Invertebrate traits for the biomonitoring of large European rivers: an assessment of specific types of human impact

1. The power of selected biological invertebrate traits for discriminating different types of human impact (heavy metal pollution and cargo‐ship traffic) were tested using ecological reasoning and linear Discriminant Function Analysis (DFA). 2. Frequency distributions of individual traits and categories of traits from 68 least impacted river reaches (LIRRs) and 304 impacted river reaches were used to define simple assessment rules based on ecological reasoning for specific impairments in large European rivers. In calibration, a maximum of three variables with a priori predictions and two different impairment threshold levels were used. Similarly, DFA was performed on the same variables included in the ecological reasoning approach, but also on all available traits or trait categories. 3. Validation with an independent data set (40 LIRRs, 291 variously impacted river reaches) and using the ecological reasoning approach showed that 75–78% of the reaches were correctly assign with rules on all impact types, 35–57% with rules on heavy metal pollution and 78–93% with rules on cargo‐ship traffic. By comparison, validation showed that DFA performed globally poorer than the ecological reasoning approach. In addition, the performance of the rules based on ecological reasoning remained stable, whereas DFA performance changed between calibration and validation. 4. Although not defined for this purpose, our study provided alarming evidence regarding the impact of cargo‐ship traffic on invertebrate communities in river reaches. Reaches with cargo‐ship traffic were found to have more genera with long life cycles that reproduce repeatedly by ovoviviparity and have a sessile life. 5. The performance of our trait‐based approach to correctly assign reaches to either least impacted or impacted conditions should promote further research on the topic across larger geographic areas (without regionalization) and across smaller stream types to provide a powerful biomonitoring tool that fulfils current European Union directives.     

Biological trait composition of European stream invertebrate communities: assessing the effects of various trait filter types

Understanding the action of filters on the biological trait composition of communities is constrained by the multitude of filter types (e.g. abiotic vs biotic, actual vs historical) that may cause changes of a multitude of traits (e.g. small vs large body size, short vs long life cycle) at a multitude of spatial scales (e.g. continent vs landscape vs local site). Using published data on the as natural as possible abundances and 11 biological traits (described through 63 categories) of 254 European stream invertebrate genera, we assessed how already available knowledge can serve to identify the importance of the action of different types of trait filters at two spatial scales. Therefore, we analysed observed and simulated abundance‐weighted trait compositions at the local scale of 384 running water sites (RWS) and at the landscape scale of 14 large biogeographical regions (LER). Actual abiotic filters acted significantly and independently of the taxonomic richness on the invertebrate traits at the RWS‐ and LER‐scale, whereas biotic filters had no significant effect. Evidence for the action of historical trait filters across Europe was only weak at both scales. Size, reproductive cycle, respiration and locomotion technique, feeding habits and vulnerability to disturbance responded to altitude and stream width of the RWS according to existing views about the effects of riparian, physiological, interstitial or disturbance controls of these traits. These controls acted independently on trait categories that did not co‐occur within the genera, because correlations of size categories with other trait categories were higher in the abundance‐weighted trait array (across communities) than in the original trait array (across genera). Overall, many of the 63 trait categories were scarcely affected by the trait filters considered in this study. Therefore, we briefly discuss potential effects of continental filters and of stream system‐specific, local physical filters, as the latter should produce similar trait patterns on a global scale. Our study suggests that analyses of the currently available knowledge can simplify the complicated hypothetical framework on trait filter actions, which sharpens the focus on future research needs.     

A potential role for overland dispersal in shaping aquatic invertebrate communities in arid regions

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Rethinking the conceptual foundations of habitat fragmentation research

The conceptual foundations of habitat fragmentation research have not kept pace with empirical advances in our understanding of species responses to landscape change, nor with theoretical advances in the wider disciplines of ecology. There is now real debate whether explicit recognition of ‘habitat fragmentation’ as an over‐arching conceptual domain will stimulate or hinder further progress toward understanding and mitigating the effects of landscape change. In this paper, we critically challenge the conceptual foundations of the discipline, and attempt to derive an integrated perspective on the best way to advance mechanistic understanding of fragmentation processes. We depict the inherent assumptions underlying the discipline as a ‘conceptual phase space’ of contrasting false dichotomies in fragmentation ‘problem space’. In our opinion, the key determinant of whether ‘habitat fragmentation’ can remain a cohesive framework lies in the concept of ‘interdependence’: 1) interdependence of landscape effects on species and 2) interdependence of species responses to landscape change. If there is non‐trivial interdependence among the various sub‐components of habitat fragmentation, or non‐trivial interdependence among species responses to landscape change, then there will be real heuristic value in ‘habitat fragmentation’ as a single conceptual domain. At present, the current paradigms entrenched in the fragmentation literature are implicitly founded on strict independence of landscape effects (e.g. the debate about the independent effects of habitat loss versus fragmentation per se) and strict independence of species responses (e.g. the individualistic species response models underpinning landscape continuum models), despite compelling evidence for interdependence in both effects and responses to fragmentation. We discuss how strong ‘interdependence’ of effects and responses challenges us to rethink long‐held views, and re‐cast the conceptual foundations of habitat fragmentation in terms of spatial context‐dependence in the effects of multiple interacting spatial components of fragmentation, and community context‐dependence in the responses of multiple interacting species to landscape change.     

MigClim: Predicting plant distribution and dispersal in a changing climate

Aim Many studies have forecasted the possible impact of climate change on plant distributions using models based on ecological niche theory, but most of them have ignored dispersal‐limitations, assuming dispersal to be either unlimited or null. Depending on the rate of climatic change, the landscape fragmentation and the dispersal capabilities of individual species, these assumptions are likely to prove inaccurate, leading to under‐ or overestimation of future species distributions and yielding large uncertainty between these two extremes. As a result, the concepts of ‘potentially suitable’ and ‘potentially colonizable’ habitat are expected to differ significantly. To quantify to what extent these two concepts can differ, we developed Mig Clim, a model simulating plant dispersal under climate change and landscape fragmentation scenarios. Mig Clim implements various parameters, such as dispersal distance, increase in reproductive potential over time, landscape fragmentation or long‐distance dispersal. Location Western Swiss Alps. Methods Using our Mig Clim model, several simulations were run for two virtual species by varying dispersal distance and other parameters. Each simulation covered the 100‐year period 2001–2100 and three different IPCC‐based temperature warming scenarios were considered. Results of dispersal‐limited projections were compared with unlimited and no‐dispersal projections. Results Our simulations indicate that: (1) using realistic parameter values, the future potential distributions generated using Mig Clim can differ significantly (up to more than 95% difference in colonized surface) from those that ignore dispersal; (2) this divergence increases under more extreme climate warming scenarios and over longer time periods; and (3) the uncertainty associated with the warming scenario can be as large as the one related to dispersal parameters. Main conclusions Accounting for dispersal, even roughly, can importantly reduce uncertainty in projections of species distribution under climate change scenarios.     

The importance of canopy complexity in shaping seasonal spider and beetle assemblages in saltmarsh habitats

1. Habitat structure, including vegetation structural complexity, largely determines invertebrate assemblages in semi‐natural grasslands. The importance of structural complexity to the saltmarsh invertebrate community, where the interplay between vegetation characteristics and tidal inundation is key, is less well known. 2. It was hypothesised that canopy complexity would be a more important predictor of spider and beetle assemblages than simple vegetation attributes (e.g. height, community type) and environmental variables (e.g. elevation) alone, measured in two saltmarsh regions, south‐east (Essex) and north‐west (Morecambe Bay) U.K. Canopy complexity (number of non‐vegetated ‘gaps’ in canopy ≥ 1 mm wide) was assessed using side‐on photography. Over 1500 spiders and beetles were sampled via suction sampling, winter and summer combined. 3. In summer, saltmarshes with abundant spider and beetle populations were characterised by high scores for canopy complexity often associated with tussocky grass or shrub cover. Simple vegetation attributes (plant cover, height) accounted for 26% of variation in spider abundance and 14% in spider diversity, rising to 46% and 41%, respectively, with the addition of canopy complexity score. Overwintering spider assemblages were associated with elevation and vegetation biomass. Summer beetle abundance, in particular the predatory and zoophagous group, and diversity were best explained by elevation and plant species richness. 4. Summer canopy complexity was identified as a positive habitat feature for saltmarsh spider communities (ground‐running hunters and sheet weavers) with significant ‘added value’ over more commonly measured attributes of vegetation structure.     

Partitioning the diversity of riverine fish: the roles of habitat types and non-native species

1. Quantifying how biological diversity is distributed in the landscape is one of the central themes of conservation ecology. For this purpose, landscape classifications are being intensively used in conservation planning and biodiversity management, although there is still little information about their efficacy. 2. I used data from 158 running water sites in Hungary to examine the contribution of six a priori established habitat types to regional level diversity of fish assemblages. Three community measures [species richness, diversity (Shannon, Simpson indices), assemblage composition] were examined at two assemblage levels (entire assemblage, the native assemblage). The relative role of non‐native species was quantified to examine their contribution to patterns in diversity in this strongly human influenced landscape. 3. Additive diversity partitioning revealed the primary importance of beta diversity (i.e. among‐site factors) to patterns in species richness. Landscape‐scale patterns in species richness were best explained by between‐habitat type (beta₂: 41.2%), followed by within‐habitat type (beta₁: 37.7%) and finally within‐site (alpha: 21.1%) diversity. Diversity indices showed patterns different from species richness, indicating the importance of relative abundance distributions on the results. Exclusion of non‐natives from the analysis gave similar results to the entire‐assemblage level analysis. 4. Canonical analysis of principal coordinates, complemented with indicator species analysis justified the separation of fish assemblages among the habitat types, although classification error was high. Multivariate dispersion, a measure of compositional beta diversity, showed significant differences among the habitat types. Contrary to species diversity (i.e. richness, diversity indices), patterns in compositional diversity were strongly influenced by the exclusion of non‐natives from the analyses. 5. This study is the first to quantify how running water habitat types contribute to fish diversity at the landscape scale and how non‐native species influence this pattern. These results on riverine fish assemblages support the hypothesis that environmental variability (i.e. the diversity of habitat types) is an indication of biodiversity and can be used in large‐scale conservation designs. The study emphasises the joint application of additive diversity partitioning and multivariate statistics when exploring the contribution of landscape components to the overall biodiversity of the landscape mosaic.     

A species‐centered approach for uncovering generalities in organism responses to habitat loss and fragmentation

Theoretical models predict strong influences of habitat loss and fragmentation on species distributions and demography, but empirical studies have shown relatively inconsistent support across species and systems. We argue that species’ responses to landscape‐scale habitat loss and fragmentation are likely to appear less idiosyncratic if it is recognized that species perceive the same landscapes in different ways. We present a new quantitative approach that uses species distribution models (SDMs) to measure landscapes (e.g. patch size, isolation, matrix amount) from the perspective of individual species. First, we briefly summarize the few efforts to date demonstrating that once differences in habitat distributions are controlled, consistencies in species’ responses to landscape structure emerge. Second, we present a detailed example providing step‐by‐step methods for application of a species‐centered approach using freely available land‐cover data and recent statistical modeling approaches. Third, we discuss pitfalls in current applications of the approach and recommend avenues for future developments. We conclude that the species‐centered approach offers considerable promise as a means to test whether sensitivity to habitat loss and fragmentation is mediated by phylogenetic, ecological, and life‐history traits. Cross‐species generalities in responses to habitat loss and fragmentation will be challenging to uncover unless landscape mosaics are defined using models that reflect differing species‐specific distributions, functional connectivity, and domains of scale. The emergence of such generalities would not only enhance scientific understanding of biotic processes driving fragmentation effects, but would allow managers to estimate species sensitivities in new regions.     

Mating timing,dispersal and local adaptation in patchy environments

Dispersal is a life‐history trait that can evolve under various known selective pressures as identified by a multitude of theoretical and empirical studies. Yet only few of them are considering the succession of mating and dispersal. The sequence of these events influences gene flow and consequently affects the dynamics and evolution of populations. We use individual‐based simulations to investigate the evolution of the timing of dispersal and mating, i.e. mating before or after dispersal. We assume a discrete insect metapopulation in a heterogeneous environment, where populations may adapt to local conditions and only females are allowed to disperse. We run the model assuming different levels of species habitat tolerance, carrying capacity, and temporal environmental variability. Our results show that in species with narrow habitat tolerance, low to moderate dispersal evolves in combination with mating after dispersal (post‐dispersal mating). With such a strategy dispersing females benefit from mating with a resident male, as their offspring will be better adapted to the local habitat conditions. On the contrary, in species with wide habitat tolerance higher dispersal rates in combination with pre‐dispersal mating evolves. In this case individuals are adapted to the ‘average’ habitat where pre‐dispersal mating conveys the benefit of carrying relatives’ genes into a new population. With high dispersal rates and large population size, local adaptation and kin structure both vanish and the temporal sequence of dispersal and mating may become a (nearly) neutral trait.     

Projected gains and losses of wildlife habitat from bioenergy‐induced landscape change

Domestic and foreign renewable energy targets and financial incentives have increased demand for woody biomass and bioenergy in the southeastern United States. This demand is expected to be met through purpose‐grown agricultural bioenergy crops, short‐rotation tree plantations, thinning and harvest of planted and natural forests, and forest harvest residues. With results from a forest economics model, spatially explicit state‐and‐transition simulation models, and species–habitat models, we projected change in habitat amount for 16 wildlife species caused by meeting a renewable fuel target and expected demand for wood pellets in North Carolina, USA. We projected changes over 40 years under a baseline ‘business‐as‐usual’ scenario without bioenergy production and five scenarios with unique feedstock portfolios. Bioenergy demand had potential to influence trends in habitat availability for some species in our study area. We found variation in impacts among species, and no scenario was the ‘best’ or ‘worst’ across all species. Our models projected that shrub‐associated species would gain habitat under some scenarios because of increases in the amount of regenerating forests on the landscape, while species restricted to mature forests would lose habitat. Some forest species could also lose habitat from the conversion of forests on marginal soils to purpose‐grown feedstocks. The conversion of agricultural lands on marginal soils to purpose‐grown feedstocks increased habitat losses for one species with strong associations with pasture, which is being lost to urbanization in our study region. Our results indicate that landscape‐scale impacts on wildlife habitat will vary among species and depend upon the bioenergy feedstock portfolio. Therefore, decisions about bioenergy and wildlife will likely involve trade‐offs among wildlife species, and the choice of focal species is likely to affect the results of landscape‐scale assessments. We offer general principals to consider when crafting lists of focal species for bioenergy impact assessments at the landscape scale.     

An empirical evaluation of the African elephant as a focal species for connectivity planning in East Africa

Aim Large, charismatic and wide‐ranging animals are often employed as focal species for prioritizing landscape linkages in threatened ecosystems (i.e. ‘connectivity conservation’), but there have been few efforts to assess empirically whether focal species co‐occur with other species of conservation interest within potential linkages. We evaluated whether the African elephant (Loxodonta africana), a world‐recognized flagship species, would serve as an appropriate focal species for other large mammals in a potential linkage between two major protected area complexes. Location A 15,400 km² area between the Ruaha and Selous ecosystems in central Tanzania, East Africa. Methods We used walking transects to assess habitat, human activity and co‐occurrence of elephants and 48 other large mammal species (> 1 kg) at 63 sites using animal sign and direct sightings. We repeated a subset of transects to estimate species detectability using occupancy modelling. We used logistic regression and AIC model selection to characterize patterns of elephant occurrence and assessed correlation of elephant presence with richness of large mammals and subgroups. We considered other possible focal species, compared habitat‐based linear regression models of large mammal richness and used circuit theory to examine potential connectivity spatially. Results Elephants were detected in many locations across the potential linkage. Elephant presence was highly positively correlated with the richness of large mammals, as well as ungulates, carnivores, large carnivores and species > 45 kg in body mass (‘megafauna’). Outside of protected areas, both mammal richness and elephant presence were negatively correlated with human population density and distance from water. Only one other potential focal species was more strongly correlated with species richness than elephants, but detectability was highest for elephants. Main conclusions Although African elephants have dispersal abilities that exceed most other terrestrial mammals, conserving elephant movement corridors may effectively preserve habitat and potential landscape linkages for other large mammal species among Tanzanian reserves.     

Limiting similarity and functional diversity along environmental gradients

Recent developments in community models emphasize the importance of incorporating stochastic processes (e.g. ecological drift) in models of niche‐structured community assembly. We constructed a finite, spatially explicit, lottery model to simulate the distribution of species in a one‐dimensional landscape with an underlying gradient in environmental conditions. Our framework combines the potential for ecological drift with environmentally‐mediated competition for space in a heterogeneous environment. We examined the influence of niche breadth, dispersal distances, community size (total number of individuals) and the breadth of the environmental gradient on levels of species and functional trait diversity (i.e. differences in niche optima). Three novel results emerge from this model: (1) niche differences between adjacent species (e.g. limiting similarity) increase in smaller communities, because of the interaction of competitive effects and finite population sizes; (2) immigration from a regional species pool, stochasticity and niche‐assembly generate a bimodal distribution of species residence times (‘transient’ and ‘resident’) under a heterogeneous environment; and (3) the magnitude of environmental heterogeneity has a U‐shaped effect on diversity, because of shifts in species richness of resident vs. transient species. These predictions illustrate the potential importance of stochastic (although not necessarily neutral) processes in community assembly.     

Forest and Landscape Structure as Predictors of Capercaillie Occurrence

ABSTRACT Capercaillie (Tetrao urogallus) is a large, endangered forest grouse species with narrow habitat preferences and large spatial requirements that make it susceptible to habitat changes at different spatial scales. Our aim was to evaluate the relative power of variables relating to forest versus landscape structure in predicting capercaillie occurrence at different spatial scales. We investigated capercaillie-habitat relationships at the scales of forest stand and forest-stand mosaic in 2 Swiss regions. We assessed forest structure from aerial photographs in 52 study plots each 5 km². We classified plots into one of 3 categories denoting the observed local population trend (stable, declining, extinct), and we compared forest structure between categories. At the stand scale, we used presence-absence data for grid cells within the plots to build predictive habitat models based on logistic regression. At this scale, habitat models that included only variables relating to forest structure explained the occurrence of capercaillie only in part, whereas variables selected by the models differed between regions. Including variables relating to landscape features improved the models significantly. At the scale of stand mosaic, variables describing forest structure (e.g., mean canopy cover, proportion of open forest, and proportion of multistoried forest) differed between plot categories. We conclude that small-scale forest structure has limited power to predict capercaillie occurrence at the stand scale, but that it explains well at the scale of the stand mosaic. Including variables for landscape structure improves predictions at the forest-stand scale. Habitat models built with data from one region cannot be expected to predict the species occurrence in other regions well. Thus, multiscale approaches are necessary to better understand species-habitat relationships. Our results can help regional authorities and forest-management planners to identify areas where suitable habitat for capercaillie is not available in the required proportion and, thus, where management actions are needed to improve habitat suitability.     

Climate and land use changes will degrade the configuration of the landscape for titi monkeys in eastern Brazil

Land use changes have profound effects on populations of Neotropical primates, and ongoing climate change is expected to aggravate this scenario. The titi monkeys from eastern Brazil (Callicebus personatus group) have been particularly affected by this process, with four of the five species now allocated to threatened conservation status categories. Here, we estimate the changes in the distribution of these titi monkeys caused by changes in both climate and land use. We also use demographic‐based, functional landscape metrics to assess the magnitude of the change in landscape conditions for the distribution predicted for each species. We built species distribution models (SDMs) based on maximum entropy for current and future conditions (2070), allowing for different global circulation models and contrasting scenarios of glasshouse gas concentrations. We refined the SDMs using a high‐resolution map of habitat remnants. We then calculated habitat availability and connectivity based on home‐range size and the dispersal limitations of the individual, in the context of a predicted loss of 10% of forest cover in the future. The landscape configuration is predicted to be degraded for all species, regardless of the climatic settings. This include reductions in the total cover of forest remnants, patch size and functional connectivity. As the landscape configuration should deteriorate severely in the future for all species, the prevention of further loss of populations will only be achieved through habitat restoration and reconnection to counteract the negative effects for these and several other co‐occurring species.     

A unified framework for diversity gradients: the adaptive trait continuum

Aim Adaptive trait continua are axes of covariation observed in multivariate trait data for a given taxonomic group. These continua quantify and summarize life‐history variation at the inter‐specific level in multi‐specific assemblages. Here we examine whether trait continua can provide a useful framework to link life‐history variation with demographic and evolutionary processes in species richness gradients. Taking an altitudinal species richness gradient for Mediterranean butterflies as a study case, we examined a suite of traits (larval diet breadth, adult phenology, dispersal capacity and wing length) and species‐specific habitat measures (temperature and aridity breadth). We tested whether traits and species‐specific habitat measures tend to co‐vary, whether they are phylogenetically conserved, and whether they are able to explain species distributions and spatial genetic variation in a large number of butterfly assemblages. Location Catalonia, Spain. Methods We formulated predictions associated with species richness gradients and adaptive trait continua. We applied principal components analyses (PCAs), structural equation modelling and phylogenetic generalized least squares models. Results We found that traits and species‐specific habitat measures covaried along a main PCA axis, ranging from multivoltine trophic generalists with high dispersal capacity to univoltine (i.e. one generation per year), trophic specialist species with low dispersal capacity. This trait continuum was closely associated with the observed distributions along the altitudinal gradient and predicted inter‐specific differences in patterns of spatial genetic variability (F_ST and genetic distances), population responses to the impacts of global change and local turnover dynamics. Main conclusions The adaptive trait continuum of Mediterranean butterflies provides an integrative and mechanistic framework to: (1) analyse geographical gradients in species richness, (2) explain inter‐specific differences in population abundances, spatial distributions and demographic trends, (3) explain inter‐specific differences in patterns of genetic variation (F_ST and genetic distances), and (4) study specialist–generalist life‐history transitions frequently involved in butterfly diversification processes.     

Synergistic impacts of sediment contamination and dam presence on river functioning

1. Dam presence is commonly associated with strong accumulation of polluted sediments. In spite of this context of multiple stressors, physical effects are often solely considered in the ecological assessment of the dam impacts. 2. We studied four ‘reservoir/downstream reach’ systems differing in levels of sediment contamination in reservoirs. Using assemblages and biotrait (i.e. ecological or biological attribute) responses of macroinvertebrate communities and leaf litter breakdown, we examined the individual effects and potential interactions between sediment contamination and dam presence along the gradient of ecotoxic pressure. 3. Leaf breakdown rates ranged from 0.0044° per day in the most contaminated reservoir to 0.0120° per day in the reference reservoir. Comparisons of community trait profiles among reservoirs highlighted a gradient of trait responses to sediment contamination. 4. In the absence of toxic contamination, the dam‐induced modifications in biotraits of invertebrate assemblages were not related to a reduction of leaf litter breakdown. Conversely, contaminated sediment in reservoir induced strong functional disturbances (i.e. bioecological shifts and reduction of leaf litter breakdown) downstream of dams. 5. Key biotrait categories positively related to leaf litter breakdown rate have been identified. They corresponded mainly to shredders and/or small‐sized (<0.5 cm) insects, using aquatic (e.g. crawlers) or aerial (e.g. fliers) active dispersal strategies. In addition, trait categories positively correlated to contamination level have been considered as ‘response’ traits. They corresponded to large‐sized (>4 cm) species, having several generations per year (polyvoltin), using asexual reproduction and/or disseminating by drift (aquatic, passive). 6. In the current context of ecological continuity restoration, this study has identified the risks associated with the presence of historical contamination in the run‐of‐river reservoirs for downstream ecosystem health.     

Habitat filtering and adult dispersal determine the taxonomic composition of stream insects in an urbanizing landscape

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Stream communities across a rural–urban landscape gradient

Rapid urbanization throughout the world is expected to cause extensive loss of biodiversity in the upcoming decades. Disturbances associated with urbanization frequently operate over multiple spatial scales such that local species extirpations have been attributed both to localized habitat degradation and to regional changes in land use. Urbanization also may shape stream communities by restricting species dispersal within and among stream reaches. In this patch-dynamics view, anthropogenic disturbances and isolation jointly reduce stream biodiversity in urbanizing landscapes. We evaluated predictions of stream invertebrate community composition and abundance based on variation in environmental conditions at five distinct spatial scales: stream habitats, reaches, riparian corridors and watersheds and their spatial location within the larger three-river basin. Despite strong associations between biodiversity loss and human density in this study, local stream habitat and stream reach conditions were poor predictors of community patterns. Instead, local community diversity and abundance were more accurately predicted by riparian vegetation and watershed landscape structure. Spatial coordinates associated with instream distances provided better predictions of stream communities than any of the environmental data sets. Together, results suggest that urbanization in the study region was associated with reduced stream invertebrate diversity through the alteration of landscape vegetation structure and patch connectivity. These findings suggest that maintaining and restoring watershed vegetation corridors in urban landscapes will aid efforts to conserve freshwater biodiversity.     

Properties of cell death models calibrated and compared using Bayesian approaches

Using models to simulate and analyze biological networks requires principled approaches to parameter estimation and model discrimination. We use Bayesian and Monte Carlo methods to recover the full probability distributions of free parameters (initial protein concentrations and rate constants) for mass‐action models of receptor‐mediated cell death. The width of the individual parameter distributions is largely determined by non‐identifiability but covariation among parameters, even those that are poorly determined, encodes essential information. Knowledge of joint parameter distributions makes it possible to compute the uncertainty of model‐based predictions whereas ignoring it (e.g., by treating parameters as a simple list of values and variances) yields nonsensical predictions. Computing the Bayes factor from joint distributions yields the odds ratio (～20‐fold) for competing ‘direct’ and ‘indirect’ apoptosis models having different numbers of parameters. Our results illustrate how Bayesian approaches to model calibration and discrimination combined with single‐cell data represent a generally useful and rigorous approach to discriminate between competing hypotheses in the face of parametric and topological uncertainty.