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"Batchelor, Kathryn"
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Detect, Consolidate, Delineate: Scalable Mapping of Field Boundaries Using Satellite Images
Digital agriculture services can greatly assist growers to monitor their fields and optimize their use throughout the growing season. Thus, knowing the exact location of fields and their boundaries is a prerequisite. Unlike property boundaries, which are recorded in local council or title records, field boundaries are not historically recorded. As a result, digital services currently ask their users to manually draw their field, which is time-consuming and creates disincentives. Here, we present a generalized method, hereafter referred to as DECODE (DEtect, COnsolidate, and DElinetate), that automatically extracts accurate field boundary data from satellite imagery using deep learning based on spatial, spectral, and temporal cues. We introduce a new convolutional neural network (FracTAL ResUNet) as well as two uncertainty metrics to characterize the confidence of the field detection and field delineation processes. We finally propose a new methodology to compare and summarize field-based accuracy metrics. To demonstrate the performance and scalability of our method, we extracted fields across the Australian grains zone with a pixel-based accuracy of 0.87 and a field-based accuracy of up to 0.88 depending on the metric. We also trained a model on data from South Africa instead of Australia and found it transferred well to unseen Australian landscapes. We conclude that the accuracy, scalability and transferability of DECODE shows that large-scale field boundary extraction based on deep learning has reached operational maturity. This opens the door to new agricultural services that provide routine, near-real time field-based analytics.
Journal Article
Two decades of progress targeting boneseed (Chrysanthemoides monilifera subsp. monilifera): a global review to inform eradication in Western Australia
Boneseed [Chrysanthemoides monilifera subsp. monilifera (L.) Norl.; syn. Osteospermum moniliferum subsp. moniliferum L.] is a perennial shrub native to the southwestern and southern coasts of South Africa. It was introduced to Australia in about 1852 and now represents a significant threat to natural ecosystems. Despite C. monilifera subsp. monilifera being listed as a Weed of National Significance, momentum on improving its management has dissipated at a national level, beginning in 2008 (when a national research initiative finished) and increasingly after 2013 (when funding for national coordination ceased). A recent synthesis of past management for C. monilifera subsp. monilifera and recommendations for guiding future priorities has rekindled interest in Western Australia. To complement this synthesis and to identify improvements for program efficiency and effectiveness, we reviewed research and management findings on this weed with a focus on the past two decades. We collated information across the ecology and biology of C. monilifera subsp. monilifera, and the near relative, bitou bush [Chrysanthemoides monilifera subsp. rotunda (DC.) J.C. Manning & Goldblatt; syn. Osteospermum moniliferum subsp. rotundatum (DC.)], as well as useful insight from C. monilifera subsp. monilifera management programs applied elsewhere. As part of this review, we assessed the classical biological control work that has been done on C. monilifera subsp. monilifera, focusing on likely explanations for why, despite nine agents and a naturalized fungus, biological control is not an effective management tool. Our synthesis suggests that for the limited populations with low-abundance plants in Western Australia, eradication from the state remains a realistic target. This objective, however, needs to build on the collated baseline of past management efforts and deploy a carefully planned management program over the coming two decades. Systematic surveillance using the latest techniques, combined with manual or herbicide removal and controlled burns where possible, remain the most suitable methods to deploy. The long-lived soil seedbank requires detailed monitoring following initial plant removals and long-term funding to ensure the sustained effort required to deliver the goal of eradication of C. monilifera subsp. monilifera in Western Australia.
Journal Article
Informing eradication feasibility: ecological context and delimitation for boneseed (Chrysanthemoides monilifera subsp. monilifera) in Western Australia
The southern African shrub boneseed [Chrysanthemoides monilifera subsp. monilifera (L.) Norl.] is a perennial shrub that is a significant threat to natural ecosystems and is listed as a Weed of National Significance in Australia. In Western Australia (WA) it has spread across peri-urban and natural environments. We assembled a single standardized database containing more than 2,050 presence records for individual plants and 135 absence records at a local population level. We further refined the populations into 89 sites that require different management trajectories due to topography and capacity of land managers to implement control. Forty-nine of these sites were in urban regions and 40 sites were in regional WA. We split these 89 sites into three near-term management goals: watch (12), extirpate (68), and contain (9). The 12 watch sites are those where all available evidence suggests that there have been no new inputs into the seedbank for 15 yr. The 68 sites marked for extirpation are those where delimitation is already achieved or easily achievable, where there have been minimal seed inputs into the soil seedbank in recent years due to consistent surveillance and control, and where surveys for new plants are likely to be efficient to conduct. Finally, for nine sites in urban regions around Perth, we recommend containment in the near term with a longer-term goal to achieve delimitation and extirpation. To achieve the objective of state-level eradication, a coordinated and sustained campaign involving three components—delimitation of all sites, prevention of further inputs into the soil seedbank, and systematic field surveys to remove plants—must commence without delay. While resourcing requirements for delimitation and overall program management are not possible to estimate, our prior experience suggests that it will take at least 1,900 h of on-ground surveying by experienced personnel to achieve extirpation of C. monilifera subsp. monilifera in WA.
Journal Article
Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African–Australian biotic exchange
Many plants exchanged in the global redistribution of species in the last 200 years, particularly between South Africa and Australia, have become threatening invasive species in their introduced range. Refining our understanding of the genetic diversity and population structure of native and alien populations, introduction pathways, propagule pressure, naturalization, and initial spread, can transform the effectiveness of management and prevention of further introductions. We used 20,221 single nucleotide polymorphisms to reconstruct the invasion of a coastal shrub, Chrysanthemoides monilifera ssp. rotundata (bitou bush) from South Africa, into eastern Australia (EAU), and Western Australia (WAU). We determined genetic diversity and population structure across the native and introduced ranges and compared hypothesized invasion scenarios using Bayesian modeling. We detected considerable genetic structure in the native range, as well as differentiation between populations in the native and introduced range. Phylogenetic analysis showed the introduced samples to be most closely related to the southern‐most native populations, although Bayesian analysis inferred introduction from a ghost population. We detected strong genetic bottlenecks during the founding of both the EAU and WAU populations. It is likely that the WAU population was introduced from EAU, possibly involving an unsampled ghost population. The number of private alleles and polymorphic SNPs successively decreased from South Africa to EAU to WAU, although heterozygosity remained high. That bitou bush remains an invasion threat in EAU, despite reduced genetic diversity, provides a cautionary biosecurity message regarding the risk of introduction of potentially invasive species via shipping routes. Bitou bush is a coastal shrub, native to Southern Africa, and invasive in Australia. We used single nucleotide polymorphisms to reconstruct the invasion history of bitou bush into eastern and Western Australia. We found strong genetic structure in the native range, and detected bottlenecks through the introduction process. Our results highlight the risk of introduction of potentially invasive species via shipping routes, even from a small number of propagules.
Journal Article
Aerial photography and dendrochronology as tools for recreating invasion histories: do they work for bitou bush (Chrysanthemoides monilifera subsp. rotundata)?
There is an increasing need to understand demographic change to improve management outcomes for controlling invasive alien species. We applied three emerging techniques for recreating past population dynamics—high resolution aerial photography time series, stem growth ring analysis and population level field surveys—to recreate the introduction and invasion history for bitou bush (Chrysanthemoides monilifera subsp. rotundata) in Western Australia. We also compared across dating techniques to test the validity of using stem rings produced by successive cambia for dating purposes, and analysed for the influence of ontogenetic, environmental and morphological factors on stem ring formation. Aerial photography allowed for an accurate recreation of plant presence over time and individual plant age for 18 plants. In a sample of over 500 plants with up to 42 rings, canopy area was related to plant age and ring number, while stem diameter was related to canopy size and ring number. However, stem rings were not produced in a temporally consistent manner and could not be predicted reliably. Up to eight stem rings were produced in younger plants, for which the rate of ring production was greatest. While there was an ontogenetic growth pattern for ring width, no inter-plant synchronisation of ring size was detected, as would be expected if ring size were a response to landscape level climate factors. With aerial imagery and stem ring analysis providing new ways to recreate plant population dynamics at the individual plant level, managers can use this insight to refine conservation and invasion management programs. For bitou bush, such information will focus the duration and location of the current eradication program in Western Australia.
Journal Article
Can honey bees be used to detect rare plants? Taking an eDNA approach to find the last plants in a weed eradication program
The detection of rare taxa, crucial to conservation and biosecurity, presents many challenges that emerging technologies have the potential to address or avoid. Analysis of environmental DNA (eDNA) is a promising tool for the detection of rare species, especially when applied in a way that exploits natural processes to accumulate biological material (natural aggregation). This study investigated the potential of using honey bees as aggregators of pollen eDNA to detect Chrysanthemoides monilifera subsp. monilifera (boneseed), an introduced species targeted for eradication in Western Australia. We developed a species‐specific polymerase chain reaction (PCR)‐based assay that detected boneseed pollen at levels as low as 70 grains per million in a constructed pollen mixture. The assay was successfully used on wild‐caught bees from large boneseed populations, confirming they collect boneseed pollen. However, our results did not detect boneseed DNA in honey bee pollen collected from hive pollen traps near isolated boneseed plants. We hypothesize that a combination of low abundance of boneseed individuals, vast alternative flower resources at the time of boneseed flowering, and honey bee behavior and ecology may have led to lack of detection. We propose ways in which future work using honey bees to detect rare species can be improved. We also outline how other eDNA substrates (e.g., air and water samples) could be used with the PCR assay we have developed. More broadly, our work highlights the potential of eDNA techniques to detect rare species in biosecurity and conservation contexts and contributes to the development of pollinator‐based detection. Study to determine if rare taxa can be detected using molecular methods in hive pollen collected from a nearby apiary. Honey bees were confirmed to visit the target taxa when abundant but were not detected in the hive pollen while they were rare.
Journal Article
Long term monitoring of recruitment dynamics determines eradication feasibility for an introduced coastal weed
Bitou bush (Chrysanthemoides monilifera subsp. rotundata) is a Weed of National Significance in Australia and has impacted a significant portion of the eastern coastline. Its discovery in Western Australia was, therefore, a cause for concern. Assessment and control of the isolated and well-defined population began in 2012. To assess the feasibility of eradication in Western Australia as a management outcome for bitou bush, we applied a rigorous data-driven quantification and prediction process to the control program. Between 2012 and 2018 we surveyed over 253 ha of land and removed 1766 bitou bush plants. Approximately 97 person-days were spent over the six years of survey. We measured the seed bank viability for five years starting in 2013, with the 2017 survey results indicating a decline of mean viable seeds/m 2 from 39.3 ± 11.4 to 5.7 ± 2.2. In 2018 we found only ten plants and no newly recruited seedlings in the population. No spread to other areas has been recorded. Soil core studies indicate that the soil seed bank is unlikely to persist beyond eight years. Eradication of the population in Western Australia, defined as five years without plants being detected, therefore remains a realistic management goal. The information generated from the documentation of this eradication program provides invaluable insight for weed eradication attempts more generally: novel detection methods can be effective in making surveys more efficient, all survey methods are not entirely accurate and large plants can escape detection, bitou bush seeds persist in the soil but become effectively undetectable at low densities, and migration of seed was unquantifiable, possibly compromising delimitation. Continued monitoring of the Western Australian population will determine how much of a risk these factors represent to eradication as the outcome of this management program.
Journal Article
Multilingualism and strategic planning for HIV/AIDS-related health care and communication
Background: Many lower and middle income countries (LMICs) have high levels of linguistic diversity, meaning that health information and care is not available in the languages spoken by the majority of the population. This research investigates the extent to which language needs are taken into account in planning for HIV/AIDS-related health communication in development contexts. Methods: We analysed all HIV/AIDS-related policy documents and reports available via the websites of the Department for International Development UK, The Global Fund, and the Ministries of Health and National AIDS commissions of Burkina Faso, Ghana and Senegal. We used quantitative and qualitative analysis to assess the level of prominence given to language issues, ascertain the level at which mentions occur (donor/funder/national government or commission), and identify the concrete plans for interlingual communication cited in the documents. Results: Of the 314 documents analysed, 35 mention language or translation, but the majority of the mentions are made in passing or in the context of providing background socio-cultural information, the implications of which are not explored. At donor level (DFID), no mentions of language issues were found. Only eight of the documents (2.5%) outline concrete actions for addressing multilingualism in HIV/AIDS-related health communication. These are limited to staff training for sign language, and the production of multilingual resources for large-scale sensitization campaigns. Conclusions: The visibility of language needs in formal planning and reporting in the context of HIV/AIDS-related health care is extremely low. Whilst this low visibility should not be equated to a complete absence of translation or interpreting activity on the ground, it is likely to result in insufficient resources being dedicated to addressing language barriers. Further research is needed to fully understand the ramifications of the low prominence given to questions of language, not least in relation to its impact on gender equality.
Journal Article
Management of Chrysanthemoides monilifera subsp. rotundata in Western Australia
One of Australia's most serious weeds, Chrysanthemoides monilifera subsp. rotundata (bitou bush) was recently found for the first time in Western Australia as a well established population in Kwinana, a major port and industrial area south of Perth, the State's capital. This population is remote from other bitou bush infestations in Australia and had escaped detection despite extensive surveys in the same State for the other subspecies that is present in Australia, Chrysanthemoides monilifera subsp. monilifera (boneseed). The main reasons it went undetected are thought to be the tightly controlled access to this area because of mineral processing and port activities, the unusual invasion route via a heavy industrial area and the morphological similarity to a native species when it is not flowering. Two surveys defined the core population of 1038 plants that are spread along the coast over a 25-ha semi-circle with about a 500-m (1640 ft) diameter. Subsequent surveys of first a 500 m buffer zone and later a 1-km (0.621 mi) buffer found four additional plants, indicating that there is considerable potential for dispersal. We concluded that the survey has not delimited the distribution because of the potential and evidence for long distance dispersal. Cooperation by the various land managers has led to all plants being killed, as an initial step to management of this species. Other steps to be undertaken include an awareness campaign in the area that would need to be surveyed for delimitation of the spatial distribution and seed bank assessment to measure potential dispersal both in space and through time. It remains to be determined what is the best strategic response: eradication or containment. Nomenclature: Bitou bush, Chrysanthemoides monilifera (L.) T. Norl. subsp. rotundata (DC.) T. Norl.
Journal Article