Freshwater Biology

Quagga mussels (Dreissena rostriformis bugensis) are ecosystem engineers that can alter nutrient cycling, benthic-pelagic coupling, and food-web structure in deep lakes. Although their invasion trajectories are well documented in the Laurentian Great Lakes in North America, depth-specific population dynamics remain poorly resolved in recently invaded European perialpine lakes. We analyzed five annual lake-wide surveys (2021-2025) from 54 stations spanning 2.4-253 m depth in Lake Constance to quantify changes in quagga mussel density, biomass, and shell-length distribution. Contrary to expectations of lake-wide exponential growth, shallow-water populations (< 20 m) showed no significant increase during the study period and appear to have reached carrying capacity before monitoring began. In contrast, densities increased monotonically at intermediate depths (40-125 m), indicating ongoing expansion into deeper strata. Mean shell length declined with depth, and size distributions in shallow waters shifted toward larger individuals, consistent with a transition from active recruitment to somatic growth of established mussels. Compared with the Laurentian Great Lakes, Lake Constance already has substantially higher shallow-water biomass, whereas deeper invasion trajectories are broadly similar. These results show that quagga mussel invasion in deep European lakes can combine rapid littoral saturation with slower profundal expansion, complicating direct transfer of predictions from the Great Lakes. Continued depth-stratified monitoring will be essential for anticipating future ecosystem effects in perialpine lakes.

Inland waters in the Northern Hemisphere are experiencing increased annual runoff due to higher overall precipitation as well as intensified short-term events such as heavy rainfall, floods and storms. These events affect the total loading and variability of inputs of allochthonous, coloured dissolved organic matter (cDOM) and inorganic nutrients into lakes. Previous studies have shown that increased total cDOM and inorganic nutrient loads affect phytoplankton biomass and metabolic rates, but it is unknown how the effects of different cDOM and nutrient pulse scenarios are modified by spatial and seasonal differences in lake characteristics. Here, we conducted a coordinated, standardized mesocosm experiment across three lakes with different ambient cDOM and nutrient concentrations. In two of these lakes, the experiment was implemented in two seasons. The same total amounts of cDOM, nitrate and phosphate were added to all mesocosms, but in pulses that differed in intensity and frequency. We found that pulse intensity and frequency affected chlorophyll a and phycocyanin concentrations and metabolic rates, i.e. gross primary production and respiration, differently. Specifically, more pronounced effects were found in response to the extreme pulse scenario compared to those with more frequent, smaller pulse additions. Furthermore, the effects were mainly temporary and varied more among lakes than between seasons. The clearest differences between the extreme and more gradual runoff scenarios were found in the lake with the lowest background cDOM and nitrate concentrations, likely because lower light limitation and possibly stronger initial N-limitation caused a faster response to the nutrient addition. Our results highlight that both antecedent lake conditions and characteristics of runoff events can affect phytoplankton biomass and metabolic rates and that comparative experimental approaches are needed to reveal the complexity of the responses.

The global study of freshwater clams in the genus Corbicula is frequently confounded by invasive androgenetic lineages that experience mitochondrial DNA capture and clonal propagation. In contrast, the endemic Corbicula of Sulawesi's ancient lakes reproduce sexually, offering a uniquely reliable system for mitochondrial population genetics. This study provides the first population-genetic framework for two endemic species, Corbicula possoensis (Lake Poso) and C. linduensis (Lake Lindu), using the cytochrome c oxidase subunit I (COI) marker. We analysed 90 newly generated COI sequences from C. possoensis (six stations) and C. linduensis (three stations), integrated with reference sequences from GenBank, to assess genetic diversity, population structure, and phylogeographic patterns. Hierarchical AMOVA revealed deep divergence between the two lakes ({Phi}_CT = 0.607), consistent with prolonged independent isolation rather than a single shared vicariance event, as the two species do not form a sister pair in the phylogeny. Within Lake Poso, C. possoensis exhibited exceptionally high genetic diversity (24 haplotypes; h = 0.876; {pi} = 0.016) and pronounced micro-geographic structuring into three phylogeographic zones (North: Tentena and Siuri; East: Tando Nceppo and Busogo Beach; Southwest: Bancea and Pendolo), each characterised by distinct haplogroups. Remarkably, the maximum divergence between zones (K2P = 2.33%) approached the interspecific distance between C. possoensis and C. linduensis (K2P = 2.42%), indicating that within-lake mitochondrial divergence has reached near-interspecific levels. Conversely, C. linduensis displayed near-panmixia and extreme genetic depauperation (3 haplotypes; h = 0.246; {pi} = 0.0004), indicating long-term demographic stasis within a restricted habitat. The deep phylogeographic zonation in C. possoensis suggests that its discrete populations should be treated as separate Management Units (MUs) in conservation planning to preserve locally adapted gene complexes, whereas the severely depauperate gene pool of C. linduensis renders it critically vulnerable to environmental disturbance and invasive species, warranting urgent IUCN Red List assessment. To validate these mitochondrial boundaries and inform future conservation strategies, multi-marker and genome-wide reassessments are strongly recommended.

Freshwater salinization is of increasing concern for integrity and functioning of freshwater habitats worldwide. Experiments so far often have studied drastic salt additions, while gradient designs have been performed less commonly. We tested the effect of freshwater salinization in a mesocosm exposing the plankton community of the oligotrophic Lake Lunz, Austria, to a four-fold salinization gradient (control, 0.2, 1, a 5 ppt salt). Salinity was manipulated in a factorial design with enrichment, with 10 g L-1 and 30 g L-1 phosphorus, resulting in 8 treatments with 3 replicates each. We followed the effects of salinization on diversity, community composition and resource use over 36 days. Community composition was assessed by amplicon sequencing, Diversity loss and community turnover followed upon salt addition. All levels of salinization caused pronounced changes in community composition, with 5 ppt causing the most drastic changes. Salinization caused trophic downgrading by kicking out especially protistan consumers and rotifers, while some green algae and chrysophytes were especially tolerant, resulting in reduced phylogenetic and functional diversity with increasing salinization. In line with reduced top down control, salinization affected temporal variability in chlorophyll-a (chl-a) and resource use (RUE), with higher salinity causing more extreme fluctuations in chl-a and RUE. Enrichment overall aggravated salinization, enhancing temporal turnover and temporal fluctuations in resource use.

Lake Constance is a pre-Alpine, monomictic, oligotrophic lake situated at the southern end of Germany composed of two main water bodies: deep, oligotrophic Upper Lake Constance (ULC) and the shallow, more mesotrophic Lower Lake Constance (LLC). To date, no sequencing-based study exists of the seasonal succession of the microbial plankton in Lake Constance. Over one-year, microbial plankton communities were sampled biweekly from the top 20 m of the water column in both sites and separated into nanoplankton (NP) and picoplankton (PP). Communities were analysed using rDNA amplicon sequencing: NP samples were analysed by 18S rDNA, and PP samples by 18S and 16S rDNA sequencing. Temporal community diversity was compared between sites and the effect of two major environmental perturbations, winter vertical mixing in ULC and oxygen depletion of the bottom-water layer in LLC, on the community was examined. Despite strong environmental contrasts, microbial plankton communities exhibited conserved seasonal temporal dynamics across basins. In contrast, pronounced compositional shifts occurred during mixing and oxygen depletion events. Approximately 20% of detected taxa were positively associated with these events, with log fold changes reaching 9.82, reflecting rare or undetectable taxa outside these periods. Taxa favoured by these perturbations commonly exhibited high metabolic flexibility, including mixotrophy, fermentation, or anaerobic respiration, or possessed functional traits conferring tolerance to altered redox and mixing regimes. Our results suggest that the temporal dynamics of freshwater microbial plankton communities are driven by deterministic processes and highlight the profound impact of large, and less known, environmental changes on these communities.

Benthic algae integrate catchment-and reach-scale pressures in streams. We assessed land-use effects on benthic algal assemblage structure, chlorophyll-a, ash-free dry mass (AFDM), and autotrophic index across 24 headwater streams in the Sondu-Miriu River basin, Kenya, and explored wet-dry patterns in two monitoring streams. We sampled across four land-use categories: natural forest (NF), tea and tree plantations (TTP), smallholder agriculture (SHA), and smallholder tea (SHT). Synoptic sampling occurred in August 2025, and one NF stream and one SHA stream were sampled five times between November 2024 and May 2025. Shannon and Simpson diversity were highest in NF streams and lowest in SHT streams. Chlorophyll-a and AFDM were highest in SHA streams; chlorophyll-a was lowest in SHT, while AFDM and autotrophic index were lowest in NF. Relative abundance patterns showed that SHA streams were dominated by Lyngbya and Stigeoclonium, whereas SHT streams were dominated mainly by Stigeoclonium; NF streams supported persistent diatom-rich assemblages. Non-metric multidimensional scaling showed land-use separation of benthic algal assemblages, while redundancy analysis indicated weak, non-significant evidence of environmental associations in the synoptic dataset. Composition and biomass metrics tracked land-use gradients and wet-dry patterns, supporting periphyton-based bioassessment for monitoring disturbance in Afrotropical headwater streams.

Sustainable management of commercial and recreational fisheries depends on accurately resolving population connectivity, across both ecological and evolutionary timescales. However, dispersal can vary markedly among life stages, making stock connectivity difficult to resolve using single-method approaches that often differ in spatio-temporal resolution. Here, we integrated population genomics, otolith stable isotope chemistry, and mark-recapture analyses to provide a multi-faceted assessment of stock connectivity in mulloway (Argyrosomus japonicus). Mulloway are a commercially, culturally, and recreationally important estuary associated fish distributed throughout the Indo-Pacific region, including south-eastern Australia where this study was conducted. Genome-wide single nucleotide polymorphism (SNP) analyses revealed significant genetic differentiation between regions influenced by different current systems, but limited structure within regions across distances exceeding 900 km. In contrast, otolith {delta}13C and {delta}18O signatures revealed fine-scale spatial structuring among estuaries, consistent with prolonged occupancy of local habitats. Mark-recapture analyses supported this interpretation, with most fish exhibiting strong estuarine fidelity over extended periods despite occasional long-distance coastal movements. Reconstructed age structures from fish otoliths revealed remarkably similar cohort composition among estuaries, with populations dominated by cohorts originating from a major recruitment pulse centred on 2011-2012, likely associated with a broad-scale flood-driven spawning and recruitment event. Together, our findings indicate that mulloway fisheries function as regionally connected networks of partially independent estuarine assemblages, where strong local residency is periodically offset by dispersive individuals and episodic recruitment events that maintain long-term demographic and genetic connectivity. Consequently, local estuarine populations may be vulnerable to localised depletion despite broader regional connectivity, particularly where sustained fishing pressure coincides with reductions in freshwater flows that constrain spawning and recruitment. More broadly, our study demonstrates the value of integrating complementary approaches to identify biological connections and define meaningful management units in species with complex life histories.

Passive sampling is the deployment of a collection material in the environment to continuously capture environmental DNA (eDNA) over time, offering the potential to integrate biodiversity signals while reducing the need for repeated active water collection. However, the mechanisms governing eDNA capture and retention on passive samplers remain poorly understood, limiting the interpretation of passive eDNA signals and their broader application. Here, we investigated the mechanistic performance of glass fibre passive samplers using controlled mesocosm experiments with three invasive freshwater bivalves: zebra mussels (Dreissena polymorpha), quagga mussels (Dreissena bugensis), and Asian clams (Corbicula fluminea). Specifically, we quantified eDNA accumulation dynamics, evaluated the contribution of different eDNA states, tested the persistence of captured eDNA, and compared passive sampler signals with conventional active sampling. Passive samplers rapidly accumulated target eDNA within hours of deployment, after which concentrations either plateaued or continued to increase depending on species. Sequential transfer of passive samplers between mesocosms containing different species showed that previously captured eDNA declined while new target eDNA accumulated to concentrations comparable to freshly deployed samplers, demonstrating continual turnover rather than permanent retention. Dissolved eDNA showed little evidence of accumulation beyond the concentration retained in the pore water within the membrane, suggesting that it is unlikely to be the dominant contributor to long-term passive sampler signals. Instead, the observed variability among replicate samplers, together with the physical properties of glass fibre membranes, suggests that membrane-bound and particulate eDNA are the primary contributors to passive eDNA capture. Collectively, these findings support a model in which glass fibre passive sampler signals reflect a dynamic equilibrium between ongoing eDNA capture and concurrent loss processes rather than cumulative accumulation over time. This mechanistic framework provides a foundation for interpreting passive eDNA data and informs the future development of passive sampling materials, deployment strategies, and biodiversity monitoring applications.

Microorganisms, found in every environment, play an important role in recycling matter and providing energy to the ecosystem. Here, we used 18S and 16S metabarcoding to study bacteria, cyanobacteria and protist community diversity and functional ecology among different environments of typical lake, river, marine and soil from the Yangtze Delta of China. The results showed that the similarity of cyanobacteria and protozoa communities in soil and aquatic environments was both higher than that of bacteria and microalgae communities. While the diversity of cyanobacteria and bacteria in lake was higher than that in river, marine and soil, the diversity of microalgae and protozoa in river was higher than that in lake, marine and soil. The {beta} diversity of cyanobacteria and bacteria marked differences in lake from other environments. But The distribution of dominant families of cyanobacteria, bacteria, microalgae and protozoa is similar to diversity. While significant positive correlations were found among dominant species of cyanobacteria, protozoa, bacteria and microalgae in lake the dominant species among bacteria, microalgae and protozoa in river, marine and soil all showed more negative correlations. Our study provides the basis for understanding the functional ecology of microbes in the micro-food webs of different environments.

Untargeted metabolomics offers a powerful lens for quantifying high-dimensional phenotypic variation within and among species in nature, but has yet to be widely adopted in evolutionary ecology. Some important initial questions are whether metabolome composition differs among populations, and to what extent such variation is genetic or plastic. Here, we use untargeted liquid chromatography tandem mass spectrometry to characterize the relative abundance of 5,939 molecular features of the threespine stickleback (Gasterosteus aculeatus) liver metabolome. Native lake populations differ in metabolome composition, reflecting effects of sex, size, geography, and population ecotype (benthic versus limnetic). Stickleback from these lakes were translocated to found new populations in nine recently fishless lakes, permuting fish ecotypes across benthic and limnetic lake habitats. Several generations later, metabolomes in these experimental populations reflect effects both of their genetic ancestry (e.g., taurocholic acid, a cholane steroid bile acid, was elevated in limnetic-ancestries), as well as their present habitat (e.g., acylcarnitines). Additionally, ecotypes transplanted into a habitat to which they were maladapted exhibited a distinctive metabolomic profile. We conclude that stickleback exhibit both heritable and plastic among-population differences in liver metabolome, which could represent an important phenotypic basis of rapid evolution, population divergence, and perhaps local adaptation.

Thiamine Deficiency Complex (TDC) is a reproductive disorder that affects recruitment of diverse salmonine populations globally. Typical symptoms include behavioral and neurological abnormalities and high offspring mortality. TDC is common in hatcheries that rear salmonines obtained from wild populations, and symptoms are mitigated by thiamine treatment. However, no studies have quantified thiamine concentrations in wild embryos. Here, we evaluated whether fertilized eggs and/or embryos may acquire thiamine from natural sources (e.g., biotic breakdown products and diet) during development. Lake trout (Salvelinus namaycush) gametes were obtained from feral adults in Lake Champlain and fertilized eggs were grouped by family with paired rearing under natural (Lake Champlain) and artificial (controlled laboratory) conditions. Average thiamine concentrations were similar between lake-reared and laboratory-reared fish prior to hatch; however, lake-reared fish experienced significant increases in thiamine concentrations at and after hatching compared to previous stages and compared to laboratory-reared fish; laboratory-reared fish experienced no increases in thiamine concentrations. Water samples revealed an abundance of thiamine precursors and byproducts in the natural environment, which may serve as sources of thiamine for developing embryos. These results demonstrate that salmonine embryos can acquire thiamine from natural sources during development, which may mitigate effects of TDC.

Capelin (Mallotus villosus), a key forage fish in the Northwest Atlantic, links zooplankton to predators including commercial fishes, seabirds, and marine mammals, yet its life-cycle movements in the Gulf of St. Lawrence (GSL) remain poorly understood. Between 2022 and 2024, otoliths from 927 individuals collected during and after spawning were analysed by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS). Building on previous work on regional structuring, seven trace elements (Li, B, Mg, K, Zn, Sr, Ba) were used to discriminate three regions. Early-life regional signatures were inferred through an edge-to-core approach, assigning otolith core chemistry to one of these regions using quadratic discriminant analysis. The core was treated as an integrated early-life signal (late-larval to early juvenile period) rather than a strictly natal signature. Spatial variation in core chemistry was consistent across cohorts, mirroring the stability documented on the otolith edge. Results revealed widespread dispersal alongside partial regional residency: individuals with northeastern early-life signatures showed the strongest correspondence between early-life and capture regions, whereas other regions were more connected. Fish sampled during spawning were more often reassigned to their inferred early-life region than post-spawning fish, a regional-scale homing-like pattern consistent with regional spawning fidelity. This coexistence of dispersive and resident strategies likely generates a portfolio effect buffering the population against environmental variability and localised reproductive failures.

Knowledge regarding variation in habitat use among individuals is crucial for understanding population dynamics and for management and conservation measures. This is especially important for diadromous fishes that shift between habitats, being affected by external pressures and environmental change in different habitats over ontogeny. Herer, we assessed individual variation in habitat use of European eel along a salinity gradient, ranging from fully marine to freshwater in northern Europe, using otolith microchemistry data from >3600 eel together with established time-series segmentation and clustering methods. We show that eel display high degree of individual variation in habitat use. Assigned life-histories included coastal resident, freshwater resident, and coastal and freshwater habitat shifting individuals. Coastal resident eels were observed in a large range of salinities. Given the widespread occurrence of migration barriers in freshwater, it is unknown whether the coastal resident eel preferred that habitat, or if it was the only available habitat for them. Our findings nonetheless highlight the need to include coastal habitats when assessing population development and silver eel production of the critically endangered European eel.

Environmental DNA (eDNA) methodology is widely applied in the biomonitoring of organisms, but it requires the target DNA to be detected in a simple, stable, and highly sensitive manner. Detection sensitivity of eDNA measurement becomes particularly critical when monitoring species present at low abundance. In this study, we aimed to improve the detection sensitivity through a method of DNA-extract reconcentration. This approach involves reconcentrating eDNA samples that were originally extracted using the widely adopted DNeasy Blood and Tissue Kit (Qiagen), utilizing the same kits reagents, and does not require any additional equipment or reagents. We evaluated the ability of this DNA reconcentration method using field samples including river, lake and costal marine habitats. Evaluation of this DNA reconcentration method showed that when ten conventionally extracted samples were pooled, the DNA concentration increased by approximately sevenfold, as confirmed by DNA quantification and quantitative PCR analyses, demonstrating enhanced detection sensitivity.

Many dinoflagellates are mixotrophic and regulate their vertical position to navigate dynamic gradients in light, nutrients, and prey. Here, it is shown that the obligate kleptoplastidic mixotroph, Dinophysis acuminata, transitions from diel vertical migration to formation of a stationary, sub-surface thin layer in response to prolonged prey deprivation. An inshore bloom within a salt marsh kettle pond was recorded through continuous in-situ imaging, automated oxygen and fluorescence depth profiling, and targeted water chemistry measurements. During the blooms initial development, D. acuminata cells were photosynthetically active and divided vegetatively while vertically migrating. As photosynthesis and growth slowed, vertical migration ceased and cells formed a stable thin layer that promoted conditions for local acidification and nitrogen remineralization. Surface avoidance by the thin layer drove selective retention of cells within the relatively deep kettle hole. Together, these findings illustrate linkage of metabolic state and swimming behavior in D. acuminata and show how swimming behavior can drive development of toxic blooms within inshore systems. They also illustrate how D. acuminata and other eurytolerant bloom-forming species can exploit and shape physicochemical gradients associated with coastal eutrophication.

Quantitative stable isotope probing (qSIP) allows researchers to calculate taxon-specific carbon incorporation from sequencing of natural microbial communities, which can be used as a proxy for metabolic activity rates and subsequently as an input for biogeochemical modeling. While qSIP is widely utilized in soils to investigate the identity and metabolic activity of largely unculturable microbes, the application of qSIP in marine and aquatic ecosystems is more recent. Here, we investigated how bioreactor type (batch vs. chemostat) and carbon substrate complexity (single vs. multiple substrates) affect the incorporation of {superscript 1}3C-labeled glucose into rRNA after 24 hours using excess atomic fraction (EAF) as a proxy for metabolic activity rate. We found that the growth dynamics and community composition of the {superscript 1}3C-incorporating bacteria differed significantly for each treatment. EAF was positively correlated with both 16S gene copy number and a genomic index of copiotrophy in both batch treatments, but not in the chemostat, suggesting that chemostats dampen the competitive advantage of fast-growing copiotrophic taxa. Our results demonstrate that both substrate complexity and experimental regime influence qSIP-derived metabolic activity estimates and provide guidance for future applications of qSIP in aquatic environments.

Future climate change may reshape ecological communities not only by increasing mean temperature, but also by altering the consequences of increasingly frequent heatwaves. Predicting these effects requires understanding how background warming interacts with short heatwaves in natural communities, where responses can arise through direct thermal stress and species interactions. We tested this using 32 outdoor freshwater mesocosms exposed to sustained near-future warming while capturing a documented natural heatwave. Warming raised temperature maxima that exceeded the thermal threshold of the pond snail, a main grazer in the community. Warmed communities showed lower grazer abundance, increased macrophyte and insect herbivore abundance, reduced phytoplankton biomass, and lower zooplankton density. Complementary assays showed that heatwave-level temperatures promoted macrophyte growth and reduced grazer survival, whereas reduced zooplankton performance mainly reflected indirect warming effects via food-web cascades. Thus, near-future warming can amplify natural heatwave impacts by exceeding consumer thermal thresholds and propagating through species interactions.

Understanding the evolutionary history of species within a geographic context is key to historical biogeography, as it reveals how geological and climatic changes shaped biodiversity. This is especially important in ecologically significant regions like the Amazon and Orinoco basins. Together, they host the worlds greatest freshwater fish diversity ([~]3,500 species), sharing a common but not yet fully understood evolutionary history. The gilded catfish (Brachyplatystoma rousseauxii), an ancient species widely distributed as a metapopulation in Neotropics, is an important model for studying past connectivity, divergence, and historical processes shaping fish diversity between these basins. This study analyzed the genetic structure, connectivity routes, and demographic history of B. rousseauxii using nuclear (microsatellite and ddRADseq) and mitochondrial DNA. Population structure analyses and coalescent models indicate that B. rousseauxii populations from the Orinoco and Amazon basins are genetically distinct, with no evidence of current gene flow. However, our results support the occurrence of a possible secondary contact event after the divergence, with the Boa Vista population retaining the genetic signal of this process. The ancestral population split occurred at the Rupununi Portal around 2.54 Ma (ddRAD) or 1.31 Ma (mtDNA). Then, the species colonized the Branco and Orinoco Rivers [~]1.90 Ma (ddRAD) or 0.6 Ma (mtDNA), rapidly expanding in the Orinoco (>1.3 or >0.29 Ma), while colonization of the Amazon from the Branco River was more recent ([&le;]1.0 or [&le;]0.15 Ma). Population expansion signal was detected in the Orinoco ([~]0.20 Ma), whereas the Amazon remained stable. Our findings suggest that the rise of the Vaupes Arch in the Late Miocene does not explain the observed genetic divergence. Likewise, the Casiquiare Canal and Japura-Guaviare headwaters are not connectivity routes between basins. Instead, the Rupununi Portal, including the recent capture of the Branco River by the Negro River, was the last point of connection and played a key role in shaping B. rousseauxiis distribution. These findings provide insights into Neotropical fish biogeography and the historical configuration of the Orinoco and Amazon basins.

Understanding the genetic structure of keystone species within river networks is essential for effective conservation and management. While population differentiation of anadromous species often occurs between river systems, less research has been conducted on differentiation within rivers with smaller catchment areas. In this study, we investigated the population genetic structure of wild Atlantic salmon (Salmo salar) across the small-scale river Ronne [a] system in southernmost Sweden using Restriction-site Associated DNA sequencing (RADseq). Although the Admixture analysis did not detect clearly defined genetic clusters, significant pairwise FST values and DAPC revealed emerging population differentiation among the Ronne [a] tributaries. The observed patterns are consistent with a system characterized by connectivity, where genetic flow is present but can be reduced by behavioral and ecological factors such as spawning homing behavior and selective movements. These findings suggest that, despite overall connectivity, Atlantic salmon populations in the Ronne [a] catchment area may function as partially independent sub-populations. This highlights the importance of conservation and management strategies in fragmented river systems to consider population genetic structure to support resilient salmon populations under ongoing anthropogenic pressures.

Japanese chum salmon supported by one of the world largest hatchery programs have experienced severe declines in marine survival and egg size. To investigate the underlying mechanisms, we analyzed a 21-year time series (1999-2019) of reproductive traits of age-4 chum salmon from 13 rivers together with climate and salmon abundance data using a bootstrap-supported Bayesian network. Here, we assumed that environmental variables can affect the chum salmon populations, but not vice versa, and that there could be maternal effect on reproductive traits, but not the other way around. These constraints enabled us to infer the causal links that shaped the biogeography of North Pacific chum salmon. Global warming caused a decline in Japanese chum salmon abundance, resulting in the increase of the competing Russian chum, which in turn decreased the female body size, fecundity, and egg size of Japanese chum. These findings suggest that climate-driven warming may have exposed genetic effects of hatchery practices, contributing to fitness decline in Japanese chum salmon and the ecological reorganization of chum salmon populations in the North Pacific.