, Saccostrea glomerata (Gould, 1850)

Thu, 01 Jan 2026 00:00:00 GMT

Climate-change resilience and positive scope for growth in wild adult Sydney rock oysters, Saccostrea glomerata (Gould, 1850) Pereira, Roberta R. C.; Parker, Laura M.; O’Connor, Wayne A.; Ross, Pauline M. Context. Oysters have ecological and economic importance worldwide because they provide ecosystem services and sustain profitable aquaculture industries. Calcifying bivalves including oysters have been found to be sensitive to ocean warming and acidification caused by anthropogenic climate change. Aims. This study tested whether adult wild Sydney rock oysters, Saccostrea glomerata, have resilience and can maintain sufficient scope for growth or are pushed into a suboptimal state. Methods. Oysters were exposed to elevated pCO2 (335 and 857 μatm) and temperature (24 and 28°C) in an orthogonal design for 5weeks. At the end of the exposure, growth, condition index, clearance, ingestion and absorption efficiency and rates were measured and scope for growth calculated. Key results. Sydney rock oysters responded to elevated pCO2 and temperature with no change in overall growth or condition index, but with significantly increased metabolic, clearance, ingestion, and absorption rates and positive scope for growth. Conclusions. Our results indicated that adult S. glomerata can cope with the moderate level of climate-change stress predicted for 2100, through increased standard metabolic rate and increased energetic processes. Implications. If food availability becomes limiting, and other environmental stressors interact with climate change stressors, then resilience thresholds maybe breached for this economically, ecologically and indigenous significant and iconic oyster species.

United Nations Groundwater Data Reveals 320,000 kilotons of Nitrogen "Dark Matter" in River Bottoms

Thu, 01 Jan 2026 00:00:00 GMT

United Nations Groundwater Data Reveals 320,000 kilotons of Nitrogen "Dark Matter" in River Bottoms Hall, Chris The podcast describes the results of analyses of water volume data in United Nations reports at the UNESCO IGRAC resource, linking water volumes with major nitrates supply routes in waters reaching rivers and lakes. At a frequent average nitrate concentration reported country by country in government literature, the world's land systems have nitrates in approximately a 200,000 up to 500,000 kilotons range to process by natural means per annum, with around 300,000 kilotons being the most likely figure. A range of around 140,000 kilotons is the quantity likely being produced from human activity, but the news comes with a potential key to reduce these quantities at the world scales required. The microbes responsible for converting the majority of this nitrate into ammonium when it reaches river bottoms, can potentially be farmed for ammonium conversion to Hydrogen fuels and commercial fertilisers. The news has been released initially at the European Geosciences Union (EGU) in Vienna session in May, 2026 with supplementary materials for hearing and sight-impaired audiences.

Warming but not food limitation alters metabolism during larval development in crown-of-thorns sea stars (Acanthaster sp.)

Wed, 22 Apr 2026 00:00:00 GMT

Warming but not food limitation alters metabolism during larval development in crown-of-thorns sea stars (Acanthaster sp.) Hill, Ronan Thomas; Byrne, Maria; Pettersen, Amanda Respiration data of Acanthaster sp. reared as both fed and unfed larvae at four temperature treatments (control: 26°C; warm: 28°C, 30°C, 32°C) based on current and projected OW and measured metabolic rate (oxygen consumption, V O2) across development to the late larval stage. Dataset includes size (larval area, length and width), developmental stage and plate reader details.

Data from "Behavioural, physiological, and biochemical responses of two species of Scleractinian coral to butterflyfish predation"

Wed, 25 Mar 2026 00:00:00 GMT

Data from "Behavioural, physiological, and biochemical responses of two species of Scleractinian coral to butterflyfish predation" Hsu, Tsai-Hsuan Tony; Hoey, Andrew S.; Warren, Charles R.; Marrable, Isabella; Figueira, Will F. The negative effects of coral loss on fish assemblages are well established, particularly for obligate corallivores. In contrast, the impacts of corallivorous fish on corals themselves have received less attention, though chronic predation is expected to impose sublethal costs. This study examined how two scleractinian corals, Acropora samoensis and Pocillopora damicornis, responded to varying levels of predation by the polyp-feeding butterflyfish, Chaetodon rainfordi, in a 17-day tank experiment. We assessed the effects of predation on behaviour (polyp withdrawal), physiology (growth, ash-free dry weight, photosynthetic efficiency), and biochemistry (fatty acid content) of coral colonies; with fatty acid profiles further providing insight into energy balance (structural vs. storage lipids), trophic strategy, and coral health. The two species showed contrasting responses. A. samoensis withdrew most polyps even at low predation (88% withdrawn at 0.5 bites min-1 colony-1), likely suppressing heterotrophy and leading to reduced growth, although other physiological and biochemical traits remained unaffected. In contrast, P. damicornis, a relatively heterotrophic species, maintained ~71% of polyps extended under the same intensity, sustaining feeding but incurring greater tissue loss and declining health condition. Nevertheless, growth and ash-free dry weight were maintained, likely through mobilization of storage fatty acids derived from both autotrophic and heterotrophic sources. These results highlight the resilience of corals to chronic butterflyfish predation, as most colonies maintained positive growth even under relatively high per-colony bite rates. However, the observed energy trade-offs suggest potential consequences for reproduction and susceptibility to environmental stress, indicating that chronic predation by non-skeletal feeding corallivores may subtly shape coral performance and persistence. If used in full or in part, please cite this dataset and the original publication: Hsu, T.-H. T., Hoey, A. S., Warren, C. R., Marrable, I., & Figueira, W. F. (2026). Behavioural, physiological, and biochemical responses of two species of scleractinian coral to butterflyfish predation. Marine Environmental Research, 108026. https://doi.org/10.1016/j.marenvres.2026.108026. The R script to replicate the analyses is available on GitHub (https://github.com/THTonyHsu/Coral-predation-stress.git).

Carry-over effects of decreased salinity on larval metamorphosis and the early juvenile in context with eReefs hydrodynamic models

Wed, 11 Mar 2026 00:00:00 GMT

Carry-over effects of decreased salinity on larval metamorphosis and the early juvenile in context with eReefs hydrodynamic models Clements, Matthew; Byrne, Maria The environmental conditions experienced by marine invertebrate larvae can have carry-over effects on later life stage performance, affecting population dynamics.For crown-of-thorns sea stars (CoTS; Acanthaster spp.), the terrestrial runoff hypothesis (TRH) suggests that eutrophic runoff plumes boost larval phytoplankton food supply, increasing metamorphic success and seeding outbreaks. However, river plumes also decrease salinity which can be deleterious to sea star larvae. We investigated the impact of decreased salinity (17–30 PSU) across a range of exposure durations on survival, normal development, and the ability of settlement-ready brachiolaria larvae to produce a juvenile. Salinity performance curves identified salinity levels with deleterious effects and the tipping points for 50% normal development and survival. Decreased salinity and prolonged exposure reduced larval survival and morphology. To examine carry-over effects on metamorphosis and juvenile production, competent brachiolaria that had been exposed to decreased salinity were induced to settle. Juvenile production was highest in slightly reduced (30 PSU) and control (34 PSU) salinity treatments, with faster transition to the juvenile under extended 30 PSU exposures. However, by 5 days post-settlement juveniles produced by larvae from the 30 PSU treatment were smaller indicating the presence of negative carry-over effects that reduce juvenile quality.

UOS2301-003RTX Overseas wheat phenotyping 2025/26

Thu, 01 Jan 2026 00:00:00 GMT

UOS2301-003RTX Overseas wheat phenotyping 2025/26 Singh, Davinder; Ziems, Laura; Zhang, Peng; Miah, Hanif; Bhavani, Sridhar With support from GRDC project UOS2301-003RTX, we tested 427 modern and historical Australian wheat varieties (Ausvars) in Kenya against stem rust (Ug99 lineage pathotypes – TTKSK, TTKST, TTKTT, TTTTF and TTKTT+Sr8115B) and stripe rust (race PstS16) to identify rust resistant/susceptible germplasm to these exotic rust races. High quality stripe rust and stem rust phenotypic data was generated on these varieties. For each variety, there are 3 readings for stripe rust (YR) and 2 readings for stem rust (SR) recorded on a modified Cobb scale capturing Disease severity (% leaf area) and Disease response (reaction).

UOS2301-003RTX Overseas (Mexico) barley phenotyping 2025

Thu, 01 Jan 2026 00:00:00 GMT

UOS2301-003RTX Overseas (Mexico) barley phenotyping 2025 Singh, Davinder; Ziems, Laura; Zhang, Peng; Qureshi, Naeela; Bhavani, Sridhar With support from GRDC project UOS2301-003RTX, we tested 52 Australian barley varieties and 365 CAIGE (CIMMYT ICARDA Australia Germplasm Enhancement) barley lines against exotic pathogen Puccinia strifformis f. sp hordei (Psh) race 24 (PshMEX-1) at Toluca, Mexico (CIMMYT; International Maize and Wheat Improvement Centre) to identify rust resistant/susceptible germplasm to barley yellow rust. High quality phenotypic data was generated on these lines (data file uploaded). Data for Ausbars and CAIGE are in two separate worksheets in the uploaded file. For each line, there are 3 readings recorded on a modified Cobb scale capturing Disease severity (% leaf area) and Infection type (disease response).

Towards transparent and replicable flower selection in agricultural flower strips

Wed, 05 Nov 2025 00:00:00 GMT

Towards transparent and replicable flower selection in agricultural flower strips Latty, Tanya; Mourmourakis, Faelan Flower strips are increasingly employed as ecologically sustainable methods for attracting beneficial insects to agricultural landscapes. Since flowers differ substantially in an array of characteristics including morphology, nutritional content, and phenology, selecting ‘the right flowers for the right job’ requires the designer to make careful decisions about which flowers to include. These decisions ultimately determine the success of flower strips. Given the importance of flower selection, how do researchers choose which flowers to plant? We conducted a quantitative content analysis to examine how researchers make flower selection decisions in studies aimed at supporting or attracting natural enemies or pollinators to target crops. We collected data on the criteria used to justify selection decisions and we recorded the type of evidence (experiential evidence such as “expert recommendations” or “personal communication” vs peer reviewed evidence) used to support selection decisions. We found that the majority of studies relied on experiential data to inform their flower choices. Specific selection criteria varied, but 'attractiveness' and 'native to region' were most frequently cited for both natural enemies and pollinators. Overall, we found that the prevalent use of experiential evidence for flower selection may limit the replicability and transparency of studies. To address this concern, we introduce a flexible framework aimed at ensuring the clear communication of the flower selection process. Our framework emphasizes evidence-based practices to enhance both replicability and transparency in flower strip design, offering a path toward more rigorous and effective ecological interventions.

Biotic interactions with a native urban exploiter limit occupancy by an avian flagship species in urban ecosystem

Mon, 27 Oct 2025 00:00:00 GMT

Biotic interactions with a native urban exploiter limit occupancy by an avian flagship species in urban ecosystem Heggarty, Genevieve A; Hochuli, Dieter F; Parsons, Holly M This dataset is the product of bird, mammal, vegetation and landscape surveys conducted in Sydney, NSW between May 2023 and September 2023. It is associated with the paper 'Biotic interactions with a native urban exploiter limit occupancy by an avian flagship species in urban ecosystem'.

Software pipelines from the 3D PAWC & constraint mapping project that process soil analysis data and proximal data to create automated models which produce maps of soil properties and soil constraints to depth

Thu, 02 Oct 2025 00:00:00 GMT

Software pipelines from the 3D PAWC & constraint mapping project that process soil analysis data and proximal data to create automated models which produce maps of soil properties and soil constraints to depth Bishop, Thomas; Filippi, Patrick; Hoskin, Nikolas; Whelan, Brett; Pozza, Liana The 3D PAWC and constraints mapping project utilised R to create software pipelines that process field boundaries, access privately available proximal surveys, and download private and publicly available terrain and climate data. These datasets are stored as a datacube which is used in the following 3 steps of the project: producing a stratified random sample design, summarising lab analysis results to report to growers, and running an automated modelling process to map soil properties. Within each section, there is a working script that can run on a predefined farm from the project. Sample design: This pipeline transforms the compiled datacube into strata across a farm and then randomly samples these strata given a predefined sample size. The R code can be made available for this summary reporting process, subject to an agreement with the University of Sydney and the GRDC. Models and mapping: This pipeline extracts covariates from a farm's datacube to the point locations of lab analysis sites. For any measured soil property, several models are compared for prediction quality over analysis depth intervals (0-15 cm, 15-30 cm, 30-60 cm, 60-100 cm). The best performing model is selected for each soil property and used to produce maps across the sampled fields of the farm. The R code can be made available for this automated modelling, subject to an agreement with the University of Sydney and the GRDC. Files are stored in .rmd format and require input from .csv files. The software pipelines are stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-MLCons. Data access is restricted as the code links to private APIs with access to restricted and sensitive private farm data. Third-parties will need to request access from GRDC and the University of Sydney. For further enquiries, please contact Dr Patrick Filippi at patrick.filippi@sydney.edu.au

Return of the lamingtons - boom-and-bust populations of the barrens forming sea urchin Tripneustes australiae on Lord Howe Island Marine Park

Mon, 08 Sep 2025 00:00:00 GMT

Return of the lamingtons - boom-and-bust populations of the barrens forming sea urchin Tripneustes australiae on Lord Howe Island Marine Park Byrne, Maria; McLaren, Emily; Cooper, Antonia; Davey, Madeline; Sommer, Brigitte; Wilson, Liam Sea urchins in the genus Tripneustes have fast growth and boom-and-bust population dynamics. Tripneustes australiae is endemic to southeast Australia and northwest New Zealand and is currently undergoing a population increase (‘boom’ phase) in Lord Howe Island Marine Park (LHIMP). Grazing pressure in population outbreaks of this species creates barrens-type habitat. We used Reef Life Survey data to document the density of T. australiae spanning 18 years (2006-2024). Two outbreaks were evident, the first started in 2006 followed by a marked decline and the second started in 2022. The Admiralty Islands appear to be a recruitment hot spot for this species. The size of T. australiae in 2024 (most < 5 cm test diameter) indicated recent recruitment. Most individuals were found at 6-12 m depth and were juveniles as confirmed by the absence of gonads. Over 18 years there was no difference in the densities of T. australiae in ‘no take’ sanctuary zones and habitat protection zones of LHIMP with the exception of the recent outbreak in 2024. The drivers of the boom-and-bust population dynamics of T. australiae are likely related to inherent demographic traits of the genus associated with fast growth to reproductive maturity and a short life span. Recruitment anomalies of T. australiae to LHIMP may be related to climate warming and altered current connectivity from the Australian continent. The population dynamics of and ecological impacts T. australiae are important to understand in the high conservation value Lord Howe Island World Heritage Area ecosystems

Freshwater-induced coral bleaching following extreme rainfall in Pioneer Bay, Orpheus Island, Great Barrier Reef

Thu, 04 Sep 2025 00:00:00 GMT

Freshwater-induced coral bleaching following extreme rainfall in Pioneer Bay, Orpheus Island, Great Barrier Reef Waller, Alexander; Webb, Monique; Sommer, Brigitte; Maria, Byrne; Foo, Shawna A. This dataset provides benthic cover and coral assemblage data from three sites at Pioneer Bay, Orpheus Island, assessed across three time points (July 2023, July 2024, and April 2025)

Software pipelines for processing soil water data and predicting plant available water using approaches from the SoilWaterNow project

Mon, 01 Sep 2025 00:00:00 GMT

Software pipelines for processing soil water data and predicting plant available water using approaches from the SoilWaterNow project Bishop, Thomas; Filippi, Patrick; Yu, Yi; Zhang, Yuxi; Wimalathunge, Niranjan; Tian, Siyuan The SoilWaterNow project utilised both Python and R to create software pipelines that process soil moisture data and can be used for predicting plant available water. There is 4 different parts, processing CosmOz surveys, SMAP data assimilation, a water balance model, and a data driven model for predicting agriculture systems. Within each section, there is a working script with an example dataset. This allows users to repeat the analysis with the example data in order to understand the data inputs and formats required to run the analysis on their own study area. CosmOz survey - Data processing: This pipeline transforms raw neutron count data from cosmic ray probe survey data into soil moisture measurements. The pipeline was used with the associated CosmOz survey data and soil data. The R code is available along with an example dataset. SMAP Data Assimilation: This pipeline assimilates Soil Moisture Active Passive (SMAP) satellite estimates of soil moisture into an API model for soil moisture reanalysis. Sample data is provided for CosmOz sites and their locations of these points are in "cosmoz_site_info.csv". The Python code for the API model is available. The forcing data used was GPM rainfall and air temperature anomalies. These parameters were calibrated and are listed in "API_parameters.csv". Water balance model: There are two models available, one that is point-based and used for running on small datasets, e.g. soil moisture probes, and one that is raster-based, which is faster and can be used for obtaining maps of soil moisture. Both models rely on daily evapotranspiration (ET), bucket size, and rainfall as the 3 inputs. These data for these 3 inputs can be accessed publicly: 8-day MODIS evapotranspiration data can be downloaded from the USGS website or directly from google earth engine, rainfall data can be accessed from SILO through the Long Paddock website, and soil data can be accessed from the eSoil website. 5 bucket sizes were used for both models, 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, and 60-100 cm. The "ET&rain4WBmodel.r" file contains code that organises daily data for model execution. Alternatively, provided example datasets can be used to run the model. R code is available for both models. Data-driven approach: This pipeline uses a Gaussian Process regression model/workflow that can be used to predict soil moisture in space and time. This model uses a complex base function that can capture underlying trends in soil data. Each workflow consists of 4 steps: 1. data-preprocessing 2. feature analysis and selection 2. model training, optimisation, evaluation, and selection 4. generating prediction and uncertainty maps. Python code is available for this model and an example dataset is available that is already pre-processed. The "Methods.pdf" file discusses feature selection and model details and the "README.md" file contains in depth information about how this model works and gives example outputs. The software pipelines are stored in a public GitHub repository (https://github.com/thomasfabishop/soilwaternow) and are also stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-soilwaternowarchive. The pipelines are open access under a creative commons license (CC-BY 4.0). Please contact Dr Patrick Filippi (patrick.filippi@sydney.edu.au) for further information.

Proximal sensing surveys (EM & Gamma) across 36 farms from the grain growing regions of Australia

Tue, 12 Aug 2025 00:00:00 GMT

Proximal sensing surveys (EM & Gamma) across 36 farms from the grain growing regions of Australia Bishop, Thomas; Filippi, Patrick; Whelan, Brett; Pozza, Lianna; Hoskin, Nikolas; Collyer, Bryn; Wright, Jenna Proximal soil electromagnetic induction (EM) & gamma radiometric (gamma) surveys from 36 farms across Australia's dryland cropping regions. Surveyed fields correspond to those sampled in the '3D PAWC and constraint mapping' project. Soil proximal surveys were compiled between 2023 and 2025. These surveys were collected to be used as modelling covariates in digital 3D soil maps that describe on-farm soil constraints and PAWC in a given area and can be used to inform management decisions. These have been collected at many sites across Australia to give an idea of the investment value for proximal surveys in different environments and soil types. Surveyed areas range from 200 - 2,000 ha at specific farms, while the total surveyed area represented in this dataset exceeds 26,000 ha of dryland cropping soils. Proximal surveys were collected at 36 m swathe widths using gator mounted EM & gamma sensors. EM & gamma surveys are stored seperately in .csv format for each farm. EM data consists of 4 x depth slices to a maximum of 300 cm from a DualEM sensor. Gamma data collected by an RSX-1 gamma-ray spectrometer consists of Potassium, Uranium & Thorium concentrations as well as total count. Coordinates are present in 'EPSG:4326' projection. Farms were surveyed between 2023 and 2025. The date of survey is available for all farms. GRDC Project UOS2206-009RTX The datasets with raw values are stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-MLCons. This data has restricted access and the data is de-identified as it contains information from private properties. Third-parties may be able to access the data subject to terms agreed to by the GRDC and the University of Sydney and/or a data supply and licence agreement. Please contact Dr Patrick Filippi (patrick.filippi@sydney.edu.au) to request access to the data.

Seasonality & Sensitivity Of Microbial Decomposition in Semi-Arid Grasslands

Mon, 11 Aug 2025 00:00:00 GMT

Seasonality & Sensitivity Of Microbial Decomposition in Semi-Arid Grasslands Pino, Vanessa; Vervoort, Willem; McBratney, Alex; Gambrill, Ella; Graaf, Amanda; Fajardo, Mario This dataset captures seasonal soil microbial decomposition dynamics in semi-arid grasslands of northern NSW, Australia, under regenerative grazing and landscape rehydration practices. It includes Tea Bag Index metrics (TBI_k, TBI_S), soil moisture and temperature readings, and remote sensing indicators (ET, LST, EVI), highlighting the influence of hydrological conditions on decomposition and carbon stability.

Soil moisture probe data from 15 probes within the Liverpool Plains region and Muttama in NSW

Mon, 04 Aug 2025 00:00:00 GMT

Soil moisture probe data from 15 probes within the Liverpool Plains region and Muttama in NSW Bishop, Thomas; Filippi, Patrick; Yu, Yi; Zhang, Yuxi; Amir, Muqeet; Wright, Jenna Soil moisture probe measurements from 15 different probes in the Liverpool Plains and Muttama, NSW. There are 15 files, with one for each probe and each is named after the location. These measurements are taken as ground-truth soil moisture data (%VWC) at depths from 30-110 cm, with a measurement every 10 cm, that is used to validate predictive modelling. A file named "USYD PROBE INFO.csv" contains the name of each probe, the corresponding API, and the coordinates. All data is obtained using the irrimaxlive API. This file is stored as "USYD API.py" and uses the "USYD PROBE INFO.csv" file as input. Once run, it outputs an up-to-date soil moisture probe measurement file named after its location. This data is uncalibrated. Each probe measurement file has the following columns: Date Time, A (soil moisture (%VWC) readings), and T (soil temperature (degrees Celsius) readings. The number inside the bracket after "A" or "T" is the depth (cm) of the measurement. "USYD PROBE INFO.csv" has the following columns: API Probe Name (Name of the site in the API database, Product Name (what the site is known as in all documentation and in file names), Latitude, and Longitude. The datasets are stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-soilwaternowarchive. This data is available under terms and conditions to be agreed by the University of Sydney and GRDC and/or under a data supply and licence agreement. Please contact Dr Patrick Filippi (patrick.filippi@sydney.edu.au) to request access to the data.

Cosmic ray probe survey data of soil surface neutron counts and associated soil analysis data across grain growing regions in NSW and QLD

Fri, 01 Aug 2025 00:00:00 GMT

Cosmic ray probe survey data of soil surface neutron counts and associated soil analysis data across grain growing regions in NSW and QLD Bishop, Thomas; Filippi, Patrick; Yu, Yi; Zhang, Yuxi; Amir, Muqeet; Wright, Jenna This dataset includes cosmic ray probe survey data that details soil neutron counts detected using CSIRO's CosmOz Rover. Cosmic ray probes measure the flux of fast neutrons which is inversely proportional to the amount of hydrogen atoms. Water molecules are the dominant source of hydrogen atoms in soil so they can be measured close to the Earth's surface and used to infer soil moisture content. In addition to the neutron count, the survey data also contains barometric pressure (mb), temperature (℃) and relative humidity (%). These measurements are needed to correct the raw neutron count data by removing influences from atmospheric pressure and water content above the soil surface. Surveys were carried out across the grain growing regions in NSW and QLD, particularly Northern NSW, South-Eastern NSW, and South-Eastern QLD, and were completed over a period of 4 years from 2020-2023. Surveys were completed between 1 and 4 times within this 4 year period for each of the farms. The mobile system has 16 capsules that each measure neutron count at 1-minute intervals and log the GPS locations of each measurement. Survey data is in .csv format with 20 surveys completed across 8 farms. Soil sampling campaigns were completed concurrently with the CosmOz surveys and the data is available in this collection. Soil moisture, bulk density, soil organic carbon, and clay content was measured from each sample and was used to calibrate the neutron count from the surveys. 20 cores were taken at each farm to a depth of 30 cm. Sampling sites were defined using a stratified random sampling scheme based on k-means clustering, where strata were defined using farm characteristics. The available soil data for each farm is in .csv format. The datasets are stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-soilwaternowarchive. This data has restricted access, third-parties need to contact the University of Sydney and the GRDC to access the data according to agreed terms and/or with a data supply and licence agreement. Please contact Dr Patrick Filippi (patrick.filippi@sydney.edu.au) to request access to the data.

Comprehensive soil analysis data across 75 farms from the grain-growing regions of Australia

Tue, 29 Jul 2025 00:00:00 GMT

Comprehensive soil analysis data across 75 farms from the grain-growing regions of Australia Filippi, Patrick; Bishop, Thomas; Hoskin, Nikolas; Whelan, Brett; Pozza, Lianna; Wright, Jenna; Collyer, Bryn Soil analysis data from 75 farms across Australia's dryland cropping regions sampled in the '3D PAWC and constraint mapping' project. Sampling and analysis was compiled from several campaigns between 2023 and 2025. This data was collected to be used as one of the inputs to digital 3D soil maps that can describe the constraints and PAWC in a given area and can be used to inform management decisions. Using many sites across Australia gives an idea of how this approach works in different environments and soil types. Sites were selected using a stratified sampling approach where variation in spatial data layers was considered. Soil analysis results from 75 farms are stored in .csv format Soil analysis of 25 datapoints at 4 depth intervals to 1 m. Unless otherwise stated, depth intervals are 0 - 15 cm, 15 - 30 cm, 30 - 60 cm and 60 - 100cm. All analysis conducted by CSBP labs, aside from gravel content (determined in-house by USyd staff). Analysis of PSA texture (MIR), OC (Walkley-Black), electrical conductivity (1:5), pH (H20), pH (CaCl2), exchangeable cations (without prewash), Ammonium, Nitrate, Phosphorous, PBI and Gravel. units* Coordinates are present in 'EPSG:4326' projection. Farms were sampled in 3 different campaigns, with 30 farms sampled in 2023, 42 sampled in 2024, and the last 3 sampled in 2025. The date of sampling is available for all farms. GRDC Project UOS2206-009RTX The datasets with raw values are stored on the USYD-RDS at \\shared.sydney.edu.au\research-data\PRJ-MLCons. This data has restricted access and the data is de-identified as it contains information from private properties. Third-parties may be able to access the data subject to terms agreed to by the GRDC and the University of Sydney and/or a data supply and licence agreement. Please contact Dr Patrick Filippi (patrick.filippi@sydney.edu.au) to request access to the data.

The gibberellic acid responsive GmbHLHm1 transcription factor influences nodule development, nitrogen fixation activity and shoot nitrogen content in soybean (Glycine max)

Wed, 01 Jan 2025 00:00:00 GMT

The gibberellic acid responsive GmbHLHm1 transcription factor influences nodule development, nitrogen fixation activity and shoot nitrogen content in soybean (Glycine max) Hu, Die; Wen, Zhengyu; Imin, Nijat; Dhugga, Kanwarpal S.; Kaiser, Brent N. GmbHLHm1 is a basic Helix-Loop-Helix membrane (bHLHm1) DNA binding transcription factor localized to the symbiosome membrane and nucleus in soybean (Glycine max) nodules. Overexpression of GmbHLHm1 significantly increased nodule number and size, nitrogen fixation activity, and nitrogen delivery to the shoots. This contrasts with reduced nodule numbers per plant, nitrogen fixation activity and poor plant growth when silenced using RNAi. The promoter of GmbHLHm1 was found to be sensitive to exogenous GA supply, decreasing the level of GUS expression in transformed hairy roots in both nodules and roots and reducing native GmbHLHm1 expression in wild-type nodules. In summary, our study suggests that GmbHLHm1 positively regulates soybean nodulation and nitrogen fixation, and that GA can negatively regulate GmbHLHm1 expression in soybean nodules.

Historical changes in marine communities uncovered in diverse data sources highlight impacts over half a century

Wed, 01 Jan 2025 00:00:00 GMT

Historical changes in marine communities uncovered in diverse data sources highlight impacts over half a century Turnbull, John W.; Booth, David J.; Clark, Graeme F. Context. Historical records and citizen scientist data are a useful resource for long-term ecological studies, yet their quality and validity have been challenged. Aims. We aimed to investigate how traditional structured surveys and unstructured, opportunistic data sources can be used to understand historical ecological change over half a century. Methods. We studied ~6000 records between 1965 and 2020 from the Shiprock site in the Sydney region, to understand ecological changes and insights that could be derived from these diverse data sources. Key results. We reportthe local disappearance ofsome fish and invertebrate species, declinesin the abundance of many taxa including kelp, potential impacts of the implementation of a marine reserve and range extensions consistent with climate change. Structured surveys provided broadly scientifically useful ecological information, whereas unstructured opportunistic data provided long-term retrospective community information and species presence information. Conclusions. We have described scientifically and managerially relevant insights encompassing foundation, threatened, protected and invasive species, community shifts and the impacts of local and global processes over historical timescales. Implications. Unstructured, opportunistic data sources can document long-term ecological changes arising from local and global processes, but are limited in the ability to provide population and community structure information.

Who’s been lost from the landscape? Identifying missing terrestrial fauna to inform urban rewilding

Wed, 01 Jan 2025 00:00:00 GMT

Who’s been lost from the landscape? Identifying missing terrestrial fauna to inform urban rewilding Wauchope, Mareshell; Finnerty, Patrick B.; Pierson, Jennifer C.; Banks, Peter B.; Carthey, Alexandra J. R.; Newsome, Thomas M. Context. Urbanisation has driven native species declines and local extinctions, eroding ecological processes. However, urban areas with remnant native vegetation patches may offer opportunities for native wildlife rewilding. Aims. We sought to identify potential urban rewilding candidates across a target landscape. We then examined their ecological traits to understand if those traits were shared by rewilding candidate species. Methods. We developed and applied a decision framework to occurrence records of terrestrial, non-volant mammals and reptiles to identify two status groups: (1) extant; and (2) rewilding candidates. Data on four ecological traits (diet, size, habit, and habitat) were then analysed using multivariate statistics. Key results. We identified 39 mammal and 47 reptile species historically present, with up to 62% of mammals and 93% of reptiles persisting since 2000. Eighteen species were categorised as locally missing, 11 of which are threatened. Two families (Canidae and Potoridae) were found to be locally extinct. Foraging habit (P-value = 0.047) and diet breadth (P-value = 0.024) were significantly different between our status groups. Conclusions. Locally missing and/or declined species represent potential urban rewilding candidates with broadest geographic applicability in patchy urban contexts, and align with a rewilding goal to restore pre-disturbance assemblages. In an urban context,where the list ofspecieslost might be high, additional factorsrequire consideration to aid rewilding candidate prioritisation in resource constrained environments. Implications. The decision framework efficiently pinpointed an initial suite of urban rewilding candidates. This framework can be applied by urban conservation managers. Trait analyses highlighted vulnerabilities critical to informing development of successful urban rewilding strategies.

Insect-plant interactions of the Sydney Region

Mon, 12 May 2025 00:00:00 GMT

Insect-plant interactions of the Sydney Region Lequerica Tamara, Manuel; Latty, Tanya; Threlfall, Caragh; Hochuli, Dieter This data set contains the interactions and behaviours of of insects (Honey bees and hover flies) with plants recorded in Sydney, NSW between Winter 2019 and Autumn 2022

Teratogenic effects of larval low salinity experience in development of the juvenile body in Acanthaster sp

Tue, 01 Apr 2025 00:00:00 GMT

Teratogenic effects of larval low salinity experience in development of the juvenile body in Acanthaster sp Clements, Matthew This item is the dataset and the Rscript supporting the manuscript titled - Teratogenic effects of larval low salinity experience in development of the juvenile body in Acanthaster sp. This dataset captures experimental results investigating the effects of reduced salinity during the larval stage on the morphological development of juvenile crown-of-thorns starfish (Acanthaster sp.). The data reflect teratogenic outcomes such as abnormal body plans, arm number deviations, and survival metrics under different salinity and exposure durations. The Excel file contains five sheets: Juvenile growth Measurements of juvenile body diameter (µm) by larval salinity treatment, exposure duration, and age (1 or 5 days). Includes replicate IDs. Proportion normal Proportions and percentages of juveniles categorized as "normal" or "abnormal" based on morphology, by treatment and exposure time. Proportional arm count Relative frequencies of different arm numbers (e.g., 4, 5 arms) in juveniles across treatments and ages. Arm# Detailed arm count data per individual juvenile, including counts of individuals with 0, 4, or 5 arms and corresponding treatment metadata. Juvenile morphology scores Individual-level scoring of morphological abnormalities (e.g., fleshy body, swelling) by treatment, replicate, and juvenile ID. Key Variables: Larval salinity treatment (‰) Larval salinity exposure duration (e.g., 2 or 4 days) Juvenile age (days post-settlement) Morphological traits (arm number, body diameter, abnormality scores) Proportional outcomes (normal vs. abnormal development) This R Markdown file contains all statistical analyses and data visualizations supporting the manuscript "Teratogenic effects of larval low salinity experience in development of the juvenile body in Acanthaster sp." (Clements et al., 2025). The code enables full reproducibility of the analyses, including data import, summary statistics, linear and generalized linear mixed models, and diagnostic assessments. Contents: Packages used: readxl, dplyr, ggplot2, cowplot, lme4, car, emmeans, DHARMa, lattice, arm Main analyses include: Juvenile growth (1- and 5-day-old) Body and arm morphometrics Normal vs. abnormal morphology scoring Five-arm development likelihood Residual and random effects diagnostics Data linkage: External Excel file (.xlsx) referenced for input data Usage: This file is intended for transparent and reproducible research. Users can rerun all analyses and regenerate figures by updating the file paths to match their system.

Fine-scale associational effects: single plant neighbours can alter susceptibility of focal plants to herbivores

Wed, 01 Jan 2025 00:00:00 GMT

Fine-scale associational effects: single plant neighbours can alter susceptibility of focal plants to herbivores Finnerty, Patrick Benjamin The neighbourhood of plants in a patch can shape vulnerability of focal plants to herbivores, known as an associational effect. Associational effects of plant neighbourhoods are widely recognised. But whether a single neighbouring plant can exert an associational effect is unknown. Here, we tested if single neighbours indeed do influence the likelihood that a focal plant is visited and eaten by a mammalian herbivore. We then tested whether any refuge effect is strengthened by having more neighbours in direct proximity to a focal plant. We used native plant species and a browser/mixed feeder mammalian herbivore (swamp wallabies (Wallabia bicolor)) free-ranging in natural vegetation. We found that a single neighbouring plant did elicit associational effects. Specifically, plant pairs consisting of one high-quality seedling next to a single low-quality plant were visited and browsed by wallabies later and less than pairs of two high-quality seedlings. Having more neighbours did not strengthen these associational effects. Compared with no neighbours, one or five low-quality neighbours had the same effect in delaying time taken for wallabies to first visit a plot and browse on a high-quality focal seedling. While traditionally a 'patch' refers to a broad sphere-of-influence neighbouring plants have on a focal plant, our findings suggest the influence of plant neighbours can range from the nearest individual neighbour to the entire plant neighbourhood. Such fine-scale associational effects are fundamentally important for understanding intricate plant-herbivore interactions, and ecologically important by potentially having knock-on effects on plant survival, in turn influencing plant community structure.

Indigenous Ecological Knowledge of marine and freshwater organisms and ecosystems on Sea Country: from past absences to future inclusion

Wed, 01 Jan 2025 00:00:00 GMT

Indigenous Ecological Knowledge of marine and freshwater organisms and ecosystems on Sea Country: from past absences to future inclusion Gibbs, Mitchell C.; Rotolo-Ross, Raphaela S.; Parker, Laura M.; Scanes, Elliot; Gibbs, James; Ross, Pauline M. For over 60,000 years, Aboriginal and Torres Strait Islander peoples of Australia have developed an enduring knowledge of marine and freshwater organisms and ecosystems on Sea Country. However, it has taken more than 200 years since colonisation, and a biodiversity and habitat crisis for Australia, to begin to recognise and value Indigenous Ecological Knowledge (IEK). This perspective piece builds on previous work to define IEK in the context of Sea Country research, particularly within Australia. It discusses reasons for the rarity of IEK in marine and freshwater literature, the loss of intergenerational transmission of IEK, the erosion of cultural heritage and the tensions between Western science and IEK, and strategies for change. The elevation of Aboriginal and Torres Strait Islander knowledge in national research priorities offers an opportunity to correct historical wrongs and develop effective strategies for the inclusion of IEK and Indigenous researchers. Together we need to protect what has been lost and restore and sustain marine and freshwater organisms and ecosystems on Sea Country.

Growth and ontogenetic change in juvenile crown-of-thorns sea star (Acanthaster sp.) morphology: Can morphometrics be used as an aging tool?

Mon, 03 Mar 2025 00:00:00 GMT

Growth and ontogenetic change in juvenile crown-of-thorns sea star (Acanthaster sp.) morphology: Can morphometrics be used as an aging tool? Wilson, Liam J; Byrne, Maria The crown-of-thorns seastar (COTS, Acanthaster sp.) is a coral predator that, during population outbreaks, causes major coral loss in Indo-Pacific reefs. Current paradigms explaining the cause of outbreaks focus on the larval and adult stages, while the early herbivorous juvenile stage remains a black box in our understanding of COTS. We followed growth in a large laboratory population of juveniles from settlement to 300 days. Ontogenetic changes in eight traits over time were quantified, including those typically used to track growth in seastars (total diameter, arm number) and traits not previously quantified (e.g., spine number/type). Combinations of traits were modeled against age to explore their potential as indicators of age. Total diameter exhibited a strong association with age, as did covarying traits: central disk diameter, mouth diameter, and arm length. The number of pointed spines was also strongly associated with age, more strongly than arm number. Our results indicate that the use of a combination of morphological traits has potential as an indicator of juvenile age. In particular, pointed spines appear to have potential as an age marker for juveniles. Using size-at-age data, we investigated the fit of growth models to estimate age-size relationships. A Gompertz model provided the best fit to the growth/age data and is consistent with the size/time of the diet shift (herbivory to corallivory) in juvenile COTS. Addressing knowledge gaps on these juveniles to inform age modeling using morphological traits contributes to the understanding of the biology and ecology of this cryptic life stage.

Zieria obcordata DArT data

Fri, 21 Feb 2025 00:00:00 GMT

Zieria obcordata DArT data McMaster, Eilish S.; Duretto, Marco; Yap, Jia-Yee Samantha; Rosetto, Maurizio Data supporting the analysis of Zieria obcordata in the paper "Conservation genomics uncovers disjunct subspecies and critically low diversity in Zieria obcordata A.Cunn. (Rutaceae)"

Behavioural responses of Australian lizards towards visual cues of feral cats

Wed, 01 Jan 2025 00:00:00 GMT

Behavioural responses of Australian lizards towards visual cues of feral cats Lishmund, Owen T.; Nimmo, Dale G.; Doherty, Tim S. Invasive mammalian predators have caused population declines and extinctions of wildlife worldwide. Many of these species exhibit some form of prey naïveté, which heightens their vulnerability to novel predators. In Australia, introduced feral cats (Felis catus) and red foxes (Vulpes vulpes) have had a particularly negative effect on native fauna, with the impacts of cats on mammals and birds well documented. Although feral cats are known to regularly prey on Australian reptiles, little is known about the behavioural responses of reptiles to cats, including whether native reptiles can recognise cats as a predation risk, and if so, which cues they use. Aims. We investigated behavioural responses of two Australian lizard species, the shrubland morethia skink (Morethia obscura) and eastern striped skink (Ctenotus robustus), to the visual cues of feral cats in semiarid, south-eastern Australia. Methods. We used arena trials to test lizards for predator recognition by using visual cues of an alien mammal predator (taxidermied cat, Felis catus), a native mammal predator (taxidermied western quoll, Dasyurus geoffroyi) and a mammal non-predator (taxidermied European rabbit, Oryctolagus cuniculus), as well as a procedural control (bucket) and a negative control (nothing). Key results. We found little evidence of behavioural change when lizards were exposed to the taxidermied cat. Morethia obscura basked less when exposed to all treatments and C. robustus increased vigilance when in the presence of the taxidermied cat, but overall responses were similar among treatments. Conclusions. Our findings suggest that stationary visual cues of cats do not trigger behavioural responses in these two lizard species. Implications. Future research should assess behavioural responses to combinations of cat cues (e.g. movement, scent). Developing a deeper understanding of predator recognition systems and prey naïveté in reptile communities will be crucial for conservation of Australian reptiles that are negatively affected by feral cats.

UOS2301-003RTX Overseas wheat phenotyping 2024/25

Wed, 12 Feb 2025 00:00:00 GMT

UOS2301-003RTX Overseas wheat phenotyping 2024/25 Singh, Davinder; Ziems, Laura; Zhang, Peng; Bhavnai, Sridhar; Park, Robert A total of 519 lines were tested in Kenya against stem rust (Ug99 lineage pathotypes – TTKSK, TTKST, TTKTT, TTTTF and TTKTT+Sr8115B) and stripe rust (race PstS16). The tested lines were derived from two resistant genotypes: Kenya Kudu (an east African line) and Kingbird (a CIMMYT line released in Ethiopia) both of which have showed good levels of resistance (characterized and/or uncharacterized) to all three rusts in field trials at PBI Cobbitty. These lines were crossed with Avocet to develop DH populations. High quality data was generated on these lines with two readings each for stem rust and stripe rust at 10-day interval (data file attached).

UOS2301-003RTX Overseas (Mexico) barley phenotyping 2024

Wed, 12 Feb 2025 00:00:00 GMT

UOS2301-003RTX Overseas (Mexico) barley phenotyping 2024 Singh, Davinder; Ziems, Laura; Zhang, Peng; Qureshi, Naeela; Bhavani, Sridhar; Park, Robert A set comprising of 48 released Australian barley cultivars, and 861 breeding lines (plus 25 parents/controls) were screened at Toluca, Mexico for assessing barley stripe/yellow rust (BYR) resistance and susceptibility against Puccinia striiformis f. sp. hordei (Psh) race 24 (PshMEX-1). The breeding lines were derived from the Australian cultivars La Trobe and Flagship, crossed with 17 donor lines (Chinese lines: YAN 90260, Zug31, Zug161, Fumai8; European lines: Volla, Dash, Line 17, Carafe, Halla, Atem, Gilbert, Universe, Titan, Belfor, Andapi, Egmond and Uta) carrying adult plant resistance (APR) to barley leaf rust. High quality phenotypic data was generated on these lines (file attached).

Life in the big smoke: terrestrial vertebrate assemblages and their drivers along an urbanisation gradient in Sydney, Australia

Wed, 01 Jan 2025 00:00:00 GMT

Life in the big smoke: terrestrial vertebrate assemblages and their drivers along an urbanisation gradient in Sydney, Australia Boer-Cueva, Martín; Cairncross, Rhys; Crowther, Mathew S.; Finnerty, Patrick B.; Rana, Angela F.; Banks, Peter B.; Newsome, Thomas M. Context. Urban areas are rapidly expanding, increasing anthropogenic pressure on global biodiversity. There are many threats associated with urbanisation,such as habitat loss and the spread of invasive species. Thus, to effectively manage urban greenspaces for native species, we need to understand species assemblages, and the factors that influence their diversity. Aims. We assessed how assemblages of terrestrial vertebrate species differ across urbanisation levels in northern Sydney, Australia, and whether habitat characteristics influenced them. We also investigated the role of invasive species in these areas by comparing daily activity patterns between invasive and native species. Methods. Nine forest (dry sclerophyll) patches, surrounded by three urbanisation levels (high-urban, mid-urban and low-urban), each with five motion-sensor cameras, were used to survey terrestrial fauna in northern Sydney from May to July 2023. Five vegetation variables and eight spatial variables were also recorded at each patch. Key results. There were differences in terrestrial vertebrate assemblages across the three urbanisation levels, with more invasive species, including red foxes (Vulpes vulpes) and black rats (Rattus rattus), in high-urban areas. We also found native species assemblages (particularly superb lyrebirds, Menura novaehollandiae; long-nosed bandicoots, Perameles nasuta; and bush rats, Rattus fuscipes) to differ with tall and low shrub cover, whereas invasive species did not differ. Furthermore, mean activity peaks did not differ between red foxes and a critical weight range (CWR) mammal was recorded in high-urban sites. Last, we observed a significant negative relationship between invasive species richness and native species diversity. Conclusions. Urbanisation has a strong effect on the assemblages, activity and interactions of native and invasive terrestrial vertebrate species in Sydney. Whereas remnant patches may support native species, the prevalence of invasive fauna in areas that are more highly urbanised may compound other factors affecting biodiversity. Implications. This study has provided a baseline understanding of urban terrestrial vertebrate assemblages in northern Sydney, and has shown that mid-urban areas may be good candidates for reintroduction sites. Our findings can be used to guide management actions to support the conservation or re-establishment of native species in the region or other urban areas.

The effects of clipping frequency and nitrogen fertilisation on greenhouse gas emissions and net ecosystem exchange in an Australian temperate grassland

Wed, 01 Jan 2025 00:00:00 GMT

The effects of clipping frequency and nitrogen fertilisation on greenhouse gas emissions and net ecosystem exchange in an Australian temperate grassland Padashbarmchi, Zahra; Minasny, Budiman; Shirvan, Milad Bagheri; González, Luciano A.; Dijkstra, Feike A. Grassland ecosystems store significant amounts of organic carbon (C) and have the potential to function as a source or sink of greenhouse gases (GHGs) under different environmental conditions and management practices. However, the effects of management (clipping frequency and N fertilisation) on the GHGs remain uncertain. In this study, a field-based experiment with automated-lid gas exchange chambers was conducted to simultaneously measure different GHG fluxes (CO 2 , N 2 O, CH 4 ), their overall global warming potential (GWP-100) impact, and net ecosystem exchange (NEE) from a grassland. The experiment had two clipping frequencies (simulating moderate and high grazing intensity) and two nitrogen (N) fertiliser treatments (0 and 40 kg N ha −1 year −1 ). The measurements were conducted during two periods (each approximately 2 weeks long) of varied temperature and moisture in early autumn. High clipping frequency caused higher daily NEE emissions, higher GWP-100 impact and lower photosynthesis; however, it did not significantly affect these parameters. Nitrogen fertilisation effects were lower than the clipping frequency treatment, but the impact on N on the time of N application. Methane (CH 4 ) 2 O fluxes was likely to be dependent was predominantly controlled by soil moisture, whereas nitrous oxide (N 2 O) was more strongly affected by temperature. N O emissions increased significantly after the break-point temperature of 20°C. Our results have highlighted the sensitivity of CH 4 2 uptake and N 2 2 O emissions to environmental conditions, particularly their increase under warmer temperatures. The main contributor of GWP-100 impact in this study was CO emissions and uptake. For the observation period, the grassland was a small C sink. For a comprehensive understanding, longer-term studies spanning over several years are needed to accurately assess the impact of different management practices on GHG emissions.

Soil Moisture daily data for the Llara Landscape Rehydration Project

Thu, 30 Jan 2025 00:00:00 GMT

Soil Moisture daily data for the Llara Landscape Rehydration Project Vervoort, Rutger Willem; Graaf, Amanda Landscape rehydration is a method that aims to regenerate the agricultural landsacpe while remaining productive. This dataset consists of data from uncalibrated soil moisture probes installed at Llara in Narrabri on the landscape rehydration project. The data is collected from 32 soil moisture probes in two 40 ha experimental pasture fields down to 1m20 and 1m60 depth and summarised to daily values. The two fields called Weir West and Weir East consist of one half "control" and one half "treatment" where landscape rehydration practices have been implemented. The data covers 2022 - 2024, but will be updated over time.

A detailed streamflow and groundwater salinity dataset for Muttama Creek Catchment, NSW, Australia

Thu, 30 Jan 2025 00:00:00 GMT

A detailed streamflow and groundwater salinity dataset for Muttama Creek Catchment, NSW, Australia Vervoort, Rutger Willem; van Ogtrop, Floris; Tambrchi, Mina; Akter, Farzina; Buzacott, Alexander; Lessels, Jason; Moloney, James; Kundu, Dipangkar; Dijkstra, Feike; Bishop, Thomas Dryland salinity remains a major natural resource management concern, specifcially in Australia, but also globally. However, a lack of detailed space-time data sets with observations of stream and groundwater salinity has limited further understanding of the range of processes that can lead to dryland salinity problems in landscapes. The aim of this study is to report on the open data available as a result of a 10-year data collection effort in a subcatchment of the Murrumbidgee catchment in New South Wales, Australia. Over a 10 year period a series of different sampling campaigns has resulted in a large dataset with hydrogeochemical data which includes both in-situ (field) data and post laboratory analysis of major anions and cations. The data set covers 23 groundwater sample sites and 37 surface water sites. Because the data was collected by four distinct groups and over many years we analyse if this has caused a bias in the dataset. In addition we show the major spatial and temporal trends to provide an overview of the dataset and analyse any posible biases. The dataset is made open access to encourage further research and the basic description already shows the richness of the collected data and opportunities for further research. The associated paper is submitted to Earth System Science Data: https://www.earth-system-science-data.net/

Glebe's Hill: unravelling its biodiversity secrets and potential

Mon, 01 Jan 2024 00:00:00 GMT

Glebe's Hill: unravelling its biodiversity secrets and potential Hochuli, Dieter Fritz; Lequerica Tamara, Manuel Eduardo; Heggarty, Genevieve Amber Context: Urban greenspaces play a vital role in enhancing biodiversity and promoting human well-being. Despite their importance, creating high-quality greenspaces in cities is often constrained by limited availability of suitable land. The Glebe Hill project addresses this challenge by demonstrating how a small degraded site in Sydney can be transformed into a valuable greenspace. Approach: The project was divided into four components, contextualising the ecological value of small urban greenspaces within Sydney; surveying the current biodiversity and habitat traits of Glebe Hill; analysing landscape drivers and ecological constraints; and proposing actionable recommendations for restoration and long-term management. Key results: Field surveys revealed 31 plant species at the site, dominated by invasive species such as Chinese Hackberry (Celtis sinensis) and Lantana (Lantana camara). Faunal surveys documented a range of bird, mammal, reptile, and invertebrate species, demonstrating the site's potential to support a more diverse wildlife community. Implications: The project proposes habitat enhancement through the planting of native, weed-resistant woody meadows and the phased removal of invasive species. Community engagement is central to fostering local stewardship, with initiatives targeting schools and residents. Monitoring and evaluation strategies are emphasised to ensure adaptive management, while collaboration with adjacent local government areas is encouraged to create a cohesive urban landscape scale restoration framework.

Data and R markdown to replicate analyses in “Optimizing remote underwater video sampling to quantify relative abundance, richness, and corallivory rates of reef fish”

Thu, 09 Jan 2025 00:00:00 GMT

Data and R markdown to replicate analyses in “Optimizing remote underwater video sampling to quantify relative abundance, richness, and corallivory rates of reef fish” Hsu, Tsai-Hsuan Tony; Gordon, Sophie; Ferrari, Renata; Hoey, Andrew S.; Figueira, Will F. Remote underwater videos (RUVs) are valuable for studying fish assemblages and behaviours, but analyzing them is time-consuming. To effectively extract data from RUVs while minimizing sampling errors, this study developed optimal subsampling strategies for assessing relative abundance, richness, and bite rates of corallivorous fish across eight geographically dispersed reef sites on the Great Barrier Reef and in the Torres Strait. Analyzing 40 frames per 60-minute video yielded precise and accurate estimates of the mean number of individuals per frame (i.e., MeanCount), with systematic sampling (one frame every 90 seconds) proved as effective as or better than random sampling, depending on the survey sites. However, this approach underestimated species richness by ~40%, missing the less common species. For estimating bite rates, 30 minutes or 15 feeding events were optimal, with no significant gains in precision and accuracy with further effort. These strategies enhance data standardization and process efficiency, reducing the time required for MeanCount and bite rate estimates by nine and two times, respectively, compared to full video annotation. If used in full or in part, please cite the data and the original publication: Hsu TH.T, Gordon S, Rerrari R, Hoey A.S, Figueira W.F (2025) Optimizing remote underwater video sampling to quantify relative abundance, richness, and corallivory rates of reef fish (accepted in Coral Reefs).

Understanding extractable metal species relationships with phosphorus sorption and organic carbon in soils

Mon, 01 Jan 2024 00:00:00 GMT

Understanding extractable metal species relationships with phosphorus sorption and organic carbon in soils Amenkhienan, Bright E.; Dijkstra, Feike; Warren, Charles; Singh, Balwant Context. Iron and aluminium oxides are important in phosphate sorption capacity of soils and preservation of soil organic carbon (SOC). However, there is a complex interplay between among Fe/Al oxides, SOC, and P in soils. Aims. We aimed to evaluate the relationships between extractable Fe and Al, SOC concentration and P sorption capacity using generalised additive mixed models. Methods. We compiled and analysed data from 77 published articles from Scopus and Web of Science. Key results. Ammonium oxalate extractable aluminium (Alox) had astrong significant relationship (P < 0.0001) with P sorption capacity, but this was stronger with dithionite-citratebicarbonate extractable aluminium (Ald). A positive 1:1 relationship between Alox and Ald suggests that the pool of Al dissolved by ammonium oxalate and dithionite citrate bicarbonate (DCB) was nearly similar. A strong significant relationship was found between ammonium oxalate extractable iron (Feox) and Alox, and SOC concentration, but Alox had a stronger statistically significant relationship with SOC concentration. This may be due to various interactions of SOC with Al oxides, which can directly or indirectly influence P sorption capacity in soils. Conclusions. From these relationships, we show that: (1) that Ald is a better predictor for P sorption capacity than Alox; and (2) Alox is a better predictor of SOC than Feox. Implications. DCB and ammonium oxalate extractable Al (and Fe) that represent Al in crystalline and poorly crystalline, or amorphous form of Al may be used as a routine soil test, and may be able to predict P sorption capacity and SOC preservation potential, particularly in acid soils.

Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

Mon, 01 Jan 2024 00:00:00 GMT

Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer Campbell, Matthew A.; Becker, Joy A. Context. Lates calcarifer is a widespread Indo-Pacific fish that is important in aquaculture, recreational and commercial fisheries. Genetic divergences from different data sources and sampling schemes have been reported. Aims. To conduct phylogenetic and population genetic analyses from a geographically and phylogenetically representative data set to identify hierarchical divisions within L. calcarifer. We further test the evolutionary significance of genetic units in terms of signatures of adaptation. Methods. Using a whole-genome sequence data set of 61 fish, including an outgroup, we conducted phylogenetic and population genetic analyses. We also generated measures of fixation index (Fst), nucleotide diversity (π) and Tajima’s D (D). Key results. We identified three main lineages of L. calcarifer, corresponding to the Indian subcontinent, South-east Asia and Australasia. Subdivision within each of the three main lineages was also identified and characterised. Adaptively significant differences are indicated within and among the three main lineages. Conclusions. L. calcarifer exhibits genetic divergences at different levels that originate before and during the Pleistocene. These divergences are associated with adaptive divergence but unclear phenotypic changes. Implications. This study has highlighted the need for comprehensive sampling and integrative study of genotypes and phenotypes across the range of L. calcarifer.

‘It’s dangerous to put a number on them’. Media coverage of koalas during the 2019–2020 ‘Black Summer’ bushfires in Australia

Mon, 01 Jan 2024 00:00:00 GMT

‘It’s dangerous to put a number on them’. Media coverage of koalas during the 2019–2020 ‘Black Summer’ bushfires in Australia Stalenberg, Eleanor; Lunney, Daniel; Moon, Chris Context. The unprecedented scale and severity of the 2019–2020 ‘Black Summer’ bushfires in Australia were an environmental disaster, and koalas became the public face of the fires’ toll on wildlife. Aims. We investigated the media stories on koalas during the fires to identify what was reported, and how the numbers of koalas killed by the fires were sourced and reported. Methods. We searched for media articles published in major Australian print and online news outlets, local sources, press releases and international outlets for the terms ‘koala’, ‘fire’, ‘bushfire’, ‘emergency’, ‘disaster’ and ‘burn’, published between 15 October 2019 and 31 October 2020, and recorded any numbers of koalas given in those reports. This places our methods in a qualitative realm of investigation. Key results. We reviewed 371 media articles on the bushfires and koalas in New South Wales (NSW). Almost half included an estimate of the numbers of koalas killed in NSW. Almost a third stated that koalas are going extinct in NSW, however almost two thirds did not mention that koalas were already in decline from threats other than fire. Conclusions. We concluded that it was dangerous to put numbers on koalas. Misinformation, half-truths, and neglecting the important role of science and scientists, can erode public trust in the media and in science. Implications. The obsession with numbers has left a legacy that can drown out the more considered narrative of science and lead to distortions of policy and management, as well as distract from other critical attributes of koala conservation.

Catastrophic bleaching in protected reefs of the Southern Great Barrier Reef Running head: Catastrophic bleaching in the Southern GBR

Thu, 31 Oct 2024 00:00:00 GMT

Catastrophic bleaching in protected reefs of the Southern Great Barrier Reef Running head: Catastrophic bleaching in the Southern GBR Byrne, Maria; Waller, Alexander; Clements, Matthew; Kelly, Aisling S.; Kingsford, Michael J.; Liu, Bailu; Reymond, Claire E.; Vila Concejo, Ana; Webb, Monique; Foo, Shawna A. This dataset provides health assessments for 459 coral colonies tracked at One Tree Island from February to July 2024 with health categories assigned across 4 time points (Feb, Apr, May, Jul).

Islands in the sky – could complex topography help us rewild beyond the fence?

Mon, 01 Jan 2024 00:00:00 GMT

Islands in the sky – could complex topography help us rewild beyond the fence? Brewster, Rob; Jameson, Tom; Roncolato, Francesca; Crowther, Mathew S.; Finnerty, Patrick B.; Newsome, Thomas M. Context. The protection of threatened species in fenced safe havens has become a vital component of conservation management in Australia. However, despite their success, fenced safe havens face several ecological and economic constraints. There is a need to explore additional approaches to restore species beyond the fence. Aims. To explore naturally occurring mesas as potential ‘sky-island safe havens’, created by natural barriers in elevation and relief, which may restrict the movement of introduced predators and other mammals. Methods. We examined species occurrences at a mesa site (Mt. Talaterang in south-east NSW, Australia) as well as a nearby lower-lying site (Little Forest Plateau). We then provide a geospatial analysis of other mesas in NSW to investigate the number of potential sky-island safe havens in the state. Key results. Species assemblages differed between the two sites, with red foxes (Vulpes vulpes), dingoes/domestic dogs (Canis dingo/familiaris), and European rabbits (Oryctolagus cuniculus) absent from the mesa site, while Antechinus spp. were not detected from the lower-lying site. Feral cats (Felis catus) occurred at significantly lower densities on the mesa site compared to the lower-lying site. In NSW, we identified 91 other mesas of ≥10 ha with similar topology as Mt. Talaterang. Conclusions. Although differences in species assemblages are expected between different habitats, the absence of red foxes and lower number of feral cat detections at the mesa site suggest the need to further explore the potential for mesas in conservation initiatives. Implications. Our findings introduce a supplementary conservation strategy that could augment existing fenced safe haven approaches.

The decline, fall, and rise of a large urban colonising bird

Mon, 01 Jan 2024 00:00:00 GMT

The decline, fall, and rise of a large urban colonising bird Hall, Matthew J.; Martin, John M.; Burns, Alicia L.; Hochuli, Dieter F. Context. The process of urbanisation results in dramatic landscape changes with long-lasting and sometimes irreversible consequences for the biota as urban sensitive species are eliminated. The Australian brush-turkey (Alectura lathami) is a recent urban colonist despite atypical traits for an urban adapter. Contrary to observed range declines and initial reports of decreased reproductive success in cities, Australian brush-turkeys have increased their range in urban areas. Aims. Historical atlas and present citizen science data were used to examine the changing distribution of the Australian brush-turkey at continental and city scales, and the changing land use in urban areas occupied by the species. We assess which environmental and landscape features are driving observed distribution changes over time. Methods. We describe and map changes at the continental scale between 1839–2019. We then assessed colonisation of the cities of Brisbane and Sydney (located 900 km apart) over the period 1960–2019. At the city scale, we quantified the changing land use within Australian brush-turkey occupied areas over time using classification of satellite imagery. Key results. The Australian brush-turkey’s geographical range has shifted over the last century, with the species receding from the western and southwestern parts of their range, while expanding in the northwest. Areas occupied in the cities of Brisbane and Sydney have expanded, with more recently occupied areas containing less vegetation and more developed land than previously occupied areas. Conclusions. Our results confirm that Australian brush-turkeys are successfully colonising urban areas, including major cities, and are likely to continue moving into urban areas, despite declines elsewhere in their natural range. The species is not limited to suburbs with a high proportion of greenspace, as Australian brush-turkeys are increasingly occurring in highly developed areas with limited vegetation. Implications. This study highlights that species which were locally extirpated from urban areas, and thought to be unlikely candidates for recolonisation, can successfully occupy human modified habitats. Successful expansion is likely to be associated with key behavioural traits, urban greening, and legal protection from human persecution.

UOS2301-003RTX Overseas wheat phenotyping 2024

Tue, 28 May 2024 00:00:00 GMT

UOS2301-003RTX Overseas wheat phenotyping 2024 Ziems, Laura; Zhang, Peng; Park, Robert; Singh, Davinder 614 wheat lines were evaluated in Njoro Kenya for resistance and susceptibility against stem rust (Ug99 lineage) and stripe rust (race PstS16) in year 2024

UOS2301-003RTX Overseas barley phenotyping 2023

Tue, 28 May 2024 00:00:00 GMT

UOS2301-003RTX Overseas barley phenotyping 2023 Ziems, Laura; Zhang, Peng; Park, Robert; Singh, Davinder 218 barley lines were screened in Toluca Mexico for assessing barley stripe/yellow rust (BYR) resistance and susceptibility against exotic race 24 (PshMEX-1) in year 2023

Data from: Embracing Biodiversity: Multispecies Population Genomics of Leafless Bossiaeas Reveals Novel Taxa, Population Dynamics, and Conservation Strategies

Mon, 22 Apr 2024 00:00:00 GMT

Data from: Embracing Biodiversity: Multispecies Population Genomics of Leafless Bossiaeas Reveals Novel Taxa, Population Dynamics, and Conservation Strategies McMaster, Eilish Summer; Yap, Jia-Yee Samantha; McDougall, Keith L.; James, Elizabeth A.; Walsh, Neville; Jario, Nic; Peterie, Jess; Rossetto, Maurizio Leafless Bossiaea species are a unique group of plants endemic to Australia which present intriguing challenges in taxonomy and conservation due to their morphological simplicity and often small, disjunct populations. We employed whole genome reduced representation sequencing to enhance our understanding of the population dynamics, diversity, and taxonomy of leafless Bossiaea species. Our dataset comprised 52,539 SNPs across 283 samples from seven leafless Bossiaea species, including six listed threatened species. We examined population structure, phylogenetic relationships, kinship, and gene flow within and between populations. Based on our population genomic analyses we propose recognition of the novel taxon Bossiaea vombata subsp. orientalis and a change in status from species (B. milesiae) to subspecies for B. fragrans subsp. milesiae. Additionally, we reveal extensive clonal reproduction across species and limited gene flow at distances > 1 km, shedding light on the challenges faced by these species. We advocate a coordinated approach to conservation, focusing on restoring self-sustaining populations and leveraging genetic rescue strategies. By addressing the population dynamics of multiple species simultaneously in taxonomically challenging lineages, we can make informed choices to safeguard biodiversity and evolutionary potential.

Paternal protein provisioning to embryos during male seahorse pregnancy

Mon, 01 Jan 2024 00:00:00 GMT

Paternal protein provisioning to embryos during male seahorse pregnancy Skalkos, Zoe; Van Dyke, James; Dowland, Samson; Whittington, Camilla In brief: Seahorses exhibit male pregnancy and are thus valuable comparative models for the study of the physiology and evolution of pregnancy. This study shows that protein is transported from fathers to developing embryos during gestation, and provides new knowledge about paternal contributions to embryonic development. Abstract: Syngnathid embryos (seahorses, pipefishes and seadragons) develop on or in the male in a specialised brooding structure (brood pouch). Seahorse brood pouches supply nutrients, including lipids, to developing embryos (patrotrophy). We tested the hypothesis that proteins, vital for gene regulation and tissue growth during embryogenesis, are also transported from father to embryos, using the Australian pot-bellied seahorse, Hippocampus abdominalis. We used dry masses and total nitrogen content to estimate the total protein content of newly fertilised egg and neonate H. abdominalis. Neonates contained significantly greater protein mass than newly fertilised eggs. This result indicates that paternal protein transport to developing embryos occurs during H. abdominalis pregnancy. This study is the first to show paternal protein transport during pregnancy in seahorses, and furthers our understanding of paternal influence on embryonic development in male pregnant vertebrates.

Odour information: the key to associational effects of neighbours on focal plant susceptibility to mammalian herbivores

Mon, 04 Mar 2024 00:00:00 GMT

Odour information: the key to associational effects of neighbours on focal plant susceptibility to mammalian herbivores Finnerty, Patrick (1) Neighbouring plants can alter the susceptibility of high-quality focal plants to herbivores by affecting herbivore patch choice. Many herbivores use plant odour to make patch-scale foraging decisions from afar, but the actual information they rely on within complex plant odours is largely unknown. Defining the information herbivores use provides a mechanistic link underpinning herbivore patch-scale foraging decisions. Revealing the information driving herbivore patch selection is key if we are to understand and predict associational effect outcomes of these decisions. (2) Here, our first aim was to test whether herbivores can use odour cues alone to make patch selection decisions facilitating predictable associational effects on high-quality focal plants. Our second aim was then to test whether artificial odour, designed to mimic the informative odour component of low-quality neighbours, is as effective as real plants in providing associational refuge. (3) We tested patch choice by African elephants, Loxodonta africana using a giant Y-maze and real or artificial plant odours as the only cues for the neighbours of a high-quality focal plant. We quantified the probability of various odour treatments being chosen in comparison with the odour of a focal plant alone. (4) Compared with focal plants alone, we found that elephants were more likely to choose patches with the focal plant and either moderate or high-quality neighbours, but less likely to choose patches with the focal plant and low-quality neighbours. We also demonstrated that an artificial subset of odours, designed to be informative, were as effective as real low-quality neighbours in providing associational refuge to the focal plant. (5) Our results demonstrate a key role of plant odour – and specifically informative components within complex odour profiles – in patch choice decisions facilitating plant associational effects on high-quality focal plants. Understanding what olfactory information herbivores use when deciding which patches to visit or avoid, and how it affects focal plant susceptibility is important ecologically. Herbivores' patch selection not only affects individual fitness, but also shapes plant community structure through impacting plant survival and recruitment, causing trophic cascades. Synthesizing odour information could offer a new tool to influence herbivore foraging decisions, with implications for wildlife management and conservation, including plant protection.

Decoupled cycling of carbon, nitrogen, and phosphorus in a grassland soil along a hillslope mediated by clay and soil moisture

Sat, 01 Jan 2022 00:00:00 GMT

Decoupled cycling of carbon, nitrogen, and phosphorus in a grassland soil along a hillslope mediated by clay and soil moisture Bicharanloo, Bahareh; Bagheri Shirvan, Milad; Dijkstra, Feike A. Grasslands extend across a variety of topographies including non-flat hilly areas with varied soil texture and moisture that can mediate soil biogeochemical cycling of carbon (C), nitrogen (N) and phosphorus (P). In this study we examined soil organic C, total N and P pools (both inorganic and organic), as well as gross N mineralisation (GNM, as a measure of microbial activity and N dynamics) and microbial C, N and P in winter and spring along a grassland hillslope. Our results showed that variation in soil clay and associated soil moisture were the most important mediators affecting C and N dynamics along the grassland elevational gradient. Total organic C pools were highest where the clay content was highest, likely because of the sorption capacity of clay stabilising organic matter against microbial decomposition. Likewise, the variation in soil organic N pools along the hillslope was mostly controlled by clay and soil moisture effects on microbial stabilisation of organic N. Furthermore, microbial C, N and GNM increased with increased soil moisture, suggesting that microbial activity was limited by soil moisture. In contrast, soil P pools were not related to clay and soil moisture, while soil organic P was decoupled from soil organic C and N pools along the hillslope. Possibly, differences in microbial stabilisation and mineralisation pathways (oxidation for C and N, hydrolysis for P), microbial homeostatic regulation of C, N and P, and P fixation resulted in a decoupling of P from C and N cycling in this grassland. We conclude that variation in clay and associated soil moisture along grassland hillslopes can have important but nonunidirectional effects on soil C, N and P cycling.

Ameliorating soil acidity with calcium carbonate and calcium hydroxide: effects on carbon, nitrogen, and phosphorus dynamics

Sun, 01 Jan 2023 00:00:00 GMT

Ameliorating soil acidity with calcium carbonate and calcium hydroxide: effects on carbon, nitrogen, and phosphorus dynamics Yu, Xing; Keitel, Claudia; Dijkstra, Feike A. Calcium carbonate (CaCO3) is frequently used to ameliorate soil acidity in agricultural soils. An alternative is calcium hydroxide (Ca(OH)2), which is more soluble than CaCO3. However, the associated change in soil parameters remains unclear. We aimed to evaluate the different responses of available nitrogen (N) and phosphorus (P), microbial biomass carbon (C), N, and P (MBC, MBN, and MBP), and dissolved organic C and N (DOC and DON) to CaCO3 and Ca(OH)2. We amended an acidic soil (pH of 5.6) with CaCO3 or Ca(OH)2 at 5 different loadings of hydroxide (OH−, 0.025, 0.05, 0.1, 0.25, and 0.75 mmol g−1) in a 30-day incubation experiment. Both Ca(OH)2 and CaCO3 rapidly increased soil pH, but soil pH increased to 10 with the highest loading rate of Ca(OH)2, while soil pH levelled off at 7.5 with an OH− loading of 0.25 mmol g−1 as CaCO3. Higher ammonium and lower nitrate concentration with high OH− loading of Ca(OH)2 (>0.25 mmol g−1) suggests that nitrification was constrained under basic soil conditions, while adding CaCO3 showed the opposite results. Ca(OH)2 addition increased DOC and DON, along with MBC and MBN, suggesting that desorption of organic matter stimulated microbial growth. High OH− loading with CaCO3 reduced available P due to high P-fixation more than Ca(OH)2. Our study shows that while both Ca(OH)2 and CaCO3 can be used to ameliorate soil acidity, Ca(OH)2 may be able to reduce nitrification and thus N loss at high OH− loading and enhance available P more than CaCO3.