ShadowBoxer and LocusEater: programs to optimise experimental design and multiplexing strategies for genetic mark-recapture

Genetic mark–recapture requires efficient methods of uniquely identifying individuals. 'Shadows' (individuals with the same genotype at the selected loci) become more likely with increasing sample size, and bias harvest rate estimates. Finding loci is costly, but better loci reduce analysis costs and improve power. Optimal microsatellite panels minimize shadows, but panel design is a complex optimization process. locuseater and shadowboxer permit power and cost analysis of this process and automate some aspects, by simulating the entire experiment from panel design to harvest rate estimation.

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.

Comparative performance of Corymbia hybrids and parental species in subtropical Queensland and implications for breeding and deployment.

Eighty six full-sib Corymbia F1 hybrid families (crosses between C. torelliana and four spotted gum taxa: C. citriodora subsp. variegata, C. citriodora subsp. citriodora, C. henryi and C. maculata), were planted in six trials across six disparate sites in south-eastern Queensland to evaluate their productivity and determine their potential utility for plantation forestry. In each trial, the best-growing 20% of hybrid families grew significantly faster (P=0.05) than open-pollinated seedlots of the parent species Corymbia citriodora subsp. variegata, ranging from 107% to 181% and 127% to 287% of the height and diameter respectively. Relative performance of hybrid families growing on more than one site displayed consistency in ranking for growth across sites and analysis showed low genotype-by-environment interaction. Heritability estimates based on female and male parents across two sites at age six years for height and diameter at breast height, were high (0.62±0.28 to 0.64±0.35 and 0.31±0.21 to 0.69±0.37 respectively), and low to moderate (0.03±0.04 to 0.33±0.22) for stem straightness, branch size, incidence of ramicorns, and frost and disease resistance traits at ages one to three years. The proportion of dominance variance for height and diameter had reduced to zero by age six years. Based on these promising results, further breeding and pilot-scale family forestry and clonal forestry deployment is being undertaken. These results have also provided insights regarding the choice of a future hybrid breeding strategy.

Male traits and herd reproductive capability in tropical beef cattle. 1. Experimental design and animal measures

Research into the genetics of whole herd profitability has been a focus of the Beef Cooperative Research Centre for Beef Genetic Technologies over the past decade and it has been identified that measures of male reproduction may offer a potential indirect means of selecting for improved female reproduction. This paper describes the experimental design and provides a descriptive analysis of an array of male traits in Brahman and Tropical Composite genotypes managed under the medium to high stress, semi-extensive to extensive production systems of northern Australia. A total of 1639 Brahman and 2424 Tropical Composite bulls with known pedigrees, bred and raised in northern Australia, were evaluated for a comprehensive range of productive and reproductive traits. These included blood hormonal traits (luteinising hormone, inhibin and insulin-like growth factor-I); growth and carcass traits (liveweight, body condition score, ultrasound scanned 12-13th rib fat, rump P8 fat, eye muscle area and hip height); adaptation traits (flight time and rectal temperature); and a bull breeding soundness evaluation (leg and hoof conformation, sheath score, length of everted prepuce, penile anatomy, scrotal circumference, semen mass activity, sperm motility and sperm morphology). Large phenotypic variation was evident for most traits, with complete overlap between genotypes, indicating that there is likely to be a significant opportunity to improve bull fertility traits through management and bull selection.

Design and assessment of weirs for fish passage under drowned conditions

In aquatic systems, in-stream structures such as dams, weirs and road crossings can act as barriers to fish movement along waterways. There is a growing array of technological fish-pass solutions for the movement of fish across large structures such as weirs and dams. However, most existing weir structures lack dedicated fishways, and fish often have to rely on drowned conditions to move upstream. In order to assess the adequacy of a given or proposed weir for upstream fish passage under drowned conditions, it is necessary to determine, firstly, the hydraulic properties of the drowned weir with respect to the requirements of the fish community and, secondly, the duration and timing of drowning flows with respect to the hydrograph for the site and the likely timing of fish movements. This paper primarily addresses the first issue. A computer program has been developed and incorporated in a simple-to-operate spreadsheet for the determination of the hydraulic characteristics of a drowned weir which are important to fish movement. The program is based on a theoretical analysis of drowned weirs and subsequent extensive verification in laboratory experiments. Inputs to the program include site information comprising channel cross-section data, channel slope, and channel roughness, and weir information comprising weir height and the required minimum drowned depth over the weir for migrating fish passage. The program then calculates the flow rate at which the required level of drowning occurs, the velocity characteristics above the weir (including transverse distributions), and flow depths and velocities upstream and downstream of the weir. The paper discusses (briefly) the theoretical background of the program and its experimental verification. A case study is then presented that illustrates the use of the program in the field to assess fish passage opportunities at an existing weir and to develop a case for retrofitting a fishway. Some discussion is also provided on the contribution of a modelled drownout volume to the assessment of how significant a barrier a weir is to fish passage. It is shown that the program is an important new additional tool in the assessment of the adequacy of weir structures in providing for fish movement and informing associated fish passage solutions. (C) 2011 Elsevier B.V. All rights reserved.

Profiling of carotenoids and antioxidant capacity of microalgae from subtropical coastal and brackish waters

Carotenoids are associated with various health benefits, such as prevention of age-related macular degeneration, cataract, certain cancers, rheumatoid arthritis, muscular dystrophy and cardiovascular problems. As microalgae contain considerable amounts of carotenoids, there is a need to find species with high carotenoid content. Out of hundreds of Australian isolates, twelve microalgal species were screened for carotenoid profiles, carotenoid productivity, and in vitro antioxidant capacity (total phenolic content (TPC) and ORAC). The top four carotenoid producers at 4.68-6.88 mg/g dry weight (DW) were Dunaliella salina, Tetraselmis suecica, Isochrysis galbana, and Pavlova salina. TPC was low, with D. salina possessing the highest TPC (1.54 mg Gallic Acid Equivalents/g DW) and ORAC (577 μmol Trolox Equivalents/g DW). Results indicate that T. suecica, D. salina, P. salina and I. galbana could be further developed for commercial carotenoid production.