Biology subjects

Safi, K.

Publications and source records attributed to Safi, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Fine-scale flight behaviour reveals eagles' response to different uplift sources and highlights observational gaps in high-resolution weather models.

Understanding how animals respond to their physical environment requires environmental observations at the scale at which behavioural decisions are made. For soaring birds, the coarse resolution of weather products has long hindered the analysis of their behavioural response to fine-scale atmospheric dynamics, forcing uplift sources to be inferred largely from behaviour itself. Here, we combined high-resolution movement data from 24 golden eagles with the kilometre-scale COSMO weather model. We first classified thermal, orographic, and gravity-wave uplifts using independent atmospheric predictors and then quantified the birds' use of each uplift type and their fine-scale behavioural responses. Eagles relied predominantly on thermals, but opportunistically adjusted their use of uplift sources seasonally. The birds' flight behaviour could not reliably indicate which uplift type was primarily used, and thus suggests that both atmospheric processes and behavioural responses are better described as continua than discrete categories. Finally, we compared vertical wind velocities derived from eagles soaring behaviour with those modelled by the COSMO weather model, showing that most of the thermals exploited by eagles remain unresolved at kilometre-scale model resolution. Our results demonstrate how high-resolution weather models provide new insights into bird movement decisions, while also highlighting the potential of soaring birds as biologically embedded atmospheric sensors that could help closing the resolution gap in atmospheric models.

ecology↗

bioRxiv2026

Self-thresholding hierarchical outlier-detection for animal movement tracks

1. Erroneous locations are ubiquitous in animal tracking data and notoriously difficult to remove without supervision. Whether caused by poor satellite geometry, atmospheric interference, tag malfunction, or deliberate GNSS jamming and spoofing, they propagate into estimates of movement rates, home ranges, habitat selection and behavioural states. Existing procedures rely on fixed speed or distance thresholds, require regular sampling, depend on model-based smoothing that is hard to fit to heterogeneous data, or stop at diagnostic plots leaving the decision to the analyst. Most also share a structural blind spot: they catch fixes whose transitions to neighbours are extreme, but miss spatially coherent blocks whose interiors look metrically normal. 2. I introduce mt_clean_track(), a function in the R package move2utils that returns a track with outlier flags and a categorical read-out of what kind of evidence triggered each flag. It combines four ideas: data-driven thresholds the user need not specify; four complementary detectors, each catching an error class the others structurally cannot (a Brownian-bridge geometric residual, a movement-metric probability test, a scale-invariant path-versus-displacement detour ratio, and a step-level physiological speed cap); a graph-based block-expansion step recovering coherent error trains beyond the reach of per-fix scoring; and an agreement-based rule building a consensus flag from the number of single-method flags and their certainty. 3. I evaluate the cascade on synthetic trajectories spanning isolated spikes, drift segments, spoofing blocks, stationary-halo jitter and multi-state migration anomalies, against four established alternatives (naive speed cap, atlastools, trip::sda, SDLfilter). It recovers the injected outliers on every track, achieves the highest cross-cohort mean $F_1$ ($0.86$ at zero user parameters; nearest competitor $0.80$ hand-tuned), and alone recovers the coherent spoofing block with usable precision (30/30 versus 1-3/30). On a clean reference track only trip::sda produces substantial false positives. A directional decomposition of the bridge residual further reframes detection as error classification: a fix's position in a two-dimensional residual plane reveals whether the error is perpendicular drift, along-track jump, or extreme on both axes. 4. Per-location scores, data-driven thresholds, an error-morphology read-out and a parameter-free default entry point are intended to make outlier screening a routine, reproducible step in the movement-ecology pipeline. The outlier removal cascade is part of the move2utils package and available at https://github.com/move2universe/move2utils.

ecology↗

bioRxiv2026

move2utils: a utility toolkit for the move2 ecosystem

1. Studying animal movement at the population scale requires a stable, modern software substrate. Within R, the legacy move package supplied that substrate for over a decade, but its sp/rgeos backbone has been retired. The successor package move2 deliberately confined its scope to the data class and core movebank API functions. 2. The analytical machinery of move, namely dynamic Brownian-bridge utilisation distributions, the directional bivariate-Gaussian variant, corridor segmentation, and along-track thinning, was left to port to the modern sf/terra stack. 3. We present move2utils, an R package that completes and complements that transition. move2utils provides move2-native ports of the move analytical functions, preserves the original C kernels where they exist, and replaces the deprecated spatial scaffolding around them. It additionally ports some of the legacy R code to faster C kernels. move2utils also exposes novel outlier-detection methodology described in detail in a companion paper. 4. The package is open-source (GPL [≥] 3), is developed on the MPCDF GitLab and mirrored on GitHub for public installation, and ships with vignettes and a CI-tested check suite. We illustrate it with a worked example on real tracking data and synthetic datasets.

ecology↗

bioRxiv2026

Early avoidance of human-dominated landscapes by juvenile Alpine golden eagles

O_LIThe expanding human footprint drives profound transformations in species, including not only morphological trait loss but also behavioural trait extinction. In contrast to behavioural trait extinction, which entails a reduction in genetic variability, behavioural plasticity maintains behavioural trait diversity and the associated genetic variability required for evolutionary adaptation. Yet, while behavioural plasticity shaping non-human capacity to coexist with humans has evolved under past, human-modified, environmental conditions, few studies have examined whether species retain a level of behavioural plasticity after past interactions with humans. C_LIO_LIUsing data from 64 juveniles golden eagles (Aquila chrysaetos) from a population demographically recovering after centuries of persecution, yet still restricted to less human-dominated alpine massifs, we tested whether human avoidance is innate or learned through experience during dispersal or parental influences during the pre-dispersal period. We performed a Principal Component Analysis (PCA) on landscape features used during the pre-dispersal and the first fifteen weeks of the dispersal phase, and used Mahalanobis distance as an indicator for quantifying changes in individual spatial behaviour over time. C_LIO_LIThe lower frequency of use of human-dominated landscape features, compared with the more sparsely populated mid- and high-elevation landscape features, resulted from individuals consistent use of similar landscape features across the pre-dispersal and dispersal periods. Avoidance of humans was therefore better explained by a learning or imprinting process prior to dispersal, which predisposed individuals to use landscape features similar to those experienced during pre-dispersal, rather than by learning during dispersal, or by an innate avoidance. C_LIO_LIImprinting on natal habitat features corroborates the observed limited range expansion of the alpine population beyond the massif borders. Differences among European populations in range recolonisation suggest contrasting histories of persecution, which may have left varying degrees of behavioural plasticity across populations. C_LIO_LIAs a guide for future conservation priorities, these findings underscore the need to reconstruct past conditions and/or to document contemporary animal behaviour in order to build a library of behaviours that can be used in the future to track behavioural changes. C_LI

animal behavior and cognition↗

bioRxiv2025

Overcoming Innate Lateralization Improves Avian Flight Performance

Behavioural lateralization--side-bias or handedness--enhances neurological processing efficiency but creates a dilemma for behaviours requiring symmetry. Flight demands symmetric execution, particularly when optimising energy extraction from atmospheric updrafts during soaring. Using high-resolution biologging of 31 juvenile European honey buzzards from fledging through their first intercontinental migration leg, we show that strong lateralised circling was prevalent immediately after fledging (74%). This proportion declined to parity by migration onset, indicating developmental adjustment with increasing experience. During migration, side-biased circling was linked to wider turns, reduced altitude gain, and daily travel distances shortened by 13%. These findings reveal a direct trade-off between the neurological efficiency of lateralization and the aerodynamic requirements of efficient soaring. Our results challenge the notion that lateralization is universally adaptive and highlight how experience and ontogeny modulate the balance between task difficulty, neural specialization, and ecological performance.

animal behavior and cognition↗

bioRxiv2025

Cascading carry-over effects of early activity phenotypes in golden eagles

1.Early-life conditions are often associated with fitness of animals later in life. Although recent studies show that environmental conditions during development affect the formation of early behavioural phenotypes we have a limited understanding of the cascade of life-history transitions from early phenotypes to fitness relevant behaviours in later life stages. Here, we used GPS and body-acceleration data of 35 juvenile golden eagles (Aquila chrysaetos) to investigate the association between nestling body condition and activity levels (ODBA), the relationship of nestling activity with the timing of fledging and post-fledging activity, and the effects of post-fledging activity on post-fledging movements and the timing of dispersal. We found that nestlings with good body condition also showed increased activity levels. Active nestlings fledged earlier and remained more active after fledging than passive nestlings during early post-fledging. Increased post-fledging activity levels were related to an increased number of pre-dispersal forays and an early timing of dispersal. Even though some effects showed reduced certainty, our results provide evidence for downstream effects of behavioural differences due to early-life conditions. They suggest that early activity phenotypes of nestlings drive the timing of subsequent life-history transitions, thereby representing a key mechanism that links early life conditions with future performance.

ecology↗

bioRxiv2025

Timing of independence is explained by movement ability, but depends on how independence is defined for a long-lived raptor

Many young animals must gain independence from parental care by acquiring the necessary skills for survival. Thus, the rate of skill acquisition can predict how long juveniles remain with their parents before emigrating from the natal territory. Yet in some systems, young animals acquire adult-like skills and the capacity to be independent long before they emigrate. This raises the question of why the timing of emigration decouples from the rate of skill acquisition, resulting in extended parental care. We addressed this by leveraging GPS tracking data from juvenile golden eagles (Aquila chrysaetos), which learn to fly and to hunt while remaining with their parents for 61-283 days after fledging. Young golden eagles often go on excursions without their parents outside of their natal territories before emigration. We expected flight performance to predict the timing of excursions better than the timing of emigration, which should be more influenced by external factors. In a set of time-to-event models, we predicted the rate of excursions and of emigration using metrics of soaring flight performance or of daily movement. Contrary to our prediction, we found that soaring performance failed to predict the rate of either excursions or emigration, whereas daily movement predicted both rates, but inconsistently. This was likely because those coarser metrics captured motivation and weather in addition to flight skills. Thus external factors seem more likely to explain the timing of independence and internal development--in this case of flight skills--may be completed quickly. Juveniles may delay emigration not due to lack of skill, but because the costs of leaving parental care outweigh the benefits. The difference we discovered between when individuals were capable of independence and when they committed to it may obscure the more general link between skill acquisition and the end of parental care in other systems as well.

animal behavior and cognition↗

bioRxiv2025

MoveTraits - A database for integrating animal behaviour into trait-based ecology

Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits - standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure, and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species acclimation and adaptive capacity to environmental change. We outline a vision for a living global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology, and (3) providing information on multi-level (species, individual, within-individual) trait variation. We present a proof-of-concept MoveTraits database with 55 mammal and 108 bird species, demonstrating calculation workflows for 5 traits across multiple time scales. Movement traits have significant potential to improve trait-based global change predictions and contribute to global biodiversity assessments as Essential Biodiversity Variables. By making animal movement data more accessible and interpretable, this database could bridge the gap between movement ecology and biodiversity policy, facilitating evidence-based conservation.

ecology↗

bioRxiv2024

Golden eagles regularly use gravity waves to soar in the Alps: new insights from high-resolution weather data

1Soaring flight developed as a result of behavioural and morphological adaptations that allow birds to reduce the metabolic cost of flight by harnessing the energy available in the atmosphere. Despite an increased attention given in the last decades to the physics and ecology that allow soaring flight, its study has been limited by the generally low spatio-temporal resolution of available atmospheric data. This constrained our ability to quantify the atmospheric conditions that allow soaring, and limited our understanding of its flexibility in different uplift conditions. While the use of updraughts such as thermals and orographic lifting are well described in the literature (albeit only quantified through atmospheric proxies), the use of others, such as gravity waves, was hypothesised but largely undocumented. Recent advancements in high-resolution atmospheric modelling, with hourly output available at the kilometer-scale grid spacing, offer new opportunities to investigate the flexibility of soaring flight in response to complex atmospheric dynamics. In this study, we used a combination of a high-resolution atmospheric analysis and high-resolution GPS tracking data to characterise the updraught sources used by golden eagles, Aquila chrysaetos, in the European Alps. We document that golden eagles in this region repeatedly use gravity waves, and that while thermals were still the main updraught source used for soaring, gravity waves were involved in at least 19% of the inspected soaring segments. In winter, when thermals were more scarce, the quasi-totality of soaring events were powered by gravity waves or orographic lifting, largely expanding the environmental energy available to soaring birds and therefore the landscape connectivity in topographically complex regions. Our results also emphasise the difficulty to distinguish between convective (thermals) and dynamic updraught sources, as these co-occur within the boundary layer over complex terrain.

ecology↗

bioRxiv2023

Wild sulphur-crested cockatoos match human activity rhythms to access food in the urban environment

AO_SCPLOWBSTRACTC_SCPLOWUrban areas are growing rapidly across the globe, and wild species are occupying this new environment. Despite offering potential resources, disparities in the urban matrix can lead to specific challenges, with pathways and resources fragmented in space and time. Urban-dwelling species would therefore benefit from learning when and where to exploit human derived food. Here, we investigate whether birds synchronize the exploitation of the most urbanized areas to match food-provisioning patterns, using the example of the popular hand-feeding of sulphur-crested cockatoos (Cacatua galerita) in Sydney, Australia. We monitored the provisioning behaviour of people via a large-scale citizen science program, and tested for synchrony with the spatial behaviour of eight birds equipped with GPS loggers. Our data show that sulphur-crested cockatoos exploited the urban environment, relying on the green areas of the city; importantly, they also visited buildings within more urbanized areas. Sulphur-crested cockatoos used urban space with specific time patterns particularly matching human recreational feeding routines, suggestive of time-place learning. We show that urban environments provide daily temporal foraging resources for which species adjust behaviorally. Thus, our data support the general claim that retaining green spaces in cities is essential to sustainable urban planning, and key to allow species to exploit the urban environment, particularly in areas of high human density. This study builds on the literature investigating human-animal interactions, expanding our understanding of animals exploitation of human behavior. Further research should include the impact of such interactions on urban wildlifes fitness according to their cognitive and behavioral traits.

animal behavior and cognition↗

bioRxiv2023

Gaining proficiency in flight transforms energy landscapes during ontogeny

The heterogeneity of the physical environment determines the cost of transport for animals, shaping their energy landscape. Animals respond to this energy landscape by adjusting their distribution and movement to maximize gains and reduce costs. Much of our knowledge about energy landscape dynamics focuses on factors external to the animal, particularly the spatio-temporal variations of the environment. However, an animals internal state can significantly impact its ability to perceive and utilize available energy, creating a distinction between the "fundamental" and the "realized" energy landscapes. Here we show that the realized energy landscape varies along the ontogenetic axis. Locomotor and cognitive capabilities of individuals change over time, especially during the early life stages. We investigate the development of the realized energy landscape in the Central European Alpine population of the golden eagle Aquila chrysaetos, a large predator that requires negotiating the atmospheric environment to achieve energy-efficient soaring flight. We quantified weekly energy landscapes using environmental features for 55 juvenile golden eagles, demonstrating that energetic costs of traversing the landscape decreased with age. Consequently, the potentially flyable area within the Alpine region increased 2,170-fold during their first three years of independence. Our work contributes to a predictive understanding of animal movement by presenting ontogeny as a mechanism shaping the realized energy landscape.

animal behavior and cognition↗

bioRxiv2022

EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action

The global biodiversity crisis threatens the natural world and its capacity to provide benefits to humans into the future. The conservation of evolutionary history, captured by the measure phylogenetic diversity (PD), is linked to the maintenance of these benefits and future options. The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to identify species for conservation action that embody large amounts of threatened evolutionary history. In 2017, we convened a workshop to update the EDGE metric to incorporate advances in the field of phylogenetically-informed conservation. Building on that workshop, we devised the metric EDGE2, which we present here. EDGE2 uses a modular, tiered approach to provide priority rankings--and associated measures of uncertainty in both phylogenetic and extinction risk data--for all species in a clade. EDGE2 takes into account the extinction risk of closely-related species to better reflect the contribution a species is expected to make to overall PD in the future. We applied EDGE2 to the worlds mammals to identify an updated list of priority EDGE species and compare the results with the original EDGE approach. Despite similarity in the priority lists produced between EDGE and EDGE2, EDGE2 places greater priority on species with fewer close relatives on the Tree of Life. As we approach a crossroads for global biodiversity policy, EDGE2 exemplifies how academic and applied conservation biologists can collaborate to guide effective priority-setting to conserve the most irreplaceable components of biodiversity upon which humanity depends.

zoology↗

bioRxiv2022

Extreme tolerable winds for seabirds are determined by morphology

Storms can cause widespread seabird strandings and wrecking1,2,3,4,5, yet little is known about the maximum wind speeds that birds are able to tolerate or the conditions they avoid. We analyzed > 300,000 hours of tracking data from 18 seabird species, including flapping and soaring fliers, to assess how flight morphology affects wind selectivity, both at fine scales (hourly movement steps) and across the breeding season. We found no general preference or avoidance of particular wind speeds within foraging tracks. This suggests seabird flight morphology is adapted to a "wind niche", with higher wing loading being selected for in windier environments. In support of this, wing loading was positively related to the median wind speeds on the breeding grounds, as well as the maximum wind speeds in which birds flew. Yet globally, the highest wind speeds occur in the tropics (in association with tropical cyclones) where birds are morphologically adapted to low median wind speeds. Tropical species must therefore show behavioral responses to extreme winds, including long-range avoidance of wind speeds that can be twice their operable maxima. In contrast, procellariiformes flew in almost all wind speeds they encountered at a seasonal scale. Despite this, we describe a small number of cases where albatrosses avoided strong winds at close-range, including by flying into the eye of the storm. Extreme winds appear to pose context- dependent risks to seabirds, and more information is needed on the factors that determine the hierarchy of risk, given the impact of global change on storm intensity 6,7.

animal behavior and cognition↗

bioRxiv2022

Experience does not change the importance of wind support for migratory route selection by a soaring bird

Migration is a complex behavior that is costly in terms of time, energy, and risk of mortality. Thermal soaring birds rely on airflow, specifically wind support and uplift, to offset their energetic costs of flight. Their migratory routes are a record of movement decisions to negotiate the atmospheric environment and achieve efficiency. Because thermal soaring is a complex flight type that young birds need to learn, we expected that, as individuals gain more experience, their movement decisions will also increasingly favor the best thermal uplift conditions. We quantified how route choice during autumn migration of young European honey buzzards (Pernis apivorus) was adjusted to wind support and uplift over up to four years of migration and compared this to the choices of adult birds. We found that wind support was important in all migrations. However, we did not find an increase in the use of thermal uplifts, which could be an artifact of the uplift proxies that we used. Age-specific variations in response to airflow might occur at a smaller spatio-temporal scale than we investigated.

animal behavior and cognition↗

bioRxiv2022

MoveApps - a serverless no-code analysis platform for animal tracking data

BackgroundBio-logging and animal tracking datasets continuously grow in volume and complexity, documenting animal behaviour and ecology in unprecedented extent and detail, but greatly increasing the challenge of extracting knowledge from the data obtained. A large variety of analysis methods are being developed, many of which in effect are inaccessible to potential users, because they remain unpublished, depend on proprietary software or require significant coding skills. ResultsWe developed MoveApps, an open analysis platform for animal tracking data, to make sophisticated analytical tools accessible to a global community of movement ecologists and wildlife managers. As part of the Movebank ecosystem, MoveApps allows users to design and share workflows composed of analysis modules (Apps) that access and analyse tracking data. Users browse Apps, build workflows, customise parameters, execute analyses and access results through an intuitive web-based interface. Apps, coded in R or other programming languages, have been developed by the MoveApps team and can be contributed by anyone developing analysis code. They become available to all user of the platform. To allow long-term and cross-system reproducibility, Apps have public source code and are compiled and run in Docker containers that form the basis of a serverless cloud computing system. To support reproducible science and help contributors document and benefit from their efforts, workflows of Apps can be shared, published and archived with DOIs in the Movebank Data Repository. The platform was beta launched in spring 2021 and currently contains 44 Apps that are used by 156 registered users. We illustrate its use through two workflows that (1) provide a daily report on active tag deployments and (2) segment and map migratory movements. ConclusionsThe MoveApps platform is meant to empower the community to supply, exchange and use analysis code in an intuitive environment that allows fast and traceable results and feedback. By bringing together analytical experts developing movement analysis methods and code with those in need of tools to explore, answer questions and inform decisions based on data they collect, we intend to increase the pace of knowledge generation and integration to match the huge growth rate in bio-logging data acquisition.

ecology↗

bioRxiv2022

Salp blooms increase carbon export 5-fold in the Southern Ocean

The Southern Ocean (SO) contributes substantially to the global biological carbon pump (BCP). Salps in the SO, in particular Salpa thompsoni, are keystone grazers that produce large, fast-sinking fecal pellets with high export potential. In a first study of this kind, we conducted Lagrangian experiments to quantify the salp bloom impacts on export pathways by contrasting locations differing in salp bloom presence/absence. We show that blooms increased particle export by ~5-fold, and exported up to 46% of net primary production out of the euphotic zone. BCP efficiency increased from 5% in non-salp areas to up to 28% in salp areas, which is among the highest recorded in the global ocean. Using SO salp abundances from KRILLBASE, we estimate they can consume ~ 13% of regional production, mediating 13-40% of the SO BCP. Consideration in models forecasting the SO BCP is recommended considering long-term increases in SO salp abundances.

ecology↗

bioRxiv2021

Effect of tag attachment on flight parameters and energetic cost across five raptor species

Bio-logging devices play a fundamental and indispensable role in movement ecology studies, particularly in the wild. However, researchers are becoming increasingly aware of the influence that attaching devices can have on animals, particularly on their behaviour, energy expenditure and survival. The way a device is attached to an animals body has also potential consequences for the collected data, and quantifying the type and magnitude of such potential effects is fundamental to enable researchers to combine and compare data from different studies, as much as it is to improve animal welfare. For over two decades, large terrestrial birds have been in the focus of long-term movement ecology research, employing bio-logging devices attached with different types of harnesses. However, comparative studies investigating the effects of different harness types used on these species are scarce. In this study, we tested for potential differences in data collected by two commonly used harness types, backpack and leg-loop, on the flight performance of 10 individuals from five raptor species, equipped with high resolution bio-logging devices, in the same area and time. We explored the effect of harness type on vertical speed, horizontal speed, glide ratio, height above sea level, distance travelled, proportion of soaring and flapping behaviour, and VeDBA (a proxy for energy expenditure) between and within individuals, all used as fine-scale measures of flight performance. Birds equipped with leg-loops climbed up to 0.65 ms-1 faster, reached 19% greater heights while soaring, and spent less time in active flight compared to birds equipped with backpacks, suggesting that backpack harnesses, compared to leg-loops, might cause additional drag affecting the birds flight performance. A lower rate of sinking while gliding, a slightly higher glide ratio, higher horizontal speed while soaring, and lower VeDBA, were also indicative of less drag using leg-loops. Our results add to the existing literature highlighting the design-related advantages of leg-loops, and support the use of leg-loops as a better alternative to backpack harnesses for large soaring birds, when possible. Our study also highlights how apparently small changes in device attachment can lead to notable improvements in tagging practice, with implications for animal welfare, data interpretation and comparability.

animal behavior and cognition↗

bioRxiv2021

Planktonic protist diversity across contrasting Subtropical and Subantarctic waters of the southwest Pacific

Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific sector (33-58{degrees}S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises (n = 482, 0-2000 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) water masses and the Subtropical Front (STF) that separates them. Diversity decreased with latitude and temperature but tended to be lowest in the STF. Sample ordination resulting from the abundance of amplicon single variants (ASVs) corresponded to the different water masses. Overall, Dinophyceae (34% of standardized total number of reads) and Chlorophyta (27%) co-dominated the euphotic zone, but their relative abundance and composition at class and lower taxonomic levels varied consistently between water masses. Among Chlorophyta, several picoplanktonic algae species of the Mamiellophyceae class including Ostreococcus lucimarinus dominated in STW, while the Chloropicophyceae species Chloroparvula pacifica was most abundant in SAW. Bacillariophyta (7%), Prymnesiophyceae (5%), and Pelagophyceae (3%) classes were less abundant but showed analogous water mass specificity at class and finer taxonomic levels. Protist community composition in the STF had mixed characteristics and showed regional differences with the southern STF (50{degrees}S) having more resemblance with subantarctic communities than the STF over the Chatham Rise region (42-44{degrees}S). Below the euphotic zone, Radiolaria sequences dominated the dataset (52%) followed by Dinophyceae (27%) and other heterotrophic groups like Marine Stramenopiles and ciliates (3%). Among Radiolaria, several unidentified ASVs assigned to Spumellarida were most abundant, but showed significantly different distribution between STW and SAW highlighting the need to further investigate the taxonomy and ecology of this group. This study represents a significant step forward towards characterizing protistan communities composition in relation to major water masses and fronts in the South Pacific providing new insights about the biogeography and ecological preferences of different taxa from class to species and genotypic level. HighlightsO_LIWater-mass preference of different taxa emerged at class, species and genotypic level. C_LIO_LIMamiellophyceae green algae dominated in subtropical waters. C_LIO_LIDinophyceae and Chloropicophyceae green algae dominated in subantarctic waters. C_LIO_LIA diverse assemblage of Radiolaria dominated the mesopelagic zone. C_LIO_LISmall rather than large taxa dominated phytoplankton blooms in subtropical waters. C_LI

ecology↗