Bernd Gruber

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• PhD
• Professor at University of Canberra

Identifying the habitat area used by animals is vital for understanding species-level life-history traits and ecological requirements. The Maximilian's Snake-necked Turtle (Hydromedusa maximiliani) is an endemic and endangered freshwater turtle from the Atlantic Rainforest in Brazil. We tracked 14 adult Hydromedusa maximiliani (seven males and seve...

Aim We examine the phylogeographic genetic structure of the endangered pig‐nosed turtle Carettochelys insculpta, the last remaining member of a once globally widespread family, now restricted to northern Australia and southern New Guinea, a region with a complex geological and eustatic history. We examine their historical biogeography, demographic...

We conducted the first comprehensive global assessment of the extinction risk of Australia's native freshwater fishes. Using International Union for Conservation of Nature (IUCN) criteria, 37 % (88 species) of the 241 assessed species were threatened (Critically Endangered, Endangered or Vulnerable), with one being Extinct. Lepidogalaxiidae and Neo...

Increasing environmental threats and more extreme environmental perturbations place species at risk of population declines, with associated loss of genetic diversity and evolutionary potential. While theory shows that rapid population declines can cause loss of genetic diversity, populations in some environments, like Australia’s arid zone, are rep...

Reconstructing biological invasions from historical sources can provide insights into how they occur but are difficult to do when invasions are poorly documented. Genetic signatures left by invaders can also offer insights into invasion routes, points of origin and general biology but often present conclusions that are contradictory to expectations...

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 standalone simulation software and R is currently not well developed. Here, we present slimr, a...

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks result...

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 sit...

Distance measures are widely used for examining genetic structure in datasets that comprise many individuals 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...

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 divergent populations, the underlying...

Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproducti...

Ectotherms are considered vulnerable to climate change as many operate at close to their thermal maxima. Exposure to higher temperatures could reduce activity by forcing animals to shelter in thermal refugia to avoid exceeding lethal limits. While rising temperatures should reduce activity in tropical species, the situation is less clear for temper...

Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting geneflow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying...

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...

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 polymorphis...

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-...

Grouping and description of all the functions currently available in dartR.

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 (...

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 an...

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...

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...

Community‐level resource management efforts are cornerstones in ensuring sustainable use of natural resources. Yet, understanding how community characteristics influence management practices remains contested. With a sample size of ≥725 communities, we assessed the effects of key community (i.e., socioeconomic) characteristics (human population siz...

There is currently a significant gap in knowledge about the emission and deposition of mercury (Hg) from coal-fired power plants in Australia. To fill this gap, we propose a novel method that combines several sources of information (stratigraphic data, hydrodynamic modelling and atmospheric modelling), to identify the sources and fates of Hg emitte...

Agricultural modification is one of the main drivers of global biodiversity decline. Vegetation clearance, tillage, grazing, and the application of fertilisers and pesticides have significantly affected native plants and animals. Reptiles can be vulnerable to agricultural practices, and localised declines in reptile biodiversity have been detected....

In 2019 the nine ACT Wedge-tailed Eagle territories we check each year fledged 1.11 young per territory, with three nests fledging twins. ACT Little Eagle breeding success in 2019 was much lower, at 0.30 young per territory, and attributed to drought (Rae et al. 2019). We suggest that drought is not the only cause of low breeding success in ACT Lit...

Conservation translocations are becoming more common to assist in the management of threatened native species. While many translocation programs focus on maximizing survival in newly established populations, consideration is also required for the persistence of source populations. Here, we present and test a theoretical framework that assesses the...

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 dis...

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 dis...

Non‐native species can dominate plant communities by competitively displacing native species, or because environmental change creates conditions favourable to non‐native species but unfavourable to native species. We need to disentangle these mechanisms so that management can target competitively dominant species and reduce their impacts. Joint‐spe...

Taxonomic research is of fundamental importance in conservation management of threatened species, providing an understanding of species diversity 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...

Imperfect detection can bias estimates of site occupancy in ecological surveys but can be corrected by estimating detection probability. Time‐to‐first‐detection (TTD) occupancy models have been proposed as a cost‐effective survey method that allows detection probability to be estimated from single site visits. Nevertheless, few studies have validat...

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, previous...

The post-breeding migration of an adult male little eagle (Hieraaetus morphnoides) was followed from south-eastern Australia to the Northern Territory using a GPS satellite transmitter. The bird bred in open woodland habitat on the edge of the city of Canberra, Australian Capital Territory (ACT), before it flew more than 3300 km in 18 days, to wint...

First satellite-tagging of a Swamp Harrier Circus approximans

1.Non-native plant species can dominate communities by competitively excluding native species. However, quantifying the competitive impact of non-native species is difficult because they may simply be abundant where native species are not due to different environmental requirements, meaning that the effects of environmental and competitive variatio...

Understanding the evolutionary history of diversifying lineages and the delineation of evolutionarily significant units and species remain major challenges for evolutionary biology. Low cost representational sampling of the genome for single nucleotide polymorphisms (SNPs) shows great potential at the temporal scales that are typically the focus of...

Metal concentrations are reported for a seagrass ecosystem receiving industrial inputs. δ13C and δ15N isotope ratios were used to establish trophic links. Copper concentrations (dry mass) ranged from <0.01 μg/g in fish species to 570 μg/g (μ = 49 ± SD = 90 μg/g) in the oyster Saccostrea glomerata. Zinc concentrations ranged from 0.6 μg/g in the sea...

Figure 2 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data

Figure 3 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data

Figure 1 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data

Figure 4 from Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data

Supplementary file for Campbell et al (2018) Diversity and Distributions When is a native species invasive? Incursion of a novel predatory marsupial detected using molecular and historical data

Aim Range expansions facilitated by humans or in response to local biotic or abiotic stressors provide the opportunity for species to occupy novel environments. Classifying the status of newly expanded populations can be difficult, particularly when the timing and nature of the range expansion are unclear. Should native species in new habitats be c...

The geographical distribution of a species is limited by factors such as climate, resources, disturbances and species interactions. Environmental niche models attempt to encapsulate these limits and represent them spatially but do not always incorporate disturbance factors. We constructed MaxEnt models derived from a remotely sensed vegetation clas...

Though 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 qu...

A juvenile Little Eagle Hieraaetus morphnoides was radio-tagged and followed from the day it left the nest until it dispersed 12 weeks later. Two methods, minimum convex polygons (MCP) and kernel analysis, were used to estimate its home range. Home range increased in size progressively over the 12 weeks of the post-fledging period, from 0.001 km 2...

Accumulating evidence has demonstrated considerable impact of climate change on biodiversity, with terrestrial ectotherms being particularly vulnerable. While climate‐induced range shifts are often addressed in the literature, little is known about the underlying ecological responses at individual and population levels. Using a 30‐yr monitoring stu...

Temporary emigration is widespread in animals and plants and has important implications for ecological processes, evolution and the conservation of species. It is increasingly studied with capture–mark–recapture (CMR) models. Temporary emigration provides particular challenges to CMR analyses if it involves movement to an unobservable state. A mult...

Predicting the consequences of climate change for biodiversity is critical to conservation efforts. Extensive range losses have been predicted for thousands of individual species, but less is known about how climate change might impact whole clades and landscape-scale patterns of biodiversity. Here, we show that climate change scenarios imply signi...

Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definiti...

Anthropogenic mercury (Hg) is a global pollutant capable of undergoing long-range atmospheric transport. Understanding biogeochemical controls on the spatial distribution of Hg in Australia at the continental scale with its unique biota, soil types, and climatic variables, is critical for modelling Hg emission rates and transport at regional and gl...

Anthropogenic mercury (Hg) is a global pollutant capable of undergoing long-range atmospheric transport. Understanding the continental-scale biogeochemical controls on the spatial distribution of Hg in Australia with its unique biota, soils, and climate, is critical for modelling Hg emission rates and transport at regional to global scales. We hypo...

Supplementary material 1 Supplementary Fig. 1: Estimates of average pairwise relatedness within Canberra and Monaro sampling sites for T. pinguicolla. Sites with 2 individuals or less are not included. A value of 0.5 indicates a parent-sibling or full sibling relationship, 0.25 indicates half-siblings and below 0.125 indicates unrelated individuals...

Supplementary material 2 Supplementary Fig. 4: Supplemental Figure XXX Deviance information criterion (DIC) plot for each replicate of K (replicates = 20) for K = 2 to 10 (grey points). Durand et al. (2009) recommend examining the DIC values of the lowest 10 to 20 % of replicate values for each K in order to identify the ideal number of clusters as...

Changes in morphological traits, such as body size, body condition, and leg length, are important indicators of changes to life history or habitat quality, which can affect the performance of individuals and therefore the persistence of populations under environmental change. Only very few studies assessed the effect of fragmentation on morphologic...

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. Though the approach has been shown to...

In New South Wales (NSW), Australia, the availability of water from estuarine lakes combined with the use of coal as an energy source has resulted in coal-fired power stations on the margins of coastal lakes. The purpose of this study was to use a multi-proxy method to evaluate the extent and trends of historical metal inputs from a coal-fired powe...

Abstract In New South Wales (NSW), Australia, the availability of water from estuarine lakes combined with the use of coal as an energy source has resulted in coal-fired power stations on the margins of coastal lakes. The purpose of this study was to use a multi-proxy method to evaluate the extent and trends of historical metal inputs from a coal-...

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 diversity and therefor...

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple...

Appendix S1. Phylogenies for each taxa (maximum likelihood RAxML).

Appendix S3. Examples of meta‐analysis as a PDF with R scripts and instructions to run the basic calculations.

Appendix S4. Examples of meta‐analysis as an .rmd format to create a PDF or word document.

Appendix S6. Data subsets including acaciaex_grid.csv, fish_grid.csv, fishex_grid.csv, frogsex_grid.csv, plantgenex_grid.csv, knitbutton.png, pd_pairs_all.csv, pe_pairs_all.csv,sr_pairs_all.csv, we_pairs_all.csv, mdb.dbf, mdb.sbn, mdb.sbx, mdb.shp and mdb.shx.

Appendix S2. Comparison of the diversity patters using the mean for all grid cells analyses (upper panels) when fish data were excluded (lower panels) and the mean for concordant.

Appendix S5. Helper functions as an R script.

Despite considerable knowledge on aspects of the ecology of the Wedge-tailed Eagle Aquila audax, information on home range size has been limited to estimates based on visual observations and nesting densities. This study aims to provide a methodological and theoretical framework for the potential applications and recommendations for the use of sate...

Ethics committees that are required to oversee research activities involving the capture and handling of wild animals tend to take a cautious attitude because little has been published that quantifies their effects on animals. However, to address questions in ecology and evolution, it is often essential to be able to identify individual animals. To...

Quantifying population status is a key objective in many ecological studies, but is often difficult to achieve for cryptic or elusive species. Here, non-invasive genetic capture-mark-recapture (CMR) methods have become a very important tool to estimate population parameters, such as population size and sex ratio. The Eurasian otter ( Lutra lutra )...

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 210Pb and 137Cs dating. The distributions of copper, zinc, arsenic, seleniu...

As a consequence of coal-fired power station operations, elevated selenium concentrations have been reported in the sediments and biota of Lake Macquarie (NSW, Australia). In the present study, we applied an ecosystem-scale model to determine how selenium in a seagrass food web is processed from sediments and water through diet to predators, using...

Nest site characteristics of the Wedge-tailed Eagle Aquila audax were investigated during the 2011 breeding season within the Australian Capital Territory (ACT). Our objectives were to determine the nesting habitat requirements of this species in the ACT by surveying nest sites and identifying differences between habitat characteristics of nest tre...

Tasmania supports a number of native Australian mammals whose mainland counterparts have severely declined or disappeared since European settlement. This provides a unique opportunity to study ecosystem changes occurring through the ongoing collapse of the Tasmanian devil (Sarcophilus harrisii) population along with the recent introduction of the f...

Understanding how mammal populations interact with each other and their immediate environment is of critical importance to predicting responses to environmental change while knowledge on diet and distribution of emerging invasive species is vital to management efforts. However, estimating species distributions, let alone interactions among them, ha...

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 popu...

Reliable estimates of population size are fundamental in many ecological studies and biodiversity conservation. Selecting appropriate methods to estimate abundance is often very difficult, especially if data are scarce. Most studies concerning the reliability of different estimators used simulation data based on assumptions about capture variabilit...

Using scripting languages such as R to perform population genetic analyses can improve the reproducibility of research, but using R can be challenging for many researchers due to its steep learning curve. P op G en R eport is a new R package that simplifies performing population genetics analyses in R, through the use of a new report‐generating fun...

Key Points • Community based monitoring of water quality and aquatic ecosystems such as Waterwatch in Australia comprise an important portion of worldwide community monitoring efforts. • Waterwatch data have traditionally been criticised as being of inferior quality compared with professionally collected data yet there are few published comparisons...

The main goal of non-invasive genetic capture-mark-recapture (CMR) analysis is to gain an unbiased and reliable population size estimate of species that cannot be sampled directly. The method has become an important and widely used tool to research and manage wildlife populations. However, researchers have to struggle with low amplification success...

Evolutionary transitions between sex-determining mechanisms (SDMs) are an enigma. Among vertebrates, individual 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...