Bayesian Classification and Regression Trees for Predicting Incidence of Cryptosporidiosis

Background Classification and regression tree (CART) models are tree-based exploratory data analysis methods which have been shown to be very useful in identifying and estimating complex hierarchical relationships in ecological and medical contexts. In this paper, a Bayesian CART model is described and applied to the problem of modelling the cryptosporidiosis infection in Queensland, Australia. Methodology/Principal Findings We compared the results of a Bayesian CART model with those obtained using a Bayesian spatial conditional autoregressive (CAR) model. Overall, the analyses indicated that the nature and magnitude of the effect estimates were similar for the two methods in this study, but the CART model more easily accommodated higher order interaction effects. Conclusions/Significance A Bayesian CART model for identification and estimation of the spatial distribution of disease risk is useful in monitoring and assessment of infectious diseases prevention and control

On plexus representation of dissimilarities

Correspondence analysis has found widespread application in analysing vegetation gradients. However, it is not clear how it is robust to situations where structures other than a simple gradient exist. The introduction of instrumental variables in canonical correspondence analysis does not avoid these difficulties. In this paper I propose to examine some simple methods based on the notion of the plexus (sensu McIntosh) where graphs or networks are used to display some of the structure of the data so that an informed choice of models is possible. I showthat two different classes of plexus model are available. These classes are distinguished by the use in one case of a global Euclidean model to obtain well-separated pair decomposition (WSPD) of a set of points which implicitly involves all dissimilarities, while in the other a Riemannian view is taken and emphasis is placed locally, i.e., on small dissimilarities. I showan example of each of these classes applied to vegetation data

Mapping Oil and Gas Development Potential in the US Intermountain West and Estimating Impacts to Species

Many studies have quantified the indirect effect of hydrocarbon-based economies on climate change and biodiversity, concluding that a significant proportion of species will be threatened with extinction. However, few studies have measured the direct effect of new energy production infrastructure on species persistence. in the western US and translate the build-out scenarios into estimated impacts on sage-grouse. We project that future oil and gas development will cause a 7–19 percent decline from 2007 sage-grouse lek population counts and impact 3.7 million ha of sagebrush shrublands and 1.1 million ha of grasslands in the study area.Maps of where oil and gas development is anticipated in the US Intermountain West can be used by decision-makers intent on minimizing impacts to sage-grouse. This analysis also provides a general framework for using predictive models and build-out scenarios to anticipate impacts to species. These predictive models and build-out scenarios allow tradeoffs to be considered between species conservation and energy development prior to implementation

Disturbance and the Dynamics of Coral Cover on the Great Barrier Reef (1995–2009)

Coral reef ecosystems worldwide are under pressure from chronic and acute stressors that threaten their continued existence. Most obvious among changes to reefs is loss of hard coral cover, but a precise multi-scale estimate of coral cover dynamics for the Great Barrier Reef (GBR) is currently lacking. Monitoring data collected annually from fixed sites at 47 reefs across 1300 km of the GBR indicate that overall regional coral cover was stable (averaging 29% and ranging from 23% to 33% cover across years) with no net decline between 1995 and 2009. Subregional trends (10–100 km) in hard coral were diverse with some being very dynamic and others changing little. Coral cover increased in six subregions and decreased in seven subregions. Persistent decline of corals occurred in one subregion for hard coral and Acroporidae and in four subregions in non-Acroporidae families. Change in Acroporidae accounted for 68% of change in hard coral. Crown-of-thorns starfish (Acanthaster planci) outbreaks and storm damage were responsible for more coral loss during this period than either bleaching or disease despite two mass bleaching events and an increase in the incidence of coral disease. While the limited data for the GBR prior to the 1980's suggests that coral cover was higher than in our survey, we found no evidence of consistent, system-wide decline in coral cover since 1995. Instead, fluctuations in coral cover at subregional scales (10–100 km), driven mostly by changes in fast-growing Acroporidae, occurred as a result of localized disturbance events and subsequent recovery

Dissimilar responses of fungal and bacterial communities to soil transplantation simulating abrupt climate changes.

Both fungi and bacteria play essential roles in regulating soil carbon cycling. To predict future carbon stability, it is imperative to understand their responses to environmental changes, which is subject to large uncertainty. As current global warming is causing range shifts toward higher latitudes, we conducted three reciprocal soil transplantation experiments over large transects in 2005 to simulate abrupt climate changes. Six years after soil transplantation, fungal biomass of transplanted soils showed a general pattern of changes from donor sites to destination, which were more obvious in bare fallow soils than in maize cropped soils. Strikingly, fungal community compositions were clustered by sites, demonstrating that fungi of transplanted soils acclimatized to the destination environment. Several fungal taxa displayed sharp changes in relative abundance, including Podospora, Chaetomium, Mortierella and Phialemonium. In contrast, bacterial communities remained largely unchanged. Consistent with the important role of fungi in affecting soil carbon cycling, 8.1%-10.0% of fungal genes encoding carbon-decomposing enzymes were significantly (p < 0.01) increased as compared with those from bacteria (5.7%-8.4%). To explain these observations, we found that fungal occupancy across samples was mainly determined by annual average air temperature and rainfall, whereas bacterial occupancy was more closely related to soil conditions, which remained stable 6 years after soil transplantation. Together, these results demonstrate dissimilar response patterns and resource partitioning between fungi and bacteria, which may have considerable consequences for ecosystem-scale carbon cycling

Connectivity and systemic resilience of the Great Barrier Reef

Australia’s iconic Great Barrier Reef (GBR) continues to suffer from repeated impacts of cyclones, coral bleaching, and outbreaks of the coral-eating crown-of-thorns starfish (COTS), losing much of its coral cover in the process. This raises the question of the ecosystem’s systemic resilience and its ability to rebound after large-scale population loss. Here, we reveal that around 100 reefs of the GBR, or around 3%, have the ideal properties to facilitate recovery of disturbed areas, thereby imparting a level of systemic resilience and aiding its continued recovery. These reefs (1) are highly connected by ocean currents to the wider reef network, (2) have a relatively low risk of exposure to disturbances so that they are likely to provide replenishment when other reefs are depleted, and (3) have an ability to promote recovery of desirable species but are unlikely to either experience or spread COTS outbreaks. The great replenishment potential of these ‘robust source reefs’, which may supply 47% of the ecosystem in a single dispersal event, emerges from the interaction between oceanographic conditions and geographic location, a process that is likely to be repeated in other reef systems. Such natural resilience of reef systems will become increasingly important as the frequency of disturbances accelerates under climate change

Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest Pacific

Glaciation-induced environmental changes during the last glacial maximum (LGM) have strongly influenced species' distributions and genetic diversity patterns in the northern high latitudes. However, these effects have seldom been assessed on sessile species in the Northwest Pacific. Herein, we chose the brown alga Sargassum thunbergii to test this hypothesis, by comparing present population genetic variability with inferred geographical range shifts from the LGM to the present, estimated with species distribution modelling (SDM). Projections for contrasting scenarios of future climate change were also developed to anticipate genetic diversity losses at regional scales. Results showed that S. thunbergii harbours strikingly rich genetic diversity and multiple divergent lineages in the centre-northern range of its distribution, in contrast with a poorer genetically distinct lineage in the southern range. SDM hindcasted refugial persistence in the southern range during the LGM as well as post-LGM expansion of 18 degrees of latitude northward. Approximate Bayesian computation (ABC) analysis further suggested that the multiple divergent lineages in the centre-northern range limit stem from post-LGM colonization from the southern survived lineage. This suggests divergence due to demographic bottlenecks during range expansion and massive genetic diversity loss during post-LGM contraction in the south. The projected future range of S. thunbergii highlights the threat to unique gene pools that might be lost under global changes.UIDB/04326/2020 - PTDC/BIA-CBI/6515/2020 - DL57/2016/CP1361/CT0035info:eu-repo/semantics/publishedVersio

Predicting Coral Species Richness: The Effect of Input Variables, Diversity and Scale

Coral reefs are facing a biodiversity crisis due to increasing human impacts, consequently, one third of reef-building corals have an elevated risk of extinction. Logistic challenges prevent broad-scale species-level monitoring of hard corals; hence it has become critical that effective proxy indicators of species richness are established. This study tests how accurately three potential proxy indicators (generic richness on belt transects, generic richness on point-intercept transects and percent live hard coral cover on point-intercept transects) predict coral species richness at three different locations and two analytical scales. Generic richness (measured on a belt transect) was found to be the most effective predictor variable, with significant positive linear relationships across locations and scales. Percent live hard coral cover consistently performed poorly as anindicator of coral species richness. This study advances the practical framework for optimizing coral reef monitoring programs and empirically demonstrates that generic richness offers an effective way to predict coral species richness with a moderate level of precision. While the accuracy of species richness estimates will decrease in communities dominated byspecies-rich genera (e.g. Acropora), generic richness provides a useful measure of phylogenetic diversity and incorporating this metric into monitoring programs will increase the likelihood that changes in coral species diversity can be detected

Biogeographical Survey Identifies Consistent Alternative Physiological Optima and a Minor Role for Environmental Drivers in Maintaining a Polymorphism

The contribution of adaptive mechanisms in maintaining genetic polymorphisms is still debated in many systems. To understand the contribution of selective factors in maintaining polymorphism, we investigated large-scale (>1000 km) geographic variation in morph frequencies and fitness-related physiological traits in the damselfly Nehalennia irene. As fitness-related physiological traits, we investigated investment in immune function (phenoloxidase activity), energy storage and fecundity (abdomen protein and lipid content), and flight muscles (thorax protein content). In the first part of the study, our aim was to identify selective agents maintaining the large-scale spatial variation in morph frequencies. Morph frequencies varied considerably among populations, but, in contrast to expectation, in a geographically unstructured way. Furthermore, frequencies co-varied only weakly with the numerous investigated ecological parameters. This suggests that spatial frequency patterns are driven by stochastic processes, or alternatively, are consequence of highly variable and currently unidentified ecological conditions. In line with this, the investigated ecological parameters did not affect the fitness-related physiological traits differently in both morphs. In the second part of the study, we aimed at identifying trade-offs between fitness-related physiological traits that may contribute to the local maintenance of both colour morphs by defining alternative phenotypic optima, and test the spatial consistency of such trade-off patterns. The female morph with higher levels of phenoloxidase activity had a lower thorax protein content, and vice versa, suggesting a trade-off between investments in immune function and in flight muscles. This physiological trade-off was consistent across the geographical scale studied and supports widespread correlational selection, possibly driven by male harassment, favouring alternative trait combinations in both female morphs