Biology subjects

Barbosa, M.

Publications and source records attributed to Barbosa, M..

10 recordsLinked to original sources

bioRxiv2026

Age-specific Jensen contrasts reveal how ontogenetic responses to thermal variability shape lifetime performance in Daphnia magna

1. Temperature shapes life histories through its effects on energy allocation among growth, reproduction and maintenance. The resulting temperature dependence of performance is commonly characterised using thermal performance curves (TPCs), which are often treated as static descriptions that apply uniformly throughout life. Yet the response to thermal variability may change across ontogeny. 2. We recorded growth, reproduction and survival throughout the lifetimes of individual Daphnia magna under four thermal regimes: Constant Low (15C), Constant Rearing (20C), Constant High (25C) and Variable (15C to 25C). The mean temperature under Variable closely matched that under Constant Rearing. Using an allometric energy-allocation model, we derived age specific and lifetime performance measures and quantified their uncertainty with a stratified individual-level bootstrap. Our principal quantity was the Jensen contrast, defined as performance under Variable minus that under Constant Rearing. 3. Age specific point estimates of the Jensen contrast changed sign across ontogeny. A positive aggregate contrast in full trajectory growth concealed a negative mid-life contrast; reproductive point estimates were positive during early and mid life but negative later. Bootstrap support was strong for the positive early life and negative mid-life growth contrasts, and for the positive early life reproductive contrast. Under a second-order approximation, this pattern of estimated signs is consistent with ontogenetic changes in effective thermal curvature. 4. The positive early life reproductive response did not carry through to the lifetime outcome: expected lifetime reproduction was lower under Variable than under Constant Rearing, with strong bootstrap support for the negative lifetime contrast. Because lifetime reproduction is survival weighted, lower survival under Variable reduced later reproductive contributions; across the estimated trajectories, the accumulated negative late life contribution out-weighed the earlier positive contributions. 5. These results show why forecasts based on mean temperature, a single life stage or an aggregate TPC may misrepresent lifetime performance under variable thermal regimes. Accounting for both ontogeny and temperature variability may therefore improve forecasts of life-history performance in increasingly variable thermal environments.

ecology↗

bioRxiv2026

Benthic composition drives functional composition of fish assemblages despite varying recreational diving intensity

Human activities are driving widespread degradation of natural ecosystems, with coral reefs among the most affected. While the impacts of climate change and pollution on coral reefs are well documented, the ecological consequences of recreational scuba diving, a rapidly growing industry, remain less understood. Namely, few studies have explored how diving influences trait diversity of coral reef fish assemblages, a key dimension of ecosystem resilience. Here, we investigated spatial variation in benthic composition and fish trait diversity across reef sites in Utila, Honduras, an island heavily reliant on dive tourism. We surveyed five sites of varying levels of diving intensity to quantify benthic cover and fish assemblages. Contrary to expectations, sites with high diving intensity did not show reduced coral cover, with the most heavily dived site (Stingray Point) maintaining the highest overall coral cover. Algae, however, dominated the benthos across all sites. While functional richness was maintained across the diving intensity gradient, functional composition shifted significantly among sites. This compositional shift was driven primarily by the Von Bertalanffy growth coefficient (k). Sites with low hard coral cover but higher benthic heterogeneity harboured fish communities dominated by fast-growing, early maturing species, whereas high hard coral cover sites supported assemblages of slower-growing, later-maturing species. Benthic composition, rather than diving intensity, emerged as the primary filter of fish life-history strategies. These findings suggest that while current diving intensity may not erode the volume of functional trait space, it is associated with distinct benthic states that filter for specific life-history strategies. Our results highlight the importance of maintaining benthic heterogeneity in reef systems, even in the absence of obvious coral loss. As functional diversity underpins key ecosystem services, it is important that coral reef monitoring focuses on changes in trait composition rather than just simpler taxonomic diversity metrics. Achieving this in collaboration with dive operators to promote low-impact diving is essential to sustaining reef resilience in tourism-dependent regions like Utila.

ecology↗

bioRxiv2023

Invasive traits of freshwater fish database (ITOFF)

AIMSpecies invasions are a major driver of global biodiversity loss, but only a minority of invasions are successful. Evidence suggests that invasive success is linked to life-history traits. Yet, data on invasive success and species traits remain fragmented across multiple sources. Here we present the Invasive Traits of Freshwater Fish (ITOFF) database, an interdisciplinary framework that integrates multiple datasets to elucidate the role of life-history traits in shaping invasive success. ITOFF allows seamless access to invasive species data and fosters collaborative actions through knowledge sharing. ITOFF is supported by an innovative web-application that makes complex relationships between invasive and native species accessible to a broad audience. The scientific contribution of ITOFF is illustrated by examining the role of life-history traits and phylogeny in invasion success. LOCATIONGlobal. METHODSGeneralized linear models were used to test the contribution of generation time, trophic level, longevity, and temperature range to invasive success. Through divisive cluster analysis we investigate the role of multiple traits in determining invasive success. Finally, we construct phylogenetic trees to investigate the role of evolutionary history in the invasion process. RESULTSITOFF unifies data for 1917 freshwater fish species representative of invasive species, those species they endanger, and species impacted by invasives but not considered endangered. Invasive species are generally characterized by greater temperature ranges, but are indistinguishable from impacted, endangered, and critically endangered species for the remaining life-history traits. Further, we show that invasive species are generally not distinct from impacted or endangered species when considering multiple traits or phylogeny. MAIN CONCLUSIONSITOFF provides an accessible platform for the improved forecasting of species invasions. ITOFF data shows that classical predictions of life-history traits determining invasive success do not hold amongst freshwater fish species. Forecasting of invasive species must therefore shift towards a wholistic approach encompassing the species and the environment.

ecology↗

bioRxiv2021

Coral settlement and recruitment responses to reef fish foraging and trait diversity

The process of coral recruitment is crucial to the functioning of coral reef ecosystems, as well as recovery of coral assemblages following disturbances. Fishes can be key mediators of this process by removing benthic competitors like algae, but their foraging impacts are capable of being facilitative or harmful to coral recruits depending on species traits. Reef fish assemblages are highly diverse in foraging strategies and the relationship between this diversity with coral settlement and recruitment success remains poorly understood. Here, we investigate how foraging trait diversity of reef fish assemblages covaries with coral settlement and recruitment success across multiple sites at Lizard Island, Great Barrier Reef. Using a multi-model inference approach incorporating six metrics of fish assemblage foraging diversity (foraging rates, trait richness, trait evenness, trait divergence, herbivore abundance, and sessile invertivore abundance), we found that herbivore abundance was positively related to both coral settlement and recruitment success. However, the correlation with herbivore abundance was not as strong in comparison with foraging trait diversity metrics. Coral settlement and recruitment exhibited a negative relationship with foraging trait diversity, especially with trait divergence and richness in settlement. Our findings provide further evidence that fish play a role in making benthic habitats more conducive for coral settlement and recruitment. Because of their ability to shape the reef benthos, the variation of fish biodiversity is likely to contribute to spatially uneven patterns of coral recruitment and reef recovery.

ecology↗

bioRxiv2021

Coral niche construction: coral recruitment increases along a coral-built structural complexity gradient

Niche construction is the process through which organisms modify environmental states in ways favourable to their own fitness. Here, we test experimentally whether scleractinian corals can be considered niche constructors. In particular, we demonstrate a positive feedback involved in corals building structures which facilitate recruitment. Coral larval recruitment is a key process for coral reef persistence. Larvae require low flow conditions to settle from the plankton, and hence the presence of colony structures that can break the flow is expected to facilitate coral recruitment. Here, we show an increase in settler presence on artificial tiles deployed in the field along a gradient of coral-built structural complexity. Structural complexity had a positive effect on settlement, with an increase of 15,71% of settler presence probability along the range of structural complexity considered. This result provides evidence that coral built structural complexity creates conditions that facilitate coral settlement, while demonstrating that corals meet the criteria for ecological niche construction.

ecology↗

bioRxiv2021

Shaping coral traits: plasticity more than filtering

The structure of ecosystems is usually determined by the shape of the organisms that build it, commonly known as ecosystem engineers. Understanding to what extent plasticity and environmental filtering determine variation in ecosystem engineer physical structure is necessary to predict how ecosystem structure may change. Here, we explored coral survival and the plasticity of morphological traits that are critical for habitat provision in coral reefs. We conducted a reciprocal clonal transplant experiment in which branching corals from the genus Porites and Acropora were moved to and from a deep and a shallow site within a lagoon in the Maldives. Survival and trait analyses showed that transplant destination consistently induced the strongest changes, particularly among Acropora spp. The origin of the corals only marginally affected some of the traits. We also detected variation in the way individuals from the same species and site differentiate their shape, showing that traits linked to habitat provision are phenotypically plastic. The results suggest coral phenotypic plasticity plays a stronger role than environmental filtering, in determining zonation of coral morphologies, and consequently the habitats they provide for other taxa.

ecology↗

bioRxiv2020

The mistletoe Struthanthus flexicaulis reduces dominance and increases diversity of plants in campo rupestre

The interaction between hemiparasites and their host plants is an important structuring mechanism for plant communities. The mistletoe Struthanthus flexicaulis (Loranthaceae) is widely distributed in the campo rupestre ecosystem and likely has an important role in structuring the communities of which its hosts are part. The main goals of this study were to investigate the effects of parasitism by S. flexicaulis on host plants in a degraded area of campo rupestre and to determine how parasitism affects characteristics of the structure of this plant community over time. We found that parasitized plants had smaller crowns and branch growth, and suffered lower mortality compared to non-parasitized plants. Parasitism by S. flexicaulis decreased dominance and increased the diversity and evenness of plants in the community over time. Parasitism leads to competition with the host for water and nutrients, which may decrease the performance of the host and, consequently, leading to host death. The high mortality of the most abundant plant species led to a restructured woody plant community. These results reinforce the importance of parasitic plants as key species for maintaining species diversity in plant communities.

ecology↗

bioRxiv2020

Episignatures stratifying ADNP syndrome show modest correlation with phenotype

ADNP syndrome, also known as Helsmoortel-van Der Aa syndrome, is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. ADNP syndrome is caused by mutations in the activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with ADNP syndrome, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with ADNP syndrome into two groups, based on the location of the mutations. Here, we conducted an independent study on 24 individuals with ADNP syndrome and replicated the existence of the two, mutation-dependent ADNP episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of ADNP syndrome. We found limited phenotypic differences between the two ADNP groups, and no evidence that individuals with more widespread methylation changes are more severely affected. Also, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with ADNP syndrome. Our data warrant caution in harnessing methylation signatures in ADNP syndrome as a tool for clinical stratification, at least with regards to behavioral phenotypes.

developmental biology↗

bioRxiv2018

Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk

We present the largest exome sequencing study to date focused on rare variation in autism spectrum disorder (ASD) (n=35,584). Integrating de novo and case-control variation with an enhanced Bayesian framework incorporating evolutionary constraint against mutation, we implicate 99 genes in ASD risk at a false discovery rate (FDR) [≤] 0.1. Of these 99 risk genes, 46 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 50 show higher frequencies in individuals ascertained for ASD, and comparing ASD cases with disruptive mutations in the two groups shows differences in phenotypic presentation. Expressed early in brain development, most of the risk genes have roles in neuronal communication or regulation of gene expression, and 12 fall within recurrent copy number variant loci. In human cortex single-cell gene expression data, expression of the 99 risk genes is also enriched in both excitatory and inhibitory neuronal lineages, implying that disruption of these genes alters the development of both neuron types. Together, these insights broaden our understanding of the neurobiology of ASD.

genetics↗

bioRxiv2018

Identification of rare de novo epigenetic variations in congenital disorders

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. With recent dramatic advances in genomic technologies, genome-wide surveys of cohorts of patients with ND/CAs for point mutations and structural variations have greatly advanced our understanding of their genetic etiologies1,2. However, even after whole genome sequencing (WGS), a substantial fraction of such disorders remain unexplained3. In contrast, the possibility that constitutive epigenetic variations (epivariations) might underlie such traits has not been well explored. We hypothesized that some cases of ND/CA are caused by aberrations of DNA methylation that lead to a dysregulation of normal genome function. By comparing DNA methylation profiles from 489 individuals with ND/CAs against 1,534 population controls, we identified epivariations as a frequent occurrence in the human genome. De novo epivariations were significantly enriched in cases when compared to controls. RNAseq data from population studies showed that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detected and replicated an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations. Thus, some epivariations occur secondary to cis-linked mutations in regulatory regions, providing a rationale for interpreting non-coding genetic variation. We propose that epivariations likely represent the causative genomic defect in 5-10% of patients with unexplained ND/CAs. This constitutes a yield comparable to CNV microarrays, and as such has significant diagnostic relevance.

genomics↗