Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. IV. Abundance and conservation status

Urban encroachment on dense, coastal koala populations has ensured that their management has received increasing government and public attention. The recently developed National Koala Conservation Strategy calls for maintenance of viable populations in the wild. Yet the success of this, and other, conservation initiatives is hampered by lack of reliable and generally accepted national and regional population estimates. In this paper we address this problem in a potentially large, but poorly studied, regional population in the State that is likely to have the largest wild populations. We draw on findings from previous reports in this series and apply the faecal standing-crop method (FSCM) to derive a regional estimate of more than 59 000 individuals. Validation trials in riverine communities showed that estimates of animal density obtained from the FSCM and direct observation were in close agreement. Bootstrapping and Monte Carlo simulations were used to obtain variance estimates for our population estimates in different vegetation associations across the region. The most favoured habitat was riverine vegetation, which covered only 0.9% of the region but supported 45% of the koalas. We also estimated that between 1969 and 1995 -30% of the native vegetation associations that are considered as potential koala habitat were cleared, leading to a decline of perhaps 10% in koala numbers. Management of this large regional population has significant implications for the national conservation of the species: the continued viability of this population is critically dependent on the retention and management of riverine and residual vegetation communities, and future vegetation-management guidelines should be cognisant of the potential impacts of clearing even small areas of critical habitat. We also highlight eight management implications.

Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium aphanidermatum populations infecting cucumber in Oman

Seventy three isolates of Pythium aphanidermatum obtained from cucumber from four different regions of Oman and 16 isolates of muskmelon from the Batinah region in Oman were characterized for aggressiveness, sensitivity to metalaxyl and genetic diversity using AFLP fingerprinting. Twenty isolates of P. aphanidermatum from diverse hosts from different countries were also included in the study. Most isolates from Oman were found to be aggressive on cucumber seedlings and all were highly sensitive to metalaxyl (EC50 < 0•80 µg mL−1). Isolates from cucumber and muskmelon were as aggressive as each other on both hosts (P > 0.05), which implies a lack of host specialization in P. aphanidermatum on these two hosts in Oman. AFLP analysis of all isolates using four primer-pair combinations resolved 152 bands, of which 61 (~40%) were polymorphic. Isolates of P. aphanidermatum from Oman and other countries exhibited high genetic similarity (mean = 94.1%) and produced 59 different AFLP profiles. Analysis of molecular variance indicated that most AFLP variation among populations of P. aphanidermatum in Oman was associated with geographical regions (FST = 0.118; P < 0.0001), not hosts (FST = -0.004; P = 0.4323). These data were supported by the high rate of recovery (24%) of identical phenotypes between cucumber and muskmelon fields in the same region as compared to the low recovery (10%) across regions in Oman, which suggests more frequent movement of Pythium inoculum among muskmelon and cucumber fields in the same region compared to movement across geographically separated regions. However, recovering clones among regions and different countries may imply circulation of Pythium inoculum via common sources in Oman and also intercontinental spread of isolates.

The risk of pollen-mediated gene flow from exotic Corymbia plantations into native Corymbia populations in Australia

Sectors of the forest plantation industry in Australia are set to expand in the near future using species or hybrids of the spotted gums (Corymbia, Section Politaria). Plantations of these taxa have already been introduced across temperate and subtropical Australia, representing locally exotic introductions from native stands in Queensland and New South Wales. A literature review was undertaken to provide insights into the potential for pollen-mediated gene flow from these plantations into native populations. Three factors suggest that such gene flow is likely; (1) interspecific hybridisation within the genus has frequently been recorded, including between distantly related species from different sections, (2) apparent high levels of vertebrate pollinator activity may result in plantation pollen being moved over hundreds of kilometres, (3) much of the plantation estate is being established among closely related taxa and therefore few barriers to gene flow are expected. Across Australia, 20 of the 100 native Corymbia taxa were found to have regional level co-occurrence with plantations. These were located most notably within regions of north-east New South Wales and south-east Queensland, however, co-occurrence was also found in south-west Western Australia and eastern Victoria. The native species found to have co-occurrence were then assessed for the presence of reproductive barriers at each step in the process of gene flow that may reduce the number of species at risk even further. The available data suggest three risk categories exist for Corymbia. The highest risk was for gene flow from plantations of spotted gums to native populations of spotted gums. This was based on the expected limited existence of pre- and post-zygotic barriers, substantial long-distance pollen dispersal and an apparent broad period of flowering in Corymbia citriodora subsp. variegata plantations. The following risk category focussed on gene flow from Corymbia torelliana × C. c. variegata hybrid plantations into native C. c. variegata, as the barriers associated with the production and establishment of F1 hybrids have been circumvented. For the lowest risk category, Corymbia plantations may present a risk to other non-spotted gum species, however, further investigation of the particular cross-combinations is required. A list of research directions is provided to better quantify these risks. Empirical data will need to be combined within a risk assessment framework that will not only estimate the likelihood of exotic gene flow, but also consider the conservation status/value of the native populations. In addition, the potential impacts of pollen flow from plantations will need to be weighed up against their various economic and environmental benefits.

Baseline responses of Alphitobius diaperinus (Coleoptera : Tenebrionidae) to cyfluthrin and detection of strong resistance in field populations in eastern Australia

Resistance to cyfluthrin in broiler farm populations of lesser mealworm, Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae), in eastern Australia was suspected to have contributed to recent control failures. In 2000-2001, beetles from 11 broiler farms were tested for resistance by comparing them to an insecticide-susceptible reference population by using topical application. Resistance was detected in almost all beetle populations (up to 22 times the susceptible at the LC50), especially in southeastern Queensland where more cyfluthrin applications had been made. Two from outside southeastern Queensland were found to be susceptible. Dose-mortality data generated from the reference population over a range of cyflutbrin concentrations showed that 0.0007% cyfluthrin at a LC99.9 level could be used as a convenient dose to discriminate between susceptible and resistant populations. Using this discriminating concentration, from 2001 to 2005, the susceptibilities of 18 field populations were determined. Of these, 11 did not exhibit complete mortality at the discriminating concentration (mortality range 2.8-97.7%), and in general, cyfluthrin resistance was directly related to the numbers of cyfluthrin applications. As in the full study, populations outside of southeastern Queensland were found to have lower levels of resistance or were susceptible. One population from an intensively farmed broiler area in southeastern Queensland exhibited low mortality despite having no known exposure to cyfluthrin. Comparisons of LC50 values of three broiler populations and a susceptible population, collected in 2000 and 2001 and recollected in 2004 and 2005 indicated that values from the three broiler populations had increased over this time for all populations. The continued use of cyfluthrin for control of A. diaperinus in eastern Australia is currently under consideration.

Baseline responses of Alphitobius diaperinus (Coleoptera: Tenebrionidae) to spinosad, and susceptibility of broiler populations in eastern and southern Australia

Spinosad was proposed as a potential chemical for control of lesser mealworm, Alphitobius diaperinus (Panzer) (Coleoptera: Tenebrionidae), in Australian broiler houses after the detection of strong cyfluthrin resistance in many beetle populations. In 2004-2006, spinosad susceptibility of 13 beetle populations from eastern and southern Australian broiler houses and a cyfluthrin/fenitrothion-resistant reference population was determined using topical application, and was compared with the susceptibility of an insecticide-susceptible reference population. Comparisons of dose-response curves and baseline data showed that all populations, including the insecticide-susceptible population, were roughly equivalent in their response to spinosad, indicating no preexisting spinosad resistance. Two field populations, including the resistant reference population, which had confirmed cyfluthrin/fenitrothion- resistance, showed no cross-resistance to spinosad. There was no significant correlation between beetle weight and LC99.9. A discriminating concentration of 3% spinosad was set to separate resistant and susceptible individuals. Considering the levels of spinosad resistance that have been recorded in other insect pests, the sustained future usefulness of spinosad as a broiler house treatment will rely on effective integrated beetle management programs combined with carefully planned chemical use strategies.

Identification of QTL for sugar-related traits in a sweet x grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population

QTL for stem sugar-related and other agronomic traits were identified in a converted sweet (R9188) × grain (R9403463-2-1) sorghum population. QTL analyses were conducted using phenotypic data for 11 traits measured in two field experiments and a genetic map comprising 228 SSR and AFLP markers grouped into 16 linkage groups, of which 11 could be assigned to the 10 sorghum chromosomes (SBI-01 to SBI-10). QTL were identified for all traits and were generally co-located to five locations (SBI-01, SBI-03, SBI-05, SBI-06 and SBI-10). QTL alleles from R9188 were detected for increased sucrose content and sugar content on SBI-01, SBI-05 and SBI-06. R9188 also contributed QTL alleles for increased Brix on SBI-05 and SBI-06, and increased sugar content on SBI-03. QTL alleles from R9403463-2-1 were found for increased sucrose content and sucrose yield on SBI-10, and increased glucose content on SBI-07. QTL alleles for increased height, later flowering and greater total dry matter yield were located on SBI-01 of R9403463-2-1, and SBI-06 of R9188. QTL alleles for increased grain yield from both R9403463-2-1 and R9188 were found on SBI-03. As an increase in stem sugars is an important objective in sweet sorghum breeding, the QTL identified in this study could be further investigated for use in marker-assisted selection of sweet sorghum.

Congruence in QTL for adventitious rooting in Pinus elliottii x Pinus caribaea hybrids resolves between and within-species effects

Targeting between-species effects for improvement in synthetic hybrid populations derived from outcrossing parental tree species may be one way to increase the efficacy and predictability of hybrid breeding. We present a comparative analysis of the quantitative trait loci (QTL) which resolved between from within-species effects for adventitious rooting in two populations of hybrids between Pinus elliottii and P. caribaea, an outbred F1 (n=287) and an inbred-like F2 family (n=357). Most small to moderate effect QTL (each explaining 2-5% of phenotypic variation, PV) were congruent (3 out of 4 QTL in each family) and therefore considered within-species effects as they segregated in both families. A single large effect QTL (40% PV) was detected uniquely in the F2 family and assumed to be due to a between-species effect, resulting from a genetic locus with contrasting alleles in each parental species. Oligogenic as opposed to polygenic architecture was supported in both families (60% and 20% PV explained by 4 QTL in the F 2 and F1 respectively). The importance of adventitious rooting for adaptation to survive water-logged environments was thought in part to explain oligogenic architecture of what is believed to be a complex trait controlled by many hundreds of genes.

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.

Flour yield QTLs in three Australian doubled haploid wheat populations

Flour yield quantitative trait loci (QTLs) were identified in 3 Australian doubled haploid populations, Sunco × Tasman, CD87 × Katepwa, and Cranbrook × Halberd. Trial data from 3 to 4 sites or years were available for each population. QTLs were identified on chromosomes 2BS, 4B, 5AL, and 6BL in the Sunco × Tasman population, on chromosomes 4B, 5AS, and 6DL in the CD87 × Katepwa population, and on chromosomes 4DS, 5DS, and 7AS in the Cranbrook × Halberd population. In the Sunco × Tasman cross the highest genetic variance was detected with the QTL on chromosome 2B (31.3%), in the CD87 × Katepwa cross with the QTL on chromosome 4B (23.8%), and in the Cranbrook × Halberd cross with the QTL on chromosome 5D (18%). Only one QTL occurred in a similar location in more than one population, indicating the complexity of the flour yield character across different backgrounds.

Resistance to insect growth regulator insecticides in populations of sheep lice as assessed by a moulting disruption assay

Low-volume, backline applications with the benzoylphenyl urea insecticides triflumuron and diflubenzuron represent in excess of 70% of treatments for the control of sheep lice, Bovicola ovis (Schrank) (Phthiraptera: Trichodectidae), in Australia. Reports of reduced effectiveness from 2003 and subsequent controlled treatment trials suggested the emergence of resistance to these compounds in B. ovis populations. A laboratory assay based on the measurement of moulting success in nymphs was developed and used to assess susceptibility to diflubenzuron and triflumuron in louse populations collected from sheep where a control failure had occurred. These tests confirmed the development of resistance to triflumuron and diflubenzuron in at least two instances, with estimated resistance ratios of 67-94X at LC50.

Effects of fishing on tropical reef associated shark populations on the Great Barrier Reef

Three data sets were examined to define the level of interaction of reef associated sharks with the commercial Coral Reef Fin Fish Fishery within the Great Barrier Reef (GBR). Data were examined from fishery logbooks, an observer program within the fishery and a fishery-independent survey conducted as part of the Effects of Line Fishing (ELF) Experiment. The majority of the identified catch was comprised of grey reef (62-72%), whitetip reef (16-29%) and blacktip reef (6-13%) sharks. Logbook data revealed spatially and temporally variable landings of shark from the GBR. Catch per unit effort (CPUE) through time was stable for the period from 1989 to 2006 with no evidence of increase or decline. Data from observer and ELF data sets indicated no differences in CPUE among regions. The ELF data set demonstrated that CPUE was higher in Marine National Park zones (no fishing) when compared to General Use zones (open to fishing). The ongoing and consistent catches of reef sharks in the fishery and effectiveness of no-fishing zones suggest that management zones within the GBR Marine Park are effective at protecting a portion of the reef shark population from exploitation.

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Phenotypic variation in natural populations of kikuyu in Australia

The quality of tropical grasses is a major limitation to animal production in tropical and subtropical areas. This is mainly associated with the lower digestibility because C4 grasses have higher fibre levels. Any improvement in quality would require a reduction in the lignin and an increase in the digestion of the neutral detergent fibre content of these plants (Clark and Wilson 1993). Kikuyu (Pennisetum clandestinum) is an important grass for the dairy and beef industries of the subtropics of Australia, South Africa and New Zealand (Mears 1970). Increased digestibility could substantially improve animal production in these industries. These experiments investigated the variation in agronomic and quality of natural populations selected from diverse regions within Australia. Runners of 14 kikuyu selections were collected by project staff or local agronomists from areas considered to have grown kikuyu for over 30 years while Whittet and Noonan were established by seed. Entries were established as single spaced plants on a 1.5 m grid in a randomised block with 3 replicates and evaluated under irrigation at Mutdapilly (brown podsol) and Wollongbar (red ferrosol). Foliage height, forage production and runner yield were assessed along with crude protein (CP), in vitro dry matter digestibility (IVDMD), metabolisable energy (ME), acid detergent fibre (ADF) and neutral detergent fibre (NDF) content of the leaf in autumn, winter and spring.

Simple sequence repeat markers associated with three quantitative trait loci for black point resistance can be used to enrich selection populations in bread wheat

Black point in wheat has the potential to cost the Australian industry $A30.4 million a year. It is difficult and expensive to screen for resistance, so the aim of this study was to validate 3 previously identified quantitative trait loci (QTLs) for black point resistance on chromosomes 2B, 4A, and 3D of the wheat variety Sunco. Black point resistance data and simple sequence repeat (SSR) markers, linked to the resistance QTLs and suited to high-throughput assay, were analysed in the doubled haploid population, Batavia (susceptible) × Pelsart (resistant). Sunco and Pelsart both have Cook in their pedigree and both have the Triticum timopheevii translocation on 2B. SSR markers identified for the 3 genetic regions were gwm319 (2B, T. timopheevii translocation), wmc048 (4AS), and gwm341 (3DS). Gwm319 and wmc048 were associated with black point resistance in the validation population. Gwm341 may have an epistatic influence on the trait because when resistance alleles were present at both gwm319 and wmc048, the Batavia-derived allele at gwm341 was associated with a higher proportion of resistant lines. Data are presented showing the level of enrichment achieved for black point resistance, using 1, 2, or 3 of these molecular markers, and the number of associated discarded resistant lines. The level of population enrichment was found to be 1.83-fold with 6 of 17 resistant lines discarded when gwm319 and wmc048 were both used for selection. Interactions among the 3 QTLs appear complex and other genetic and epigenetic factors influence susceptibility to black point. Polymorphism was assessed for these markers within potential breeding material. This indicated that alternative markers to wmc048 may be required for some parental combinations. Based on these results, marker-assisted selection for the major black point resistance QTLs can increase the rate of genetic gain by improving the selection efficiency and may facilitate stacking of black point resistances from different sources.