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    A seventeen-year soil analysis dataset for ecosystem management

    AbstractThe Sol_Run dataset compiles seventeen years (2008–2024) of soil analysis data for Reunion Island. It includes 266,304 records from 24,857 unique soil samples, detailing numerous chemical and physical properties such as pH, cation exchange capacity, and nutrient content. These were analyzed using standardized physicochemical methods. Sol_Run supports an agronomic decision-support tool, providing specific recommendations for liming and fertilization. It enables monitoring of long-term soil degradation trends, like acidification, and informs local public policies for soil management. With its high sampling density and temporal repetition, Sol_Run offers local-scale information, complementing broader global datasets, and aiding the development and validation of soil modeling tools.

    Data availability

    The dataset described in this paper is publicly available from the Cirad data repository. It is a single CSV (Comma Separated Values) file and contains 266,304 records from 24,857 unique soil samples, including 22 different types of chemical and physical analyses.
    The dataset can be acessed via the following link:

    Code availability

    The geographical representation of the soil units and sampling points in Fig. 1 was carried out using QGis software version 3.40. Static data processing was carried out using RStudio 2025.05.1 Build 513 and R version 4.5.1.
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    Download referencesAcknowledgementsThe authors would like to thank the staff currently present and involved: D. Diot, L. Llose, B. Senis, K. Diblar and M. Payet. The authors would also like to thank the technical and administrative staff, both permanent and non-permanent, who have worked in the laboratory since 1985, processing samples, analysing them and producing analytical data. The research was supported by the CIRAD, France, the Conseil Regional de La Reunion, France, the French Ministry of Agriculture and Food, France, and the European Union as part of the CAPTERRE project (Feader – REU77071–1–000010 and Feder-2024–1248–005756 programs) and all the previous funding (Feader and Feder) from European Union.Author informationAuthors and AffiliationsCIRAD, UPR Recyclage et Risque, F-97490, Saint-Denis, FranceMarion Collinet & Jean-Christophe SouliéCIRAD, UPR Recyclage et Risque, F-34398, Montpellier, FranceFrédéric FederRecyclage et Risque, Univ Montpellier, CIRAD, F-34398, Montpellier, FranceFrédéric FederAuthorsMarion CollinetView author publicationsSearch author on:PubMed Google ScholarJean-Christophe SouliéView author publicationsSearch author on:PubMed Google ScholarFrédéric FederView author publicationsSearch author on:PubMed Google ScholarContributionsM.C., Validation, Investigation, Ressources, Writing – Original Draft, Writing – Review & Editing. J.C.S., Data Curation, Formal analysis. F.F., Writing – Original Draft, Writing – Review & Editing, Formal analysis, Visualization, Project administration. All authors reviewed the manuscript.Corresponding authorCorrespondence to
    Marion Collinet.Ethics declarations

    Competing interests
    The authors declare no competing interests.

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    Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
    Reprints and permissionsAbout this articleCite this articleCollinet, M., Soulié, JC. & Feder, F. A seventeen-year soil analysis dataset for ecosystem management.
    Sci Data (2026). https://doi.org/10.1038/s41597-026-07254-8Download citationReceived: 15 September 2025Accepted: 09 April 2026Published: 18 April 2026DOI: https://doi.org/10.1038/s41597-026-07254-8Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    Controlled mild water stress as a priming tool to inherent defense mechanisms of navel orange against citrus nematode, Tylenchulus semipenetrans

    Abstract

    Citrus nematode, Tylenchulus semipenetrans Cobb, 1913 is a major economically important plant-parasitic nematode responsible for citrus slow decline worldwide. This study aimed to evaluate the efficacy of controlled mild water stress on priming defences in navel orange (Citrus sinensis “Navel”) seedlings and to model nematode-host interactions under stress. Five greenhouse treatments were applied: negative control (C-, 100% field capacity), positive control (C+, 100%), pre-infection water stress (T1, 40%), post-infection water stress (T2, 40%), and continuous water stress (T3, 70%). Nematode reproduction criteria, plant growth and physiological and biochemical parameters were evaluated. Results indicate that the controlled mild water stress significantly (p ≤ 0.05) reduced nematode reproduction. The final nematode population (Pf) and reproduction factor decreased from 6.176 to 2.47 in positive control to 2.034 and 0.81 in continuous water stress. Shoot length and fresh weight declined from 31.47 cm to 29.22 g in negative control to 7.30 cm and 6.58 g in continuous water stress. Regression based model indicated that a strong positive correlation between nematode final population and orange seedlings growth performance (R2 = 0.995–0.999), demonstrated that the controlled mild water stress plays a critical role in mediating the interaction between T. semipenetrans and its host plant. Stressed plants accumulated higher flavonoids (up to 4.563 mg QE g− 1 FW), phenolics (6.498 mg g− 1 FW min− 1), and proline (11.50 mg g− 1 FW), while chlorophyll a and b decreased to 0.607 and 0.207 mg g− 1 FW, respectively. These findings suggest that controlled mild water stress, particularly when applied as a pre- or post-infection, can reduce T. semipenetrans reproduction and enhance citrus defense mechanisms. However, continuous water stress limits plant growth, highlighting a balance between nematode suppression and host adaptation for sustainable management.

    IntroductionPlant-parasitic nematodes (Phylum: Nematoda) constitute a major biotic constraint to citrus production worldwide. Among them, the citrus nematode Tylenchulus semipenetrans Cobb, 1913 (Nematoda: Tylenchida) is recognized as one of the most destructive pathogens, responsible for the slow decline disease of citrus1. This sedentary semi-endoparasite establishes permanent feeding sites in the root cortex by partial penetration of the female body, leading to chronic root dysfunction. The citrus nematode can cause yield losses of 10–30% globally, with higher losses under favorable soil and climate conditions2. Citrus nematodes have been found throughout the main citrus production regions of Egypt and in a large measure jeopardize the losses of the yield and quality of the final crop. The management of T. semipenetrans on navel orange, Citrus sinensis L. Osbeck (Family: Rutaceae) the main cultivated variety of orange in Egypt by 3.7 Million tons in season of 2023–20243,4,5.Management of T. semipenetrans has traditionally relied on chemical nematicides6. However, increasing concerns regarding environmental pollution, pesticide residues in fruit and soil, regulatory restrictions, and the potential development of nematode resistance have substantially limited the long-term sustainability of chemical control7. These constraints have intensified the search for alternative, environmentally sound strategies that reduce nematode pressure while maintaining crop productivity8.One promising approach is the exploitation of plant resistance mechanisms. In plant physiology, the concept of priming or induced resistance describes a state in which exposure to a mild stimulus prepares the plant for faster and stronger defense activation upon subsequent biotic stress9. Abiotic factors, including controlled water deficit, are known to function as effective priming agents by activating complex signaling pathways and enhancing the accumulation of defensive metabolites10,11. While severe drought stress negatively affects plant growth, accumulating evidence suggests that mild and transient water stress can act as a physiological elicitor rather than a damaging factor12,13.Despite growing interest in priming-based strategies, little is known about the role of controlled water stress in enhancing citrus root defense specifically against T. semipenetrans. In particular, the extent to which mild water deficit can modify root susceptibility, nematode penetration, and establishment remains poorly understood14,15. This represents a critical knowledge gap, especially for citrus production systems seeking sustainable alternatives to chemical nematicides.Therefore, the objective of this study was to evaluate the potential of controlled mild water stress as a priming strategy to enhance the defensive capacity of navel orange seedlings against T. semipenetrans under greenhouse conditions. We hypothesize that a transient, non-lethal water deficit acts as an early warning signal that pre-activates root defense mechanisms, thereby reducing nematode infection and development. This host-mediated approach aims to manipulate plant suitability rather than directly targeting the nematode, offering a sustainable and eco-friendly component for integrated nematode management in citrus cultivation.ResultsReproduction and survival of T. semipenetrans
    The results in Table 1; Fig. 1 demonstrate that controlled mild water stress significantly (p ≤ 0.05) affected the reproduction and survival of T. semipenetrans infecting navel orange seedlings. The number of second-stage juveniles (J2s) extracted from soil decreased progressively from the control mean of 2463 to 1729, 1376, and 1123 under pre-stress (T1), post-stress (T2), and continuous stress (T3) treatments, respectively. This reduction was highly significant (F = 474.45, R2 = 0.9393), reflected a strong relationship between stress intensity and nematode suppression. The number of adult females per root system followed a similar trend, declining from 55 in the control to 52, 48, and 31 in T1, T2, and T3, respectively. The difference among treatments was statistically significant, confirming that mild water stress limited female maturation.Table 1 Influence of controlled mild water stress on the reproduction and survival of T. semipenetrans infecting navel orange seedlings under greenhouse conditions (25 ± 3 °C).Full size tableFig. 1The alternative text for this image may have been generated using AI.Full size imageMicroscopic examination of citrus nematode individuals in response to different levels of mild water stress (magnification ×100). (A) C+, Individuals show normal body length and curvature, high turgidity, and well-defined internal tissues. The cuticle is smooth and continuous, and the cytoplasm is uniformly distributed without any voids, indicating high physiological fitness and a healthy homeostatic state. (B) T1, specimens exhibit a slight reduction in body turgor and minor changes in curvature. While internal structures are largely preserved, there is the onset of internal vacuolization (visible as small, transparent circular voids). This reflects a mild stress impact and the beginning of cellular adaptation to the water-stressed environment. (C) T2, individual display clearer stress symptoms, including reduced turgidity and a less uniform body shape. There is a visible darkening of the internal contents and progressive internal degradation. The vacuoles have increased in size and frequency along the intestinal tract, suggesting compromised physiological performance and disrupted osmotic regulation. (D) T3Individual show the most pronounced stress response, characterized by an evident loss of turgor and irregular or constricted posture. This panel demonstrates severe cytoplasmic disintegration and extensive vacuolization. The internal organelles appear disorganized (cellular lysis), leading to diminished internal clarity and indicating significantly reduced vitality and fitness.Egg production per egg mass also decreased significantly with increasing stress intensity, with means of 93, 76, 65, and 46 for C+, T1, T2, and T3, respectively. The number of egg masses per root exhibited a comparable reduction trend, dropping from 39 in the control to 33, 28, and 19 under the same sequence of treatments. The Pf followed a clear descending pattern among treatments. The highest value was recorded in C+ (6176), while a significant decrease was observed in T1 treatment (4326). The Pf declined further in T2 (3222) and reached its lowest level under continuous stress T3 (2034). A similar pattern was obtained for the reproduction factor (Rf), which was highest in C+ (2.47), then decreased in T1 (1.73) and T2 (1.29), attaining its minimum in T3 (0.81). In addition, the high coefficients of determination (R2 = 0.8371 to 0.9907) confirmed the strong linear association between increasing water-stress intensity and the reduction in nematode reproduction and survival.Moreover, the least significant difference (LSD 0.05) values indicate that all nematode reproduction criteria including J2s in soil, females, eggs, and egg masses (87.222, 4.210, 4.482 and 2.490) respectively, were differed significantly among treatments at the 5% probability level. Those low values showed that the reductions recorded under the different water stress levels were statistically distinct and not due to random variation.Vegetative growthThe vegetative growth of navel orange seedlings was significantly influenced by the interactive effects of tested water stress and infection with T. semipenetrans (Tables 2 and 3). All measured growth parameters; shoot length (SL), shoot and root biomass (fresh and dry weights), root length (RL), and leaf relative water content (LRWC), showed revealed highly significant differences (p ≤ 0.05) reductions with increasing water stress intensity. Shoot length was greatest in the negative control (C-) (31.47 cm) and significantly reduced in the positive control (C+) (19.80 cm). Further declines were observed in the pre-stress (T1) (14.20 cm), post-stress (T2) (11.80 cm), and continuous stress (T3, 7.30 cm) treatments. The reduction was highly significant, confirming a strong negative relationship between stress intensity and shoot elongation.Table 2 Interactive effects of controlled mild water stress on shoot traits of navel orange seedlings infecting with T. semipenetrans under greenhouse conditions (25 ± 3 °C).Full size tableTable 3 Interactive effects of controlled mild water stress on root traits of navel orange seedlings infecting with T. semipenetrans under greenhouse conditions (25 ± 3 °C).Full size tableA similar pattern was recorded for shoot fresh weight (SFW), which decreased from 29.22 g in C- to 21.33 g in C+, 15.61 g in T1, 10.49 g in T2, and 6.58 g in T3. The corresponding dry weight (SDW) declined steadily from 9.84 g in the control to 6.72, 6.36, 4.50, and 3.60 g in the same sequence of treatments, with a highly significant F-value (253.64) and R2 = 0.9316, indicating a strong linear association between the level of stress and biomass reduction. Root length (RL) followed the same descending pattern, ranging from 24.30 cm in C- to 17.03 cm in C+, and dropping further to 14.50, 13.40, and 12.33 cm under T1, T2, and T3, respectively. Similarly, root fresh weight (RFW) and root dry weight (RDW) showed continuous decreases from 5.13 g to 3.71 g in C- to 1.87 g and 1.58 g in C+, reaching their lowest values of 1.20 g and 0.23 g under T3. These reductions were statistically significant (R2 = 0.644 for RFW and 0.8479 for RDW). Leaf relative water content (LRWC) also declined sharply with stress application, dropping from 89.71% in C- to 84.03% in C+, and further to 68.77%, 56.45%, and 47.31% under T1, T2, and T3, respectively. The high F-value (429.714) and R2 (0.9847) reflected a strong dependence of leaf hydration status on water availability. Furthermore, the consistently high coefficients of determination (R2 = 0.64 to 0.98) across all parameters indicate a strong negative linear relationship between water stress and vegetative performance of nematode-infected citrus seedlings. In addition, LSD 0.05 values for all vegetative growth parameters; SL, SFW, RFW, SDW, RDW, RL and LRWC (0.907, 0.820, 0.476, 0.664, 0.429, 0.265, and 2.721), respectively indicate that significant differences existed among treatments at the 5% probability level, and not attributed to random variation.Interaction of T. semipenetrans with vegetative growthTo evaluation the interaction between nematode population dynamics and navel orange seedlings performance under controlled mild water stress levels under greenhouse conditions, a regression-based model (integrated matrix) was used to integrate T. semipenetrans and plant growth parameters. The data presented in Table 4; Fig. 2 indicated that a strong positive correlation between nematode final population and orange seedlings growth performance, suggesting that mild water stress plays a critical role in mediating the interaction between T. semipenetrans and its host plant.Table 4 Integrated matrix to evaluation of the interaction between T. semipenetrans criteria and navel orange seedlings growth parameters with regression model outputs under greenhouse conditions (25 ± 3 °C).Full size tableFig. 2The alternative text for this image may have been generated using AI.Full size imageIntegrated regression-based matrix illustrating the interaction between T. semipenetrans and orange seedling growth parameters. The model demonstrates a strong positive correlation between the nematode final population (Pf) (right Y-axis), reproduction factor (Rf) and plant growth parameters (left Y-axis) (total plant fresh weight, TPFW; and total plant length, TPL), suggesting that controlled mild water stress significantly influences the relationship between T. semipenetrans and navel orange seedlings.In the control treatment, the Pf reached 6,176 individuals, with a reproduction factor (Rf) of 2.47. Plants grown under this condition exhibited the highest growth performance, recording a total plant fresh weight (TPFW) of 34.34 g and a total plant length (TPL) of 36.83 cm. Under pre- and post-stress conditions, both Pf and Rf values declined moderately (4,326, 3,222) and (1.73, 1.29) respectively, accompanied by noticeable reductions in TPFW (23.21 and 17.13 g) and TPL (28.70 and 25.20 cm). The lowest nematode reproduction and poorest plant growth were observed under continuous stress, where Pf dropped to 2,034 and Rf to 0.81, while plant fresh weight and length decreased to 11.88 g and 19.63 cm, respectively.Regression analyses confirmed strong correlations between nematode parameters and plant growth indicators. The simple linear regression between Rf and TPFW (R2 = 0.9950, p = 0.00247) and between Pf and TPFW (R2 = 0.9954, p = 0.00232) showed highly significant relationships, indicating that nematode reproductive potential is closely linked to plant biomass production. Multiple regression models combining Pf and Rf as predictors improved the coefficient of determination (R2 up to 0.9988). Similarly, the model relating plant length (TPL) to Pf and Rf (R2 = 0.9978).Physiological and biochemical responsesTo evaluate the biochemical basis of the citrus seedlings defensive response against T. semipenetrans infection under greenhouse conditions, a set of key physiological and biochemical indicators the non-enzymatic antioxidants (total flavonoids and total phenolics), osmolytes acting as stress osmoprotectants (proline), enzymatic antioxidants associated with oxidative stress regulation (peroxidase, polyphenol oxidase, and catalase), and photosynthetic pigments (chlorophyll a and b) was assessed.Data presented in Fig. 3 resulted in significant (p ≤ 0.05) physiological and biochemical modifications in orange seedlings. Which indicates the integrated impact of nematode parasitism and mild water stress intensity, through a consistent progression in antioxidant and osmoprotectant accumulation with increasing stress intensity, counterbalanced by a steady decline in photosynthetic pigments. In the negative control (C-), plants maintained balanced metabolic activity, as indicated by the modest levels of total flavonoids (1.269 mg QE g− 1 FW) and total phenolics (2.320 mg g− 1 FW min− 1). Proline accumulation was relatively low (1161.195 mg g− 1 FW), and the enzymatic antioxidant system remained at baseline, with POD (0.173 mg g− 1 FW min− 1), PPO (0.079− 1 g− 1 FW), and CAT (6.400 µmol H₂O₂ min− 1 g− 1 FW). The photosynthetic pigments were highest in this treatment, with chlorophyll a (2.001 mg g− 1 FW) and chlorophyll b (0.803 mg g− 1 FW). Once infection was introduced in the positive control (C+), plants exhibited early biochemical stress responses, including slight increases in total flavonoids (1.455 mg QE g− 1 FW) and phenolics (2.523 mg g− 1 FW min− 1). Proline accumulation (1260.901 mg g− 1 FW) and elevated antioxidant enzyme activities; POD (0.247), PPO (0.106), and CAT (6.673) suggested a mild oxidative challenge triggered by nematode invasion. Meanwhile, chlorophyll a (1.915 mg g− 1 FW) and b (0.725 mg g− 1 FW) slightly declined, reflecting an initial disruption in photosynthetic efficiency. Under pre-stress conditions (T1), biochemical defense mechanisms intensified considerably. The synthesis of total flavonoids rose to 2.678 mg QE g− 1 FW, and phenolic content nearly doubled (4.529 mg g−1FW min− 1). A substantial proline build-up (4032.818 mg g− 1 FW) marked enhanced osmotic regulation, while antioxidant enzymes became highly active; POD (0.656), PPO (0.246), and CAT (12.017). Simultaneously, chlorophyll a and b declined to 1.409 and 0.511 mg g− 1 FW, respectively, suggesting early pigment degradation due to stress-induced ROS formation. In the post-stress treatment (T2), these responses became more pronounced. Total flavonoids increased further to 3.234 mg QE g− 1 FW, while total phenolics stabilized around 4.012 mg g− 1 FW min− 1. Proline content reached 4371.149 mg g− 1 FW, supporting its role in osmotic adjustment and membrane stabilization. The antioxidant system remained highly active, as POD (0.922), PPO (0.333), and CAT (14.021) continued to rise. Conversely, photosynthetic pigment levels dropped further chlorophyll a (1.250 mg g− 1 FW) and b (0.450 mg g− 1 FW) indicating sustained oxidative damage to chloroplasts. The continuous stress treatment (T3) induced the strongest biochemical and physiological responses. Flavonoid content reached its peak (4.563 mg QE g− 1 FW), while total phenolics accumulated substantially (6.498 mg g− 1 FW min− 1). Proline content exhibited a remarkable increase to 11491.667 mg g− 1 FW, confirming a critical osmotic defense state. Antioxidant enzymes showed their highest activities, with POD (1.230 mg g− 1 FW min− 1), PPO (0.503− 1 g− 1 FW), and CAT (18.093 µmol H₂O₂ min− 1 g− 1 FW). Meanwhile, the pronounced decline in chlorophyll a (0.607 mg g− 1 FW) and b (0.207 mg g− 1 FW) revealed severe impairment of the photosynthetic machinery.Fig. 3The alternative text for this image may have been generated using AI.Full size imagePhysiological and biochemical response of navel orange seedlings infecting with T. semipenetrans under controlled mild water stress under greenhouse conditions (25 ± 3 °C). Each value represents the mean of three replicates. Values followed by the same letter (s) in a column do not significantly differ according to according to Duncan’s multiple-range test.Overall, all tested stressed treatments differed significantly from the controls, exhibiting a uniform ascending order for antioxidant and osmolyte parameters, and an inverse pattern for chlorophyll content. This reciprocal relationship underscores the adaptive trade-off between enhanced stress defence and reduced photosynthetic capacity in Citrus under the combined impact of nematode infection and water stress.DiscussionThe present experiment was conducted under greenhouse conditions to evaluate the efficacy of mild water stress in priming defenses of navel orange seedlings to citrus nematode T. semipenetrans control with water management. Through eco-physiological strategies that could contribute to the development of sustainable nematode management programs in citrus production systems.The observed reduction in nematode population density and reproduction factor under water stress suggests that host suitability is strongly influenced by stress-mediated changes in root function and rhizosphere conditions16. Altered cell turgor, reduced nutrient flux, and modified root exudation patterns under limited water availability may collectively constrain nematode feeding efficiency and reproductive success, as previously reported for other sedentary and migratory nematodes under moderate drought scenarios17,18.In addition to physical and nutritional limitations, stress-induced biochemical adjustments in roots may play a regulatory role in nematode suppression. The accumulation of secondary metabolites under mild water stress conditions has been linked to enhanced basal resistance against soil-borne pathogens, including nematodes, through deterrent or inhibitory effects on penetration and development19. In this context, the reduced nematode performance observed in moderately stressed plants likely reflects an indirect consequence of host metabolic reprogramming rather than a direct nematicidal effect of water stress itself20.Plant growth reduction under combined nematode infection and water limitation reflects the additive physiological burden imposed by biotic and abiotic stressors. Declines in shoot and root biomass, organ length, and relative water content indicate that nematode parasitism amplifies the cost of water deficit by impairing root hydraulic conductivity and increasing internal water imbalance21. Similar growth penalties have been reported in potato infected with nematodes, where reductions in biomass and hydration status were associated with enhanced oxidative stress markers, including malondialdehyde and hydrogen peroxide22. These responses are consistent with broader evidence that nematode-induced tissue disruption accelerates oxidative imbalance and compromises membrane integrity, thereby limiting plant capacity for sustained growth under water deficit23.Nevertheless, the partial maintenance of vegetative growth under moderate stress treatments (T1 and T2) indicates the activation of compensatory physiological mechanisms that mitigate stress damage. Such responses may involve improved water-use efficiency, selective resource allocation, or enhanced antioxidant buffering capacity, as suggested in citrus and other perennial crops exposed to transient or mild stress conditions24,25. These findings emphasize that stress intensity and duration critically determine whether defense activation translates into functional tolerance or growth suppression.The pronounced increase in antioxidant metabolites and enzymes under nematode and water stress reflects a coordinated response to elevated reactive oxygen species (ROS) production. The accumulation of phenolics and flavonoids contributes to ROS scavenging and structural reinforcement of cell walls, which may indirectly restrict nematode establishment26. Proline accumulation further supports osmotic adjustment and redox balance, enhancing membrane stability under combined stress conditions27. Concurrent increases in POD, PPO, and CAT activities indicate an enzymatic reinforcement of oxidative stress mitigation pathways, consistent with observations in citrus and other crops infected with sedentary nematodes28,29.In contrast, the progressive decline in chlorophyll a and b contents with increasing water stress reflects the vulnerability of the photosynthetic apparatus to prolonged oxidative pressure. Chlorophyll degradation under combined stress conditions is commonly associated with impaired carbon assimilation and reduced energy availability, potentially constraining both growth and defense metabolism30,31. The relatively higher chlorophyll retention observed in pre- and post-stress treatments suggests that moderate stress exposure allows plants to activate protective antioxidant systems without inducing irreversible damage to chloroplast structures, highlighting a critical threshold beyond which stress becomes detrimental rather than adaptive32.Overall, the interaction between nematode infection and water stress reveals a non-linear physiological response, where moderate stress promotes defense-related metabolic adjustments, while continuous stress leads to metabolic exhaustion and functional decline20,33. Although this response pattern is consistent with the conceptual framework of hormesis, the present findings should be interpreted as physiological trends rather than definitive experimental validation of hormetic mechanisms34,35.ConclusionThe current study demonstrates that controlled mild water stress can act as an ecological tool to strengthen plant defence and reduce nematode infection pressure in citrus production systems. The combined enhancement of antioxidant metabolism, osmolyte accumulation, and reduced nematode reproduction supports the potential for integrating such physiological manipulations into sustainable citrus nematode management frameworks. Among the tested treatments, pre-infection and post-infection mild water stress appear most promising for integrated management, as they moderately suppress nematode reproduction while maintaining reasonable plant growth. In practical field applications, careful monitoring of irrigation and soil moisture is essential to implement such priming regimes effectively. Future research should focus on optimizing stress thresholds and irrigation schedules to achieve the desired balance between plant defense activation and productivity, potentially coupled with biological control agents or organic amendments for a comprehensive eco-friendly management system.MethodsSource of T. semipenetrans inoculumA population of T. semipenetrans was established from an inoculum collected from the rhizosphere of mature sweet orange, Citrus sinensis L. Osbeck trees, exhibiting characteristic symptoms of slow decline, in a commercial orchard located in the Sahel Selim province, Assiut Governorate, Egypt. Soil and root samples were transported to the laboratory for nematode extraction. Second-stage juveniles (J2s) were extracted from the soil using a combination of sieving and a modified Baermann funnel technique36. Actively motile juveniles collected in the water were concentrated, identified morphologically to species level based on description keys of Thorne (1962)37, and counted under a stereomicroscope by Hawksley counting slide. The resulting J2s suspension was adjusted with distilled water to a density of 2,500 J2s per 5 ml for subsequent inoculation.Plant material and growth conditionsThe trial was conducted at natural growing of 2024 (February to March) in a greenhouse under moderate temperature conditions (25 ± 3 °C), natural light, and daylight period approximately 11 to 13 h. Uniform, six-month-old seedlings of navel orange (grafted onto a commonly used citrus rootstock: sour orange, Citrus aurantium L.) were used. Each seedling was transplanted into a 3-kg plastic pot containing a sterilized sandy loam soil mixture (1:3 v/v, autoclaved at 120 °C for 2.5 h) containing 1.2% organic matter. The soil had a pH of 7.85, with an electrical conductivity (EC) of 2.87 dS m− 1 and a saturation percentage of 20%. Chemical analysis of the soil saturation extract revealed soluble cations including sodium (26.0 meq L− 1), calcium (11.10 meq L− 1), magnesium (7.10 meq L− 1), and potassium (0.29 meq L− 1). The soluble anions comprised chloride (41.43 meq L− 1), sulfate (16.37 meq L− 1), bicarbonate (7.30 meq L− 1), and carbonate (0.26 meq L− 1)38.Experimental design and treatmentsThe pots were arranged in a completely randomized design (CRD), with five treatments and three replications (one pot with one seedling for each replicate) per treatment. The treatments were defined as follows:C− (Negative control) = (optimum): Regular irrigation at 100% of field capacity (no water stress) + no nematodes.C+ (Positive control) = Regular irrigation at 100% of field capacity + with nematodes.T1 = Mild pre-infection stress: Apply mild water stress (irrigation at 40% of field capacity) for 14 days before nematode inoculation, then return to optimal irrigation during and after inoculation.T2 = Mild post-infection stress: Apply mild water stress (irrigation at 40% of field capacity) for 14 days immediately after nematode inoculation, then return to optimal irrigation.T3 = Mild continuous stress: Continuous irrigation at 70% of field capacity throughout the experiment (before and after inoculation).Inoculation and irrigation managementAn acclimatization period (two weeks) was provided for all orange seedlings prior to treatment initiation to ensure uniform growth and adaptation to greenhouse conditions under optimal irrigation. A balanced fertilizer (NPK 12-12-12) was applied uniformly to all treatments to ensure adequate nutrient availability. For T. semipenetrans inoculation, each pot assigned to the C+, T1, T2, and T3 treatments were inoculated with 2500 J2s of T. semipenetrans, which were introduced into three holes (5 cm deep) around the base of each seedling. The negative control (C-) received an equal volume of distilled water.Irrigation treatments were applied according to the experimental design using precise soil moisture sensors to maintain the targeted FC levels. Soil moisture was monitored and adjusted daily using a portable soil moisture sensor (Intelligent soil detector- EK572411, Guangdong, China) and verified gravimetrically by weighing a subset of pots39. The 100% FC level represented the soil water content at field capacity, while the deficit levels (40% and 70% FC) were calculated and maintained accordingly. Throughout the experimental period, plants were monitored daily for visible stress symptoms to ensure that the imposed water stress remained within a mild, non-lethal range.Data collectionSixty days after inoculation for each treatment, the following parameters were recorded:Plant growth parametersFor plant growth analysis, shoot length (SL) and roots length (RL) (cm) were measured directly. The entire shoot and root systems were then carefully separated. The fresh weight of both shoots (SFW) and roots (RFW) (g) was recorded immediately after harvesting. Subsequently, the plant materials were placed in a forced-air oven at 70 °C for 72 h until a constant weight was achieved, after which the dry weight of shoots (SDW) and roots (RDW) (g) was determined. The reduction percentage in growth parameters (reduction % over control) were calculated by the following formula: Reduction %= ((C-T) /C) x100.Where C = Parameter value in control (C+), T= Parameter value in treatment.T. semipenetrans criteriaFor the nematological evaluation, the root system of each plant was gently but thoroughly washed to remove soil particles. The cleaned roots were stained with acid fuchsin according to Bybd et al.(1983)40 to count numbers of females, eggs and egg masses per root system under a stereomicroscope. Simultaneously, a 250 g soil sample was taken from the rhizosphere of each pot for count the number of J2s using the Cobb decanting and sieving technique41. The nematode final population (Pf) per root calculated by the following formula:$$Pf{text{ }} = {text{ }}left( {Number{text{ }}egg{text{ }}masses{text{ }} times {text{ }}Mean{text{ }}eggs{text{ }}per{text{ }}egg{text{ }}masse} right){text{ }} + {text{ }}Females{text{ }} + Developmental{text{ }}stages + J2s{text{ }}in{text{ }}250{text{ }}g{text{ }}soil)$$Pf = (Number egg masses × Mean eggs per egg masse) + Females + Developmental stages + J2s in 250 g soil).The reproduction factor (Rf) was calculated for each treatment using the formula Rf = Pf / Pi, where Pi is the initial inoculation density of 2500 nematodes per plant. The percentage reduction in nematode Pf were calculated by the following formula42:$${Reduction% {text{ }} = {text{ }}left( {left( {Pf{text{ }}of{text{ }}control{text{ }} – {text{ }}Pf{text{ }}of{text{ }}treatment} right){text{ }}/Pf{text{ }}of{text{ }}control} right)){text{ }}x100;}$$Physiological and biochemical markersRoot tissues were sampled for the analysis of key physiological and biochemical compounds, including:Photosynthetic pigmentsConcentrations of chlorophyll a and b were measured by using spectrophotometry in accordance by approach of Lichtenthaler (1987)43. Fresh leaf tissue was heated to 60–70 °C until it was entirely colourless, then extracted in ethanol 95% (v/v). Following centrifugation of the extract, measurements of the supernatant absorbance were read at 663, 644, and 452 nm. Each concentration of pigment was determined using standard formulas and is given as milligrams per gram of fresh weight (mg g− 1 FW).Plant extract preparationFor the analysis of primary metabolites and enzymatic, non-enzymatic antioxidants, fresh leaf samples were homogenized in an ice-cold extraction buffer containing 50 mM Tris-HCl (pH 7.0), 1 mM sodium EDTA, and 3 mM MgCl2 using a pre-chilled mortar and pestle. The homogenate was centrifuged at 5,000 rpm for 10 min at 4 °C, and the resulting supernatant was collected and stored at -20 °C until subsequent biochemical analyses44.Non-enzymatic antioxidantsTotal FlavonoidsTotal flavonoid contents were determined spectrophotometrically according to the method of Zhishen et al. (1999)45. Briefly, fresh leaf tissue was homogenized in a methanol extraction solvent. The homogenate was centrifuged, and an aliquot of the supernatant was mixed with sodium nitrite solution, followed by the addition of aluminium chloride. The reaction was terminated by adding sodium hydroxide, and the absorbance of the resulting pink-colored solution was measured at 510 nm. The total flavonoid content was calculated using a quercetin standard curve and expressed as mg QE g− 1 FW.Total phenolsTotal phenols were determined by mixing 0.1 ml sample extract with 10 drops of concentrated HCL and boiled in a water bath for 10 min, then left to cool. 1.0 ml Folin and 5 ml of 20% Na2Co3 were added. The mixture was diluted to 10 ml as the final volume by distilled water. Colour optical density of the reacted mixture was measured on absorbance spectrophotometer (Miltonroy Spectronic) at 520 nm after 30 min according to Snell and Snell (1953)46. Phenol content was determined as mg g− 1 FW min− 1.OsmolyteThe proline concentration was determined according to the method described by Moore and Stein (1948)47. 1 ml of the sample extract was reacted with acid ninhydrin reagent, glacial acetic acid and the mixture was heated in a boiling water bath for 1 h. After cooling, the chromophore was extracted using toluene, and the absorbance of the colored layer was measured at 520 nm using a spectrophotometer. The proline concentration was calculated from a standard calibration curve prepared with known concentrations of pure proline and expressed as milligrams per gram of fresh weight (mg g− 1 FW).Enzymatic antioxidants (Oxidative-stress enzymes)Peroxidase (POD)Peroxidase was assayed using photochemical approach as outlined by Amako et al. (1994)48. The following sequences were added to the reacted mixture: 50.0 mmol/L K-phosphate buffer (PH 7.0), 1.0 mmol/L EDTA, 0.5 mmol/L Na ascorbate, 0.25 mmol/L H2O2 and 0.1 ml enzyme solution. The absorbance increase at 430 nm was determined relative blank with phosphate buffer instead of enzyme extract. Under normal test conditions, one unit of enzyme activity was defined as the quantity of the enzyme that changed the optical density at 430 nm per minute at 25 °C. The units of specific activity were expressed in mg g− 1 FW min− 1.Polyphenol Oxidase (PPO)The photochemical approach, as outlined by Coseteng and Lee (1987)49, was used to determine polyphenol oxidase. The following sequences were added to the reacted mixture: 0.25 ml of 00.9 M catechol, 200mM potassium buffer, pH 6.2, and 0.1 ml of enzyme extract. At 420 nm and at 30 °C, the rise in absorbance was detected. The quantity of an enzyme that raises absorbance by 0.001 units per minute at 25 °C is referred to as one unit of enzyme activity (min− 1 g− 1 FW).Catalase (CAT)The catalase activity was measured according to the description of Aebi (1974)50. Where, 2.9 ml of a reactive mixture comprised 0.1M H2O2 5% and 50mM sodium phosphate buffer (pH 7.6) was mixed with 0.1 ml of enzyme extract. By tracking the decrease in absorbance at 240 nm brought on by H2O2 consumption, the activity of catalase was determined. The unit of catalase activity was mg/g/fresh weight/min. The breakdown of 1µmol of H2O2 per minute was considered to be one unit of enzyme activity (µmol H2O2 min− 1 g− 1 FW).Data analysis and processingMultiple statistical parameters were used to address the multidimensional nature of the data. All experimental data were subjected to normality tests using Shapiro-Wilk test51 and for homogeneity of variances using Levene test52 prior to performing analysis of one-way analysis of variance (ANOVA) by COSTAT software package (CoHort Software). Treatment means were separated using Duncan Multiple Range Test (DMRT) at a 5% probability level (P ≤ 0.05)53, and the least significant difference (LSD 0.05) was also calculated at the 5% probability level. In addition, the coefficient of determination (R2) was computed using Microsoft Excel without modification to assess the strength of these relationships54. Where, R2 value ranges between 0 and 1 (0 ≤ R2≤ 1); values closer to 1 indicate a meaningful relationship and a higher accuracy of the regression model in explaining the variability of the data. Finally, the calculated values were integrated to establish a regression-based model (integrated matrix)55 describing the interactive influence of T. semipenetrans reproduction dynamics on plant growth performance under tested water stress levels.

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    Reprints and permissionsAbout this articleCite this articleEl-Sagheer, A.M., Saad, M.A. & Abdelghany, A.M.M. Controlled mild water stress as a priming tool to inherent defense mechanisms of navel orange against citrus nematode, Tylenchulus semipenetrans.
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    KeywordsPhytonematodesCitrus nematode managementSlow decline diseaseCitrus physiological responseDrought-induced defenseBiological control More

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    Checklist of edaphic endemic plants in northeastern Iran: diversity, distribution patterns, and conservation

    AbstractSoil variability is a key driver of plant diversity and endemism, yet the ecological roles of specific soil types remain poorly understood. In the Khorassan-Kopet Dagh floristic province of northeastern Iran and southern Turkmenistan, the coexistence of gypsum, calcareous, and serpentine soils provides a unique setting to explore these relationships. We carried out extensive field surveys and soil analyses across nine habitats to refine the classification of edaphic endemic plants and reassess their conservation status. Using elemental analyses and standard soil tests, we characterized chemical properties such as carbonates, organic matter, gypsum, pH, and conductivity. Our results documented 71 plant taxa from 30 families, including 35 regional endemics and six Iranian endemics. Based on soil affinity, species were grouped as gypsophiles (3%), gypsovags (20%), obligate calcicoles (25%), and facultative calcicoles (52%). Several species required reclassification from gypsum to calcareous specialists. Hemicryptophytes (45%) and chamaephytes (28%) were the dominant groups, especially among calcicoles, with the highest species richness found at elevations between 1,500 and 2,300 m. Updated distribution data revealed that facultative calcicoles are largely secure, while obligates remain vulnerable. This study offers the first integrated account of edaphic endemism in the region, providing essential insights for biodiversity monitoring and conservation under rising anthropogenic and climatic pressures.

    Data availability

    The datasets generated during this study are available from the corresponding author on reasonable request.
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    Download referencesAcknowledgementsThis work was conducted as part of the Ph.D. dissertation of the first author, supported by Grant number 3/60075, from the Office of the Vice-President for Research and Technology of Ferdowsi University of Mashhad and partly by European Union’s Horizon 2020 (H2020-MSCA RISE-777803). The authors wish to express deep gratitude to Mohammad Reza Joharchi in Herbarium of Ferdowsi University of Mashhad (FUMH) for helping with species determination. Thanks to Elaheh Tabasi for help with fieldwork and data collection.FundingThis work was supported by Grant number 3/60075 from the Office of the Vice-President for Research and Technology of Ferdowsi University of Mashhad for H.R., and partly by the European Union’s Horizon 2020 (H2020-MSCA RISE-777803) for F.M.Author informationAuthors and AffiliationsQuantitative Plant Ecology and Biodiversity Research Lab, Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, IranHossein Rahmaninia & Hamid EjtehadiDepartment of Range and Watershed Management, Faculty of Natural Resources and Environment, Ferdowsi University of Mashhad, Mashhad, IranFarshid MemarianiHerbarium FUMH, Ferdowsi University of Mashhad, Mashhad, IranFarshid MemarianiDepartment of Range Management, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, IranMehdi AbediInstituto Pirenaico de Ecología (IPE-CSIC), Av. Nuestra Señora de la Victoria, 16, Jaca, Huesca, 22700, SpainSara PalacioAuthorsHossein RahmaniniaView author publicationsSearch author on:PubMed Google ScholarHamid EjtehadiView author publicationsSearch author on:PubMed Google ScholarFarshid MemarianiView author publicationsSearch author on:PubMed Google ScholarMehdi AbediView author publicationsSearch author on:PubMed Google ScholarSara PalacioView author publicationsSearch author on:PubMed Google ScholarContributionsAuthor contributions H.R., H.E., and F.M. conceived and designed the study; H.R. and F.M. collected and analyzed the data and H.R. wrote the first draft. H.E., F.M., M.A., and S.P. helped with revising drafts of the paper. All authors read and approved the final draft.Corresponding authorsCorrespondence to
    Hamid Ejtehadi or Farshid Memariani.Ethics declarations

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    The authors declare no competing interests.

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    All field studies and collection of wild plant material were performed in accordance with relevant institutional, national, and international guidelines under formal permission from the Iranian Natural Resources and Watershed Management Organization. Voucher specimens were deposited at the FUMH herbarium under accession numbers included in the manuscript.

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    Reprints and permissionsAbout this articleCite this articleRahmaninia, H., Ejtehadi, H., Memariani, F. et al. Checklist of edaphic endemic plants in northeastern Iran: diversity, distribution patterns, and conservation.
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    KeywordsCalciphytesEdaphismGypsophytesIrano-TuranianKhorassan-Kopet Dagh More

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    Sources, seasonal trends and urban exposure to airborne particulate matter-bound pollutants

    AbstractSize-fractionated airborne particulate matter was collected over 1 year (2023–2024) at five urban pedestrian and cycling locations in Slovenia. PM10, PM2.5, PM0.1 were collected using a low-volume sampler with polytetrafluoroethylene filters, and PM<0.1 fraction was retained in ultrapure-water. Metal(loid)s and polycyclic aromatic hydrocarbons (PAHs) were determined to assess the potential health and environmental risks. Metal(loid) concentrations were the highest in PM10, with most elevated levels of Zn (7 ng m−3), Ba (4.5 ng m−3), Cu (2.8 ng m−3) and Cr (1.5 ng m−3). Significant enrichment in PM<0.1 was observed for Ba, Cu, Ni, Pb and Zn, with Ce-normalised values indicating a strong anthropogenic contribution. Tailpipe tracers were dominant in (ultra)fine PM fractions, while non-exhaust emission markers (Ba, Cu, Zn) strongly correlated with Ce and La in PM10. Among PAHs, BbF (0.05 ng m−3), BghiP and IP (0.04 ng m−3) exhibited the highest concentrations. BaP, BghiP and IP were enriched in ultra-fine particles, indicating fresh vehicular combustion emissions. Peak pollutant concentrations occurred during the heating period (HP) and in densely populated, high-traffic cities. Source apportionment revealed a dominance of pyrogenic sources, including: (i) vehicular exhaust emissions from diesel engines (5–6-ring PAHs, Ni, V and Pb), (ii) resuspended mineral dust and non-exhaust traffic particles (Ba, Cu, Zn), and (iii) coal and biomass combustion during HP (4-ring PAHs, Co, Mo, Tl). Incremental lifetime cancer risk for As (2 × 10−7), Co (1 × 10−6) and Cr (6 × 10−6) was minimal. Hazard quotient values were below 1. Children cycling during HP experienced the highest exposure levels. The European PM10 limit values for As (6 ng m−3), Cd (5 ng m−3), Pb (500 ng m−3), Ni (20 ng m−3) and BaP (1 ng m−3) were not exceeded.

    Data availability

    Data will be made available on request from corresponding author.
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    Download referencesAcknowledgementsAnja Ilenič acknowledges Jožef Stefan International Postgraduate School as the institution where her PhD studies are carried out. In addition, authors would like to thank the Municipality of Maribor, Municipality of Murska Sobota, Municipality of Dobrova–Polhov Gradec, National Institute of Biology (NIB)Marine Biology Station Piran, as well as the Pavlič family (Ana, Maša, Dana, Bojan) for their valuable cooperation and assistance in installing the sampling devices.FundingThis research was funded by the Slovenian Research Agency, financial support programme groups P2-0273, P1-0143 and P1-0008, and research project J7-60124.Author informationAuthors and AffiliationsDepartment of Materials, Slovenian National Building and Civil Engineering Institute, 1000, Ljubljana, SloveniaAnja Ilenič, Alenka Mauko Pranjić & Marija ĐurićJožef Stefan International Postgraduate School, 1000, Ljubljana, SloveniaAnja Ilenič, Radmila Milačič Ščančar & Janez ŠčančarDepartment of Environmental Sciences, Jožef Stefan Institute, 1000, Ljubljana, SloveniaRadmila Milačič Ščančar & Janez ŠčančarFaculty of Natural Sciences and Engineering, University of Ljubljana, 1000, Ljubljana, SloveniaNina ZupančičZRC SAZU Ivan Rakovec Institute of Paleontology, 1000, Ljubljana, SloveniaNina ZupančičAuthorsAnja IleničView author publicationsSearch author on:PubMed Google ScholarRadmila Milačič ŠčančarView author publicationsSearch author on:PubMed Google ScholarAlenka Mauko PranjićView author publicationsSearch author on:PubMed Google ScholarNina ZupančičView author publicationsSearch author on:PubMed Google ScholarMarija ĐurićView author publicationsSearch author on:PubMed Google ScholarJanez ŠčančarView author publicationsSearch author on:PubMed Google ScholarContributionsAI: Writing–original draft, methodology, analysis, data curation, conceptualisation. RMŠ: Writingreview & editing, supervision, methodology, conceptualisation. AMP: Resources, project administration, funding acquisition, review & editing. NZ: Data curation, writing–review & editing. MĐ: Analysis, methodology. JŠ: Funding acquisition writingreview & editing, supervision, methodology.Corresponding authorCorrespondence to
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    Reprints and permissionsAbout this articleCite this articleIlenič, A., Milačič Ščančar, R., Mauko Pranjić, A. et al. Sources, seasonal trends and urban exposure to airborne particulate matter-bound pollutants.
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    The effect of the fitness gradient on fixation probability

    AbstractEvolutionary biology examines how the genetic and phenotypic composition of populations changes over time. An important goal is to determine the fixation probability of a single advantageous mutant that arises in a homogeneous population of N residents. Many real populations experience environmental gradients that cause mutations to be beneficial in some spatial regions but harmful in others. Here, we study the fixation probability of a mutant placed on a simple one-dimensional spatial structure that experiences such a gradient. The mutant’s fitness varies linearly from 1 − s to 1 + s, whereas the resident fitness is constant and equal to 1. The existing literature suggests that such heterogeneity in the mutant’s fitness should lead to a decrease in its fixation probability. However, in this work, we find that small, non-negligible gradients ((s < 1/sqrt{N})) substantially increase the fixation probability, while larger gradients ((s > (log N)/sqrt{N})) substantially decrease it. Moreover, we quantify the strength of this phenomenon analytically and we precisely delimit the range of the gradients for which it occurs. Our computer simulations closely match those findings. Altogether, our results indicate that subjecting a simple population structure to natural environmental conditions can produce strong counterintuitive effects.

    Data availability

    The data generated in this study have been deposited in the Figshare database under accession code https://doi.org/10.6084/m9.figshare.29271674.
    Code availability

    The related computer code has been deposited in the Figshare database under the accession code https://doi.org/10.6084/m9.figshare.29271674.
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    Download referencesAcknowledgementsJ.S. and K.C. were supported by the European Research Council (ERC) CoG 863818 (ForM-SMArt) and Austrian Science Fund (FWF) 10.55776/COE12. J.T. was supported by GAČR grant 25-17377S and by Charles Univ. projects UNCE 24/SCI/008 and PRIMUS 24/SCI/012.Author informationAuthors and AffiliationsISTA, Klosterneuburg, AustriaJakub Svoboda & Krishnendu ChatterjeeDartmouth College, Hanover NH, USAJakub SvobodaUtrecht University, Utrecht, NetherlandsHossein NematiComputer Science Institute, Charles University, Prague, Czech RepublicJosef TkadlecIndependent researcher, Toronto, CanadaKamran KavehAuthorsJakub SvobodaView author publicationsSearch author on:PubMed Google ScholarHossein NematiView author publicationsSearch author on:PubMed Google ScholarJosef TkadlecView author publicationsSearch author on:PubMed Google ScholarKamran KavehView author publicationsSearch author on:PubMed Google ScholarKrishnendu ChatterjeeView author publicationsSearch author on:PubMed Google ScholarContributionsConceptualization: H.N., K.K., and K.C. Investigation: J.S., H.N., J.T., K.K., and K.C. Visualization: H.N., J.T., and K.K. Formal analysis: J.S., J.T. Project administration: K.K., K.C. Writing–original draft: J.S., H.N., J.T., K.K., and K.C. Writing–editing: J.S., H.N., J.T., K.K., and K.C.Corresponding authorCorrespondence to
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    Nat Commun (2026). https://doi.org/10.1038/s41467-026-71777-2Download citationReceived: 27 June 2025Accepted: 30 March 2026Published: 17 April 2026DOI: https://doi.org/10.1038/s41467-026-71777-2Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    A parasite-inclusive food web for the California rocky intertidal zone

    AbstractWe present a highly resolved, species-rich food web, including parasitic interactions, for the California rocky intertidal zone. The food web, which is a meta-web inclusive of all rocky intertidal taxa in California, is comprised of 1994 nodes, representing 1901 taxa, and 15,485 links that illustrate trophic interactions between nodes. While only 4.4% of links represent parasitic interactions, we have assembled possibly the most speciose parasite-inclusive food web ever published. The inclusion of all nodes and links are justified using multiple lines of evidence which are built into the dataset. In addition, metadata, including trophic strategy, taxonomic information, habitat, and other ecological attributes allow the data user to filter the food web to their specifications. The food web is a powerful and flexible tool for researchers with questions about large network properties, ecological dynamics of rocky shores, and the role of parasites in ecosystems. Our food web can be used to predict how complex ecosystems like the California rocky intertidal will respond to anthropogenic change and management strategies.

    Data availability

    The California rocky intertidal food-web dataset is available from the Dryad digital repository: https://doi.org/10.5061/dryad.3ffbg79sb67.
    Code availability

    Annotated code for assembling the food web and generating network figures is available on our Dryad digital repository (https://doi.org/10.5061/dryad.3ffbg79sb)74 in the cariz_foodweb_visualization.Rmd file. We have also included some suggested code for subsetting the food-web network in the example_web_subset_code.Rmd file.
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    Zoe L. Zilz.Ethics declarations

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    Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
    Reprints and permissionsAbout this articleCite this articleZilz, Z.L., Hascall, E., DiBartolo, A. et al. A parasite-inclusive food web for the California rocky intertidal zone.
    Sci Data (2026). https://doi.org/10.1038/s41597-026-07259-3Download citationReceived: 03 July 2024Accepted: 09 April 2026Published: 17 April 2026DOI: https://doi.org/10.1038/s41597-026-07259-3Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    No evidence that hominin dispersal across Eurasia was part of a wider turnover in mammal distributions

    AbstractThe drivers and consequences of hominin dispersals out of Africa remain debated. The spatial and temporal distribution of large mammal faunas contemporaneous with early Homo provides direct evidence for their ecological context and impact. In this study, we conduct taxonomic and functional similarity analyses on fossil and extant Eurasian and African large mammal communities of the last 10 Ma. We test two hypotheses: 1) the dispersal of hominins across Eurasia around or shortly after ~2 Ma was part of a wave of faunal dispersals out of Africa; 2) the arrival of hominins at Eurasian sites coincided with major changes in the functional structure of large mammal communities. Our results indicate that hominin dispersals from Africa to Eurasia during the Plio-Pleistocene were not part of a larger faunal expansion. Instead, the most significant faunal interchange during the Plio-Pleistocene occurred between Europe and Asia, while African faunas have mostly remained distinct from Eurasian faunas since ~7 Ma. Our results suggest relative homogeneity in community functional structure across Eurasia and Africa since at least 10 Ma. In contrast to fossil communities, modern Eurasian and African terrestrial large mammal faunas show strong geographic functional structure, which might reflect the selectivity of Late Pleistocene extinctions.

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    IntroductionFor most of their evolutionary history, hominins were restricted to Africa. The driving factors behind their dispersal out of Africa, as well as their influence on contemporaneous Eurasian mammal communities, are subjects of interest and debate. There were at least two major out-of-Africa events. The first was during the Early Pleistocene, possibly ~2 Ma based on artifacts from Shangchen, China1 and Grăunceanu in Romania dated to 1.95 Ma2. From around 1.8 Ma, there is conclusive evidence of the presence of hominins in Eurasia3, 4 based on fossils from Dmanisi, Georgia5. Shortly thereafter, stone artifacts or hominin remains are reported from the Yuanmou Formation in southern China, dated to 1.7 Mya6, Majuangou III and Shangshazui in the Nihewan Basin, dated to 1.6–1.7 Mya7,8, Ubeidiya in the Levant dated to 1.4 Ma9 as well as Atapuerca and Orce in Spain, dated to 1.1–1.3 Mya10.Different scenarios have been proposed to explain Early Pleistocene dispersals, including intrinsic evolutionary factors11,12 (e.g., brain expansion and technological advances) and external factors13,14,15,16,17,18,19,20 (e.g., environmental conditions including climate change as well as tectonics, and accompanying faunal dispersal). There is significant speculation about the ecological context and adaptive capacities of these early hominin dispersers. Messager et al. (2011), for instance, have claimed that, during the Early Pleistocene, hominins gradually increased their capacity of adaptation to diversified environments4.A second major out-of-Africa event occurred during the Late Pleistocene when Homo sapiens dispersed outside Africa. There are different hypotheses on possible driving factors of this dispersal, including environmental, fauna, or cognitive changes and technological advances21,22,23,24,25.The hypothesis that Pleistocene hominins might have followed other large mammals out of Africa is based on assumptions of predator-prey relationships of hominins and herbivores, or a coevolutionary relationship between hominins and large carnivores15,26,27. The spatial and temporal distribution of large mammal faunas contemporaneous with early Homo could help us understand the context and impact of hominin dispersal out of Africa. Large mammals that are believed to have dispersed into Eurasia during the Plio-Pleistocene include Theropithecus, Panthera, Megantereon, Crocuta, Pachycrocuta, Hippopotamus, Palaeoloxodon, Hippotragus, Oryx, Damalops, Pelorovis, Kolpochoerus, Parahyaena, Giraffa, Vishnukobus and Potamochoerus19,28. During their first dispersal, H. erectus might follow large herbivores15, with cervids, bovids, and likely suids serving as important prey in Southeast Asia29.Among large mammalian species, carnivores might have played a significant role in hominin dispersals12. Hominins might have incurred in an intense competition with carnivores for both resources and space30. Lewis and Werdelin (2010) proposed that large carnivores likely influenced hominin dispersal based on a significant overlapping of diet and habitat31. Rodríguez et al. (2023) suggested that early hominins were capable of competing with giant hyaenas for carcasses generated by saber-toothed felids32. Thus, whether hominins played a role as predators or scavengers was possibly determined by the competition stress from carnivores30. Among carnivores, Panthera gombaszoegensis, Pachycrocuta brevirostris33,34, Crocuta crocuta35, Megantereon whitei34 and Panthera leo36 dispersed into Eurasia during the Early Pleistocene33,34,35,36. But whether Pachycrocuta and Crocuta originated in Africa is still unclear36, and it should be taken into account that carnivores tend to have a wider geographic distribution than herbivores and can disperse quickly and widely37,38.Nonetheless, some hold the view that faunal exchanges were not correlated with hominin dispersals out of Africa27,39. Analysis based on the first appearance of African and Eurasian mammals showed little evidence for waves of dispersal during Plio-Pleistocene19. Tong (2011) pointed out that, although there was some faunal exchange between Africa and Eurasia during the Neogene, there are few taxa in northern China that directly originated from sub-Saharan African faunas during the Pleistocene36. And some genera might also have dispersed into Africa from Eurasia, such as Equus, Nyctereutes, Lycaon, and Antilope19.Additionally, there are questions about the impact of hominins on Eurasian faunal communities after their arrival from Africa. Some researchers suggested that the reduction of functional richness of the large carnivore (>21.5 kg) guild starting from 2 Mya may have been caused by competition with hominins40. In contrast, other studies found evidence for long-term declines in African large mammal diversity and abundance since ~4 Ma, precluding a role for hominins41,42. Hominin dispersals in the Early and Middle Pleistocene were found not to be correlated with faunal turnover39. During the Late Pleistocene dispersal of H. sapiens, hunting activities are likely to have had a significant influence on the extinction of large mammals43,44,45,46. Studies suggested that Late Quaternary large mammal extinction with selectivity for large body sizes appeared on all continents except Africa and the unusual body-size selectivity is correlated with human arrival, through both direct (hunting) and indirect (competition and habitat alteration) effects47. Mammal extinctions in Africa during the Late Pleistocene and Holocene were suggested to be driven by environment changes48. Megafaunal declines in Europe have been proposed to be driven by H. sapiens49. A notable decline of species richness after 10 Ma was also found in European fauna50.Based on the information above, we analyze Eurasian and African large mammal faunas of the last 10 Ma to obtain a continental-scale perspective of faunal change and dispersal in this study. We examine the taxonomic and functional similarity of fossil communities to better understand the faunal context and potential impact of hominin dispersals out of Africa. We test two hypotheses: (1) the dispersal of hominins across Eurasia around or shortly after ~2 Ma was part of a larger wave of faunal dispersal out of Africa; (2) the arrival of hominins in Eurasia resulted in major changes in the functional structure of large mammal communities. Our results show no evidence of faunal dispersal waves out of Africa and a rather similar functional community structure across Eurasian and African fossil sites, in contrast to extant communities, which show strong latitudinal differences.ResultsFossil taxonomic analysisThe result of silhouette coefficient analysis indicated the number of k should be 3 for the fossil taxonomic clustering (Supplementary Fig. 1A), while the average membership degree (AMD) analysis indicated just 2 groups in the data (Supplementary Fig. 1E). With k = 3, the three resulting clusters basically comprised an African cluster, a mainly Late Miocene cluster and a mainly Pliocene to Pleistocene Eurasian cluster (Fig. 1A). From 10 to 7 Ma, all communities across Eurasia and Africa, including two African communities (Chorora site and Ngeringerowa site), belonged to a single cluster (cluster 1 in Fig. 1). The ten most frequently occurring genera were Hipparion, Gazella, Hippopotamodon, Palaeotragus, Tragoportax, Adcrocuta, Chilotherium, Cremohipparion, Hyaenicthitherium and Ictitherium. The Plio-Pleistocene Eurasian cluster (cluster 2 in Fig. 1), characterized by Cervus, Equus, Sus, Ursus, Panthera, Canis, Stephanorhinus, Mammuthus, Bison and Rhinoceros, appeared between 7 and 5 Ma in western Eurasia, then dispersed to replace the Miocene cluster entirely across Eurasia by 3 Mya. Late-surviving genera of the Late Miocene cluster in Asia included Canis, Gazella, and Hipparion. Around the same time, a distinct African cluster began to develop at 7-6 Ma (cluster 3 in Fig. 1). The ten most frequently occurring genera in this cluster were Tragelaphus, Gazella, Aepyceros, Kobus, Elephas, Kolpochoerus, Ceratotherium, Hippopotamus, Giraffa and Equus. Overall, from this time on, African faunas remained basically different from those of Eurasia and were not affected by the faunal turnover that took place in Eurasia between 6 and 3 Ma. We also visualized the clustering by epoch, with similar results (Supplementary Fig. 2A).Fig. 1: Clustering of African and Eurasian fossil and extant large mammals.The alternative text for this image may have been generated using AI.Full size imageA Taxonomic clustering shows strong temporal and geographic differences across continents in fossil data (shown in 1 myr intervals). Miocene faunas (cluster 1) survive longest in Asia, to be replaced by genera that first emerged between 7 and 4 Ma in Europe (cluster 2). African faunas (cluster 3) remained distinct from 7 mya on. Extant communities similarly show strong latitudinal structure. B Clustering of fossil communities by functional traits (diet, locomotion, size) shows no apparent geographic structure, in contrast to extant communities, which have strong latitudinal structure. All analyses were conducted at the genus level, with the number of clusters set to three.The chronofauna similarity analysis of the Shanshenmiaozui (SSMZ) fauna revealed a peak similarity of both European and Asian communities during the Early Pleistocene (Fig. 2A). In contrast, persistently low similarity of the African fauna with SSMZ confirms little to no mixing of genera between Africa and eastern China at this time. The chronofauna analyses of other communities from the Pleistocene of Spain (Atapuerca TDW4 & TDE5), Miocene of Anatolia (Akkasdagi), and Pleistocene of Kenya (Karari Ridge 2) confirm the high similarity of Asian and Eurasian faunas during the Late Miocene (Akkasdagi) and their later divergence during the Pleistocene (Atapuerca), and the highly endemic nature of African Plio-Pleistocene faunas (Karari Ridge) (Fig. 2B–D).Fig. 2: Taxonomic similarity chronofauna plots.The alternative text for this image may have been generated using AI.Full size imageTaxonomic similarity chronofauna plots. Shown is genus-level taxonomic similarity to (A), Shanshenmiaozu (SSMZ, China), B Atapuerca TDW4 & TDE5 (Spain), C Akkasdagi (Turkey), D Karari Ridge 2 (Kenya), and other fossil sites in Eurasia and Africa. All analyses indicate African faunas remained distinct from those of Eurasia. The gray shaded area is the 95% confidence interval.The nMDS analyses of all communities by genera confirmed the high overlap of Eurasian fossil communities, and the distinctiveness of African communities since the Miocene (plotted by epoch in Fig. 3A). A stress value of 0.17 indicates an acceptable ordination fit, with the major patterns being represented. Similarly, the correspondence analysis of communities by genera confirmed the strong continental taxonomic differentiation between Eurasia and Africa (Fig. 4A). In both the nMDS and correspondence analyses, the first axis separates between older (to the right) and younger (left) Eurasian communities, confirming the turnover between taxonomic clusters 1 and 2 shown in Fig. 1A. In both analyses the second axis consistently distinguished Eurasian from African communities.Fig. 3: Non-metric multidimensional scaling analysis.The alternative text for this image may have been generated using AI.Full size imageEach point is a paleo-community, colored by continent. A Genus-level taxonomic dissimilarity, confirming a consistent separation of African from Eurasian faunas through time. B Functional dissimilarity, showing a lack of continental differentiation. Analyses were conducted using all data, then visualized by epoch.Fig. 4: Correspondence analyses of fossil data.The alternative text for this image may have been generated using AI.Full size imageA Analysis of fossil communities by genera. B Analysis of extant communities by genera. Only a subset of genera is labeled for readability in (A and B); C Analysis of fossil communities by traits. D Analysis of extant communities by traits.Fossil functional analysisThe same method was applied to the functional clustering. The silhouette coefficient analysis indicated that the best number of k should be 2, while the AMD analysis indicated 3 clusters (Supplementary Fig. 1B, F). For a better comparison between the taxonomic and functional analyses, k was set to be 3. The resulting three functional clusters show high overlap with no apparent structure across temporal intervals or geographic regions. Visualizing the data by epoch shows a similar result (Supplementary Fig. 2B). A sensitivity analysis using just two traits (body mass, diet) showed a similar result, indicating that any uncertainty of locomotion assignment was not significantly biasing the results (Supplementary Fig. 3).The functional nMDS analysis based on total dissimilarity similarly showed no patterns of difference among the three continents (Fig. 3B). Stress value was 0.087.The correspondence analysis of community by traits also showed a high overlap of sites across all three continents. Ground dwelling herbivores between 45 kg and 10 tons were the most common large mammals on all three continents. Trait distributions therefore do not show major differences among continents in the fossil data.Extant taxonomic analysisBoth the silhouette coefficient and AMD analyses of the extant taxonomic data showed a best cluster number of 3 (Supplementary Fig. 1C, G). Taxonomic clustering with k = 3 showed pronounced latitudinal variation separating the Old World into northern and southeastern Eurasia, North Africa to South Asia, and sub-Saharan Africa (Fig. 1A). Analyses using variations of the PHYLACINE dataset (including estimates of where species would live without anthropogenic pressures) showed a similar pattern with only slight differences to the IUCN data shown in Fig. 1A (Supplementary Fig. 4).Extant functional analysisThe silhouette coefficient analysis showed a result of 2 for the functional clustering, while in the AMD analysis the result showed a result of 3. (Supplementary Fig. 1D, H) The functional clustering also showed a latitudinal pattern, with clusters uniting northern Eurasia with North Africa, central Asia with the Middle East as well as part of southern Europe, and South and Southeast Asia with sub-Saharan Africa (Fig. 1B: present). Similar to the fossil functional analysis, we conducted an analysis based on 2 traits (body mass, diet) for the extant IUCN data in the study. The result showed a similar pattern with minor differences in the distributions. We also conducted the analysis based on both PHYLACINE current ranges and present natural ranges for the functional clustering. The result showed differences from clustering based on IUCN data. One cluster basically occupied north Africa while the other two clusters occupied Eurasia in different regions. The pattern, however, still showed a latitudinal distribution of different clusters here (Supplementary Fig. 4).DiscussionNo evidence for waves of faunal dispersal out of AfricaThe first hypothesis we sought to test is whether hominins arriving in northern China ~2 Ma were part of a larger wave of faunal dispersal from Africa to Eurasia. Our analysis of taxonomic similarity at the genus level does not support the presence of a major wave of large mammal dispersal out of Africa at this time, or at any other time during the last 10 Ma. Though African data for the Late Miocene is sparse, communities at 9-8 Ma show greater similarity to contemporaneous Eurasian communities than later African ones, perhaps supporting the proposition of an Old World Savanna Paleobiome51. However, by 7-6 Ma African faunas cluster more closely with later African communities than Eurasian faunas. Around the same time in Eurasia, a major faunal interchange took place whereby genera appearing first in Europe at 7-5 Ma totally replaced more archaic Asian taxa by the late Pliocene. African and Eurasian faunas remained highly dissimilar throughout the Pliocene and Pleistocene. The results from the nMDS and correspondence analyses were consistent with the taxonomic clustering analysis, showing a high similarity of European and Asian communities, and a consistent separation of African communities (Figs. 3A, 4A).Our results support previous studies that found a lack of correlation between hominin and faunal dispersals during the Early Pleistocene39. Claims that H. erectus passively followed15 the dispersal routes of large herbivores during their dispersal out of Africa are not supported by our continental-scale perspective. If anything, African and Eurasian faunas were most dissimilar during this time (Figs. 1–4). The dispersal of Homo out of Africa therefore likely not a result of major extrinsic (e.g., climatic) factors that would have significantly affected other large mammals as well. Any driving factors for Homo and other dispersers during this time were likely lineage-specific, such as new technological, behavioral, or dietary adaptations. We therefore conclude that the dispersal of Homo out of Africa, if driven by any factors at all, occurred in a context largely specific to Homo.No evidence for changes in functional community structure in the fossil recordThe second hypothesis we sought to test was whether the arrival of hominins in Eurasia coincided with major changes in the functional structure of communities, as defined by diversity of body size, diet, and locomotion. We found that, over the last 10 Ma, functional communities across Africa and Eurasia showed no clear geographic structure, neither across time nor by continent. We additionally found no evidence for significant changes to functional community structure in Eurasia associated with the arrival of Homo from Africa after 2 Ma.Evidence for highly altered extant functional community structureExtant large mammal communities show taxonomic clustering that is latitudinally and continentally structured (Fig. 1A). While this is more nuanced than the fossil geographic clusters, the main distinction of African and Eurasian realms is a strong common feature. This is similar to classical zoogeographic regions based on the distributions of amphibians, birds, and mammals, with identifiable Afrotropical, Saharo-Arabian, and a combination of Palearctic, Sino-Japanese and Oriental regions52,53(Fig. 1A).In contrast, the geographic structure of functional similarity of extant communities is starkly different from that of the fossil assemblages. Unlike fossil communities, which showed no apparent geographic functional structure over the last 10 million years, extant communities reveal clear latitudinal structure, with major differences between mainly Afrotropical, Saharan, and northern Eurasian, and southern Eurasian regions. There are possibly two explanations for these differences: (1) The fossil datasets may be inaccurate or incomplete; or (2) A fundamental rearrangement of functional groups appeared in the time between the fossil and modern dataset, i.e. during the Late Pleistocene and Holocene. We think it is unlikely that this pattern is the result of inaccurate data, particularly given that the attribution of such fundamental traits as size, diet, and locomotion to both fossil and extant genera was in most cases done with a relatively high degree of confidence, allowing also for uncertainty via randomization. The second possibility is more plausible, as much evidence indicates major losses of taxonomic diversity from the Eurasian record during the Middle and Late Pleistocene (e.g., lions, hyenas, proboscideans, rhinos, monkeys, hippos, etc.)48,54,55,56,57. These taxonomic losses appear to have had disproportionately large functional consequences at higher latitudes, producing the latitudinal variation in functional structure we observed for extant communities. Our correspondence analysis of the extant functional communities shows that the Eurasian regions differ from sub-Saharan Africa mainly in the lack of amphibious and arboreal genera as well as mammals with body mass of 405 to 3675 kg.This finding suggests that the functional structure appearing in modern large mammal faunas across Africa and Eurasia today may be an artifact of (possibly human-induced) Late Pleistocene and Holocene extinctions. This should be confirmed by further studies, but it adds further supports for the idea fossil communities were functionally non-analogous to those today (even in Africa54). It also provides significant support for the importance of the fossil record to determining natural baselines and forecasting climate change effects58.MethodsWe compiled a large dataset of occurrences of fossil large mammals (Artiodactyla, Carnivora, Creodonta, Perissodactyla, Primates, and Proboscidea) from BICAEHGIS, a geographic information system database that includes data from the Paleobiology Database (https://paleobiodb.org/), NOW Database59, and additional data on 92 Chinese sites and one Romanian site that was entered for this study. All the additional data were collected from published literature. Site age was calculated as the midpoint between the maximum age and minimum age. If the age was provided as a geological interval (e.g., Late Pleistocene), site age was calculated as the midpoint age of the geological interval. Data is available in Supplementary Data 1. Geographic distribution data for extant large mammals was downloaded from the IUCN Red List website60 and Phylacine61,62. The Phylacine dataset includes species ranges and diversity estimated while accounting for large human impact61, which documents current or historical ranges, providing an alternative to the IUCN Red List. Both extant and fossil taxonomic data were analyzed at the genus level. Both taxonomic and functional clustering for the extant data used 1° by 1° grid cells as one community. Grid cells are referred to as community throughout this paper. Communities with age uncertainty covering more than one geological epoch (e.g., Pliocene-Pleistocene) were removed. The final dataset includes 570 fossil genera comprising 1513 fossil communities and 204 extant genera comprising 13837 extant communities.In order to examine community structure changes, we compiled data for three traits: body mass, diet, and locomotion. These traits capture the functional role of taxa in a community, reflecting survival strategies, habitat and resource use, energetic requirements, and trophic level63,64. Body mass categories are logarithmic, following Bibi and Cantalapiedra42, and classified into 10 groups: 1: <1.67 kg; 2: 1.67–5 kg; 3: 5–15 kg; 4: 15–45 kg; 5: 45–135 kg; 6: 135–405 kg; 7: 405–1215 kg; 8: 1215–3645 kg; 9: 3645–10935 kg; 10: >10935 kg. Dietary categories were: herbivore, carnivore, and omnivore. Locomotion categories were: ground dwelling, scansorial, arboreal, amphibious, and semifossorial. Trait data was from the Paleobiology Database, PanTHERIA65, CarniFOSS66, Kissling et al.67, and Faith et al.54, and from literature describing individual taxa. If a genus has species in different diet categories, all the categories will be assigned to the genus. Data is available in Supplementary Data 2. Taxa belonging to marine habitats were excluded. Synonyms used in this study were provided in Supplementary Data 3. Since the study was based on genus level, one genus might contain more than one body mass or diet category. We used a code to randomize the category used in the study then ran the analyses several times to make sure the randomization choice of the body mass and diet had no significant influence on the final result. Due to size bias against the recovery of very small fossils, taxa belonging to body mass categories 1 and 2 (i.e. <5 kg) were excluded from all analysis. While omnivory can be difficult to define consistently, we note that only 46 out of 625 genera (7.4%) were classified as omnivores, while 32 out of 625 have omnivore in their diet category. Reclassifying genera into or out of the omnivore category would likely have little impact on our results.The data was analyzed and visualized using R (v 4.3.0)68 using custom script69. We removed all occurrences of indeterminate genera (which are classified as “Indet.” or “Gen.”) and then kept only communities with at least five genera (e.g.,51) to create a presence-absence matrix. Sørensen pair-wise dissimilarity was calculated for beta diversity using the betapart package70,71. Sørensen pair-wise dissimilarity measures the dissimilarity between two different communities based on their faunal composition. A value of 0 means the two communities are identical while a value of 1 means the two communities shares no common genera. The result consisted of three dissimilarity matrices: total dissimilarity, turnover, and nestedness. Total dissimilarity contains the latter two components without any weight: turnover, which refers to the replacement of taxa between communities; and nestedness, which refers to the degree that a less diverse community is a subset of a more diverse community70. Total diversity was used to represent the overall difference among the communities in this study. Communities were clustered using Partitioning Around Medoid (PAM)72 with the number of clusters (k) set to three, based on the result of silhouette coefficient analysis and average membership degree (AMD) analysis. (Supplementary Fig. 1). PAM is a method similar to k-means but can be applied to a distance matrix. We used the silhouette coefficient as implemented in the cluster package73 to independently check the best value of k. Additionally, AMD analysis was also applied to the pairwise dissimilarity clustering analysis. AMD analysis is a method for detecting the actual functional groups within the data74. The silhouette coefficient and AMD analyses shown in panels A, C, F, G, and H in Supplementary Fig. 1 identified 3 as the optimal number of clusters. Thus, 5 of the 8 analyses supported k = 3 as the best choice. Based on this result, we used k = 3 for all analyses throughout the study. All the data were analyzed together then visualized in 10 intervals of 1 million years duration. Communities with an age uncertainty of more than 2 million years were removed from the visualization but were not removed from the analysis (34 communities). The data was also visualized in three larger time bins: Late Miocene, Pliocene, and Pleistocene. The same method was applied to the extant mammal data compiled from PHYLACINE and IUCN Red List datasets for taxonomic analysis. The result of the IUCN extant data was plotted together with the result of the fossil data for comparison. In the analysis of the PHYLACINE data, we used both current ranges which show current species ranges, and present natural ranges which represent estimates of where species would live without anthropogenic pressures61 providing an alternative to the IUCN Red List in supplementary. The map used in this study was generated using rnaturalearth package in R.Temporal and geographic dissimilarity change among communities was also investigated using the chronofauna method, which examines how similarity to a single reference community changes across geography and time51. The fossil site of Shanshenmiaozui (SSMZ) in the Nihewan Basin, northeastern China, was chosen for this comparison. SSMZ is an Early Pleistocene site (1.7 Ma) with 25 genera (22 of which met our criteria and were included in this study) representing the typical Nihewan Fauna75. Although no hominin fossils or stone tools are known from SSMZ, its taxonomic richness and distance from Africa makes it a good reference for cross-continental comparisons. Additionally, chronofauna analysis was also applied to the three medoid communities determined by the PAM analysis, (Akkasdagi, Turkey; Karari Ridge 2, Kenya; and Atapuerca TDW4 & TDE5, Spain). The medoid is the community that shares the lowest total dissimilarity with other communities in the cluster they belong to.For the functional analysis, the distribution of all three traits for all communities was calculated based on the genus-trait matrix generating a community-trait abundance matrix. This was analyzed using the beta.pair.abund function in betapart package70, employing the Bray-Curtis Index to generate an abundance-based pair-wise dissimilarity matrix. The dissimilarity matrix then was analyzed using PAM with the number of clusters (k) set to three. Silhouette coefficient and AMD analysis were also conducted to examine the best value of k. Analyses using only body mass and diet were also applied as an alternative in supplementary. All the data were analyzed together and visualized in 1-million-year time bins, as with the taxonomic clusters.To test the consistency of the results obtained by PAM, we also conducted a non-metric multidimensional scaling (nMDS) analysis on the taxonomic and functional dissimilarity matrices using the vegan package76. NMDS is an ordination technique to visualize dissimilarities for non-Euclidean data which can visualize the communities across a low number of dimensions. The closer the two communities are in the plot, the more similar their composition is. Stress values indicating the goodness-of-fit were checked, with optimal values considered to be below 0.277.Additionally, correspondence analyses of the community-genus and community-trait data matrices were conducted to visualize the relationships between communities, genera, and traits for providing visual information on which taxa and traits have the strongest influence on (i.e., most strongly define) the three continents or three clusters determined by the clustering analysis. Correspondence analysis is a multivariate statistical technique used for visualization of the relationships between multiple categorical variables.Reporting summaryFurther information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

    Data availability

    Data used to generate Figs. 1–4 can be found in Supplementary Data 1–3. The fossil data used in this study are provided in Supplementary Data 1. The trait data used in this study are provided in Supplementary Data 2. The synonym data are provided in Supplementary Data 3.
    Code availability

    The R script used in this study is available at Zenodo: https://doi.org/10.5281/zenodo.18733763.
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    Download referencesAcknowledgementsThis study was funded by the European Research Council through an Advanced Grant to I.d.l.T. (BICAEHFID, project number 832980). Additional support came from the Diversity Dynamics Department of the Museum für Naturkunde. We thank Haowen Tong, Shuwen Pei, Dongdong Ma, Xin Ding, Jingjing Bie, Jiachen Cai and Carlos Fernandez for their assistance with the faunal records and related information, members from Amniota Lab at the Museum für Naturkunde and the BICAEHFID project for discussion.FundingOpen Access funding enabled and organized by Projekt DEAL.Author informationAuthors and AffiliationsMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyJijia Sun & Faysal BibiFaculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, GermanyJijia SunPleistocene Archaeology Lab, Instituto de Historia, CSIC-National Research Council, Madrid, SpainIgnacio de la TorreAuthorsJijia SunView author publicationsSearch author on:PubMed Google ScholarIgnacio de la TorreView author publicationsSearch author on:PubMed Google ScholarFaysal BibiView author publicationsSearch author on:PubMed Google ScholarContributionsF.B. and I. de la T. conceptualized the study. J.S. and F.B. developed the methodology. J.S. and I. de la T. were responsible for data collection and curation. J.S. conducted the formal analysis and wrote the original draft of the manuscript. F.B. and I.de laT. reviewed and edited the manuscript. Funding was acquired by I. de la T. All authors approved the final version of the manuscript.Corresponding authorsCorrespondence to
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    Reprints and permissionsAbout this articleCite this articleSun, J., de la Torre, I. & Bibi, F. No evidence that hominin dispersal across Eurasia was part of a wider turnover in mammal distributions.
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    Histopathological effects of the fruit extract of Citrullus colocynthis on the integument of the female tick Hyalomma dromedarii

    AbstractHyalomma dromedarii is a hard tick species parasitizing domestic animals, particularly camels. Heavy infestation results in huge economic losses through severe blood loss and transmission of pathogens, in addition to crucial problems for camel production. Worldwide control of ticks is mainly based on acaricides, which have led to environmental pollution, resistance development, and an increase in the cost of control. To reduce the drawbacks of chemical acaricides, new tick control methods are therefore required, such as the application of natural plant extracts. Citrullus colocynthis, commonly known as bitter apple, is a desert plant found in Egypt. It has an economic importance due to its bioactive compounds with antidiabetic, antimicrobial, and potentially anticancer properties. In addition, it is used as a natural preservative, as it was historically applied to protect Egyptian manuscripts and leather from fungal damage. The goal of this work was to study the histopathological and ultrastructural changes of H. dromedarii integument after immersion in 100 mg/mL of C. colocynthis ethanolic extract. Volatile components of the extract were detected following the use of gas chromatography-mass spectrometry (GC–MS). Light, scanning, and transmission electron microscopy examinations provided evidence that C. colocynthis caused great damage to the integument. Increasing eroded areas with irregular folds and warts were observed by SEM. LM and TEM showed integumental layers separation, procuticle disorganization, subcuticular layer rupture and epidermal layer damage. GC–MS revealed volatile constituents, such as methyl linoleate, octadecadienoic, palmitic, and stearic acids. This is the first histological investigation that reported the integumentary damage caused by C. colocynthis in H. dromedarii. The present data suggest that the changes in all integument layers of the female tick H. dromedarii following treatment with C. colocynthis extract may facilitate the transport of toxic compounds into ticks’ internal systems, which can then affect other organs. As a result, C. colocynthis can be considered as a promising tick control agent.

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    IntroductionTicks are significant ectoparasites that spread disease through their saliva to both humans and animals1, consequently, there is a pressing need for their natural management2. Hyalomma dromedarii is one of a significant livestock ectoparasites3. In many parts of the Middle East, it is the biggest barrier to camel production4. According to Champour et al.5, it causes mortality, reduces weight and milk production and damages leather production, as well as reduces reproduction by lowering pregnancy rates and raising abortion rates6.Because the role of Hyalomma dromedarii in the transmission of various infectious diseases, such as Crimean-Congo hemorrhagic fever virus7, Dhori virus8, theileriosis of cattle (Theileria annulata)9, and theileriosis of camels (T. camelensis)10, it has received more attention11. So, we should manage this parasite to reduce the spread of these tick-borne diseases.The traditional method of tick control, which involves chemical acaricides usage, is currently inadequate and unsustainable11. This is because of the emergence of resistant ticks, environmental contamination, residues in livestock products, repeated applications, and the impossibility and/or high cost of creating new acaricide generations in the near future12. For these reasons, scientists are searching for alternatives to get around the drawbacks of synthetic acaricides13. Utilizing plant extracts is one of the alternate strategies2,14. This is due to its biodegradability, lack of environmental accumulation and contamination, rarity of environmental and non-targeted species toxicity, and decreased likelihood of resistance development15,16.Citrullus colocynthis is one of economically and biochemically important plants from Cucurbitaceae family17. Its fruit contains a variety of bioactive substances including fatty acids, flavonoids, alkaloids, glycosides, and essential oils18. It has exceptional pharmacological qualities such as anti-inflammatory, anti-tumor, anti-microbial, anti-mycotic, and antioxidant activities19,20,21.The various extracts of C. colocynthis demonstrated anthelminthic activity on Haemonchus contortus22, molluscidal activity against Biomphalaria arebica23, insecticidal effects against Tribolium castaneum24 and Lipaphis erysimi25, antileishmanial activity against Leishmania26, and acaricidal activity against various tick stages, including H. analoticum27, Rhipicephalus sp.28 and H. dromedarii2,29.Tick integument histological and ultrastructural changes after treatment with plant extracts and their natural components were studied in R. sanguineus30,31,32, Haemaphysalis longicornis16, and H. dromedarii33. Therefore, the aim of this study is to examine the histological and ultrastructural effects of an ethanolic extract of C. colothynthis on H. dromedarii integument. Additionally, gas chromatography-mass spectrometry (GC–MS) was used to identify volatile components in order to investigate the mode of action of the plant extract on the tick integument.MethodsTick collectionHyalomma dromedarii were collected from camels naturally infested with ticks at the Birqash camel market (30° 9′ 58.4″ N, 31° 2′ 13.2″ E), Giza Governorate, Egypt. Based on Hoogstraal and Kaiser34, ticks were identified, then grouped into non-, semi-, and engorged adults (males and females)35. Within 24 h of collection, engorged females were put in glass vials wrapped with gauze pieces. They were kept in an incubator at 28 ± 2 °C and 75–80% relative humidity until time of the experiments.Preparation of the extractCitrullus colocynthis ripen dried fruits were bought from the market. Plant materials were identified by Dr. May Taha, assistant professor in Botany Department, Faulty of Science, Ain shams University, and some were kept at CAIA (Ain Shams University Herbarium). Dried fruits were cleaned to remove dust, and ground using a stainless-steel knife mill. The method of Twaij et al.36 was followed in the preparation of ethanolic extract. Plant powder (50 g) was added to 80% ethyl alcohol (250 mL), covered with aluminium foil and kept in dark condition for 72 h, then it was filtrated using Whatman filter paper (110 mm diameter opening). The filtrate was poured into glass Petri dishes and placed in the incubator at 50 °C to evaporate the alcohol. The dried extract was then gathered, weighed, placed in glass vials, and stored at 4 °C until use. To prepare a concentration of 100 mg/mL (LC50 according to Mahamed et al. 2), 1 g of the extract was dissolved in 10 mL of distilled water.TreatmentThe adult immersion test (AIT) was conducted according to Drummond et al.37. Each engorged tick female was immersed in 10 mL of 100 mg/mL for 5 min (LC50 according to Mahamed et al.2). Then they were placed in sterile glass vials securely covered by gauze. Both untreated and treated specimens were kept inside incubator adjusted at 28 ± 2 °C temperature and 75–80% relative humidity.Morphological and histological studiesUntreated and treated females were dissected after 4 and 7 days of engorgement and treatment. Throughout the experiments, 63 spicemens were dissected. For the untreated and treated specimens at each period, three replicates each consisting of 3 females were maintained.Light microscopyDissection of tick females occurred under a dissecting binocular microscope. Females were covered with 0.85% NaCl solution in a Petri dish filled with a mixture of charcoal and paraffin wax. After removing the dorsal integument, it was repeatedly cleaned with saline solution and fixed in Bouin’s fixative (aqueous-based solution consists of saturated picric acid, formaline and glacial acetic acid) for 24 h38. Then they dehydrated in ascending series of the ethyl alcohol before being placed for 24 h in methyl benzoate. Samples were placed in 2% celloidin in methyl benzoate solution for 24 h39, cleared in benzol, submerged in three paraplast changes at 56 °C, and finally embedded in the paraplast (Fisher Scientific Inc. USA).Serial transverse sections were cut 3 µm in thick using computer microtome (YD-335-Huran Kaida Scientific Instrument Comp., China), and stained with either Mallory triple stain (MT)40 or hematoxylin–eosin stain (HE)41. Sections were photographed using a digital camera (Samsung ES95 HD) fixed on a microscope (Olympus, Japan made).Electron microscopyFemales were dissected in cold phosphate buffer (pH 7.2). After removing integument, it was fixed for 2 h in 3% cold fresh glutaraldehyde. Phosphate buffer was used to wash the samples for 30 min., then the following procedures were done for scanning and transmission electron microscopy.Scanning electron microscopy (SEM)Integument was dehydrated in ascending series of ethanol. It subjected to critical point drying, attached to aluminum stubs, and coated with gold using a sputter-coating apparatus. Then it examined and photographed under a Quanta (FEG 250) scanning electron microscope (FEI Company, Hillsboro, Oregon, USA) at the Electron Microscope Unit, Desert Research Center, Cairo, Egypt.Transmission electron microscopy (TEM)Integument samples were postfixed in cold 1% osmic acid for 2 h and washed again in fresh buffer. They were dehydrated in ascending series of ethanol and embedded in an epoxy resin39.Semithin sections (500 to 1000 nm) were cut using Leica Ultra-cut (UCT ultra-microtome) and stained with toluidine blue stain (TB)42. Then ultrathin sections (75–90 nm) were cut using a diamond knife and the same ultratome, mounted on copper grids (grid size 300 mesh × 83 µm pitch), and stained with uranyl acetate and lead citrate43. Integument samples were examined by JEOL (JEM-1400 TEM) transmission electron microscope at the Electron Microscope Unit, Faculty of Agriculture, Cairo University, Egypt.Gas chromatography-mass spectrometry (GC–MS) analysisDiethyl ether extractionVolatile components from C. colocynthis were extracted by the solvent extraction (SE) method44. Three grams of plant powder were extracted using diethyl ether (1:10, w/v) for three times (15 min each time) using ultrasonic. The solution was filtrated, and the solvent was removed using rotary evaporation under low pressure. Then the extract was diluted with 1 mL of anhydrous ethyl alcohol: n-hexane (1:1, v/v) then filtered through a membrane filter (0.22 μm). The subsequent filtrate (1 μL) was injected to GC–MS for analysis.GC–MS analysisThe analysis for volatiles was performed by the GC–MS instrument (Thermo Electron Corporation, USA) equipped with a Finnigan Trace DSQ and an electron impact (EI) ion source. The analytes were separated on a DB-5MS capillary column (30 m × 0.25 mm × 0.25 μm; Agilent, USA) coated with phenyl arylene polymer. The oven temperature program was: 50 °C initially for 1 min, increased to 145 °C at °C/min, increased to 175 °C at 7 °C/min, increased to 195 °C at 5 °C/min, and then ramped to 250 °C at 3 °C/min; 250 °C was maintained for 10 min. High pure helium (99.999%) was the carrier gas set at a constant flow rate (1 mL/min). The injection port, ion source and transfer line temperatures were set at 250 °C. 70 eV of EI was adopted, and the mass scanning range was set from 50 to 650 amu in full scan. The injection was performed by split mode with a split ratio of 10:1. For all samples generated by different methods, the solvent delay time was set for 3 min. Xcalibur 2.0 workstation was used to process data. Most volatile components were identified by comparison of their retention times and obtained mass spectra of the analytes with those of authentic standards from the NIST libraries (2005) and with the mass spectra published previously45,46,47. Peak areas of all components were calculated by Xcalibur 2.0.The protocol and procedures were approved by the Research Ethics Committee, Faculty of Science, Ain Shams University. Code: ASU-SCI/ZOOL/2024/7/1.ResultsThe female H. dromedarii has an oval body with a posterior alloscutum having festoones at the posterior border, as well as an antero-dorsal sclerite (scutum) (Fig. 1). On the dorsal surface, dermal gland apertures were dispersed (Fig. 1).Fig. 1The alternative text for this image may have been generated using AI.Full size imagePhotograph of dorsal view of untreated female H. dromedarii showing dorsal integument with anterior scutum (Sc) and posterior alloscutum (As) with many dermal gland openings (arrow in enlarged portion).Under scanning electron microscopical examination, dorsal integument of engorged female H. dromedarii is clearly expanded, with minor foldings and dispersed setae (Fig. 2a,b). Four and 7 days following feeding, there were no alterations in the alloscutum surface structure. Seven days after feeding, there was an increase in folds number (Fig. 2b). The wax substance on the external part of the integument (Fig. 2b) indicates that the dorsal integument has some apertures of dermal glands (Fig. 2a), which discharge their secretions to the cuticle surface.Fig. 2The alternative text for this image may have been generated using AI.Full size imageScanning electron micrographs of H. dromedarii integument. (a) 4 days after feeding showing slight folds (F), setae (S) and openings of dermal glands (arrow). (b) 7 days after feeding showing numerous folds (F), setae (S) and outer wax layer (W). (c) 4 days after treatment showing alloscutum (As), folds (F) and integumental eroded area (arrow). (d) 7 days after treatment showing warts on the surface (arrows) with abnormal appearance of folds (F). (e) 4 days after treatment showing the blockage and deformation of dermal gland opening by secretions (arrow) and irregular folds (F).Comparing treated and untreated female H. dromedarii integument at the aforementioned treatment stages revealed significant alterations. Four days following treatment, the alloscutum displayed damage and morphological deformation (Fig. 2c). The dorsal integument had several minor eroded areas (Fig. 2c). The integument showed increasing eroded areas with irregular folds and warts seven days after treatment (Fig. 2d). The secretion of the dermal gland blocked its opening (Fig. 2e).As revealed by light and transmission electron microscopical examination, the integument of H. dromedarii is divided into three main regions; the cuticle, subcuticular layer, and epidermis (Figs. 3a–c and 4a–e).Fig. 3The alternative text for this image may have been generated using AI.Full size imageLight micrographs of transverse sections of H. dromedarii integument. (a) Paraffin section 4 days after feeding showing the heterogenous structure of the cuticle with an external epicuticle (E) and an internal procuticle (P) which differentiated into an outer exocuticle (Ex) and an inner endocuticle (En). Ed: Epidermis. Sl: Sub-cuticular layer. H: Heamocoal. HE stain. (b) Paraffin section 7 days after feeding showing the external epicuticle (E) and the internal procuticle (P) underlined with the sub-cuticular layer (Sl) and the epidermis (Ed). En: Endocuticle, Ex: Exocuticle. H: Heamocoel. MT stain. c. Paraffin section 4 days after feeding the integument with dermal gland that consists of 2–5 dermal cells (Dc) and dermal canal (DC). Ed: Epidermis; Sl: Sub-cuticular layer. HE stain. (d) Paraffin section 4 days after treatment showing erosion, damage or destruction in epicuticular layer (E) and abnormal appearance of all integument layers. En: Endocuticle, Ex: Exocuticle, P: Procuticle. MT stain. (e) Paraffin section 7 days after treatment showing abnormal appearance of cuticle layers, damage of the epicuticle (E), and separation between exocuticle (Ex) and endocuticle (En). MT stain. (f) Paraffin section 7 days after treatment separation between the exocuticle (Ex) and the endocuticle (En), and damaged epidermal cells (Ed). E: Epicuticle. MT stain. (g) Paraffin section 7 days after treatment showing complete degeneration of dermal gland cells as well as damage of dermal canal (DC). E: Epicuticle. P: Procuticle. MT stain.Fig. 4The alternative text for this image may have been generated using AI.Full size imageTransmission electron micrographs of H. dromedarii integument. (a) 4 days after feeding showing the outer highly electron dense epicuticle (E) and the inner procuticle (P) with the exocuticle (Ex), endocuticle (En) and pore canals (arrows). (b) 4 days after feeding the epicuticle (E) multilayered structure with the outer wax layer (W), the cuticulin layer (Cl) with high density, and less dense homogenous layer (Hl) which separates the epicuticle (E) and the exocuticle (Ex). (c) 7 days after feeding showing the procuticle (P) with outer exocuticle (Ex) and inner endocuticle (En), the sub-cuticular layer (Sl) and the epidermis layer (Ed) with epidermal cells (EC). Pore canals (arrow). N: Nucleus. Nu: Nucleolus. (d) 7 days after feeding showing the cytoplasm of epidermal cell (EC) containing free ribosomes (R), mitochondria (M) and numerous rough endoplasmic reticulum (RER). Plasma membrane of epidermal cell had numerous microvilli (Mv) that direct toward the sub-cuticular layer (Sl). (e) 4 days after feeding showing the spongy appearance of the procuticle (P) with the presence of pore canals (PC). (f) 7 days after treatment showing the epicuticle (E) layer with separation between its outer wax layer (W) and the cuticulin layer (Cl). Hl: Homogenous layer. (g) 7 days after treatment showing marked deterioration of cuticle layers. En: Endocuticle; Ex: Exocuticle; PC: Pore canals; Sl: Subcuticular layer. (h) 7 days after treatment showing loss of lamellar arrangement of the endocuticle (En), specious dilation of pore canals (PC), abnormal appearance of subcuticular layer (Sl) and damaged microvilli in epidermis (Ed). (i) 7 days after treatment showing the epidermal cell with highly vacuolated cytoplasm (V), irregularly shaped enlarged nucleus (N), fragmented nucleolus (Nu) and damaged microvilli (Mv). Sl: Subcuticular layer.The exterior thin epicuticle and the interior thicker, more developed procuticle are the two main different layers that make up the cuticle’s heterogeneous appearance (Fig. 3a). After feeding, the cuticle’s thickness decreased from four to seven days (Fig. 3a,b).The outer, thinner, and slightly folded layer is called the epicuticle (Fig. 3a,b). It responded faintly with HE stain (Fig. 3a) and stained orange or mild red with MT stain (Fig. 3b). On the other hand, it appeared as a multilayered, extremely electron-dense structure (Fig. 4a,b). Three distinct layers were observed in; wax, cuticulin, and a thick, less dense, homogenous layer (Fig. 4b). One characteristic of the cuticulin layer was its high density (Fig. 4b). A layer of wax was present above the cuticulin layer (Fig. 4b).Four days of treatment, the epicuticle layer appeared damaged (Fig. 3d). In certain regions, it was either undetectable or appeared abnormal with additional folds (Fig. 3d). Additionally, the epicuticle layer, particularly the wax layer, seemed thicker after seven days of treatment compared to the untreated group (Fig. 3e). TEM examination revealed separation between wax and cuticulin layers (Fig. 4f).The procuticle had two separate layers; the exocuticle, in contact with the epicuticle, and the endocuticle, near the epidermis (Figs. 3a, b, and 4a–c). Although it reacted less intensely with HE stain (Fig. 3a), the endocuticle’s staining affinity was lower than the exocuticle’s, allowing for the differentiation between two layers (Fig. 3a). Oppositely, the procuticle was stained dark blue using MT stain with undistinguishable layers (Fig. 3b). The chitin material in the exocuticle seemed randomly structured under an electron microscope, whereas the endocuticle showed layers of more electron-dense chitin material with electron-lucid matrix creating overlaying lamellae in between (Fig. 4c).The treated integument’s procuticle layers (exocuticle and endocuticle) appeared thicker, disorganized, and their content extremely deteriorated (Fig. 3e). TEM observation revealed crumpled and disorganized lamellar arrangement found in the exocuticle and endocuticle (Fig. 4g).The subcuticular layer appeared with a faint pink color when stained by HE stain (Fig. 3a); and a dark blue color when MT stain was used, compared to other layers (Fig. 3b). Under the electron microscope, it appeared as a dark dense area (Fig. 4c).TEM examination of the treated ticks’ subcuticular layer showed an abnormal appearance and rupture in some areas (Fig. 4g). There seemed to be many vacuoles and damaged microvilli at the attachment site between the subcuticular layer and epidermis (Fig. 4h).The epidermis is a single cell layer settled on a basal lamina separating the integument from the hemocoel (Fig. 3a). These cells appeared irregular under electron microscope, contained irregular nucleus with several heterochromatin patches and a visible nucleolus (Fig. 4c). Free ribosomes, mitochondria, and many rough endoplasmic reticulum cisternae were clearly observed (Fig. 4d). The plasma membrane of epidermal cells contained numerous microvilli directed toward the subcuticular layer and vesicles containing electron-dense material below them (Fig. 4d).After extract treatment, the epidermal layer showed a significant disorganization and/or total destruction (Fig. 3f). After four and seven days of treatment, TEM showed abnormal features, including damaged microvilli, an irregularly shaped enlarged nucleus, a fragmented nucleolus, and degraded and severely vacuolated cytoplasm (Fig. 4i).Throughout the epidermal layer, dermal glands were visible and connected to the exterior via a duct open on the cuticle surface (Fig. 3c). Each gland consisted of 2–5 large polygonal cells with faintly stained cytoplasm (Fig. 3c).The treated ticks’ dermal glands showed enlarged and/or damaged dermal ducts with damaged cells (Fig. 3g).The pore canals were seen to be a highly branching system of fine channels that penetrated the entire cuticle, connecting the epicuticle with the underlying epidermal cells (Fig. 4c and e). These canals were located in various directions inside the procuticle layer (Fig. 4c). They were anastomosing, ramified, and abundant in the endocuticle, while they were fewer and less ramified in the exocuticle (Fig. 4a and c). There was less electron-dense material inside canals, which were membrane-limited (Fig. 4e).Following treatment, a fibrous-like structure was left behind by the endocuticle’s pore canals that exhibited a significant dilatation, particularly in the area connected to the subcuticular layer (Fig. 4h).Using GC–MS, a wide variety of volatile components were present in the ethaonolic extract of C. colocynthis. Peak area, retention time, molecular weight, and molecular formula are all important factors in phytochemical compound identification. The identified volatiles are trichloromethane, 4-Oleoylmorpholine, cycloheptasiloxane, tetradecamethyl, hexacosane, spathulenol, decylbenzene, dodecylbenzene, undecylbenzene, eicosane, 1-phenyl, benzene, (1-butyloctyl), palmitic acid methyl ester, stearic acid, methyl linoleate, eicosadienoic acid, 9,12-octadecadienoic acid (Z,Z) and monostearyl maleate (Table 1 and Fig. 5).Table 1 Volatiles content of ethanolic extract of Citrullus colocynthis.Full size tableFig. 5The alternative text for this image may have been generated using AI.Full size imageVolatiles profile of ethanolic extract of Citrullus colocynthis fruit by using GC–MS.DiscussionTicks’ integument is an essential organ forming the exoskeleton, which envelops the entire body and serves as a physical barrier, support, and defense against external threats48. Furthermore, it controls the water balance and has the ability to quickly stretch and expand when female ticks engorge during the blood meal, which facilitates egg formation and tick reproduction49. For these reasons, evaluating the chemical effects on the integument seems to be a reliable and straight-forward strategy to estimate the entrance and possible action of chemicals in the internal organs of ticks30,31.In the present SEM study, the dorsal integument of fed female H. dromedarii is greatly expanded with several folds. The same results were reported by Hackman50 in Boophilus microplus, Arruda et al.51 in B. microplus, Ghosh and Misra52 in Amblyomma gervaisi, Remedio et al.53 in R. sanguineus and Starck et al.35 in Ixodes ricinus. Numerous dermal gland pores and scattered setae were found in the dorsal integument during the current study. Estrada-Peña et al.54 reported nearly identical results for I. inopinatus and I. ricinus, Remedio et al.53 for R. sanguineus, and Patra et al.55 for Aponomma varanense using SEM.According to the current findings using SEM examination of the fed H. dromedarii integument following immersion in 100 mg/mL C. colocynthis ethanolic extract Remedio et al.30 similarly observed the secretion on dermal gland openings in the R. sanguineus integument treated with neem plant extract. They suggested that it was caused due to disturbed cell metabolism of dermal glands. In the present examination, the thickness decreased in treated integument layers. This may be due to extract penetration, with failure of epidermal cells to replace it, as they were affected32.Light (LM) and transmission electron microscopy (TEM) analysis of the fed female H. dromedarii integument in this work showed that the cuticle is differentiated into two distinct layers; a thin external epicuticle and a thick internal procuticle. This differentiation can be observed in the alloscutum of H. asiaticum55, H. dromedarii57, I. ricinus58, H. analoticum59, and R. sanguineus53. Similar to findings reported by Hackman and Filshie60 and Sonenshine and Roe49, LM in the present study of the cuticle revealed the presence of an outer, thinner, and slightly folded layer called the epicuticle. TEM revealed that it is extremely electron-dense and has a multilayered structure, including wax, cuticulin, and a less dense homogeneous layer. Similar findings were noted for Haem. leporspalustris61, B. microplus62, H. asiaticum63, H. dromedrii64, H. anatolicum59.In the current study, the procuticle was made up of two separate sublayers; the exocuticle, which was in contact with the epicuticle, and the endocuticle, which was close to the epidermis. According to these results, these layers are easily observed and distinguishable in B. microplus and B. decoloratus65, H. asiaticum56, H. dromedarii57, Amb. hebraeum66, R. appendiculatus67, B. microplus51, R. sanguineus53,68, and D. andersoni and D. variabilis49.According to results of the current histological study, the subcuticular layer was found below the endocuticle. Hackman69, Coons and Alberti70, and Remedio et al.53 identified this layer in R. microplus, I. ricinus, and R. sanguineus, respectively.LM and TEM examination of the integument showed the presence of an epidermis that contained irregular shaped cells, each had an irregular nucleus with peripheral heterochromatin, dispersed euchromatin and a visible nucleolus, several free ribosomes, mitochondria, and rough endoplasmic reticulum. Additionally, microvilli with vesicles containing electron-dense material were observed oriented towards the sub-cuticular layer. Such observations were in great accordance with those previously mentioned49,53,56,61,65,67,71,72.Throughout the epidermal layer, dermal glands were visible and connected to the outside through a duct that led to a cuticle surface aperture. Similarly, the present findings were detected in the integument of R. microplus68 and H. asiaticum63.In the present study, LM examination of treated integument revealed damaged epicuticle with increased folds. TEM showed that the layers of wax and cuticulin were separated. The procuticle layer lacked lamellar structure and seemed less organized with coalesced layers. Additionally, there was a noticeable dilated pore canals in the endocuticle. The subcuticular layer has damaged microvilli and vacuoles, giving it an abnormal appearance. It was also noted that the epidermal cells and the subcuticular layer separated. The epidermal layer appeared with great disorganization, as its cells suffered from cytoplasmic degeneration and vacuolization, loss of cytoplasmic organelles, and damage of nuclear membrane and the nucleolus. Morphological alterations in epidermal cells indicate that the active ingredients of the extract were capable of crossing the cuticle barrier and reaching the epidermis30.According to de Souza et al.31, changes in the epidermal cells of female R. sanguineus ticks treated with neem plant extract may result in long-term changes to the physiological characteristics of the epidermis and may even cause cell death due to the noticeable nuclear deformation73. The occurrence of nuclear alterations (characteristics of cell death) in cells of the epidermal layer can affect the synthesis and secretion of the cuticular components and hence leave the tick more susceptible to changes in the external environment73.The presence of vacuoles in epidermal cells cytoplasm is one of morphological changes that occur when organisms are exposed to stress. This is an indication that the defense mechanism is activated, which would be taking place by isolation of damaged cytoplasmic components and organelles that have lost their function, then broken down by lysosomal enzymes73,74,75,76. This strategy allows cells to preserve their internal systems and thus the efficiency of their metabolism77. Cytoplasmic retraction of the epidermal cells or dilated intercellular gaps suggested changes in tight junctions and adhesion junctions, which are frequently found in lining cells78.In the present investigation, the pore canals of treated females showed dilatation and disintegration, creating an empty network. The dermal glands were characterized by enlarged ducts with ruptured membranes, and damaged cells. The integumental glands’ enlargement suggests that the secretory cells are very active79, releasing lipids that serve as a protective barrier67.Using adult immersion tests, several authors have reported similar effects of plant extracts on the integument of semiengorged and engorged females of various tick species, including R. sanguineus30,31, Haem. longicornis16, and H. dromedarii33. Similar results were found in R. sanguineus after using chemicals derived from plants32.Gas chromatography-mass spectrometry (GC–MS) is the most widely used method for analyzing volatile chemicals80,81,82. It is a technique that combines the performance of gas chromatography, which allows the separation of compounds, and the performance of mass spectrometry, which enables the finding and identification of compounds according to their mass-to-charge ratio (m/z)83.In this study, volatiles from C. colocynthis were found mainly in the plant extract’s fruit using GC-Mass84. Its seeds also rich in stearic and palmitic acids85 that exhibit biological activity against arthropods86,87, and insecticidal effects on Melanaphis sacchari88. According to Mohamed et al.2, GC–MS analysis of the C. colocynthis ethanolic extract showed a significant diversity of fatty acid contents, which are regarded as one type of volatiles. Among these components were linoleic acid, vaccenic acid, decanoic acid, carbamic acid, and oleic acid.Volatile organic compounds (VOCs) are lipophilic with low molecular weights and high vapor pressures83. Their physical properties facilitate them to cross cell membranes89. Accordingly, it was suggested that all previous changes detected in the tick integument following treatment in the present study were attributed to the occurrence of volatiles such as methyl linoleate, octadecadienoic, palmitic and stearic acids. These compounds have lipophilic structures, and their penetration through the integument may disrupt cell membranes, altering their permeability and causing significant deformation in all integument layers. This suggestion is in great agreement with some authors90,91,92.ConclusionHistological examinations of fed female Hyalomma dromedarii integument after Citrullus colocynthis extract treatment revealed symptoms of great damage to all cuticle layers and the epidermis. Alterations in the morphology of epidermal cells because of the aggression of plant components on the cuticle were accompanied by changes in their physiological status. The data provided suggest that the used plant extract may be applied for biological control of H. dromedarii.

    Data availability

    We are the authors assure that all data and materials support the published claims and comply with field standards. The data are mentioned in the manuscript and will be available after publication.
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    Download referencesAcknowledgementsAuthors would like to thank Dr. Mostafa Hussein, a researcher in Egypt Desalination Research Center of Excellence, Desert Research Center, Cairo, Egypt and Dr. Ebtehal Hassan Mohamed, a researcher in Electron Microscope Unit, Faculty of Agriculture, Cairo University, Egypt for their helpful cooperation in photographing of electron microscopical samples.FundingOpen access funding provided by The Science, Technology & Innovation Funding Authority (STDF) in cooperation with The Egyptian Knowledge Bank (EKB). This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Author informationAuthors and AffiliationsZoology Department, Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, EgyptAshraf Ahmed Montasser, Salma Nabil Ahmed Mohamed & Asmaa Ali Baioumy AliAuthorsAshraf Ahmed MontasserView author publicationsSearch author on:PubMed Google ScholarSalma Nabil Ahmed MohamedView author publicationsSearch author on:PubMed Google ScholarAsmaa Ali Baioumy AliView author publicationsSearch author on:PubMed Google ScholarContributionsAABA and AAM contributed to the study conception and design. Material preparation, data collection and analysis were performed by AABA and SNAM. The first draft of this manuscript was written by SNAM and all authors commented on the previous versions before this final one. All authors read and approved this final manuscript. Ashraf Ahmed Montasser (Montasser AA): Conceptualization, Writing-review & editing. Salma Nabil Ahmed Mohamed (Mohamed SNA): Conceptualization, Investigation, Resources, Data curation, Writing-original draft, Writing-review & editing. Asmaa Ali Baioumy Ali (Ali AAB): Conceptualization, Validation, Investigation, Resources, Data curation, Writing-review & editing, Visualization, Supervision.Corresponding authorCorrespondence to
    Asmaa Ali Baioumy Ali.Ethics declarations

    Ethical approval
    Although this study didn’t involve any experiments on humans or animals, it was ethically approved by the Research Ethics Committee of Faculty of Science, Ain Shams University, Cairo, Egypt, Code: ASU-SCI/ZOOL/2024/7/1.

    Competing interests
    The authors declare no competing interests.

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    Reprints and permissionsAbout this articleCite this articleMontasser, A.A., Mohamed, S.N.A. & Ali, A.A.B. Histopathological effects of the fruit extract of Citrullus colocynthis on the integument of the female tick Hyalomma dromedarii.
    Sci Rep 16, 12708 (2026). https://doi.org/10.1038/s41598-026-46500-2Download citationReceived: 25 December 2025Accepted: 26 March 2026Published: 17 April 2026Version of record: 17 April 2026DOI: https://doi.org/10.1038/s41598-026-46500-2Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy shareable link to clipboard
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    Keywords
    Citrullus
    ExtractHistology
    Hyalomma
    IntegumentVolatiles More