Biology and Life Sciences

Abstract: In the Balam Beh corridor in Campeche, Mexico, 217 transects were established, yielding a total of 301 independent records of ungulates: 198 records of white-tailed deer, 65 of collared peccary, 22 of tapir, and 16 of red brocket deer. A total of 503 vegetation structure points were characterized. Vegetation variables were analyzed using Principal Component Analysis, Multidimensional Scaling, and Logistic Regression. White-tailed deer was the most frequently recorded species and was found in more open areas, which could be explained by its habitat generalist characteristics. In contrast, tapir and brocket deer are species that prefer highly conserved sites far removed from human activity and tend to have lower abundances. Vertical canopy cover was the most important variable for ungulate presence. It is necessary to conserve or restore the structural features of the Balam Beh corridor, particularly the vertical cover, as it provides protection against predators and allows ungulates to perform their basic functions.

Abstract: Natural selection is credited for giving direction to evolution. But it is also described as a filter acting on variation supplied by mutation, development and chance. These views highlight different regimes, not rival truths. In this paper, I ask when selection actually determines evolutionary direction. I define determination counterfactually, i.e. an outcome is selection determined if it recurs across replicate histories under the same selective regime and becomes much less likely when selection factor is removed. Here, I argue that four conditions must hold jointly- (i) selection must outweigh drift, (ii) the selective regime must persist, (iii) variation should not be biased enough to overturn selection's ranking and (iv) landscape must allow the favored route to be travelled. Each failure hands direction to a distinct process. Determination also falls as outcomes are described more firmly, from function to phenotype to sequence. Finally, six testable predictions are stated.

Abstract: The advent of the genetic code and translation would have been the most important event in the early evolutionary stage of primordial cells. Although many theories on the origin of the genetic code have been proposed, no definitive answer has yet been reached. In 2001, I have proposed the RNA/protein symmetry theory for the origin of life, in which both RNAs and proteins coevolved forming a stable metabolic complex from the very beginning of the origin of life. In this theory, the genetic information can be generated from existing cellular proteins through reverse translation, which proceeds in the 3′ to 5′ direction using a set of reverse transfer RNAs (rtRNAs). Here, the original model for reverse translation was revised by modifying rtRNAs to naturally include forward translation. Inspired by the structures of the modified rtRNAs, I analyzed the relation between the sizes of the 20 proteinogenic amino acids and the stability of each codon/anticodon pair for each amino acid. I found the strong correlations between the molecular weights of the 18 amino acids excluding tryptophan and arginine and the ΔG values for the formation of each codon/anticodon duplex. This correlation may partly explain the origin of the genetic code.

Abstract: The Pavlik harness works remarkably well for babies under six months and about 8 to 10 kg. Outside that window, clinicians do not use it, and for good reason. But why exactly that boundary exists has never been fully explained in biomechanical terms. This article argues that Pavlik's control-theoretic idea, soft constraint plus bounded autonomous movement, is not the problem. The problem is that both of its inputs get scrambled by variables no one currently measures: body weight, limb dimensions, muscle strength, tone, developmental stage. These variables modulate the actual mechanical environment so heavily that identical strap settings produce wildly different outcomes across patients. Clinics respond by retreating to a narrow age window. We think there is another way: measure those variables, compensate for them, and see how far the Pavlik philosophy can actually reach. We lay out four research questions under a working label, CMVDF or Controllable Motion-Variable Dynamic Fixation, place everything squarely inside the IHDI safety framework, and sketch speculative extensions to CP and SMA. This is a research agenda. It is not a clinical protocol.

Abstract: Facultative endosymbionts living within arthropod cells are known to affect several aspects their hosts’ behavior. Here we synthesize studies that measure effects of endosymbionts on arthropod behavioral traits, ranging from effects on host activity and feeding to mating and multitrophic interactions with predators and parasitoids. Our systematic review of the literature identified 70 laboratory studies that compared behavioral traits between arthropod populations where the endosymbiont was either present or absent. In a meta-analysis of 799 comparisons (639 Hedges’ g effect sizes and 160 log of odds ratios for binomial data) across different endosymbiont species and behavioral categories, we found that the presence of facultative endosymbionts tended to provide benefits to mating but costs to feeding, while for many other traits endosymbionts had no overall effect or patterns depended on the endosymbiont or host species. Measured effects of endosymbionts tended to be larger when the genetic background of the strains was not controlled. We discuss challenges with assessing effects of endosymbionts on arthropod behavior, identify avenues for future studies and highlight implications for field releases of arthropod lines carrying endosymbionts for pest and pathogen control.

Abstract: Malaria is a public health problem in Senegal, with heterogeneous transmission and little known about transmission drivers at the Senegalese border. This study aimed to determine bionomics of major vectors and malaria transmission in the Senegambian border. The study was conducted from July 2023 to March 2024 in Nemataba and Ndrame Ndimb (near the border), and in Medina Dianguette and Paoskoto (farther). Adult mosquitoes were collected using human landing catches and pyrethrum spray catches. Laboratory analyses were performed by Enzyme-Linked Immunosorbent Assay and Polymerase Chain Reaction techniques. Anopheles gambiae s.l. human biting rates (HBRs) were 1.05 bites/person/night (b/p/n) in Nemataba and 6.55 b/p/n in Ndrame Ndimb, while they were 14.73 b/p/n in Medina Dianguette and 1.47 b/p/n in Paoskoto. Anopheles funestus HBR was 2.88 b/p/n in Paoskoto and 0.37 b/p/n in Ndrame Ndimb. Human blood index for An. gambiae s.l. were 77.08% in Medina Dianguette, 66.67% in Nemataba, 2.42% in Ndrame Ndimb and 0 in Paoskoto, while for An. funestus they were 5.93% in Ndrame Ndimb and 3.65% in Paoskoto. Malaria transmission was detected in Medina Dianguette and Paoskoto, with 0.078 and 0.209 ib/p/n, respectively. This study highlights the diverse bionomic characteristics of major malaria vectors along the Senegambian border.

Abstract: Genome-wide association studies (GWAS) and LD Score regression are closely related in practice, yet the quantities used in these approaches have apparently different mathematical definitions. GWAS evaluates the association between a genetic variant and a phenotype, whereas the LD Score of a locus is defined from pairwise correlations among genetic variants. Here, we show that these apparently different quantities can be represented within a common geometric framework.We represent standardized genetic variants as vectors in the sample space and construct a symmetric positive semidefinite matrix from their outer products. Spectral decomposition of this matrix provides a common orthogonal eigenbasis for the genetic variation observed in the sample. Both individual genetic variants and the component of the phenotype contained in the SNP space can be represented using coordinates defined with respect to this same eigenbasis. LD Score and phenotype--genotype association can consequently be expressed as different operations on these common coordinates.We numerically verified these relationships using simulated genotype data containing correlated groups of loci and a phenotype vector constructed from components both within and orthogonal to the SNP space. Direct calculations of LD Score and phenotype--genotype association agreed with their corresponding spectral representations to numerical precision.These results show that GWAS association and LD Score are not quantities defined in unrelated mathematical spaces, but can be viewed as different operations performed within a common coordinate system. We term this representation Genetic Geometry. This framework provides a unified view of GWAS and LD Score regression and provides a basis for investigating why their locus-specific quantities exhibit the relationship exploited by LD Score regression.

Abstract: Why simple carbon-containing small molecules can evolve stepwise into complex, diverse, and ordered living organisms and social organizations remains an unresolved core scientific question. Existing evolutionary theories each apply to only one stage—chemical, biological, or social evolution—thereby fragmenting the complete evolutionary picture. This article develops Carbon-Based Evolutionary Theory (CBET), a framework theory deduced from six scientific principles and two universal mathematical rules through an eight-step process. CBET identifies two mechanisms shared by chemical, biological, and social evolution: the dual-loop feedback mechanism, which generates changes ceaselessly, and the persistence selection mechanism, which filters changes ceaselessly and encompasses natural selection and artificial selection. CBET decouples natural selection from biological inheritance and calculates logarithmic fitness of various CBMs using the Malthusian formula. CBET accommodates major evolutionary phenomena—including niche construction, horizontal gene transfer, epigenetics, non-random mutation, coevolution, and neutral mutations—and subsumes the core viewpoints of the major theories of chemical, biological, and social evolution, yielding three derivative theories. It further proposes that human society has already entered a preliminary Global Unified Cooperative Society (GUCS). CBET also provides a systematic, positive, and balanced ethical reference that has the potential to dispel the negative ethical influence of Social Darwinism.

Abstract: Population genomics can improve mosquito control when genetic measurements are linked to specific design, deployment, and monitoring decisions. Here, we provide a decision-oriented framework for integrating population genetic data into conventional sterile insect technique (SIT), female-specific Release of Insects carrying a Dominant Lethal (fsRIDL), CRISPR-based precision-guided SIT (pgSIT), gene drives, Wolbachia-based incompatible insect technique (IIT), and Wolbachia population modification. These approaches have distinct biological requirements and failure modes. Immigration can replenish vector populations targeted by repeated sterile male or IIT releases; standing or newly generated functional escape alleles can impede the performance of homing gene drives; and Wolbachia establishment depends on cytoplasmic incompatibility, maternal transmission, host fitness, and spatial structure. We show how target site surveys, functional and compatibility assays, movement measurements, contained experiments, and spatial models can inform target selection, release stock preparation, release geography, and surveillance. We distinguish evidence from field trials—including mosquito suppression with IIT and reductions in dengue following IIT-SIT or Wolbachia population-modification releases—from gene-drive outcomes that remain pre-field. We argue that population genetic measurements are most useful when they lead to prespecified, testable decisions: local inputs should define forecast ranges, endpoints, and decision rules that can be evaluated against independent observations. Genomic structure alone cannot establish current movement, biological compatibility, field efficacy, or epidemiological benefit. Linking population genetic measurements to intervention-specific decisions and prospective validation provides a practical framework for translating mosquito genetic control from laboratory design toward responsible field deployment.

Abstract: Long terminal repeats (LTRs) of endogenous retroviruses (ERVs) contain transcription factor (TF)-binding motifs involved in interactions between ERVs and the host genome. We analyzed two LTR fragments from bovine placenta-expressed betaretroviruses, BERVK1 and BERV-beta3, to identify factors contributing to their sequence conservation across three distantly related species: Bos taurus, Oryctolagus cuniculus, and Apis cerana. Both fragments contain GGAGA, a noncanonical binding motif of the ETS-family transcription factor PU.1. Homologous sequences were identified in protein-coding genes, predominantly those associated with cytoskeletal remodeling, cell adhesion, and intercellular interactions. In several cases, these sequences occurred within conserved protein domains. Homologous sequences were also found in piRNAs involved in suppression of ERV activity, miRNA precursors in cattle and honey bees, and lncRNAs. Several factors may therefore contribute to the sequence conservation of K1 and beta3 fragments, including exaptation of ERV fragments, host regulatory motifs, localization within conserved domains of protein-coding genes, and a balance between TF binding and inhibition of ERV transcription. Multiple potential sources of conservation may provide a basis for more targeted genotyping by combining a conserved ERV LTR fragment with a protein-coding gene fragment from a specific functional module.

Abstract: Genetic engineering deliberately alters biological material, but the transmission, spread, and continued function of engineered variation remain subject to evolutionary processes. This structured narrative review compares engineered crops, insect gene drives, and engineered microbes through an origin–transmission–population fate framework, distinguishing control at the sequence, inheritance, and ecological levels. Crop studies document pollen-mediated gene flow, multi-year transgene persistence in a weedy relative, and pest resistance alongside regional pest suppression. Gene-drive studies demonstrate biased inheritance and collapse of particular cage populations, while resistance and ecological heterogeneity constrain extrapolation to other settings. Microbial studies show that construct burden, genetic exchange, and selection can undermine intended functions despite successful initial engineering and host colonization. Together, these findings distinguish molecular precision from control over inheritance, population persistence, and ecological outcomes: initial technical success does not establish lasting practical benefit. The review maps research designs to the claims they can support and identifies difficulties in comparison across systems, interpretation of evidence, and observation over relevant evolutionary time scales. Priorities include multigenerational monitoring, comparable measures of genetic persistence and functional stability, and staged, context-sensitive evaluation. The framework connects molecular intervention with population processes and clarifies the evidence needed for biosafety and governance decisions.

Abstract: Psychrophilic dinoflagellates are a group of microalgae that, together with psychrophilic diatoms, contribute to the functioning of cold-water ecosystems. One of the important species in these ecosystems is Peridiniella catenata, which is capable of developing both in under-ice waters and within sea ice. The species has been reported from northern marine waters ranging from the Baltic Sea to the coast of Canada. In the present study, we provide the first 18S and ITS2 rDNA sequences for this species and clarify its phylogenetic position based on three ribosomal markers (18S, ITS2, and 28S rDNA). We confirm the ability of P. catenata to develop under very low-salinity conditions. An extensive search for P. catenata-like sequences in DNA metabarcoding datasets indicates a broad distribution of closely related Peridiniella taxa. In particular, our results suggest that P. catenata or a closely related Peridiniella species may occur not only in the Northern Hemisphere but also in Antarctic waters.

Abstract: Understanding the interactions between agricultural management and seasonal climate variability is essential for maintaining soil biological sustainability and resilience. This study evaluated the effects of irrigation regime (irrigated vs. rainfed) and seasonality (autumn vs. spring) on rhizosphere microbiome diversity and composition using 16S and ITS amplicon metabarcoding during 2024–2026. Rainfed vineyards showed substantially higher bacterial richness (median Chao1: ≈1,220 vs. 710) and greater fungal diversity and richness than irrigated vineyards (Shannon H′: 4.71 vs. 3.86; Chao1: ≈595 vs. 335, re-spectively). PERMANOVA based on Bray–Curtis dissimilarity confirmed irrigation re-gime as the main structuring factor for bacterial (R² = 0.264, p = 0.042) and fungal communities (R² = 0.272, p = 0.005), whereas seasonality had no significant effect (p > 0.30). Taxonomic analysis revealed a marked dominance of Ascomycota under irrigation (80–98% relative abundance), accompanied by reduced fungal evenness. The bacte-ria-to-fungi ratio indicated a higher bacterial proportion under rainfed conditions and in autumn. These results suggest a plant-mediated buffering effect in the rhizosphere and indicate that continuous irrigation may promote microbial homogenization, potentially reducing soil biodiversity. Controlled deficit irrigation strategies may therefore help preserve microbial diversity and support soil functionality and resilience in Mediterra-nean vineyards.

Abstract:

The independent origins of plant parasitism in nematodes offer a classic model for studying the evolution of parasitic adaptations. Using comparative genomics, we analyzed representative nematodes from the superfamilies Aphelenchoidea and Tylenchoidea within the suborder Tylenchina, uncovering the genetic basis of cross-superfamily molecular convergence and lineage-specific divergence. Overall, sequence-level molecular convergence was relatively weak, reflecting dilution of evolutionary contrast by closely related ancestral genetic backgrounds and the diverse genetic mechanisms by which different lineages attain the plant-parasitic phenotype. Nevertheless, these two independently evolved parasitic lineages exhibited a predictable, general-purpose molecular arsenal for breaching host physical and immune barriers. At the metabolic level, the unsaturated fatty acid biosynthesis pathway (ko01040) underwent concordant and significant contraction across plant-parasitic lineages throughout the suborder, suggesting a possible shift toward greater reliance on host-derived lipids, although this remains to be functionally tested. At the sequence level, the two superfamilies displayed strong site-level convergence in core genes including host recognition (GRK, Tr-type G), effector protein folding (PDI), plant nitrogen assimilation (asparagine synthetase), and interfacial stress perception (DOMON, alkaline ceramidase), which may contribute to the molecular framework for breaching parasitic barriers and warrant further experimental validation. Building on this foundation, life-history and niche differentiation drove a dual-track paradigm. The Tylenchoidea lineage, represented by sedentary endoparasites, followed a path of large-scale genome-wide streamlining, with extensive outsourcing and degeneration of autonomous metabolic pathways, highly adapted to the stable internal environment of specialized root feeding sites. In contrast, the migratory parasitic Aphelenchoidea displayed a dual paradigm of conserved genome-wide metabolic versatility coupled with precise micro-level remodeling of stress-resistance networks, which we propose, as candidate hypotheses, may facilitate adaptation to the high-stress aerial environment and multiple hosts through micro-scale remodeling of mitochondrial stress responses, host-lipid utilization, and medium-sensing proteins. This contrast between macro-scale degeneration and micro-scale specialization provides a genomic perspective that may help inform future work on the origin and evolutionary radiation of parasitism in invertebrates.

Abstract: The crested francolin complex comprises geographically variable populations assigned to three African species, Ortygornis grantii, O. rovuma and O. sephaena. We examined phenotypic differentiation across Africa using 272 photographic records, museum specimens and mitochondrial data. Seven plumage characters were scored, with repeatability assessed by blind intra-observer rescoring of 61 stratified records. Breast markings, gorget-line position, abdominal feather structure and abdominal colour were retained for formal statistical inference. Gower ordination showed geographic structuring among eight historical forms, and PERMANOVA confirmed this pattern (R² = 0.717), although morphospace overlap persisted. Northeastern/eastern populations were predominantly high-gorget, whereas southern populations were mainly low-gorget, with intermediate combinations in eastern contact areas. Ugandan ochrogaster were high-gorget with a predominantly weak or fine abdominal vermiculation, differing strongly from neighbouring grantii. The form spilogaster showed weaker centroid separation from grantii than from rovuma, although mean Gower dissimilarities were similar. Mitochondrial divergence was lower between spilogaster and grantii (1.4%) than between spilogaster and rovuma (3.8%), supporting qualified placement with O. grantii. Southern O. sephaena forms also showed phenotypic structure despite shallow mitochondrial divergence. Overall, the results support geographically structured phenotypes and selected subspecific units within the established three-species framework. Several transitions remained clinal or overlapping rather than sharply bounded.

Abstract: Sea skaters of the genus Halobates (Heteroptera: Gerridae) are the only insects known to inhabit the open ocean, yet the relative importance of the environmental factors shaping their distributions remains poorly resolved. Prior work has emphasized sea-surface temperature as the primary constraint, but temperature, salinity, productivity, and ocean dynamics are tightly coupled in the ocean, and conventional importance metrics struggle to disentangle their contributions under collinearity. Here we apply SHAP (SHapley Additive exPlanations) analysis — combined with pairwise permutation testing and false discovery rate (FDR) correction — to quantify and compare the environmental drivers of distribution in three Halobates species: the widespread oceanic H. micans, the range-restricted H. sobrinus, and the coastal/neritic H. sericeus. Using spatially thinned occurrence records and eleven environmental predictors organized into physiological, physical habitat, and trophic tiers, we built species-specific Maxent models and decomposed their predictions into mean absolute and mean signed SHAP values. Contrary to the temperature-first emphasis of the prior literature, temperature, chlorophyll-a, and dissolved oxygen showed no significant pairwise differences between species in their net directional effects. Instead, only wind speed, annual variance in sea-surface salinity, and sea-surface height differed significantly between species after the FDR correction.

Abstract: The endangered Chinese horseshoe crab (Tachypleus tridentatus) suffers severe habitat degradation and coastal tourism disturbance across its nursery habitats along the Southeast China coast. Community based conservation (CBC) acts as a valuable complementary Other Effective area based Conservation Measure (OECM); yet few integrated domestic case studies combine ecological field monitoring with quantitative social ecological assessment. Based on the “Action for the Sea” supported Tangdong Horseshoe Crab Conservation Community in Fujian Province, this study integrates non destructive seasonal juvenile horseshoe crab surveys, questionnaire driven social ecological evaluation, coupling coordination and obstacledegree modelling, together with multi year project archival records. Results reveal that overlyingwater physicochemical parameters (temperature, salinity, pH) at Antenna Beach maintain suitable ranges for juvenile T. tridentatus across seasons, while juvenile abundance peaks temporally coincide with the peak tourist season. The tourism disturbance resilience socialecological system exhibits moderate coupling accompanied by mild dysfunctional coordination. Major bottlenecks include fragile volunteer capacity, incomplete conservation livelihood feedback loops, and tourism induced sociocultural pressures. This “science led local participation cultural tourism integration” practical model has obtained both domestic and international recognition. Targeted adaptive management measures are further proposed to support community based intertidal biodiversity conservation across the Asia Pacific region.

Abstract: This study assessed honeybee forage plant diversity, seasonal phenology, and beekeepers’ knowledge of forage resources and flowering calendars in selected zones of Tigray, Ethiopia. A cross-sectional survey using multistage sampling included 378 households from the Southern, Southeastern, and Eastern Zones. Data were collected through questionnaires, key informant interviews, and focus group discussions. Respondents identified 82 honeybee forage species belonging to 22 families, including 37 herbaceous species, 27 trees, and 18 shrubs, with Fabaceae, Asteraceae, and Lamiaceae among the dominant families. Forage resources showed pronounced seasonal variation in flowering richness, growth form complementarity, and nectar and pollen availability. Flowering richness ranged from 10 species in February to 38 in September. The forage gap index was highest in February (0.737), January (0.632), and March (0.553), identifying January–March as the critical forage dearth period, whereas September–November was resource rich. Nectar and pollen richness peaked in September. Age, education, and family size significantly influenced beekeepers’ forage knowledge, while education predicted flowering-calendar knowledge. Deforestation, agricultural expansion, and fuelwood production were major threats. Conserving diverse native forage plants and strengthening seasonal management are essential for sustaining floral resources and honeybee productivity in seasonally variable agroecosystems.

Abstract: Habitat degradation caused by anthropogenic disturbance is a major threat to global biodiversity, yet the spatiotemporal dynamics of the ecological intactness of giant panda habitat and the associated population responses remain poorly quantified. Focusing on the Sichuan section of the Giant Panda National Park and the Liangshan Mountains, using multi-source anthropogenic disturbance data and three national giant panda surveys, we integrated fuzzy overlay analysis, Theil–Sen trend analysis, Geodetector, and the Mann–Whitney U test to analyze the spatiotemporal dynamics, driving factors, and population responses of habitat intactness. The mean habitat intactness in 2020 was 6.70. Intactness declined slowly during 1980–2020, and 73.7% of the habitat remained stable. Land-use type and road construction were the dominant driving factors, and the explanatory power of any two interacting factors exceeded that of either factor alone. The intactness of giant panda occurrence sites was higher than that of random background points (significant in five of the six survey-by-region comparisons) and was higher in the Liangshan Mountains than in the national park. However, intactness was not significantly correlated with population density. These results indicate that wild giant pandas prefer high-intactness habitat, although intactness alone does not predict population density, and they provide empirical evidence for intactness-oriented conservation management.

Abstract: Large-language models (LLMs) are rapidly becoming part of human culture, reshaping how information is produced, transmitted, and used. Here we propose that their diffusion can be understood through a viral analogy, with LLM use spreading through populations, becoming embedded in cognitive and cultural practices. We model transitions among uncoupled, coupled, and persistently dependent users, and show that the interplay between social transmission, recovery, and collective reinforcement can generate tipping points and technological lock-in. A central consequence is the possibility of runaway dynamics: once a critical threshold is crossed, small increases in adoption can trigger rapid population-level shifts toward persistent dependence, with abrupt losses in cognitive competence. The same framework, however, identifies conditions for cognitive immunization, based on reducing transmission and facilitating reversibility. Our results highlight how LLM adoption may involve nonlinear collective transitions with important consequences for cognitive autonomy.