Independent Populations Research Articles

BIA-assessed cellular hydration and strength in healthy older adults

ObjectivesThe objective of this research was to evaluate the differential relationships between various BIA-estimated compartments of body water and strength, among healthy older adults, by age range and sex. DesignDescriptive and correlational study. Setting and ParticipantsA total of 234 healthy older adults (72.59±7.60 years) participated in the study. Participants were recruited from community centers around Portugal and Spain. Data were recorded during May 2023. This is a physically active sample: all the participants are physically active for a minimum of three days a week. MethodsFor the study of body composition the variables extracted from the Tanita were: fat mass (FM), fat free mass (FFM), visceral fat rating (VFR), total body water (TBW), extracellular water (ECW) and intracellular water (ICW). Handgrip Strength was used to evaluate upper body strength and the Chair Stand Test for lower body strength. ResultsDifferences across the various data sets were recorded in the gender variable.When looking into the gender variable, significant correlations were recorded for the body composition variables analyzed for all age groups in the upper body strength test, except for BMI(r=0.125-0.878) and Fat mass (0.056 - -0.634). For the lower body strength test, no significant correlations were recorded for the Fat-Free mass variables (r= 0.164 - 0.380), as well as for the Visceral Fat Rating(r= 0.082 - 0.213) and the body water variables (TBW, ECW, ICW). ConclusionsThe hydration parameters analyzed can be related to muscle performance for Handgrip in an independent older adult population with ages ranging from 60 to 90 years.

Inference about a Common Mean Vector from Several Independent Multinormal Populations with Unequal and Unknown Dispersion Matrices

This paper addresses the problem of making inferences about a common mean vector from several independent multivariate normal populations with unknown and unequal dispersion matrices. We propose an unbiased estimator of the common mean vector, along with its asymptotic estimated variance, which can be used to test hypotheses and construct confidence ellipsoids, both of which are valid for large samples. Additionally, we discuss an approximate method based on generalized p-values. The paper also presents exact test procedures and methods for constructing exact confidence sets for the common mean vector, with a comparison of the local power of these exact tests. The performance of the proposed methods is demonstrated through a simulation study and an application to data from the Current Population Survey (CPS) Annual Social and Economic (ASEC) Supplement 2021 conducted by the U.S. Census Bureau for the Bureau of Labor Statistics.

Past activity of Sgr A⋆ is unlikely to affect the local cosmic-ray spectrum up to the TeV regime

Context The presence of kiloparsec-sized bubble structures on both sides of the Galactic plane suggests active phases of Sgr A⋆, the central supermassive black hole of the Milky Way in the last 1–6 Myr. We investigated the contribution of such events to the cosmic-ray (CR) flux measured in the solar neighborhood with numerical simulations. Aims. We evaluate whether the population of high-energy charged particles emitted by the Galactic center could be sufficient to significantly impact the CR flux measured in the solar neighborhood. Methods. We present a set of 3D magnetohydrodynamical simulations following the anisotropic propagation of CRs in a Milky Way-like Galaxy. We followed independent populations of CRs through time. We followed CRs originating from two different source types, namely supernovae and the Galactic center. To assess the evolution of the CR flux spectrum properties, we split these populations into two independent energy groups of 100 GeV and 10 TeV. Results. We find that the anisotropic nature of CR diffusion dramatically affects the amount of CR energy received in the solar neighborhood. The typical timescale required to observe measurable changes in the CR spectrum slope is of the order 10 Myr, largely surpassing estimated ages of the Fermi bubbles in the active galactic nuclei (AGN) jet-driven scenario. Conclusions. We conclude that a CR outburst from the Galactic center in the last few million years is unlikely have produced any observable feature in the local CR spectrum in the TeV regime within times consistent with current estimates of the age of the Fermi bubbles.

Unveiling vertical migration patterns of the mesopelagic fish Ceratoscopelus warmingii in cold seep ecosystems: A trophic niche perspective

Ceratoscopelus warmingii, a common mesopelagic fish in cold seep ecosystems, plays a crucial role in transferring energy and materials between different water layers, thereby influencing deep-sea carbon cycling and storage. In August 2023, we collected samples from four depths (75 m, 400 m, 500 m, and 600 m) in cold seep waters to analyze the trophic niche characteristics of C. warmingii using stable isotope techniques. The results indicated significant differences in δ13C and δ15N values among the water layers, with mean δ13C and δ15N values of −19.85 ‰±0.33 ‰ and 8.41 ‰±0.62 ‰, respectively. Indicators of trophic structure showed distinct vertical differentiation, with the width of the trophic niche decreasing as depth increased. At 75 m and 400 m, the consistency of CR and NR indicators and high trophic niche overlap indicated similar food sources, confirming vertical migration behavior. In contrast, at 500 m, the MNND and SDNND values suggested a more stable trophic structure, while at 600 m, changes in feeding sources pointed to a distinct population. The Standard Ellipse Area of Overlap (SEAc) was highest between 75 m and 400 m, while the divergence of trophic ecological niches at 600 m, with different food sources, suggests that cold seep ecosystems at this depth provide a relatively stable trophic structure for C. warmingii and support the formation of an independent population. In cold seep ecosystems, C. warmingii employs adaptive trophic strategies to optimize survival under varying habitat conditions at different depths. This vertical trophic differentiation reduces intraspecific competition and enhances population stability in deep-sea habitats. This study enhances our understanding of the trophic niche and vertical migration of C. warmingii in cold seep ecosystems, significantly contributing to our knowledge of biodiversity, energy flow, and material cycling in these unique environments.

Tracking the pre-clinical progression of transthyretin amyloid cardiomyopathy using artificial intelligence-enabled electrocardiography and echocardiography.

Diagnosing transthyretin amyloid cardiomyopathy (ATTR-CM) requires advanced imaging, precluding large-scale testing for pre-clinical disease. We examined the application of artificial intelligence (AI) to echocardiography (TTE) and electrocardiography (ECG) as a scalable strategy to quantify pre-clinical trends in ATTR-CM. Across age/sex-matched case-control datasets in the Yale-New Haven Health System (YNHHS) we trained deep learning models to identify ATTR-CM-specific signatures on TTE videos and ECG images (area under the curve of 0.93 and 0.91, respectively). We deployed these across all studies of individuals referred for cardiac nuclear amyloid imaging in an independent population at YNHHS and an external population from the Houston Methodist Hospitals (HMH) to define longitudinal trends in AI-defined probabilities for ATTR-CM using age/sex-adjusted linear mixed models, and describe discrimination metrics during the early pre-clinical stage. Among 984 participants referred for cardiac nuclear amyloid imaging at YNHHS (median age 74 years, 44.3% female) and 806 at HMH (69 years, 34.5% female), 112 (11.4%) and 174 (21.6%) tested positive for ATTR-CM, respectively. Across both cohorts and modalities, AI-defined ATTR-CM probabilities derived from 7,423 TTEs and 32,205 ECGs showed significantly faster progression rates in the years before clinical diagnosis in cases versus controls (p time × group interaction ≤0.004). In the one-to-three-year window before cardiac nuclear amyloid imaging sensitivity/specificity metrics were estimated at 86.2%/44.2% [YNHHS] vs 65.7%/65.5% [HMH] for AI-Echo, and 89.8%/40.6% [YNHHS] vs 88.5%/35.1% [HMH] for AI-ECG. We demonstrate that AI tools for echocardiographic videos and ECG images can enable scalable identification of pre-clinical ATTR-CM, flagging individuals who may benefit from risk-modifying therapies.

Long-term effects of widespread pharmaceutical pollution on trade-offs between behavioural, life-history and reproductive traits in fish.

In our rapidly changing world, understanding how species respond to shifting conditions is of paramount importance. Pharmaceutical pollutants are widespread in aquatic ecosystems globally, yet their impacts on animal behaviour, life-history and reproductive allocation remain poorly understood, especially in the context of intraspecific variation in ecologically important traits that facilitate species' adaptive capacities. We test whether a widespread pharmaceutical pollutant, fluoxetine (Prozac), disrupts the trade-off between individual-level (co)variation in behavioural, life-history and reproductive traits of freshwater fish. We exposed the progeny of wild-caught guppies (Poecilia reticulata) to three field-relevant levels of fluoxetine (mean measured concentrations: 0, 31.5 and 316 ng/L) for 5 years, across multiple generations. We used 12 independent laboratory populations and repeatedly quantified activity and risk-taking behaviour of male guppies, capturing both mean behaviours and variation within and between individuals across exposure treatments. We also measured key life-history traits (body condition, coloration and gonopodium size) and assessed post-copulatory sperm traits (sperm vitality, number and velocity) that are known to be under strong sexual selection in polyandrous species. Intraspecific (co)variation of these traits was analysed using a comprehensive, multivariate statistical approach. Fluoxetine had a dose-specific (mean) effect on the life-history and sperm trait of guppies: low pollutant exposure altered male body condition and increased gonopodium size, but reduced sperm velocity. At the individual level, fluoxetine reduced the behavioural plasticity of guppies by eroding their within-individual variation in both activity and risk-taking behaviour. Fluoxetine also altered between-individual correlations in pace-of-life syndrome traits: it triggered the emergence of correlations between behavioural and life-history traits (e.g. activity and body condition) and between life-history and sperm traits (e.g. gonopodium size and sperm vitality), but collapsed other between-individual correlations (e.g. activity and gonopodium size). Our results reveal that chronic exposure to global pollutants can affect phenotypic traits at both population and individual levels, and even alter individual-level correlations among such traits in a dose-specific manner. We discuss the need to integrate individual-level analyses and test behaviour in association with life-history and reproductive traits to fully understand how animals respond to human-induced environmental change.

Swordtail fish hybrids reveal that genome evolution is surprisingly predictable after initial hybridization.

Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common-not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni × X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.

Genome-wide re-sequencing reveals selection signatures for important economic traits in Taihang chickens

Taihang chickens is precious genetic resource with excellent adaptability and disease resistance, as well as high-quality eggs and meat. However, the genetic mechanism underlying important economic traits remain largely unknown. To address this gap, we conducted whole-genome resequencing of 66 Taihang and 15 White Plymouth rock chicken (Baiyu). The population structure analysis revealed that Taihang chickens and Baiyu are 2 independent populations. The genomic regions with strong selection signals and some candidate genes related to economic and appearance traits were identified. Additionally, we found a continuously selected 1.2 Mb region on chromosome 2 that is closely related to disease resistance. Therefore, our findings were helpful in further understanding the genetic architecture of the Taihang chickens and provided a worthy theoretical basis and technological support to improve high-quality Taihang chickens.

Association between calcium-channel blockers and gingival enlargement: A case-control study

ObjectivesAs reported by the existing literature, calcium-channel blockers (CCB) can lead to gingival enlargement. The aims of this study were to investigate the factors associated with gingival enlargement in patients on CCB and to assess the saliva and gingival crevicular fluid (GCF) profile of patients on CCB with gingival enlargement. MethodsA total of 131 participants were included. Data were collected from 91 patients taking CCB for treatment of systemic hypertension. The presence of drug-induced gingival enlargement (DIGE) was assessed clinically and associated with patient factors. Patients with DIGE were group-matched for gender and ethnicity with an equal number of consecutive CCB non-DIGE patients (control 1), no-CCB no-DIGE (control 2) and periodontally healthy with no DIGE (control 3) for the saliva and GCF analysis. A bead-based multiplex immunoassay was used to assess a panel of biomarkers. ResultsTwenty-two percent of patients on CCB were diagnosed with DIGE. Lack of daily interdental cleaning and self-reported diagnosis of type II diabetes were associated with the diagnosis of DIGE. When analysing patients only on CCB, those with DIGE had higher GCF levels of vascular endolthelial growth factor (VEGF) (p = 0.032), epidermal growth factor (EGF) (p = 0.030) and matrix metalloproteinase-8 (MMP-8) (p = 0.008). Among the salivary markers, only MMP-8 showed a statistically significant difference across groups (p < 0.001). ConclusionsThis is the first study investigating saliva and GCF biomarkers in patients with DIGE and different control groups, suggesting that causes of the overgrowth might involve inflammatory processes, tissue damage pathways, and potentially an impact on growth factors like VEGF. Future research should verify these results in independent populations and explore the underlying pathogenic mechanisms in-depth. Clinical significanceCalcium-channel blockers (CCB) can lead to gingival enlargement. This study confirms lack of interdental cleaning and type II diabetes as risk factors. Elevated levels of VEGF, EGF, and MMP-8 in gingival crevicular fluid and MMP-8 in saliva suggest inflammatory processes and growth factors might play roles in this condition.

A unified approach to long-term population monitoring of grizzly bears in the Greater Yellowstone Ecosystem

Long-term wildlife research and monitoring programs strive to maintain consistent data collections and analytical methods. Incorporating new techniques is important but can render data sets incongruent and limit their potential to discern trends in demographic parameters. Integrated population models (IPMs) can address these limitations by combining data sources that may span different periods into a unified statistical framework while providing a holistic view of population dynamics. We developed an IPM in a Bayesian framework for grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem. We coupled demographic data with multiple, independent population count data to link annual changes in abundance with vital rates over 4 decades (1983–2023). Abundance increased threefold from an estimated 270 individuals in 1984 to 1030 individuals in 2023. Parameter estimates indicated survival of bears ≥2 years of age was high, contributing to robust population growth during the 1980s (λ = 1.023 [50 % interquartile range = 0.993–1.082]) and 1990s (λ = 1.064 [1.023–1.103]). A slowing of population growth started around 2000 (2000s: λ = 1.030 [0.989–1.068]) and continued into the 2010s (λ = 1.021 [0.985–1.057]), due primarily to reductions in survival of bears <2 years of age. These findings corroborate previous research that identified density-dependent effects as a likely cause. The IPM framework provided greater certainty and understanding regarding the dynamic demographic characteristics of the population and serves as a powerful monitoring tool for this long-lived species. Implementation of the IPM allows timely dissemination of demographic data to help inform adaptive management strategies and policy decisions necessary for the continued management and conservation of this population. This robust and flexible monitoring system allows scientists to investigate the effects of a changing ecosystem on population dynamics, incorporate new data sources and statistical models, and respond to changes in monitoring needs for the population. We highlight the efficacy of the IPM in estimating and tracking demographic parameters for a long-lived species, while accommodating shifts in monitoring techniques and data collections typical of long-term wildlife conservation programs worldwide.

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs.

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

Plasmodium falciparum population dynamics in East Africa and genomic surveillance along the Kenya-Uganda border

East African countries accounted for ~ 10% of all malaria prevalence worldwide in 2022, with an estimated 23.8 million cases and > 53,000 deaths. Despite recent increases in malaria incidence, high-resolution genome-wide analyses of Plasmodium parasite populations are sparse in Kenya, Tanzania, and Uganda. The Kenyan-Ugandan border region is a particular concern, with Uganda confirming the emergence and spread of artemisinin resistant P. falciparum parasites. To establish genomic surveillance along the Kenyan-Ugandan border and analyse P. falciparum population dynamics within East Africa, we generated whole-genome sequencing (WGS) data for 38 parasites from Bungoma, Western Kenya. These sequences were integrated into a genomic analysis of available East African isolate data (n = 599) and revealed parasite subpopulations with distinct genetic structure and diverse ancestral origins. Ancestral admixture analysis of these subpopulations alongside isolates from across Africa (n = 365) suggested potential independent ancestral populations from other major African populations. Within isolates from Western Kenya, the prevalence of biomarkers associated with chloroquine resistance (e.g. Pfcrt K76T) were significantly reduced compared to wider East African populations and a single isolate contained the PfK13 V568I variant, potentially linked to reduced susceptibility to artemisinin. Overall, our work provides baseline WGS data and analysis for future malaria genomic surveillance in the region.

ARTEMIS: An independently validated prognostic prediction model of breast cancer incorporating epigenetic biomarkers with main effects and gene-gene interactions

IntroductionBreast cancer, a heterogeneous disease, is influenced by multiple genetic and epigenetic factors. The majority of prognostic models for breast cancer focus merely on the main effects of predictors, disregarding the crucial impacts of gene-gene interactions on prognosis. ObjectivesUsing DNA methylation data derived from nine independent breast cancer cohorts, we developed an independently validated prognostic prediction model of breast cancer incorporating epigenetic biomarkers with main effects and gene-gene interactions (ARTEMIS) with an innovative 3-D modeling strategy. ARTEMIS was evaluated for discrimination ability using area under the receiver operating characteristics curve (AUC), and calibration using expected and observed (E/O) ratio. Additionally, we conducted decision curve analysis to evaluate its clinical efficacy by net benefit (NB) and net reduction (NR). Furthermore, we conducted a systematic review to compare its performance with existing models. ResultsARTEMIS exhibited excellent risk stratification ability in identifying patients at high risk of mortality. Compared to those below the 25th percentile of ARTEMIS scores, patients with above the 90th percentile had significantly lower overall survival time (HR=15.43, 95 % CI: 9.57–24.88, P=3.06 × 10-29). ARTEMIS demonstrated satisfactory discrimination ability across four independent populations, with pooled AUC3-year = 0.844 (95 % CI: 0.805–0.883), AUC5-year = 0.816 (95 % CI: 0.775–0.857), and C-index = 0.803 (95 % CI: 0.776–0.830). Meanwhile, ARTEMIS had well calibration performance with pooled E/O ratio 1.060 (95 % CI: 1.038–1.083) and 1.090 (95 % CI: 1.057–1.122) for 3- and 5-year survival prediction, respectively. Additionally, ARTEMIS is a clinical instrument with acceptable cost-effectiveness for detecting breast cancer patients at high risk of mortality (Pt = 0.4: NB3-year = 0.019, NB5-year = 0.062; NR3-year = 69.21 %, NR5-year = 56.01 %). ARTEMIS has superior performance compared to existing models in terms of accuracy, extrapolation, and sample size, as indicated by the systematic review. ARTEMIS is implemented as an interactive online tool available at http://bigdata.njmu.edu.cn/ARTEMIS/. ConclusionARTEMIS is an efficient and practical tool for breast cancer prognostic prediction.

The Promoter Polymorphism rs3918226 of the Endothelial Nitric Oxide Synthase Gene as a Novel Susceptibility Marker for Peripheral Artery Disease

This pilot study aimed to investigate the association between the single nucleotide polymorphism (SNP) rs3918226 in the promoter of the nitric oxide synthase (NOS3) gene and the risk of peripheral artery disease (PAD). DNA samples from 1,263 unrelated subjects of Slavic origin, including 620 patients with PAD and 643 controls, were genotyped for the SNP rs3918226 using the MassArray-4 system. The rs3918226 polymorphism was found to be strongly associated with an increased risk of PAD regardless of coronary artery disease, hypertension, or cigarette smoking (odds ratio [OR]=2.86; 95% confidence interval [CI] 1.89-4.32; Pperm < 0.0001). The SNP-PAD association was almost 3 times stronger in females (OR=8.31; 95% CI 3.07-22.48) than in males (OR=1.79; 95% CI 1.10-2.93). SNP rs3918226 was correlated with ankle-brachial index and total plasma cholesterol in patients with PAD (Рperm < 0.05). The NOS3 polymorphism was closely associated with SNPs rs7692387 and rs13139571 in guanylate cyclase soluble subunit alpha-3 (GUCY1A3) to determine the risk of PAD, suggesting that the rs3918226 polymorphism may disrupt signaling in the NO-soluble guanylyl cyclase pathway. Diplotypes with wild-type alleles, such as NOS3 rs3918226-C/C×GUCY1A1 rs7692387G/G and NOS3 rs3918226-C/C×GUCY1A1 rs13139571C/C, showed strong protection against disease risk (false discovery rate ≤ 0.001). Functional SNP annotation revealed that the allele rs3918226-T was associated with decreased expression of NOS3, most strongly in the tibial arteries than in the coronary artery or aorta. The present study is the first to show that the rs3918226 polymorphism of NOS3 is a novel susceptibility marker for PAD. Further research in independent populations is necessary to reproduce the association between polymorphism rs3918226 and disease risk.

Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.

Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC1F2:5) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.

Smallmouth buffalo (Ictiobus bubalus Rafinesque) population trends and demographics in the Upper Mississippi River System

AbstractSmallmouth buffalo (Ictiobus bubalus Rafinesque) are a large-bodied fish highly valued and commercially exploited across most of their range. Despite this, relatively little is known of their population demographics compared to other exploited species. To fill these knowledge gaps, we analyzed two independent long-term datasets (30 and 57 years, respectively) and population demographic data (age structure, growth, mortality, age at maturity, and recruitment) from multiple pools of the Upper Mississippi River System (UMRS) and Illinois River (Illinois, USA). Long-term data (30-year dataset) generally show downward trends or significant declines in catch per unit effort in the UMRS, while the 57-year dataset shows a stable trend or a significant increase in the Illinois River. The oldest smallmouth buffalo were estimated to be 39 years old, with nearly every pool sampled having individuals estimated to exceed 30 years of age. Except for Pool 13 of the UMRS, 90% of smallmouth buffalo were estimated to mature between 411 and 470 mm in length or between 8.7 and 11.2 years old. Recruitment was variable: strong year classes were generally preceded by multiple years of weak year classes. Our results indicate that the smallmouth buffalo population may be stable in portions of the UMRS and Illinois River systems, but significant declines in the northern extent of the UMRS may warrant conservation concern. Recent research into ages of buffalofishes shows that consideration should be given to the idea that the UMRS population could be age truncated. Results also emphasize the importance of long-term data and the ability to show changes in exploited populations over time.

Intelligent optimization of inspection route based on multi-population integer coding particle swarm optimization algorithm

Aiming at the problems of premature convergence and slow convergence speed in the optimization process of single population particle swarm optimization algorithm, in order to improve the global convergence performance of particle swarm optimization algorithm, a hierarchical three-population integer coded particle swarm optimization algorithm based on grade evaluation with parallel structure is proposed and used to solve the traveling salesman problem (TSP). The algorithm imitates the form of biological aggregation in nature. In the initialization stage, three independent populations are generated according to different particle fitness, including an elite population composed of small-scale individuals with high fitness and two large-scale civilian populations composed of remaining individuals. The three populations apply the immigration strategy based on grade evaluation to exchange particles after a certain number of evolutionary generations. By applying the grade evaluation strategy, the natural law of the biological cluster is integrated into the particle swarm optimization algorithm, which effectively improves the optimization efficiency of the particle swarm optimization algorithm. The above algorithm is applied to the inspection route optimization of one of the traveling salesman problems. The results show that the improved algorithm is superior to the single population particle swarm optimization algorithm in terms of convergence speed, global optimization ability and stability.

Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population.

Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.

Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice.

The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.

Characterisation of phenotypic patterns in equine exercise-associated myopathies.

Equine exercise-associated myopathies are prevalent, clinically heterogeneous, generally idiopathic disorders characterised by episodes of myofibre damage that occur in association with exercise. Episodes are intermittent and vary within and between affected horses and across breeds. The aetiopathogenesis is often unclear; there might be multiple causes. Poor phenotypic characterisation hinders genetic and other disease analyses. The aim of this study was to characterise phenotypic patterns across exercise-associated myopathies in horses. Historical cross-sectional study, with subsequent masked case-control validation study. Historical clinical and histological features from muscle samples (n = 109) were used for k-means clustering and validated using principal components analysis and hierarchical clustering. For further validation, a blinded histological study (69 horses) was conducted comparing two phenotypic groups with selected controls and horses with histopathological features characterised by myofibrillar disruption. We identified two distinct broad phenotypes: a non-classic exercise-associated myopathy syndrome (EAMS) subtype was associated with practitioner-described signs of apparent muscle pain (p < 0.001), reluctance to move (10.85, p = 0.001), abnormal gait (p < 0.001), ataxia (p = 0.001) and paresis (p = 0.001); while a non-specific classic RER subtype was not uniquely associated with any particular variables. No histological differences were identified between subtypes in the validation study, and no identifying histopathological features for other equine myopathies identified in either subtype. Lack of an independent validation population; small sample size of smaller identified subtypes; lack of positive control myofibrillar myopathy cases; case descriptions derived from multiple independent and unblinded practitioners. This is the first study using computational clustering methods to identify phenotypic patterns in equine exercise-associated myopathies, and suggests that differences in patterns of presenting clinical signs support multiple disease subtypes, with EAMS a novel subtype not previously described. Routine muscle histopathology was not helpful in sub-categorising the phenotypes in our population.