Freshwater Biology

The rapid global expansion of dams has significantly reshaped freshwater ecosystems, yet long-term trophic dynamics and food-web stability within reservoirs remain underexplored. This study examines the reorganization of fish communities induced by the trophic surge following dam construction and river impoundment. We used the predator-to-consumer mass ratio (PCMR) as a proxy for trophic pyramid structure to track changes in fish biomass distribution across three large boreal reservoirs in Quebec, Canada, over 20 years, using data from before and after impoundment. We found transient top-heaviness events (i.e., PCMR values > 1; predator accumulation), characterized by a hump-shaped trajectory of the PCMR values in two reservoirs (Opinaca and Robert Bourassa). The third reservoir (Caniapiscau) showed a gradual increase in top-heaviness but did not exhibit a clear transient pattern. The magnitude and duration of top-heaviness varied across reservoirs, potentially due to differences in the system's capacity to receive and accumulate nutrients, which are driven by water residence time and reservoir size. This research provides a conceptual framework for understanding the long-term trophic dynamics of reservoirs, which can help inform the development of more effective management strategies to preserve ecological health in these ecosystems.

Hydropower development has emerged as a major driver of global environmental change, causing significant ecological damage to freshwater ecosystems and threatening aquatic biodiversity. However, the impact of cascade dams on fish communities in large river systems remains poorly understood, particularly in biodiversity hotspots such as China. Here, we used environmental DNA (eDNA) metabarcoding to assess the spatiotemporal patterns of fish diversity and community structure in the Ganjiang River, the largest tributary of the Yangtze River, in relation to cascade hydropower development. We collected water samples from 19 sites along the main stem and major tributaries in both wet and dry seasons, and analyzed the eDNA data using high-throughput sequencing and advanced bioinformatics pipelines. Our results revealed significant seasonal and spatial variations in fish diversity and community composition, with lower species richness and distinct assemblages in the impounded sections upstream of the dams compared to the downstream reaches. The fish communities were strongly influenced by environmental factors such as water temperature, pH, dissolved oxygen, and nutrients, which exhibited complex interactions with dam operation and land use practices. Spatial scale analyses further indicated that the impact of dams on fish diversity was most pronounced at the local scale, but also detectable at the regional scale. Our findings provide novel insights into the ecological consequences of cascade hydro-power development on fish communities and highlight the importance of considering spatial scales and environmental heterogeneity in assessing the impacts of human activities on freshwater biodiversity. Our study demonstrates the power of eDNA metabarcoding as a cost-effective and non-invasive tool for biodiversity assessment and conservation planning in large river systems facing multiple stressors and knowledge gaps.

Boreal forested streams receive substantial inputs of terrestrial carbon (C) from riparian vegetation in the form of leaf litter, which is processed by litter-associated microorganisms. In addition to these leaf-litter C inputs, boreal streams also receive significant concentrations of dissolved organic carbon (DOC), which may represent an alternative major resource pool for litter-associated microorganisms. As leaf litter quality decreases over the process of decomposition, DOC may increasingly become a more suitable C source for the microbial communities. We investigated how DOC availability, litter type, and microbial succession influenced respiration and decomposition. Alder, birch, and spruce litter were incubated for 65 days in 12 outdoor experimental channels supplied with natural boreal stream water. Higher time-adjusted DOC concentrations were associated with higher respiration and lower relative mass remaining, whereas DOC flux received less support. Respiration and mass loss followed litter-specific trajectories, with birch showing a respiration peak that was not matched by proportional mass loss. Prokaryotic and eukaryotic communities differed among litter types and changed through time but explained process variation only for specific litter types and responses. Our results suggest that DOC can sustain litter-associated microbial activity and partly decouple respiration from litter decomposition, thereby affecting boreal stream C processing.

The decline in fishery yields in Japan's enclosed coastal seas has been accompanied by a reduction in phytoplankton biomass, suggesting a widespread decrease in ecosystem productivity. Oligotrophication in Mikawa Bay has caused substantial declines in phytoplankton biomass and Manila clam (Ruditapes philippinarum) production. To assess whether external nutrient enhancement could stimulate phytoplankton growth, a controlled demonstration experiment using treated effluent from two sewage treatment plants (WWTPs) was conducted (spanning fiscal years 2022 to 2024) based on analysis using a three-dimensional non-hydrostatic model. Although effluent DIP and nitrogen concentrations were increased, model results showed that WWTP-derived nutrients represent only a minor portion of the total nutrient budget. Field observations revealed limited increases in surface water phosphorus, strong seasonal variability, and only temporary rises in chlorophyll-a and clam harvests. Monthly TP data demonstrated that seasonal DIP pulses, especially spring phosphorus bursts, dominate nutrient dynamics and overshadow external loading effects. Laboratory experiments further showed that phosphate is efficiently fixed by Fe(III) under oxidizing conditions and rapidly released during reductive dissolution of [FeOOH-HPO4]2- complexes, confirming iron as the principal regulator of internal P cycling. Because current numerical models omit iron-driven internal cycling, they cannot accurately predict bioavailable P or ecosystem responses. Overall, the study indicates that localized nutrient enhancement is insufficient to counter long-term oligotrophication, and effective management must integrate nitrogen limitation, internal Fe and P cycling, oceanic exchange, and seasonal variability in Ise and Mikawa Bays.

Animal movements can transport materials across ecosystem boundaries, while simultaneously modifying habitats through physical engineering. We integrated GPS telemetry, camera trapping, sediment measurements and physicochemical sampling of ponds on Santa Cruz Island, Galapagos, to evaluate how giant tortoises connect and shape terrestrial and freshwater ecosystems. Telemetry revealed 2,254 visits by 21 tortoises to 12 ponds, with visits lasting up to 21.38 h and showing strong seasonal and diel variation, while camera traps showed peak pond use in January and during early morning and late afternoon. Greater tortoise abundance was associated with higher ammonium, dissolved organic carbon and total phosphorus concentrations, while ponds with persistently greater tortoise abundance had higher total suspended solids. Departing tortoises carried a mean 505.9 g of sediment, yielding a conservative potential export of 8.20 kg per tortoise per year and tens of tonnes annually. These findings identify giant tortoises as mobile zoogeochemical engineers linking terrestrial and freshwater ecosystems through physical and biogeochemical pathways.

Okanagan sockeye salmon have shown a strong recovery over the past three decades, but the contribution of environmental conditions and management actions to this recovery has not been determined. We developed a hierarchical Bayesian model linking spawner abundances to fry emergence observations to evaluate how flow and water temperature during adult upstream migration and incubation periods influence spawner-to-fry production. Production declined by 62% in years with earlier onset and longer duration of periods when warm river temperatures created barriers to adult migration, indicating that migration conditions can have carry-over effects on reproductive success even when spawners successfully reach the spawning grounds. Additionally, production was 46% lower when flows fell above or below the management target range designed to minimize scour and desiccation during egg incubation. In contrast, we found little support for effects of pre-spawning flows or incubation temperature on production. These findings provide quantitative evidence that current flow management is increasing freshwater spawner-to-fry production and has likely contributed to the Okanagan sockeye recovery. Effective flow management may therefore help offset climate-driven impacts that increasingly threaten this population.

Hormesis is an important consideration in chemical risk assessment across most aquatic environments. Evidence suggests that hormetic responses are shaped by organismal physiological processes. Accordingly, predictions of hormesis under environmentally realistic conditions should account for physiological traits. Yet the role of these traits remains largely unexplored. This study investigated how baseline growth rate modulates antibiotic responses in the harmful cyanobacterium Microcystis and the underlying mechanisms. Results showed that at an antibiotic concentration of 200 ng L-1 (representing environmental concentration levels), slow-growing Microcystis populations exhibited an obvious growth enhancement more than 4-fold greater than that of fast-growing populations, and this enhancement was positively correlated with cellular reserves. A baseline growth rate below 0.19 day-1 emerged as the threshold below which hormetic responses were consistently observed. This study provides pioneering insights into how organisms' physiological states influence pollutant-induced hormetic responses in aquatic environments. Our findings point to a central principle for extrapolation that laboratory-derived toxicological responses may not translate directly to the field unless key physiological traits of the organisms are explicitly considered. In this regard, baseline growth rate and energy reserves may be key physiological traits for reliably predicting toxic effects at the population level. This study also makes an initial attempt to conceptualize a physiology-anchored framework for strengthening risk assessment of low-level emerging contaminants.

Background: Cyanobacteria are the major phototrophs in many endolithic ecosystems, yet their genomic diversity and metabolic adaptations remain poorly characterized. Here, we investigated cyanobacterial diversity in endolithic dolomite rocks from the Piora Valley in the southern Swiss Alps using genome-resolved metagenomics. Results: We reconstructed 138 medium-quality metagenome-assembled genomes (MAGs) from four neighboring endolithic rock communities, including 15 cyanobacterial MAGs distributed across six order-level lineages. The cyanobacterial communities showed limited taxonomic overlap among rocks, and most recovered MAGs represented potentially novel species. Only one Gloeobacter lineage occurred in all sampled rocks, which we propose as Gloeobacter dolomitensis sp. nov., representing the first Gloeobacter genome recovered from an endolithic environment. Comparative genomic analyses identified a cynS gene encoding cyanase unique to G. dolomitensis among the Gloeobacter. Phylogenetic analyses support its horizontal acquisition from Pseudomonadota. Interestingly, the genome of G. dolomitensis lacks a canonical CynABD cyanate transporter and instead contains a distinct ATP-synthase binding cassette (ABC) transporter adjacent to cynS. Although the available genomic and structural evidence does not establish cyanate transport, its genomic association with cynS suggests a potentially non-canonical mechanism. We further show that horizontal gene transfer was unevenly distributed among cyanobacterial lineages, with Acaryochloridales acting predominantly as donors, Chroococcidiopsidales as recipients, and Gloeobacterales showing a comparatively high frequency of interphylum gene exchange. Conclusions: The Piora Valley dolomite environment represents an underexplored reservoir of cyanobacterial diversity, including basal and previously undescribed lineages. The discovery of G. dolomitensis and its unusual cyanate-associated genomic architecture expands our understanding of Gloeobacterales diversity and highlights the potential importance of horizontal gene acquisition and metabolic innovation in endolithic microbial communities.

Introduction: Despite decades of investment, stream restoration often fails to recover diverse benthic macroinvertebrate communities, as restored reaches tend to remain dominated by pollution-tolerant taxa. This shortfall in recovery is commonly attributed to either poor habitat quality or dispersal limitation of aquatic macroinvertebrate taxa, yet these hypotheses are rarely tested directly. Objectives: We conducted a manipulative field experiment in the eastern Piedmont region (Maryland, USA) within the Chesapeake Bay Watershed to evaluate whether restored streams can support pollution-sensitive taxa when dispersal barriers are removed. Methods: We translocated whole macroinvertebrate communities from three nearby reference streams into three restored streams using standardized habitat substrates and quantified macroinvertebrate survival after 28 days. We also assessed how effective leaf vs rock substrates were for accumulating diverse and abundant macroinvertebrate communities for translocation. Results: Across all sites, 77% of translocated individuals and 16 of 22 taxa sensitive and moderately sensitive to pollution persisted under restored stream conditions, demonstrating that restored reaches can support short-term survival of pollution-sensitive taxa that typically fail to recover. Substrate comparisons revealed that leaf packs accumulated higher macroinvertebrate abundances, whereas both substrates accumulated macroinvertebrate communities with similar taxa richness, EPT richness, and Shannon Diversity. Conclusions: This work suggests that dispersal limitation, rather than unsuitable habitat, may be an underappreciated constraint limiting macroinvertebrate recovery in restored streams. These findings challenge the assumption that habitat restoration alone is sufficient for biological recovery and highlight the potential for whole-community translocations to accelerate recovery and ecological uplift as part of stream restoration practices. Implication for Practice: Our study highlights the need to consider habitat connectivity and dispersal pathways during stream restoration designs. Restoring streams to meet habitat requirements of pollution-sensitive macroinvertebrate taxa may not be sufficient for their populations to recover if these taxa are unable to reach the restored stream. In scenarios where restoring connectivity to source populations is infeasible, whole community translocations may offer a novel restoration tool to overcome dispersal barriers and accelerate biological recovery in restored streams.

Hydractiniidae is a diverse family of colonial hydrozoans exhibiting substantial variation in colony organization, reproduction and life-cycle strategies, including species with and without a medusa stage. Several hydractiniids are also established model organisms, yet species boundaries and distributions remain incompletely resolved, limiting comparisons of reproductive and developmental traits across taxa. Here, we combine morphological and molecular data to reassess hydractiniid diversity, species identities, and life-cycle variation in material from the North Atlantic and Arctic Ocean. We integrate detailed observations of colonies and reproductive structures with DNA barcoding and mitochondrial genomes to evaluate species boundaries and provide molecular support for taxonomic identifications. Our results confirm 10 species in the study area, occurring from shallow waters to 2600 m depth and from coastal fjords to deep-sea hydrothermal vents. We further show that some historical species identifications and distribution records require reassessment. We establish a new genus for Arctic hydractiniid species (Bonneviactinia gen. nov.) and reassign two species to Schuchertinia. Mapping reproductive strategies onto the phylogeny reveals a broad pattern of increasing retention of medusa characters, from fixed sporosacs through reduced and fixed medusoids and non-liberated eumedusoids to fully developed, free-swimming feeding medusae, suggesting a progressive evolutionary trajectory in life-cycle complexity across Hydractiniidae. Furthermore, we clarify the identity of Podocoryna carnea and, through rearing experiments from polyp stage to medusae, characterize its morphological variation and developmental stages. By linking morphologically documented specimens and vouchers to genetic data, we establish reference resources that will facilitate future taxonomic, phylogenetic and biodiversity studies, including molecular surveys of marine communities. Together, these results demonstrate the value of integrative taxonomy for resolving hydractiniid diversity and provide a comparative foundation for investigating the evolution of reproductive strategies and life-cycle complexity in Medusozoa.

Riverine and riparian food webs are connected via 'allochthonous' resource flows from neighboring ecosystems. These resources, such as terrestrial leaf litter, contribute to benthic macroinvertebrate diets, supporting higher trophic levels. While allochthony occurs in streams globally, its sensitivity to broad environmental gradients remains poorly understood. We explored the drivers of allochthony across six river basins within the contiguous United States, including climate, stream size, and flow permanence. We used Bayesian mixing models to estimate macroinvertebrate dietary proportions in four functional feeding groups. Air temperature best predicted allochthony, with consumers relying less on allochthonous resources with increasing temperature. Our models indicate that macroinvertebrate diets become primarily autochthonous at approximately 15{degrees}C mean annual air temperature, with leaf litter-consuming shredders showing a slightly higher threshold for this shift. We also found increased allochthony in smaller, non-perennial streams. These findings highlight the complexity of stream allochthony and responses to multi-scale environmental factors.

1. Temperature shapes life histories through its effects on energy allocation among growth, reproduction and maintenance. The resulting temperature dependence of performance is commonly characterised using thermal performance curves (TPCs), which are often treated as static descriptions that apply uniformly throughout life. Yet the response to thermal variability may change across ontogeny. 2. We recorded growth, reproduction and survival throughout the lifetimes of individual Daphnia magna under four thermal regimes: Constant Low (15C), Constant Rearing (20C), Constant High (25C) and Variable (15C to 25C). The mean temperature under Variable closely matched that under Constant Rearing. Using an allometric energy-allocation model, we derived age specific and lifetime performance measures and quantified their uncertainty with a stratified individual-level bootstrap. Our principal quantity was the Jensen contrast, defined as performance under Variable minus that under Constant Rearing. 3. Age specific point estimates of the Jensen contrast changed sign across ontogeny. A positive aggregate contrast in full trajectory growth concealed a negative mid-life contrast; reproductive point estimates were positive during early and mid life but negative later. Bootstrap support was strong for the positive early life and negative mid-life growth contrasts, and for the positive early life reproductive contrast. Under a second-order approximation, this pattern of estimated signs is consistent with ontogenetic changes in effective thermal curvature. 4. The positive early life reproductive response did not carry through to the lifetime outcome: expected lifetime reproduction was lower under Variable than under Constant Rearing, with strong bootstrap support for the negative lifetime contrast. Because lifetime reproduction is survival weighted, lower survival under Variable reduced later reproductive contributions; across the estimated trajectories, the accumulated negative late life contribution out-weighed the earlier positive contributions. 5. These results show why forecasts based on mean temperature, a single life stage or an aggregate TPC may misrepresent lifetime performance under variable thermal regimes. Accounting for both ontogeny and temperature variability may therefore improve forecasts of life-history performance in increasingly variable thermal environments.

This study assesses the spatial dynamics of heavy metals and associated trace elements in the water and sediment of the Slana River approximately one and half year after an environmental accident and river contamination caused by mining effluent. Using PCA and standardized environmental indices (CF, PLI), we modelled the distribution of contaminants across the macro-gradient of the river and within the micro-gradient surrounding the source of pollution. We found that although the situation in the water column has improved and stabilized, the sediment remains the primary reservoir of trace elements, including toxic arsenic, with the highest concentrations recorded near the source and in its immediate vicinity. Although the concentration of primary mining indicators decreases relatively rapidly along the stream, this is systematically offset by the accumulation of other elements, including sulphur and aluminium. As a result of these geochemical processes, the total pollution load index (PLI) remains statistically unchanged along the entire stream, but indicates a chronic, spatially uniform (PLI = 1.06-1.16) toxicological burden on the ecosystem.

Environmental nucleic acid (eRNA and eDNA) metabarcoding is a promising tool for biodiversity assessment as it supports low-cost, noninvasive biological surveys. A critical challenge for eRNA/eDNA analyses is accounting for nucleic acid contamination that can compromise the accuracy of biomonitoring results. The primary aim of the current study was to examine carcasses as potential sources of eRNA/eDNA contamination, a contribution that remains poorly understood. Using Japanese medaka (Oryzias latipes), we quantified the detectability and persistence of carcass-derived eRNA/eDNA in water through two complementary experiments: (i) a shedding study comparing eRNA/eDNA release from live and dead individuals and (ii) a decay experiment measuring temperature-dependent degradation from 4 to 34 {degrees}C. Dead fish released detectable amounts of both eDNA and eRNA, indicating that eRNA-based surveys cannot fully eliminate carcass-derived signals. Arrhenius-based analysis showed that eRNA degradation was more temperature-dependent than eDNA degradation. These results suggest that eRNA may improve temporal resolution for recent organismal presence under warm conditions, whereas carcass-derived eRNA may persist under cold conditions and complicate interpretation of positive detections. Overall, eRNA may help reduce carcass-related false positives, particularly in warm conditions, but should be paired with temperature-aware sampling strategies and temporal replication during colder periods.

Freshwater biodiversity is declining at alarming rates globally, yet our capacity to monitor it depends heavily on the methods used for biodiversity assessment. Stream benthic macroinvertebrates are widely used as bioindicators, but traditional morphological identification is labor-intensive and limited by taxonomic expertise, while DNA metabarcoding offers a promising but incompletely evaluated alternative. Here, we compared biodiversity patterns detected by four macroinvertebrate sampling and identification methods (morphological identification of benthic samples, morphological identification of combined benthic and stream-edge samples, eDNA metabarcoding of bulk benthic samples, and eDNA metabarcoding of streamwater) across 62 sites in seven watersheds spanning the southern continental United States. We compared methods across three facets of biodiversity (gamma diversity, alpha diversity, and taxonomic composition) and three taxonomic levels (family, genus, and species). We found that which method detected more taxa shifted with taxonomic resolution: morphological methods detected more families and genera, while metabarcoding methods detected more species. Bulk benthic metabarcoding detected more families and genera than water eDNA metabarcoding, consistent with the "watered-down biodiversity" effect of DNA dilution in water samples, but the two metabarcoding methods did not differ significantly in species richness. All four methods detected largely distinct suites of taxa, with metabarcoding methods yielding more unique taxa than morphological methods. Notably, taxa uniquely detected by water eDNA were dominated by soft-bodied organisms (oligochaetes, leeches, earthworms) and water-column-associated taxa, while benthic eDNA uniquely detected hard-bodied EPT insects. We attribute this pattern to fundamental differences in eDNA shedding, transport, and deposition dynamics across organism types. These results demonstrate that no single method captures a complete picture of stream macroinvertebrate biodiversity, and that method choice should be guided by the taxonomic resolution and community components most relevant to the goals of the bioassessment program.

Background: Long non protein coding (lnc)RNAs are ubiquitous transcripts known to be major regulators of cellular processes in eukaryotes. In diatoms, specific lncRNA expression is tightly correlated to nutrient fluctuations, which suggests function, but their biological relevance remains to be established. In order to fill this knowledge gap, we sought to design a protocol to generate diatom lncRNA knockout mutants by CRISPR-Cas9 enabling subsequent functional studies to shed light into their mechanistic roles. Since lncRNAs do not contain open reading frames that can be targeted by point mutations for the generation of functional knockouts, we designed a multiplexed CRISPR-Cas9 plasmid harboring two independent gRNA for the specific ablation of lncRNA loci in P. tricornutum. As proof of concept, we used our plasmid-based system to target three phosphate depletion responsive lncRNAs. Results: Using the golden gate based uLoop system, we assembled a single plasmid containing all the necessary components to generate CRISPR-Cas9 large genomic ablations of lncRNAs in P. tricornutum using bacterial conjugation. Three intergenic lncRNAs (Linc91, Linc77 and Linc24) responsive to phosphate fluctuations were selected and independently targeted. Around 32% of the exconjugants presented a monoallelic ablation of the targeted loci and 11% presented a biallelic ablation on the first PCR-screening round. Mutated lines, harboring biallelic lncRNAs ablations for each lncRNA targeted, were successfully generated for each of the targeted lncRNAs. Additionally, a first line of phenotypic analysis revealed significant growth rate differences for one of the mutants ({Delta}Lnc24) under both full and phosphate depleted conditions, suggesting its involvement in cell division regulation under nutrient fluctuations. Conclusions: This work provides a simple and efficient method for the generation of lncRNA knock-out mutants in P. tricornutum. Furthermore, this approach can be easily adapted to other microalgae amenable to transformation, enabling the enhancement of our understanding of these important cellular regulatory transcripts in the marine environment.

Aquaporin-10 (AQP10) is an aquaglyceroporin that transports small, uncharged molecules, such as water and glycerol. In some species, such as mice and cattle, the AQP10 gene (Aqp10) is pseudogenized. In rodents, pseudogenization of Aqp10 is limited to the Myomorpha suborder, while Aqp10 remains intact in other rodent lineages. The order Cetartiodactyla encompasses diverse species, including Suina, Tylopoda, Ruminantia, and Whippomorpha. The distribution of intact Aqp10 across the entire Cetartiodactyla and analyses estimating the timing of Aqp10 pseudogenization have not been sufficiently investigated. In this study, we identified species within Cetartiodactyla that retain intact Aqp10 and analyzed the detailed patterns of pseudogenization to elucidate the specifics of pseudogenization within this order. We collected Aqp10 loci by BLAST and synteny analyses of publicly available genome databases of 51 cetartiodactyl species from 17 families. Dot plot and alignment analyses revealed that seudogenization of Aqp10 occurred in 42 Cetartiodactyla species, including the Camelidae, warthog (Suidae), Antilocapridae, okapi (Giraffidae), Cervidae, Bovidae, Hippopotamidae, and Cetacea. In contrast, nine species retained an intact Aqp10: pig and babirusa (Suidae), peccary (Tayassuidae), mouse deeres (Tragulidae), giraffes (Giraffidae), and musk deers (Moschidae). The timing of pseudogenization was estimated by comparing patterns of exon deletions, frameshifts, and nonsense mutations in Aqp10 pseudogenes. RT-PCR analysis of cattle and sheep tissues revealed that these species express Aqp3 and Aqp7 in their intestines, but not Aqp10. Collectively, these findings indicate that Aqp10 pseudogenization occurred independently in multiple cetartiodactyl lineages and provide new insights into the evolutionary history of Aqp10 loss within this order.

Mesophotic coral ecosystems are commonly interpreted as thin biological veneers over relict shallow-water reef structures, but their capacity to generate late Holocene carbonate deposits remains poorly quantified. Here we combine diver excavations, rubble-bed thickness surveys, radiocarbon age-depth modelling, sediment grain-size analyses, coral-rubble assemblages, trace-element geochemistry, and modern Alveopora allingi growth measurements from two 40-65 m deep coral-rubble fields in the northern Gulf of Eilat/Aqaba, Red Sea. Rubble deposits are at least 1.0-1.5 m thick and accumulated at mean rates of 2.21 {+/-} 0.52 mm yr-1 at the Dekel site and 1.33 {+/-} 0.13 mm yr-1 at the IUI site, implying persistent carbonate accumulation over centuries to >1 kyr. Age-depth models indicate quasi-continuous deposition despite pronounced faunal changes, including a shift from A. allingi-dominated rubble to upper layers enriched in Euphyllia paradivisa at Dekel. The dominant modern rubble-forming coral, A. allingi, extends at 3.04 {+/-} 0.87 mm yr-1 and has skeletal density of 1.17 {+/-} 0.27 g cm-3. First-order cover-based accretion estimates at present coral cover fall well below the radiocarbon-derived rates, indicating that long-term mesophotic rubble accumulation integrates historical cover, secondary calcification and sediment retention rather than present live coral cover alone. These data demonstrate that mesophotic rubble fields can act as active carbonate factories and palaeoecological archives, challenging the assumption that modern mesophotic habitats are geomorphologically passive.

The palaeogeographic history of the Neotropics has inspired multiple diversification models, emphasizing either the Andes or Amazonia as primary drivers of biodiversity. However, the extensive Pebas wetland system that covered western Amazonia during the Miocene has gained attention as a potential barrier to dispersal and diversification. This system may have contributed to the modern diversity imbalance between the Andes and Amazonia, known as the Gentry pattern. Most evidence for this hypothesis comes from isolated case studies and fossils. Here, we conduct a meta-analysis including 1,361 species of Neotropical butterflies to evaluate the role of the Pebas wetland on the dynamics of dispersal and diversification. We found that Andean- and Amazonian-centred clades show complementary but temporarily distinct biogeographic patterns. High Andean diversity reflects an Andean origin, with early occupancy and diversification occurring within the Andes, followed by post-Pebas dispersal into Amazonia. By contrast, Amazonian-centred clades, reflect an Amazonian origin, with an early diversification in Amazonia and subsequent post-Pebas colonization of the Andes. While several clades show little evidence of Pebas influence, our study suggests that the Pebas wetland did not uniformly restrict diversification, but rather selectively constrained dispersal between the Andes and Amazonia, preventing simultaneous diversification in both regions and thereby creating a diversity imbalance that characterizes the modern Neotropic.

Coastal organisms experience natural and anthropogenic stressors simultaneously, yet the interactive effects of multiple stressors are largely unknown. In urbanized estuaries, coastal acidification (CA) is coupled to sewage effluent (SE): nutrient loading from SE stimulates microbial CO2 production, and this lowers the pH. The genomic targets of selection of CA and SE have been characterized separately but never together in early life stages of marine organisms. Here, we exposed eastern oyster (Crassostrea virginica) larvae to control, CA (~2800 atm pCO2), SE (5% by volume), and the combination (CASE) for 24 h across independent spawns, and used expressed exome capture sequencing to measure allele-frequency change before and after exposure, removing loci that also shifted in controls. CASE generally produced the lowest survival, although mortality was driven primarily by effluent and did not exceed the additive expectation. The size of allele-frequency change under CASE stayed close to the additive sum of the single stressors, but it showed compositional synergy: CASE had more outlier loci than CA and SE combined with 1,941 loci (747 genes) detected only under the combined treatment. CASE outliers were enriched for proteostasis, ciliary function, mitochondrial calcium handling, and a steroid-metabolizing (CYP17) module consistent with effluent endocrine disruptors. Selection acted repeatedly on standing variation across spawns and genetic backgrounds, with the largest allele-frequency shifts at rare, spawn-private loci. Enriched biological functions recurred across spawns more often than expected, while most outlier loci were specific to one or two spawns, consistent with genotypic redundancy. Our results show that combined stressors can recruit a compositionally synergistic genomic response, at loci and functions not detected under either stressor alone, even when survival and the size of allele-frequency change are additive.