Biology subjects

Carmona, C. P.

Publications and source records attributed to Carmona, C. P..

16 recordsLinked to original sources

bioRxiv2026

Diversity without borders: partitioning continuous spaces using probabilistic equivalent numbers

Equivalent numbers represent biodiversity as the effective number of equally distinct units, typically species, and can be partitioned across scales. In practice, they summarize each unit of biodiversity by a single value and compare units pairwise, misrepresenting units that are better described as distributions and the relationships between several units that share the same space. We introduce an equivalent-number index for assemblages of units represented as probability density functions (PDFs) over a continuous space, estimated as the integral of the pointwise maximum across abundance-weighted PDFs. Resulting equivalent PDF numbers fulfil elementary properties of classical equivalent numbers, and support additive partitioning across any number of nested scales. We illustrate the framework with case studies across three domains: (1) measuring trait diversity considering intraspecific variability in grasslands, (2) partitioning realized bioclimatic niches among clades of Carnivora, and (3) understanding seasonal changes in the partitioning of fish home ranges in geographic space.

ecology↗

bioRxiv2025

A functional Red List Index for monitoring trends in functional diversity

Functional diversity supports ecosystem function and resilience but is in decline due to ongoing extinctions. Despite this, no functional diversity metrics are included in the set of indicators adopted by governments to measure progress towards the Global Biodiversity Framework. Monitoring changes in functional diversity is essential to understand differences between taxonomic and functional diversity trends. The Red List Index (RLI) is a widely used metric in conservation policy, and tracks trends in aggregate extinction risk across sets of species over time. We present a functional Red List Index (fRLI), which weights species by their morphological uniqueness at either local or global scales, to indicate the risk that future extinctions could pose to functional diversity. We applied the fRLI on birds and found higher aggregate extinction risk for both local and global fRLI compared with the standard RLI. Species with higher local uniqueness were more likely to be at higher risk of extinction while we found no difference for globally unique species. Globally or locally unique species were not more likely to show escalation in extinction risk between 1988 and 2024 than less unique species; however, locally unique birds had a lower proportion of their resident range covered by site-based conservation measures, leaving them vulnerable to future decline. The fRLI provides a tool to monitor the impact of extinction risk on functional diversity and could be applied to other taxonomic groups with comprehensive or representative coverage of Red List assessments and trait data.

ecology↗

bioRxiv2025

Threat reduction must be coupled with targeted recovery programmes to conserve global bird diversity

Biodiversity is undergoing severe declines while threats to natural populations continue to escalate worldwide. Ambitious international commitments have been made to preserve biodiversity, with the goal of preventing extinctions and maintaining ecosystem resilience, yet the efficacy of large-scale protection remains unclear. Here we use a trait-based approach to show that global actions - such as the immediate abatement of all threats across at least half of species ranges for [~]10,000 bird species - will only prevent half of projected species extinctions and functional diversity loss attributable to current and future threats in the next 100 years. Nonetheless, targeted recovery programmes prioritizing protection of the 100 most functionally unique threatened birds could avoid 68% of projected functional diversity loss. Actions targeting habitat loss and degradation will prevent the greatest number of species extinctions and proportion of functional diversity loss relative to other drivers of extinction, whereas control of hunting and collection and disturbance and accidental mortality would save fewer species but disproportionately boost functional richness. These findings show that conservation of avian diversity requires action partitioned across all drivers of decline, and highlights the importance of understanding and mitigating the ecological impacts of species extinctions predicted to occur even under optimistic levels of conservation action.

ecology↗

bioRxiv2024

A skewed picture of functional diversity in global drylands

Recently, Gross et al. (Nature 632, 808-814) found that plant phenotypic diversity dramatically increases with aridity globally, challenging conventional environmental filtering theories. However, some methodological choices by Gross et al. might overestimate the effect of aridity on phenotypic diversity: (i) We detected a skewed distribution of sampling sites towards the arid end of the analyzed gradient; (ii) We posited that fine-tuning of some statistical parameters might further challenge their estimates. We reanalyzed Gross et al. data accounting for these effects and found a substantially reduced change of phenotypic diversity with increasing aridity. Gross et al. surely represents a cornerstone for future research on trait diversity in a drier world, but their interpretations need to be considered alongside our findings. Importantly, the points raised by our reanalysis provide general guidelines for future research on plant phenotypic diversity changes along environmental gradients.

ecology↗

bioRxiv2024

Intraspecific and intraindividual trait variability decrease with tree species richness in a subtropical tree biodiversity experiment

Phenotypic variability within tree species responds to local tree species richness. However, we lack evidence on how different sources of trait variation shape tree-tree interactions. Along a diversity gradient from one to eight tree species, we sampled 4,568 leaves from 381 trees to study changes in intraspecific and intraindividual leaf trait variability and assessed their contribution to community functional diversity. Intraspecific variability decreased with tree species richness, while intraindividual variability barely responded. Functional overlap between conspecific trees increased with tree species richness and through intraindividual variation, but was reduced through intraspecific variability, meaning that intraspecific variability may reduce intraspecific competitive interactions while intraindividual variability could arise due to varying microenvironmental conditions within the canopy. Last, intraspecific and intraindividual variability explained high community functional richness and divergence, respectively, especially in mixtures. Our findings emphasize that fine-scale variability influences tree-tree interactions and can be a driver of local functional diversity. TeaserTrait variability within tree species decreases with diversity and explains high forest functional diversity.

ecology↗

bioRxiv2024

Diseases and invasive species have synergistic effects with other anthropogenic threats on the functional and phylogenetic diversity in Testudines and Crocodilia

Understanding how multiple threats interact is crucial for the prioritization of conservation measures. Here, we investigate how interactions between six common threats (climate change, habitat disturbance, global trade, overconsumption, pollution, and emerging diseases/invasive species) affect the functional and phylogenetic diversity of 230 species of Testudines and 21 of Crocodilia. We classify two-way threat interactions into additive, synergistic, and antagonistic according to their effects on functional and phylogenetic diversity. Most threat interactions are antagonistic, the effect of threats jointly is lower than the sum of the effects of threats separately. However, we find that the interaction between emerging diseases or invasive species with other threats has synergistic and additive effects, meaning that the combined effects are greater or equal to the effects of threats separately. Our work can help target conservation strategies and detect key places to address multiple threats when they appear together.

ecology↗

bioRxiv2023

"Flower power": how flowering affects spectral diversity metrics and their relationship with plant diversity

Biodiversity monitoring is constrained by cost- and labour-intensive field sampling methods. Increasing evidence suggests that remotely sensed spectral diversity (SD) is linked to plant diversity, holding promise for monitoring applications. However, studies testing such a relationship reported conflicting findings, especially in challenging ecosystems such as grasslands, due to their high temporal dynamism and variety. It follows that a thorough investigation of the key factors, such as the metrics applied (i.e., continuous, categorical) and phenology (e.g., flowering), influencing such a relationship is necessary. Thus, this study aims to assess the applicability of SD for plant diversity monitoring at the local scale by testing six different SD metrics while considering the effect of the presence of flowering on the relationship and resampling the original data to assess how spatial resolution affects the results. Taxonomic diversity was calculated based on data collected in 159 plots with 1.5 m x1.5 m experimental mesic grassland communities. Spectral information was collected using a UAV-borne sensor measuring reflectance across six bands in the visible and near-infrared range at [~]2 cm spatial resolution. Our results show that, in the presence of flowering, the relationship is significant and positive only when SD is calculated using categorical metrics. Despite the observed significance, the variance explained by the models had very low values, with no evident differences when resampling spectral data to coarser pixel sizes. Such findings suggest that new insights into the possible confounding effects on the SD[~]plant diversity in grassland communities are needed to use SD for monitoring purposes.

ecology↗

bioRxiv2022

Trait diversity metrics can perform well with highly incomplete datasets

O_LICharacterizing changes in trait diversity at large spatial scales provides insight into the impact of human activity on ecosystem structure and function. However, the approach is often based on trait datasets that are incomplete and unrepresentative, with uncertain impacts on trait diversity estimates. C_LIO_LITo address this knowledge gap, we simulated random and biased removal of data from a near complete avian trait dataset (9579 species) and assessed whether trait diversity metrics were robust to data incompleteness with and without using imputation to fill data gaps. Specifically, we compared two commonly used metrics each calculated with two methods: trait richness (calculated with convex hulls and trait probabilities densities) and trait divergence (calculated with distance-based Rao and trait probability densities). C_LIO_LIWithout imputation, estimates of global avian trait diversity (richness and divergence) were robust when 30-70% of species had missing data for four out of 11 continuous traits, depending on severity of bias and the method used. However, when missing traits were imputed based on present morphological trait data and phylogeny, trait diversity metrics consistently remained representative of the true value, even when 70% of species were missing data for four out of 11 traits and data were not missing at random (biased with respect to body mass). Trait probability densities and distance-based Rao were particularly robust to missingness and bias when combined with imputation, with convex hull-based trait richness being less reliable. C_LIO_LIExpanding global morphometric datasets to represent more taxa and traits, and to quantify intraspecific variation, remains a priority. In the meantime, our results show that widely used methods can successfully quantify large-scale trait diversity even when data are missing for two-thirds of species, so long as missing traits are estimated using imputation. C_LI

ecology↗

bioRxiv2022

The extinction of threatened species by anthropogenic threats endangers the functional diversity of turtles and crocodiles

The Anthropocene is tightly associated with a drastic loss of species worldwide and the disappearance of their key ecosystem functions. The on-going reduction in ecosystem functionality is driven by global and local threats. The orders Testudines (turtles and tortoises) and Crocodilia (crocodiles, alligators, and gharials) contain numerous threatened, long-lived species for which their functional diversity and potential erosion by anthropogenic impacts remains unknown. Here, we examine 259 (69%) of the existing 375 species of Testudines and Crocodilia, quantifying their life history strategies (i.e., schedules of survival, development, and reproduction) from open-access data on their demography, ancestry, and threats. We find that the loss of functional diversity in simulated extinction scenarios of threatened species is greater than expected by chance. Moreover, the effects of unsustainable local consumption, diseases, and pollution are associated with specific functional strategies. In contrast, climate change, habitat disturbance, and global trade affect all species independent of their life history strategy. Importantly, the loss of functional diversity for threatened species by habitat disturbance is twice that for all other threats. Our findings highlight the importance of conservation programmes focused on preserving the functional diversity of life history strategies jointly with the phylogenetic representativity of these highly threatened groups.

ecology↗

bioRxiv2021

An updated framework to account for inter-individual variability when quantifying phenotypic variation

O_LIIn trait-based ecology, phenotypic variation (PVar) is often quantified with measures that express average differences between populations standardized in the range 0-1. A major problem with these measures is that they disregard the within-population trait variability. In addition, most of these measures cannot be decomposed across scales. This can alter their interpretation, thus limiting their applicability. C_LIO_LITo overcome these problems, we propose a new measure, the Phenotypic Dissimilarity Index (PhD) that is insensitive to the within-population interindividual trait variability. Likewise, PhD can be used to quantify PVar between individuals in a population while accounting for the PVar within individuals. C_LIO_LIUsing simulated and real data, we showed that PhD index correctly quantifies PVar when the within-population trait variability is not negligible, as in many ecological studies. By accounting for within-population trait variability, the PhD index generally provides a more parsimonious quantification of PVar across an environmental gradient compared to other estimators. C_LIO_LITraits sampled within a species have an inherent variability. Accounting for such variability is essential to understand species phenotypic responses to environmental cues. As such, the PhD index will provide ecologists with an asset to reliably quantify and compare PVar within and between species across environmental gradients at different scales. We also provide an R function to calculate the PhD index. C_LI

ecology↗

bioRxiv2021

Combining taxonomic, phylogenetic and functional diversity reveals new global priority areas for tetrapod conservation

Human activities have eroded biodiversity, yet the varying influence of past versus recent impacts across the distinct facets of biodiversity is still poorly understood. Weighting taxonomic information by phylogenetic and functional diversity in a novel multifaceted index (-Diversity) across more than 17,000 tetrapod species, we show the geography of multifaceted tetrapod diversity, and the role of climate stability and water-energy dynamics coupled with the timing of inception of agriculture in explaining broad-scale patterns of tetrapod diversity. In particular, the varying geography of the timing of agriculture expansion since the Neolithic affected -Diversity at least as much as recent human impacts, especially in birds, mammals, and reptiles, suggesting that human imprints may have shaped tetrapod diversity for millennia through legacy effects of past land use modifications. The long-lasting effect of humans will only accelerate, as the most diverse areas for -Diversity (tropical Africa, South East Asia and Central and South America) are disproportionally exposed to both future climate and land-use change.

ecology↗

bioRxiv2020

Including intraspecific trait variability to avoid distortion of functional diversity and ecological inference: lessons from natural assemblages

O_LIFunctional diversity assessments are crucial and increasingly used for understanding ecological processes and managing ecosystems. The functional diversity of a community is assessed by sampling traits at one or more scales (individuals, populations, species) and calculating a summary index of the variation in trait values. However, it remains unclear how the scale at which traits are sampled and the indices used to estimate functional diversity may alter the patterns observed and inferences about ecological processes. C_LIO_LIFor 40 plant and 61 ant communities, we assess functional diversity using six methods - encompassing various mean-based and probabilistic methods - chosen to reflect common scenarios where different levels of detail are available in trait data. We test whether including trait variability at different scales (from individuals to species) alter functional diversity values calculated using volume-based and dissimilarity-based indices, Functional Richness (FRic) and Rao, respectively. We further test whether such effects alter the functional diversity patterns observed across communities and their relationships with environmental drivers such as abiotic gradients and occurrences of invasive species. C_LIO_LIIntraspecific trait variability strongly determined FRic and Rao. Methods using only species mean trait values to calculate FRic (convex hulls) and Rao (Gower-based dissimilarity) distorted the patterns observed when intraspecific trait variability was considered. These distortions generated Type I and Type II errors for the effects of environmental factors structuring the plant and ant communities. C_LIO_LIThe high sensitivity of FRic to individuals with extreme trait values was revealed in comparisons of different probabilistic methods including among-individual and among-population trait variability in functional diversity. By contrast, values and ecological patterns in Rao were consistent among methods including different scales of intraspecific trait variability. C_LIO_LIDecisions about where traits are sampled and how trait variability is included in functional diversity can drastically change the patterns observed and conclusions about ecological processes. We recommend sampling the traits of multiple individuals per species and capturing their intraspecific trait variability using probabilistic methods. We discuss how intraspecific trait variability can be reasonably estimated and included in functional diversity in the common circumstance where only limited trait data are available. C_LI

ecology↗

bioRxiv2020

Mycorrhizal symbiosis alleviates plant drought stress within and across plant generations via plasticity

O_LIPhenotypic plasticity is essential for organisms to adapt to local ecological conditions. It is expected that mutualistic interactions, such as arbuscular mycorrhizal (AM) symbiosis, mediate plant phenotypic plasticity, although it is not clear to what extent this plasticity may be heritable (i.e., transgenerational plasticity). C_LIO_LIWe tested for plant plasticity within- and across-generations in response to AM symbiosis and varying water availability in a full factorial experiment over two generations, using a genetically uniform line of a perennial apomictic herb, Taraxacum brevicorniculatum. We examined changes in phenotype, performance, and AM fungal colonization of the offspring throughout plant development. C_LIO_LIAM symbiosis and water availability triggered phenotypic changes during the life cycle of plants. Additionally, both triggered adaptive transgenerational effects, especially detectable during the juvenile stage of the offspring. Water deficit and absence of AM fungi caused concordant plant phenotypic modifications towards a "stress-coping phenotype", both within- and across-generations. AM fungal colonization of offspring was also affected by the parental environment. C_LIO_LIAM symbiosis can trigger within-generation and transgenerational plasticity in terms of functional traits related to resource-use acquisition and AM fungal colonization. Thus, transgenerational effects of mycorrhizal symbiosis are not limited to plant fitness, but also improve plants ability to cope with environmental stress. C_LI

ecology↗

bioRxiv2020

Mapping extinction risk in the global functional spectra across the tree of life

Although one quarter of the species of plants and vertebrates are threatened with extinction, little is known about how the potential effect of extinctions on the global diversity of ecological strategies. Using trait and phylogenetic information for more than 75,000 species of plants, mammals, birds, reptiles, amphibians and freshwater fishes, we characterized the global functional spectra of each of these groups. Mapping of extinction risk within these spectra revealed that larger species with slower pace of life are universally threatened. Simulated potential extinctions revealed extensive internal reorganizations in the global functional spectra, which are particularly severe for mammals and amphibians. Considering the disproportionate importance of the largest species for ecological processes, our results emphasize the importance of actions to prevent the extinction of the megabiota.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2019

Estimating probabilistic dark diversity based on the hypergeometric distribution

O_LIThe biodiversity of a site includes the absent species from the region that are theoretically able to live in the sites particular ecological conditions. These species constitute the dark diversity of the site. Unlike present species, dark diversity is unobservable and can only be estimated. Most existing methods to designate dark diversity act in a binary fashion. However, dark diversity is more suitably defined as a fuzzy set--in which the degree of certainty about species membership is expressed as a probability.\nC_LIO_LIWe present a new method to estimate probabilistic dark diversity based on the hypergeometric distribution. The method relies on co-occurrences to infer the strength of the association between pairs of species and assign probabilistic adscription to dark diversity to absent species. We compare it with two established methods to estimate dark diversity (Beals index and favorability correction). To test the methods, we created simulations based on individual agents in which the suitability of each species in each site is known. We compared the ability of the methods to accurately predict suitability and the size of dark diversity, and compared their sensitivity to data availability. Further, we assessed the methods in two real datasets with nested sampling designs.\nC_LIO_LIOur simulations revealed that predictions of the Beals method were extremely sensitive to species frequency, and predicted suitability poorly. The Favorability transformation corrected this relationship, but did still predicted extremely low probabilities for species with very little information. The Hypergeometric method outperformed the Beals and Favorability methods in all considered aspects in the simulations and displayed better characteristics in the real datasets.\nC_LIO_LIProbabilistic consideratiosn of biodiversity will help to acknowledge the uncertainty associated with ecological information. Although the Beals method has been described as the best estimator of dark diversity, it should be preferred only when the goal is to predict future apperances of species. However, studies on dark diversity should focus on the ecological affinities of species. The Hypergeometric method is the most promising method to estimate probabilistic dark diversity and species pool composition based on co-occurrences.\nC_LI

ecology↗

bioRxiv2019

Trait plasticity of intensive pasture species due to growth in mixture across seasons and nutrient addition levels

QuestionsHow do the traits of pastoral species respond to growth in mixture, nitrogen addition and season? What are the impacts of trait plasticity on community aggregate trait values?\n\nStudy siteA large-scale field experiment on intensively managed dairy pastures in New Zealand.\n\nMethodsWe measured traits linked to rate of return on investment in leaves - leaf nitrogen content (leaf N) and specific leaf area (SLA) - and biomass investment in leaf area - leaf area ratio (LAR). We collected trait data for 5 pasture species (one grass, two forbs, and two N2-fixing legumes) grown in monoculture or a five-species mixture across three levels of nitrogen (N) addition in four seasons. For each species in each season we tested for significant effects of growth in mixture, N addition, and their interaction. We calculated community-weighted mean (CWM) values in mixture plots using traits collected either from mixtures or monocultures. We tested for significant mixture and N addition effects on CWM, and for significant interactions between mixture and N addition.\n\nResultsSLA and LAR for all non-N2-fixers were significantly higher in spring, summer or autumn, and never significantly lower in mixture than in monoculture. All three non-N2-fixers experienced higher leaf N in mixture during summer, but two species had significantly lower leaf N in either winter or autumn. Mixture effects on CWM values for all three traits were negative in winter and positive in either spring or summer.\n\nConclusionsThe direction of trait plasticity effects on community level trait means was highly seasonally dependent.

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