Freshwater snails of the genus Biomphalaria include several species of major public health importance as intermediate hosts of schistosomiasis and represent a key group for evolutionary and taxonomic research within Hygrophila. However, complete mitochondrial genomes are available for only a limited number of Biomphalaria species, restricting comparative assessments of mitogenome evolution and the ability of mitogenomic data to resolve contentious relationships within Planorbidae and across Hygrophila. Here, we generate and analyse six complete mitochondrial genomes from four Neotropical Biomphalaria species collected in Argentina, including the first mitogenomes for B. peregrina and B. orbignyi, and evaluate genomic architecture, molecular evolutionary patterns, and phylogenetic relationships using multiple mitogenome-based approaches. All six mitogenomes contained the standard complement of 37 mitochondrial genes and exhibited a fully conserved gene order and strand orientation across Biomphalaria. Genomes were highly compact, with numerous gene overlaps. An unusually long non-coding region (210–242 bp) was detected exclusively in B. peregrina, contributing to its slightly larger mitogenome size. Intraspecific variation in the secondary structure of tRNACys, including arm truncation, was also observed within B. peregrina. All genomes showed negative AT-skew and positive GC-skew, indicating conserved strand asymmetry across Hygrophila. Protein-coding genes displayed strong codon-usage bias and were predominantly shaped by purifying selection, with atp8 identified as the most variable and least constrained gene. Phylogenetic analyses recovered two closely related topologies across datasets, supported monophyly of Bulinidae and Lymnaeidae, and consistently placed bulinids within planorbids, rendering Planorbidae non-monophyletic. Amphipepleinae was monophyletic, whereas Lymnaeinae was paraphyletic in a pattern sensitive to taxon sampling. Within Biomphalaria, B. peregrina was consistently resolved as the earliest-diverging lineage among sampled species. These six newly generated mitogenomes substantially expand genomic resources for Neotropical Biomphalaria and reveal strong conservation of mitochondrial genome organisation alongside pronounced heterogeneity in gene-specific evolutionary dynamics. Complete mitochondrial genomes enhance phylogenetic resolution within Hygrophila and provide independent evidence relevant to ongoing debates in planorbid systematics, including the affinity between Bulininae and Planorbinae. Nevertheless, broader taxon sampling and the integration of nuclear genomic data will be essential to fully resolve subfamilial relationships and species boundaries within this medically important group. The online version contains supplementary material available at 10.1186/s12862-026-02520-0.
The phylogeny, classification, diversity, and distribution of cave species have always been difficult problems for taxonomists. In this study, we aim to clarify the phylogeny and evolutionary history of the cave-dwelling fish genus Sinocyclocheilus, a group that is not only difficult to collect but is also frequently under-recognized due to its cryptic nature, in order to elucidate its evolutionary patterns and dynamics. Our phylogeny supports the monophyly of the five current species groups (S. angularis, S. cyphotergous, S. jii, S. microphthalmus, and S. tingi groups), but a variety of evidence suggests that corresponding subgenera should be elevated. Our species delimitation analysis identified 84 species, including 18 cryptic. Molecular dating and biogeographic analyses revealed that Sinocyclocheilus originated in the late Eocene, ~ 40.32 millions of years ago (Ma), that the most recent common ancestor inhabited the Guijiang-Hejiang River and the Nanpanjiang River, ~ 34.61 Ma, and dispersed outward from the Nanpanjiang River Basin, and that an acceleration of speciation rates occurred during the late Eocene. A biogeographic dynamic meta-analysis showed that lineage divergence and in situ diversification began at ~ 38 Ma and increased sharply at ~ 24 Ma, with two peaks at ~ 15 and ~ 2.5 Ma and a valley at 2.5 Ma. Dispersal events began at ~ 28 Ma and increased sharply at ~ 12 Ma, with a distinct peak at ~ 5 Ma. The speciation rate increased rapidly between approximately 40 and 32 Ma, followed by a sustained, gradual decline. The diversity of Sinocyclocheilus has been severely underestimated and requires a comprehensive reassessment integrating both morphological and genetic evidence. The revised classification comprises seven species groups or subgenera. The origin and diversification history of the genus were likely coupled with orogenic activities and the intensification of the Asian monsoon rainfall, which facilitated the formation of extensive subterranean voids, thereby creating ecological opportunities for speciation. Early high-temperature events may have initially triggered a rapid increase in speciation rates, whereas the relatively stable and cooler conditions of cave environments likely became less conducive to subsequent speciation. Our results also suggest a four-phase model of karst cave formation in southwestern China, with accelerating and decelerating periods in each phase. These evolutionary dynamics can be viewed as a response to shifts in paleogeoclimatic events since the Eocene. The online version contains supplementary material available at 10.1186/s12862-026-02496-x.
Species-rich grasslands (SRGs) provide unique ecosystem services, yet they are some of the most understudied environments in Scotland. This is because their true extent is unknown, and their locations are often in unreachable areas. Remote sensing may ameliorate this by helping to distinguish between SRG classes and increase monitoring efforts. However, these applications have not been conducted across highly diverse grasslands at national scales. We aimed to address this by applying remote sensing techniques to multiple classes of species-rich grasslands, nationally. Using an Unmanned Aerial Vehicle (UAV), we investigated the Spectral Variation Hypothesis, testing the relationship between species diversity (species richness) and spectral diversity (variation in surface reflectance using the coefficient of variation and standard deviation). Additionally, data was acquired from Sentinel-2 and Planetscope satellites, as well as the UAV data, assessing the prediction of grassland community traits (above ground biomass, sward height, and SPAD-measured chlorophyll) across multiple spatial (8 cm − 10 m) and spectral (8–13 bands) resolutions. The results contrast with prior studies of single sites and less diverse grasslands, indicating that there was no significant relationship between species diversity and the spectral diversity metrics, standard deviation (p = 0.120) and the coefficient of variation (p = 0.141), across seven of our study sites. The accuracy of grassland trait prediction varied largely with spatial and spectral resolution and the combination of predictor variables used. The UAV mounted multispectral Micasense predictor variables were most successful in predicting all traits: sward height, above ground biomass, and SPAD-measured chlorophyll (R2 = 0.545, R2 = 0.221, R2 = 0.167 respectively). The results suggest monitoring across species-rich grassland classes using remote sensing may be hampered by increased variation and confounding factors in these highly diverse habitats. Further methodological advancements are needed for wide scale cross-grassland habitat differentiation and monitoring, and field guidelines for remote sensing species-rich grasslands must be elaborated. The online version contains supplementary material available at 10.1186/s12862-026-02500-4.
Accurate species delimitation is essential for understanding biodiversity patterns and guiding conservation, yet cryptic species with minimal morphological variation often obscure the assessment of true species diversity, making the identification of reliable diagnostic characters critical. Island radiations exemplify this challenge by concentrating endemic diversity in restricted areas, which accentuates both the urgency of conservation and the need for accurate taxonomy, while often presenting species divergences masked by subtle morphological differences. Here, we investigated patterns of morphological differentiation in Ailuronyx geckos, a genus endemic to the Seychelles archipelago, comprising deeply divergent lineages and unresolved, possibly cryptic species boundaries. We applied 3D and 2D morphometric analyses across the range (16 islands) of the three recognised species: the bronze-eyed gecko A. seychellensis, dwarf bronze gecko A. tachyscopaeus, and giant bronze gecko A. trachygaster. 3D geometric morphometric analyses of cranial and mandibular landmark data from 42 geckos revealed strong species-level differences. Ailuronyx trachygaster exhibits extreme skull sculpturing with rugose textures on up to ten cranial and three mandibular bones, while the other two species have smooth skull surfaces. Skull elongation and narrowing increased with decreasing body size from the larger A. trachygaster, via the medium-sized A. seychellensis, to the smaller A. tachyscopaeus. Analysis of body size-corrected 2D measurements of ten external morphological traits from 567 geckos revealed similar differences in head dimensions among the species, but also showed changes in mass and toe length. While we observed substantial morphological variation between islands, we did not find support for the previously identified northern and southern island group divergence within either A. seychellensis or A. tachyscopaeus. Nevertheless, we found strong support for the proposed divergence between northern and southern Mahé populations of A. tachyscopaeus, with variation in mass and head size between the two populations. We provide morphometric parameters to guide species identification within this gecko genus and highlight distinct population units that warrant further genomic investigation and prioritisation for conservation. Our findings illustrate the complexity of morphological diversification in archipelagos, where island-specific processes may outweigh regional biogeographic patterns. This underscores the need for integrative approaches to species delimitation and conservation in insular systems. The online version contains supplementary material available at 10.1186/s12862-026-02517-9.
The recent integration of 3D imaging and digital methodologies has revolutionized evolutionary biology, offering unprecedented opportunities for analysing and sharing morphological data. However, the transition toward open access remains incomplete due to persistent technical, legal, and institutional barriers. Issues such as lack of standardization, massive file sizes, and unclear intellectual property rights continue to hinder data verification and reproducibility. These challenges have acquired new urgency with the rapid rise of machine learning and AI-based tools for automated segmentation, landmarking, and shape analysis, which require large, standardized, and openly accessible training datasets - making inaccessible 3D data not merely an inconvenience, but a source of systematic bias in the algorithms shaping the field's future. This review synthesizes technical, legal, and behavioural perspectives on open data in digital morphology, building on prior work to address the specific challenges of the current AI era. By advocating for the adoption of FAIR principles, the use of persistent digital identifiers, and the implementation of digital watermarking, we offer recommendations for establishing minimum standards in data publication. Ultimately, a shift toward responsible data stewardship is essential to ensuring that digital morphological resources remain accessible, reproducible, and scientifically valuable for both human and computational users.
Identifying significant adaptive variation within species is a key focus of efforts to preserve evolutionary potential under environmental change. We analysed genome-wide SNPs and ecomorphological traits to define units for the conservation of Aipysurus sea snakes. This group contains nine fully-marine taxa that are primarily endemic to the northern Australian region, including two critically endangered and one endangered listed species. Results show convergent patterns of genetic and morphological divergence between coastal and offshore populations in four of five co-distributed Aipysurus lineages. In A. apraefrontalis, A. duboisii, A. foliosquama, and the A. fuscus-A. tenuis complex, individuals from the WA Coast and remote Timor Sea reefs form distinct genetic clusters with gene-tree based divergence estimates of five hundred to nine hundred and fifty thousand years. Coastal populations in all four of these lineages have longer bodies, higher vertebrate counts, and lighter colour patterns compared to offshore-reef populations. In A. laevis (the fifth co-distributed lineage), body length and colour pattern variation mirrored the coastal-offshore divisions seen in the other Aipysurus, but this species showed different patterns of geographic genetic structure that are incongruent with current species boundaries. This striking genetic and morphological convergence implicates shared patterns of biogeographic isolation and suggests local adaptation related to locomotory performance and crypsis in open soft-bottomed coastal habitats versus structurally complex reefs. We recommend that coastal and offshore-reef populations of A. duboisii, A. apraefrontalis and A. foliosquama be recognised as evolutionarily significant units (ESUs), while the current taxonomy of A. fuscus, A. laevis, A. pooleorum and A. tenuis be retained.
Dietary environments can shape host-microbe co-evolution by imposing selection pressures that favor host and microbial genotypes with enhanced fitness under specific nutritional conditions. However, the long-term evolutionary dynamics of these interactions after selection pressures are relaxed remain poorly understood. Here, we investigated the microbiome of Drosophila melanogaster populations that underwent long-term experimental evolution under three temporally variable nutritional regimes (constant high sugar, progressively decreasing protein, and fluctuating protein), and compared them to unselected controls. Following inbreeding of evolved populations, we examined how persistent evolutionary effects interact with aging to shape host-microbe relationships and survival. All selected regimes exhibited reduced survival relative to controls, indicating lasting physiological costs associated with historical selection and inbreeding. Survival differed among regimes: the deteriorating-protein regime was closest to controls, the fluctuating-protein regime was intermediate, and the high-sugar regime showed the shortest lifespan. Survival effects were sex-specific: relative to control females, those from the fluctuating-protein regime exhibited reduced early-life survival, whereas females from the deteriorating-protein regime experienced lower late-life mortality. Microbiome composition varied with both selection regime and age. Although Firmicutes and Proteobacteria dominated across groups, selected lines showed increased Firmicutes and reduced Proteobacteria, especially early in life, suggesting early-life taxonomic restructuring. The decreasing-protein regime maintained more stable microbial diversity over time, whereas high-sugar and fluctuating-protein diets were associated with progressive microbiome instability with age. Core Acetobacter species (A. aceti, A. oryzifermentans) declined in abundance in selected flies, indicating persistent disruption of microbiome integrity. A random forest model predicted fly age from microbiome composition with 78.8% accuracy, reinforcing links between microbial dynamics and host aging. Historical dietary selection and inbreeding can leave lasting signatures on survival and microbiome composition in Drosophila. Protein restriction promoted late-life longevity and microbial stability, whereas high-sugar and fluctuating diets were associated with early-life effects followed by later-life shifts in dominant taxa. Together, these findings illustrate how nutritional history and its microbial legacies influence lifespan and aging through persistent host-microbe interactions. The online version contains supplementary material available at 10.1186/s12862-026-02493-0.
Urban environments are increasingly recognized as important habitats for wildlife, yet information on how reptiles use urban environments remains scarce. The Aesculapian snake (Zamenis longissimus), a non-venomous colubrid widespread in Central Europe, is considered a habitat generalist with a frequent association with human settlements. However, data on its occurrence and ecology in metropolitan areas are limited. To address this gap, we implemented a citizen science initiative in Bratislava, Slovakia, aiming to document the distribution and habitat use of the Aesculapian snake and to evaluate the potential and limitations of citizen science for reptile monitoring in urban environments. Between April 2019 and October 2022, a citizen science initiative was implemented to monitor the distribution and ecology of the Aesculapian snake in Bratislava, Slovakia. The project relied primarily on social media, which proved to be the most effective channel for data collection, complemented by direct e-mail submissions. Altogether, volunteers provided 588 verified records of the focal species, alongside 184 misidentified observations of other native reptiles, most frequently Natrix spp. Spatial analyses showed that most observations of the Aesculapian snake in Bratislava were concentrated in natural and semi-natural areas at lower elevations below 300 m a.s.l., with a few records above 500 m. Within these areas, snakes were most often reported from built-up and forested land cover, while agricultural land yielded comparatively few sightings. Seasonal patterns indicated a pronounced peak in spring and early summer, while diurnal activity was dominated by midday and afternoon observations. Specifically, the number of reports declined with increasing urbanization intensity but was higher in more densely populated areas, reflecting both ecological patterns and the availability of observers. This study delivers one of the most comprehensive datasets on the Aesculapian snake in an urban setting, highlighting its synanthropic behavior and frequent use of anthropogenic habitats. At the same time, the results underscore both the opportunities and inherent biases of citizen science, confirming its value as a complementary tool for monitoring reptile populations in metropolitan environments.
Temperature profoundly influences the physiology, survival, and distribution of marine ectotherms, including mollusks. Transient receptor potential (TRP) channels are conserved thermosensory proteins in metazoans, yet their evolutionary diversification and functional roles in gastropod mollusks remain unclear. In this study, we present a comprehensive phylogenetic classification and expression analysis of TRP-like channel genes in Pacific abalone (Haliotis discus hannai). Through the extensive mining of genome and transcriptome datasets, we identified 49 TRP-like genes and categorized them into nine families from two major groups: Group 1 (TRPA, TRPC, TRPM, TRPN, TRPS, TRPV, and TRPVL) and Group 2 (TRPP and TRPML), along with two unclassified TRP-like genes. Phylogenetic analysis incorporating sequences from lophotrochozoans, choanoflagellates, fungi, and green algae outlined a lineage-specific TRP-like gene expansion in mollusks. Spatial expression profiling revealed distinct tissue-specific patterns: TRPC-, TRPM-, and TRPP-like genes were enriched in sensory organs (i.e., the eyes and tentacles), whereas TRPM- and TRPV-like genes were expressed predominantly in respiratory and metabolic tissues (i.e., the gills and hepatopancreas). Under acute thermal stress, RNA sequencing and real-time quantitative PCR identified several thermoresponsive TRP paralogs, including TRPA1- and TRPV-like genes, exhibiting distinct transcriptional regulation. These results elucidate the evolutionary complexity and functional diversification of TRP channels in marine gastropods, and highlight the potential role of these molecules in thermal sensing and adaptation. This study provides a molecular framework for understanding TRP-mediated environmental responses in mollusks, contributing to broader insights into marine invertebrate resilience under climate change. The online version contains supplementary material available at 10.1186/s12862-026-02505-z.
Mesozoic and Cenozoic fossils from Myanmar and the Indian subcontinent provide a crucial source of information on the global distribution of biota after the breakup of East Gondwana and the subsequent northward drift of these land masses towards Asia. While the mayfly fauna of Burmese amber is relatively well studied, data on extinct Ephemeroptera from India remain scarce. Here, we describe for the first time a fossil adult mayfly reliably assigned to the family Teloganodidae. Based on a single male imago discovered in mid-Cretaceous Burmese amber, we establish a new species and genus, Chibiphemera cretalota gen. & sp. nov. based on the following combination of characters: (i) small body and forewing size; (ii) distinctive forewing venation, including the positions of RS and MP forks; (iii) strongly reduced hind wings, with a distally positioned costal process and markedly diminished venation; (iv) presence of pad-like pretarsal claws on the forelegs together with pointed claws on the middle and hind legs; and (v) unique shape of genitalia characterized by deeply separated, stick-like penis lobes and a markedly elongated gonostyli segment I. Adult morphological characters show affinities between the fossil Chibiphemera gen. nov. and extant South African and Malagasy genera of Teloganodidae. Plesiomorphies in the forewings and genitalia of Chibiphemera gen. nov. suggest an early diverged position within the family. Additionally, we re-examine the holotype of the Cenozoic species Teloganella gurhaensis Agnihotri et al., 2020, originally described from a single larva from the late Palaeocene–early Eocene Palana Formation (India), and redescribe it. It is defined by larval characters such as (i) a broad pronotum protruding anterolaterally, (ii) strongly expanded femora that are widest centrally, (iii) tibiae moderately widened distally, (iv) robust, hooked pretarsal claws, (v) a small, styliform gill I attached to abdominal segment I near its outer margin medially, and (vi) the presence of three caudal filaments. We establish a monotypic genus Bharataganodes gen. nov. for Bharataganodes gurhaensis (Agnihotri et al., 2020) comb. nov., and discuss its systematic position within Teloganodidae and its relationships with other genera. Together, these fossils support a Gondwanan origin for Teloganodidae and highlight the importance of the Burma Terrane and the Indian Plate as key dispersal routes for aquatic insects across the Tethys to Asia during the Mesozoic–Cenozoic transition.
This study examines the patterns and storage of soil organic carbon (SOC) in the Upper and Lower Lakes of Egypt’s Wadi El-Rayan Protected Area, a hyper-arid inland lake system. The objective was to develop predictive models for estimating volumetric SOC density (SOCv, kg C/m³) and cumulative SOC stocks (SOCc, kg C/m²) at varying soil depths across both lakes. Using data from 40 soil cores comprising 400 individual samples, three mathematical models (allometric, exponential, and sigmoid) were applied to analyze SOC. Significant differences in soil bulk density (SBD), SOC content, SOCv, and SOCc were observed between the two lakes (p < 0.05–0.001). The Lower Lake exhibited the highest mean SBD (1.01 ± 0.03 g/cm³) compared with the Upper Lake (0.83 ± 0.03 g/cm³), whereas the Upper Lake showed the highest mean SOC content (29.4 ± 2.0 g C/kg), SOCv (20.3 ± 1.5 kg C/m³), and SOCc (10.2 ± 2.0 kg C/m²), with the corresponding lowest values recorded in the Lower Lake (7.0 ± 0.6 g C/kg, 6.4 ± 0.6 kg C/m³, and 3.2 ± 0.5 kg C/m², respectively). A negative correlation between SOC content and SBD was observed in both lakes (r = − 0.344 in the Upper Lake and r = − 0.188 in the Lower Lake). For SOCv predictions in the Lower Lake, the allometric and exponential models provided the best fit, with R² values of 0.989 and 0.980, respectively. In contrast, the exponential, allometric, and sigmoid models performed well for the Upper Lake, with R² values of 0.972, 0.963, and 0.958, respectively. All three modeling approaches achieved high accuracy (R² > 0.99) in simulating SOCc. The allometric and exponential models provided the best fit for the Lower Lake (R² = 0.999), while the exponential and sigmoid models yielded the best fit for the Upper Lake (R² = 0.999). These findings enhance our understanding of SOC distribution in the hyper-arid inland lakes of the Wadi El-Rayan Protected Area and provide a foundation for more accurate predictions of future carbon stocks, thereby supporting conservation, restoration, and preservation efforts. The online version contains supplementary material available at 10.1186/s12862-026-02519-7.
Clematis tientaiensis is a rare and endangered plant species endemic to Zhejiang Province, China, characterized by weak natural regeneration and a scarce extant population. To elucidate its endangerment mechanisms and formulate scientific conservation strategies, this study collected data from its natural community using the quadrat sampling method, with C. tientaiensis and its associated dominant species from the shrub layer (n = 19) and herb layer (n = 19) as the research subjects. By comprehensively applying niche analysis (niche breadth and overlap), interspecific association tests (overall association, [Formula: see text]-test, association coefficient, Pearson and Spearman correlation analyses), and cluster analysis, we systematically revealed the resource utilization strategies and interaction patterns between the target species and its associated plants. The results showed that a total of 133 associated plant species were recorded in the C. tientaiensis community, belonging to 107 genera in 58 families. The proportion of liana species accounted for only 6.77%, and a shortage of seedlings was observed. C. tientaiensis belongs to the endemic Chinese distribution type, while 83.46% of the associated species or 70.00% of the dominant species belonged to the East Asian distribution type. In both the shrub and herb layers, C. tientaiensis exhibited the widest niche breadth (BL = 10.756 and BS = 2.508), but this ecological attribute did not enhance its population survival. The niche overlap among dominant associated species was generally low (mean value < 0.30), indicating weak interspecific resource competition. Furthermore, the overall associations among dominant species were not significantly negative. The ratios of positively associated species pairs to negatively associated species pairs were all below 1.00 in the [Formula: see text], AC, Pearson, and Spearman test results. According to the hierarchical clustering analysis results, C. tientaiensis was suitable for constructing a stable shrub community with associated plants such as Rubus idaeus, Lespedeza davidii, Mallotus apelta, and Oplismenus undulatifolius. In conclusion, the C. tientaiensis community is characterized by high species richness and a relatively complete structure, currently in the early unstable stage of positive succession with independent niche differentiation and loose interspecific associations. The majority of associated species, sharing similar resource requirements, created a niche monopoly effect that significantly inhibited resource acquisition by plants from other floristic regions. This may be a primary reason for the endangered status of C. tientaiensis. For the conservation and restoration of its native habitat, in situ protection of individuals should be implemented to enhance niche occupation, accompanied by appropriate replanting and optimization of associated species composition to improve community stability. The online version contains supplementary material available at 10.1186/s12862-026-02510-2.
The construction of cascade hydropower stations on the lower Jinsha River has significantly altered natural hydrological regimes and ecological processes, posing potential impacts on aquatic ecosystems. Understanding the spatiotemporal dynamics of phytoplankton communities and their responses to environmental changes is crucial for the ecological management of reservoirs and the protection of water environments. This study investigated four cascade reservoirs in the lower Jinsha River during June (summer) and December (winter) 2023. Pronounced thermal and chemical stratification observed in June became homogenized in December, with concentrations of TN, NO3-N, DTN, and TP significantly higher in December (p < 0.05) and accumulating downstream. Phytoplankton density generally decreased with increasing depth, and community structure differed significantly among the reservoirs (PERMANOVA, p < 0.05 except for WDD, p = 0.052). The density of Cyanophyta increased significantly from June to December (p < 0.05), whereas that of Bacillariophyta and Chlorophyta decreased. Mantel tests indicated significant correlations between phytoplankton communities and temperature, dissolved oxygen, and nitrate nitrogen (p < 0.05). Hierarchical partitioning revealed seasonal shifts in key driving factors: temperature (32.58%) and dissolved oxygen (20.13%) dominated in June, whereas nitrate nitrogen (21.86%) and suspended solids (15.22%) were the key factors in December. The elevated Cyanophyta density in December was associated with enhanced nutrient release from sediments, weakened dilution effects, and increased terrestrial inputs. This study reveals that phytoplankton community dynamics in subtropical cascade reservoirs are co-regulated by thermal stratification, nutrient availability, and seasonal changes. Future reservoir management strategies should prioritize monitoring thermal stratification and surface bloom risks in June, while focusing on controlling endogenous nutrient loading and optimizing water mixing processes in December. These findings provide important guidance for water quality management and ecological conservation strategies in regulated river systems. The online version contains supplementary material available at 10.1186/s12862-026-02502-2.
Hatching failure is common in the eggs of wild birds, yet its variation in relation to ecological and life history factors remains poorly understood. Understanding these patterns is essential for explaining reproductive strategies and evolutionary trade-offs in birds. In a comprehensive comparative study, we found that the previously recognized latitudinal decline in avian hatching failure rates is driven by a greater proportion of eggs failing in larger clutches at lower latitudes. We suggest that this pattern could reflect higher exposure to ambient conditions in larger clutches, which might have more severe consequences for egg viability in warmer environments. Furthermore, hatching failure rates increased with species longevity. We predicted this from the notion that, if needed, short-lived species should invest more heavily in current reproduction, whereas longer-lived species should be more prone to prioritize self-maintenance to improve future breeding opportunities. Hatching failure rates were also higher in species with uniparental incubation compared to biparental species, higher in elevated nests than in ground nests, and negatively related to altitude. Our results reveal several novel patterns of variation in hatching failure rates in relation to aspects of ecology and life history. These results suggest that clutch size, latitude, and parental care strategies interact to shape reproductive success and highlight potential evolutionary trade-offs between current and future reproduction. Further research is needed to clarify the proximate mechanisms underlying these patterns and their implications for avian life history evolution. The online version contains supplementary material available at 10.1186/s12862-026-02515-x.
Cichlids in the genus Danakilia, endemic to the hyper-arid Danakil Depression of Eritrea and Ethiopia, represent a rare example of diversification in one of Earth’s most extreme aquatic environments. While previous mitochondrial and morphological studies have identified two species (D. franchettii and D. dinicolai), the evolutionary history of this clade remains poorly resolved. Here, we use genome-wide SNP data from 85 individuals of Danakilia, sampled across six sites to infer phylogenetic relationships, assess population structure, and explore the role of historical hydrology in shaping diversification within the genus. We analyzed double-digest RAD-seq data to generate maximum likelihood phylogenies, PCA, and admixture profiles, and calculated pairwise FST values to assess genetic differentiation. Our results support strong phylogenetic and population-level differentiation between the two described species and three additional riverine populations, with four to five discrete genetic clusters identified. Phylogenetic analyses confirm the monophyly of D. dinicolai and reveal that all riverine populations form a well-supported clade sister to D. dinicolai, suggesting a shared origin. In contrast, D. franchettii is not monophyletic, and populations from southern spring habitats near Lake Afrera show limited genetic structure. Patterns of genetic divergence are broadly consistent with a paleohydrological model in which a mid-Holocene lake system connected the northern and southern Danakil Depression, facilitating gene flow among now-isolated habitats. We also detect varying levels of admixture among the northern populations, with evidence of historical gene flow between the crater lake and riverine populations. Despite their close geographic proximity, the three riverine populations are genetically distinct and may represent independent evolutionary units. These findings suggest a complex interplay of historical connectivity, geographic isolation, and adaptation to extreme environmental gradients in driving divergence within Danakilia. Given emerging environmental threats in the region, our results underscore the urgent need for conservation attention and further exploration of unsampled populations to fully characterize the evolutionary and ecological diversity of this little-known lineage.
As ecosystem engineers, earthworms play a significant role in maintaining soil health, fertility and ecosystem functioning by enhancing organic matter decomposition, nutrient cycling, and soil structure. Their diversity and distribution are shaped by land-use practices such as urbanization, agriculture, and forests. This study investigates earthworm species richness and spatial distribution across various land-use types in Hazara Division, Pakistan. Examine key ecological drivers including soil moisture, pH, organic carbon and potassium. The research explores how land-use practices affect earthworm diversity, providing insights essential for biodiversity conservation strategies in similar ecosystems. Sampling across six districts Haripur, Abbottabad, Mansehra, Kohistan, Batagram, and Tor Ghar 2697 individuals from 16 species belonging to three families: Lumbricidae, Megascolecidae, Moniligastridae. Eisenia fetida and Amynthas morrisi were the most abundant (12% each), while Drawida japonica (Gene bank ACESSION NOPV871406.1) was documented for the first time in Pakistan, highlighting the region’s unexplored biodiversity. Species richness showed a significant positive correlation with soil moisture (r = 0.472, p < 0.05) and neutral pH levels. Population densities were highest in Haripur and Mansehra, whereas Kohistan and Tor Ghar exhibited lower densities, likely due to poor soil structure and organic carbon content. The Shannon Diversity Index (H’) ranged from 2.55 in Tor Ghar to 2.61 in Kohistan, with overall earthworm abundance highest in Mansehra. Urban and industrial areas exhibited low species richness, possibly due to soil compaction and pollution. These findings highlight the ecological importance of earthworms in promoting soil health, enhancing ecosystem services, and reinforcing soil resilience amid environmental stressors. The online version contains supplementary material available at 10.1186/s12862-026-02506-y.
Models of evolutionary dynamics have long been dominated by a paradigm of gradualism, yet the fossil record consistently points to a history defined by punctuation. This disconnect between theory and data has left major macroevolutionary events, such as punctuated equilibria, explosive radiations, and mass extinctions, without a unified first-principles explanation. We argue that this gap stems from a subtle ubiquitous assumption in theoretical models: that the underlying fitness landscapes are mathematically smooth (Lipschitz continuous). We develop a theoretical framework based on relaxing this assumption, showing that non-Lipschitz dynamics are sufficient to make punctuation the default mode of evolution. We demonstrate that non-Lipschitz singularities, which arise naturally from known biological mechanisms like developmental constraints and ecological tipping points, provide a formal dynamical-systems basis for speciation as a bifurcation event and extinction as a finite-time singularity. Furthermore, we show that these dynamics are universal, appearing in contexts ranging from viral quasispecies to global biotas. Our framework provides a new generative engine for macroevolutionary theory. It makes specific quantitative predictions for paleontological patterns, including the decoupling of disparity and diversity during adaptive radiations, and for the genomic signatures of lineages that undergo rapid evolution. By replacing the assumption of smoothness with non-Lipschitz continuity, we offer a rigorous mathematical reconciliation between gradualist models and the punctuated nature of the fossil record.
The Sardinian wildcat (Felis silvestris lybica) belongs to a felid North-African lineage that reached the Mediterranean island in Neolithic times. While numerous studies have been conducted on the European wildcat (Felis silvestris silvestris), very little is known about the Sardinian wildcat ecology, genetics, and conservation status. Therefore, it is paramount to investigate the current distribution and genetics of the Sardinian population of F. s. lybica, previously described as var. sarda. In this work we assessed morphological and molecular traits of Sardinian wildcats, ascertained areas of species presence on the island, and investigated possible occurrence of hybridization with domestic cats. An integrated approach was adopted, involving questionnaire distribution and interviews to local people, and the morphological evaluation of road-killed individuals combined with their genetic typing using 29 polymorphic autosomal microsatellite loci. Genotypes were then analyzed by Bayesian clustering and assignment analyses. Questionnaires and interviews allowed us to build a preliminary alleged distribution map of the species and select candidate areas for non-invasive monitoring. The morphological and genetic characterization of road kills and museum specimens allowed us to identify pure individuals and recent wild × domestic hybrids, paving the way for better characterizing the Sardinian wildcat. Further steps of the research will allow us to shed light on this elusive presence on the island and enhance its conservation.
The Russian desman (Desmana moschata) is a critically endangered, elusive semi-aquatic mammal. While understanding its historical population dynamics is crucial for conservation, genomic data on its evolutionary and demographic history remain scarce. Here, we present a comprehensive whole-genome phylogenetic analysis of Desmana moschata within the Talpidae family, including heterozygosity assessments and inferred population size changes, as determined by PSMC and MSMC analyses. Our results demonstrate that, similar to its closest relative the Pyrenean desman (Galemys pyrenaicus), this species has undergone a long-term population decline preceding significant human influence. The phylogenetic component of our study involved a multigene analysis based on over 2,000 exons, producing a well-resolved, dated phylogeny of the Talpidae family at the tribal level. Although anthropogenic factors have undoubtedly contributed to recent declines, our data reveal that the reduction in the desman population is primarily an ancient process driven by natural causes. This has resulted in persistent declines in both effective population size and geographic range and then subsequent evolutionary extinction of ancient taxa with limited adaptive capabilities. These findings lay the groundwork for future genomic conservation studies, incorporating expanded sampling and targeted investigation of specific genomic features.
Shade trees in coffee agro ecosystem provide ecological and socio-economic benefits, including biodiversity conservation, microclimate regulation, and soil fertility maintenance. The Sheko semi-forest coffee system in southwestern Ethiopia is a traditional low-intensity landscape, yet its shade tree diversity, structure, and regeneration dynamics remain poorly documented. Vegetation surveys were conducted across six purposively selected kebeles along an altitudinal gradient (950-1800 m a.s.l.) using 50 systematically placed plots (30 × 30 m). Each plot included five nested subplots (5 × 5 m) to assess seedlings and saplings. Shade trees were identified through field observations, local knowledge, and herbarium references. Structural attributes including density, basal area, diameter at breast height (DBH), height, and importance value index were measured. Data were analyzed using R 4.3.1 with descriptive statistics, ANOVA, correlation analyses, and Canonical Correspondence Analysis (CCA). A total of 31 shade tree species across 15 families and 23 genera were recorded, with 96.7% native. Moraceae (32.2%) and Fabaceae (16.1%) were dominant. Cordia africana Lam., Pouteria adolfi-friederici (Engl.) Baehni, and Antiaris toxicaria lesch accounted for over 50% of density and basal area, with Cordia africana having the highest IVI (36.3). DBH and height distributions indicated a mixed-aged population, yet seedlings and saplings were underrepresented, reflecting limited regeneration. Altitude showed no significant effect on species richness or density. Anthropogenic disturbances, including clearing and unsustainable harvesting, constrained natural regeneration. The Sheko semi-forest coffee system supports high shade tree diversity but faces regeneration bottlenecks that threaten long-term sustainability. Targeted management, including enrichment planting and protection of key species, is essential to maintain ecosystem services and agroforestry resilience.