A stochastic model of jaguar abundance in the Peruvian Amazon under climate variation scenarios

The jaguar (Panthera onca) is the dominant predator in Central and South America, but is now considered near-threatened. Estimating jaguar population size is difficult, due to uncertainty in the underlying dynamical processes as well as highly variable and sparse data. We develop a stochastic temporal model of jaguar abundance in the Peruvian Amazon, taking into account prey availability, under various climate change scenarios. The model is calibrated against existing data sets and an elicitation study in Pacaya Samiria. In order to account for uncertainty and variability, we construct a population of models over four key parameters, namely three scaling parameters for aquatic, small land, and large land animals and a hunting index. We then use this population of models to construct probabilistic evaluations of jaguar populations under various climate change scenarios characterized by increasingly severe flood and drought events and discuss the implications on jaguar numbers. Results imply that jaguar populations exhibit some robustness to extreme drought and flood, but that repeated exposure to these events over short periods can result in rapid decline. However, jaguar numbers could return to stability—albeit at lower numbers—if there are periods of benign climate patterns and other relevant factors are conducive

Searching for the best bet in life-strategy : a quantitative approach to individual performance and population dynamics in reef-building corals

Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe anew approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science

Searching for the best bet in life-strategy: A quantitative approach to individual performance and population dynamics in reef-building corals

© 2015 Elsevier B.V. Ecological signs of Earth's biosphere forewarn an alarming trajectory towards a global mass-extinction. Assessing species performance and susceptibilities to decline is essential to comprehend and reverse this trend. Yet it is challenging, given difficulties associated with quantifying individual and population processes that are variable across time, space, and life-stages. We describe a new approach to estimating and comparing species performances that combines empirical data, a novel theoretical consideration of population dynamics, and modern statistics. Our approach allows for a more realistic continuous representation of individual performances along development stages while taking into account non-linearity, and natural variability as captured by spatio-temporally replicated observations. We illustrate its application in a coral meta-assemblage composed of populations of the three major reef-building taxa Acropora, Pocillopora, Porites. Using a unique set of highly replicated observations of individual coral dynamics under various environmental conditions, we show how taxa differ in their investment in recruitment and size-specific aptitude for growth and survival, notably through different use of clonal shrinkage, fragmentation, fission, and fusion processes. Our results reveal contrasting life-history trade-offs among taxa which, along with differing patterns of density-dependent recruitment, modulate species responses to decline. These differences in coral life history traits reflect opposing life-strategies, imply regulation at differing life-stages, and explain divergence in species trajectories. Our findings indicate a high potential for resilience in Pocillopora and Porites populations, thanks respectively to a sustained recruitment that promotes demographic elasticity through replacement of individuals, and a steady resistance to mortality which confers persistence through lingering of individuals. Resilience in Acropora appears more arbitrary, given high susceptibility to perturbations and dependency of recruitment on presence of established local populations. We identify management actions that can complement Acropora's life history and benefit recovery of its populations following mortality events. Our regression-modelling approach to quantifying and comparing species performances in different population processes is applicable to all taxa, as illustrated even those with complex clonal life histories, and can be implemented at wide spatio-temporal and taxonomic coverage. It can promote more accurate representation of species dynamics in both descriptive and predictive modelling approaches. The semi-parametric contrast curve method we develop facilitates comparing response variables along continuous explicative metrics while accounting for multiple sources of complexity in empirical data. It should widely benefit investigations in ecology and quantitative science

Demographic structure of two populations of Porites lutea in Reunion Island indicates past and present disturbances: a modeling approach

PosterInternational audiencePoster about Demographic structure of two populations of Porites lutea in Reunion Island indicates past and present disturbances: a modeling approac

Thresholds of coral cover that support coral reef biodiversity

Global environmental change, such as ocean warming and increased cyclone activity, is driving widespread and rapid declines in the abundance of key ecosystem engineers, reef-building corals, on the Great Barrier Reef. Our ability to understand how coral associated species, such as reef fishes, respond to coral loss can be impeded by uncertainty surrounding natural spatio-temporal variability of coral populations. To address this issue, we developed a semi-parametric hierarchical Bayesian model to estimate long-term trajectories of habitat-forming coral cover as a function of three spatial scales (sub-region, habitat and site) and environmental disturbances. The relationships between coral cover trajectories and fish community structure were examined using posterior predictive distributions of estimated coral cover from the statistical model. In the absence of direct observations of fish community structure, we used the probability of coral cover being above some ecological threshold values as a proxy for potential disruptions of fish community structure. Threshold values were derived from published field studies that estimated changes in the structure of coral-reef fish communities and coral cover after major disturbances. In these studies, fish community structure did not change where post-disturbance coral cover was &amp;gt; 20%. Disruptions in the structure of these communities were observed when coral cover dropped to between 10–20% and declines in fish diversity were typical where coral cover ranged from between 5 and 10%. Based on these thresholds values, posterior probabilities of coral cover being above 20% and between 10 and 20% and between 5 and 10% were calculated across spatial scales on the Great Barrier Reef (GBR) from 1995 to 2011. At the GBR scale, probabilities of coral cover being above these thresholds remained relatively stable through time. Across years, probabilities of coral cover being at least &amp;gt; 20% remained null for the sub-regions of Cairns, Townsville, Whitsundays and Swain but highly variable between reef sites within these sub-regions, with the exception of Townsville. In the Townsville area, probabilities of coral cover being between 10–20% and 5–10% declined from 0.75 to 0 during the study period. This finding highlights potential sub-regional fish community structure disruptions which have not yet been observed at this spatial scale. As frequency and intensity of disturbance events continue to rise, and consequently, as coral cover declines further, the probabilistic Bayesian approach presented in this chapter could be used to help provide early warnings of major ecological shifts at management relevant scales in the absence of direct observations.</p

Being Bayesian in the 2020s: opportunities and challenges in the practice of modern applied Bayesian statistics

Building on a strong foundation of philosophy, theory, methods and computation over the past three decades, Bayesian approaches are now an integral part of the toolkit for most statisticians and data scientists. Whether they are dedicated Bayesians or opportunistic users, applied professionals can now reap many of the benefits afforded by the Bayesian paradigm. In this paper, we touch on six modern opportunities and challenges in applied Bayesian statistics: intelligent data collection, new data sources, federated analysis, inference for implicit models, model transfer and purposeful software products. This article is part of the theme issue 'Bayesian inference: challenges, perspectives, and prospects'.</p

Monitoring through many eyes: integrating disparate datasets to improve monitoring of the Great Barrier Reef

Numerous organisations collect data in the Great Barrier Reef (GBR), but they are rarely analysed together due to different program objectives, methods, and data quality. We developed a weighted spatio-temporal Bayesian model and used it to integrate image-based hard-coral data collected by professional and citizen scientists, who captured and/or classified underwater images. We used the model to predict coral cover across the GBR with estimates of uncertainty; thus filling gaps in space and time where no data exist. Additional data increased the model's predictive ability by 43%, but did not affect model inferences about pressures (e.g. bleaching and cyclone damage). Thus, effective integration of professional and high-volume citizen data could enhance the capacity and cost-efficiency of monitoring programs. This general approach is equally viable for other variables collected in the marine environment or other ecosystems; opening up new opportunities to integrate data and provide pathways for community engagement/stewardship.Erin E. Peterson, Edgar Santos-Fernández , Carla Chen, Sam Clifford, Julie Vercelloni, Alan Pearse, Ross Brown, Bryce Christensen, Allan James, Ken Anthony, Jennifer Loder, Manuel González-Rivero, Chris Roelfsema, M. Julian Caley, Camille Mellin, Tomasz Bednarz, Kerrie Mengerse