Frontiers in Ecology and Evolution

Strong population contractions can leave a persistent genomic legacy that can influence populations long after their demographic recovery. While bottlenecks facilitate the removal of strongly deleterious mutations, the effectiveness of purging may be limited in historically small populations. The Kirtlands warbler (Setophaga kirtlandii) is a rare North American songbird with an ancestrally small population. After narrowly evading extinction, they are one of few species that have been delisted from federal protections in the USA. Despite their recovery, a previous study showed evidence for recent inbreeding and a high burden of deleterious mutations that may have not been purged despite strong bottlenecks. Historical DNA offers a unique opportunity to understand the consequences of recent demographic declines on genetic diversity. Here, we use DNA from over 100-year-old museum specimens to estimate changes in genetic load in the Kirtlands warblers pre- and post-bottleneck. We validate our results with forward-in-time genetic simulations and explore how sample size and missing data can affect estimates. Both empirical data and simulations suggest a reduced ability to purge deleterious mutations in this historically small population. Our simulations also highlight that limited sampling design and data quality can constrain the ability to detect changes.

1Effective population size (Ne) is a critical parameter for evaluating the evolutionary and persistence potential of endangered populations and for designing sustainable conservation strategies. Captive breeding and release programs are widely used across taxa to reduce risk of extinction when natural reproduction is insufficient or no longer possible, making it essential to assess their consequences. We used the case study of the landlocked Saimaa salmon (Salmo salar), one of the most critically en-dangered salmonid populations in Europe, with unique evolutionary significance due to its isolation from other populations since the last glaciation. Using long-term demographic data (1969-2024) from wild-caught founders of a captive breeding and release program, we estimated the effective population size under multiple scenarios of variance in reproductive success. Across scenarios, Ne ranged from 33 to 81 individuals, representing 32%-75% of the census size. Captive breeding practices aimed at equalizing parental contributions during fertilization and early life stages increased Ne by 12% compared to natural reproductive conditions. However, variation in survival after early developmental stages, typically beyond direct management control, remained a key determinant of Ne. Despite recent increases in the number of founders, the population remains genetically vulnerable due to historical bottlenecks. These results highlight that while captive breeding programs can partially mitigate genetic risks, their effectiveness depends critically on both controlled and uncontrolled sources of variance in reproductive success. Strengthening such programs may require combining breeding management with habitat restoration and, where appropriate, genetic rescue to ensure the long-term evolutionary potential of such unique and endangered populations.

Elucidating how habitat degradation facilitates extinction is critical for effective conservation efforts. Here, we propose integrating physiologically-structured population models into stochastic population viability analyses to assess how differing consequences of habitat degradation interact to drive extinction dynamics in a focal population. Using the isolated spectacled caiman Caiman crocodilus population/ecomorph from the Apaporis River as a case study, we find that threatening the resource base, which individuals increasingly rely upon, to outgrow vulnerable size ranges and mature accelerates extinction. We also found that when habitat degradation impacts both the primary adult and juvenile resource bases, this can have marked synergistic effects on threatening population viability. By contrast, destroying nesting sites has only a small effect on accelerating the impact of deteriorating prey availability. Through integrating community-level feedback between habitat degradation/change and population dynamics/structure, our approach provides a comparative framework for assessing the relative importance of distinct mechanisms through which habitat degradation ultimately drives extinction risk.

Reef manta rays (Mobula alfredi) are threatened by fishing and other anthropogenic threats. Which, when coupled with conservative life history traits, have made this species vulnerable to extinction. Spatiotemporal ecological knowledge, such as site fidelity and visitation patterns to key aggregation sites, are imperative for effective conservation management of M. alfredi. A novel method of environmental sensing, remote underwater photo systems (RUPs), was employed to understand drivers of M. alfredi habitat use and resighting patterns. RUPs were deployed at four cleaning sites around Laamu Atoll, Maldives. Between March 2021 and May 2023, 455,458 photos were analysed. Generalised linear models revealed increases in M. alfredi presence in response to high chlorophyll-a concentrations, low illumination moon states, the Southwest Monsoon, and in the morning, while human presence had no effect. Branchial spot patterns allowed for 81 M. alfredi individuals to be identified, from 629 sightings, representing 51.59% of Laamu Atolls previously identified population (n = 157). Cleaning stations are visited more intensively during periods of increased productivity of the Southwest Monsoon, likely in response to greater foraging opportunities near the study areas. Additionally, moon state, used as a proxy for tidal strength, was associated with increased visitation during new moon periods, suggesting that weaker tidal states may facilitate presence. These data support integrating RUPs with observational surveys to improve inferences about habitat use and our understanding of cleaning sites frequented by M. alfredi. This study aims to inform the implementation of Laamu Atolls first marine protected area management plan.

The fitness of immigrants and their descendants determines the effectiveness of gene flow. Genetic incompatibilities or outbreeding depression can limit the spread of novel alleles, while highly fit immigrant lineages can hasten introgression. These fitness effects of gene flow can also differ between generations as immigrant and resident haplotypes recombine. Understanding the genetic factors that shape immigrant fitness over multiple generations is increasingly important as habitat fragmentation threatens populations by reducing genetic variation and leading to increased levels of inbreeding. Few studies have measured the multigenerational fitness of immigrant lineages, especially within populations that had histories of high gene flow. We used 33 years of life history and pedigree data on a population of Florida scrub-jays (Aphelocoma coerulescens) with historically high immigration to quantify the fitness of immigrants and their descendants. We compared the fitness of immigrants and residents as well as their resulting descendants (F1, F2, etc.) to determine the composite genetic effects responsible for fitness differences. We found evidence of additive benefits of immigrant ancestry and heterosis driven by non-additive effects that persists for multiple generations. These results are promising for conservation efforts aiming to increase connectivity and illustrate the complex dynamics that determine the rates of introgression in natural populations.

Designing effective spatial management for chondrichthyans (sharks, skates, rays and chimaeras) requires incorporating critical areas, sites essential for population maintenance, such as reproductive and feeding areas. Yet most area-based measures have been developed without consideration of chondrichthyan habitat use. The Important Shark and Ray Area (ISRA) initiative has been pivotal in designating priority areas through a rigorous, consultative process. To complement this, our study offers researchers a testable definition for generating robust evidence to strengthen future critical area delineations and related management decisions. We define critical areas using three criteria: 1) relative frequency of use, (2) extended within-year occupancy and (3) repeated use across years. This framework enables objective comparison among candidate sites and is generalisable across different critical area types. The definition builds upon established early-life-stage habitat concepts and applies these to broader life-history functions. The utility of this framework is then demonstrated through a systematic review of contemporary peer-reviewed literature of critical chondrichthyan areas in the European Atlantic. The review highlighted 62 critical areas with Strong evidence and 41 areas of Moderate strength evidence, which informed the European Atlantic ISRA selection process. Research effort was concentrated in inshore areas, particularly around the British Isles and Portugal, with biases towards large, threatened and commercially valuable species, whilst chimaeras were notably underrepresented. Early-life stage areas were most frequently identified, whereas resting areas were rarely documented. Evidence patterns and biases are examined in the context of evolving critical area concepts to advance their development and improve the quality and breadth of future research. By outlining a testable definition, identifying key knowledge gaps, and proposing research and reporting guidelines, this work enhances the consistency, comparability, and spatial coverage of future chondrichthyan habitat research to support its application to conservation planning.

Sky islands are high-elevation ecosystems surrounded by lowland habitats that create isolated environments with distinct climatic conditions. These factors have driven the evolution of many endemic species, separated from their larger, contiguous populations. An Individual-Based Model (IBM) was used to simulate population dynamics by modeling the behaviors and interactions of Tamiasciurus hudsonicus grahamensis (Mount Graham Red Squirrel) a subspecies of the American red squirrel (Tamiasciurus hudsonicus) that is endemic to the Pinaleno Mountains in southeastern Arizona. This approach can help predict future population trends based on historical species data leading to better conservation decisions. Using species-specific ecological preferences--including temperature, precipitation, and vegetation indices (NDVI)--an IBM was developed to simulate population dynamics and spatial distribution projections through 2100. Climate change projections, based on the best- and worst-case scenarios outlined in the 2014 National Climate Assessment, were incorporated to assess potential future population trends under changing environmental conditions. The population faces a 45-62% probability of extinction by 2100, with a significant risk of extinction within the next 50 years. A translocation experiment was conducted to evaluate the viability of relocating individuals to the Chiricahua Mountains, another sky island with a larger habitable area. However, the risk of extinction remains even higher (87-89%) due to environmental disturbances affecting both the Chiricahua and Pinaleno regions. This highlights the challenges of conservation efforts in the face of climate change and emphasizes the need for targeted management strategies to preserve this critically endangered subspecies.

O_LIFear of humans can drive persistent changes in wildlife behavioural and life-history traits, with cascading effects on entire ecosystems. Human multimodal cues and pet cues may influence impact of such fear, yet no study has tested how wildlife fear responses change when human acoustic cues and pet visual and acoustic cues are added to human visual cues. Filling this gap is important for managing human and pet outdoor activities while conserving wildlife. C_LIO_LIHere, with dogs representing the pet, we tested the effects of human and dog cues on fear responses of wild sika deer (Cervus nippon yesoensis) in approximately 800 km2 area, northern Japan, using alert distance (AD) and flight initiation distance (FID). First, we measured AD/FID with an approaching surveyor alone and with additional cues. Then, we fitted linear mixed-effects models while controlling for key covariates. C_LIO_LIFrom analyses with 266 observations, AD was estimated at 80.0 m with the human visual cue alone, and dog barking increased AD by 18.4m. FID was estimated at 57.1 m with the human visual cue alone, and human voice and the dog decoy increased FID by 11.3m and by 8.5 m, respectively. C_LIO_LIThese results demonstrate that human multimodal cues and pet cues can increase prey fear responses. Our findings also suggest that dog walking may expose wildlife to simultaneous human and pet cues more consistently than predator co-occurrence typically does in nature. The increase in FID with human acoustic cues, in contrast to previous studies, suggests that animals may shift cue weighting depending on predator species, potentially using human voices to help identify the threat as human. C_LIO_LIPrevious studies show that multimodal predator cues increase prey fear responses, and our findings extend this flamework to fear responses towards humans. Our findings can inform more tolerant management of human recreation and pet walking in sensitive areas. Reducing human and pet cues through signage, guidance, and zoning may prevent flight and associated energy expenditure, whereas mitigating vigilance may require behavioural guidance and spacing between pet-walking visitors. Overall, shaping how humans and pets behave may be more practical than blanket restriction. C_LI

The ongoing decline in biodiversity highlights the need for understanding the causes of population changes. This study uses 25-year, large-scale monitoring dataset to investigate the influence of climate and landscape structure on the annual population growth rates of 84 bird species across Poland. Our methodological framework involves the spatiotemporal decomposition of these environmental drivers to decouple demographic effects of long-term carrying capacities from the short-term effects of environmental perturbations. Using species-specific demographic models followed by a community-wide meta-analysis, we evaluated how individual species responses scale up to shape community-level dynamics. The results reveal significant variation in species-specific responses to individual drivers. At the community level, our findings suggest that bird populations are mainly regulated by the long-term spatial constraints rather than short-term disturbances. Persistent environmental heterogeneity had the strongest positive demographic effect on birds, followed by temperature, forest dominance over croplands, and precipitation. In contrast, rapid temporal shifts in environmental heterogeneity and precipitation anomalies negatively affected population growth, whereas urbanisation consistently exerted a negative effect across both spatiotemporal dimensions. Our results highlight the significance of protecting existing heterogeneous and ecotonal habitats, as well as the need to incorporate features that enhance habitat heterogeneity into urban development. Article impact statementPreserving heterogeneous habitats is essential for the conservation of bird populations.

The release of tens of millions of common pheasants (Phasianus colchicus) across the UK for shooting may pose an ecological risk to native species and sensitive habitats, particularly if the birds move into protected areas (PAs) such as Special Areas of Conservation (SAC), Special Protection Areas (SPA), and Sites of Special Scientific Interest (SSSI). The extent of this ecological risk depends on the abundance of pheasants in these sensitive sites, especially if they are attracted there after the shooting season when game management efforts to retain the birds cease. We used relative pheasant abundance measures derived from British Trust for Ornithology bird atlas data from 3793 2km tetrads across four English counties (Berkshire, Cornwall, Devon, and Hertfordshire) to determine if pheasants preferentially disperse into or reside in areas with greater PA coverage. We analysed relative abundance in both the winter shooting season and the breeding season using a Bayesian occupancy-abundance model, controlling for habitat type and diversity. Our results showed a strong influence of habitat on pheasant abundance, consistent with known habitat preferences. However, we found no evidence of a relationship between relative pheasant abundance and the proportion of ecologically relevant PA coverage in a tetrad. This lack of a relationship was consistent across all four counties and across both the winter and breeding seasons. Our finding suggests that common pheasants do not preferentially disperse into or reside in protected areas compared to surrounding, unprotected land, suggesting that the ecological impacts caused by released pheasants are no more likely to occur in protected areas than in non-protected areas.

Reef restoration practitioners aim to preserve coral genetic diversity by protecting reefs and cultivating diverse genotypes in coral nurseries. However, cryptic genetic lineages in most corals complicate restoration strategies, as the role of between-lineage genetic divergence remains unclear regarding adaptation. In Montastraea cavernosa, researchers have identified cryptic lineages, some strongly segregated by depth. We conducted a ten-week reciprocal transplantation experiment using two cryptic lineages restricted to shallow water (<10m depth), with one lineage more common on nearshore reefs and the other on offshore reefs. We aimed to quantify lineage-specific responses to the environment that explain the genetic and ecological divergence between the two lineages. Surprisingly, the strongest response was not lineage-specific. Instead, both lineages exhibited strong and similar changes in growth and metabolomic profiles, depending on the transplantation habitat. These results suggest that cryptic lineages employ similar mechanisms of adaptation and acclimatization to environmental challenges, despite their genetic distinction.

O_LITerrestrial insects are vulnerable to desiccation due to their small body size. Because insects lose most water through cuticular evaporation, cuticular traits strongly influence desiccation tolerance. Individuals with greater cuticular melanisation, i.e., darker ones, are hypothesised to tolerate desiccation better than less melanised ones. C_LIO_LIIn many butterflies, pupal colour is plastic - individuals pupating on leaves tend to be greener, while those that pupate away from leaves (off-leaf), such as on tree bark or defoliated twigs, tend to be browner. Brown pupae are hypothesised to have more cuticular melanin and are expected to experience higher desiccation stress than leaf-borne green pupae. Thus, plasticity in pupal melanisation may be an adaptation against desiccation. We tested this in the butterfly Eurema blanda. C_LIO_LIWe demonstrate that individuals pupating on on-leaf substrates are greener than those pupating on off-leaf substrates, and that desiccation stress is higher in the off-leaf substrates, a microenvironment typical of brown pupae, than in typical green pupae. Using Raman spectroscopy, we show that brown, but not green, pupal cuticles contain melanin. C_LIO_LIFollowing this, we obtained greener and browner pupae by manipulating substrate colour. When subjected to desiccation stress, browner pupae survived better than greener ones. There was no correlation between pupal colour and survival in the absence of desiccation stress. Thus, melanisation appears to confer a survival advantage to pupae by increasing desiccation tolerance. C_LIO_LISurvival under desiccating conditions was inversely related to water loss. Interestingly, melanisation did not correlate with water loss, suggesting that melanisation helps tolerate desiccation through physiological mechanisms not directly related to water loss reduction. C_LIO_LIOur findings reveal an additional, crucial, adaptive value of pupal colour plasticity, a trait that has been studied primarily from an anti-predatory perspective. C_LI

Plants, as structural elements of habitats, contribute greatly to the maintenance of local biodiversity through their biological interactions. In this study we explore whether their rarity, according to Rabinowitzs (1981) three criteria, is related to the richness and diversity of arthropods and other plants they are associated to, in a gypsum-rich steppe. We first analysed whether the geographic abundance and ecological specialisation of 32 characteristic and dominant plant species are related to the diversity (richness and phylogenetic diversity (MPD)) and degree of local specialisation of arthropods associated with them (1,694 taxa). Then, we focused on a non endemic and non specialized plant in the study area (Krascheninnikovia ceratoides) to explore the effect of population size on two types of interactions: aerial arthropods and plant facilitation. Results indicate that: 1) plant species abundance (geographical range) is not related to the richness or MPD of communities of associated arthropods, 2) plant species ecological specialization (edaphic endemisms or gypsophiles) do not contribute differentially to the maintenance of singular arthropod communities, and 3) the community of aerial arthropods and plants interacting with K. ceratoides in a small population are not necessarily less diverse than those in patches of similar size in a large population. Results also revealed that the two plant species with fewer interactions (one rare, one widespread) do show the highest singularity in their interactions with arthropods. Our study illustrates the important contribution of rare plants to the conservation of local biodiversity.

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

Oxygen limitation is a widespread environmental constraint that shapes physiological and evolutionary responses across ecosystems. A central unresolved question is whether tolerance to hypoxia reflects generalized stress responses or coordinated regulatory strategies shaped by long-term environmental exposure. Here, we use comparative transcriptomic analyses to examine gene expression responses to low oxygen in two aquifer-dwelling stoneflies (Isocapnia sp. and Paraperla frontalis) and one benthic species (Sweltsa sp.) under controlled conditions. Time-series analysis in Isocapnia sp. revealed a multi-phase transcriptional response involving early regulatory activation, metabolic reorganization, and late-stage cellular stabilization. Across aquifer taxa, hypoxia was associated with downregulation of energy-demanding processes and upregulation of pathways related to oxidative stress mitigation, metabolite transport, and protein folding, consistent with coordinated cellular adjustment to oxygen limitation. In contrast, the river benthic species exhibited transcriptional profiles dominated by neural signaling, ion channel activity, and structural remodeling, which are patterns consistent with acute physiological stress rather than coordinated regulation. Despite these differences, all taxa showed modulation of ion transport and calcium signaling pathways, suggesting conserved mechanisms of hypoxia sensing. Together, these results indicate that transcriptional responses to hypoxia differ systematically with habitat and are consistent with the evolution of distinct regulatory strategies in chronically hypoxic environments. Significant statementOxygen limitation is a common environmental challenge that affects organisms across aquatic and terrestrial ecosystems, yet the mechanisms by which species cope with low oxygen remain incompletely understood. A key question is whether tolerance to hypoxia reflects common stress responses or the evolution of coordinated metabolic regulatory strategies under chronic exposure. By comparing gene expression responses in closely related aquatic insects from oxygen-variable underground aquifers and oxygen-rich river habitats, we show that species that evolved under persistent hypoxia exhibit transcriptional patterns consistent with energy conservation and cellular stabilization, whereas those experiencing hypoxia as a transient stress display signature of physiological disruption. These findings highlight fundamental differences between evolutionarily adaptive and acute stress-driven responses to environmental change and provide insight into how organisms may respond to increasing hypoxia under global change.

O_LIThe frequency and intensity of heat events is increasing across marine and terrestrial ecosystems. Within the same ecological community, the relative exposure and sensitivity to heat stress may vary considerably among interacting species, like predators and prey. This can be especially true for species that interact at the aquatic-terrestrial interface, as well as for interactions between primarily nocturnal and diurnal species, making it difficult to predict how such communities will respond to habitat warming. C_LIO_LIThermal limit metrics such as CTmax are often assumed to equate with ecological death because such temperatures impair behavioral activity and/or physiological functioning. Prey that are diurnally active can be more frequently exposed to temperatures that approach CTmax compared to their nocturnal predators, which may use thermal refuges during the day. Yet the impacts of daytime heat exposure on nighttime predation risk remain unknown. C_LIO_LIHere, we compared the thermal environment, performance, and heat tolerance between the predatory blue crab, Callinectus sapidus and one of its prey species, the mangrove periwinkle Littoraria anguilifera in a tropical mangrove ecosystem. We examined how exposing prey to heat stress at and below their CTmax affected their capacity to avoid predation in the field at night when predation risk is highest. C_LIO_LIWe found that acute exposure to temperatures near CTmax during the day increased the prey species susceptibility to predation during recovery at night. Although both interacting predator and prey have high thermal tolerance, prey are exposed to conditions that already reach CTmax, suggesting that current extremes in temperatures may already be influencing vulnerability to predation in this ecosystem. C_LIO_LIOur results suggest that differential exposure to sublethal heat stress in diurnal prey relative to their predator, along with the subsequent impact of these exposures on predation risk, will play a role in shaping these interacting as climate warms. C_LI

Within species, individuals of the same age can differ in size. Previously, parental genetics, nutrition, space, and social interactions have been suggested to explain different growth rates. However, direct effects of larger individuals on the physiology and growth of smaller individuals are poorly understood. In this study, we investigated how larger individuals of the marine worm Platynereis dumerilii can impact the growth of smaller conspecifics. Comparing growth distributions in communally and individually reared worms, we show that larger worms suppress the growth of smaller ones. Furthermore, we were able to demonstrate that this suppression is chemically mediated. The chemical cue does not originate from faeces but is water soluble, stable for several days and smaller than 3 kDa. Our findings highlight the importance of non-reproduction related chemical signalling, showing evidence that dominant individuals can chemically suppress the growth of their conspecifics. This study provides new insights into how hierarchy can be established and maintained in a population and is particularly relevant for the growing community studying this model species.

Understanding how anthropogenic disturbance and vegetation structure influence bird abundance is important for biodiversity conservation in rapidly changing tropical landscapes. This study evaluated the effects of anthropogenic and vegetation-related variables on the abundance of the Red-cheeked Cordon-bleu (Uraeginthus bengalus) in human settlements and surrounding farmlands in Laminga Village, Jos-East Local Government Area, Plateau State, Nigeria. Bird surveys were conducted using line transects and quadrat-based vegetation assessments during November 2024. Poisson Generalized Linear Models (GLMs) were used to examine the influence of anthropogenic and vegetation predictors on abundance. Among anthropogenic variables, building density significantly reduced abundance ({beta} = -0.141, SE = 0.060, z = -2.333, p = 0.020), whereas human presence ({beta} = -0.073, p = 0.141) and noise level ({beta} = 0.009, p = 0.592) did not significantly influence abundance. Average grass height showed a marginal positive relationship with abundance ({beta} = 2.008, SE = 1.051, z = 1.910, p = 0.056), while hedgerow presence, hedgerow height, grass cover, and bare ground cover were not significant predictors. The vegetation model produced the lowest residual deviance (91.19) and AIC value (297.66), indicating comparatively stronger explanatory performance. The results suggest that structural habitat characteristics and building density may play more important roles in shaping Red-cheeked Cordon-bleu abundance than human activity or noise levels alone. These findings provide insight into species responses to environmental disturbance in human-modified savanna ecosystems.

Understanding the drivers of genomic health and their consequences for population viability is often overlooked but potentially important to effective conservation amidst the biodiversity crisis of the Anthropocene. Leatherback turtle (Dermochelys coriacea) populations have declined globally due to anthropogenic factors, with some populations losing over 90% of their abundance over the past 30-50 years. While conservation efforts have been successful in stabilizing some populations, others continue to decline, and the reasons for these differential trajectories remain unclear. To assess how recent demographic factors, such as population size and decline, influence population genomic health, we combined population monitoring information with medium depth whole-genome and reduced representation resequencing data from globally representative populations. We found that small-stable populations have lower genomic diversity and higher inbreeding than large declining populations, reflecting prolonged small population sizes and limited gene flow. Yet, small-stable populations also show evidence of deleterious allele purging, suggesting genetic resilience. This, combined with lack of detectable genomic erosion over the study period, provides hope for potential recovery of healthy leatherback populations provided that anthropogenic threats are effectively mitigated. However, potential time lags and possible recent increases in inbreeding among close relatives in recently declined populations warrant continued monitoring and assessment. Genomic and abundance-based metrics were less aligned following rapid population declines, emphasizing the different timescales of the evolutionary and demographic processes they reflect, respectively, and the strength in their complementary, integrative use for extinction risk assessments. This also supports that it is not too late to turn the tide for recently declined leatherback populations and that continued investment in conservation efforts and threat reductions are warranted. Collectively, our results highlight how recent and historical demography shapes current genomic health and recovery potential in leatherback turtles, aids understanding of current risks and informs future conservation and management strategies.

The evolutionary divergence between Henophidia (non-venomous) and Caenophidia (venomous) snakes has produced distinct cranial morphologies, digestive strategies, and presence of specialised venom systems in Caenophidia, yet the extent to which these long-standing diverging trajectories have shaped cloacal microbiota assembly remains poorly understood. We characterised cloacal microbiota in 70 captive snakes (52 Caenophidia, 18 Henophidia) by 16S rRNA amplicon sequencing. Beta diversity was tested by PERMANOVA, differential abundance by ANCOM-BC2, community types by Dirichlet Multinomial Mixture modelling (DMM), and microbial interactions by SparCC co-occurrence networks. Predicted functional potential (PICRUSt2) was analysed by ALDEx2 differential abundance testing and elastic net feature selection. Henophidia exhibited significantly higher bacterial richness and greater compositional variability than Caenophidia. Community composition showed clade-associated differences (PERMANOVA) and partitioned into two distinct DMM community types. The Henophidia network was 11.9-fold denser and more modular, with Burkholderiaceae as a keystone hub, whereas the Caenophidia network was sparse. Henophidia showed predicted enrichment in C1 metabolic pathways (ethylmalonyl-CoA, formaldehyde assimilation I, glycine betaine degradation I, methylaspartate cycle), aromatic compound catabolism, and nitrogen recycling, whilst Caenophidia showed enrichment in allantoin and glucuronate degradation. This multi-method analysis suggests Burkholderiaceae as a candidate keystone taxon in Henophidia and indicates that phylogenetic clade is a major contributor to cloacal microbiota structure. The lower richness in Caenophidia raises a testable hypothesis that broad-spectrum antimicrobial activity of their venom components may selectively filter susceptible microbial lineages, motivating future shotgun metagenomic studies in wild populations of snakes.