School of Agriculture, Food and Ecosystem Sciences - Theses
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ItemPhenological responses of select Eucalyptus species to environmental variability( 2014)The Earth’s climate is warming which will likely lead to changes in biological systems; particularly to species physiology, phenology and distribution. Phenology is the study of life cycle events of plants and animals (e.g.plant germination/ leafing/ flowering; bird migration/feeding) that is directly ruled by seasonal changes in climate. The phenological responses of species are typically sensitive to climate and can be drivers of plant distributions. In Australia, significant research gaps exist on species phenology as extensive and long-term datasets are lacking. A lack of datasets and observational studies highlights key knowledge gaps on the relationship between climate and species phenology, which in turn may limit our ability to predict the response of species to climatic change. This study investigates the key environmental drivers that affect three phenological cycles; germination, growth and reproduction (flowering) of six Eucalyptus species that co-occur in two groups, representing dry (warm-dry) and wet (cool-moist) sclerophyll forests of south-eastern Australia respectively. The six species studied were E. microcarpa, E. polyanthemos, E. tricarpa, E. obliqua, E. radiata and E.sieberi; the first three species representing the dry and the later three the wet sclerophyll forests. The study seeks to identify the relationships between these phenological events and the environmental factors temperature, soil moisture, air humidity and photoperiod length. In particular, the study seeks to identify environmental thresholds that initiate or delay phenological events. Experimental and statistical approaches were used to identify phenological response parameters for each phenological stage. Significant effects of environmental factors on germination, growth and flowering phenology of the studied species were found across all the species, however, the extent and response mechanisms varied amongst species, highlighting that some species may be more susceptible to environmental change. Based on the GCM predictions of future climate the climate change scenarios were built where temperature increases ranging from 0.4−2.75 C with a 1−9% decline in rainfall are expected to incur by the 2020s. For the 2050s, the temperature increase ranges from 0.75−2.75 C with a 3−25% decline in rainfall and for the 2080s temperature increase ranges from 1.0−4.5 C with a 4−40% decline in rainfall.The germination phenological study identified that among warm-dry species, greater germination and establishment may be exhibited by E. microcarpa under warm and dry condition of climate change. Among cool-moist species germination increased for E. obliqua under warm and dry condition of climate change, however, establishment declined. For all the species in the cool-moist group establishmet declined rapidly by the 2050s, though E. radiata exhibited capacity to establish until the 2080s. Non linear growth responses to temperature and temperature thresholds were identified using a Generalised Additive Model (GAM) analysis of 12 months of tree growth, collected from a climate-manipulation experiment study conducted in four glasshouses.The study found that amongst the warm-dry species, E. microcarpa exhibited greater resistance to high temperatures and lower air humidity conditions. E. obliqua exhibited a flexible growth rate and tolerance to moisture limitations. Temperature-dependent photoperiodic responses were quantified for all the species except E. tricarpa and E. sieberi. The flowering phenological study found that non-linear effects of temperature, rainfall and photoperiod length affected flowering intensity. The study showed that E. microcarpa displayed phenotypic plastic response to higher temperature and lower rainfall conditions. Rainfall was influential for E. polyanthemos and E. tricarpa, while flowering and umbel budding of E. obliqua increased when rainfall decreased. This study also identified temperature-dependent photoperiodic cues for all the species with flowering in E. polyanthemos reliant on longer photoperiod lengths. The longer photoperiodic cues found for E. polyanthemos suggests the species is reliant on summer conditions for flowering, however, climate change may increase summer temperature conditions which may pose a risk to the flowering. Long-term flowering phenological data sets are rare for Australian species. An analysis of flowering data using herbarium records in this study demonstrated that the herbarium approach can detect climatic effects on flowering phenology. The study identified that temperature has the largest influence on flowering time although the impacts vary among species, with the warm-dry species exhibiting earlier shifts in response to increasing temperature increment (14.1−14.9 days per 1C for E. microcarpa and E. tricarpa) while the cool-moist species exhibit a delay in flowering (8.7−14.1 days per 1C for E. obliqua, E. radiata and E. sieberi). Both the flowering dataset and herbarium approaches identified that flowering phenology of E. polyanthemos was sensitive to the majority of environmental variables. This study attempts to address the role of phenology on species distributions by integrating the germination, growth and flowering phenological response to model plant response. Phenological trait responses derived from all three studies were combined with 50 years of climate data from each species home range and climate change predictions for south-eastern Australia into the mechanistic model TACA-GEM to create the model variant TACA-PHENO (sub modules of growth and flowering phenological response added to TACA-GEM). The modelling analysis demonstrated that changes in species germination probability, yearly growth and monthly flowering intensity can be detected under observed and climate change scenarios. The results show that for the warm-dry species E. microcarpa, all three phenological stages may be positively influenced by warmer and drier condition of climate change, indicating that the species will maintain and/or increase its distribution in the future. Distributions of all the other species may constrict, however, as one or more phenological responses were negatively affected by climate change. The current distribution of E. tricarpa was the most vulnerable to warming and drying of climate change as germination failed by the 2050s. The phenological strategy of the cool-moist species E. radiata indicates that the species may maintain or increase its current distribution, compared to E. obliqua and E.sieberi by the 2080s. This study highlights that species exhibit divergent phenological responses to environmental conditions; linking all these responses with a modelling approach can help to identify species sensitivity to environmental change. The study high lights that species phenology will remain responsive to changes in temperature and moisture across the spatial scales and thus will be sensitive to climate change. The implications of this phenological shift on species adaptation to climate change is complex, however, our study was successful in providing some initial insights on how climate change may vary phenology which in turn may affect the species abundance in the future.
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ItemAssessing site quality of South Australian radiata pine plantations using airborne LiDAR data( 2011)Site quality information underpins many aspects of radiata pine plantation management in South Australia. Site quality assessment is essentially a problem of assessing the spatial variation of standing volume in unthinned stands at reference age nine or ten. Data collected during three experimental trials and two operational surveys were used to research a new site quality assessment system relying on airborne LiDAR data. A two-stage method was adopted characterised by the calibration of predictive models relating forest and LiDAR variables, and the subsequent application of these models to predict the forest variable across an area of interest. The four parts of the study examined the properties and behaviour of LiDAR prediction models, the sampling design and timing of field data collection, the spatial resolution of model application and the special case of partially thinned plantations. Single-variable, linear models, fitted to high altitude/low density LiDAR data captured across 20 sites scattered over an area of 10,000 km2 , had RMSE of 10-11% and 3-4% for stand volume and predominant height respectively. Evidence of site effects in the models was inconclusive. Models fitted to four LiDAR and field datasets acquired in 2002, 2006, 2007 and 2009 had consistent structure but model parameters were sensitive to the differences in operational LiDAR campaign parameters, indicating that prediction models should be re-calibrated each survey. Fifty field plots were found to be adequate to fit a regionally applicable volume prediction model. Sample selection methods only influenced model precision when sample sizes were small (less than twenty plots). The correlation between forest and LiDAR variables remained strong when field and LiDAR data were collected several years apart, but model parameter values changed rapidly as a result of tree growth. A time lag between LiDAR and field data collection can be tolerated but field measurements, once commenced, should be concentrated in time. The LiDAR predictor variable for volume was found to be insensitive to changes in the reference plot area indicating that volume prediction models may be applied in partitions (spatial units) with areas different than those of the calibration field plots. Comparison of alternative configurations of size, shape and arrangement of partitions, coupled with one of four spatial interpolation techniques, demonstrated significant differences in precision of predicted volume surfaces, with key factors being the dimensions of the interpolation neighbourhood and LiDAR data density. Several configurations closely approximated or, in the case of low density data, exceeded the precision of the prediction models. A method for assessment of partially thinned plantations appeared effective but requires further validation. The results of this study will be used to guide the second operational LiDAR-based site quality survey in South Australia, scheduled for early 2012.
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ItemStructural variations in the ovine genome: their detection and association with phenotypic traits( 2013)Growth and meat yield traits are important to the New Zealand sheep industry. Genomic selection (GS) of these traits uses information from high density ovine SNPs to produce estimated breeding values (EBVs). The aim of GS is to account for loci directly influencing the trait (quantitative trait loci, QTL). This relies on the assumption that high density SNPs tag QTL effects via linkage disequilibrium (LD), however, it is unlikely that all QTL are adequately tagged by high density SNPs. Copy number variants (CNVs) are a type of genetic variant that may not be well tagged by SNPs and have been shown to be involved in phenotypic variation. To date, there has been little published work on CNVs in the sheep genome. While there is a well known example of a CNV affecting coat colour (agouti) in sheep, little is known of how CNVs affect phenotypic variation of production traits. The studies in this thesis employed multiple methods to identify CNVs in the sheep genome. Animals (including trios) were assayed on a Roche NimbleGen 2.1M CGH array. CNV calls from trios were used along with known false-positive calls to build a logistic regression to predict the probability calls from the 2.1M CGH array were correct. 3,488 autosomal CNVRs were identified. On a large scale, CNVRs were hard to accurately detect without using a combination of approaches. CNVRs were verified against CNVRs detected with the Roche NimbleGen 385K CGH array, Illumina OvineSNP50 BeadChip and Illumina HiSeq 2000 sequence data. Results of this work contribute a comprehensive resource of CNV regions to the literature on sheep CNVs. Given the importance of growth and meat yield traits in the New Zealand sheep industry, and the possibly unaccounted effects of CNVs on these traits, an association analysis was carried out with these traits and loci that potentially represent CNVs. Firstly, it was determined that EBVs produced by Sheep Improvement Limited (SIL) were appropriate to use as the dependent variable in the association analysis. Loci that potentially represent CNVs were SNPs from the Illumina OvineSNP50 BeadChip that were previously discarded from GS and genome wide association studies (GWAS) because they could not be genotyped. Reasons why these SNPs can’t be genotyped include the presence of the SNP in a CNV. Raw data from these SNPs were tested to determine if they were associated with the growth and meat yield traits. Seventeen associations, involving nine SNPs, were detected and validated in independent datasets. Two SNPs were in CNVRs detected using the CNV detection methods described above - one involved the agouti CNV. Raw data from this SNP was associated with ultrasonic eye muscle depth. Associations remained significant after fitting genotypes of flanking SNPs (from surrounding ~1Mb of sequence) used in GS and GWAS, suggesting that the effect of these associations are not accounted for in GS or GWAS. Including information from these SNPs in GS could improve the reliability of EBVs, contributing to genetic improvement of growth and meat yield traits in the New Zealand sheep industry.
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ItemThe dynamics of growth in even-aged stands of Eucalyptus obliqua (l'herit)( 1968)The genus Eucalyptus contains a large number of species suitable for the commercial production of timber, but the history of their forest management is comparatively recent, being initially founded on traditional European experience. Despite this tradition and the fact that many species have certain silvicultural properties in common distinguishing them from other timber producing genera (Jacobs, 1955), there already exists a diversity in silvicultural systems, even for the one species or species association in a single region. This diversity appears to be associated with the development history of the forest region, because there has been a general tendency to perpetuate the characteristic forest structure of a particular area at the time that planned management was commenced. This structure has varied from extensive areas of even-aged stands of a single species to intimate mixtures of species of all ages and sizes in association. The variation in forest structure appears to have developed largely from a diversity in the history of settlement and early exploitation. Fire history, access history, intensity and frequency of past utilization have all played a prominent role in forming the characteristic forest structure of a particular area. Regardless of whether growing in regular or irregular forests, the determination of tree and stand age for the majority of eucalypts is extremely difficult or even impossible. The identification of annual rings is reasonably reliable only for those species growing in subalpine and alpine climatic zones of Australia. Therefore, in the absence of adequate compartment and stand history records, management planning in the eucalypts must be based on methods which do not require precise knowledge of tree and stand age. While age is not normally required for the management of irregular forests, it has been fundamental to the planned management of even-aged forests. The ability to distinguish sites of differing productive capacities is an important aid in forest management. The most popular method of site classification is the site index, which gives stand height at a particular reference age. If age is unknown this method cannot be used and alternative methods of site quality determination have not yet been developed for the eucalypts. (From Introduction)
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ItemGrowth and yield models for South Australian radiata pine plantations: incorporating fertilising and thinning( 2001)This thesis describes the development of models to predict the volume growth response of South Australian radiata pine plantations to the interaction of the silvicultural tools of thinning and fertiliser used in combination. Some years ago this issue was identified as the component of the ForestrySA yield regulation system most in need of addressing and as a result a large thinning and fertiliser experiment was established. This was designed to determine whether a thinning and fertiliser interaction existed and to enable this interaction to be modelled. At the time it was established it was believed to be the only experiment of its kind in the world and this still appears to be the case. The thinning and fertiliser interaction models described in this thesis were designed to integrate with the models already implemented in the ForestrySA yield regulation system so that more precise predictions of future log availability can be provided, and improved management decisions can be made. Three sets of component sub models are described which operate at a stand level to: • predict the total volume growth of the main crop between the time of fertilising and the next thinning, approximately seven years hence; • predict the total volume growth of the portion of the stand which will be thinned (known as the thinnings elect) at the next thinning, between the time of fertilising and the next thinning; • predict the annual volume growth response of the stand between the time of fertilising and the next thinning. Further research is described to identify the data sets that are likely to be required for future analysis and revision of the South Australian growth and yield models. Adopting the future research recommendations will ensure that the consideration of the financial and economic benefit of alternative silvicultural prescriptions is broadened to include a more diverse range of sites and include log and wood quality considerations.
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ItemThe effects of fertilisation and wastewater irrigation on the biomass and nutrient content of Pinus radiata D. Don( 1985)Detailed measurements were made of soil and stand characteristics before experimental plots were designed and laid out by collaborators from CSIRO. Fertiliser and irrigation were applied in a 2 x 2 factorial design, giving four treatment combinations. Irrigation commenced when the stand was 15 years old, and continued for 29 months; phosphorus at the rate of 5 g m- 2 was evenly broadcast as superphosphate when the stand was 16 years old. The study of biomass and nutrient uptake was comprehensive. Above-ground biomass was estimated by regression analysis of weights and dimensions of 24 sample trees, six trees being selected from each treatment. Standing litter was sampled, and root biomass estimated from core samples and by excavating the roots of one tree per treatment. Uptake of nine nutrients was estimated after measuring their concentrations in all components of the stand. Fertilisation with phosphorus had no effect on total above-ground biomass over a two-year period. Foliar analysis at the start of the study indicated that the trees were mildly deficient in phosphorus, but there was no increase in foliage biomass after fertilisation, despite substantial uptake of the applied nutrient. The lack of growth response was attributed to limiting soil moisture. This finding reinforces results of studies elsewhere that fertiliser responses are site-specific. (From Summary)