A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Mapping and characterisation of the inter-reefal benthic assemblages of the Torres Strait

A comprehensive survey of the benthic assemblages of the Torres Strait was conducted in order to provide critical baseline information for regional marine planning, assessing the environmental sustainability of fisheries and understanding the ecosystems of the region. Over 150 sites throughout the region were sampled with a modified prawn trawl, towed underwater video, pipe dredge and epibenthic sled. This manuscript provides a broad overview of the activities undertaken and data collected. Two thousand three hundred and seventy-two different nominal species were sampled by the trawl and sled, only 728 by both gears. The towed video was not able to provide the same level of taxonomic resolution of epibenthic taxa, but was particularly useful in areas where the seabed was too rough to be sampled. Data from the trawl, sled and video were combined to characterise the epibenthic assemblages of the region. Data from the towed video was also used to provide a characterisation of the inter-reefal benthic habitats, which was then analysed in combination with physical covariate data to examine relationships between the two. Levels of mud and gravel in the sediments, trawling effort and seabed current stress were the covariates most significantly correlated with the nature of the seabed habitats.

Inter-seasonal population dynamics and pest status of Bemisia tabaci (Gennadius) biotype B in an Australian cropping system

Bemisia tabaci, biotype B, commonly known as the silverleaf whitefly (SLW) is an alien species that invaded Australia in the mid-90s. This paper reports on the invasion ecology of SLW and the factors that are likely to have contributed to the first outbreak of this major pest in an Australian cotton cropping system, population dynamics of SLW within whitefly-susceptible crop (cotton and cucurbit) and non-crop vegetation (sowthistle, Sonchus spp.) components of the cropping system were investigated over four consecutive growing seasons (September-June) 2001/02-2004/05 in the Emerald Irrigation Area (EIA) of Queensland, Australia. Based on fixed geo-referenced sampling sites, variation in spatial and temporal abundance of SLW within each system component was quantified to provide baseline data for the development of ecologically sustainable pest management strategies. Parasitism of large (3rd and 4th instars) SLW nymphs by native aphelinid wasps was quantified to determine the potential for natural control of SLW populations. Following the initial outbreak in 2001/02, SLW abundance declined and stabilised over the next three seasons. The population dynamics of SLW is characterised by inter-seasonal population cycling between the non-crop (weed) and cotton components of the EIA cropping system. Cotton was the largest sink for and source of SLW during the study period. Over-wintering populations dispersed from weed host plant sources to cotton in spring followed by a reverse dispersal in late summer and autumn to broad-leaved crops and weeds. A basic spatial source-sink analysis showed that SLW adult and nymph densities were higher in cotton fields that were closer to over-wintering weed sources throughout spring than in fields that were further away. Cucurbit fields were not significant sources of SLW and did not appear to contribute significantly to the regional population dynamics of the pest. Substantial parasitism of nymphal stages throughout the study period indicates that native parasitoid species and other natural enemies are important sources of SLW mortality in Australian cotton production systems. Weather conditions and use of broad-spectrum insecticides for pest control are implicated in the initial outbreak and on-going pest status of SLW in the region.

Transition of EGA wheat breeding activities to Australian Grain Technologies

Transition of EGA wheat breeding activities to Australian Grain Technologies.

A multi-faceted approach for quantifying the estuarine-nearshore transition in the life cycle of the bull shark, Carcharhinus leucas.

Understanding the ontogenetic habitat linkages of sharks is important for conservation and managing human interactions. We used acoustic telemetry, catch data, elemental and stable isotope signatures and dietary analyses to investigate ontogenetic habitat use in south-east Queensland, Australia, by the bull shark Carcharhinus leucas, a IUCN 'near-threatened' species that is implicated in many shark attacks on humans in urban estuaries. Sequential analyses for delta(15)N and delta(13)C of vertebrae from five adult C. leucas and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) for elemental composition from 23 C. leucas, including a pregnant female, were also used to trace ontogenetic habitat dependence. Acoustic telemetry indicated large juvenile and subadult C. leucas remained in estuarine habitats. delta(15)N values across shark vertebrae showed an ontogenetic shift in diet with total length (TL), confirmed by stomach contents. LA-ICPMS data reflected the ontogenetic movements of C. leucas from natal habitats. Differences among adults were gender related. Shifts in habitat use by subadults were correlated with a sigmoidal delta(13)C relationship with TL. C. leucas have a multipartite, stage-specific dependency in their transition between habitats along the freshwater-estuarine-marine continuum, making them particularly susceptible to the habitat alteration that is occurring globally.

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual’s previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag–recapture data and tag–recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

A comparison of welfare outcomes for weaner and mature Bos indicus bulls surgically or tension band castrated with or without analgesia: 2. Responses related to stress, health and productivity

Tension banding castration of cattle is gaining favour because it is relatively simple to perform and is promoted by retailers of the banders as a humane castration method. Two experiments were conducted, under tropical conditions using Bos indicus bulls comparing tension banding (Band) and surgical (Surgical) castration of weaner (7–10 months old) and mature (22–25 months old) bulls with and without pain management (NSAID (ketoprofen) or saline injected intramuscularly immediately prior to castration). Welfare outcomes were assessed using a range of measures; this paper reports on some physiological, morbidity and productivity-related responses to augment the behavioural responses reported in an accompanying paper. Blood samples were taken on the day of castration (day 0) at the time of restraint (0 min) and 30 min (weaners) or 40 min (mature bulls), 2 h, and 7 h; and days 1, 2, 3, 7, 14, 21 and 28 post-castration. Plasmas from day 0 were assayed for cortisol, creatine kinase, total protein and packed cell volume. Plasmas from the other samples were assayed for cortisol and haptoglobin (plus the 0 min sample). Liveweights were recorded approximately weekly to 6 weeks and at 2 and 3 months post-castration. Castration sites were checked at these same times to 2 months post-castration to score the extent of healing and presence of sepsis. Cortisol concentrations (mean ± s.e. nmol/L) were significantly (P < 0.05) higher in the Band (67 ± 4.5) compared with Surgical weaners (42 ± 4.5) at 2 h post-castration, but at 24 h post-castration were greater in the Surgical (43 ± 3.2) compared with the Band weaners (30 ± 3.2). The main effect of ketoprofen was on the cortisol concentrations of the mature Surgical bulls; concentrations were significantly reduced at 40 min (47 ± 7.2 vs. 71 ± 7.2 nmol/L for saline) and 2 h post-castration (24 ± 7.2, vs. 87 ± 7.2 nmol/L for saline). Ketoprofen, however, had no effect on the Band mature bulls, with their cortisol concentrations averaging 54 ± 5.1 nmol/L at 40 min and 92 ± 5.1 nmol/L at 2 h. Cortisol concentrations were also significantly elevated in the Band (83 ± 3.0 nmol/L) compared with Surgical mature bulls (57 ± 3.0 nmol/L) at weeks 2–4 post-castration. The timing of this elevation coincided with significantly elevated haptoglobin concentrations (mg/mL) in the Band bulls (2.97 ± 0.102 for mature bulls and 1.71 ± 0.025 for weaners, vs. 2.10 ± 0.102 and 1.45 ± 0.025 respectively for the Surgical treatment) and evidence of slow wound healing and sepsis in both the weaner (0.81 ± 0.089 not healed at week 4 for Band, 0.13 ± 0.078 for Surgical) and mature bulls (0.81 ± 0.090 at week 4 for Band, 0.38 ± 0.104 for Surgical). Overall, liveweight gains of both age groups were not affected by castration method. The findings of acute pain, chronic inflammation and possibly chronic pain in the mature bulls at least, together with poor wound healing in the Band bulls support behavioural findings reported in the accompanying paper and demonstrate that tension banding produces inferior welfare outcomes for weaner and mature bulls compared with surgical castration.

A comparison of welfare outcomes for weaner and mature Bos indicus bulls surgically or tension band castrated with or without analgesia: 1. Behavioural responses

Tension-band castration of cattle is gaining favour because it is relatively simple to perform and is promoted by retailers of the devices as a humane castration method. Furthermore, retailers encourage delaying castration to exploit the superior growth rates of bulls compared with steers. Two experiments were conducted, under tropical conditions, comparing tension banding and surgical castration of weaner (7–10 months old) and mature (22–25 months old) Bos indicus bulls with and without pain management (ketoprofen or saline injected intramuscularly immediately prior to castration). Welfare outcomes were assessed using a wide range of measures; this paper reports on the behavioural responses of the bulls and an accompanying paper reports on other measures. Behavioural data were collected at intervals by direct observation and continuously via data loggers on the hind leg of the bulls to 4 weeks post-castration. Tension-banded bulls performed less movement in the crush/chute than the surgically castrated bulls during the procedures (weaner: 2.63 vs. 5.69, P < 0.001; mature: 1.00 vs. 5.94; P < 0.001 for tension-band and surgical castration, respectively), indicating that tension banding was less painful then surgical castration during conduct. To 1.5 h post-castration, tension-banded bulls performed significantly (all P < 0.05) more active behavioural responses indicative of pain compared with surgical castrates, e.g., percentage time walking forwards (weaner: 15.0% vs. 8.1%; mature: 22.3% vs. 15.1%), walking backwards (weaner: 4.3% vs. 1.4%; mature: 2.4% vs. 0.5%), numbers of tail movements (weaner: 21.9 vs. 1.4; mature: 51.5 vs. 39.4) and leg movements (weaner: 12.9 vs. 0.9; mature: 8.5 vs. 1.5), respectively. In contrast, surgically castrated bulls performed more immobile behaviours compared with tension-banded bulls (e.g., standing in mature bulls was 56.6% vs. 34.4%, respectively, P = 0.002). Ketoprofen administration appeared effective in moderating pain-related behaviours in the mature bulls from 1.5 to 3 h, e.g., reducing abnormal standing (0.0% vs. 7.7%, P = 0.009) and increasing feeding (12.7% vs. 0.0%, P = 0.048) in NSAID- and saline-treated bulls, respectively. There were few behavioural differences subsequent to 24 h post-castration, but some limited evidence of chronic pain (3–4 weeks post-castration) with both methods. Interpretation, however, was difficult from behaviours alone. Thus, tension banding is less painful than surgical castration during conduct of the procedures and pain-related behavioural responses differ with castration method (active restlessness in response to tension banding and minimisation of movement in response to surgical castration). Ketoprofen administered immediately prior to castration was somewhat effective in reducing pain, particularly in the mature bulls.

Atypical correlation of otolith strontium : calcium and barium : calcium across a marine–freshwater life history transition of a diadromous fish

Variation in strontium (Sr) and barium (Ba) within otoliths is invaluable to studies of fish diadromy. Typically, otolith Sr : Ca is positively related to salinity, and the ratios of Ba and Sr to calcium (Ca) vary in opposite directions in relation to salinity. In this study of jungle perch, Kuhlia rupestris, otolith Sr : Ca and Ba : Ca, however, showed the same rapid increase as late-larval stages transitioned directly from a marine to freshwater environment. This transition was indicated by a microstructural check mark on otoliths at 35–45 days age. As expected ambient Sr was lower in the fresh than the marine water, however, low Ca levels (0.4 mg L–1) of the freshwater resulted in the Sr : Ca being substantially higher than the marine water. Importantly, the otolith Sr : Ba ratio showed the expected pattern of a decrease from the marine to freshwater stage, illustrating that Sr : Ba provided a more reliable inference of diadromous behaviour based on prior expectations of their relationship to salinity, than did Sr : Ca. The results demonstrate that Ca variation in freshwaters can potentially be an important influence on otolith element : Ca ratios and that inferences of marine–freshwater habitat use from otolith Sr : Ca alone can be problematic without an understanding of water chemistry.