ORCID Profile
0000-0003-0078-8179
Current Organisations
The University of Canberra
,
University of Canberra Faculty of Education Science Technology and Mathematics
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Environmental Science and Management | Conservation and Biodiversity | Evolutionary Impacts of Climate Change | Ecological applications | Ecological Impacts of Climate Change | Wildlife and Habitat Management | Environmental Management | Evolutionary Biology | Horticultural crop protection (incl. pests diseases and weeds) | Biosecurity science and invasive species ecology | Sociology and social studies of science and technology | Population, Ecological and Evolutionary Genetics | Biogeography and Phylogeography | Biological Adaptation
ANZSRC Socio-Economic Objective (SEO)
Ecosystem Adaptation to Climate Change | Sparseland, Permanent Grassland and Arid Zone Flora, Fauna and Biodiversity | Ecosystem Assessment and Management of Fresh, Ground and Surface Water Environments | Climate and Climate Change not elsewhere classified | Flora, Fauna and Biodiversity at Regional or Larger Scales | Fresh, Ground and Surface Water Flora, Fauna and Biodiversity |
Related Links
Publications
Measuring competitive impact: Joint‐species modelling of invaded plant communities
Publisher: Wiley
Date: 06-10-2019
Collinearity: a review of methods to deal with it and a simulation study evaluating their performance
Publisher: Wiley
Date: 18-05-2012
Advantages of Volunteer‐Based Biodiversity Monitoring in Europe
Publisher: Wiley
Date: 16-03-2009
DOI: 10.1111/J.1523-1739.2008.01125.X
Abstract: Without robust and unbiased systems for monitoring, changes in natural systems will remain enigmatic for policy makers, leaving them without a clear idea of the consequences of any environmental policies they might adopt. Generally, bio ersity-monitoring activities are not integrated or evaluated across any large geographic region. The EuMon project conducted the first large-scale evaluation of monitoring practices in Europe through an on-line questionnaire and is reporting on the results of this survey. In September 2007 the EuMon project had documented 395 monitoring schemes for species, which represents a total annual cost of about 4 million euro, involving more than 46,000 persons devoting over 148,000 person-days/year to bio ersity-monitoring activities. Here we focused on the analysis of variations of monitoring practices across a set of taxonomic groups (birds, hibians and reptiles, mammals, butterflies, plants, and other insects) and across 5 European countries (France, Germany, Hungary, Lithuania, and Poland). Our results suggest that the overall s ling effort of a scheme is linked with the proportion of volunteers involved in that scheme. Because precision is a function of the number of monitored sites and the number of sites is maximized by volunteer involvement, our results do not support the common belief that volunteer-based schemes are too noisy to be informative. Just the opposite, we believe volunteer-based schemes provide relatively reliable data, with state-of-the-art survey designs or data-analysis methods, and consequently can yield unbiased results. Quality of data collected by volunteers is more likely determined by survey design, analytical methodology, and communication skills within the schemes rather than by volunteer involvement per se.
Taxonomy and conservation of grassland earless dragons: new species and an assessment of the first possible extinction of a reptile on mainland Australia
Publisher: The Royal Society
Date: 05-2019
DOI: 10.1098/RSOS.190233
Abstract: Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species ersity on which management plans are based. The grassland earless dragon lizards (Agamidae: Tympanocryptis ) of southeastern Australia have long been of conservation concern but there have been ongoing taxonomic uncertainties. We provide a comprehensive taxonomic review of this group, integrating multiple lines of evidence, including phylogeography (mtDNA), phylogenomics (SNPs), external morphology and micro X-ray CT scans. Based on these data we assign the lectotype of T. lineata to the Canberra region, restrict the distribution of T. pinguicolla to Victoria and name two new species: T. osbornei sp. nov. (Cooma) and T. mccartneyi sp. nov. (Bathurst). Our results have significant conservation implications. Of particular concern is T. pinguicolla , with the last confident sighting in 1969, raising the possibility of the first extinction of a reptile on mainland Australia. However, our results are equivocal as to whether T. pinguicolla is extant or extinct, emphasizing the immediate imperative for continued surveys to locate any remaining populations of T. pinguicolla . We also highlight the need for a full revision of conservation management plans for all the grassland earless dragons.
Pop Gen Report : simplifying basic population genetic analyses in R
Publisher: Wiley
Date: 02-03-2014
Phylogenetic approaches reveal biodiversity threats under climate change
Publisher: Springer Science and Business Media LLC
Date: 19-09-2016
DOI: 10.1038/NCLIMATE3126
Creating new evolutionary pathways through bioinvasion: The population genetics of brushtail possums in New Zealand
Publisher: Wiley
Date: 07-2014
DOI: 10.1111/MEC.12834
Abstract: Rapid increases in global trade and human movement have created novel mixtures of organisms bringing with them the potential to rapidly accelerate the evolution of new forms. The common brushtail possum (Trichosurus vulpecula), introduced into New Zealand from Australia in the 19th century, is one such species having been sourced from multiple populations in its native range. Here, we combine microsatellite DNA- and GIS-based spatial data to show that T. vulpecula originating from at least two different Australian locations exhibit a population structure that is commensurate with their introduction history and which cannot be explained by landscape features alone. Most importantly, we identify a hybrid zone between the two subspecies which appears to function as a barrier to dispersal. When combined with previous genetic, morphological and captive studies, our data suggest that assortative mating between the two subspecies may operate at a behavioural or species recognition level rather than through fertilization, genetic incompatibility or developmental inhibition. Nevertheless, hybridization between the two subspecies of possum clearly occurs, creating the opportunity for novel genetic combinations that would not occur in their natural ranges and which is especially likely given that multiple contact zones occur in New Zealand. This discovery has implications for wildlife management in New Zealand because multiple contact zones are likely to influence the dispersal patterns of possums and because differential susceptibility to baiting with sodium fluoroacetate between possums of different origins may promote novel genetic forms.
Solving the puzzle of mercury fate and emissions by coal-fired power plants: The potential of hydrodynamic-atmospheric modelling
Publisher: Elsevier BV
Date: 11-2021
Integrating ongoing biodiversity monitoring: potential benefits and methods
Publisher: Springer Science and Business Media LLC
Date: 18-07-2008
Habitat monitoring in Europe: a description of current practices
Publisher: Springer Science and Business Media LLC
Date: 06-06-2008
Transport and fate of metal contamination in estuaries: Using a model network to predict the contributions of physical and chemical factors
Publisher: Elsevier BV
Date: 06-2016
When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data
Publisher: Wiley
Date: 02-2018
DOI: 10.1111/DDI.12717
Necessity and reality of monitoring threatened European vascular plants
Publisher: Springer Science and Business Media LLC
Date: 16-07-2008
dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture
Publisher: Wiley
Date: 11-07-2022
Abstract: Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of lified sequence tags) by providing user‐friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR . In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy‐to‐navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
How to overcome genotyping errors in non-invasive genetic mark-recapture population size estimation-A review of available methods illustrated by a case study
Publisher: Wiley
Date: 08-10-2013
DOI: 10.1002/JWMG.604
A review and a framework for the integration of biodiversity monitoring at the habitat level
Publisher: Springer Science and Business Media LLC
Date: 26-03-2008
Erratum to “Microsite conditions dominate habitat selection of the red mason bee (Osmia bicornis, Hymenoptera: Megachilidae) in an urban environment: A case study from Leipzig, Germany” [Landsc. Urban
Publisher: Elsevier BV
Date: 03-2012
Use of a multi-proxy method to support the restoration of estuaries receiving inputs from industry
Publisher: Elsevier BV
Date: 12-2015
Otters in Saxony: A Story of Successful Conflict Resolution
Publisher: Springer Berlin Heidelberg
Date: 2013
A new method for estimating visitation rates of cryptic animals via repeated surveys of indirect signs
Publisher: Wiley
Date: 29-10-2007
Modeling food web structure and selenium biomagnification in lake macquarie, New South Wales, Australia, using stable carbon and nitrogen isotopes
Publisher: Wiley
Date: 06-02-2015
DOI: 10.1002/ETC.2847
Abstract: As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (New South Wales, Australia). In the present study, an ecosystem-scale model has been applied to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using stable isotopes (δ(13) C and δ(15) N) to establish the trophic position of organisms. Trophic position, habitat, and feeding zone were examined as possible factors influencing selenium bioaccumulation. Selenium concentrations ranged from 0.2 μg/g dry weight in macroalgae species to 12.9 μg/g in the carnivorous fish Gerres subfasciatus. A mean magnification factor of 1.39 per trophic level showed that selenium is biomagnifying in the seagrass food web. Habitat and feeding zone influenced selenium concentrations in invertebrates, whereas feeding zone was the only significant factor influencing selenium concentrations in fish. The sediment-water partitioning coefficient (Kd ) of 4180 showed that partitioning of selenium entering the lake to particulate organic material (POM) is occurring, and consequently availability to food webs from POM is high. Trophic transfer factors (invertebrate = 1.9 fish = 1.2) were similar to those reported for other water bodies, showing that input source is not the main determinant of the magnitude of selenium bioaccumulation in a food web, but rather the initial partitioning of selenium into bioavailable POM. Environ Toxicol Chem 2015 :608-617. © 2014 SETAC.
Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae)
Publisher: Springer Science and Business Media LLC
Date: 06-02-2023
DOI: 10.1007/S10577-023-09715-X
Abstract: Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of ergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population ergence in the dwarf goanna, Varanus acanthurus . Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify ergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between in iduals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric in iduals. These findings suggest that chromosomal rearrangements were widespread prior to ergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic ersity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
Linking habitat structure and orientation in an arboreal species Gehyra variegata (Gekkonidae)
Publisher: Wiley
Date: 13-09-2004
“Mind the gap!” – How well does Natura 2000 cover species of European interest?
Publisher: Pensoft Publishers
Date: 17-12-2012
Remotely sensed agricultural modification improves prediction of suitable habitat for a threatened lizard
Publisher: Informa UK Limited
Date: 21-01-2018
Some like it hot: from individual to population responses of an arboreal arid‐zone gecko to local and distant climate
Publisher: Wiley
Date: 14-05-2018
DOI: 10.1002/ECM.1301
National Responsibilities in European Species Conservation: a Methodological Review
Publisher: Wiley
Date: 06-2008
DOI: 10.1111/J.1523-1739.2008.00961.X
Abstract: One particular challenge in reducing the loss of bio ersity by 2010, as agreed on at the Earth Summit in 2002, is to assign conservation tasks to geographic or administrative entities (e.g., countries or regions) on different geographical scales. To identify conservation tasks, it is imperative to determine the importance of a specific area for the global survival of a species. So far, these national or subnational responsibilities for the conservation of species have been included differently in methods prioritizing conservation. We reviewed how 12 European and 3 non-European methods determined national conservation responsibilities and evaluated the international importance of a biological population. Different countries used different methodologies, which made a direct comparison of assessments of national responsibilities among countries extremely difficult. Differences existed in the importance criteria used. Criteria included population decline, range reduction, rarity status, degree of isolation of a population, endemism, proportional distribution, and geographic location. To increase comparability, it is imperative to develop criteria for which data are generally available and to standardize the methodology among countries. A standardized method would allow conservation decisions to be based on the conservation status of a species and on the responsibility of a geographic or administrative entity for the survival of a species. We suggest that such a method should use a scalable index of proportional distribution, taxonomic status, and the distribution pattern of a taxon or species as key elements. Such a method would allow for the creation of hierarchical lists and would be highly relevant for parts of the world with multiple political jurisdictions or state unions and for nations with regional governmental structures. Conservation priorities could then be reasonably set by combining national responsibility assessments with the international conservation status of a species.
History of metal contamination in Lake Illawarra, NSW, Australia
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.CHEMOSPHERE.2014.06.058
Abstract: Lake Illawarra has a long history of sediment contamination, particularly by metals, as a result of past and current industrial operations and land uses within the catchment. In this study, we examined the history of metal contamination in sediments using metal analysis and (210)Pb and (137)Cs dating. The distributions of copper, zinc, arsenic, selenium, cadmium and lead concentrations within sediment cores were in agreement with historical events in the lake, and indicated that metal contamination had been occurring since the start of industrial activities in Port Kembla in the late 1800 s. Most metal contamination, however, has occurred since the 1960s. Sedimentation rates were found to be 0.2 cm year(-1) in Griffins Bay and 0.3 cm year(-1) in the centre of the lake. Inputs from creeks bringing metals from Port Kembla in the northeast of the lake and a copper slag emplacement from a former copper refinery on the Windang Peninsula were the main sources of metal inputs to Lake Illawarra. The metals of highest concern were zinc and copper, which exceeded the Australian and New Zealand sediment quality guideline values at some sites. Results showed that while historical contamination persists, current management practices have resulted in reduced metal concentrations in surface sediments in the depositional zones in the centre of the lake.
Evolution of climate niches in European mammals?
Publisher: The Royal Society
Date: 14-10-2009
Abstract: Our ability to predict consequences of climate change is severely impaired by the lack of knowledge on the ability of species to adapt to changing environmental conditions. We used distribution data for 140 mammal species in Europe, together with data on climate, land cover and topography, to derive a statistical description of their realized climate niche. We then compared climate niche overlap of pairs of species, selected on the basis of phylogenetic information. In contrast to expectations, related species were not similar in their climate niche. Rather, even species pairs that had a common ancestor less than 1 Ma already display very high climate niche distances. We interpret our finding as a strong interspecific competitive constraint on the realized niche, rather than a rapid evolution of the fundamental niche. If correct, our results imply a very limited usefulness of climate niche models for the prediction of future mammal distributions.
Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short‐necked turtles (Chelidae: Emydura) of eastern Australia
Publisher: Wiley
Date: 12-2018
DOI: 10.1111/MEC.14925
Abstract: Understanding the evolutionary history of ersifying lineages and the delineation of evolutionarily significant units and species remains major challenges for evolutionary biology. Low-cost representational s ling of the genome for single nucleotide polymorphisms shows great potential at the temporal scales that are typically the focus of species delimitation and phylogeography. We apply these markers to a case study of a freshwater turtle, Emydura macquarii, whose systematics has so far defied resolution, to bring to light a dynamic system of substantive allopatric lineages erging on independent evolutionary trajectories, but held back in the process of speciation by low level and episodic exchange of alleles across drainage ides on various timescales. In the context of low-level episodic gene flow, speciation is often reticulate, rather than a bifurcating process. We argue that species delimitation needs to take into account the pattern of ancestry and descent of erging lineages in allopatry together with the recent and contemporary processes of dispersal and gene flow that retard and obscure that ergence. Underpinned by a strong focus on lineage diagnosability, this combined approach provides a means for addressing the challenges of incompletely isolated populations with uncommon, but recurrent gene flow in studies of species delimitation, a situation likely to be frequently encountered. Taxonomic decisions in cases of allopatry often require subjective judgements. Our strategy, which adds an additional level of objectivity before that subjectivity is applied, reduces the risk of taxonomic inflation that can accompany lineage approaches to species delimitation.
Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)
Publisher: Cold Spring Harbor Laboratory
Date: 24-03-2023
DOI: 10.1101/2023.03.22.533737
Abstract: Distance measures are widely used for examining genetic structure in datasets that comprise many in iduals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. We examine the application of distance measures to SNP data (both genotypes and sequence tag presence-absence) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. Missing values arise from ascertainment issues in the SNP discovery process (null alleles in the case of SNP genotyping true missing data in the case of sequence tag presence-absence data). Missing values can cause displacement of affected in iduals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of in iduals (e.g. inclusion of sibs) and lack of independence of both in iduals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation. Euclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of underlying models of ergence, population demographic history, linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data that depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should be avoided. Careful consideration should be given to which state is scored zero when applying binary distance measures to fragment presence-absence data (e.g. Jaccard distance). Filtering on missing values then imputing those that remain avoids distortion in visual representations. Presence of closely related in iduals or polymorphic haploblocks in the genomes of target species with limited genomic information occasionally emerge as challenges.
Phylogeography and species delimitation of Cherax destructor (Decapoda: Parastacidae) using genome-wide SNPs
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MF18347
Abstract: Cherax is a genus of 58 species of decapod crustaceans that are widespread across Australia and New Guinea. We use single-nucleotide polymorphisms (SNPs) to examine phylogeographic patterns in the most widespread species of Cherax, namely, C. destructor, and test the distinctiveness of one undescribed species, two C. destructor subspecies, previously proposed evolutionarily significant units, and management units. Both the phylogenetic analyses and the analysis of fixed allelic differences between populations support the current species-level taxonomy of C. setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of C. destructor albidus and C. d. destructor and the existence of one undescribed species. The two populations of C. d. albidus from the Glenelg and Wimmera rivers were significantly distinct, with eight diagnostic differences (& % fixed differences, null expectation is four fixed differences), but this low level of ergence is interpreted as within the range that might be expected of management units, that is, among allopatric populations of a single species or subspecies. A southern clade of C. d. destructor comprising the Murray River and its tributaries upstream from its confluence with the Darling River is genetically distinct from a northern clade comprising populations from the Lake Eyre Basin, the northern half of the Murray–Darling Basin (Darling River catchment) and the Lower Murray River below the Darling confluence.
Non-Invasive Genetic Mark-Recapture as a Means to Study Population Sizes and Marking Behaviour of the Elusive Eurasian Otter (Lutra lutra)
Publisher: Public Library of Science (PLoS)
Date: 14-05-2015
slimr: An R package for integrating data and tailor-made population genomic simulations over space and time
Publisher: Cold Spring Harbor Laboratory
Date: 06-08-2021
DOI: 10.1101/2021.08.05.455258
Abstract: Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between simulation software and software designed for working with empirical data is currently not well developed. Here we present slimr, an R package designed to create a seamless link between standalone software SLiM 3.0, one of the most powerful population genomic simulation frameworks, and the R development environment, with its powerful data manipulation and analysis tools. We show how slimr facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning, and manipulation, proceed to constructing empirically-based parameters and initial conditions for simulations, then to running numerical simulations, and finally to retrieving simulation results in a format suitable for comparisons with empirical data – aided by advanced analysis and visualization tools provided by R. We demonstrate the use of slimr with an ex le from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. slimr makes the powerful simulation ability of SliM 3.0 directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes.
Indices, Graphs and Null Models: Analyzing Bipartite Ecological Networks
Publisher: Bentham Science Publishers Ltd.
Date: 27-02-2009
Reproductive Strategies and Population Genetic Structure in Two Dryland River Floodplain Plants, Marsilea drummondii and Eleocharis acuta
Publisher: MDPI AG
Date: 23-08-2022
Abstract: Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems, life history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies that allow plants to persist. Using two aquatic plants, Marsilea drummondii and Eleocharis acuta, we investigated the proportions of sexual and asexual reproduction and self-fertilisation by employing next-generation sequencing approaches, and we used this information to understand the population genetic structure of a large inland floodplain in western New South Wales (NSW), Australia. Asexual vegetative reproduction and self-fertilisation were more common in M. drummondii, but both species used sexual reproduction as the main mode of reproduction. This resulted in a highly differentiated genetic structure between wetlands and a similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species, highlighting the influence of the floodplain landscape and hydrology on structuring population genetic structure. The high levels of genetic variation among wetlands and the low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for the population maintenance of plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment, and reproduction in dryland regions.
Morphological shifts in populations of generalist and specialist amphibians in response to fragmentation of the Brazilian Atlantic forest
Publisher: Pensoft Publishers
Date: 15-12-2015
Climate warming drives a temperate-zone lizard to its upper thermal limits, restricting activity, and increasing energetic costs
Publisher: Springer Science and Business Media LLC
Date: 13-06-2023
DOI: 10.1038/S41598-023-35087-7
Abstract: Lizards are considered vulnerable to climate change because many operate near their thermal maxima. Exposure to higher temperatures could reduce activity of these animals by forcing them to shelter in thermal refugia for prolonged periods to avoid exceeding lethal limits. While rising temperatures should reduce activity in tropical species, the situation is less clear for temperate-zone species where activity can be constrained by both low and high temperatures. Here, we measure the effects of natural variation in environmental temperatures on activity in a temperate grassland lizard and show that it is operating near its upper thermal limit in summer even when sheltering in thermal refuges. As air temperatures increased above 32 °C, lizard activity declined markedly as in iduals sought refuge in cool microhabitats while still incurring substantial metabolic costs. We estimate that warming over the last two decades has required these lizards to increase their energy intake up to 40% to offset metabolic losses caused by rising temperatures. Our results show that recent increases in temperature are sufficient to exceed the thermal and metabolic limits of temperate-zone grassland lizards. Extended periods of high temperatures could place natural populations of ectotherms under significantly increased environmental stress and contribute to population declines and extinction.
Can Genetic Estimators Provide Robust Estimates of the Effective Number of Breeders in Small Populations?
Publisher: Public Library of Science (PLoS)
Date: 06-11-2012
Microsite conditions dominate habitat selection of the red mason bee (Osmia bicornis, Hymenoptera: Megachilidae) in an urban environment: A case study from Leipzig, Germany
Publisher: Elsevier BV
Date: 10-2011
A model‐derived short‐term estimation method of effective size for small populations with overlapping generations
Publisher: Wiley
Date: 12-02-2016
Abstract: If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size ( N e ) is proportional to the loss of genetic ersity and therefore of considerable conservation relevance. However, estimators of N e that account for demographic parameters in species with overlapping generations require s ling of populations across generations, which is often not feasible in long‐lived species. We created an in idual‐based model that allows calculation of N e based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life‐history parameter combination. The model is freely available as an r ‐package NE ff . The model was first used in a simulation experiment observing changes in N e in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes ( N y ) but decreased N e per generation. Adding the effect of different recruitment rates only affected N e for populations with low generational overlap. The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata . Simulation results were compared to genetic analyses and matched estimates of the real population very well. Unlike other estimation methods of N e , NE ff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating N e within short time periods and comparably low costs facilitating the use of N e in applied conservation and management.
Predicting when animal populations are at risk from roads: an interactive model of road avoidance behavior
Publisher: Elsevier BV
Date: 07-2005
An optimisation approach to increase DNA amplification success of otter faeces
Publisher: Springer Science and Business Media LLC
Date: 25-04-2007
landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers
Publisher: Wiley
Date: 18-02-2015
Abstract: We describe functions recently added to the r package popgenreport that can be used to perform a landscape genetic analysis (LGA) based on landscape resistance surfaces, which aims to detect the effect of landscape features on gene flow. These functions for the first time implement a LGA in a single framework. Although the approach has been shown to be a valuable tool to study gene flow in landscapes, it has not been widely used to date, despite the type of data being widely available. In part, this is likely due to the necessity to use several software packages to perform landscape genetic analyses. To apply LGA functions, two types of data sets are required: a data set with spatially referenced and genotyped in iduals, and a resistance layer representing the effect of the landscape. The function outputs three pairwise distance matrices from these data: a genetic distance matrix, a cost distance matrix and a Euclidean distance matrix. Statistical tests are performed to test whether the cost matrix contributes to the understanding of the observed population structure. A full report on the analysis and outputs in the form of plots and tables of all intermediate steps of the LGA is produced. It is possible to customize the LGA to allow for different cost path approaches and measures of genetic distances. The package is written in the r language and is available through the Comprehensive r Archive. Comprehensive tutorials and information on how to install and use the package are provided at the authors' website (www.popgenreport.org).
How to monitor elusive lizards: comparison of capture-recapture methods on giant day geckos (Gekkonidae, Phelsuma madagascariensis grandis) in the Masoala rainforest exhibit, Zurich Zoo
Publisher: Wiley
Date: 21-06-2009
Determination of national conservation responsibilities for species conservation in regions with multiple political jurisdictions
Publisher: Springer Science and Business Media LLC
Date: 16-07-2008
Abundance and habitat preferences of the southernmost population of mink: implications for managing a recent island invasion
Publisher: Springer Science and Business Media LLC
Date: 16-10-2009
Reliability of Different Mark-Recapture Methods for Population Size Estimation Tested against Reference Population Sizes Constructed from Field Data
Publisher: Public Library of Science (PLoS)
Date: 04-06-2014
Performance of multistate mark–recapture models for temporary emigration in the presence of survival costs
Publisher: Wiley
Date: 09-10-2017
Assessing the benefits and risks of translocations in depauperate species: A theoretical framework with an empirical validation
Publisher: Wiley
Date: 25-02-2020
Has the introduction of two subspecies generated dispersal barriers among invasive possums in New Zealand?
Publisher: Springer Science and Business Media LLC
Date: 11-08-2021
DOI: 10.1007/S10530-021-02609-1
Abstract: The introduction of species into new environments provides the opportunity for the evolution of new forms through admixture and novel selection pressures. The common brushtail possum, Trichosurus vulpecula vulpecula from the Australian mainland and T.v.fuliginosus from Tasmania, were introduced multiple times to New Zealand from Australia to become one of New Zealand’s most significant pests. Although derived from two subspecies, possums in New Zealand are generally considered to be a single entity. In a previous analysis, we showed that possums in the Hawkes Bay region of New Zealand appeared to consist of at least two overlapping populations. Here, we extend that analysis using a genotype-by-sequencing approach to examine the origins and population structure of those possums and compare their genetic ersity to animals s led from Australia. We identify two populations of each subspecies in Hawkes Bay and provide clear evidence of a contact zone between them in which a hybrid form is evident. Our analysis of private alleles shows higher rates of dispersal into the contact zone than away from it, suggesting that the contact zone functions as a sink (and hence as a barrier) between the two subspecies. Given the widespread and overlapping distribution of the two subspecies across both large islands in New Zealand, it is possible that many such contact zones exist. These results suggest an opportunity for a more targeted approach to controlling this pest by recognising sub-specific differences and identifying the contact zones that may form between them.
Effect of detection heterogeneity in occupancy‐detection models: an experimental test of time‐to‐first‐detection methods
Publisher: Wiley
Date: 20-05-2019
DOI: 10.1111/ECOG.04321
What's on the horizon for macroecology?
Publisher: Wiley
Date: 18-05-2012
dartR v2: an accessible genetic analysis platform for conservation, ecology, and agriculture
Publisher: Cold Spring Harbor Laboratory
Date: 04-2022
DOI: 10.1101/2022.03.30.486475
Abstract: Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of lified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this iteration, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
On managing the red mason bee (Osmia bicornis) in apple orchards
Publisher: Springer Science and Business Media LLC
Date: 30-06-2011
Recent history of sediment metal contamination in Lake Macquarie, Australia, and an assessment of ash handling procedure effectiveness in mitigating metal contamination from coal-fired power stations
Publisher: Elsevier BV
Date: 08-2014
DOI: 10.1016/J.SCITOTENV.2014.04.055
Abstract: This study assessed historical changes in metal concentrations in sediments of southern Lake Macquarie resulting from the activities of coal-fired power stations, using a multi-proxy approach which combines (210)Pb, (137)Cs and metal concentrations in sediment cores. Metal concentrations in the lake were on average, Zn: 67 mg/kg, Cu: 15 mg/kg, As: 8 mg/kg, Se: 2mg/kg, Cd: 1.5 mg/kg, Pb: 8 mg/kg with a maximum of Zn: 280 mg/kg, Cu: 80 mg/kg, As: 21 mg/kg, Se: 5 mg/kg, Cd: 4 mg/kg, Pb: 48 mg/kg. The ratios of measured concentrations in sediment cores to their sediment guidelines were Cd 1.8, As 1.0, Cu 0.5, Pb 0.2 and Zn 0.2, with the highest concern being for cadmium. Of special interest was assessment of the effects of changes in ash handling procedures by the Vales Point power station on the metal concentrations in the sediments. Comparing sediment layers before and after ash handling procedures were implemented, zinc concentrations have decreased 10%, arsenic 37%, selenium 20%, cadmium 38% and lead 14%. An analysis of contaminant depth profiles showed that, after implementation of new ash handling procedures in 1995, selenium and cadmium, the main contaminants in Australian black coal had decreased significantly in this estuary.
Spatial and seasonal distribution of trace metals in floodplain soils. A case study with the Middle Elbe River, Germany
Publisher: Elsevier BV
Date: 12-2013
dartr: An r package to facilitate analysis of SNP data generated from reduced representation genome sequencing
Publisher: Wiley
Date: 15-01-2018
Abstract: Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new r package, dartr, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. dartr provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy-Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., newhybrids, faststructure and phylogeny applications) outside of the r environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data-therefore, the package comes with a detailed tutorial targeted to the r beginner to allow data analysis without requiring deep knowledge of r. Second, we use a single, well-established format-genlight from the adegenet package-as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The dartr package is available via the r CRAN network and GitHub.
Novel evolutionary pathways of sex-determining mechanisms
Publisher: Wiley
Date: 11-10-2013
DOI: 10.1111/JEB.12258
Abstract: Evolutionary transitions between sex-determining mechanisms (SDMs) are an enigma. Among vertebrates, in idual sex (male or female) is primarily determined by either genes (genotypic sex determination, GSD) or embryonic incubation temperature (temperature-dependent sex determination, TSD), and these mechanisms have undergone repeated evolutionary transitions. Despite this evolutionary lability, transitions from GSD (i.e. from male heterogamety, XX/XY, or female heterogamety, ZZ/ZW) to TSD are an evolutionary conundrum, as they appear to require crossing a fitness valley arising from the production of genotypes with reduced viability owing to being homogametic for degenerated sex chromosomes (YY or WW in iduals). Moreover, it is unclear whether alternative (e.g. mixed) forms of sex determination can persist across evolutionary time. It has previously been suggested that transitions would be easy if temperature-dependent sex reversal (e.g. XX male or XY female) was asymmetrical, occurring only in the homogametic sex. However, only recently has a mechanistic model of sex determination emerged that may allow such asymmetrical sex reversal. We demonstrate that selection for TSD in a realistic sex-determining system can readily drive evolutionary transitions from GSD to TSD that do not require the production of YY or WW in iduals. In XX/XY systems, sex reversal (female to male) occurs in a portion of the XX in iduals only, leading to the loss of the Y allele (or chromosome) from the population as XX in iduals mate with each other. The outcome is a population of XX in iduals whose sex is determined by incubation temperature (TSD). Moreover, our model reveals a novel evolutionarily stable state representing a mixed-mechanism system that has not been revealed by previous approaches. This study solves two long-standing puzzles of the evolution of sex-determining mechanisms by illuminating the evolutionary pathways and endpoints.
Episodic population fragmentation and gene flow reveal a trade‐off between heterozygosity and allelic richness
Publisher: Wiley
Date: 24-10-2023
DOI: 10.1111/MEC.17174
Search for lepton-flavour-violating decays of the Higgs and Z bosons with the ATLAS detector
Publisher: Springer Science and Business Media LLC
Date: 02-2017
How many conservation units are there for the endangered grassland earless dragons?
Publisher: Springer Science and Business Media LLC
Date: 09-02-2016
A conceptual framework for damage compensation schemes
Publisher: Elsevier BV
Date: 2007
Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery
Publisher: Oxford University Press (OUP)
Date: 09-10-2022
DOI: 10.1093/BIOLINNEAN/BLAB095
Abstract: A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among in iduals to identify both discrete and admixed genetic groups from first principles and to hold aside in iduals involved in contemporary admixture for independent consideration (2) apply phylogenetic techniques to identify lineages (3) assess diagnosability of those lineages as potential candidate species (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry) (5) assess significance of difference or trends in the context of s ling intensity and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.
Food web structure and biocontrol in a four-trophic level system across a landscape complexity gradient
Publisher: The Royal Society
Date: 16-02-2011
Abstract: Decline in landscape complexity owing to agricultural intensification may affect bio ersity, food web complexity and associated ecological processes such as biological control, but such relationships are poorly understood. Here, we analysed food webs of cereal aphids, their primary parasitoids and hyperparasitoids in 18 agricultural landscapes differing in structural complexity (42–93% arable land). Despite little variation in the richness of each trophic group, we found considerable changes in trophic link properties across the landscape complexity gradient. Unexpectedly, aphid–parasitoid food webs exhibited a lower complexity (lower linkage density, interaction ersity and generality) in structurally complex landscapes, which was related to the dominance of one aphid species in complex landscapes. Nevertheless, primary parasitism, as well as hyperparasitism, was higher in complex landscapes, with primary parasitism reaching levels for potentially successful biological control. In conclusion, landscape complexity appeared to foster higher parasitism rates, but simpler food webs, thereby casting doubt on the general importance of food web complexity for ecosystem functioning.
Determination of conservation priorities in regions with multiple political jurisdictions
Publisher: Springer Science and Business Media LLC
Date: 20-08-2008
Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)
Publisher: Springer Science and Business Media LLC
Date: 06-12-2022
Analysing the effect of movement on local survival: a new method with an application to a spatially structured population of the arboreal gecko Gehyra variegata
Publisher: Springer Science and Business Media LLC
Date: 16-10-2007
DOI: 10.1007/S00442-007-0866-0
Abstract: Mortality during movement between habitat patches is the most obvious cost of dispersal, but rarely it has been demonstrated empirically. An approach is presented, which uses capture-mark-recapture data of an arboreal gecko species to determine the effect of in idual movement on local survival in a spatially structured population. Because capture-mark-recapture data are widely available for a range of animal species, it should be possible to extend their application to other species. The method is based on the assumption that the tendency to be a territorial animal or to be a floating animal is fixed during the study period. The advantage of our approach is that only one additional parameter has to be estimated for describing movement risks. We further tested the power of our approach to detect an association of movement and mortality with simulated capture histories. The study revealed a strong negative effect of movement on local survival. Hence, animals that moved more often between trees had a lower survival rate. Interestingly, the mean movement rate for males was significantly higher than for females, which should lead to a biased sex ratio towards females in the population. As there was an even sex ratio in the population, we discuss not mutually exclusive explanations for this finding like differences in emigration rates between sexes, differences in survival rates between sexes, or a skewed sex ratio in offspring.
Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups
Publisher: Wiley
Date: 22-10-2015
DOI: 10.1002/ECE3.1747
Agricultural modification to vegetation drives presence and abundance of a threatened fossorial legless lizard
Publisher: Wiley
Date: 13-12-2021
DOI: 10.1111/AEC.12986
Trophic transfer of metals in a seagrass food web: Bioaccumulation of essential and non-essential metals
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.MARPOLBUL.2018.04.046
Abstract: Metal concentrations are reported for a seagrass ecosystem receiving industrial inputs. δ
Oceanic and coastal populations of a harvested macroinvertebrate Rochia nilotica in north-western Australia are isolated and may be locally adapted
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/MF19172
Abstract: Marine macroinvertebrates support important fisheries throughout the Indo-Pacific, but stocks of species such as trochus (Rochia nilotica) are easily overharvested. In north-western Australia, trochus are taken from inshore reefs by Indigenous Australians and oceanic reefs by artisanal Indonesian fishers. The management of these environmentally distinct regions relies on understanding their spatial interdependencies, yet connectivity between them has not been evaluated empirically. Here, we used genotype-by-sequencing analysis of 514 trochus s les collected from 17 locations (15 in the inshore Kimberley, 2 offshore oceanic sites). Analysis of 5428 polymorphic single nucleotide polymorphism loci revealed significant genetic sub ision between the oceanic and coastal sites, and a subset of loci exhibited significantly higher sub ision, suggesting they are subject to directional selection. Population differentiation was also evident between the two oceanic sites, but not between coastal sites. Trochus populations from the coastal Kimberley and oceanic reefs represent two genetically and demographically independent units, with preliminary evidence for local adaptation to these distinctive environments. Management strategies for R. nilotica reflect these isions, but the limited connectivity among oceanic populations indicates that they are vulnerable to overexploitation. Furthermore, their potential adaptive distinctiveness indicates that coastal stocks may be unsuitable for replenishing oceanic stocks.
Related Organisations
University Of Canberra Faculty Of Education Science Technology And Mathematics
Location: Australia
Related Funding Activities
Linkage Projects - Grant ID: LP110200029
Start Date: 07-2011
End Date: 06-2016
Amount: $395,000.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP180103844
Start Date: 2018
End Date: 12-2023
Amount: $530,496.00
Funder: Australian Research Council
View Funded ActivityLinkage Projects - Grant ID: LP140100521
Start Date: 12-2014
End Date: 06-2018
Amount: $269,692.00
Funder: Australian Research Council
View Funded ActivityIndustrial Transformation Training Centres - Grant ID: IC230100027
Start Date: 2023
End Date: 12-2027
Amount: $5,000,000.00
Funder: Australian Research Council
View Funded Activity