- Mathematics, Biology, Animal Ecology, Social behavior in animals, Bayesian, Statistics, and 11 moreComputational Statistics, Design of Experiments, Foundations of Statistics, R (Statistics), Statistical Modelling, Vertebrate Evolution, Wildlife Biology, Herpetology, Phylogenetics, Ecology, and Conservation Biologyedit
Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to... more
Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression,...
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The distribution of parasites in host populations is integral to simulations of parasite populations.We compared three methods to measure parasite aggregation, namely the Hoover, Coefficient of Variation and I10 indices, using field data... more
The distribution of parasites in host populations is integral to simulations of parasite populations.We compared three methods to measure parasite aggregation, namely the Hoover, Coefficient of Variation and I10 indices, using field data from a range of fish parasites. These included anisakid nematodes, trypanorhynch cestodes and polyopisthocotylean monogeneans from 10 previously published studies and one unpublished study.Positive correlations among the three methods were high. Standard errors and estimated biases obtained by bootstrap methods were smallest for the Hoover index. There was no evidence for a bias-variance trade-off.The analyses suggest that the Hoover index is to be preferred as a measure of aggregation although difficulties remain in deriving theoretical and operational definitions of aggregation.
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Whether contemporary human populations are still evolving as a result of natural selection has been hotly debated. For natural selection to cause evolutionary change in a trait, variation in the trait must be correlated with fitness and... more
Whether contemporary human populations are still evolving as a result of natural selection has been hotly debated. For natural selection to cause evolutionary change in a trait, variation in the trait must be correlated with fitness and be genetically heritable and there must be no genetic constraints to evolution. These conditions have rarely been tested in human populations. In this study, data from a large twin cohort were used to assess whether selection will cause a change among women in a contemporary Western ...
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Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating... more
Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add ecomorphological characterization of a young cryptic divergence within the carnivorous marsupial genus Antechinus. Specifically, we used 168 museum specimens to characterize the recently proposed clades A. stuartii ‘south’, A. stuartii ‘north’ and A. subtropicus. Beyond slight differences attributable to overall size (and, therefore, not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no su...
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Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating... more
Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add eco-morphological characterisation of a young cryptic divergence within the marsupial carnivorous genus Antechinus. Specifically, we used 168 museum specimens to characterise the recently proposed clades A. stuartii “south”, A. stuartii “north” and A. subtropicus. Beyond slight differences attributable to overall size (and therefore not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no sup...
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The composition of an open-forest lizard assemblage in eastern Australia was examined before and after a low-intensity controlled fire and concurrently compared with that in an adjoining unburnt area. The effect of fire on the available... more
The composition of an open-forest lizard assemblage in eastern Australia was examined before and after a low-intensity controlled fire and concurrently compared with that in an adjoining unburnt area. The effect of fire on the available structural environment and the habitat used by two focal species, Carlia vivax and Lygisaurus foliorum, was also examined. Lizard species richness was unaffected by the controlled burn as was the abundance of most species. C. vivax was the only species to display a significant ...
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Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets... more
Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalised linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age, or gestation length. This supports suggestions that significan...
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Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species... more
Genetic diversity within species may promote resilience to environmental change, yet little is known about how such variation is distributed at broad geographic scales. Here we develop a novel Bayesian methodology to analyse multi-species genetic diversity data in order to identify regions of high or low genetic diversity. We apply this method to co-distributed taxa from Australian marine waters. We extracted published summary statistics of population genetic diversity from 118 studies of 101 species and > 1000 populations from the Australian marine economic zone. We analysed these data using two approaches: a linear mixed model for standardised data, and a mixed beta-regression for unstandardised data, within a Bayesian framework. Our beta-regression approach performed better than models using standardised data, based on posterior predictive tests. The best model included region (Integrated Marine and Coastal Regionalisation of Australia (IMCRA) bioregions), latitude and latitud...
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For species with five or more sightings, quantitative techniques exist to test whether a species is extinct on the basis of distribution of sightings. However, 70% of purportedly extinct mammals are known from fewer than five sightings,... more
For species with five or more sightings, quantitative techniques exist to test whether a species is extinct on the basis of distribution of sightings. However, 70% of purportedly extinct mammals are known from fewer than five sightings, and such models do not include some important indicators of the likelihood of extinction such as threats, biological traits, search effort, and demography. Previously, we developed a quantitative method that we based on species traits in which we used Cox proportional hazards regression to calculate the probability of rediscovery of species regarded as extinct. Here, we used two versions of the Cox regression model to determine the probability of extinction in purportedly extinct mammals and compared the results of these two models with those of stationary Poisson, nonparametric, and Weibull sighting-distribution models. For mammals with five or more sightings, the stationary Poisson model categorized all but two critically endangered (flagged as pos...
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Despite numerous concerns raised by government agencies, private landholders, and the general public on feral horse (Equus caballus) presence in the Australian ecosystems, there is lack of collective solutions on the management of this... more
Despite numerous concerns raised by government agencies, private landholders, and the general public on feral horse (Equus caballus) presence in the Australian ecosystems, there is lack of collective solutions on the management of this overabundant species. It has been proposed that successful management of feral horses in the Australian landscape can be achieved by firstly establishing the impacts of feral horses on the environment, economy or society, and secondly by commissioning a detailed scientific study into population distribution and dynamics (Dobbie & Berman 1993). These findings should be made available to the interest groups, and coupled with community involvement before the management action is implemented. The objective of this study was to characterize the most vital parameters of a feral horse population in order to propose a long-term management plan. The study was conducted over two years in 2011-2013 on a population of feral horses, which occupies a coniferous env...
Australia has experienced dramatic declines and extinctions of its native rodent species over the last 200 years, particularly in southern Australia. In the tropical savanna of northern Australia significant declines have occurred only in... more
Australia has experienced dramatic declines and extinctions of its native rodent species over the last 200 years, particularly in southern Australia. In the tropical savanna of northern Australia significant declines have occurred only in recent decades. The later onset of these declines suggests that the causes may differ from earlier declines in the south. We examine potential regional effects (northern versus southern Australia) on biological and ecological correlates of range decline in Australian rodents. We demonstrate that rodent declines have been greater in the south than in the tropical north, are strongly influenced by phylogeny, and are consistently greater for species inhabiting relatively open or sparsely vegetated habitat. Unlike in marsupials, where some species have much larger body size than rodents, body mass was not an important predictor of decline in rodents. All Australian rodent species are within the prey-size range of cats (throughout the continent) and red...
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Evolutionary increases in mammalian brain size relative to body size are energetically costly but are also thought to confer selective advantages by permitting the evolution of cognitively complex behaviors. However, many suggested... more
Evolutionary increases in mammalian brain size relative to body size are energetically costly but are also thought to confer selective advantages by permitting the evolution of cognitively complex behaviors. However, many suggested associations between brain size and specific behaviors - particularly related to social complexity - are possibly confounded by the reproductive diversity of placental mammals, whose brain size evolution is the most frequently studied. Based on a phylogenetic generalized least squares analysis of a data set on the reproductively homogenous clade of marsupials, we provide the first quantitative comparison of two hypotheses based on energetic constraints (maternal investment and seasonality) with two hypotheses that posit behavioral selection on relative brain size (social complexity and environmental interactions). We show that the two behavioral hypotheses have far less support than the constraint hypotheses. The only unambiguous associates of brain size ...
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Nutrient enrichment is increasingly affecting many tropical ecosystems, but there is no information on how this affects tree biodiversity. To examine dynamics in vegetation structure and tree species biomass and diversity, we annually... more
Nutrient enrichment is increasingly affecting many tropical ecosystems, but there is no information on how this affects tree biodiversity. To examine dynamics in vegetation structure and tree species biomass and diversity, we annually remeasured tree species before and for six years after repeated additions of nitrogen (N) and phosphorus (P) in permanent plots of abandoned pasture in Amazonia. Nitrogen and, to a lesser extent, phosphorus addition shifted growth among woody species. Nitrogen stimulated growth of two common pioneer tree species and one common tree species adaptable to both high- and lowlight environments, while P stimulated growth only of the dominant pioneer tree Rollinia exsucca (Annonaceae). Overall, N or P addition reduced tree assemblage evenness and delayed tree species accrual over time, likely due to competitive monopolization of other resources by the few tree species responding to nutrient enrichment with enhanced establishment and/or growth rates. Absolute ...
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We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs)... more
We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has several implications: 1. Understanding the structure of the linear model for GLS regression provides insight into when and why phylogeny is important in comparative studies. 2. The limitations of the PIC regression analysis are the same as the limitations of the GLS model. In particular, phylogenetic covariance applies only to the response variable in the regression and the explanatory variable should be regarded as fixed. Calculation of PICs for explanatory variables should be treated as a mathematical idiosyncrasy of the PIC regression algorithm. 3. Since the GLS estimator is the best linear unbiased estimator (BLUE), the slope parameter estimated using PICs is also BLUE. 4. If the slope is estimated using different branch lengths for the explanatory and response variables in the PIC algorithm, the estimator is no longer the BLUE, so this is not recommended. Finally, we discuss whether or not and how to accommodate phylogenetic covariance in regression analyses, particularly in relation to the problem of phylogenetic uncertainty. This discussion is from both frequentist and Bayesian perspectives.