Biology subjects

Lees, A. C.

Publications and source records attributed to Lees, A. C..

14 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↗

bioRxiv2026

Chromosome-level genome assembly of the Endangered scaly-sided merganser Mergus squamatus with insight into its demographic history

The scaly-sided merganser, Mergus squamatus, is an Endangered piscivorous duck which has been declining since the late 1900s due to habitat loss, over-hunting, and climate change. Despite being a species of global conservation concern and subject to ex- and in-situ conservation efforts, genomic research has been limited, hindering our understanding of its population genetic status and evolutionary history. In this study, we present the first fully annotated, chromosome-level genome for the scaly-sided merganser, generated using Oxford Nanopore long reads, Illumina short reads, and Hi-C sequencing. The final assembly spans 1.1 Gb across 307 scaffolds, 64 of which are anchored into 35 chromosomes, covering 99.5% of the genome. The assembly shows high contiguity (N50 = 84.3Mb) and completeness, with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 98%. Repeat sequences comprise 9.55% of the genome. Homology-based gene annotation identified [~]15,200 protein-coding genes. A complete 16,624 bp mitochondrial genome was also assembled and annotated. Synteny analysis revealed strong chromosomal conservation across the wider Anatidae family, with evidence of lineage-specific rearrangements. Pairwise Sequential Markovian Coalescence modelling indicates recent stability in the effective population size of the species, with past declines coinciding with Pleistocene glacial cycles. Our high-quality genome provides an essential resource for conservation genomic and evolutionary studies of the scaly-sided merganser, supporting ongoing efforts to manage and protect this threatened species.

genomics↗

bioRxiv2025

The reliability of acoustic classification models for determining avian vocalisation patterns

Automated detection and classification of species vocalisations offers the potential to utilise acoustic datasets across unprecedented spatial and temporal scales. However, classification algorithms inevitably generate errors, and error rates vary with context. While methods for quantifying error rates in ecoacoustics are well established, there is limited research on what level of model performance is sufficient to reliably determine avian vocalisation patterns. Using an extensive fully expert-labelled acoustic dataset from Peru (18 hours, 6 sites), we examined changes in the probability of detecting target bird vocalisations in the first hour after dawn to address three key questions: (1) How sensitive are models predicting detection probability over time to reductions in classification accuracy? (2) To what extent does aggregating detections over longer time periods impact classification accuracy? Additionally, we used the labelled dataset to assess how the creation and composition of a test dataset for assessing classifier performance can impact the reliability of accuracy metrics: (3) Are estimates of classification precision robust when test and deployment datasets are not independent and identically distributed? Our results indicate that poor classification performance--especially low precision--can lead to misleading inferences about temporal patterns of vocalisations. Aggregating classifier predictions over longer time periods improved recall but often resulted in misleading patterns of vocal behaviour by reducing precision and temporal resolution. We also demonstrate that precision can be substantially overestimated when species presences are rarer in the deployment dataset than in test data. These findings highlight the importance of cautious application of automated classification in acoustic ecology and the need for accuracy assessment methods tailored to the intended ecological analysis.

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↗

bioRxiv2025

Land-use change undermines the stability of avian functional diversity

Land-use change causes widespread shifts in the composition and functional diversity (FD) of species assemblages, yet the impacts on ecosystem resilience remain uncertain. Stability of ecosystem functioning may increase after land-use change because the most sensitive species are removed, leaving more resilient survivors (Balmford, 1996; Clavel et al., 2010; McKinney & Lockwood, 1999). Alternatively, ecosystems may be destabilized if land-use change reduces functional redundancy, accentuating the ecological impacts of further species loss (Fonseca & Ganade, 2001; McCann, 2000). Current evidence is inconclusive, partly because trait data have not been available to quantify functional stability at sufficient scale. Here, we use morphological measurements of 3696 bird species to estimate shifts in functional redundancy following recent anthropogenic land-use change at 1281 sites worldwide, and then assess the sensitivity of these altered assemblages to future species loss. We find that the proportion of disturbance-tolerant species increases after land-use change, but that this does not increase stability. Instead, we show that functional redundancy is reduced and that further species loss will destabilize ecosystem function because relatively few additional extinctions lead to accelerated losses of FD, particularly in trophic groups delivering important ecological services such as seed dispersal and insect predation. Our analyses reveal that land-use change may have major undetected impacts on the stability of key ecological functions, hindering the capacity of natural ecosystems to absorb further declines in functionality caused by ongoing perturbations.

ecology↗

bioRxiv2024

Elevational constraints on flight efficiency shape global gradients in avian wing morphology

Wings with elongated shape or larger surface area are associated with increased flight efficiency and dispersal ability in a wide range of animals from insects to birds 1-4. Inter- and intraspecific variation in these attributes of wing shape is determined by a range of factors - including foraging ecology, migration and climatic seasonality 5-8 - all of which may drive latitudinal gradients in wing morphology 9,10. A separate hypothesis predicts that wing shape should also follow an elevational gradient because air density and oxygen supply decline with altitude 11, altering the aerodynamics of flight, and driving the evolution of more efficient wings in high-elevation species to compensate for reduced lift 12,13. However, previous analyses have found only mixed support for the thin-air hypothesis 14-18, and we currently lack a global synthesis of elevational gradients in wing design for any taxonomic group. In this study, we use phylogenetic comparative models to explore elevational effects on wing morphology in 9986 bird species, while accounting for multiple climatic and ecological attributes, including latitude, temperature seasonality, body mass, aerial lifestyle and migration. We found that relative wing elongation (hand-wing index) and wing area increase with elevation, particularly in the upper montane zone (>4 km above sea level). These results confirm a pervasive elevational gradient in avian wing morphology, highlighting the role of aerodynamic constraints as key mechanisms shaping global patterns of trait evolution in flying animals.

evolutionary biology↗

bioRxiv2023

Climate-smart prioritisation of tropical Key Biodiversity Areas for protection in response to widespread temperature novelty.

Key Biodiversity Areas (KBAs) are a cornerstone of 21st century area-based conservation targets. In tropical KBAs, biodiversity is potentially at high risk from climate change, because most species reside within or beneath the canopy, where small increases in temperature can lead to novel climate regimes. We quantify novelty in temperature regimes by modelling hourly temperatures below the forest canopy across tropical KBAs between 1990 and 2019. We find that up to 66% of KBAs with tropical forest are likely to have transitioned to novel temperature regimes. Nevertheless, 34% of KBAs are providing refuge from novelty, 58% of which are not protected. By conducting the first pan-tropical analyses of changes in below-canopy temperatures, we identify KBAs that are acting as climate refugia and should be prioritised as candidates for expansion of the conservation network in response to the post-2020 Global Biodiversity Framework target to conserve 30% of land area by 2030.

ecology↗

bioRxiv2023

Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests

1. Seed dispersal - one of the many services supplied by biodiversity - is a critical process underpinning the resilience of tropical forests. Forest loss or degradation typically leads to defaunation, altering seed transfer dynamics and impairing the ability of forested habitats to regenerate or recover from perturbation. However, the extent of defaunation, and its likely impacts on the seed dispersers needed to restore highly degraded or clear-felled areas, remains poorly understood, particularly in human-modified tropical forest landscapes. 2. To quantify defaunation of seed-dispersing birds, we used field survey data from more than 400 transects in three regions of Brazil, first comparing the recorded assemblages with those predicted by geographic range maps, and then assessing frugivore habitat associations across gradients of land cover modification at local scales. 3. We found that current bird assemblages have lower functional trait diversity than predicted by species range maps in Amazonia (4-6%), with a greater reduction (28%) for the Atlantic Forest region, which has been more heavily deforested for a longer period. These reductions are probably caused by local extinctions of forest-dependent bird species following land-use change. 4. Direct measures of seed dispersal are difficult to obtain, so we instead focused on the potential for seed transfer inferred from shared species occurrence between land cover types. Of 83 predominantly frugivorous bird species recorded in relatively intact forests, we show that 10% were absent from degraded forest, and 57% absent from the surrounding matrix of agricultural land covers, including many of the large-beaked species. Of 112 frugivorous species using degraded forest, 47% were absent from matrix habitats. 5. Our findings suggest that degraded forest can supply seed dispersal services to adjacent cleared lands, and that direct transfer of seeds from intact forest to cleared areas may be limited, particularly for large-seeded trees. We conclude that resilience of tropical forest landscapes is best achieved by protecting a mosaic of forest types, including sufficient core areas of intact forest surrounded by buffer zones of degraded forest.

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↗

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↗

bioRxiv2020

How many bird and mammal extinctions has recent conservation action prevented?

Aichi Target 12 of the Convention on Biological Diversity (CBD) aims to prevent extinctions of known threatened species. To measure its success, we used a Delphi expert elicitation method to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993 - 2020 (the lifetime of the CBD) and 2010 - 2020 (the timing of Aichi Target 12). We found that conservation prevented 21-32 bird and 7-16 mammal extinctions since 1993, and 9-18 bird and 2-7 mammal extinctions since 2010. Many remain highly threatened, and may still become extinct in the near future. Nonetheless, given that ten bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9-4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions.

ecology↗

bioRxiv2018

Climate, habitat, and geographic range overlap drive plumage evolution

Organismal appearances are shaped by selection from both abiotic and biotic drivers 1-5. For example, Glogers rule describes the pervasive pattern that more pigmented populations are found in more humid areas 1,6,7, and substrate matching as a form of camouflage to reduce predation is widespread across the tree of life 8-10. Sexual selection is a potent driver of plumage elaboration 5,11, and species may also converge on nearly identical colours and patterns in sympatry, often to avoid predation by mimicking noxious species 3,4 To date, no study has taken an integrative approach to understand how these factors determine the evolution of colour and pattern across a large clade of organisms. Here we show that both habitat and climate profoundly shape avian plumage. However, we also find a strong signal that many species exhibit remarkable convergence not explained by these factors nor by shared ancestry. Instead, this convergence is associated with geographic overlap between species, suggesting strong, albeit occasional, selection for interspecific mimicry. Consequently, both abiotic and biotic factors, including interspecific interactions, are potent drivers of phenotypic evolution.

evolutionary biology↗

bioRxiv2017

Diversification, sympatry, and the emergence of mega-diverse tropical assemblages

Geographic gradients in species richness, including latitudinal gradients, can arise from geographic variation in any of three mechanisms: the geologic age of habitats, net rates of evolutionary diversification, or rates of sympatry among diversifying lineages. Here we show that variation in rates of sympatry is a dominant force structuring geographic richness gradients in birds. Species-rich sites contain disproportionately high numbers of recently diverged sympatric species but contain lineages with slower-than-average diversification rates. The positive sympatry-diversity relationship consistently overwhelms the negative diversification-diversity relationship, particularly among high-diversity sites (>250 species). These patterns repeat across biomes and continents with striking regularity, and remain consistent across multiple timescales, including the recent evolutionary past. Biogeographic and evolutionary patterns in birds are consistent with a role for ecological conditions in promoting species coexistence, which allows sister species to co-occur and potentially lowers extinction rates.

ecology↗