Category: Statistics

Evolution. 2025 Sep 5:qpaf177. doi: 10.1093/evolut/qpaf177. Online ahead of print.

ABSTRACT

Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation, such as adaptation, operate. Work in living clades has shown standing population-level variation fuels ecological speciation and gives rise to adaptive radiations. Despite its importance in evolutionary biology, the role of intraspecific variation in shaping phylogenetic and macroevolutionary patterns and processes has remained underexplored. I introduce a model of morphological evolution that accommodates polymorphism. The model describes the stochastic gain and loss of phenotypic character states within taxa, i.e., anagenesis, and the sorting of ancestral polymorphic variation during speciation, i.e., cladogenesis. I explore the behaviour of the model using simulations, then deploy it to reconstruct evolutionary relationships between the highly variable species belonging to the Cretaceous echinoid genus Micraster. The analysis revealed strong statistical support for several contentious relationships. The clade depicts a pattern where morphological variation accumulates within a small number of ancestral lineages and then is sorted into descendants without being fully replenished by anagenetic gains. This disproportionate maintenance of variation within early taxa and loss among later taxa could provide a link between the population processes that maintain intraspecific variation and the radiation and decline of clades.

PMID:40911295 | DOI:10.1093/evolut/qpaf177

Syst Biol. 2025 Sep 5:syaf061. doi: 10.1093/sysbio/syaf061. Online ahead of print.

ABSTRACT

For many questions in ecology and evolution, the most relevant data to consider are attributes of lineage pairs. Comparative tests for causal relationships among traits like ‘diet niche overlap’, ‘divergence time’, and ‘strength of reproductive isolation (RI)’ – measured for pairwise combinations of related species or populations – have led to several groundbreaking insights, but the correct statistical approach for these analyses has never been clear. Lineage-pair traits are non-independent, but unlike the expected covariance among species’ traits, which is captured by a phylogenetic covariance matrix arising from a given model, the expected covariance among lineage-pair traits has not been explicitly formulated. Analyses of pairwise-defined data have thus employed untested workarounds for non-independence rather than direct models of lineage-pair covariance, with consequences that are unexplored. Here, we consider how evolutionary relatedness among taxa translates into non-independence among taxonomic pairs. We develop models by which phylogenetic signal in an underlying character generates covariance among pairs in a lineage-pair trait. We incorporate the resulting lineage-pair covariance matrices into modified versions of phylogenetic generalized least squares and a new phylogenetic beta regression for bounded response variables. Both outperform previous approaches in simulation tests. We find that a common heuristic method, node averaging, imparts a greater cost to model performance than does the non-independence it was designed to correct. We re-analyze two empirical datasets to find dramatic improvements in model fit and, in the case of avian hybridization data, an even stronger relationship between pair age and RI than is revealed from uncorrected analysis. We finally present a new tool, the R package phylopairs, that allows empiricists to test relationships among pairwise-defined variables in a way that is statistically robust and more straightforward to implement.

PMID:40911284 | DOI:10.1093/sysbio/syaf061

MSMR. 2025 Aug 20;32(8):9-17.

ABSTRACT

Arboviruses pose a significant health threat to U.S. military personnel deployed in the U.S. Indo-Pacific Command (INDOPACOM) region. In 2023 we conducted a sero-epidemiological study to determine the arboviruses circulating in 185 Papua New Guinea military personnel (PNGMP), using the neutralizing antibody (NAb) assay. Overall, sero-positivity rates among the 185 PNGMP tested were: anti-Zika virus (ZIKV), 87% (n=161); anti-Japanese encephalitis virus (JEV), 62.2% (n=115); anti-Ross River virus (RRV), 44.3% (n=82); anti-Murray Valley encephalitis virus (MVEV), 39.5% (n=73); anti-chikungunya virus (CHIKV), 33.5% (n=62); anti-Barmah Forest virus (BFV), 10.8% (n=20); and anti-West Nile virus (WNV), 5.9% (n=11). The monotypic NAb sero-positivity rates for dengue virus (DENV) serotypes were: anti-DENV-1 94.6% (n=175), anti-DENV-2 93% (n=172), anti-DENV-3 95.1% (n=176), and anti-DENV-4 31.4% (n=57). These findings indicate that the majority of PNGMP had prior exposure to DENV and ZIKV, with a notable proportion exposed to CHIKV, RRV, JEV, and MVEV, and lower levels of exposure to BFV and WNV. Low or moderate prior exposure may leave individual PNGMP immunologically naïve and more susceptible to infection and disease upon first exposure. Furthermore, secondary DENV infections with a different serotype can increase risk of severe disease due to immune enhancement mechanisms such as antibody-dependent enhancement. Understanding these exposure patterns is crucial for assessing population risk and informing surveillance and prevention strategies. U.S. soldiers exercising or deploying to Papua New Guinea should adhere to strict preventive measures for minimizing mosquito bites and reducing their risk of arboviral infections. To our knowledge, this study provides the first comprehensive examination of arbovirus sero-positivity rates in Papua New Guinea military personnel (PNGMP) following the COVID-19 pandemic. After examining sero-positivity of 11 arboviruses, we found a majority of PNGMP with neutralizing antibodies (NAb) to dengue and Zika viruses, with some NAb to chikungunya, Japanese encephalitis, Ross River, and Murray Valley encephalitis viruses. Sero-prevalence to Barmah Forest and West Nile viruses was less common.

PMID:40911282

Fam Cancer. 2025 Sep 5;24(4):70. doi: 10.1007/s10689-025-00494-4.

ABSTRACT

This study compares three hereditary colorectal cancer (CRC) registries-the Iranian Hereditary Colorectal Cancer Registry (IHCCR), the Singapore Polyposis Registry (SPR), and the University of Cape Town Familial CRC Registry-to illuminate diverse approaches to identification, management, and research across different healthcare systems. Each registry, while emphasizing patient diversity, employed unique strategies reflecting available resources and epidemiological contexts. The IHCCR, leveraging WES, revealed considerable genetic heterogeneity, including novel mutations. The SPR, a nationalized service, focused on structured surveillance and management of FAP and other polyposis syndromes, highlighting the challenges of cultural conservatism and limited public awareness. The UCT registry, initially concentrating on Lynch syndrome, expanded to encompass other hereditary CRC syndromes, revealing a high prevalence of these conditions within the South African population. All three registries encountered challenges related to access to genetic testing and early diagnosis. The registries’ combined experiences underscore the critical need for integrated, culturally sensitive strategies combining genetic testing, enhanced surveillance, and family-based management to improve outcomes for individuals and families affected by hereditary CRC. Future efforts should focus on addressing disparities in access to care and expanding research to improve understanding and management of this complex disease.

PMID:40911264 | DOI:10.1007/s10689-025-00494-4

Pharmacol Rep. 2025 Sep 5. doi: 10.1007/s43440-025-00784-9. Online ahead of print.

ABSTRACT

BACKGROUND: The isobolographic analysis is a gold standard in the assessment of interactions between drugs in experimental studies. Although some isobolographic approaches are available, the most popular methods to characterize drug-drug interactions are the log-probit method accompanied with statistical analysis of interactions (by Tallarida) and the method based on mass-action law using CompuSyn software (elaborated by Chou-Talalay-Martin). The aim of this study was to compare the results from these two isobolographic approaches.

METHODS: Two isobolographic methods (log-probit associated with Tallarida statistics and Chou-Talalay-Martin) were applied to analyze the interaction between two antiseizure medications – clonazepam and lamotrigine in the mouse maximal electroshock-induced seizure model.

RESULTS: Both isobolographic approaches confirmed that the combination of clonazepam with lamotrigine produced synergistic interaction and allowed for detailed characteristics of the interaction at various effect levels for the two-drug mixture. Calculation of the combination index values (at various effect levels) confirmed that synergy slightly decreased when the antiseizure effect increased (combination index values increased from 0.44 for 16% to 0.65 for 84%).

CONCLUSIONS: The log-probit method with statistical analysis of data (by Tallarida) was more subtle and precise in the assessment of the synergistic interaction, whereas the isobolographic analysis by Chou-Talalay-Martin offered more automatic options facilitating visualization of the interaction.

PMID:40911251 | DOI:10.1007/s43440-025-00784-9

J Mol Model. 2025 Sep 5;31(10):264. doi: 10.1007/s00894-025-06486-6.

ABSTRACT

CONTEXT: This study systematically investigates the growth mechanism of nitrogen-doped graphene in a plasma environment, with a particular focus on the effects of temperature and hydrogen radicals on its structural evolution. The results reveal that, at 3000 K, the formation of nitrogen-doped graphene proceeds through three stages: carbon chain elongation, cyclization, and subsequent condensation into planar structures. During this process, nitrogen atoms are gradually incorporated into the carbon network, forming various doping configurations such as pyridinic-N, pyrrolic-N, and graphitic-N. An increase in temperature accelerates the reaction kinetics and cluster growth, but concurrently reduces the stability of nitrogen incorporation. Hydrogen radicals play a dual role: they help maintain the planar structure and suppress the curling of carbon clusters; however, excessive hydrogen radicals compete for edge-active sites, thereby inhibiting nitrogen doping efficiency. This work provides deeper insight into the growth mechanism of nitrogen-doped graphene and offers theoretical guidance for its efficient and controllable synthesis.

METHODS: In this study, we employed molecular dynamics (MD) simulations using the LAMMPS software package combined with the ReaxFF reactive force field to systematically investigate the growth mechanism of nitrogen-doped graphene in a plasma environment, as well as the effects of temperature and hydrogen radicals on its structural evolution. All simulations were performed in the NVT ensemble with a time step of 0.1 fs and a total simulation duration of 15,000 ps. To reduce variability and enhance the reliability of the results, each simulation was carefully repeated three times under identical conditions for subsequent statistical analysis.

PMID:40911219 | DOI:10.1007/s00894-025-06486-6

Bull Math Biol. 2025 Sep 5;87(10):145. doi: 10.1007/s11538-025-01522-1.

ABSTRACT

Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently surveyed in a book by Fischer et al. They are used to rank rooted binary trees on a scale from the most balanced to the least balanced. We show that a wide range of subtree-size based measures satisfying concavity and monotonicity conditions are minimized by the complete or greedy from the bottom (GFB) tree and maximized by the caterpillar tree, yielding an infinitely large family of distinct new imbalance indices. Answering an open question from the literature, we show that one such established measure, the $\hat{s}$ -shape statistic, has the GFB tree as its unique minimizer. We also provide an alternative characterization of GFB trees, showing that they are equivalent to complete trees, which arise in different contexts. We give asymptotic bounds on the expected $\hat{s}$ -shape statistic under the uniform and Yule-Harding distributions of trees, and answer questions for the related Q-shape statistic as well.

PMID:40911217 | DOI:10.1007/s11538-025-01522-1

J Math Biol. 2025 Sep 5;91(3):33. doi: 10.1007/s00285-025-02254-5.

ABSTRACT

Human movement plays a key role in spreading vector-borne diseases globally. Various spatial models of vector-borne diseases have been proposed and analyzed, mainly focusing on disease dynamics. In this paper, based on a multi-patch Ross-Macdonald model, we study the impact of host migration on the local and global host disease prevalences. Specifically, we find that the local disease prevalence of any patch is bounded by the minimum and maximum disease prevalences of all disconnected patches and establish a weak order-preserving property. For global disease prevalence, we derive its formula at both zero and infinite dispersal rates and compare them under certain conditions, and calculate the right derivative at no dispersal. In the case of two patches, we give two complete classifications of the model parameter space: one is to compare the host disease prevalences with and without host dispersal, and the other is to determine the monotonicity of host disease prevalence with respect to host dispersal rate. Numerical simulations confirm inconsistence between disease persistence and host disease prevalence, as well as between host prevalence and vector prevalence in response to host movement. In general, a more uneven distribution of hosts and vectors in a homogeneous environment leads to lower host prevalence but higher vector prevalence and stronger disease persistence.

PMID:40911201 | DOI:10.1007/s00285-025-02254-5

Equine Vet J. 2025 Sep 5. doi: 10.1111/evj.70091. Online ahead of print.

ABSTRACT

BACKGROUND: Superficial digital flexor tendon (SDFT) injuries cause progressive loss of its mechanical properties. Two-dimensional shear wave elastography (2D-SWE) provides information about tissue stiffness.

OBJECTIVE: To determine the feasibility, repeatability, and reproducibility of 2D-SWE of healthy and pathological forelimb SDFT.

STUDY DESIGN: Prospective observational cohort study.

METHODS: Horses were divided into a noninjured Group (H) and a Group with tendinopathy of the SDFT (P). 2D-SWE of both fore SDFTs was performed at three metacarpal levels (A, B, and C, from proximal to distal). Qualitative and quantitative assessments were performed by two operators, and interobserver agreement was calculated. Differences between Group H and P, and between the affected and unaffected limbs of Group P and with Group H were analysed. Statistical analysis was performed with SPSS IBM. Statistical significance was set for p < 0.05.

RESULTS: Thirty horses were enrolled (13 in Group H, 17 in Group P). Interobserver agreement was excellent to good. Qualitatively, in Group H, SDFT was from light to marked blue; in Group P, it appeared marked blue. Quantitatively, Group H had lower median mean shear wave velocity (SWV, m/s) and Young’s modulus (kPa) at levels B and C (SWV: 8.19 and 8.27 m/s vs. 8.47 and 8.48 m/s; Young’s modulus: 299.21 and 204 kPa vs. 216.03 and 214.44 kPa). In longitudinal scans, the unaffected limbs of Group P were different from the affected limb and from Group H at level B and in the transverse scan. The affected limbs of Group P were different from Group H in the transverse scan at levels B and C.

MAIN LIMITATIONS: Low sample size, examination of naturally occurring lesions, observational nature.

CONCLUSIONS: 2D-SWE is feasible as a supplementary diagnostic method for detecting SDFT tendinopathies. Clinically healthy SDFTs exhibit lower SWV and Young’s modulus values, suggesting less stiffness.

PMID:40910344 | DOI:10.1111/evj.70091

J Biol Dyn. 2025 Dec;19(1):2552730. doi: 10.1080/17513758.2025.2552730. Epub 2025 Sep 5.

ABSTRACT

The fear preoften leads to changes in the physiological characteristics of the prey. Different stages of prey exhibit different physiological behaviours, such as susceptibility to predator risk, which often leads to Allee effect. Taking into account the influence of these factors, a modified Leslie-Gower predator-prey model with Allee effect and stage structure is constructed in this paper. By use of variational technique and normal form theory, the criteria assuring the appearance of transcritical bifurcation, saddle-node bifurcation, Hopf bifurcation and its direction are all established. Specially, such codimension 2 bifurcations as Bautin bifurcation and Bogdanov-Takens bifurcation are presented. The bubble phenomenon and bistability are detected. All theoretical findings are verified by numerical examples. The biological effects of fear level, Allee effect and stage structure on system stability are analysed.

PMID:40910340 | DOI:10.1080/17513758.2025.2552730