Integrating field survey data with satellite image data to improve shallow water seagrass maps : the role of AUV and snorkeller surveys

Repeatable and accurate seagrass mapping is required for understanding seagrass ecology and supporting management decisions. For shallow (< 5 m) seagrass habitats, these maps can be created by integrating high spatial resolution imagery with field survey data. Field survey data for seagrass is often collected via snorkelling or diving. However, these methods are limited by environmental and safety considerations. Autonomous Underwater Vehicles (AUVs) are used increasingly to collect field data for habitat mapping, albeit mostly in deeper waters (>20 m). Here we demonstrate and evaluate the use and potential advantages of AUV field data collection for calibration and validation of seagrass habitat mapping of shallow waters (< 5 m), from multispectral satellite imagery. The study was conducted in the seagrass habitats of the Eastern Banks (142 km2), Moreton Bay, Australia. In the field, georeferenced photos of the seagrass were collected along transects via snorkelling or an AUV. Photos from both collection methods were analysed manually for seagrass species composition and then used as calibration and validation data to map seagrass using an established semi-automated object based mapping routine. A comparison of the relative advantages and disadvantages of AUV and snorkeller collected field data sets and their influence on the mapping routine was conducted. AUV data collection was more consistent, repeatable and safer in comparison to snorkeller transects. Inclusion of deeper water AUV data resulted in mapping of a larger extent of seagrass (~7 km2, 5 % of study area) in the deeper waters of the site. Although overall map accuracies did not differ considerably, inclusion of the AUV data from deeper water transects corrected errors in seagrass mapped at depths to 5 m, but where the bottom is visible on satellite imagery. Our results demonstrate that further development of AUV technology is justified for the monitoring of seagrass habitats in ongoing management programs.

Genetics of path lengths in brain connectivity networks: HARDI-based maps in 457 adults

Brain connectivity analyses are increasingly popular for investigating organization. Many connectivity measures including path lengths are generally defined as the number of nodes traversed to connect a node in a graph to the others. Despite its name, path length is purely topological, and does not take into account the physical length of the connections. The distance of the trajectory may also be highly relevant, but is typically overlooked in connectivity analyses. Here we combined genotyping, anatomical MRI and HARDI to understand how our genes influence the cortical connections, using whole-brain tractography. We defined a new measure, based on Dijkstra's algorithm, to compute path lengths for tracts connecting pairs of cortical regions. We compiled these measures into matrices where elements represent the physical distance traveled along tracts. We then analyzed a large cohort of healthy twins and show that our path length measure is reliable, heritable, and influenced even in young adults by the Alzheimer's risk gene, CLU.

Constructing abstract maps from spatial descriptions for goal-directed exploration

This paper describes ongoing work on a system using spatial descriptions to construct abstract maps that can be used for goal-directed exploration in an unfamiliar office environment. Abstract maps contain membership, connectivity, and spatial layout information extracted from symbolic spatial information. In goal-directed exploration, the robot would then link this information with observed symbolic information and its grounded world representation. We demonstrate the ability of the system to extract and represent membership, connectivity, and spatial layout information from spatial descriptions of an office environment. In the planned study, the robot will navigate to the goal location using the abstract map to inform the best direction to explore in.

Validation of processing maps for 304L stainless steel using hot forging, rolling and extrusion

The development of a microstructure in 304L stainless steel during industrial hot-forming operations, including press forging (mean strain rate of 0.15 s(-1)), rolling/extrusion (2-5 s(-1)), and hammer forging (100 s(-1)) at different temperatures in the range 600-1200 degrees C, was studied with a view to validating the predictions of the processing map. The results have shown that excellent correlation exists between the regimes exhibited by the map and the product microstructures. 304L stainless steel exhibits instability bands when hammer forged at temperatures below 1100 degrees C, rolled/extruded below 1000 degrees C, or press forged below 800 degrees C. All of these conditions must be avoided in mechanical processing of the material. On the other hand, ideally, the material may be rolled, extruded, or press forged at 1200 degrees C to obtain a defect-free microstructure.

Predicting wood value in Queensland Caribbean pine plantations using a decision support system

A decision support system has been developed in Queensland to evaluate how changes in silvicultural regimes affect wood quality, and specifically the graded recovery of structural timber. Models of tree growth, branch architecture and wood properties were developed from data collected in routine Caribbean pine plantations and specific silvicultural experiments. These models were incorporated in software that simulates the conversion of standing trees into logs, and the logs into boards, and generates detailed data on knot location and basic density distribution. The structural grade of each board was determined by simulating the machine stress-grading process, and the predicted graded recovery provided an indicator of wood value. The decision support system improves the basis of decision-making by simulating the performance of elite genetic material under specified silvicultural regimes and by predicting links between wood quality and general stand attributes such as stocking and length of rotation.

GIS-based tools for management of pine plantations, Queensland, Australia

Two examples of GIS-based multiple-criteria evaluations of plantation forests are presented. These desktop assessments use available topographical, geological and pedological information to establish the risk of occurrence of certain environmentally detrimental processes. The first case study is concerned with the risk that chemical additives (i.e. simazine) applied within the forestry landscape may reach the drainage system. The second case study assesses the vulnerability of forested areas to landslides. The subject of the first multiple-criteria evaluation (MCE) was a 4 km2 logging area, which had been recently site-prepared for a Pinus plantation. The criteria considered relevant to the assessment were proximity to creeks, slope, soil depth to the restrictive layer (i.e. potential depth to a perched water table) and soil erodability (based on clay content). The output of the MCE was in accordance with field observations, showing that this approach has the potential to provide management support by highlighting areas vulnerable to waterlogging, which in turn can trigger overland flow and export of pollutants to the local stream network. The subject of the second evaluation was an Araucaria plantation which is prone to landslips during heavy rain. The parameters included in the assessment were drainage system, the slope of the terrain and geological features such as rocks and structures. A good correlation between the MCE results and field observations was found, suggesting that this GIS approach is useful for the assessment of natural hazards. Multiple-criteria evaluations are highly flexible as they can be designed in either vector or raster format, depending on the type of available data. Although tested on specific areas, the MCEs presented here can be easily used elsewhere and assist both management intervention and the protection of the adjacent environment by assessing the vulnerability of the forest landscape to either introduced chemicals or natural hazards.

Construction of microsatellite linkage maps for Corymbia

The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

Propagation of Wollemi pine from tip cuttings and lower segment cuttings does not require rooting hormones

Domestication of the recently discovered and highly endangered Wollemi pine has relied almost entirely upon serial propagation of cuttings from a very small conservation collection. This study assessed the requirement for applied auxin to induce rooting in tip cuttings and lower segment cuttings of Wollemi pine. Both types of cuttings proved easy-to-root, with mean rooting of 71% for tip cuttings and 82% for lower segments. Auxin application (at 1.5, 3.0 or 8.0 g indole-3-butyric acid/L) did not accelerate root protrusion from propagation tubes or affect final rooting percentages.

Long-term impacts of harvest residue management on nutrition, growth and productivity of an exotic pine plantation of sub-tropical Australia

Residue retention is an important issue in evaluating the sustainability of production forestry. However, its long-term impacts have not been studied extensively, especially in sub-tropical environments. This study investigated the long-term impact of harvest residue retention on tree nutrition, growth and productivity of a F1 hybrid (Pinus elliottii var. elliottii × Pinus caribaea var. hondurensis) exotic pine plantation in sub-tropical Australia, under three harvest residue management regimes: (1) residue removal, RR0; (2) single residue retention, RR1; and (3) double residue retention, RR2. The experiment, established in 1996, is a randomised complete block design with 4 replicates. Tree growth measurements in this study were carried out at ages 2, 4, 6, 8 and 10 years, while foliar nutrient analyses were carried out at ages 2, 4, 6 and 10 years. Litter production and litter nitrogen (N) and phosphorus (P) measurements were carried out quarterly over a 15-month period between ages 9 and 10 years. Results showed that total tree growth was still greater in residue-retained treatments compared to the RR0 treatment. However, mean annual increments of diameter at breast height (MAID) and basal area (MAIB) declined significantly after age 4 years to about 68-78% at age 10 years. Declining foliar N and P concentrations accounted for 62% (p < 0.05) of the variation of growth rates after age 4 years, and foliar N and P concentrations were either marginal or below critical concentrations. In addition, litter production, and litter N and P contents were not significantly different among the treatments. This study suggests that the impact of residue retention on tree nutrition and growth rates might be limited over a longer period, and that the integration of alternative forest management practices is necessary to sustain the benefits of harvest residues until the end of the rotation.

Preservice early childhood teachers and designers partnering for change at The Lone Pine Koala Sanctuary: An interdisciplinary education and design for sustainability project

This presentation discusses and critiques a current case study of a project in which Early Childhood preservice teachers are working in partnership with Design students to develop principles and concepts for the design and construction of an early childhood centre. This centre, to be built on the grounds of the iconic Lone Pine Koala Sanctuary in Brisbane , focuses on Education for Sustainability (EfS), sustainable design and sustainable business. Interdisciplinary initiatives between QUT staff and students from two Faculties (Education and Creative Industries) have been situated in the real –world context of this project. This practical, authentic project has seen stakeholders take an interdisciplinary approach to sustainability, opening up new ways of thinking about early childhood centre design, particularly with respect to operation and function. Interdisciplinarity and a commitment to genuine partnerships have created intellectual spaces to re-think the potential of the disciplines to be interwoven so that future professionals from different fields might come together to learn from each other and to address the sustainability imperative. The case study documents and explores the possibilities that the Lone Pine project offers for academics and students from Early Childhood and Design to collaboratively inform the Sanctuary’s vision for the Centre. The research examines how students benefit from practical, real world, community-integrated learning; how academic staff across two disciplines are able to work collaboratively within a real-world context; and how external stakeholders experience and benefit from the partnership with university staff and students. Data were collected via a series of focus group and individual interviews designed to explore how the various stakeholders (staff, students, business partners) experienced their involvement in the interdisciplinary project. Inductive and deductive thematic analysis of these data suggest many benefits for participants as well as a number of challenges. Findings suggest that the project has provided students with ‘real world’ partnerships that reposition early childhood students’ identities from ‘novice’ to ‘professional’, where their knowledge, expertise and perspectives are simultaneously validated and challenged in their work with designers. These partnerships are enabling preservice teachers to practice a new model of early childhood leadership in sustainability, one that is vital for leading for change in an increasingly complex world. This presentation celebrates, critiques and problematises this project, exploring wider implications for other contexts in which university staff and students may seek to work across traditional boundaries, thus building partnerships for change.

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

Domestication for Conservation of an Endangered Species: The Case of the Wollemi Pine

A small population of tall slender conifers was discovered in 1994 in a deep rainforest canyon of the Wollemi National Park, New SouthWales, Australia. The living trees closely resembled fossils that were more than 65 million years old, and this ‘living fossil’ was recognised as a third extant genus in the Araucariaceae (Araucaria, Agathis and now Wollemia). The species was named the Wollemi pine (W. nobilis). Extensive searches uncovered very few populations, with the total number of adult trees being less than 100. Ex situ collections were quickly established in Sydney as part of the Wollemi Pine Recovery Plan. The majority of the ex situ population was later transferred to our custom-built facility in Queensland for commercial multiplication. Domestication has relied very heavily on the species’ amenability to vegetative propagation because seed collection from the natural populations is dangerous, expensive, and undesirable for conservation reasons. Early propagation success was poor, with only about 25% of cuttings producing roots. However, small increases in propagation success have a very large impact on a domestication program because plant production can be modelled on an exponential curve where each rooted cutting develops into a mother plant that, in turn, provides more rooted cuttings. An extensive research program elevated rooting percentages to greater than 80% and also provided in vitro methods for plant multiplication. These successes have enabled international release of the Wollemi pine as a new and attractive species for ornamental horticulture.

Pre-maps : An Educational Programme for Reading Tactile Maps

It is demanding for children with visual impairment to become aware of the world beyond their immediate experience. They need to learn to control spatial experiences as a whole and understand the relationships between objects, surfaces and themselves. Tactile maps can be an excellent source of information for depicting space and environment. By means of tactile maps children can develop their spatial understanding more efficiently than through direct travel experiences supplemented with verbal explanations. Tactile maps can help children when they are learning to understand environmental, spatial, and directional concepts. The ability to read tactile maps is not self-evident; it is a skill, which must be learned. The main research question was: can children who are visually impaired learn to read tactile maps at the preschool age if they receive structural teaching? The purpose of this study was to develop an educational program for preschool children with visual impairment, the aim of which was to teach them to read tactile maps in order to strengthen their orientation skills and to encourage them to explore the world beyond their immediate experience. The study is a multiple case study describing the development of the map program consisting of eight learning tasks. The program was developed with one preschooler who was blind, and subsequently the program was implemented with three other children. Two of the children were blind from birth, one child had lost her vision at the age of two, and one child had low vision. The program was implemented in a normal preschool. Another objective of the pre-map program was to teach the preschooler with visual impairment to understand the concept of a map. The teaching tools were simple, map-like representations called pre-maps. Before a child with visual impairment can read a comprehensive tactile map, it is important to learn to understand map symbols, and how a three-dimensional model changes to a two-dimensional tactile map. All teaching sessions were videotaped; the results are based on the analysis of the videotapes. Two of the children completed the program successfully, and learned to read a tactile map. The two other children felt happy during the sessions, but it was problematic for them to engage fully in the instruction. One of the two eventually completed the program, while the other developed predominantly emerging skills. The results of the children's performances and the positive feedback from the teachers, assistants and the parents proved that this pre-map program is appropriate teaching material for preschool children who are visually impaired. The program does not demand high-level expertise; also parents, preschool teachers, and school assistants can carry out the program.

Ageing delays the cellular stages of adventitious root formation in pine.

Vegetative propagation programs internationally are affected by the significant decline of rooting success as trees mature. This study compared the cellular stages of root formation in stem cuttings from 15-week-old (juvenile) and 9-y-old (mature) stock plants of the slash x Caribbean pine hybrid (Pinus elliottii var. elliottii x P. caribaea van hondurensis). The cellular stages of root formation were the same in both juvenile and mature cuttings, beginning with cell divisions of the vascular cambium forming callus tissue. Within the callus, tracheids differentiated and elongated to form root primordia. Roots in juvenile cuttings developed faster than those in mature cuttings and the juvenile cuttings had a much higher rooting percent at the end of the study (92% and 26% respectively). Cuttings of the two juvenile genotypes had more primary roots (5.5 and 3.3) than the three mature genotypes (0.96, 0.18 and 0.07). The roots of juvenile cuttings were more evenly distributed around the basal circumference when compared with those on cuttings from the mature genotypes. Further work is needed to improve understanding of physiological changes with maturation so that the rooting success and the speed of development in cuttings from mature stock plants can be optimised, hence improving genetic gain.