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Understanding how both the mean (location) and variance (scale) of traits differ among species and lineages is fundamental to unveiling macroevolutionary patterns. Yet, traditional phylogenetic comparative methods primarily focus on modelling mean trait values, often overlooking variability and heteroscedasticity that can provide critical insights into evolutionary dynamics. Here, we introduce phylogenetic location–scale models (PLSMs), a novel framework that jointly analyses the evolution of trait means and variances. This dual approach captures heteroscedasticity and evolutionary changes in trait variability, allowing for the detection of clades with differing variances and revealing patterns of adaptation, diversification, and evolutionary constraints. Extending PLSMs to a multivariate context enables simultaneous analysis of multiple traits and their covariances, facilitating the testing of hypotheses about evolutionary trade‐offs, pleiotropy and phenotypic integration. By modelling covariances between phylogenetic effects in both the location and scale parts, we can discern whether changes in one trait's mean or variance are associated with changes in another's, thereby offering deeper insights into the mechanisms driving trait co‐evolution and co‐divergence or ‘contra‐divergence’. We also describe how an extended version of PLSMs incorporating within‐species variability can enhance our understanding of trait convergence and divergence arising from ecological and environmental factors. Our framework provides a powerful tool for exploring macroevolutionary patterns and can be used to reassess previously published comparative data, offering new insights into the mechanisms driving the diversity of life.

Persistent soil seed banks are characteristic of Arctostaphylos (Ericaceae) species in the Mediterranean‐climate California Floristic Province. While most species are obligate seeders, regeneration of stands of all Arctostaphylos species ultimately depends on post‐fire seedling recruitment. Arctostaphylos seed banks are created, in large part, by scatter‐hoarding rodents. Variation in fruit morphology, therefore, is expected to impact the Arctostaphylos–rodent interaction. Seeds produce sufficient rewards (nutritious mature embryo) to entice rodents to disperse and ultimately bury seeds in the soil. Hard seed coats increase the time required to extract the embryo, encouraging rodents to choose storage over immediate predation, and nutlets are frequently empty. We assessed the variation of fruit nutlet fusion and seed viability among 38 Arctostaphylos taxa. Factors such as latitude, elevation, life history, ploidy, and phylogenetic position were also analyzed. Generalized mixed‐effects models were used to determine the factors contributing to variation in fruit nutlet fusion and seed viability. Our results indicate that fruit volume and shape are the most important variables affecting nutlet fusion and seed viability. Additionally, other potential influences only show a weak correlation and are not predicted to significantly impact nutlet fusion or seed viability. These findings provide insights into evolved strategies used by plants to increase reproductive success via scatter‐hoarding rodents. Our study benefits the conservation and restoration of Arctostaphylos stands by emphasizing the importance of animal‐mediated dispersal and providing estimates of seed viability for different species. With the anticipated effects of climate change, such as departures from historic fire regimes, the preservation of the relationship between plants and animal foragers is crucial for the continued survival of Arctostaphylos and California's evergreen chaparral. We assessed the variation of fruit nutlet fusion and seed viability among 38 Arctostaphylos taxa. Our results indicate that fruit volume and shape are the most important variables affecting nutlet fusion and seed viability. These findings provide insight into evolved strategies used by plants to increase reproductive success via scatter‐hoarding rodents.

Mammalian generalist mesopredators can reach high densities in forest–farmland mosaic landscapes in the absence of top‐down control. The abundance of generalist mesopredators is a potentially limiting factor for prey populations, especially ground breeding birds such as grouse. High mesopredator abundance has been associated with reduced reproductive success in grouse. There is little evidence, however, on how variation in mesopredator abundance affects grouse population trends while considering other environmental covariates. We make use of range maps spanning two decades (1993–2013) of a locally threatened capercaillie (Tetrao urogallus) population in the Black Forest, Germany, to assess whether range loss of grouse in forest–farmland mosaic landscapes can be explained by a gradient in red fox abundance, while accounting for other potential determinants of grouse range loss. We show that capercaillie range persistence was favored by increasing snow cover, decreasing index of red fox abundance, slightly increasing index for soil quality, and increasing population connectivity. Red fox abundance had the largest relative impact in areas already facing an elevated capercaillie extinction risk due to unsuitable site conditions, dense forests, or lack of connectivity, but the negative effect was compensated under otherwise optimal conditions. This indicates that the relative importance of predator abundance for prey population dynamics is mediated by environmental attributes, emphasizing the threat to remnant populations but also indicating potential for species conservation.

Question: What are the drivers of structural changes and mortality in oak— beech forests over 50 yrs of natural succession? Location: Twelve unmanaged forest sites, comprising a large environmental gradient in the Swiss lowlands. Method: By using repeated inventory data from more than 17 600 individually tagged trees, the dynamics of oak—beech stands over the past 50 yrs were analysed. Generalized linear mixed-effects models were fitted to quantify annual mortality rates of oak and beech based on DBH, stand basal area, precipitation and slope. Results: Stand basal area increased, whereas tree density decreased over time. At most sites, the relative importance of oak decreased gradually compared to beech. Mortality increased over time for both oak and beech, but the increase was stronger for oak. Oak and beech mortality decreased with increasing DBH and tended to increase with precipitation. Additionally, oak mortality increased with stand basal area, whereas no such trend was found for beech. Conclusion: Our study indicates that mortality in Central European oak—beech forests is driven by a combination of stand structures (i.e. tree size and stand basal area) and climate. However, the influence of climate on oak mortality is comparably low. Increasing oak mortality with stand basal area is a plausible consequence of its lower relative competitiveness and higher demand for light. Thus, in forests developing towards higher stand basal area, the ecologically important oak is increasingly outcompeted by beech, unless competition is reduced through management or disturbances.

Conservation policies often take for granted the importance of protected areas for supplying ecosystem services. The first edition of the State of Protected and Conserved Areas in Eastern and Southern Africa report contained limited information on ecosystem services, so for the 2nd edition we statistically compared 561 standardized economic values of various types of ecosystem services inside and outside of protected areas. We found that data from local and sub‐national case studies in the Ecosystem Service Valuation Database were biased geographically, highlighting major evidence gaps for most of the region. For well‐studied countries (Botswana, Ethiopia, Kenya, South Africa, Tanzania, Uganda), the value of ecosystem services varied considerably across different types of services but were—on average—three to six times higher outside protected areas. This trend was not universal, however, given that opportunities for recreation and tourism tended to be higher within protected areas. Combined, these findings suggest that conservation authorities across Eastern and Southern Africa (1) prioritize ecosystem service valuation studies; (2) expand the focus of ecosystem service policies to include wider landscapes beyond protected area boundaries; and (3) avoid generic assumptions about ecosystem services by identifying the services that are most compatible with the broader goals of protected areas. This study reports on an analysis of the value of ecosystem services in protected areas in Eastern and Southern Africa. Although data were biased geographically, ecosystem services in countries with sufficient data were generally more valuable outside of protected areas. However, certain types of ecosystem services were more valuable in protected areas, suggesting that more nuanced approaches are needed to identify types of services most compatible with the broader goals of protection.

We developed predictive models of coral reef fish species richness and abundance that account for both broad-scale environmental gradients and fine-scale biotic processes, such as dispersal, and we compared the importance of absolute geographical location (i.e. geographical coordinates) versus relative geographical location (i.e. distance to domain boundaries). Great Barrier Reef, Australia. Four annual surveys of coral reef fishes were combined with a 0.01°-resolution grid of environmental variables including depth, sea surface temperature, salinity and nutrient concentrations. A principal component-based method was developed to select candidate predictors from a large number of correlated variables. Generalized linear mixed-effects models (GLMMs) were used to gauge the respective importance of the different spatial and environmental predictors. An error covariance matrix was included in the models to account for spatial autocorrelation. (1) Relative geographical descriptors, represented by distances to the coast and to the barrier reef, provided the highest-ranked single model of species richness and explained up to 36.8% of its deviance. (2) Accounting for spatial autocorrelation doubled the deviance in abundance explained to 71.9%. Sea surface temperature, salinity and nitrate concentrations were also important predictors of abundance. Spatially explicit predictions of species richness and abundance were robust to variation in the spatial scale considered during model calibration. This study demonstrates that distance-to-domain boundaries (i.e. relative geographical location) can offer an ecologically relevant alternative to geographical coordinates (i.e. absolute geographical location) when predicting biodiversity patterns, providing a proxy for multivariate and complex environmental processes that are often difficult or expensive to estimate.

Aim: There is global consensus that marine protected areas offer a plethora of benefits to the biodiversity within and around them. Nevertheless, many organisms threatened by human impacts also find shelter in unexpected or informally protected places. For coral reef organisms, refuges can be tourist resorts implementing local environment-friendly bottom-up management strategies. We used the coral reef ecosystem as a model to test whether such practices have positive effects on the biodiversity associated with de facto protected areas. Location: North Ari Atoll, Maldives. Methods: We modelled the effects of the environment and three human management regimes (tourist resorts, uninhabited and local community islands) on the abundance and diversity of echinoderms and commercially important fish species, the per cent cover of reef benthic organisms (corals, calcareous coralline algae, turf and macroalgae) and the proportion of coral disease. We used multivariate techniques to assess the differences between reef components among the management regimes. Results: Reefs varied between the management regimes. A positive \"resort effect\" was found on sessile benthic organisms, with good coral cover and significantly less algae at resort islands. Corals were larger and had fewer diseases in uninhabited islands. Minor \"resort effect\" was detected on motile species represented by commercial fish and echinoderms. Main conclusions: In countries where natural biodiversity strongly sustains the tourist sector and where local populations rely on natural resources, a balance between tourism development, local extraction practices and biodiversity conservation is necessary. The presence of eco-friendly managed resorts, which practices would need to be certified on the long term, is beneficial to protect certain organisms. House reefs around resorts could therefore provide areas adding to existing marine protected areas, while marine protection efforts in local community islands should focus on improving fishing management.

Societal Impact Statement We found evidence that larger fruited plant species are more likely to be found in aseasonal wet areas of Malesia. These areas are likely to be impacted by increasing human encroachment, which threatens both large‐fruited species and the large fauna that are most likely responsible for their dispersal. This synergistic threat could drive the loss of fruit‐crop relatives that potentially have key traits for resilient fruit crops of the future. Summary It is unclear how fruit size determines distributions of megadiverse tropical flora. Energetic constraints of ecosystems suggest plant species with larger fruit should be found in the higher productivity, aseasonal wet tropics. However, the probability of seed dispersal over large scales should be increased by fruits being smaller, due to being available to a greater number of dispersal agents. We use a Bayesian phylogenetic model of species occurrence for >3400 species in Malesia to test how fruit size and environment interact to determine species distributions across the archipelago. We show that larger fruited species are more likely to occur in aseasonal wet areas. We also found that smaller fruit size was associated with species occurrence in more mountainous areas. Fruit size interacts with environmental variables to shape plant distributions across the megadiverse Malesian islands. The evolutionary processes that influence the patterns we have observed require further examination. We found evidence that larger fruited plant species are more likely to be found in aseasonal wet areas of Malesia. These areas are likely to be impacted by increasing human encroachment, which threatens both large‐fruited species and the large fauna that are most likely responsible for their dispersal. This synergistic threat could drive the loss of fruit‐crop relatives that potentially have key traits for resilient crops of the future.

The coefficient of determination R2 quantifies the amount of variance explained by regression coefficients in a linear model. It can be seen as the fixed-effects complement to the repeatability R (intra-class correlation) for the variance explained by random effects and thus as a tool for variance decomposition. The R2 of a model can be further partitioned into the variance explained by a particular predictor or a combination of predictors using semi-partial (part) R2 and structure coefficients, but this is rarely done due to a lack of software implementing these statistics. Here, we introduce partR2, an R package that quantifies part R2 for fixed effect predictors based on (generalized) linear mixed-effect model fits. The package iteratively removes predictors of interest from the model and monitors the change in the variance of the linear predictor. The difference to the full model gives a measure of the amount of variance explained uniquely by a particular predictor or a set of predictors. partR2 also estimates structure coefficients as the correlation between a predictor and fitted values, which provide an estimate of the total contribution of a fixed effect to the overall prediction, independent of other predictors. Structure coefficients can be converted to the total variance explained by a predictor, here called ‘inclusive’ R2, as the square of the structure coefficients times total R2. Furthermore, the package reports beta weights (standardized regression coefficients). Finally, partR2 implements parametric bootstrapping to quantify confidence intervals for each estimate. We illustrate the use of partR2 with real example datasets for Gaussian and binomial GLMMs and discuss interactions, which pose a specific challenge for partitioning the explained variance among predictors.

Rapid losses and degradation of natural habitats in the tropics are driving catastrophic declines and extinctions of native biotas, including angiosperms. Determining the ecological and life-history correlates of extinction proneness in tropical plant species may help reveal the mechanisms underlying their responses to habitat disturbance, and assist in the pre-emptive identification of species at risk from extinction. We determined the predictors of extinction proneness in 1884 locally extinct (n = 454) and extant (n = 1430) terrestrial angiosperms (belonging to 43 orders, 133 families, and 689 genera) in the tropical island nation of Singapore (699.4 km²), which has lost 99.6% of its primary lowland evergreen rainforest since 1819. A wide variety of traits such as geographical distribution, pollination system, sexual system, habit, habitat, height, fruit/seed dispersal mechanism, and capacity for vegetative re-sprouting were used in the analysis. Despite controlling for phylogeny (as approximated by family level classification), we found that only a small percentage of the variation in the extinction probability could be explained by these factors. Epiphytic, monoecious, and hermaphroditic species and those restricted to inland forests have higher probabilities of extinction. Species dependent on mammal pollinators also probably have higher extinction probabilities. More comparative studies that use species traits to identify extinction-prone plant species are needed to guide the enormous, but essential task of identifying species most in need of conservation action.