A review of the application of molecular genetics for fisheries management and conservation of sharks and rays

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective. (C) 2012 The Authors Journal of Fish Biology (C) 2012 The Fisheries Society of the British Isles

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.

Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

Demographics, pollination syndrome and conservation status of Macrozamia platyrhachis (Zamiaceae), a geographically restricted Queensland cycad

To assess the International Union for Conservation of Nature (IUCN) status of Macrozamia platyrhachis F.M.Bailey, we surveyed this central Queensland cycad for its population abundance and health and its pollinator type and pollination syndrome (thermogenesis and volatile emissions). Plants are locally abundant within the 11 discrete populations surveyed, with an estimated population of 611 315 adult plants. Plants are highly restricted to a small area of occupancy, seed dispersal is nearly non-existent and extreme fires appear to have destroyed almost all seeds and seedlings and decimated the pollinators. Of known Macrozamia pollinators, only the thrips, Cycadothrips chadwicki Mound, were found on cones, and these were found in very low numbers. The pollination syndrome for this cycad appears to be unique, based on two cone traits. For one, thermogenesis peaks in early evening, a contrast with daytime peaks of other Cycadothrips-pollinated Macrozamia, but matches that of the Tranes weevil-pollinated Macrozamia machinii. In addition, cone volatiles include both previously unreported compounds as well as those reported exclusively on either Cycadothrips- or Tranes-pollinated species. Based on its small, fragmented area of occupancy, projected population declines and the unique pollination syndrome, we recommend that M. platyrhachis retain its current status as 'Endangered'. Habitat management plans should stipulate that controlled burns be avoided during cycad coning season and that wildfires be controlled to minimise damage to seedlings and pollinators.

Biology, ecology and conservation of the Mobulidae

The Mobulidae are zooplanktivorous elasmobranchs comprising two recognized species of manta rays (Manta spp.) and nine recognized species of devil rays (Mobula spp.). They are found circumglobally in tropical, subtropical and temperate coastal waters. Although mobulids have been recorded for over 400 years, critical knowledge gaps still compromise the ability to assess the status of these species. On the basis of a review of 263 publications, a comparative synthesis of the biology and ecology of mobulids was conducted to examine their evolution, taxonomy, distribution, population trends, movements and aggregation, reproduction, growth and longevity, feeding, natural mortality and direct and indirect anthropogenic threats. There has been a marked increase in the number of published studies on mobulids since c. 1990, particularly for the genus Manta, although the genus Mobula remains poorly understood. Mobulid species have many common biological characteristics although their ecologies appear to be species-specific, and sometimes region-specific. Movement studies suggest that mobulids are highly mobile and have the potential to rapidly travel large distances. Fishing pressure is the major threat to many mobulid populations, with current levels of exploitation in target fisheries unlikely to be sustainable. Advances in the fields of population genetics, acoustic and satellite tracking, and stable-isotope and fatty-acid analyses will provide new insights into the biology and ecology of these species. Future research should focus on the uncertain taxonomy of mobulid species, the degree of overlap between their large-scale movement and human activities such as fisheries and pollution, and the need for management of inter-jurisdictional fisheries in developing nations to ensure their long-term sustainability. Closer collaboration among researchers worldwide is necessary to ensure standardized sampling and modelling methodologies to underpin global population estimates and status.

Spatial and temporal effects of grazing management and rainfall on the vertebrate fauna of a tropical savanna

Grazing by domestic livestock is one of the most widespread uses of the rangelands of Australia. There is limited information on the effects of grazing by domestic livestock on the vertebrate fauna of Australia and the establishment of a long-term grazing experiment in north-eastern Queensland at Wambiana provided an opportunity to attempt an examination of the changes in vertebrate fauna as a consequence of the manipulation of stocking rates. The aim was to identify what the relative effects of vegetation type, stocking rate and other landscape-scale environmental factors were on the patterns recorded. Sixteen 1-ha sites were established within three replicated treatments (moderate, heavy and variable stocking rates). The sites were sampled in the wet and dry seasons in 1999-2000 (T-0) and again in 2003-04 (T-1). All paddocks of the treatments were burnt in 1999. Average annual rainfall declined markedly between the two sampling periods, which made interpretation of the data difficult. A total of 127 species of vertebrate fauna comprising five amphibian, 83 bird, 27 reptile and 12 mammal species were recorded. There was strong separation in faunal composition from T-0 to T-1 although changes in mean compositional dissimilarity between the grazing stocking rate treatments were less well defined. There was a relative change in abundance of 24 bird, four mammal and five reptile species from T-0 to T-1. The generalised linear modelling identified that, in the T-1 data, there was significant variation in the abundance of 16 species explained by the grazing and vegetation factors. This study demonstrated that vertebrate fauna assemblage did change and that these changes were attributable to the interplay between the stocking rates, the vegetation types on the sites surveyed, the burning of the experimental paddocks and the decrease in rainfall over the course of the two surveys. It is recommended that the experiment is sampled again but that the focus should be on a rapid survey of abundant taxa (i.e. birds and reptiles) to allow an increase in the frequency of sampling and replication of the data. This would help to articulate more clearly the trajectory of vertebrate change due to the relative effects of stocking rates compared with wider landscape environmental changes. Given the increasing focus on pastoral development in northern Australia, any opportunity to incorporate the collection of data on biodiversity into grazing manipulation experiments should be taken for the assessment of the effects of land management on faunal species.

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.

A survey of management and economic impact of weeds in dryland cotton cropping systems of subtropical Australia

In dryland cotton cropping systems, the main weeds and effectiveness of management practices were identified, and the economic impact of weeds was estimated using information collected in a postal and a field survey of Southern Queensland and northern New South Wales. Forty-eight completed questionnaires were returned, and 32 paddocks were monitored in early and late summer for weed species and density. The main problem weeds were bladder ketmia (Hibiscus trionum), common sowthistle (Sonchus oleraceus), barnyard grasses (Echinochloa spp.), liverseed grass (Urochloa panicoides) and black bindweed (Fallopia convolvulus), but the relative importance of these differed with crops, fallows and crop rotations. The weed flora was diverse with 54 genera identified in the field survey. Control of weed growth in rotational crops and fallows depended largely on herbicides, particularly glyphosate in fallow and atrazine in sorghum, although effective control was not consistently achieved. Weed control in dryland cotton involved numerous combinations of selective herbicides, several non-selective herbicides, inter-row cultivation and some manual chipping. Despite this, residual weeds were found at 38-59% of initial densities in about 3-quarters of the survey paddocks. The on-farm financial costs of weeds ranged from $148 to 224/ha.year depending on the rotation, resulting in an estimated annual economic cost of $19.6 million. The approach of managing weed populations across the whole cropping system needs wider adoption to reduce the weed pressure in dryland cotton and the economic impact of weeds in the long term. Strategies that optimise herbicide performance and minimise return of weed seed to the soil are needed. Data from the surveys provide direction for research to improve weed management in this cropping system. The economic framework provides a valuable measure of evaluating likely future returns from technologies or weed management improvements.

Integrated pest management and supply chain improvement for mangoes in the Philippines and Australia

This project will incorporate two strategies for improving industry sustainability in the Philippines and Australia: (a) developing improved field management and quarantine monitoring and detection of mango pests and diseases; and (b) working with selected mango supply chains to identify and test areas for improvement.

Macadamia Breeding and Conservation

DEEDI is tendering for this project because it considers that macadamia breeding is essential for long-term industry viability and that new productive cultivars will be the basis for the industry to withstand future competition from overseas and from other nut crops.

Biology, Management and Genetic Stock Structure of Mangrove Jack, (Lutjanus argentimaculatus) in Australia.

This project has contributed to the ecologically sustainable management of mangrove jack in Australia by providing comprehensive information on its biology, habitat requirements, population parameters and stock structure. Specifically, the project has resulted in an enhanced understanding of the life history of Australian mangrove jack, the levels of exploitation in its local fishery and the likely existence of a single genetic stock throughout Queensland.

An overview on the role of Hexanchiformes in marine ecosystems: biology, ecology and conservation status of a primitive order of modern sharks

The large size, high trophic level and wide distribution of Hexanchiformes (cow and frilled sharks) should position this order as important apex predators in coastal and deep-water ecosystems. This review synthesizes available information on Hexanchiformes, including information not yet published, with the purpose of evaluating their conservation status and assessing their ecological roles in the dynamics of marine ecosystems. Comprising six species, this group has a wide global distribution, with members occurring from shallow coastal areas to depths of c. 2500 m. The limited information available on their reproductive biology suggests that they could be vulnerable to overexploitation (e.g. small litter sizes for most species and suspected long gestation periods). Most of the fishing pressure exerted on Hexanchiformes is in the form of commercial by-catch or recreational fishing. Comprehensive stock and impact assessments are unavailable for most species in most regions due to limited information on life history and catch and abundance time series. When hexanchiform species have been commercially harvested, however, they have been unable to sustain targeted fisheries for long periods. The potentially high vulnerability to intense fishing pressure warrants a conservative exploitation of this order until thorough quantitative assessments are conducted. At least some species have been shown to be significant apex predators in the systems they inhabit. Should Hexanchiformes be removed from coastal and deep-water systems, the lack of sympatric shark species that share the same resources suggests no other species would be capable of fulfilling their apex predator role in the short term. This has potential ecosystem consequences such as meso-predator release or trophic cascades. This review proposes some hypotheses on the ecology of Hexanchiformes and their role in ecosystem dynamics, highlighting the areas where critical information is required to stimulate research directions.

The importance of grasslands for animal production and other functions: a review on management and methodological progress in the tropics

The global importance of grasslands is indicated by their extent; they comprise some 26% of total land area and 80% of agriculturally productive land. The majority of grasslands are located in tropical developing countries where they are particularly important to the livelihoods of some one billion poor peoples. Grasslands clearly provide the feed base for grazing livestock and thus numerous high-quality foods, but such livestock also provide products such as fertilizer, transport, traction, fibre and leather. In addition, grasslands provide important services and roles including as water catchments, biodiversity reserves, for cultural and recreational needs, and potentially a carbon sink to alleviate greenhouse gas emissions. Inevitably, such functions may conflict with management for production of livestock products. Much of the increasing global demand for meat and milk, particularly from developing countries, will have to be supplied from grassland ecosystems, and this will provide difficult challenges. Increased production of meat and milk generally requires increased intake of metabolizable energy, and thus increased voluntary intake and/or digestibility of diets selected by grazing animals. These will require more widespread and effective application of improved management. Strategies to improve productivity include fertilizer application, grazing management, greater use of crop by-products, legumes and supplements and manipulation of stocking rate and herbage allowance. However, it is often difficult to predict the efficiency and cost-effectiveness of such strategies, particularly in tropical developing country production systems. Evaluation and on-going adjustment of grazing systems require appropriate and reliable assessment criteria, but these are often lacking. A number of emerging technologies may contribute to timely low-cost acquisition of quantitative information to better understand the soil-pasture-animal interactions and animal management in grassland systems. Development of remote imaging of vegetation, global positioning technology, improved diet markers, near IR spectroscopy and modelling provide improved tools for knowledge-based decisions on the productivity constraints of grazing animals. Individual electronic identification of animals offers opportunities for precision management on an individual animal basis for improved productivity. Improved outcomes in the form of livestock products, services and/or other outcomes from grasslands should be possible, but clearly a diversity of solutions are needed for the vast range of environments and social circumstances of global grasslands.

Effect of crop establishment methods and weed control treatments on weed management, and rice yield

Lower water availability coupled with labor shortage has resulted in the increasing inability of growers to cultivate puddled transplanted rice (PTR). A field study was conducted in the wet season of 2012 and dry season of 2013 to evaluate the performance of five rice establishment methods and four weed control treatments on weed management, and rice yield. Grass weeds were higher in dry-seeded rice (DSR) as compared to PTR and nonpuddled transplanted rice (NPTR). The highest total weed density (225-256plantsm-2) and total weed biomass (315-501gm-2) were recorded in DSR while the lowest (102-129plantsm-2 and 75-387gm-2) in PTR. Compared with the weedy plots, the treatment pretilachlor followed by fenoxaprop plus ethoxysulfuron plus 2,4-D provided excellent weed control. This treatment, however, had a poor performance in NPTR. In both seasons, herbicide efficacy was better in DSR and wet-seeded rice. PTR and DSR produced the maximum rice grain yields. The weed-free plots and herbicide treatments produced 84-614% and 58-504% higher rice grain yield, respectively, than the weedy plots in 2012, and a similar trend was observed in 2013.