Biology subjects

Dornelas, M.

Publications and source records attributed to Dornelas, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Adult corals enhance juvenile recruitment through cumulative ecological niche construction

Ecosystem engineers are ecological niche constructors: by modifying local environments, they alter the conditions under which organisms establish, persist and interact. Although niche construction is often framed as a population-level evolutionary feedback, it could also operate at the assemblage level when communities collectively shape their environments and filter future recruitment. Reef-building corals provide a perfect system to test this idea because adult colonies form three-dimensional carbonate structures that can persist after colony death, creating an inherited habitat for subsequent coral generations. Here, we tested whether coral recruitment to the juvenile stage was associated with local adult coral abundance, reef structure, and larval settlement supply. Combining spatially explicit coral censuses, photogrammetric reef digital elevation models and data from settlement tiles across 15 reef sites at two time points at Jiigurru, Great Barrier Reef, we found that juvenile abundance increased additively on the log scale with adult abundance and with fractal dimension, a metric of fine-scale structural complexity. Surface rugosity had weaker effects, and interactions between adult abundance and habitat structure were limited, indicating largely additive, rather than synergistic or antagonistic, effects. Our results show that both adult assemblages and the concurrent structural complexity, consistent with assemblage-level niche construction and ecological inheritance theory, shape coral recruitment.

ecology↗

bioRxiv2026

Coral reef ecosystem functions in a human-dominated world

The metabolic processes sustaining coral reefs, from carbonate and primary production to secondary production, remain poorly integrated and rarely quantified simultaneously at global scales. This hampers our ability to predict global responses to accelerating human pressures and manage coral reef functioning. Using metabolic scaling and bioenergetic models applied to surveys from 1,100 reefs worldwide, we provide a global, standardized quantification of 14 ecosystem functions spanning benthic (corals and algae) and fish communities. Our analysis reveals a continuous functional spectrum of global coral reefs organized along four dominant axes: 1) primary production, 2) calcification and habitat structure, 3) secondary biomass production and consumption, and 4) biomass turnover. Functions mediated by fish and benthic communities show weak associations at the global scale rather than tight coupling. Climate stressors reduced calcification and local human impacts lowered secondary production. Yet these directional effects unfolded against a backdrop of substantial natural variability in reef functional configurations, such that heavily and minimally impacted reefs overlap substantially in the global functional space. Temporal analyses across three representative reef systems further revealed that functional trajectories following disturbance are context-dependent, with no universal pattern of recovery across locations. This continuous and context-dependent functional spectrum challenges the notion of universal functional benchmarks and supports locally tailored conservation strategies.

ecology↗

bioRxiv2025

Tracking morphological development in stony corals

The shape of reef-building corals largely determines how they interact with their environment and the ecosystem services they provide. However, morphology is not fixed. As corals grow and develop from singular polyps to mature adult colonies, they experience pronounced changes in their morphology. This developmental trait variation remains poorly quantified in corals, despite their importance as ecosystem engineers. To address this gap, we used photogrammetry to track the morphological development of wild coral colonies across six size-independent metrics designed to capture variation in volume compactness, surface complexity, and top-heaviness. Size-trait models and analyses of colony movement through morphological trait space revealed that small colonies shared compact morphologies and only later diverged along growth-form-specific developmental trajectories. Massive corals largely retained stable shapes as they grew, whereas non-massive colonies became less compact, more top-heavy, and in most cases, more complex. Despite these differences, there was still overlap between growth forms in their developmental trajectories through morphospace. These findings highlight that traditional categorical growth forms mask important developmental variation, particularly early in coral ontogeny. By applying a quantitative trait-based framework, this study improves understanding of coral morphological development and provides a foundation for linking individual growth trajectories to broader reef ecosystem dynamics.

ecology↗

bioRxiv2024

Habitat complexity defines global biological and societal landscapes

The three-dimensional structure of land- and seascapes links biotic and abiotic processes to shape how organisms use their environments. Much effort has been dedicated to understanding this relationship between structural complexity and biodiversity. However, tailored, system-specific approaches to quantifying structural complexity preclude cross-system comparisons. Expanding a geometric framework developed for quantifying the structural complexity of local-scale surface environments, we generate high-resolution, global maps of the key complexity measures of height range, rugosity, and fractal dimension. We illustrate how patterns in these complexity attributes correspond with the distribution of ecosystems, land cover types, and the presence of people across the globe. Using geometric tools to understand how structural complexity is associated with the arrangement of natural and socio-ecosystems, we can better predict their responses to ongoing global change.

ecology↗

bioRxiv2024

Coral reef habitat complexity decreases and diversifies local availability of light

The spatial distribution of environmental conditions can determine where organisms can and cannot live. When the distribution of microhabitats within a landscape is mediated by the shape of its surface, structural complexity can indirectly affect environmental niche distributions. This study investigates how light availability patterns change along a gradient of landscape complexity measured as surface rugosity and height range in tropical shallow reefs. We used 260,000 high frequency and high spatial resolution light measurements across 903 locations to determine the proportion of light that is available at the reef surface. We find that light available on the reef surface is highly variable, with close locations within reef sites experiencing up to 25.7 mol/m2d of daily photon input difference. After accounting for light attenuation due depth, light availability decreases with increasing surface rugosity: a unit increase in local surface rugosity corresponds to an 11-29% decrease in light availability. Local surface complexity can affect the distributions of light availability at local scales, while broader extent site metrics do not capture this variability. Our results suggest that structural complexity enhances local environmental variability, and its indirect effects on other environmental variables and their interactions are essential for understanding ecosystem processes.

ecology↗

bioRxiv2024

Degradation of fish food webs in the anthropocene

The Anthropocene is marked by profound changes in biodiversity and the ecosystems in which species live 1-4. A primary signature of this change is the often rapid change in species composition through time (i.e., species turnover) rather than changes in the numbers of species per se 5-7. Less well known, however, is which types of species are winning and which are losing as ecosystems change through time 8,9, as well as whether and how these changes influence higher-level processes in the food webs in which species are embedded 10,11. Here, we combine a compilation of long-term observations of [~]15,000 freshwater and marine fish communities surveyed for 1949-2019 years, together with information about their diets and trophic status in order to evaluate how the food webs in which these fish communities are embedded are changing through time. We found widespread alteration to fish food web topology and functioning. This includes an increase in connectance and generalism in food webs, which has led to greater predation pressure, as indicated by higher diet overlap and increased prey vulnerability. We also identified a decrease in modularity, which has reduced the compartmentalization within local networks. These changes extend across the trophic structure of food webs, causing a cascading shift in the proportion of species across trophic levels. Our study highlights the complex responses of biodiversity change of fish food webs in the Anthropocene, which can ultimately influence the functions of these ecosystems and human well-being 12,13.

ecology↗

bioRxiv2024

habtools: an R package to calculate 3D metrics for surfaces and objects

O_LITechnological advances in three-dimensional imaging techniques have opened the door to advanced morphological analyses and habitat mapping for biologists and ecologists. C_LIO_LIAt the same time, the challenge of translating complex 3D data into meaningful metrics that can be used in conjunction with biological data currently hinders progress and accessibility. C_LIO_LIWe introduce habtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow. C_LIO_LIWe expect the functionality of habtools to continue to expand as new metrics and faster methods become available, and welcome new contributions and ideas. C_LI

ecology↗

bioRxiv2023

Disentangling non-random structure from random placement when estimating β-diversity through space or time

There is considerable interest in understanding patterns of {beta}-diversity that measure the amount of change in species composition through space or time. Most hypotheses for {beta}-diversity evoke nonrandom processes that generate spatial and temporal within species aggregation; however, {beta}-diversity can also be driven by random sampling processes. Here, we describe a framework based on rarefaction curves that quantifies the non-random contribution of species compositional differences across samples to {beta}-diversity. We isolate the effect of within-species spatial or temporal aggregation on beta-diversity using a coverage standardized metric of {beta}-diversity ({beta}C). We demonstrate the utility of our framework using simulations and an empirical case study examining variation in avian species composition through space and time in engineered versus natural riparian areas. The primary strengths of our approach are that it provides an intuitive visual null model for expected patterns of biodiversity under random sampling that allows integrating analyses across -, {gamma}-, and {beta}-scales. Importantly, the method can accommodate comparisons between communities with different species pool sizes, and can be used to examine species turnover both within and between meta-communities. Open Research statement: all code and data used in this manuscript are available at the following link: https://github.com/MoBiodiv/beta_concept

ecology↗

bioRxiv2023

Widespread reductions in body size are paired with stable assemblage biomass.

Biotic responses to global change include directional shifts in organismal traits. Body size, an integrative trait that determines demographic rates and ecosystem functions, is often thought to be shrinking in the Anthropocene. Here, we assess the prevalence of body size change in six taxon groups across 5,032 assemblage time-series spanning 1960-2020. Using the Price equation to partition this change into within-species body size versus compositional changes, we detect prevailing decreases in body size through time. Change in assemblage composition contributes more to body size changes than within-species trends, but both components show substantial variation in magnitude and direction. The biomass of assemblages remains remarkably stable as decreases in body size trade-off with increases in abundance. One-Sentence SummaryVariable within-species and compositional trends combine into shrinking body size, abundance increases and stable biomass.

ecology↗

bioRxiv2022

Synthesis reveals biotic homogenisation and differentiation are both common

It is commonly thought that the biodiversity crisis includes widespread decreases in the uniqueness of different sites in a landscape (biotic homogenization). Using a typology relating homogenization and differentiation to local and regional diversity changes, we synthesize patterns across 283 metacommunities surveyed for 10-91 years, and 54 species checklists (13-500+ years). On average, there is a 0.2% increase in species shared among communities/year (i.e., weak homogenization), but across data sets, differentiation frequently occurs, with no statistically significant change being most common. Local (not regional) diversity frequently underlies composition change, and homogenization is strongly associated with checklist data that have longer durations and large spatial scales. Conservation and management can benefit from the multiscale perspective used here as it disentangles the implications of both the differentiation and homogenization currently unfolding. One-Sentence SummaryBiotic homogenization is most prevalent at large temporal and spatial scales.

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

Local biodiversity change reflects interactions among changing abundance, evenness and richness

Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet understanding covariation of changes to the numbers of individuals, the evenness of species relative abundances, and the total number of species remains limited. Using individual-based rarefaction curves, we introduce a conceptual framework to understand how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined interdependencies between changes in abundance, evenness and richness in more than 1100 assemblages sampled either through time or across space. As predicted, richness changes were greatest when abundance and evenness changed in the same direction, and countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site-to-site changes in abundance, evenness, and richness were often decoupled, and pairwise relationships between changes in these components across assemblages were weak. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages varying through time. Temporal changes in local biodiversity showed greater inertia and stronger relationships between the component changes when compared to site-to-site variation. Local variation in assemblage diversity was rarely due to a passive sample from a more or less static species abundance distribution. Instead, changing species relative abundances often dominated local variation in diversity. Moreover, how changing relative abundances combined with changes to total abundance frequently determined the magnitude of richness changes. Embracing the interdependencies between changing abundance, evenness and richness can provide new information for better understanding biodiversity change in the Anthropocene.

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↗

bioRxiv2021

A millennium of increasing ecosystem diversity until the mid-20th century

Land-use change is widely regarded as a simplifying and homogenising force in nature. In contrast, analysing global land-use reconstructions from the 10th to 20th centuries, we found progressive increases in the number, evenness, and diversity of ecosystems (including human-modified land-use types) across the globe. Ecosystem diversity increased more rapidly after [~]1700CE, then slowed or partially reversed (depending on the metric) following the mid-20th century acceleration of human impacts. Differentiation also generally increased across space, with homogenization only evident in the presence-absence analysis of ecosystem types at the global scale. Our results suggest that human land-use changes have primarily driven increases in ecosystem diversity over the last millennium.

ecology↗

bioRxiv2020

Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs. MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

evolutionary biology↗

bioRxiv2020

Disturbance-induced changes in size-structure promote coral biodiversity

Reef-building coral assemblages are typically species-rich, yet the processes maintaining coral biodiversity remain poorly understood. Disturbance has long been believed to promote coral species coexistence by reducing the strength of competition. However, such disturbance-induced effects have since been shown to be insufficient on their own to prevent competitive exclusion. Nevertheless, Modern Coexistence Theory has revealed other mechanisms by which disturbance and, more generally, environmental variation can favour coexistence. Here, we formulate, calibrate, and analyze a size-structured, stochastic coral competition model using field data from two common colony morphologies. These two coral morphologies, tabular and digitate, differ in their size-dependent vulnerability to dislodgement caused by wave action. We confirm that fluctuations in wave action can promote coral species coexistence. However, using a recently proposed partitioning framework, we show that, contrast to previous expectations, temporal variability in strength of competition did not promote coexistence. Instead, coexistence was enabled by differential fluctuations in size-dependent mortality among competitors. Frequent and intense disturbances resulted in monocultures of digitate corals, which are more robust to wave action than tabular corals. In contrast, infrequent or weak disturbances resulted in monocultures of tabular corals. Coexistence was only possible under intermediate levels of disturbance frequency and intensity. Given the sensitivity of coexistence to disturbance frequency and intensity, anthropogenic changes in disturbance regimes are likely to affect biodiversity in coral assemblages in ways that are not predictable from single population models.

ecology↗

bioRxiv2019

Temperature-related biodiversity change across temperate marine and terrestrial systems

Climate change is reshaping global biodiversity as species respond to changing temperatures. However, the net effects of climate-driven species redistribution on local assemblage diversity remain unknown. Here, we relate trends in species richness and abundance from 21,500 terrestrial and marine assemblage time series across temperate regions (23.5-60.0{degrees}) to changes in air or sea surface temperature. We find a strong coupling between biodiversity and temperature changes in the marine realm, which is conditional on the baseline climate. We detect increases in species richness with increasing temperature that is twice as pronounced in warmer locations, while abundance declines with warming in the warmest marine locations. In contrast, we did not detect systematic temperature-related richness or abundance trends on land, despite a greater magnitude of warming. We also found no evidence for an interaction between biodiversity change and latitude, further emphasizing the importance of baseline climate in structuring assemblages. As the world is committed to further warming, significant challenges remain in maintaining local biodiversity amongst the non-uniform inflow and outflow of "climate migrants" across distinct regions, especially in the ocean.

ecology↗