On Systems Thinking, Systems Biology, and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

The life history of Phalacrognathus Muelleri (Macleay) (Coleoptera: Lucanidae)

The life history of Phalacrognathus muelleri (Macleay) is described and aspects of its biology discussed. The species is restricted to the wet tropics of northern Queensland where it breeds in rotting wood in rainforest. Larvae have been extracted from the wood of 27 tree species in 13 families. All larvae found were in wood attacked by white rot fungi. The final instar larva is described. Larva, pupa, and parasites are figured.

A new data source for fisheries resource assessment: genetic estimates of the effective number of spawners. Final Report to the Fisheries Research and Development Corporation.

The development of innovative methods of stock assessment is a priority for State and Commonwealth fisheries agencies. It is driven by the need to facilitate sustainable exploitation of naturally occurring fisheries resources for the current and future economic, social and environmental well being of Australia. This project was initiated in this context and took advantage of considerable recent achievements in genomics that are shaping our comprehension of the DNA of humans and animals. The basic idea behind this project was that genetic estimates of effective population size, which can be made from empirical measurements of genetic drift, were equivalent to estimates of the successful number of spawners that is an important parameter in process of fisheries stock assessment. The broad objectives of this study were to 1. Critically evaluate a variety of mathematical methods of calculating effective spawner numbers (Ne) by a. conducting comprehensive computer simulations, and by b. analysis of empirical data collected from the Moreton Bay population of tiger prawns (P. esculentus). 2. Lay the groundwork for the application of the technology in the northern prawn fishery (NPF). 3. Produce software for the calculation of Ne, and to make it widely available. The project pulled together a range of mathematical models for estimating current effective population size from diverse sources. Some of them had been recently implemented with the latest statistical methods (eg. Bayesian framework Berthier, Beaumont et al. 2002), while others had lower profiles (eg. Pudovkin, Zaykin et al. 1996; Rousset and Raymond 1995). Computer code and later software with a user-friendly interface (NeEstimator) was produced to implement the methods. This was used as a basis for simulation experiments to evaluate the performance of the methods with an individual-based model of a prawn population. Following the guidelines suggested by computer simulations, the tiger prawn population in Moreton Bay (south-east Queensland) was sampled for genetic analysis with eight microsatellite loci in three successive spring spawning seasons in 2001, 2002 and 2003. As predicted by the simulations, the estimates had non-infinite upper confidence limits, which is a major achievement for the application of the method to a naturally-occurring, short generation, highly fecund invertebrate species. The genetic estimate of the number of successful spawners was around 1000 individuals in two consecutive years. This contrasts with about 500,000 prawns participating in spawning. It is not possible to distinguish successful from non-successful spawners so we suggest a high level of protection for the entire spawning population. We interpret the difference in numbers between successful and non-successful spawners as a large variation in the number of offspring per family that survive – a large number of families have no surviving offspring, while a few have a large number. We explored various ways in which Ne can be useful in fisheries management. It can be a surrogate for spawning population size, assuming the ratio between Ne and spawning population size has been previously calculated for that species. Alternatively, it can be a surrogate for recruitment, again assuming that the ratio between Ne and recruitment has been previously determined. The number of species that can be analysed in this way, however, is likely to be small because of species-specific life history requirements that need to be satisfied for accuracy. The most universal approach would be to integrate Ne with spawning stock-recruitment models, so that these models are more accurate when applied to fisheries populations. A pathway to achieve this was established in this project, which we predict will significantly improve fisheries sustainability in the future. Regardless of the success of integrating Ne into spawning stock-recruitment models, Ne could be used as a fisheries monitoring tool. Declines in spawning stock size or increases in natural or harvest mortality would be reflected by a decline in Ne. This would be good for data-poor fisheries and provides fishery independent information, however, we suggest a species-by-species approach. Some species may be too numerous or experiencing too much migration for the method to work. During the project two important theoretical studies of the simultaneous estimation of effective population size and migration were published (Vitalis and Couvet 2001b; Wang and Whitlock 2003). These methods, combined with collection of preliminary genetic data from the tiger prawn population in southern Gulf of Carpentaria population and a computer simulation study that evaluated the effect of differing reproductive strategies on genetic estimates, suggest that this technology could make an important contribution to the stock assessment process in the northern prawn fishery (NPF). Advances in the genomics world are rapid and already a cheaper, more reliable substitute for microsatellite loci in this technology is available. Digital data from single nucleotide polymorphisms (SNPs) are likely to super cede ‘analogue’ microsatellite data, making it cheaper and easier to apply the method to species with large population sizes.

Achievements in forest tree improvement in Australia and New Zealand 6: Genetic improvement and conservation of Araucaria cunninghamii in Queensland

Araucaria cunninghamii (hoop pine) typically occurs as an emergent tree over subtropical and tropical rainforests, in a discontinuous distribution that extends from West Irian Jaya at about 0°30'S, through the highlands of Indonesian New Guinea and Papua New Guinea, along the east coast of Australia from 11°39'S in Queensland to 30°35'S in northern New South Wales. Plantations established in Queensland since the 1920s now total about 44000 ha, and constitute the primary source for the continuing supply of hoop pine quality timber and pulpwood, with a sustainable harvest exceeding 440 000 m3 y-1. Establishment of these managed plantations allowed logging of all native forests of Araucaria species (hoop pine and bunya pine, A. bidwillii) on state-owned lands to cease in the late 1980s, and the preservation of large areas of araucarian forest types within a system of state-owned and managed reserves. The successful plantation program with this species has been strongly supported by genetic improvement activities since the late 1940s - through knowledge of provenance variation and reproductive biology, the provision of reliable sources of improved seed, and the capture of substantial genetic gains in traits of economic importance (for example growth, stem straightness, internode length and spiral grain). As such, hoop pine is one of the few tropical tree species that, for more than half a century, has been the subject of continuous genetic improvement. The history of commercialisation and genetic improvement of hoop pine provides an excellent example of the dual economic and conservation benefits that may be obtained in tropical tree species through the integration of gene conservation and genetic improvement with commercial plantation development. This paper outlines the natural distribution and reproductive biology of hoop pine, describes the major achievements of the genetic improvement program in Queensland over the past 50+ y, summarises current understanding of the genetic variation and control of key selection traits, and outlines the means by which genetic diversity in the species is being conserved.

Soil sorption-desorption of phosphorus from piggery effluent compared with inorganic sources

The leaching of phosphorus (P) within soils can be a limiting consideration for the sustainable operation of intensive livestock enterprises. Sorption curves are widely used to assist estimation of P retention, though the effect of effluent constituents on their accuracy is not well understood. We conducted a series of P-sorption-desorption batch experiments with an Oxic Haplustalf (soil 1), Haplusterts (soils 2 and 3), and a Natrustalf (soil 4). Phosphorus sources included effluent, orthophosphate-P in a matrix replicating the effluent's salt constituents (the reference solution), and an orthophosphate-P solution. Treated soils were incubated for up to 193 days before sequential desorption extraction. Effluent constituents, probably the organic or particulate components, temporarily increased the vulnerability of sorbed-P to desorption. The increase in vulnerability was removed by 2-113 days of incubation (25 degrees C). Despite vigorous extraction for 20 consecutive days, some P sorbed as part of the treatments of soils 1 and 2 was not desorbed. The increased vulnerability due to effluent constituents lasted a maximum of about one cropping season and, for all other treatments, adsorption curves overestimated vulnerability to desorption. Therefore, adsorption curves provide a conservative estimate of vulnerability to desorption where effluent is used in continued crop production in these soils.

Apparent digestibility of some nutrient sources by juvenile mud crab, Scylla serrata (Forskal 1775)

As part of preliminary work aimed at the development of a formulated diet for the mud crab, Scylla serrata, an experiment was conducted with juvenile mud crabs (95.65±2.17 g) to determine apparent digestibility coefficients (ADC) for cellulose, fish meal, shrimp meal, blood meal, soybean meal, wheat flour and cod liver oil. Apparent digestibility coefficients for dry matter (ADCdm), energy (ADCenergy) and protein (ADC protein) were in the ranges 70.0-95.7%, 77.4-97.1% and 57.7-97.9% respectively. Soybean meal had the highest ADCdm and wheat flour had the lowest value (P<0.05), while the ADCdm for fish meal, blood meal and shrimp meal were not different (P?0.05). Similarly, soybean meal had the same ADCenergy as that of fish meal, but higher than those of cod liver oil, blood meal and shrimp meal (P<0.05). Moreover, the ADC protein for blood meal or shrimp meal were not significantly different from fish meal (P?0.05); nevertheless, they were lower than that of soybean meal and higher than that of wheat flour (P<0.05). Of significant interest was the ADCdm (78.0%) and ADCenergy (77.4%) for cellulose, which indicates that plant-based nutrient sources may well be a useful component of formulated diets for mud crabs.

The effect of habitat and environmental history on otolith chemistry of barramundi Lates calcarifer in estuarine populations of a regulated tropical river

We examine the microchemistry of otoliths of cohorts of a fished shed population of the large catadromous fish, barramundi Lates calcarifer from the estuary of a large tropical river. Barramundi from the estuary of the large, heavily regulated Fitzroy River, north eastern Australia were analysed by making transects of 87Sr/86Sr isotope and trace metal/Ca ratios from the core to the outer edge. Firstly, we examined the Sr/Ca, Ba/Ca, Mg/Ca and Mn/Ca and 87Sr/86Sr isotope ratios in otoliths of barramundi tagged in either freshwater or estuarine habitats that were caught by the commercial fishery in the estuary. We used 87Sr/86Sr isotope ratios to identify periods of freshwater residency and assess whether trace metal/Ca ratios varied between habitats. Only Sr/Ca consistently varied between known periods of estuarine or freshwater residency. The relationships between trace metal/Ca and river flow, salinity, temperature were examined in fish tagged and recaptured in the estuary. We found weak and inconsistent patterns in relationships between these variables in the majority of fish. These results suggest that both individual movement history within the estuary and the scale of environmental monitoring were reducing our ability to detect any patterns. Finally, we examined fish in the estuary from two dominant age cohorts (4 and 7 yr old) before and after a large flood in 2003 to ascertain if the flood had enabled fish from freshwater habitats to migrate to the estuary. There was no difference in the proportion of fish in the estuary that had accessed freshwater after the flood. Instead, we found that larger individuals with each age cohort were more likely to have spent a period in freshwater. This highlights the need to maintain freshwater flows in rivers. About half the fish examined had accessed freshwater habitats before capture. Of these, all had spent at least their first two months in marine salinity waters before entering freshwater and some did not enter freshwater until four years of age. This contrasts with the results of several previous studies in other parts of the range that found that access to freshwater swamps by larval barramundi was important for enhanced population productivity and recruitment.

Comparison of odour emission rates measured from various sources using two sampling devices

Two commonly used sampling devices (a wind tunnel and the US EPA dynamic emission chamber), were used to collect paired samples of odorous air from a number of agricultural odour sources. The odour samples were assessed using triangular, forced-choice dynamic olfactometry. The odour concentration data was combined with the flushing rate data to calculate odour emission rates for both devices on all sources. Odour concentrations were consistently higher in samples collected with a flux chamber (ratio ranging from 10:7 to 5:1, relative to wind tunnel samples), whereas odour emission rates were consistently larger when derived from wind tunnels (ratio ranging from 60:1 to 240:1, relative to flux chamber values). A complex relationship existed between emission rate estimates derived from each device, apparently influenced by the nature of the emitting surface. These results have great significance for users of odour dispersion models, for which an odour emission rate is a key input parameter.

Identifying major contributing sources to odour annoyance using a non-specific gas sensor array

Identification of major contributors to odour annoyance in areas with multiple emission sources is necessary to address and resolve odour disputes. In an effort to develop an appropriate tool for this task, odour samples were collected on-site at a piggery and an abattoir (the major odour sources in the area) and at surrounding off-site areas, then analysed using a commercial non-specific chemical sensor array to develop an odour fingerprint database. The developed odour fingerprint database was analysed using two pattern recognition algorithms including a partial least squares-discriminant analysis (PLS-DA) and a Kohonen self-organising map (KSOM). The KSOM model could identify odour samples sourced from the piggery shed 15, piggery pond 8, piggery pond 9, abattoir, motel and others with mean percentage values of 77.5, 65.0, 90.2, 75.7, 44.8 and 64.6%, respectively.

Development of a synthetic plant volatile-based attracticide for female noctuid moths. I. Potential sources of volatiles attractive to Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae).

This paper is the first of a series which will describe the development of a synthetic plant volatile-based attracticide for noctuid moths. It discusses potential sources of volatiles attractive to the cotton bollworm, Helicoverpa armigera (Hubner), and an approach to the combination of these volatiles in synthetic blends. We screened a number of known host and non-host (for larval development) plants for attractiveness to unmated male and female moths of this species, using a two-choice olfactometer system. Out of 38 plants tested, 33 were significantly attractive to both sexes. There was a strong correlation between attractiveness of plants to males and females. The Australian natives, Angophora floribunda and several Eucalyptus species were the most attractive plants. These plants have not been recorded either as larval or oviposition hosts of Helicoverpa spp., suggesting that attraction in the olfactometer might have been as nectar foraging rather than as oviposition sources. To identify potential compounds that might be useful in developing moth attractants, especially for females, collections of volatiles were made from plants that were attractive to moths in the olfactometer. Green leaf volatiles, floral volatiles, aromatic compounds, monoterpenes and sesquiterpenes were found. We propose an approach to developing synthetic attractants, here termed 'super-blending', in which compounds from all these classes, which are in common between attractive plants, might be combined in blends which do not mimic any particular attractive plant.

The effect of data sources and quality on the predictive capacity of CLIMEX models: an assessment of Teleonemia scrupulosa and Octotoma scabripennis for the biocontrol of Lantana camara in Australia

Understanding the effects of different types and quality of data on bioclimatic modeling predictions is vital to ascertaining the value of existing models, and to improving future models. Bioclimatic models were constructed using the CLIMEX program, using different data types – seasonal dynamics, geographic (overseas) distribution, and a combination of the two – for two biological control agents for the major weed Lantana camara L. in Australia. The models for one agent, Teleonemia scrupulosa Stål (Hemiptera:Tingidae) were based on a higher quality and quantity of data than the models for the other agent, Octotoma scabripennis Guérin-Méneville (Coleoptera: Chrysomelidae). Predictions of the geographic distribution for Australia showed that T. scrupulosa models exhibited greater accuracy with a progressive improvement from seasonal dynamics data, to the model based on overseas distribution, and finally the model combining the two data types. In contrast, O. scabripennis models were of low accuracy, and showed no clear trends across the various model types. These case studies demonstrate the importance of high quality data for developing models, and of supplementing distributional data with species seasonal dynamics data wherever possible. Seasonal dynamics data allows the modeller to focus on the species response to climatic trends, while distributional data enables easier fitting of stress parameters by restricting the species envelope to the described distribution. It is apparent that CLIMEX models based on low quality seasonal dynamics data, together with a small quantity of distributional data, are of minimal value in predicting the spatial extent of species distribution.

Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management

Aim: Resolving the origin of invasive plant species is important for understanding the introduction histories of successful invaders and aiding strategies aimed at their management. This study aimed to infer the number and origin(s) of introduction for the globally invasive species, Macfadyena unguis-cati and Jatropha gossypiifolia using molecular data. Location: Native range: Neotropics; Invaded range: North America, Africa, Europe, Asia, Pacific Islands and Australia. Methods: We used chloroplast microsatellites (cpSSRs) to elucidate the origin(s) of introduced populations and calculated the genetic diversity in native and introduced regions. Results: Strong genetic structure was found within the native range of M. unguis-cati, but no genetic structuring was evident in the native range of J. gossypiifolia. Overall, 27 haplotypes were found in the native range of M. unguis-cati. Only four haplotypes were found in the introduced range, with more than 96% of introduced specimens matching a haplotype from Paraguay. In contrast, 15 haplotypes were found in the introduced range of J. gossypiifolia, with all invasive populations, except New Caledonia, comprising multiple haplotypes. Main conclusions: These data show that two invasive plant species from the same native range have had vastly different introduction histories in their non-native ranges. Invasive populations of M. unguis-cati probably came from a single or few independent introductions, whereas most invasive J. gossypiifolia populations arose from multiple introductions or alternatively from a representative sample of genetic diversity from a panmictic native range. As introduced M. unguis-cati populations are dominated by a single haplotype, locally adapted natural enemies should make the best control agents. However, invasive populations of J. gossypiifolia are genetically diverse and the selection of bio-control agents will be considerably more complex.

Life history and host range of Alagoasa extrema (Coleoptera: Chrysomelidae: Alticinae), a potential biological control agent of Lantana spp. (Verbenaceae) in Australia

The life history and host range of the lantana beetle, Alagoasa extrema, a potential biocontrol agent for Lantana spp. were investigated in a quarantine unit at the Alan Fletcher Research Station, Brisbane, Australia. Adults feed on leaves and females lay batches of about 17 eggs on the soil surface around the stems of plants. The eggs take 16 days to hatch and newly emerged larvae move up the stem to feed on young leaves. Larvae feed for about 23 days and there are three instars. There is a prepupal non-feeding stage that lasts about 12 days and the pupal stage, which occurs in a cocoon in the soil, lasts 16 days. Teneral adults remain in the cocoon for 3 days to harden prior to emergence. Males live for about 151 days while females live for about 127 days. The pre-oviposition period is 19 days. In no-choice larval feeding trials, nine plant species, representing three families, supported development to adult. Three species, Aloysia triphylla, Citharexylum spinosum and Pandorea pandorana were able to support at least two successive generations. These results confirm those reported in South Africa and suggest that A. extrema is not sufficiently specific for release in Australia. Furthermore, it is not recommended for release in any other country which is considering biological control of lantana.

Recruitment sources of brown trout identified by otolith trace element signatures.

This study examined whether element: Ca ratios within the otoliths of juvenile brown trout could provide accurate trace element signatures for specific natal tributaries, and attempted to match these to trace element natal signatures found within the otoliths of adult trout caught in the main stem rivers of the same catchment. The trace element signatures of juvenile trout otoliths were analysed from a sample of eight tributaries representing the main sub-catchments of the Motueka River catchment, New Zealand. Trace element signatures were determined using laser ablation inductively coupled plasma mass spectrometry, and differentiated using linear discriminant function analysis with an overall cross-validated classification success of 96.8%. Temporal stability in element: Ca ratios was investigated by repeat collections of juvenile fish over two years. Natal signatures from 11 of 23 adult trout sampled from the catchment main stems were matched to one of the eight tributary signatures showing recruitment sources to be spread relatively evenly throughout the catchment. This study demonstrates the potential of using otolith trace element analysis to determine the natal origins of freshwater fish within a catchment.

Spatial variation in life history reveals insight into connectivity and geographic population structure of a tropical estuarine teleost: king threadfin, Polydactylus macrochir

Understanding the life history of exploited fish species is not only critical in developing stock assessments and productivity models, but has a dual function in the delineation of connectivity and geographical population structure. In this study, patterns in growth and length and age at sex change of Polydactylus macrochir, an ecologically and economically important protandrous estuarine teleost, were examined to provide preliminary information on the species' connectivity and geographic structure across northern Australia. Considerable variation in life history parameters was observed among the 18 locations sampled. Both unconstrained and constrained (t(0) = 0) estimates of von Bertalanffy growth function parameters differed significantly among all neighbouring locations with the exception of two locations in Queensland's east coast and two in Queensland's Gulf of Carpentaria waters, respectively. Comparisons of back-calculated length-at-age 2 provided additional evidence for growth differences among some locations, but were not significantly different among locations in the south-eastern Gulf of Carpentaria or on Queensland's east coast. The length and age at sex change differed markedly among locations, with fish from the east coast of Australia changing sex from males to females at significantly greater lengths and ages than elsewhere. Sex change occurred earliest at locations within Queensland's Gulf of Carpentaria, where a large proportion of small, young females were recorded. The observed differences suggest that P. macrochir likely form a number of geographically and/or reproductively distinct groups in Australian waters and suggest that future studies examining connectivity and geographic population structure of estuarine fishes will likely benefit from the inclusion of comparisons of life history parameters. (C) 2012 Elsevier B.V. All rights reserved.