Biology and Life Sciences

Abstract: Background: Aquaculture supplies over half of global fish consumption but faces challenges including disease outbreaks, oxidative stress, antimicrobial resistance, and reliance on finite fishmeal and fish oil resources. Methods: This review synthesizes research on freshwater and marine microalgae, focusing on their bioactive compounds and functional roles in aquaculture nutrition and health. Results: Microalgae provide proteins, carotenoids, vitamins, polyunsaturated fatty acids, and immunostimulants that act via immunomodulation, antioxidant defense, gut microbiota regulation, anti-inflammatory activity, growth promotion, and pigmentation enhancement. Applications include live feed in larval rearing, dried biomass in compound feeds, and microalgal oils as fish oil substitutes. Conclusions: Incorporating microalgal nutraceuticals into aquafeeds offers a sustainable strategy to improve aquaculture productivity, animal health, and product quality, supporting the transition toward resilient and ecologically sustainable systems within the One Health framework.

Abstract: To optimize spat stocking rates for Pacific calico scallop (PCS, Argopecten ventricosus) during nursery culture, two consecutive 8-week trials were conducted to evaluate growth in land-based downweller and upweller systems. Four stocking rates (60%, 70%, 80%, and 90% of silo bottom coverage) were tested in the downweller system, whereas three stocking rates (50%, 70%, and 90% of silo bottom coverage) were evaluated in the upweller system. In the downweller system, spat stocked at 60% generally exhibited the best growth performance, with significantly higher relative growth rate (RGR, mm/day) in shell height compared with higher stocking rates. In the upweller system, spat stocked at 50% and 70% showed similar growth performance and both outperformed the 90% stocking rate treatment in shell height, dry weight, RGR, specific growth rate (SGR, %/day), and condition index (CI). These results suggest that moderate stocking rates, approximately 60% in downweller systems and 50–70% in upweller systems, provide favorable conditions for PCS spat growth under the present culture conditions. The present study demonstrates the feasibility of PCS spat nursery culture in land-based systems and provides practical information for hatchery production and nursery management of this emerging aquaculture species.

Abstract:

Integrated proteomics and untargeted metabolomics were employed to systematically characterize molecular differences between high-quality (HQ) and low-quality (PQ) eggs of Acipenser schrenckii. Among 1,636 proteins and 1,102 metabolites, 220 differentially expressed proteins (DEPs) and 365 differential metabolites (DMs) were identified. Functional enrichment demonstrated that HQ eggs were predominantly enriched in pathways associated with amino acid biosynthesis, glycolysis/tricarboxylic acid cycle, nucleotide metabolism, and mRNA surveillance, which collectively supported material accumulation, energy supply, and embryonic developmental competence. In contrast, PQ eggs were mainly enriched in oxidative phosphorylation, mitochondrial stress response, arachidonic acid metabolism, and immune and inflammatory signaling pathways, indicating severe lipid metabolic disorders and excessive oxidative stress. Spearman correlation analysis identified L-pyroglutamic acid and ascorbic acid as core metabolic hubs responsible for maintaining high egg quality, whereas natamycin and tetrahydrocorticosterone served as characteristic metabolic biomarkers of deteriorated eggs. Key protein hubs closely associated with egg quality included GAPDH, glutathione S-transferase, and CYP450 2E1. Collectively, this study elucidates distinct molecular regulatory patterns and establishes a reliable multi-omics biomarker for evaluating sturgeon egg quality formation and deterioration.

Abstract: This study evaluated the use of finishing diets to reduce fish oil (FO) inclusion in European sea bass feeds while preserving fillet quality and n-3 fatty acid content. Fish (197 g) were fed for 25 weeks with a control FO diet, based on 9% FO and 6% plant oil, or diets where 6% FO was replaced by rapeseed oil (RO) or microalgae (AO; Nannochloropsis sp. and Schizochytrium sp.). After 13 weeks, 2 groups of fish fed the RO diet were switched to the FO or AO finishing diets for the final 12 weeks. Growth, feed efficiency, body composition, and health were unaffected by dietary treatments. However, long-term RO feeding reduced EPA and DHA and increased monounsaturated and n-6 fatty acids compared to fish fed AO or FO. Finishing diets effectively restored morphometric traits, fatty acid profiles, liver histology, and overall fish quality, with FO outperforming AO in recovering the original fatty acid composition of FO-fed fish. Longer finishing periods may further enhance fillet quality when using microalgae-based oils.

Abstract: This study presents the development and application of an integrated Geographic Information System (GIS)-based Marine Spatial Planning (MSP) framework for identifying suitable offshore aquaculture development zones in Cyprus. The methodology, developed within the OS AQUA project, combines environmental exclusion analysis, weather and proximity assessment, stakeholder and policy evaluation, and carrying-capacity estimation within a unified spatial decision-support framework. A sequential three-phase analytical workflow was applied to progressively refine candidate offshore areas under environmental, operational, infrastructural, regulatory, and governance considerations. The analysis identified four candidate offshore aquaculture zones in Cyprus — Xylofagou West, Larnaka (Faros area), Governor’s Beach, and Aphrodite Hills/Avdimou — demonstrating comparatively favourable conditions for offshore aquaculture development. The results highlight the importance of integrating environmental compatibility, operational feasibility, accessibility, stakeholder acceptance, and sustainability considerations within offshore aquaculture planning processes. Carrying-capacity assessment further indicated substantial offshore production potential under precautionary operational assumptions. Beyond the Cyprus case study, the proposed GIS-MSP framework offers a transferable methodological roadmap for offshore aquaculture zoning, Allocated Zones for Aquaculture (AZA) establishment, and sustainable marine spatial planning in the Mediterranean region.

Abstract: Using marine resources’ colouring agents as nutrients, medicaments and in luxury products colouring is rooted in human history. The handy obtainable marine biological pigments (MBPs), consider as inexpensive materials since colourants. They were a part e of blue technology for colouring purposes, as nutrient additives, cosmetic gradients, beauty products, staining addresses and fashion colour in luxury. Today, they still broaden many new applications. They can be concentrated on the bodies of marine creatures providing unique colour, properties and complement activities. They can stand alone to process unique activities. In addition, some are essential for host survival. Out of their primary hosts, they stay either unmodified or can be changed or associated with other micro and/or macromolecules in their secondary hosts (consumers). Few were extracted, purified, identified and formulated as drugs. Many share properties like being antioxidants, having the ability to protect from sunlight (as UV waves) and improving eye vision. They are involved in health protection or illness treatment, as anticancer, anti-inflammatory, anti-neuro-degradation, antiaging, anti-wrinkle, and as antimicrobial. Even they hold many undiscovered properties that make them an uncountable source for de nevo applications with innumerable chances that mastery the colourful fields. This review summarizes the importance of marine pigments and addresses important applicable properties that made them interesting in nutraceutical, medicinal, pharmaceutical, cosmeceutical and industrial applications. In addition, it is concerned with discussing some facts that have attracted the attention of humans in the past today and some expectations for the MBPs future.

Abstract: Linking community variation to environmental gradients is central to reservoir ecology and monitoring, yet the strength of detected associations can depend on how community change is represented. Using phytoplankton surveys from a tropical reservoir (Corumbá River, Brazil) sampled across wet and dry seasons, we compared taxonomic beta diversity with two functional representations: Reynolds functional groups and a set of widely used morphological traits combined into functional beta-diversity indices. We partitioned beta diversity into turnover and richness-difference components and quantified environment–community associations with constrained ordination. Overall, the representation chosen altered both the magnitude and the seasonal consistency of environmental associations: trait-based indices (particularly dendrogram-based metrics weighted by biovolume) tended to show stronger associations with environmental gradients related to mixing, light availability and nutrients, whereas functional groups and species-level data emphasized complementary aspects of community change. Turnover and richness-difference components did not respond uniformly across representations, highlighting that component choice can shift ecological interpretation. Rather than providing a universal ‘best’ approach, our results suggest practical trade-offs among representations when the goal is to detect and interpret environmental structuring along reservoir gradients, especially during highly dynamic conditions typical of early post-impoundment phases.

Abstract: Reliable age information is needed for fisheries assessment, but conventional otolith reading requires trained readers and considerable time. This study evaluated whether convolutional neural networks could classify reader assigned age classes of Japanese jack mackerel Trachurus japonicus directly from sagittal otolith images. Otolith images from fish aged 0 to 4 years were used to compare three image only backbones: Inception v3, Xception, and EfficientNet B4. The models were trained under the same data split, preprocessing, augmentation, and evaluation framework. In Stage 1, Inception v3 showed the highest validation macro F1 score (0.933) and was selected as the image only baseline. After additional optimization, the selected model reached a validation macro F1 score of 0.944, validation exact accuracy of 0.935, and validation agreement within one age class of 1.000. On the independent test set, the optimized image only model achieved exact accuracy of 0.866, macro F1 score of 0.873, and agreement within one year of 1.000. These results indicate that otolith images contain useful age related visual information. Convolutional neural networks may support age class screening in T. japonicus, although they should complement rather than replace expert otolith reading.

Abstract: (1) Background: Nile tilapia is a cornerstone of global aquaculture, yet hypoxia remains a critical constraint. This study investigates the hypoxia response mechanisms in the gill tissue of a selectively bred Egyptian strain to elucidate the metabolic pathways and genetic regulators governing its tolerance. (2) Methods: We evaluated antioxidant and metabolic enzyme activities alongside gill histology after hypoxia exposure. Furthermore, transcriptome profiling was conducted to identify enriched pathways, with expression patterns validated via qPCR to distinguish between acute and long-term adaptive responses. (3) Results: Hypoxia significantly altered enzyme activities and caused time-dependent gill damage, ranging from mild swelling to severe rupture. Transcriptomics highlighted starch/sucrose metabolism and PPAR signaling. qPCR confirmed that specific genes peak at 6 h for acute responses, while others gradually increase for long-term adaptation. (4) Conclusions: These findings link energy metabolism with immune regulation, revealing the molecular mechanisms underlying hypoxia tolerance. The identified genes offer valuable insights and genetic resources for breeding resilient Nile tilapia.

Abstract: Assessing water quality in lotic ecosystems using biological indicators is essential for their conservation. This study analyzed the influence of physicochemical parameters (pH, conductivity, dissolved oxygen, total nitrogen, nitrates, total phosphorus, phosphates, alkalinity, and hardness) on the diversity, abundance, and distribution of protozoa in 15 sites of the upper Soto la Marina River basin, Tamaulipas, Mexico, including the Corona, Purificación, Pilón, San Felipe rivers and the Vicente Guerrero Reservoir. Through bimonthly sampling over an annual cycle (February-December), 24 protozoan morphospecies were identified, with a dominance of Ciliophora (10 morphospecies) and Amoebozoa (4 morphospecies). Chi-square analyses revealed that morphospecies frequency was significantly dependent on the sampling site (χ² = 246.72, df = 69, p < 0.001) but independent of seasonality (χ² = 0.86, df = 15, p = 1.0). Beta diversity (Sorensen-Dice index) showed low faunistic similarity among most sites (<60%), suggesting high species turnover and a local environmental filter. Using Outlying Mean Index (OMI) analysis, most morphospecies exhibited a generalist niche (low marginality, high tolerance), showing no significant relationship with the measured environmental variables. However, Vorticella sp. emerged as an exception, showing a significant association (p = 0.0329) and positive correlation with maximum pH and alkalinity values, and at sites with high NO₃⁻ and PO₄³⁻ concentrations, suggesting its potential as a bioindicator of organic enrichment conditions in the region. The lack of a strong environmental signal in most species underscores the complexity of these systems and the need to integrate multiple levels of bioindicators. This study provides the first baseline on the protozoan community in the area and discusses its relevance for water quality monitoring in a region of high conservation value, such as the area of influence of the Sierra de Tamaulipas.

Abstract: The striped mullet (Mugil cephalus) and white mullet (Mugil curema) support artisanal fishing at the mouth of the Soto La Marina River, Gulf of Mexico, an area of great ecological value within the Laguna Madre and Rio Bravo Delta Protected Natural Area, the Terrestrial Priority Region RTP-83, and the Marine Priority Region RMP-44. Given the absence of historical catch and effort time series—a typical constraint of data limited fisheries—a length based frequency approach was used to estimate growth parameters, mortality rates, and the exploitation rate (E = F/Z). During 2018–2019, 1,134 specimens of M. cephalus and 339 of M. curema were sampled. Due to sexual dimorphism in M. cephalus, analyses were performed separately for females, males, and combined sexes, while M. curema was analyzed with sexes combined. Growth (L∞, k) and mortality (Z, M, F) parameters for combined sexes were: M. cephalus (562 mm, 0.14 year⁻¹; 3.72, 0.21, 3.51 year⁻¹); M. curema (329 mm, 0.15 year⁻¹; 1.46, 0.25, 1.21 year⁻¹). Exploitation rates (E) substantially exceeded Gulland (E = 0.5) and Patterson (E = 0.4) reference points: M. cephalus females (0.891), males (0.915), combined sexes (0.944); M. curema (0.828). It is concluded that both stocks are experiencing severe overexploitation, revealing a disconnect between the area's conservation designations and the actual condition of the resource.

Abstract: To elucidate the characteristics of fatty acid composition in different tissues of Anguilla japonica before and after their seaward spawning migration, this study measured the fatty acid contents in the muscle, liver, and ovary of eels collected from the Yangtze River Estuary and offshore waters, and analyzed the distribution characteristics and transformation patterns of various fatty acids in different tissues. The results showed that the fatty acid composition in different tissues of eels from both the Yangtze River Estuary and offshore waters was essentially similar. Among all fatty acids, C18:1n9c had the highest proportion, accounting for over 31% of the total fatty acids in each tissue. Comparing different tissues, in eels from the Yangtze River Estuary, the muscle had the highest content of EPA, the liver had the highest content of DHA and EPA+DHA, and the ovary had the highest contents of ARA, n6-PUFA and SFA. In offshore eels, the muscle had the highest contents of C16:1, C18:1n9c and MUFA; the liver had the highest content of C16:0; and the ovary had the highest contents of C18:0, DPA, HUFA, n3-PUFA and PUFA. Comparing eels before and after seaward migration, the contents of C16:0, ARA, n6-PUFA, SFA, and the DHA/EPA ratio in the ovary of Yangtze River Estuary eels were higher than those in offshore eels. Conversely, the contents of C18:0, C16:1, C18:1n9c, EPA, DPA, DHA, EPA+DHA, HUFA, n3-PUFA, MUFA, PUFA, as well as the EPA/ARA, n3/n6 PUFA and PUFA/SFA ratios in the ovary of offshore eels were higher than those in Yangtze River Estuary eels. The ovary of Yangtze River Estuary eels mainly contained fatty acids for energy provision and precursors for long-chain fatty acid synthesis, whereas the ovary of offshore eels had preliminarily accumulated PUFA nutrients required for egg and embryonic development. Thus, the distribution patterns of different fatty acids among tissues are closely related to the seaward spawning migration process of A. japonica. Before migration, eels in the Yangtze River Estuary primarily focus on energy accumulation and liver metabolism; after entering the sea, eels gradually accumulate PUFA such as EPA, DPA+DHA and n3-PUFA as gonads develop. The selective reservation of different fatty acids in the ovary represents a physiological regulation in response to the nutritional demands of gonadal development.

Abstract: The Tilapia (Oreochromis aureus) sustains more than 90% of the fishery value and volume in the Vicente Guerrero Reservoir (VGR), Northeast Mexico, but stock status is uncertain due to lack of assessments. A total of 1,792 individuals (2020-2021) were analyzed. Von Bertalanffy growth, total (Z), natural (M) and fishing (F) mortality, and exploitation rate (E) were estimated. Under a data-limited framework, four complementary approaches were applied: the LBB model, length-based indicators, empirical reference points, and ecological risk assessment. Growth was negatively allometric (b=2.89). Estimated parameters were: L∞=464 mm, K=0.2275 yr⁻¹, Z=3.591 yr⁻¹, M=0.3894 yr⁻¹, F=3.302 yr⁻¹, E=0.892. The LBB model estimated a relative biomass B/B₀=0.057 (95% CI: 0.042-0.072) and an F/M ratio of 8.48. Only 7.5% of individuals exceeded maturity length, 4.8% were at optimal length, and 2.6% were mega-spawners. Estimated fishing mortality exceeded the reference points (F_MSY=0.339 yr⁻¹; F_limit=0.508 yr⁻¹; F_crash=0.678 yr⁻¹) by 9.7, 6.5, and 4.9 times, respectively, classifying the stock as extreme high risk. The O. aureus stock in VGR is in biological collapse (B/B₀=5.7%; F/M=8.48). Increasing minimum capture length to at least 290 mm and reducing fishing effort by 80-90% is urgently required. The convergence of independent methods validates data-limited approaches for artisanal fisheries.

Abstract: Hyperspectral imaging (HSI) is emerging as a promising tool in scientific endeavours, including non-invasive quantification of pigments, an area of research with many use cases. Here, we tested the efficacy of a low-cost (~USD $200) and open-source HSI device (400 – 1000 nm, a spectral resolution of ~2 nm FWHM) in coral bleaching research. Specifically, we evaluated its ability to quantify the concentration of key photosynthetic pigments (chlorophyll a, chlorophyll c2, diadinoxanthin, peridinin, and total pigment content) was compared against a research-grade (~USD $70,000) commercial hyperspectral camera using coral fragments subjected to varying levels of thermal stress. The low-cost HSI acquired coral reflectance spectra that were similar to the commercial hyperspectral camera, with a mean spectral angle of 11.38 ± 3.82°. However, the low-cost device was unable to resolve differences in spectral magnitude to the same accuracy as the commercial HSI and did not detect differences among coral fragments at different levels of thermal stress. Thus, the current HSI device prototype is better suited for classification and diagnostic applications where spectral shape is of greater importance than spectral magnitude. Partial Least Squares Regression models built from the reflectance spectra of each HSI instrument showed very similar yet moderate performance when predicting key coral pigments (Commercial HSI mean %RMSEP = 22.8%, low-cost HSI = 22.12%). While the current design of the low-cost HSI device has clear limitations, the results show potential in a system that costs a fraction of commercial alternatives. Continued development of low-cost HSI platforms is accelerating rapidly across a variety of fields in environmental research, and improved designs have the potential to enhance coral reef monitoring and restoration efforts globally.

Abstract: As part of conservation efforts for Pinna nobilis, a critically endangered bivalve endemic to the Mediterranean Sea, laboratory programs have been developed to maintain and breed specimens. However, progress in the ex situ conservation of the species remains limited and challenging. This study aims to advance the knowledge required to establish effective reproductive protocols for P. nobilis, specifically focusing on the population in the Mar Menor lagoon, one of the last two surviving populations along the Spanish coast. The first phase of this study involved characterizing the reproductive events in the lagoon. Subsequently, two ex situ reproduction experiences were conducted under conditions designed to replicate the lagoon's natural environment. Three reproductive events were detected in the lagoon between 2019 and 2022, and five successful spawning events occurred across the two ex situ experiences. The conditions for maintenance, maturation, and induction of the individuals are described. In all cases, the percentage of fertilized oocytes released was remarkably high, suggesting internal fertilization, but not self-fertilization, within the pallial cavity. Additionally, ex situ individuals exhibited simultaneous hermaphroditism, with synchronous maturation and alternating release of gametes, effectively preventing self-fertilization. These findings represent a significant step forward in understanding the reproductive biology of P. nobilis and contribute to efforts aimed at ensuring the species’ long-term survival.

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Blue crab (Callinectes sapidus) populations are of substantial ecological and economic importance. As a keystone species, C. sapidus plays a critical role in maintaining estuarine food webs while also supporting one of the most consumed and economically valuable seafood industries in Delaware and Maryland. This study investigated the presence of Callinectes sapidus Reovirus 1 (CsRV1) in C. sapidus collected from Rehoboth Bay, Delaware, USA, using reverse transcription–quantitative polymerase chain reaction (RT-qPCR) and evaluated potential associations between viral occurrence and physicochemical parameters, including temperature, salinity, pH, turbidity, alkalinity, calcium hardness, nitrite, and chlorophyll-a. A total of 18 traps were deployed across six study sites encompassing oyster aquaculture areas, artificial oyster reefs, and control sites with minimal structural habitat. CsRV1 was detected in blue crabs from Rehoboth Bay, confirming the presence of the virus within the Delaware Inland Bays; however, detections were limited to a small subset of sampled individuals. Among the environmental parameters examined, salinity exhibited the greatest interannual variability, while other physicochemical conditions remained relatively consistent across site types and sampling periods. Overall, environmental conditions during the study period were within ranges considered suitable for C. sapidus, indicating that the population is likely to experience limited environmental stress and minimal disease-related impacts under current conditions.

Abstract:

Recently, a strain of Streptococcus agalactiae serotype Ia sequence type 7 clonal complex 1 (SaIa ST7 CC1) has emerged in Latin American tilapia aquaculture as an international threat. This study evaluated outbreaks of acute streptococcosis occurring between 2021 and 2025 on commercial Nile tilapia (Oreochromis niloticus) farms located in six Latin American countries, with an aim to combine molecular, clinical, pathological and environmental data. In total, 360 moribund or recently dead fish at various production stages (larvae/fry, pre grow-out and grow out) were examined, and 25 S. agalactiae isolates were serotyped, subjected to real time PCR analysis multilocus sequence typing (MLST), virulence and antimicrobial resistance gene profiling and antimicrobial susceptibility testing. All isolates belonged to SaIa and had the same ST7 CC1 MLST profile, which created a highly homogeneous cluster that grouped with reference SaIa ST7 CC1 strains previously isolated from tilapia farms in Asia. These results are consistent with the regional spread of a single clonal line. At larval and fry stage, SaIa ST7 CC1 was associated with hyperacute septicemia, gastrointestinal hemorrhage and frequent intestinal intussusception; while in pre grow out and grow out fish neurological signs were more prominent followed by ocular signs, systemic hemorrhages and coelomic lesions. Histopathological examination showed profuse colonization of brain, spleen, liver, and intestine by Gram positive cocci accompanied by significant acute circulatory and inflammatory lesions and few chronic granulomatous responses consistent with a fast-progressing high aggressive infectious process. All outbreaks occurred during extended episodes of hot water (>32°C) with large day–night thermal gradients and reduced dissolved oxygen, suggesting that thermal stress may exacerbate disease expression in systems affected. All SaIa ST7 CC1 strains exhibited phenotypic susceptibility to florfenicol and amoxicillin, but 84% (21/25) and 100% (25/25) of them exhibited intermediate susceptibility to oxytetracycline and enrofloxacin, respectively. Five of the 21 isolates (23,8%) with intermediate susceptibility to oxytetracycline carried tetracycline resistance genes (tetM, tetO). These findings identify SaIa ST7 CC1 as a clinically relevant threat of emerging thermally facilitated and geographically expanded streptococcosis for tilapia production in Latin America. Immediate priorities include screening of imported broodstock using MLST or whole genome sequencing, harmonized regional molecular surveillance, climate adaptive farm management practices, prudent antimicrobial use and serotype matched vaccination and breeding strategies that improve both disease- as well as heat-resilience.

Abstract: Systematic surveillance of World Organization for Animal Health (WOAH)-listed protozoan parasites is essential for maintaining sanitary status for seafood export and detecting the introduction of exotic pathogens into coastal ecosystems. In 2023, we examined wild Mediterranean mussels Mytilus galloprovincialis and Pacific oysters Crassostrea gigas collected from small harbors adjacent to ten major trading ports along the west and south coasts of Korea to assess the occurrence of WOAH-listed protozoan parasites and emerging Perkinsus species. A total of 1,080 mussels and 1,080 oysters from 18 sites were sampled in spring and autumn, and gill and digestive gland tissues were pooled from six individuals for DNA extraction. Species-specific PCR assays targeting Perkinsus marinus, P. olseni, P. beihaiensis, Bonamia ostreae, B. exitiosa, and Marteilia refringens were performed using previously validated primer sets and positive controls. All PCR assays were negative for the six protozoan parasite species in both host species across all sampling sites, indicating no detectable infections in port-adjacent wild mussel and oyster populations during the survey period. These negative results contrast with recent reports of P. marinus in wild C. gigas and B. ostreae in Ostrea denselamellosa on the west coast of Korea, suggesting that infections may currently be focal, transient, and host-specific rather than widespread in port-associated M. galloprovincialis and C. gigas populations. The present study provides baseline data on the distribution of protozoan parasites in bivalves inhabiting high-risk harbor environments and underscores the need for continued surveillance of transboundary shellfish disease that is closely coupled with environmental monitoring.

Abstract: Aquatic macroinvertebrates inhabit virtually all freshwater ecosystems, yet communities in extreme saline environments remain largely undescribed, particularly in the Tropical Andes. This study characterizes the taxonomic diversity of aquatic macroinvertebrates in a travertine-fed saline stream (salinity: 12.5 ± 0.2 g/L; 2520 m a.s.l., southern Ecuador) and compares it with an adjacent freshwater stream. Macroinvertebrates were sampled on four occasions (n = 4 events per stream) using a multi-habitat D-net technique; physicochemical variables were compared with Mann–Whitney U exact tests, and diversity metrics with exact permutation tests (C(8,4) = 70 permutations) supplemented with Cliff’s delta as effect-size estimator. Community composition was assessed with ANOSIM and non-metric multidimensional scaling (NMDS). A total of 919 individuals were collected. The freshwater stream harbored significantly greater richness (49 genera, 28 families), abundance, and Shannon diversity than the saline stream (14 genera, 8 families; all p = 0.029, Cliff’s δ = 1.00), while Pielou’s evenness did not differ between stream types. Community composition was fully separated (ANOSIM R = 1.00, p = 0.028), with salinity (R² = 0.95, p &lt; 0.01) and water temperature (R² = 0.79, p = 0.03) as the primary environmental drivers. The saline stream was dominated by halotolerant Diptera (Ceratopogonidae, Stratiomyidae) and water mites (Hydrachnidae), with virtually no EPT (Ephemeroptera–Plecoptera–Trichoptera) representation. These findings establish the first macroinvertebrate diversity baseline for a travertine-associated saline stream in the Tropical Andes, highlighting salinity and temperature as key environmental filters of aquatic biodiversity in extreme Andean lotic ecosystems.

Abstract: To explore the genetic diversity and adaptive evolutionary mechanism of Mastacembelus armatus in the Dongjiang and Ganjiang River Sources, whole-genome resequencing was performed on three populations of M. armatus from Xunwushui (XW) and Jiuqu River (DN) in the Dongjiang River Source, and Taojiang (XF) in the Ganjiang River Source. Population genetics methods were integrated to analyze their genetic structure, differentiation characteristics and selection signals. The results showed that a total of 209.05 Gbp of Clean Data was obtained from the three populations, with the Q30 base percentage reaching 94.42% and the average mapping rate to the reference genome being 97.85%, indicating high reliability of the sequencing data. A mean of 7,459,686 single nucleotide polymorphisms (SNPs) were detected, with a transition/transversion ratio of 1.52 and a heterozygous SNP ratio of 2.22%. The total number of genome-wide insertions and deletions (InDels) was 1,902,722±23,247. Gene Ontology (GO) functional annotation revealed a consistent variation pattern of core genes among the three populations. Phylogenetic tree, Admixture and principal component analysis (PCA) confirmed that the three populations belonged to a single evolutionary clade and shared a genetic origin from two ancestral populations (the lowest cross-validation error at K=2), while significant genetic differentiation was observed among populations: XW and DN populations had similar genetic backgrounds and closer genetic relationships, both biased towards the blue ancestral component, whereas XF population was inclined to the red ancestral component, with the DN population showing the highest degree of genetic admixture. Individuals within the XF population had more distant genetic relationships and the longest linkage disequilibrium (LD) decay distance, which was speculated to be associated with its small population size and low recombination rate; in contrast, the XW population had the shortest LD decay distance, corresponding to the characteristics of large population size and high recombination rate. Analysis of population genetic diversity indicated that XW and DN populations were classified as the high-diversity group (with more than 440,000 polymorphic markers, expected heterozygosity >0.31 and polymorphism information content (PIC) ≈0.25), while the XF population was the low-diversity group (with 342,646 polymorphic markers, expected heterozygosity of 0.2608 and PIC of 0.2073). Only the minor allele frequency (MAF) of the XF population (0.2829) was slightly higher than that of the other two populations. This study systematically elucidated the characteristics of genetic differentiation and diversity differences of M. armatus in the Dongjiang and Ganjiang River Sources, providing a genome-level scientific basis for the conservation of genetic resources, development of molecular markers and analysis of environmental adaptive mechanisms of this species.