Biology subjects

Berenguer, E.

Publications and source records attributed to Berenguer, E..

8 recordsLinked to original sources

bioRxiv2026

Unsupervised source separation and clustering of soundscape recordings predicts avian richness in hyperdiverse systems

1: Passive Acoustic Monitoring (PAM) has emerged as a leading approach for biodiversity research, but analysing the vast quantities of data produced by this method remains challenging. Acoustic indices are often employed to estimate species richness in soundscape recordings, but their generalisability and overall efficacy in speciose regions has increasingly been challenged. An alternative, multi-species classification models, still suffer from performance limitations, particularly in the tropics. 2: We introduce an unsupervised approach that estimates avian species richness using an integrated source separation model trained on birds (BirdMixIT), a leading bird vocalization embedding model (Perch 2.0), and hierarchical agglomerative clustering. We count the clusters of embeddings generated from separated channels to estimate the species richness in recordings at differing timescales. 3: We test the generalisability and predictive performance of our approach, "source-clustering", using a large combined dataset featuring 103 total hours of manually-annotated soundscape recordings from the Amazon rainforest in Peru and Brazil. To compare the performance of source-clustering to existing approaches, we estimated species richness in the same recordings with both traditional acoustic indices and Perch classifications at various confidence thresholds. 4: Our source-clustering method performed consistently well between our separate datasets. Source-clustering performed better for predicting avian species richness than traditional acoustic indices at all levels, and was complementary with Perch, performing similarly overall to its best settings combinations, though it was more robust for short recordings, and should be more resilient in locations with less training data. Source-clustering generally predicted species richness better than the best-performing Perch settings at the 15-second, 1-minute, and 15-minute temporal resolutions, while most settings of Perch performed better at the 1-hour resolution. 5: Source-clustering can complement or exceed the performance of presently established methods for estimating avian species richness from soundscape recordings, namely traditional acoustic indices and the out-of-box versions of leading automated identification modes. This is particularly true at narrow temporal resolutions, in systems where training data is scarce, and where species density is high enough to generate significant overlapping vocalisations, rendering it especially useful in hyperdiverse tropical ecosystems where other methods for interpreting soundscape recordings face persistent challenges.

bioinformatics↗

bioRxiv2026

Anthropogenic disturbance inverts microclimate stratification in tropical forests

Tropical rainforests generate and maintain their own microclimate regimes and the resultant cooler, more humid and stable environments foster the hyperdiversity typical of these ecosystems. Although the temporal and spatial (horizontal) distributions of microclimates have been relatively well studied, the vertical dimension has received less attention, and little is known about how forest disturbance affects the vertical stratification of microclimates in tropical forests. In this study, we examine how the vertical distribution of temperatures varies between undisturbed and burned Amazonian forests. We installed five vertical transects with temperature dataloggers distributed at 7 different heights to collect data over multiple days during the end of the dry season. We investigated how anthropogenic disturbance (fire) mediates the vertical stratification of microclimate and whether microclimate buffering (i.e, the difference between understorey and canopy temperatures) varies according to the forest structure. We showed that anthropogenic disturbance can cause an inversion in the vertical stratification of microclimates, with burned forests having hotter temperatures (up to 2 {degrees}C) in the understorey than in the canopy during the day - the opposite of what is found in undisturbed forests (typically 3 {degrees}C cooler). During the night, while understorey and canopy temperatures are similar in undisturbed forests, we found that, in burned forests, understorey temperatures were up to 2 {degrees}C cooler than in the canopy. Microclimate buffering by day was best explained by aboveground carbon stocks, with higher temperature buffering in more carbon rich forests. Our study shows that anthropogenic disturbance alters the vertical stratification of temperatures in Amazonian forests, leading to significant temporal changes along the diel cycle. Future research should focus on understanding these changes across a wider range of disturbance regimes, and explore the consequences for biodiversity and ecosystem functions from the canopy to the forest floor.

ecology↗

bioRxiv2025

Hyperdominance and rarity in Amazonian secondary forests

Recent studies have shown that a few tree species dominate abundance and carbon storage in undisturbed Amazonian forests. However, this pattern remains poorly understood in forests regrowing after deforestation. Understanding dominance patterns in secondary forests is important as it could improve insights into their functioning and guide management and restoration efforts. We used unweighted and novel plot-weighted approaches to assess hyperdominance in abundance and carbon storage of trees and palms during secondary forest recovery, using data from 102 plots across four regions in the eastern Amazon, separated by an average distance of 600 km (range: 150-1,000 km). Secondary forests show extreme hyperdominance in all approaches, with just 16-25 species ([~]3.6-5.6%) accounting for over 50% of abundance and carbon storage. A small subset of species ([~]9%) were found across all regions and successional stages, highlighting their key role in ecosystem structure and function during forest regrowth. Annona exsucca, Cecropia palmata, Tapirira guianensis, Inga alba, Attalea maripa, Amphiodon effusus, Banara guianensis, and Vismia guianensis consistently emerged as hyperdominant across stem size classes, approaches, and metrics, jointly accounting for roughly 16-27% of total abundance and carbon in Amazonian secondary forests. For larger stems >10cm DBH, hyperdominant species exhibited lower wood density compared to non-hyperdominant species across all successional stages, suggesting these specialist pioneers have distinct ecological strategies from the rest of the community. Our findings indicate that secondary forest functioning can be largely predicted by a relatively limited set of species, providing a framework for future research ranging from ecophysiology to remote sensing of canopy traits and restoration planning.

ecology↗

bioRxiv2025

Combined interventions are required to reverse biodiversity and carbon losses in tropical forest frontiers

Halting deforestation and promoting restoration are at the core of biodiversity and climate strategies in tropical forest regions. Avoiding forest disturbances is also critically important but has received far less attention, and there is a lack of clarity about the cost-effectiveness of these three different interventions. We provide the first comparison of the biodiversity and carbon benefits and costs associated with each intervention, comparing observed and counterfactual outcomes based on in-depth field assessments and high-resolution remote sensing in Amazonian Brazil. Avoiding forest disturbances delivered the greatest benefits and was more cost-effective than either avoiding deforestation or restoration, with results being robust to a range of benefit and cost assumptions. However, combined interventions delivered the greatest gains and were essential to reverse biodiversity and carbon losses.

ecology↗

bioRxiv2023

Listening to tropical forest soils

PAM has proven to be an effective tool for monitoring biotic soundscapes in the marine, terrestrial, and aquatic realms. Recently it has been suggested that it could also be an effective method for monitoring soil fauna, but has so far been used in only four studies in temperate and polar regions. We present the first study of soil soundscapes in tropical forests, using a novel analytical pipeline allowing for the use of in-situ recording of soundscapes with minimal soil disturbance. We found significant differences in soil soundscapes between burnt and unburnt forests and the first indications of a diel cycle in soil soundscapes. These promising results and methodological advances highlight the potential of PAM for large-scale and long-term monitoring of soil biodiversity. We use the results to discuss research priorities, including relating soil biophony to biodiversity, community structure and ecosystem functioning, and the use of appropriate hardware and analytical techniques.

ecology↗

bioRxiv2022

Heterologous expression of a lycophyte protein enhances angiosperm seedling vigor

Seedling vigor is a key agronomic trait that determines juvenile plant performance. Angiosperm seeds develop inside fruits and are connected to the mother plant through vascular tissues. Their formation requires plant-specific genes, such as BREVIS RADIX (BRX) in Arabidopsis thaliana roots. BRX family proteins are found throughout the angiosperms but also occur in non-vascular bryophytes and non-seed lycophytes. They consist of four conserved domains, including the tandem "BRX-domains". We found that bryophyte or lycophyte BRX homologs can only partially substitute for Arabidopsis BRX (AtBRX) because they miss key features in the linker between the BRX-domains. Intriguingly however, expression of a BRX homolog from the lycophyte Selaginella moellendorffii (SmBRX) in A. thaliana wildtype background confers robustly enhanced root growth vigor that persists throughout the life cycle. This effect can be traced back to a substantial increase in seed and embryo size, and can be reproduced with a modified, "SmBRX-like" variant of AtBRX. Our results thus suggest that BRX variants could serve as biotechnological tools to boost seedling vigor and shed light on the activity of ancient, non-angiosperm BRX family proteins.

plant biology↗

bioRxiv2021

Global trade-offs in tree functional traits

AO_SCPLOWBSTRACTC_SCPLOWDue to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. When considering trait relationships across the entire plant kingdom, plant trait frameworks typically must omit traits unique to large woody species, thereby limiting our understanding of how these distinct ecological pressures shape trait relationships in trees. Here, by considering 18 functional traits--reflecting leaf economics, wood structure, tree size, reproduction, and below-ground allocation--we quantify the major axes of variation governing trait expression of trees worldwide. We show that trait variation within and across angiosperms and gymnosperms is captured by two independent processes: one reflecting tree size and competition for light, the other reflecting leaf photosynthetic capacity and nutrient economies. By exploring multidimensional relationships across clusters of traits, we further identify a representative set of seven traits which captures the majority of variation in form and function in trees: maximum tree height, stem conduit diameter, specific leaf area, seed mass, bark thickness, root depth, and wood density. Collectively, this work informs future trait-based research into the functional biogeography of trees, and contributes to our fundamental understanding of the ecological and evolutionary controls on forest biodiversity and productivity worldwide.

ecology↗

bioRxiv2020

Optimising tropical forest bird surveys using passive acoustic monitoring and repeated short-duration point counts

Estimation of avian biodiversity is a cornerstone measure of ecosystem condition, with turnover in avian community composition underpinning many studies of land-use change in tropical forests. Surveys conducted using autonomous recorders have been frequently found to be more efficient than traditional point-count surveys. However, there has been limited research into optimal survey duration, despite autonomous recordings allowing for many more repeats of short-duration surveys with relative ease in comparison to traditional survey methods. We use an acoustic dataset collected from a region of very high avian biodiversity - the eastern Brazilian Amazon - to test the effect of using short-duration surveys to increase temporal coverage without increasing total survey duration. We use this dataset to assess whether a survey protocol consisting of 240 15-second surveys at 29 locations, short-duration surveys, has an influence on resulting alpha and gamma diversity, and detection frequency, than standard-duration surveys of four 15-minute surveys per location. We find that repeated short-duration surveys outperform longer duration surveys in every metric considered herein, with short-duration surveys predicted to detect approximately 50% higher alpha diversity, and 10% higher gamma diversity. Short-duration surveys also detect species more often, at more survey locations. Conversely, standard-duration surveys are almost four times more likely to produce false negatives (i.e. to fail to detect species presence). Whilst there is no difference between the proportion of uncommon species detected by the two methods, when considering species detected multiple times at multiple locations, short-duration surveys detected three times more uncommon species than standard-duration surveys. We conclude that short-duration recorded surveys should be considered the primary method for sampling the species richness of bird communities in tropical forests and is likely to be preferable to longer duration or traditional surveys in most environments.

ecology↗