Achievements in forest tree genetic improvement in Australia and New Zealand 2: Development of Corymbia species and hybrids for plantations in eastern Australia

This paper describes the establishment of provenance seedling seed orchards of three spotted gums and cadaga (all species of Corymbia ex Eucalyptus). It also discusses the limitations of growing the spotted gums as pure species including: lack of mass flowering, susceptibility to a fungal shoot blight and low amenability to vegetative propagation. These limitations, together with observation of putative natural hybrids of the spotted gums with cadaga, and the early promise of manipulated hybrids, led to an intensive breeding and testing program. Many hybrid families have significant advantages in growth and tolerance to disease, insects and frost, and can be vegetatively propagated. They also exhibit broad environmental plasticity, allowing the best varieties to be planted across a wider range of sites than the spotted gums, resulting in more land being suitable for plantation development.

Evaluating temperate species for the subtropics. 1. Annual ryegrasses

In the subtropics of Australia, irrigated temperate species are the key to reliable cool season feed on dairy farms. Persistence of perennial species is a major limitation to achieving reliable production from irrigated areas and yearly sowings of annual ryegrasses have replaced them as the most productive cool season forage production system in the subtropics. This series of experiments evaluated the yield, and resistance to rust damage, of commercially available cultivars and breeders' lines of annually sown ryegrasses (Lolium multiflorum, L. rigidum, L. x boucheanum and L perenne) in pure, nitrogen-fertilised swards under irrigation in the subtropics over a 22-year period. Barberia and Aristocrat 2 were the most adapted cultivars for subtropical conditions, producing high yields (119 and 114% of mean yield, respectively) and demonstrating the least rust damage. Newer selections from New Zealand, South African, United States of America and European breeding programs are performing better under subtropical conditions than older cultivars, particularly if a component of the selection process has been conducted in that environment. Cultivars such as Passerei Plus, Crusader, Hulk, Status and Warrior are examples of this process, producing between 105 and 115% of mean yield. Yields of annual ryegrass cultivars, which have been available or still are available for sale in Australia, ranged from 14-30 t/ha DM, depending on cultivar, site and seasonal conditions. Yields were lower at the site, which had inferior soil structure and drainage. Up to 50% of yield was produced in the 3 winter months. There was a trend towards improved yields and better tolerance of crown rust from experimental lines in the subtropics, as breeders strive for wider adaptation. Around 70% of the variation in total yield of annual ryegrass and 50 and 60% of the variation in winter and spring yield, respectively, were significantly explained by cultivar, site and climatic variables in autumn, winter and spring. While level of rust damage had no effect on total or seasonal yields, it affected the amount of green leaf available in spring. Under subtropical conditions, winter, spring and overall (autumn to mid-summer) temperatures influenced the- development of rust, which along with cultivar, accounted for 46% of the variation in rust damage. Cultivars showed a range of adaptation, with some performing well only under adverse conditions, some being well adapted to all conditions and some which performed well only under favoured conditions. Cultivars with high winter yields were most suited to subtropical conditions and included Aristocrat 2 (now released as CM 108), Barberia, Warrior, Crusader, Status, Passerei Plus and Hulk. Short growing season types such as Winter Star and T Rex performed well in winter but achieved lower total production, and long season cultivars such as Flanker rarely achieved their potential because of unfavourable conditions in late summer.

Two new species and a new Australian record of Bactrocera Macquart (Diptera : Tephritidae : Dacinae) from Northern Queensland, Torres Strait and Papua New Guinea

Bactrocera (Bactrocera) speewahensis Fay & Hancock sp. n. is described from northern Queensland and B. (B.) torresiae Huxham & Hancock sp. n. is described from Boigu, Saibai and Dauan islands in Torres Strait and southern Papua New Guinea. Bactrocera (B.) nigrovittata Drew is newly recorded from Australia. All records are of male flies responding to chemical lures.

An annotated check list of Ramularia species in Australia

An annotated check list of Ramularia species in Australia, based on re-examinations of collections deposited at BRIP, DAR and VPRI, is presented. Twenty-eight species are reported in Australia, most of them on introduced host plants. The new species Cladosporium myrtacearum, Ramularia craspediicola and R. muehlenbeckiae are described. Collections of Cladosporium uredinicola, Neoramularia karelii, Passalora perfoliati and Pseudocercospora pongamiae-pinnatae, previously deposited in Australian herbaria under 'Ramularia sp.', are newly recognised for Australia.

Weed species richness, density and relative abundance on farms in the subtropical grain region of Australia

Weed management is one of the most important economic and agronomic issues facing farmers in Australia's grain regions. Weed species occurrence and abundance was monitored between 1997 and 2000 on 46 paddocks (sites) across 18 commercial farms located in the Northern Grain Region. The sites generally fell within 4 disjunct regions, from south to north: Liverpool Plains, Moree, Goondiwindi and Kingaroy. While high species richness was found (139 species or species groups), only 8 species occurred in all 4 regions and many (56 species) only occurred at 1 site or region. No species were observed at every site but 7 species (Sonchus spp., Avena spp., Conyza spp., Echinochloa spp., Convolvulus erubescens, Phalaris spp. and Lactuca serriola) were recorded on more than 70% of sites. The average number of species observed within crops after treatment and before harvest was less than 13. Species richness tended to be higher in winter pulse crops, cotton and in fallows, but overall was similar at the different sampling seasons (summer v. winter). Separate species assemblages associated with the Goondiwindi and Kingaroy regions were identified by correspondence analysis but these appeared to form no logical functional group. The species richness and density was generally low, demonstrating that farmers are managing weed populations effectively in both summer and winter cropping phases. Despite the apparent adoption of conservation tillage, an increase in opportunity cropping and the diversity of crops grown (13) there was no obvious effect of management practices on weed species richness or relative abundance. Avena spp. and Sonchus spp. were 2 of the most dominant weeds, particularly in central and southern latitudes of the region; Amaranthus spp. and Raphanus raphanistrum were the most abundant species in the northern part of the region. The ubiquity of these and other species shows that continued vigilance is required to suppress weeds as a management issue.

An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310.2000.2100 for S. fertilis and S. africanus; and ORA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the 'S. indicus complex'. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat

Pratylenchus thornei and P. neglectus are two species of root-lesion nematode that cause substantial yield losses in wheat. No commercially available wheat variety has resistance to both species. A doubled-haploid population developed from a cross between the synthetic hexaploid wheat line CPI133872 and the bread wheat Janz was used to locate and tag quantitative trait loci (QTLs) associated with resistance to both P. thornei and P. neglectus. Wheat plants were inoculated with both species of nematode in independent replicated glasshouse trials repeated over 2 years. Known locations of wheat microsatellite markers were used to construct a framework map. After an initial single-marker analysis to detect marker-trait linkages, chromosome regions associated with putative QTLs were targetted with microsatellite markers to increase map density in the chromosome regions of interest. In total, 148 wheat microsatellite markers and 21 amplified fragment length polymorphism markers were mapped. The codominant microsatellite marker Xbarc183 on the distal end of chromosome 6DS was allelic for resistance to both P. thornei and P. neglectus. The QTL were designated QRlnt.lrc-6D.1 and QRlnn.lrc-6D.1, for the 2 traits, respectively. The allele inherited from CPI133872 explained 22.0-24.2% of the phenotypic variation for P. thornei resistance, and the allele inherited from Janz accounted for 11.3-14.0% of the phenotypic variation for P. neglectus resistance. Composite interval mapping identified markers that flank a second major QTL on chromosome 6DL (QRlnt.lrc-6D.2) that explained 8.3-13.4% of the phenotypic variation for P. thornei resistance. An additional major QTL associated with P. neglectus resistance was detected on chromosome 4DS (QRlnn.lrc-4D.1) and explained a further 10.3-15.4% of the phenotypic variation. The identification and tagging of nematode resistance genes with molecular markers will allow appropriate allele combinations to be selected, which will aid the successful breeding of wheat with dual nematode resistance.

Screening selected myrtaceous tree species for production of essential oils in northern Queensland

Trials to identify alternative cropping options to Melaleuca alternifolia for northern Queensland essential oil growers were established at Dimbulah and Innot Hot Springs in 2001. Seed sources of Asteromyrtus symphyocarpa (1,8-cineole form), Eucalyptus staigeriana (citral), Melaleuca cajuputi subsp. cajuputi (trans-nerolidol), M. ericifolia (d-linalool), M. quinquenervia (trans-nerolidol and viridiflorol forms) and M. viridiflora (methyl cinnamate) with potential to produce commercial foliar oils were evaluated. Information was gathered on their adaptability, growth and oil yields over 49 months and 52 months (two harvests) from planting at Dimbulah and Innot Hot Springs, respectively. Of the species and chemotypes evaluated, M. quinquenervia showed potential for commercial production of trans-nerolidol, a compound used in perfumery. It had a very high survival rate (96%) and yields could be expected to improve dramatically from the average 100 kg/ha per harvest achieved in these trials with further research into selection of seed source, control of insect damage and breeding for genetic improvement. M. cajuputi subsp. cajuputi gave a similar performance to M. quinquenervia. The rarity of the trans-nerolidol form of this species and remoteness of its natural occurrence are impediments to further planting and research. E. staigeriana, with second harvest yields of ~600 kg/ha, performed exceptionally well on both sites but potential for development is limited by the ready availability of competitively priced E. staigeriana oil produced in South America. Survival of M. ericifolia ranged from 62% to 82% at 32 months (second harvest) at Innot Hot Springs and was deemed a failure at Dimbulah with poor growth and low survival, raising a major question about the suitability of this species for cultivation in the seasonally dry tropics. Planting of this species on a wider scale in northern Queensland cannot be recommended until more is known about factors affecting its survival. A. symphyocarpa and M. viridiflora were too slow-growing to warrant further consideration as potential oil-producing species at this time.

Phototropic growth in a reef flat acroporid branching coral species

Many terrestrial plants form complex morphological structures and will alter these growth patterns in response to light direction. Similarly reef building corals have high morphological variation across coral families, with many species also displaying phenotypic plasticity across environmental gradients. In particular, the colony geometry in branching corals is altered by the frequency, location and direction of branch initiation and growth. This study demonstrates that for the branching species Acropora pulchra, light plays a key role in axial polyp differentiation and therefore axial corallite development - the basis for new branch formation. A. pulchra branches exhibited a directional growth response, with axial corallites only developing when light was available, and towards the incident light. Field experimentation revealed that there was a light intensity threshold of 45 mu mol m(-2) s(-1), below which axial corallites would not develop and this response was blue light (408-508 nm) dependent. There was a twofold increase in axial corallite growth above this light intensity threshold and a fourfold increase in axial corallite growth under the blue light treatment. These features of coral branch growth are highly reminiscent of the initiation of phototropic branch growth in terrestrial plants, which is directed by the blue light component of sunlight.

Delineating environmental envelopes to improve mapping of species distributions, via a hurdle model with CART &/or MaxEnT

Species distribution modelling (SDM) typically analyses species’ presence together with some form of absence information. Ideally absences comprise observations or are inferred from comprehensive sampling. When such information is not available, then pseudo-absences are often generated from the background locations within the study region of interest containing the presences, or else absence is implied through the comparison of presences to the whole study region, e.g. as is the case in Maximum Entropy (MaxEnt) or Poisson point process modelling. However, the choice of which absence information to include can be both challenging and highly influential on SDM predictions (e.g. Oksanen and Minchin, 2002). In practice, the use of pseudo- or implied absences often leads to an imbalance where absences far outnumber presences. This leaves analysis highly susceptible to ‘naughty-noughts’: absences that occur beyond the envelope of the species, which can exert strong influence on the model and its predictions (Austin and Meyers, 1996). Also known as ‘excess zeros’, naughty noughts can be estimated via an overall proportion in simple hurdle or mixture models (Martin et al., 2005). However, absences, especially those that occur beyond the species envelope, can often be more diverse than presences. Here we consider an extension to excess zero models. The two-staged approach first exploits the compartmentalisation provided by classification trees (CTs) (as in O’Leary, 2008) to identify multiple sources of naughty noughts and simultaneously delineate several species envelopes. Then SDMs can be fit separately within each envelope, and for this stage, we examine both CTs (as in Falk et al., 2014) and the popular MaxEnt (Elith et al., 2006). We introduce a wider range of model performance measures to improve treatment of naughty noughts in SDM. We retain an overall measure of model performance, the area under the curve (AUC) of the Receiver-Operating Curve (ROC), but focus on its constituent measures of false negative rate (FNR) and false positive rate (FPR), and how these relate to the threshold in the predicted probability of presence that delimits predicted presence from absence. We also propose error rates more relevant to users of predictions: false omission rate (FOR), the chance that a predicted absence corresponds to (and hence wastes) an observed presence, and the false discovery rate (FDR), reflecting those predicted (or potential) presences that correspond to absence. A high FDR may be desirable since it could help target future search efforts, whereas zero or low FOR is desirable since it indicates none of the (often valuable) presences have been ignored in the SDM. For illustration, we chose Bradypus variegatus, a species that has previously been published as an exemplar species for MaxEnt, proposed by Phillips et al. (2006). We used CTs to increasingly refine the species envelope, starting with the whole study region (E0), eliminating more and more potential naughty noughts (E1–E3). When combined with an SDM fit within the species envelope, the best CT SDM had similar AUC and FPR to the best MaxEnt SDM, but otherwise performed better. The FNR and FOR were greatly reduced, suggesting that CTs handle absences better. Interestingly, MaxEnt predictions showed low discriminatory performance, with the most common predicted probability of presence being in the same range (0.00-0.20) for both true absences and presences. In summary, this example shows that SDMs can be improved by introducing an initial hurdle to identify naughty noughts and partition the envelope before applying SDMs. This improvement was barely detectable via AUC and FPR yet visible in FOR, FNR, and the comparison of predicted probability of presence distribution for pres/absence.

Three new species of Tilletia on native grasses from northern Australia

Three new species of Tilletia are reported from grasses in northern Australia, namely T. pseudoraphidis on Pseudoraphis spinescens, T. sehimicola on Sehima nervosum and T. majuscula on Yakirra majuscula.

Approaches to selecting native plant replacements for fleshy-fruited invasive species

Invasive plants are a serious threat to biodiversity. Yet, in some cases, they may play an important ecological role in heavily modified landscapes, such as where fleshy-fruited invasive plants support populations of native frugivores. How can such conservation conflicts be managed? We advocate an approach in which native fleshy-fruited plants are ranked on their ability to provide the fruit food resources for native frugivores currently being provided by invasive plants. If these native taxa are preferentially used, where ecologically appropriate, in plantings for restoration and in park and garden settings, they could help support native frugivore populations in the event of extensive invasive plant control. We develop and critically examine six approaches to selecting candidate native plant taxa: a multivariate approach based on the frugivore assemblage, a scoring model, and several multivariate approaches (including trait combinations having the greatest correlation with the diet of the native frugivore assemblage) based on the functional traits of fruit morphology, phenology, conspicuousness, and accessibility. To illustrate these approaches, we use a case study with Bitou bush (Chrysanthemoides monilifera subsp. rotundata) (Asteraceae), an Australian Weed of National Significance. The model using a dissimilarity value generated from all available traits identified a set of species used by the frugivores of C. monilifera more than null models. A replacement approach using species ranked by either all traits available or the frugivore community appears best suited to guide selection of plants in restoration practice.

Predicting invasiveness in exotic species: do subtropical native and invasive exotic aquatic plants differ in their growth responses to macronutrients?

We investigated whether plasticity in growth responses to nutrients could predict invasive potential in aquatic plants by measuring the effects of nutrients on growth of eight non-invasive native and six invasive exotic aquatic plant species. Nutrients were applied at two levels, approximating those found in urbanized and relatively undisturbed catchments, respectively. To identify systematic differences between invasive and non-invasive species, we compared the growth responses (total biomass, root:shoot allocation, and photosynthetic surface area) of native species with those of related invasive species after 13 weeks growth. The results were used to seek evidence of invasive potential among four recently naturalized species. There was evidence that invasive species tend to accumulate more biomass than native species (P = 0.0788). Root:shoot allocation did not differ between native and invasive plant species, nor was allocation affected by nutrient addition. However, the photosynthetic surface area of invasive species tended to increase with nutrients, whereas it did not among native species (P = 0.0658). Of the four recently naturalized species, Hydrocleys nymphoides showed the same nutrient-related plasticity in photosynthetic area displayed by known invasive species. Cyperus papyrus showed a strong reduction in photosynthetic area with increased nutrients. H. nymphoides and C. papyrus also accumulated more biomass than their native relatives. H. nymphoides possesses both of the traits we found to be associated with invasiveness, and should thus be regarded as likely to be invasive.

Ontogenetic depth partitioning by juvenile freshwater sawfish (Pristis microdon: Pristidae) in a riverine environment

The freshwater sawfish (Pristis microdon) is a critically endangered elasmobranch. Ontogenetic changes in the habitat use of juvenile P. microdon were studied using acoustic tracking in the Fitzroy River, Western Australia. Habitat partitioning was significant between 0+ (2007 year class) and larger 1+ (2006 year class) P. microdon. Smaller 0+ fish generally occupied shallower water (<0.6 m) compared with 1+ individuals, which mainly occurred in depths >0.6 m. Significant differences in hourly depth use were also revealed. The depth that 1+ P. microdon occupied was significantly influenced by lunar phase with these animals utilising a shallower and narrower depth range during the full moon compared with the new moon. This was not observed in 0+ individuals. Habitat partitioning was likely to be related to predator avoidance, foraging behaviours, and temperature and/or light regimes. The occurrence of 1+ P. microdon in deeper water may also result from a need for greater depths in which to manoeuvre. The present study demonstrates the utility of acoustic telemetry in monitoring P. microdon in a riverine environment. These results demonstrate the need to consider the habitat requirements of different P. microdon cohorts in the strategic planning of natural resources and will aid in the development of management strategies for this species.

Dispersal and establishment of bird-dispersed weed and native species in early successional subtropical habitats

Eve White, Anna Barnes and Gabrielle Vivian-Smith recently published their paper 'Dispersal and establishment of bird-dispersed weed and native species in early successional subtropical habitats' in Proceedings of the 16th Australian Weeds Conference. Eve also presented this paper at the conference. They investigated patterns of dispersal and establishment of bird-dispersed weeds and native species in early successional habitats in northern New South Wales. Patterns varied among growth forms, between native species and weeds, and among vegetation types. Their results indicated that the number of seeds dropped by birds is not necessarily a good predictor of recruitment and that post-dispersal factors, such as microsite characteristics, may be more important influences on seedling recruitment. This knowledge will assist with designing management strategies for bird-dispersed weeds in natural areas.