The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy

Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data‐derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.     

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus, R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.     

高光谱技术——生态学领域研究的新方法

高光谱技术是一种新的地物探测技术,该技术以其敏锐的地物光谱特征探测能力为精准识别地物属性提供了强有力的手段,在生态系统过程与属性研究中具有广阔的应用前景。该文以可见光-近红外光谱分析技术为例概述了高光谱技术的原理、特点与优势,以及高光谱技术分析的流程;总结并归纳了其在土壤、植物生理、农产品品质检测、凋落物分解方面的研究应用,指出高光谱技术与遥感成像技术结合在生态监测研究中的优势;归纳了高光谱技术应用中面临的问题,并希望高光谱技术在生态学领域研究中得到更广泛的应用。     

Effects of residual hydrocarbons on the reed community after 10 years of oil extraction and the effectiveness of different biological indicators for the long-term risk assessments

The selection of certain indicators is critical to undertake ecological risk assessments of long-term oil pollution and other environmental changes. The indicators should be easily and routinely monitored, be sensitive to pollution, respond to pollution in a predictable manner, and match the spatial and temporal scales of investigations. To compare the effectiveness of indicators for the long-term risk assessments, this study investigated the multiple ecological effects of chronic oil pollution on the plant community dominated by reed (Phragmites australis). The physiology, growth and reproduction of reed, together with the composition and productivity of the reed community, were measured around oil wells that have operated for approximately 10 years in the Yellow River Delta, eastern China. The predictive power of each indicator was evaluated using the coefficients of determination (R²) of linear regression models established for each indicator and soil Total Petroleum Hydrocarbons (TPH) concentration. The sensitivities of indicators were evaluated by comparing slopes of new established regression lines using standardized data. The top three indicators in terms of predictive power were leaf length, width and number, followed by the Shannon–Wiener index, Pielou evenness index and Simpson's diversity index. Community aboveground biomass, foliar projective coverage and species richness showed predictive power lower than those of the three diversity indexes, but higher than those of leaf net photosynthetic rate, reed height, aboveground biomass and vertical projective coverage of reed plants. Leaf transpiration, chlorophyll concentration and reed stem density showed no significant linear response to elevated soil TPH concentration. In terms of sensitivity, the top three biological indicators were Pielou evenness index, Simpson's diversity index and Shannon–Wiener index, followed by community vertical projective coverage, community aboveground biomass, and species richness. Leaf number, length and width were moderately sensitive, followed by reed coverage, aboveground biomass and height. The sensitivity of net photosynthetic rate was the lowest. The predictive power and sensitivities of indicators were compared in terms of their spatial and temporal scales. In conclusion, scale can be used to facilitate the selection of indicators, and the combination of different indicators may yield improved understanding of the various effects of elevated soil TPH concentration at the different biological levels.     

Ecological indicators of fruit and vegetable consumption (EIFVCs): A case study

Food and drink consumption was found to be responsible for around 20–30% of environmental impacts. Environmental impacts occur during all stages of the food production chain. However, households influence these impacts with through their choice of diet and habits, thus directly affecting the environment through food-related energy consumption and waste generation. With the multiplication of local policies for sustainable consumption, it has become increasingly useful to gather information on the evolution of the ecological impacts associated with household food consumption. Dealing with the indicators of household consumption of fruits and vegetables will enable changes in the population's lifestyles and the effectiveness of local policies to be monitored.The aims of this article are twofold: to provide a conceptual framework on the purposes of ecological indicators of fruit and vegetable consumption (EIFVCs) and to provide a methodological approach for selecting and measuring the most relevant EIFVCs at a local scale. Considering the great diversity of ecological impacts, the large number of potential EIFVCs must be reduced to obtain fewer EIFVCs, but that are relevant at local scale. To be relevant, the EIFVCs must provide information on the three phases of consumption (acquisition, use, and disposal) and on the upstream and downstream phases of the consumption process; they should evaluate the more problematic ecological impacts at the local scale (level of concern); and they have to only point out the ecological impacts that households can significantly reduce through their consumption rates. To measure relevant EIFVCs, three approaches must be combined: monitoring the ecological impacts, measuring the material and energy fluxes associated with household consumption, and analysing the consumer behaviours that result in the observed ecological impacts.As an illustration, the methodology is applied to the Bordeaux Metropolitan Area (France). In this area, eleven EIFVCs seem relevant. The use of surveys characterises all eleven of the EIFVCs, despite the difficulty of establishing quantified relationships between household behaviours and measured ecological impacts. The measuring of fluxes is possible for eight of them, whereas the monitoring of ecological impacts is only feasible for two of them.     

A null model test of Floristic Quality Assessment: Are plant species’ Coefficients of Conservatism valid?

Floristic Quality Assessment (FQA) was developed as a tool for quantifying the conservation value of natural areas based on their plant species composition and richness. Floristic Quality Assessment is based on Coefficients of Conservatism (C values) assigned to each plant species in a region or state. Each species i, is assigned a value C_i, on a scale of 0–10 by expert botanists, based on its fidelity to undegraded natural areas. A criticism of Floristic Quality Assessment is the subjective nature of these C values. Our objective was to determine if C values of individual species are indicative of the C values of species with which they co-occur. If subjectively assigned species’ C values carry meaningful information about plant assemblages and the conservation value of particular habitats, then individual species should tend to co-occur with species of similar C. We tested this hypothesis using occurrences of 1014 species in 388 forests and wetlands across Illinois, USA. Using a null model approach, we found that species co-occurred with species of similar C far more often than would be expected by chance; affirming the predictive ability of subjectively assigned C values. Furthermore, we quantified the extent to which each species was under- or overvalued relative to its co-occurring species assemblages to assess if any species C values were mis-assigned. Woody plants and perennial herbs, as groups, were undervalued as ecological indicators, i.e. their C values were too low. Several non-native species, which, by convention, are assigned a C of zero, were over- or under-valued relative to native species with a C of zero. Based on species occurrences across hundreds of sites, our results indicated that, despite their subjective basis, C values carry considerable ecological information, such that a given species can be used to predict the C values of its co-occurring assemblage. However, some species C values appeared less accurate than others. Our methodological approach could be applied in other states or regions to validate and refine C value assignments.     

Structural–functional approach to identify post-disturbance recovery indicators in forests from northwestern Patagonia: A tool to prevent state transitions

The disruption of the natural post-disturbance recovery process, either by changes in disturbance regime or by another disturbance, can trigger transitions to alternative degraded states. In a scenario of high disturbance pressure on ecological systems, it is essential to detect recovery indicators to define the period when the system needs more protection as well as the period when the system supports certain use pressure without affecting its resilience. Recovery indicators can be identified by non-linear changes in structural and functional variables. Fire largely modulates the dynamic and stability of plant communities worldwide, and is this the case in northwestern (NW) Patagonia. The ultimate goal of this study is to propose a structural–functional approach based on a reference system (i.e. chronosequence) as a tool to detect post-disturbance recovery indicators in forests from NW Patagonia. In NW Patagonia (40–42°S), we sampled 25 Austrocedrus chilensis and Nothofagus spp. communities differing in post-fire age (0.3–180 years). In each community we recorded structural (woody species cover and height, solar radiation, air temperature, relative humidity) and functional (annual recruitment of woody and tree species) attributes. We modeled these attributes in function of post-fire age and analized the relationship between a functional attribute and a Structural Recovery Index (SRI). Communities varying in time-since-last-fire were structurally and functionally different. Moreover, response variables showed non-linear changes along the chronosequence, allowing the selection of recovery indicators. We suggest to use vegetation variables instead of environmental variables as structural recovery indicators. Horizontal and Vertical Vegetation Heterogeneity indices provided the information necessary to describe vegetation spatial reorganization after fire. Tree species annual recruitment was a good indicator of the functional recovery of forest communities. The relationship between a functional attribute and SRI allowed us to detect phases with high- and low-risk of degradation during post-fire succession. High-risk phases (<36 years old) had the highest horizontal vegetation heterogeneity and scarce tree seedling density (<7000 seedlings ha⁻¹ year⁻¹). Whereas, low-risk phases (>36 years old) had the highest vertical vegetation heterogeneity and tree species seedling density (>10,000 seedlings ha⁻¹ year⁻¹). Due to the low structural–functional levels, communities at high-risk phases would be more vulnerable to antropic pressure (e.g. livestock raising, logging) than communities at low-risk phases. The proposed approach contributes to the sustainable management of forest communities because it allows to estimate the minimum structural–functional levels from which forest communities could be harvested.     

Impact of the terrestrial-aquatic transition on disparity and rates of evolution in the carnivoran skull

Background

Which factors influence the distribution patterns of morphological diversity among clades? The adaptive radiation model predicts that a clade entering new ecological niche will experience high rates of evolution early in its history, followed by a gradual slowing. Here we measure disparity and rates of evolution in Carnivora, specifically focusing on the terrestrial-aquatic transition in Pinnipedia. We analyze fissiped (mostly terrestrial, arboreal, and semi-arboreal, but also including the semi-aquatic otter) and pinniped (secondarily aquatic) carnivorans as a case study of an extreme ecological transition. We used 3D geometric morphometrics to quantify cranial shape in 151 carnivoran specimens (64 fissiped, 87 pinniped) and five exceptionally-preserved fossil pinnipeds, including the stem-pinniped Enaliarctos emlongi. Range-based and variance-based disparity measures were compared between pinnipeds and fissipeds. To distinguish between evolutionary modes, a Brownian motion model was compared to selective regime shifts associated with the terrestrial-aquatic transition and at the base of Pinnipedia. Further, evolutionary patterns were estimated on individual branches using both Ornstein-Uhlenbeck and Independent Evolution models, to examine the origin of pinniped diversity.

Results

Pinnipeds exhibit greater cranial disparity than fissipeds, even though they are less taxonomically diverse and, as a clade nested within fissipeds, phylogenetically younger. Despite this, there is no increase in the rate of morphological evolution at the base of Pinnipedia, as would be predicted by an adaptive radiation model, and a Brownian motion model of evolution is supported. Instead basal pinnipeds populated new areas of morphospace via low to moderate rates of evolution in new directions, followed by later bursts within the crown-group, potentially associated with ecological diversification within the marine realm.

Conclusion

The transition to an aquatic habitat in carnivorans resulted in a shift in cranial morphology without an increase in rate in the stem lineage, contra to the adaptive radiation model. Instead these data suggest a release from evolutionary constraint model, followed by aquatic diversifications within crown families.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0285-5) contains supplementary material, which is available to authorized users.