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.

An evaluation of genetic analyses, skull morphology and visual appearance for assessing dingo purity: implications for dingo conservation

The introgression of domestic dog genes into dingo populations threatens the genetic integrity of 'pure' dingoes. However, dingo conservation efforts are hampered by difficulties in distinguishing between dingoes and hybrids in the field. This study evaluates consistency in the status of hybridisation (i.e. dingo, hybrid or dog) assigned by genetic analyses, skull morphology and visual assessments. Of the 56 south-east Queensland animals sampled, 39 (69.6%) were assigned the same status by all three methods, 10 (17.9%) by genetic and skull methods, four (7.1%) by genetic and visual methods; and two (3.6%) by skull and visual methods. Pair-wise comparisons identified a significant relationship between genetic and skull methods, but not between either of these and visual methods. Results from surveying 13 experienced wild dog managers showed that hybrids were more easily identified by visual characters than were dingoes. A more reliable visual assessment can be developed through determining the relationship between (1) genetics and phenotype by sampling wild dog populations and (2) the expression of visual characteristics from different proportions and breeds of domestic dog genes by breeding trials. Culling obvious hybrids based on visual characteristics, such as sable and patchy coat colours, should slow the process of hybridisation.

Assessing the taxonomic status of dingoes Canis familiaris for conservation

1. The conservation status of the dingo Canis familiaris dingo is threatened by hybridization with the domestic dog C. familiaris familiaris. A practical method that can estimate the different levels of hybridization in the field is urgently required so that animals below a specific threshold of dingo ancestry (e.g. 1/4 or 1/2 dingoes) can reliably be identified and removed from dingo populations. 2. Skull morphology has been traditionally used to assess dingo purity, but this method does not discriminate between the different levels of dingo ancestry in hybrids. Furthermore, measurements can only be reliably taken from the skulls of dead animals. 3. Methods based on the analysis of variation in DNA are able to discriminate between the different levels of hybridization, but the validity of this method has been questioned because the materials currently used as a reference for dingoes are from captive animals of unproven genetic purity. The use of pre-European materials would improve the accuracy of this method, but suitable material has not been found in sufficient quantity to develop a reliable reference population. Furthermore, current methods based on DNA are impractical for the field-based discrimination of hybrids because samples require laboratory analysis. 4. Coat colour has also been used to estimate the extent of hybridization and is possibly the most practical method to apply in the field. However, this method may not be as powerful as genetic or morphological analyses because some hybrids (e.g. Australian cattle dog × dingo) are similar to dingoes in coat colour and body form. This problem may be alleviated by using additional visual characteristics such as the presence/absence of ticking and white markings.

Domestication for Conservation of an Endangered Species: The Case of the Wollemi Pine

A small population of tall slender conifers was discovered in 1994 in a deep rainforest canyon of the Wollemi National Park, New SouthWales, Australia. The living trees closely resembled fossils that were more than 65 million years old, and this ‘living fossil’ was recognised as a third extant genus in the Araucariaceae (Araucaria, Agathis and now Wollemia). The species was named the Wollemi pine (W. nobilis). Extensive searches uncovered very few populations, with the total number of adult trees being less than 100. Ex situ collections were quickly established in Sydney as part of the Wollemi Pine Recovery Plan. The majority of the ex situ population was later transferred to our custom-built facility in Queensland for commercial multiplication. Domestication has relied very heavily on the species’ amenability to vegetative propagation because seed collection from the natural populations is dangerous, expensive, and undesirable for conservation reasons. Early propagation success was poor, with only about 25% of cuttings producing roots. However, small increases in propagation success have a very large impact on a domestication program because plant production can be modelled on an exponential curve where each rooted cutting develops into a mother plant that, in turn, provides more rooted cuttings. An extensive research program elevated rooting percentages to greater than 80% and also provided in vitro methods for plant multiplication. These successes have enabled international release of the Wollemi pine as a new and attractive species for ornamental horticulture.

An improved technique for estimating short-term survival of released line-caught fish, and an application comparing barotrauma-relief methods in red emperor (Lutjanus sebae Cuvier 1816).

Promotion of better procedures for releasing undersize fish, advocacy of catch-and-release angling, and changing minimum legal sizes are increasingly being used as tools for sustainable management of fish stocks. However without knowing the proportion of released fish that survive, the conservation value of any of these measures is uncertain. We developed a floating vertical enclosure to estimate short-term survival of released line-caught tropical and subtropical reef-associated species, and used it to compare the effectiveness of two barotrauma-relief procedures (venting and shotline releasing) on red emperor (Lutjanus sebae). Barotrauma signs varied with capture depth, but not with the size of the fish. Fish from the greatest depths (40-52 m) exhibited extreme signs less frequently than did those from intermediate depths (30-40 m), possibly as a result of swim bladder gas being vented externally through a rupture in the body wall. All but two fish survived the experiment, and as neither release technique significantly improved short-term survival of the red emperor over non-treatment we see little benefit in promoting either venting or shotline releasing for this comparatively resilient species. Floating vertical enclosures can improve short-term post-release mortality estimates as they overcome many problems encountered when constraining fish in submerged cages.

Adaptation and management of Australian buffalograss cultivars for shade and water conservation

Soft-leaf buffalo grass is increasing in popularity as an amenity turfgrass in Australia. This project was instigated to assess the adaptation of and establish management guidelines for its use in Australias vast array of growing environments. There is an extensive selection of soft-leaf buffalo grass cultivars throughout Australia and with the countrys changing climates from temperate in the south to tropical in the north not all cultivars are going to be adapted to all regions. The project evaluated 19 buffalo grass cultivars along with other warm-season grasses including green couch, kikuyu and sweet smother grass. The soft-leaf buffalo grasses were evaluated for their growth and adaptation in a number of regions throughout Australia including Western Australia, Victoria, ACT, NSW and Queensland. The growth habit of the individual cultivars was examined along with their level of shade tolerance, water use, herbicide tolerance, resistance to wear, response to nitrogen applications and growth potential in highly alkaline (pH) soils. The growth habit of the various cultivars currently commercially available in Australia differs considerably from the more robust type that spreads quicker and is thicker in appearance (Sir Walter, Kings Pride, Ned Kelly and Jabiru) to the dwarf types that are shorter and thinner in appearance (AusTine and AusDwarf). Soft-leaf buffalo grass types tested do not differ in water use when compared to old-style common buffalo grass. Thus, soft-leaf buffalo grasses, like other warm-season turfgrass species, are efficient in water use. These grasses also recover after periods of low water availability. Individual cultivar differences were not discernible. In high pH soils (i.e. on alkaline-side) some elements essential for plant growth (e.g. iron and manganese) may be deficient causing turfgrass to appear pale green, and visually unacceptable. When 14 soft-leaf buffalo grass genotypes were grown on a highly alkaline soil (pH 7.5-7.9), cultivars differed in leaf iron, but not in leaf manganese, concentrations. Nitrogen is critical to the production of quality turf. The methods for applying this essential element can be manipulated to minimise the maintenance inputs (mowing) during the peak growing period (summer). By applying the greatest proportion of the turfs total nitrogen requirements in early spring, peak summer growth can be reduced resulting in a corresponding reduction in mowing requirements. Soft-leaf buffalo grass cultivars are more shade and wear tolerant than other warm-season turfgrasses being used by homeowners. There are differences between the individual buffalo grass varieties however. The majority of types currently available would be classified as having moderate levels of shade tolerance and wear reasonably well with good recovery rates. The impact of wear in a shaded environment was not tested and there is a need to investigate this as this is a typical growing environment for many homeowners. The use of herbicides is required to maintain quality soft-leaf buffalo grass turf. The development of softer herbicides for other turfgrasses has seen an increase in their popularity. The buffalo grass cultivars currently available have shown varying levels of susceptibility to the chemicals tested. The majority of the cultivars evaluated have demonstrated low levels of phytotoxicity to the herbicides chlorsulfuron (Glean) and fluroxypyr (Starane and Comet). In general, soft leaf buffalo grasses are varied in their makeup and have demonstrated varying levels of tolerance/susceptibility/adaptation to the conditions they are grown under. Consequently, there is a need to choose the cultivar most suited to the environment it is expected to perform in and the management style it will be exposed to. Future work is required to assess how the structure of the different cultivars impacts on their capacity to tolerate wear, varying shade levels, water use and herbicide tolerance. The development of a growth model may provide the solution.

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

Scale- and Context-Dependent Selection of Recreational Harvest Estimation Methods: The Australasian Experience

Fisheries managers are becoming increasingly aware of the need to quantify all forms of harvest, including that by recreational fishers. This need has been driven by both a growing recognition of the potential impact that noncommercial fishers can have on exploited resources and the requirement to allocate catch limits between different sectors of the wider fishing community in many jurisdictions. Marine recreational fishers are rarely required to report any of their activity, and some form of survey technique is usually required to estimate levels of recreational catch and effort. In this review, we describe and discuss studies that have attempted to estimate the nature and extent of recreational harvests of marine fishes in New Zealand and Australia over the past 20 years. We compare studies by method to show how circumstances dictate their application and to highlight recent developments that other researchers may find of use. Although there has been some convergence of approach, we suggest that context is an important consideration, and many of the techniques discussed here have been adapted to suit local conditions and to address recognized sources of bias. Much of this experience, along with novel improvements to existing approaches, have been reported only in "gray" literature because of an emphasis on providing estimates for immediate management purposes. This paper brings much of that work together for the first time, and we discuss how others might benefit from our experience.

Evaluating and validating abundance monitoring methods in the absence of populations of known size: review and application to a passive tracking index

Rarely is it possible to obtain absolute numbers in free-ranging populations and although various direct and indirect methods are used to estimate abundance, few are validated against populations of known size. In this paper, we apply grounding, calibration and verification methods, used to validate mathematical models, to methods of estimating relative abundance. To illustrate how this might be done, we consider and evaluate the widely applied passive tracking index (PTI) methodology. Using published data, we examine the rationality of PTI methodology, how conceptually animal activity and abundance are related and how alternative methods are subject to similar biases or produce similar abundance estimates and trends. We then attune the method against populations representing a range of densities likely to be encountered in the field. Finally, we compare PTI trends against a prediction that adjacent populations of the same species will have similar abundance values and trends in activity. We show that while PTI abundance estimates are subject to environmental and behavioural stochasticity peculiar to each species, the PTI method and associated variance estimate showed high probability of detection, high precision of abundance values and, generally, low variability between surveys, and suggest that the PTI method applied using this procedure and for these species provides a sensitive and credible index of abundance. This same or similar validation approach can and should be applied to alternative relative abundance methods in order to demonstrate their credibility and justify their use.

Cryopreservation of somatic embryos for avocado germplasm conservation

Presently avocado germplasm is conserved ex situ in the form of field repositories across the globe including Australia. The maintenance of germplasm in the field is costly, labour and land intensive, exposed to natural disasters and always at the risk of abiotic and biotic stresses. The aim of this study was to overcome these problems using cryopreservation to store avocado (Persea americana Mill.) somatic embryos (SE). Two vitrification-based methods of cryopreservation were optimised (cryovial and droplet-vitrification) using four avocado cultivars (‘A10′, ‘Reed’, ‘Velvick’ and ‘Duke-7′). SE of the four cultivars were stored for short-term (one hour) in liquid nitrogen using the cryovial-vitrification method and showed a viability of 91%, 73%, 86% and 80% respectively. While when using the droplet vitrification method viabilities of 100%, 85% and 93% were recorded for ‘A10′, ‘Reed’ and ‘Velvick’. For long-term storage, SE of cultivars ‘A10′, ‘Reed’ and ‘Velvick’ were successfully recovered with viability of 65–100% after 3 months of LN storage. For cultivar ‘Reed’ and ‘Velvick’ SE were recovered after 12 months of LN storage with viability of 67% and 59%, respectively. The outcome of this work contributes towards the establishment of a cryopreservation protocol that is applicable across multiple avocado cultivars.

Milk Production Responses to Oversowing a Portion of Tropical Grass Pasture with Summer Crop Legumes on Sub-tropical Dairy Farms

Northern Australian dairy farms have a large area of tropical dryland grass pasture available for use as summer pastures. Late summer-autumn in sub-tropical Australia is traditionally a difficult period in which to produce milk because of the decline in both quality and quantity of tropical grasses (Ehrlich et al. 1994). Options to improve autumn feed on dairy farms include introducing forage crops and conservation, increasing concentrate feeding and introducing legumes. Perennial tropical legumes have not been successful at this time of year because of their inability to sustain stocking rates above one cow/ha. This experiment, conducted on farms, was designed to test if annual crop legumes could be successfully oversown into tropical grass areas using minimal till methods to measure the subsequent impact on milk production on farms. Previous experiments using annual legumes in plots at Mutdapilly Research Station had demonstrated yields up to 10 t/ha can be achieved using annual tropical legumes with protein levels as high as 20% in the whole legume plant. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia.

A Comparison of Methods for Describing Irregular Animal Growth and Testing for Treatment Effects

In many designed experiments with animals liveweight is recorded several times during the trial. Such data are commonly referred to as repeated measures data. An aim of such experiments is generally to compare the growth patterns for the applied treatments. This paper discusses some of the methods of analysing repeated measures data and illustrates the use of cubic smoothing splines to describe irregular cattle growth data. Animal production for a consuming world : proceedings of 9th Congress of the Asian-Australasian Association of Animal Production Societies [AAAP] and 23rd Biennial Conference of the Australian Society of Animal Production [ASAP] and 17th Annual Symposium of the University of Sydney, Dairy Research Foundation, [DRF]. 2-7 July 2000, Sydney, Australia.

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.

Using simulation techniques to investigate methods to determine resistance of helminths to anthelmintic treatment

The widespread and increasing resistance of internal parasites to anthelmintic control is a serious problem for the Australian sheep and wool industry. As part of control programmes, laboratories use the Faecal Egg Count Reduction Test (FECRT) to determine resistance to anthelmintics. It is important to have confidence in the measure of resistance, not only for the producer planning a drenching programme but also for companies investigating the efficacy of their products. The determination of resistance and corresponding confidence limits as given in anthelmintic efficacy guidelines of the Standing Committee on Agriculture (SCA) is based on a number of assumptions. This study evaluated the appropriateness of these assumptions for typical data and compared the effectiveness of the standard FECRT procedure with the effectiveness of alternative procedures. Several sets of historical experimental data from sheep and goats were analysed to determine that a negative binomial distribution was a more appropriate distribution to describe pre-treatment helminth egg counts in faeces than a normal distribution. Simulated egg counts for control animals were generated stochastically from negative binomial distributions and those for treated animals from negative binomial and binomial distributions. Three methods for determining resistance when percent reduction is based on arithmetic means were applied. The first was that advocated in the SCA guidelines, the second similar to the first but basing the variance estimates on negative binomial distributions, and the third using Wadley’s method with the distribution of the response variate assumed negative binomial and a logit link transformation. These were also compared with a fourth method recommended by the International Co-operation on Harmonisation of Technical Requirements for Registration of Veterinary Medicinal Products (VICH) programme, in which percent reduction is based on the geometric means. A wide selection of parameters was investigated and for each set 1000 simulations run. Percent reduction and confidence limits were then calculated for the methods, together with the number of times in each set of 1000 simulations the theoretical percent reduction fell within the estimated confidence limits and the number of times resistance would have been said to occur. These simulations provide the basis for setting conditions under which the methods could be recommended. The authors show that given the distribution of helminth egg counts found in Queensland flocks, the method based on arithmetic not geometric means should be used and suggest that resistance be redefined as occurring when the upper level of percent reduction is less than 95%. At least ten animals per group are required in most circumstances, though even 20 may be insufficient where effectiveness of the product is close to the cut off point for defining resistance.