Divergence Analysis Research Articles

GENETIC DIVERSITY ANALYSIS IN SOME LOW LAND RICE LANDRACES USING AGRO-MORPHOLOGICAL TRAITS

Forty four landraces of lowland rice were assessed for genetic diversity using D2 statistics based on various grain yielding parameters. Significant variability was found among the traits studied. Eight diverse clusters were made to set them into groups. The pattern of distribution of genotypes from different eco geographic regions into various clusters was at random indicating that geographical diversity and genetic diversity were not related. The maximum inter-cluster distance was observed between cluster III and IV (1033.15), followed by clusters II and VIII (935.07). Maximum intra-cluster distance was observed in cluster IV (731.01). Divergence analysis revealed significant variation among the parental lines for all the agro-morphological traits. Cluster analysis showed that superior cultivars like ‘Kanakchur’ from cluster IV; cv. ‘FR13A’, ‘Jaladhi2’, ‘Matla’ and ‘Purni’ from cluster III; cv. ‘Latisail’, ‘Pimpu Dibasa’, ‘Jeeringa Samba’ and ‘Shib Chato’ from cluster II; and cv. ‘ARC11210’, ‘Kumar Gore’, ‘NC678’, ‘Sada Mota’ and ‘Kantaranga’ from cluster VI may be taken in hybridization program, based on the genetic distance, relative contribution of characters towards total divergence and yield potential of genotypes. The characters viz., days to 50% flowering, plant height, panicle weight and number of grains panicle-1contributed maximum towards the divergence among genotypes taken for this study. So, allelic diversity among the genotypes and the concerned traits taken for this experiment should be taken into consideration while framing a rice breeding programme.

Validating the Turkish Adaptation of the Fear of Being Single Scale

AbstractPeople may experience anxiety regarding their future romantic relationship status. Fear of being single (FOBS) is a potential cause of this anxiety, characterized by distress about the idea of being single and assessed through the FOBS Scale. In the current study, the FOBS Scale was adapted into Turkish. The study included 349 individuals aged 28–55 years (M = 23.63 years, SD = 6.45 years). The reliability and validity of the measure and the associations with particular variables were investigated for the first time in the cultural context of Turkey. The confirmatory factor analysis revealed an acceptable model fit for the single‐factor structure. Measurement invariance of the scale across relationship status was supported at configural and metric levels, but not at the scalar level. The convergent and divergent validity analyses indicated that FOBS is distinct from generalized anxiety, attachment anxiety, and the personality trait of neuroticism. FOBS was found to be related to the need to belong but not to the inclusion of close others into the self. It has been determined that FOBS is a distinctive phenomenon, and the Turkish version of the FOBS Scale is a valid and reliable tool for assessing FOBS in Turkey.

Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Correlates.

Chimpanzees (Pan troglodytes) are humans' closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.

Short-term Kullback–Leibler divergence analysis to extract unstable periods in financial time series

Short-term Kullback–Leibler divergence analysis to extract unstable periods in financial time series

Genomics of hybrid parallel origin in Aquilegia ecalcarata

BackgroundThe parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear.ResultsIn this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata.ConclusionsOur results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.

First detection of Tetraparvovirus ungulate 1 in diseased cattle (Chinese Simmental) from Hunan province, China

Tetraparvovirus is an emerging parvovirus infecting a variety of mammals and humans, and associated with human diseases including severe acute respiratory infection and acute encephalitis syndrome. In the present study, a Tetraparvovirus ungulate 1 (formerly known as bovine hokovirus) strain HNU-CBY-2023 was identified and characterized from diseased Chinese Simmental from Hunan province, China. The nearly complete genome of HNU-CBY-2023 is 5346 nt in size and showed genomic identities of 85-95.5% to the known Tetraparvovirus ungulate 1 strains from GenBank, indicating a rather genetic variation. Phylogenetic and genetic divergence analyses indicated that Tetraparvovirus ungulate 1 could be divided into two genotypes (I and II), and HNU-CBY-2023 was clustered into genotype II. This study, for the first time, identified Tetraparvovirus ungulate 1 from domestic cattle from mainland China, which will be helpful to understand the prevalence and genetic diversity of Tetraparvovirus ungulate 1.

Cross-cultural adaptation, reliability and validity of the Greek version of the Spinal Appearance Questionnaire (SAQ) in patients with adolescent idiopathic scoliosis.

The Spinal Appearance Questionnaire (SAQ) is a widely validated tool for assessing perceptions of spinal deformity in adolescent idiopathic scoliosis (AIS) patients. This study aimed to develop and validate a Greek version of the SAQ (GR-SAQ). A cross-cultural adaptation of the SAQ following international guidelines was performed. Internal consistency and test-retest reliability were evaluated. Convergent validity was assessed by correlating the GR-SAQ with the Appearance domain of Scoliosis Research Society-22 (SRS-22) and the Cobb angle with the Trunk Shift domain of GR-SAQ. Divergent validity was examined through the relationship between GR-SAQ, patient characteristics, and clinical measures including Cobb angle, DIERS Formetric 4D angle, and scoliometer readings. The study included 61 AIS patients (52 females, 13.91 ± 2.57years, 25.33 ± 10.14° Cobb angle). GR-SAQ exhibited good internal consistency (Cronbach's α = 0.794) and excellent test-retest reliability (ICC = 0.931, 95%CI: 0.880-0.960). Correlations between GR-SAQ and SRS-22 showed a low-to-moderate negative correlation (r = -0.351, p = 0.006). The Trunk Shift domain moderately correlated with the Cobb Angle (r = 0.393, p = 0.002). Divergent validity analyses did not demonstrate statistical significance (p > 0.05). The GR-SAQ is a valid and reliable tool for evaluating spinal deformity perception in Greek AIS patients.

Genetic Divergence and Cluster Analysis for Bulb Yield and Related Traits in Garlic Genotypes at Fogera, Northwestern, Ethiopia

Identifying morphological variations among garlic genotypes is crucial for enhancing garlic breeding schemes. This study aimed to assess genetic diversity based on morphological traits of garlic genotypes. The experiment was conducted at the Fogera National Rice Research and Training Center, utilizing a simple lattice design with two replications for planting the genotypes. A total of 49 Ethiopian garlic genotypes were included in the study. Multivariate analysis methods were employed to assess approximately sixteen morphological characteristics. The genotypes were classified into five distinct clusters based on divergence analysis. Clusters 5 and 4 exhibited the highest inter-cluster distance (29.448), indicating genetic diversity. Conversely, clusters 3 and 1 showed the minimum inter-cluster distance, suggesting genetic similarity. Cluster 5 had the highest mean genotypes, indicating its potential for increasing genetic gain through heterosis breeding. Plant height contributed the most to variance, followed by leaf length, number of cloves per bulb, and total soluble solids. The first two principal components explained 74% of the overall variance. Therefore, this study underscores significant diversity in genotypes based on phenotypic characteristics, which could be valuable for future heterosis breeding programs.

Phylogenetic inferences based on distinct molecular markers reveals a novel Babesia (Babesia pantanalensis nov. sp.) and a Hepatozoon americanum-related genotype in crab-eating foxes (Cerdocyon thous)

Piroplasmids and Hepatozoon spp. Are apicomplexan protozoa that may cause disease in several canid species. The present study aimed to expand the knowledge on the diversity of piroplasmids and Hepatozoon in crab-eating foxes (Cerdocyon thous; n = 12) sampled in the Pantanal of Mato Grosso do Sul State, central-western Brazil. PCR assays based on the 18S rRNA were used as screening. Three (25%) and 11 (91.7%) were positive for piroplasmids and Hepatozoon spp., respectively. Co-infection was found in three C. thous. Phylogenetic analyses based on the near-complete 18S rRNA, cox-1 and hsp70 genes evidenced the occurrence of a novel of Babesia spp. (namely Babesia pantanalensis nov. sp.) closely related to Rangelia vitalii and Babesia sp. ‘Coco’. This finding was supported by the genetic divergence analysis which showed (i) high divergence, ranging from 4.17 to 5.62% for 18 S rRNA, 6.16% for hps70 and 4.91–9.25% for cox-1 and (ii) the genotype network (which displayed sequences separated from the previously described Piroplasmida species by median vectors and several mutational events). Also, phylogenetic analysis based on the 18S rRNA gene of Hepatozoon spp. positioned the sequences obtained herein in a clade phylogenetically related to Hepatozoon sp. ‘Curupira 2’, Hepatozoon sp. detected in domestic and wild canids from Uruguay and Hepatozoon americanum. The present study described Babesia pantanalensis nov sp. and Hepatozoon closely related to H. americanum in crab-eating foxes from Brazil. Moreover, the coinfection by piroplasmids and Hepatozoon sp. for the first time in crab-eating foxes strongly suggesting that this wild canid species potentially acts as a bio-accumulate of hemoprotozoan in wild environment.

Assessing genetic diversity of tomato (Solanum lycopersicum) genotypes cultivated under protected condition

Present study was carried out during 2018–19 and 2019–20 at ICAR-Indian Agricultural Research Institute, New Delhi to evaluate 16 quantitative and qualitative traits of 36 genotypes of Tomato (Solanum lycopersicum L.) and to examine the genetic variability and character association between yield and its component traits. This investigation involved correlation and genetic divergence analyses to gain insights into the relationships among the various traits. The variance analysis revealed notable variations among genotypes, indicating a substantial level of genetic diversity among them. Among the genotypes, 178 and 115 were found promising for both yield and quality traits. Genotype no. 178 was found superior for fruit weight and yield. The principal component analysis indicated that the first 3 components i.e. component 1 (equatorial diameter, average fruit weight and fruit weight uniformity); component 2 (number of locule and equatorial/polar index); and component 3 (number of fruit and number of fruit/cluster) collectively accounted for 81.48% of the variability. The yield exhibited significant positive correlation with average fruit weight (g), pericarp thickness (cm), polar diameter of fruit (cm), equatorial diameter of fruits (cm) and average fruit weight after each harvest (kg).

Characteristics and phylogenetic analysis of the complete chloroplast genome of Cornus hongkongensis Hemsl. 1888 (Cornaceae)

Cornus hongkongensis Hemsl. 1888, native to Hong Kong, belongs to the subgenus Syncarpea within the Cornus genus of the Cornaceae family. The complete chloroplast genome of C. hongkongensis spans 156,954 bp, comprising four subregions: a large single-copy region (86,290 bp), a small single-copy region (18,394 bp), and a pair of inverted repeats (26,135 bp). Within the chloroplast genome of C. hongkongensis, we identified 113 unique genes, including 80 protein-encoding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome of 30 related taxa of the Cornus genus indicates that C. hongkongensis has not formed a monophyletic lineage. Analyses of sequence divergence found three intergenic regions including rps19-rpl22, ccsA-ndhD, and atpH-atpI, exhibiting a high degree of variations. The first chloroplast genome of C. hongkongensis was reported in this work contributes to the enrichment of genomic data for the genus Cornus.

Studies on the Variability of Indigenous Mulberry Germplasm for Growth and Yield Traits

Twenty two indigenous mulberry accessions were evaluated for growth and yield traits in three seasons. ANOVA on growth and yield showed significant variation among the accessions for the traits. The interaction between accession and season was highly significant for all traits. The co-efficient of variation was maximum for single leaf weight (17.08%) and minimum for total shoot length (0.08%). The divergence analysis grouped 22 indigenous mulberry accessions into 5 clusters. Maximum accessions were grouped in clusters I & II (8 acc.) followed by cluster V (4 acc.). The diversity among the accessions measured by inter-cluster distance (D2) showed variation. The cluster group indicates that mulberry accessions were distributed in different clusters irrespective of geographical distribution.

In-Depth Characterization of bZIP Genes in the Context of Endoplasmic Reticulum (ER) Stress in Brassica campestris ssp. chinensis.

Numerous studies have been conducted to investigate the genomic characterization of bZIP genes and their involvement in the cellular response to endoplasmic reticulum (ER) stress. These studies have provided valuable insights into the coordinated cellular response to ER stress, which is mediated by bZIP transcription factors (TFs). However, a comprehensive and systematic investigations regarding the role of bZIP genes and their involvement in ER stress response in pak choi is currently lacking in the existing literature. To address this knowledge gap, the current study was initiated to elucidate the genomic characteristics of bZIP genes, gain insight into their expression patterns during ER stress in pak choi, and investigate the protein-to-protein interaction of bZIP genes with the ER chaperone BiP. In total, 112 members of the BcbZIP genes were identified through a comprehensive genome-wide analysis. Based on an analysis of sequence similarity, gene structure, conserved domains, and responsive motifs, the identified BcbZIP genes were categorized into 10 distinct subfamilies through phylogenetic analysis. Chromosomal location and duplication events provided insight into their genomic context and evolutionary history. Divergence analysis estimated their evolutionary history with a predicted divergence time ranging from 0.73 to 80.71 million years ago (MYA). Promoter regions of the BcbZIP genes were discovered to exhibit a wide variety of cis-elements, including light, hormone, and stress-responsive elements. GO enrichment analysis further confirmed their roles in the ER unfolded protein response (UPR), while co-expression network analysis showed a strong relationship of BcbZIP genes with ER-stress-responsive genes. Moreover, gene expression profiles and protein-protein interaction with ER chaperone BiP further confirmed their roles and capacity to respond to ER stress in pak choi.

Automatic Associations between Sexual Function Problems and Pursuing Help in Pelvic Physical Therapy Practice: The Psychometric Investigation of an Implicit Association Test

Not all women experiencing pelvic floor complaints and sexual function problems seek help in pelvic physical therapy practice. Decisions to seek help can result from explicit and implicit cognitive processes. Having found some explicit predictive factors for receiving help in this setting, this study examines possible complementary implicit associations between sexual function problems and pursuing help that might also be predictive. The Pursuing Help for Sexual Problems Implicit Association Test (PHSP-IAT) was specially developed for this purpose. The instrument’s reliability and validity were evaluated. High reliability was found (Spearman’s Rho = .95). Convergent and divergent validity analyses resulted in low and non-significant correlations between the PHSP-IAT and the chosen self-report measures. The PHSP-IAT was predictive for receiving help in pelvic physical therapy practice. Further research is necessary to determine the PHSP-IAT’s validity and its predictive value in other healthcare settings.

Exploring Genetic Divergence in Cowpea: A Comprehensive Review

Genetic divergence in cowpea (Vigna unguiculata L. Walp) presents a compelling area of study with profound implications for breeding programs, crop improvement strategies, and agricultural sustainability. This abstract encapsulates a comprehensive review of the genetic divergence observed within cowpea populations. By examining the genetic diversity, population structure, and molecular markers employed in cowpea research, this review aims to elucidate the underlying genetic mechanisms driving divergence within the species. The review explores the ecological and geographical factors influencing genetic differentiation, as well as the implications for breeding objectives and germplasm conservation. Furthermore, it discusses the potential applications of genetic divergence analysis in enhancing crop adaptation, resilience, and productivity in diverse agroecological contexts. Through a synthesis of current research findings and emerging trends, this review provides valuable insights into the genetic architecture of cowpea and its implications for sustainable crop improvement strategies.

Analysis of genetic divergence in Psidium cattleyanum Sabine accessions based on morphological fruit descriptors

Analysis of genetic divergence in Psidium cattleyanum Sabine accessions based on morphological fruit descriptors

Port Access Fluidity Management during a Major Extension Project: A Simulation-Based Case Study

The increasing demand for freight services and the use of larger vessels to meet this demand has led to challenges related to storage space and logistics activities, highlighting the need for improvements in port infrastructure for better logistics management. At a crucial phase in its growth, the Port of Trois-Rivières in Canada is planning a major expansion, including the construction of a new terminal to enhance its hosting capacities and freight services. This expansion faces potential access congestion problems during the planned construction, exacerbated by the port’s urban setting. In response to the needs identified by the port authorities for this event, the study’s objective is to assess the implications of increased construction and freight truck flows on access gate fluidity and the impact of additional access infrastructure investment to mitigate potential congestion. These evaluations aim to define effective access management strategies throughout the construction period of the new terminal. To address these complexities, our approach is based on scenario analysis in variants co-constructed with the partner. These scenarios are evaluated using simulation models, configured according to parameters calibrated with a granularity that allows congestion detection. The results enabled an evaluation of the capability of existing and potential gates to manage access. Subsequently, recommendations were shaped in accordance with the expected objectives to manage access traffic effectively. These recommendations concern the optimization of construction activity planning, the layout and planning of access, and the importance of enhanced collaboration between municipal and port authorities for more controlled road traffic management. Recognizing the importance of synchromodality, road network centrality management, and the outsourcing of capacity through inter-port cooperation and with dry ports to manage congestion, these tools will be discussed in this work. The study proposes an approach that reconciles scientific rigor with the implementation constraints of the proposed solutions, allowing this study wider applicability in various port contexts facing challenges in this field of study.

Effect of Correlation and Path Analysis in Brinjal (Solanum melongena L.)

The present investigation was carried out in thirty two genotypes of brinjal with a view to estimate the extent of variability, analysis of variance and genetic divergence. The experiment was conducted in Randomized Block Design with three replications at Department of Vegetable Science, Acharya Narendra Deva University of Agriculture and Technology Narendra Nagar, (Kumarganj), Ayodhya (U.P.), during Kharif, 2020-21. Each treatment consisted of twelve plant in two rows, having spacing of 60 cm x 50 cm with net plot size of 1.2 m x 3.00 m2. The magnitudes of genotypic correlation was higher than the phenotypic correlation coefficients for all the character combinations. The most important trait, total fruit yield per plant had exhibited highly significant and positive phenotypic correlation with average fruit weight (0.747), number of fruits per plant (0.672) and fruit circumference (0.468) at both phenotypic and genotypic levels. Positive direct effect on total fruit yield was exerted by total sugars (0.474), average fruit weight (0.396), fruit circumference (0.358), number of fruits per plant (0.254), plant height (0.242), fruit polar length (0.194) and day to 50 % flowering (0.168). The higher magnitude of positive direct effect on total fruit yield was exerted by total sugars (0.474), average fruit weight (0.396), fruit circumference (0.358), number of fruits per plant (0.254), plant height (0.242), fruit polar length (0.194), day to 50 % flowering (0.168).

Chromosomal-Level Reference Genome for the Chinese Endemic Pygmy Grasshopper, Zhengitettix transpicula, Sheds Light on Tetrigidae Evolution and Advancing Conservation Efforts.

The pygmy grasshopper, Zhengitettix transpicula, is a Chinese endemic species with an exceedingly limited distribution and fragile population structure, rendering it vulnerable to extinction. We present a high-continuity, chromosome-scale reference genome assembly to elucidate this species' distinctive biology and inform conservation. Employing an integrated sequencing approach, we achieved a 970.40 Mb assembly with 96.32% coverage across seven pseudo-chromosomes and impressive continuity (N50 > 220 Mb). Genome annotation achieves identification with 99.2% BUSCO completeness, supporting quality. Comparative analyses with 14 genomes from Orthoptera-facilitated phylogenomics and revealed 549 significantly expanded gene families in Z. transpicula associated with metabolism, stress response, and development. However, genomic analysis exposed remarkably low heterozygosity (0.02%), implying a severe genetic bottleneck from small, fragmented populations, characteristic of species vulnerable to extinction from environmental disruptions. Elucidating the genetic basis of population dynamics and specialization provides an imperative guideline for habitat conservation and restoration of this rare organism. Moreover, divergent evolution analysis of the CYP305m2 gene regulating locust aggregation highlighted potential structural and hence functional variations between Acrididae and Tetrigidae. Our chromosomal genomic characterization of Z. transpicula advances Orthopteran resources, establishing a framework for evolutionary developmental explorations and applied conservation genomics, reversing the trajectory of this unique grasshopper lineage towards oblivion.

Genetic Divergence Analysis of Wheat (Triticum aestivum L.) Genotypes

A laboratory experiment was carried out with 30 indigenous genotypes of bread wheat along with three checks in a complete randomized design for divergence analysis. The trial was conducted at Seed Technology laboratory of Acharya Narendra Deva University of Agriculture and Technology Kumarganj, Ayodhya during 2020-21. The observations were recorded on thirteen-character Test weight (1000-grain weight), seed width (mm), seed length (mm), shoot length, root length, seedling length, seedling dry weight, germination (%), first count, final count, vigour index-I, vigour index-II. The 30 genotypes grouped into 5 clusters resulted in cluster I and V emerging with highest number of entries as both were constituted by 9 entries followed by Cluster III having 6 genotypes and cluster II and VI having 4 genotypes respectively. The maximum intra cluster distance was estimated in the case of Cluster II (2.630) followed by cluster I (2.618), Cluster III (2.545), cluster IV (2.512), and cluster V (2.148). The highest inter-cluster distance was observed between clusters III and IV (6.062) Followed by clusters III and V (4.632), II and IV (4.489), cluster II and V ( 4.304). The minimum inter cluster was observed between II and III (3.317) followed by cluster IV and V ( 3.337) and cluster I and V (3.404). The cluster mean of 13 different characters for most of the character's highest cluster mean was observed in clusters IV and V and lowest cluster mean observed in cluster III and II.