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Item Metadata only 14th Australasian Fluid Mechanics Conference - Preface(Elsevier Science Inc, 2003) Dally, B.; Kelso, R.; Nathan, G.; Denier, J.Item Metadata only A biochemical-biophysical study of hemoglobins from woolly mammoth, asian elephant, and humans(Amer Chemical Soc, 2011) Yuan, Y.; Shen, T.; Gupta, P.; Ho, N.; Simplaceanu, V.; Tam, T.; Hofreiter, M.; Cooper, A.; Campbell, K.; Ho, C.This study is aimed at investigating the molecular basis of environmental adaptation of woolly mammoth hemoglobin (Hb) to the harsh thermal conditions of the Pleistocene ice ages. To this end, we have carried out a comparative biochemical-biophysical characterization of the structural and functional properties of recombinant hemoglobins (rHb) from woolly mammoth (rHb WM) and Asian elephant (rHb AE) in relation to human hemoglobins Hb A and Hb A(2) (a minor component of human blood). We have obtained oxygen equilibrium curves and calculated O(2) affinities, Bohr effects, and the apparent heat of oxygenation (ΔH) in the presence and absence of allosteric effectors [inorganic phosphate and inositol hexaphosphate (IHP)]. Here, we show that the four Hbs exhibit distinct structural properties and respond differently to allosteric effectors. In addition, the apparent heat of oxygenation (ΔH) for rHb WM is less negative than that of rHb AE, especially in phosphate buffer and the presence of IHP, suggesting that the oxygen affinity of mammoth blood was also less sensitive to temperature change. Finally, (1)H NMR spectroscopy data indicates that both α(1)(β/δ)(1) and α(1)(β/δ)(2) interfaces in rHb WM and rHb AE are perturbed, whereas only the α(1)δ(1) interface in Hb A(2) is perturbed compared to that in Hb A. The distinct structural and functional features of rHb WM presumably facilitated woolly mammoth survival in the Arctic environment.Item Metadata only A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning(Blackwell Publishing Ltd., 2010) Scoble, J.; Lowe, A.AbstractAim We seek to demonstrate that whilst information derived from phylogeographic and landscape genetic approaches has been used broadly to further ecological and evolutionary hypothesis testing, it can also be used to further species modelling approaches, particularly where bioclimatic and demographic methodologies are to be combined to tackle climate change adaptation and conservation planning.Location General application.Methods We start with a review of species distribution modelling studies that have used data derived from molecular marker studies, and identify which parameters can realistically be derived from molecular marker studies for inclusion in species and ecosystem distribution prediction and conservation planning.Results We find that the uptake of phylogeographic and landscape genetic methods to inform species distribution modelling studies has to date been limited (particularly the latter approaches), despite offering clear potential to improve species modelling approaches that aim to combine climatic envelope and demographic parameters. Using a series of cases studies, we demonstrate that phylogeographic approaches can be particularly useful for identifying biogeographic barriers and refugia, testing alternative demographic models, identifying concordant demographic patterns between species within a single ecosystem and testing temporal niche conservatism. We also find that landscape genetic approaches are particularly useful for quantifying landscape permeability and source/sink dynamics of meta‐populations and identifying adaptive variation in the landscape. A summary of parameters that are derivable from such studies for modelling and conservation applications is provided.Main conclusions Molecular marker methods have much to offer species distribution modelling, particularly in the field of climate adaptation. Molecular information can inform on species historical dynamics and contemporary demography necessary to advance species modelling paradigms that seek to integrate climatic and demographic drivers. Furthermore, recognizing diversity below species level and incorporating this information into modelling frameworks will enable conservation managers to plan for the capture of areas of evolutionary potential.Item Metadata only A case for Indigenous feral pest management(Charles Darwin University Press, 2007) Bradshaw, C.; Gorman, J.Item Metadata only A combination of molecular markers identifies evolutionarily significant units in Cedrela odorata L. (Meliaceae) in Costa Rica(Springer-Verlag Dordrecht, 2003) Cavers, S.; Navarro, C.; Lowe, A.The necessity for conservation of the genetic component of biodiversity is now widely recognised. A broad genetic base is required to maintain evolutionary potential and the population erosion occurring in much of the world's forests threatens the genetic integrity of many tree species. Spanish Cedar (Cedrela odorata L.) has been under severe pressure for generations and is now the focus of a study aimed at assessing the levels and distribution of genetic diversity in remaining populations. Ten Costa Rican populationswere analysed using chloroplast and AFLP markers. The overall level of diversity was as expected for an outcrossing, long-lived, woody species (HT = 0.27). However, this concealed a deep divergence within the species, for chloroplast and AFLP (CT = 0.83) markers. Populations were differentiated in two groups that exhibited contrasting habitat preferences and two ecotypes, wet and dry, were identified. Within the ecotypes, all but one population were fixed for a single chloroplast haplotype and within populations, total genomic diversity levels were low (HS = 0.03-0.13). Populations possessing the dry ecotype maintained significantly more diversity than those from wet regions. Within the wet ecotype group, pairwise genetic distance between populations fitted an isolation by distancemodel. The group was strongly subdivided and showed isolation by distance around the southern edge of the central mountain ranges. The genetic divergence of the two ecotypes, observed at both organellar and nuclear loci, identifies evolutionarily significant units that, taken together with previous studies of the species, provide a rational basis on which to build a conservation policy for the species.Item Metadata only A common boundary between distinct northern and southern morphotypes in two unrelated Tasmanian rainforest species(C S I R O Publishing, 2000) Barnes, R.; Jordan, G.; Hill, R.; McCoull, C.The variation in selected leaf morphological traits was examined across the geographic ranges of two Tasmanian rainforest species, Tasmannia lanceolata (Poiret) A.C.Smith and Eucryphia milliganii Hook.f. Comparisons of field- and glasshouse-grown plants for both species showed that there is strong genetic control of all the morphological characters measured. Two distinct morphotypes, occupying similar areas of Tasmania, were identified in each species. The geographic boundary between the morphotypes is similar in both species and runs more or less east–west, separating each species into northern and southern forms. Southern E. milliganii differs from the northern form in having ovate leaves with dense marginal trichomes and a pubescent abaxial leaf lamina. A new subspecies, E. milliganii ssp. pubescens, is described to encompass this intra-specific variation in southern Tasmania. Southern T. lanceolata has encrypted stomata, contrasting with the superficial stomata of the northern form, but is not considered sufficiently different to warrant separate taxonomic status. The boundary is difficult to explain in terms of modern environmental factors. A past period of significantly different climate from the present, perhaps combined with anthropogenic fire regimes, may have enabled allopatric differentiation within each species.Item Metadata only A comparison of indices and measured values of eggshell thickness of different shell regions using museum eggs of 230 European bird species(British Ornithologists Union, 2012) Maurer, G.; Portugal, S.; Cassey, P.; Rasmussen, P.The thickness of avian eggshells is used to assess shell quality in wild and domestic species, as an indicator of environmental pollution and as an adaptive explanation for shell maculation. Both direct measurements and calculated eggshell thickness indices (ETI) are used in such research, yet this is the first study to quantify, across a large spectrum of bird families (and thus egg shapes), the correlation between measured thicknesses and ETI. Furthermore, few studies have quantified thickness variation across the entire length of the shell, although this variation may influence both gas transfer and embryonic development. We measured the thickness of 942 eggshells of 230 European bird species from the Class II material at the Natural History Museum, Tring, UK, both in the conventional manner, at the equator through the blowhole and, uniquely, after a single longitudinal, cut at its equator at the blunt and pointed ends. Over half of the samples revealed shell defects, cautioning against the indiscriminate use of museum specimens. Strong positive associations were found between species-specific means of shell thickness with each other and also with ETI, especially those derived from Schönwetter’s Handbuch der Oologie method, validating the interspecific comparative use of ETI. Thickness measurements and ETI factors are provided for all 230 species. Eggshells were usually thinner at the blunt end (the location of the air sac) than at the equator, but of equal thickness in passerine eggs. This difference was greatest in species producing elongate eggs and suggests that there is a functional significance of shell thickness variation among species that requires further investigation.Item Metadata only A comparison of phosphorus and DOC leachates from different types of leaf litter in an urban environment(Blackwell Publishing Ltd, 2008) Wallace, T.; Ganf, G.; Brookes, J.1. The leaching rates of filterable reactive phosphorus (FRP) and dissolved organic carbon (DOC) from five leaf litter types commonly occurring in urban environments in Mediterranean regions of Southern Australia were compared. The relative composition, bioavailability and oxygen demand of this DOC were also assessed. Four tree species were assessed, including the native river red gum (Eucalyptus camaldulensis) and three introduced deciduous species, the English elm (Ulmus procera), London plane (Platanus acerifolia) and white poplar (Populus alba). Grass cuttings (mixed species) were selected as a common garden waste. 2. Except for English elm, the majority of FRP and DOC was released within the first 48 h. Grass cuttings released the highest amount of FRP with white poplar releasing the most DOC. Species that released relatively high amounts of DOC (white poplar, English elm, river red gum) released relatively low amounts of FRP. Conversely, species that released relatively low amounts of DOC (grass cuttings and London plane) tended to release relatively high amounts of FRP. 3. Analysis of DOC composition, combined with the differing oxygen demand and DOC depletion curves, demonstrated that there were substantial differences in the DOC leached from the leaf litter of the different species. Biochemical oxygen demand and the biodegradability of the DOC was positively correlated with the proportion of hydrophilic and hydrophobic acids present in the leachate. 4. These results demonstrate that simple measurements of nutrient release per gram of leaf litter would be insufficient to predict the ecological impact on receiving waters resulting from changes in dominant vegetation. Furthermore, the use of traps to prevent particulate leaf material from entering streams may have limited potential for reducing the load of dissolved nutrients. We conclude that any changes to vegetation type which substantially alter the timing of leaf fall or the composition of leaf leachates should be avoided.Item Metadata only A comparison of the spatio-temporal emission of sodium from standard and dewatered loy yang coal using PLIF(Monash University, 2003) Nathan, G.; Ashman, P.; Alwahabi, Z.; Lucas, O.; Meeuwissen, K.; Australian Symposium on Combustion (2003 : Melbourne, Vic.); Honnery, D.Item Metadata only A cryptic and critically endangered species revealed by mitochondrial DNA analyses: the Western Ground Parrot(Springer-Verlag Dordrecht, 2011) Murphy, S.; Joseph, L.; Burbidge, A.; Austin, J.We examined cytochrome b sequence data to resolve the intraspecific taxonomy of ground parrots Pezoporus wallicus. The species occurs in fragmented coastal heaths in south-eastern and south-western Australia. Net nucleotide divergences among all eastern populations were very low (0.0â 0.6%) and genetic diversity unstructured, suggesting relatively recent common ancestry. Gene flow among them was probably maintained via land bridges and the persistence of suitable habitat during the Pleistocene. In contrast, net nucleotide divergence was high (4.4â 5.1%) between western and eastern populations, suggesting more ancient divergence about 2Â million years ago. The magnitude of divergence between eastern and western lineages is similar to a wide range of avian congeners. Our data support the need to reconsider the intraspecific taxonomy of ground parrots, and we cautiously suggest the recognition of Western Ground Parrots as a species, P. flaviventris, for conservation prioritization, planning and management purposes. Given their recent precipitous decline to approximately 110 individuals, most of which occur at one location, this makes Western Ground Parrots one of the worldâ s most threatened bird species.Item Metadata only A DNA method to verify the integrity of timber supply chains; Confirming the legal sourcing of merbau timber from logging concession to sawmill(Sauerlanders Verlag, 2010) Lowe, A.; Wong, K.; Tiong, Y.; Iyerh, S.; Chew, F.Several methods are employed by the timber industry to try to restrict the flow of products from illegal or unsustainable sources into timber supply chains. The most commonly applied are systems of log marking and associated documentation that accompany the logs. However this system is open to falsification, particularly between the logging concession and the timber mill, where the majority of illegally logged timber enters the supply chain. This paper describes the development of a methodology to track a unique genetic fingerprint for single logs of merbau, Intsia palembanica (Leguminosae), a high-value Indonesian timber species, from logging concession to the mill, where the DNA profile of individual logs is difficult or impossible to falsify. We find that whilst the ability to extract DNA and amplify a PCR product from logs decreases slightly between forest concession (59.2%) and mill (41.9%) samples, that overall enough samples worked across the 14 microsatellite markers to provide an exact genotype match between forest and sawmill samples for 27 out of 32 logs. Furthermore for these 27 samples, the probability that an illegal log with an exact genotype match to forest samples had been substituted was very low (less than 10–5) for 18 samples, was low (between 10–2 and 10–4) for 7 samples and was moderate (10–1) for 2 samples. Improvements to DNA extraction and amplification success are recommended to improve this protocol, and there was a negative correlation between locus size and amplification success but a positive correlation with allele number. However, overall we propose that this methodology is now suitable for broad-scale industry application to track legally harvested timber and check for illegal substitutions along supply chains.Item Metadata only A future for the Coorong and Lower Lakes(Surrey Beatty & Sons, 2009) Paton, D.; Rogers, D.; Aldridge, K.; Deegan, B.; Brookes, J.The Coorong and Lower Lakes are listed as a Wetland of International Significance under the Ramsar Convention. This wetland system was nominated because of the diversity of wetlands that were supported: fresh, estuarine and hypermarine; and because of the importance of the area to vast numbers of water birds: ducks, swans, pelicans, terns, grebes, and migratory sandpipers and endemic shorebirds (stilts, avocets). But the region has changed and is about to change again: a consequence of failing to allocate the necessary maintenance and environmental flows to the River Murray. The Coorong has not received upstream flows of freshwater for at least six years and in just the last two years the water levels in the Lakes have dropped to well below sea-level unprecedented. These changes threaten to eliminate the key features that made this system of international significance.Item Metadata only A generic, process-based model of microbial pollution in aquatic systems(Amer Geophysical Union, 2008) Hipsey, M.; Antenucci, J.; Brookes, J.Based on a comprehensive synthesis of data available within the literature, a new process-based model of microbial pollution is presented, which is applicable for surface and coastal waters. The model is based on a generic set of parameterisations that describe the dynamics of most protozoan, bacterial and viral organisms of interest, including pathogens and microbial indicator organisms. The parameterisations dynamically account for the effects of temperature, salinity, pH, dissolved oxygen, sunlight, nutrients and turbidity on the growth and mortality of enteric organisms. Parameters for a range of organisms are also presented which are based on collation of literature data. The model has been implemented within an aquatic ecology model, Computational Aquatic Ecosystem Dynamics Model (CAEDYM), which can couple to multidimensional hydrodynamic models. Without adjustment of the literature derived parameter values, a 3-D implementation is validated against observed data from three freshwater systems that differ in their climatic zone, trophic status and operation. The simulations highlight the spatial and temporal variability that may be encountered by operators. Additionally, large differences in the fate and distribution of different species originate from variable rates of growth, mortality and sedimentation and it is emphasized that the use of surrogates for quantifying risk is problematic. The model can be used to help design targeted monitoring programs, explore differences between species, and to support real-time decision-making. Areas where insufficient understanding and data exist are discussed.Item Open Access A genome scan and linkage disequilibrium analysis among chromosomal races of the Australian grasshopper Vandiemenella viatica(Public Library of Science, 2012) Jackson, B.; Kawakami, T.; Cooper, S.; Galindo, J.; Butlin, R.; Etges, W.J.In the past decade the interest surrounding the role of recombination in speciation has been re-kindled by a new generation of chromosomal speciation models that invoke the recombination-suppression properties of some types of chromosomal rearrangement. A common prediction of recombination-suppression models is that gene exchange between diverging populations will be more restricted in regions of the genome that experience low recombination. We carried out a genome scan of three chromosomal races of the grasshopper Vandiemenella viatica (Orthoptera: Morabinae), occurring on Kangaroo Island, South Australia, using 1517 AFLP loci, with a view to elucidating the roles that selection and chromosomal variation have played in the formation of these taxa. An analysis of molecular variance demonstrated that chromosomal race accounted for a significant proportion of the genetic variance in the total dataset, which concurred with the findings of an earlier study. Sampling across one previously-identified hybrid zone, and the identification of outlier loci between parental races allowed us to establish that, in admixed populations, outlier loci which potentially pre-date the isolation of populations of races on Kangaroo Island exhibit higher levels of linkage disequilibrium with each other than putatively neutral loci. In turn this suggests that they might reside within genomic regions of low recombination, or be closely linked with each other.Item Metadata only A global molecular phylogeny of the small Puffinus shearwaters and implications for systematics of the the little-Audubon's shearwater complex(Amer Ornithologists Union, 2004) Austin, J.; Bretagnolle, V.; Pasquet, E.A molecular phylogeny based on 917 base pairs (bp) of the mitochondrial (mt) DNA cytochrome-b gene was used to test and reassess the systematics and conflicting taxonomic treatments of the small, black-and-white Puffinus shearwaters, including the P. assimilis-lherminieri species complex. Three geographically discrete clades were identified in the North Atlantic, Southern (Australasia) and tropical Pacific and Indian oceans that contain most of the P. assimilis-lherminieri taxa. Together with four other lineages (P. puffinus, P. opisthomelas, P. mauretanicus-P. yelkouan, P. newelli-P. myrtae), they form an unresolved polytomy. Puffinus hultoni-P. gavia, P. nativitatis, and P. subalaris are basal to this. The phylogenetic positions of P. myrtae and P. subalaris are unexpected and warrant further investigation. None of the competing taxonomic treatments of the P. assimilis-lherminieri complex art, supported. Instead, our phylogeny suggests that 14 taxa should be recognized, whereas five others (loyemilleri, colstoni, nicolae, polynesiae, and atrodorsalis) are phylogenetically undifferentiated from more widespread species (lherminieri, dichrous, and bailloni) and are probably not valid. Similarities in plumage and external morphological characters between unrelated species and differences between closely related species suggest that those traditional taxonomic characters are poor indicators of phylogenetic relatedness.Item Metadata only A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens(Royal Soc London, 2002) Ericson, P.; Christidis, L.; Cooper, A.; Irestedt, M.; Jackson, J.; Johansson, U.; Norman, J.Zoogeographic, palaeontological and biochemical data support a Southern Hemisphere origin for passerine birds, while accumulating molecular data suggest that most extant avian orders originated in the mid-Late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and here we demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We propose that (i) the acanthisittids were isolated when New Zealand separated from Gondwana (ca. 82-85 Myr ago), (ii) suboscines, in turn, were derived from an ancestral lineage that inhabited western Gondwana, and (iii) the ancestors of the oscines (songbirds) were subsequently isolated by the separation of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.Item Metadata only A highly modified stygobiont diving beetle of the genus Copelatus (Coleoptera, Dytiscidae): taxonomy and cladistic analysis based on mitochondrial DNA sequences(Blackwell Publishing Ltd, 2004) Balke, M.; Watts, C.; Cooper, S.; Humphreys, W.; Vogler, A.We report the discovery of a new species of Copelatus that is morphologically highly modified for life in groundwater. Copelatus abditus sp.n. was collected from a 4m deep bore in central Australia. It was placed in Copelatinae based on morphological evidence. This is the first known stygobiont diving beetle that does not belong to the subfamily Hydroporinae. Sequences from the mitochondrial DNA cytochrome oxidase 1, 16S rRNA, tRNAL and NADH dehydrogenase subunit 1 genes suggest that the species belongs to the subgenus Papuadytes, the morphological apomorphies of which are reduced in the new groundwater species. Copelatus (Papuadytes) abditus very much resembles other world stygobiont dytiscids, which all belong to the subfamily Hydroporinae. We suggest that this striking convergence is due to similar selective pressures imposed on all groundwater beetles. We suggest a scenario in which species from temporary habitats evade drought by entering the hyporheic zone, and may be driven to a subterranean existence by desertification of their ancestral habitats, as can be observed in Australia.Item Metadata only A hybrid approach to monthly streamflow forecasting: integrating hydrological model outputs into a Bayesian artificial neural network(Elsevier, 2016) Humphrey, G.; Gibbs, M.; Dandy, G.; Maier, H.Abstract not availableItem Open Access A hymenopterists' guide to the hymenoptera anatomy ontology: utility, clarification, and future directions(Pensoft Publishers, 2012) Seltmann, K.; Austin, A.; Jennings, J.Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resourc¬es are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, “preferred terms”, and “structural equivalency”. We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the “URI table”) by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the “Analyzer”) to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.Item Metadata only A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird(Blackwell Publishing Ltd, 2009) Pavlacky, D.; Goldizen, A.; Prentis, P.; Nicholls, J.; Lowe, A.Landscape genetics is an important framework for investigating the influence of spatial pattern on ecological process. Nevertheless, the standard analytic frameworks in landscape genetics have difficulty evaluating hypotheses about spatial processes in dynamic landscapes. We use a predictive hypothesis-driven approach to quantify the relative contribution of historic and contemporary processes to genetic connectivity. By confronting genetic data with models of historic and contemporary landscapes, we identify dispersal processes operating in naturally heterogeneous and human-altered systems. We demonstrate the approach using a case study of microsatellite polymorphism and indirect estimates of gene flow for a rainforest bird, the logrunner (Orthonyx temminckii). Of particular interest was how much information in the genetic data was attributable to processes occurring in the reconstructed historic landscape and contemporary human-modified landscape. A linear mixed model was used to estimate appropriate sampling variance from nonindependent data and information-theoretic model selection provided strength of evidence for alternative hypotheses. The contemporary landscape explained slightly more information in the genetic differentiation data than the historic landscape, and there was considerable evidence for a temporal shift in dispersal pattern. In contrast, migration rates estimated from genealogical information were primarily influenced by contemporary landscape change. We discovered that landscape heterogeneity facilitated gene flow before European settlement, but contemporary deforestation is rapidly becoming the most important barrier to logrunner dispersal.