International Journal of Molecular Ecology and Conservation, 2025, Vol.15 http://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
International Journal of Molecular Ecology and Conservation, 2025, Vol.15 http://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. EcoEvoPublisher is an international Open Access publishing platform that publishes scientific journals in the field of ecology and evolution registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher EcoEvo Publisher Editedby Editorial Team of International Journal of Molecular Ecology and Conservation Email: edit@ijmec.ecoevopublisher.com Website: http://ecoevopublisher.com/index.php/ijmec Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada International Journal of Molecular Ecology and Conservation (ISSN 1927-663X) is an open access, peer reviewed journal published online by EcoEvoPublisher. The journal is considering all the latest and outstanding research articles, letters and reviews in all aspects of molecular ecology and conservation, containing the contents of the ranges from the applied to the theoretical in molecular ecology and nature conservation, the policy and management with comprehensive and applicable information; the ecological bases for the conservation of ecosystems, species, genetic diversity, the restoration of ecosystems and habitats; as well as the expands the field of ecology and conservation work. All the articles published in International Journal of Molecular Ecology and Conservation are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. EcoEvoPublisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
International Journal of Molecular Ecology and Conservation (online), 2025, Vol. 15, No.2 ISSN 1927-663X https://ecoevopublisher.com/index.php/ijmec © 2025 EcoEvoPublisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Phylogenetic Reconstruction and Genomic Adaptive Evolution in Siniperca spp. Chengmin Sun, Rudi Mai International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2, 54-62 Research on Biological Control Technologies and Mechanism Analysis of Common Pests and Diseases in Chrysanthemum morifolium(Hangbaiju) Jianli Lu, Chuchu Liu International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2, 63-73 Population Structure and Genetic Adaptation of Domestic and Wild Ducks Across Different Climatic Regions Xian Li, Qibin Xu International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2, 74-82 Genetic and Environmental Factors Controlling Tuber Shape in Commercial Varieties Dandan Huang, Zhen Li International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2, 83-90 The Research on Green Control Strategies and Techniques for Major Pests and Diseases of Sapindus mukorossi Jie Zhang, Jianhui Li International Journal of Molecular Ecology and Conservation, 2025, Vol. 15, No. 2, 91-100
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 54 Research Insight Open Access Phylogenetic Reconstruction and Genomic Adaptive Evolution inSinipercaspp. Chengmin Sun1, RudiMai 2 1 Center for Tropical Marine Fisheries Research, Hainan Institute of Tropical Agricultural Resouces, Sanya, 572025, Hainan, China 2 Tropical Biological Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding author: rudi.mai@hitar.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2 doi: 10.5376/ijmec.2025.15.0006 Received: 18 Jan., 2025 Accepted: 24 Feb., 2025 Published: 06 Mar., 2025 Copyright © 2025 Sun and Mai, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Sun C.M., and Mai R.D., 2025, Phylogenetic reconstruction and genomic adaptive evolution in Siniperca spp., International Journal of Molecular Ecology and Conservation, 15(2): 54-62 (doi: 10.5376/ijmec.2025.15.0006) Abstract Siniperca or Chinese perch is a freshwater fish family indigenous to East Asia, of great economic value and ecological particularity. Though of great significance in aquaculture, the phylogenetic histories of the Siniperca genus are unclear due to morphological convergence and a dearth of molecular data. We rebuilt the genome-wide single-copy orthologous genes-based phylogenetic framework of Siniperca and inferred divergence times between species using a molecular clock model in this study. We further performed comparative genomics to identify expansions of gene families, positive selection signals, and adaptive evolutionary trajectories linked with ecological specialization. Several genetic candidates for environmental tolerance, immune response, and sensory systems were detected, suggesting lineage-specific adaptation to various freshwater environments. This study not only illuminates the phylogenetic history of Siniperca, but also reveals the genetic mechanism of its adaptive divergence, providing theoretical evidence for species conservation, utilization of resources, and molecular breeding in aquaculture. Keywords Siniperca; Phylogenetic reconstruction; Comparative genomics; Adaptive evolution; Freshwater fish 1 Introduction The Siniperca genus is a family of freshwater fish endemic to East Asia in the Sinipercidae family. It contains some of its species such as S. chuatsi, S. scherzeri, S. kneri, and S. undulata, which are found mainly in the Yangtze, Pearl, and Amur river basins. They are carnivorous species, solitary, and prefer clean, slow-moving freshwater environments. Despite their ecological divergence, their phylogenetic relationships and placements within the genus are controversial due to convergent morphological features coupled with limited molecular markers (Liang et al., 2019; Zhang et al., 2023). Advances in genome sequencing coupled with phylogenomic methods in the past few years have paved new ways in resolving these taxonomic ambiguities as well as their evolution. Siniperca chuatsi (mandarin fish) and S. scherzeri are two of the most valuable Chinese freshwater aquaculture species, with high consumer demand and excellent meat quality, and they grow rapidly. The production of S. chuatsi has been more than 300,000 tons each year, becoming China's pillar of carnivorous fish production (Zhao et al., 2017; Chen et al., 2020). However, high-level production has brought with it new issues, including more frequent outbreak of disease, reduced genetic variation, and depression in inbreeding. They have generated growing interest in using molecular technologies like whole-genome selection, marker-assisted breeding, and genome-wide association studies to improve desirable traits including disease resistance, growth rate, and feed efficiency (Chen et al., 2020). A good understanding of the evolutionary and genetic basis of these traits is required to guide upcoming breeding programmes. Phylogenetic analysis forms the foundation of understanding speciation, the evolution of traits, and the conservation of biodiversity. In this genomics era, having the capability to combine high-throughput sequencing with phylogenomics enables scientists to have the ability to uncover ancient evolutionary relationships and identify genomic regions under selection. In Siniperca spp., where there has been ecological divergence and niche specialization, the integration of phylogenetic reconstruction and adaptive evolution analysis encapsulates how these fishes evolve to respond to environmental stresses such as temperature, turbidity, and prey availability. In addition, investigations of positively selected genes and fast-evolving gene families can reveal genetic
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 55 mechanisms of carnivory, metabolic thrift, and immunity. These findings not only enhance evolutionary biology but also have applied relevance to genetic improvement and conservation strategies. 2 Genetic Basis and Evolutionary Characteristics of Siniperca Species 2.1 Species composition and current research on phylogenetic relationships Siniperca is comprised of a series of freshwater species that are spread across East Asia, mainly China, with two dominant genera, Siniperca and Coreoperca. Interspecific relationships, Sinipercidae monophyly, and species boundaries have been explained through recent phylogenetic analysis using thousands of nuclear coding sequences and next-generation sequencing methods. For example, S. scherzeri has been determined to be the most basal taxon of Siniperca, and species delimitation analyses confirmed the singularity of S. chuatsi and S. kneri, within closely related species pairs. Estimates of divergence times suggest that Sinipercidae's ancestor evolved in southern China over 50 million years ago and was shaped by the subsequent historical climatic and geological events (Zhao et al., 2017). 2.2 Genetic diversity and phenotypic differentiation of germplasm resources Genetic diversity in F1 and F2 generations of interspecific hybrids between S. chuatsi and S. scherzeri is extensive, as shown by hybrids and natural populations analyses. F1 and F2 generations from the hybridization between S. chuatsi and S. scherzeri possess greater genetic diversity and extensive morphological differentiation, especially for F1 hybrids. Microsatellite and SNP analyses indicate that hybrid and backcross populations maintain intermediate or higher levels of heterozygosity than parental species, indicative of their vigorous breeding power. There are particular molecular markers used in identifying hybrids and genetic breeding schemes. Population analysis of S. scherzeri within the Pearl River drainage also identified particular genetic lineages due to vicariance and demographic history, highlighting the genetic intricacy of the genus (Zhang et al., 2022; Chen et al., 2024) (Figure 1). Figure 1 Morphology of the S. chuatsi ♀ ×S. scherzeri ♂, F1, F2, and backcross hybrids (Adopted from Chen et al., 2024) Image caption: a: S. chuatsi, b: S. scherzeri, c: F1 (CS), d: CS-C (81%), e: C-CS (19%), f: F2 large size (97%), g: F2 small size (3%) (Adopted from Chen et al., 2024) 2.3 Potential adaptive traits and mechanisms of ecological divergence Comparative and genomic studies have revealed adaptive characters and molecular routes of ecological divergence in Siniperca. Differentially expressed genes for metabolism, pigmentation, and the immune system are triggered by structural variants impacting cis-regulatory elements leading to phenotypic diversity among closely related species, e.g., S. chuatsi and S. scherzeri. Gene family expansion and positive selection are linked to features like predatory feeding, growth, and habitat tolerance. For instance, adaptive gene evolution for feeding and aggression-related genes occurs quickly, while gene family diversity for growth, immunity, and mobility explains niche preference between species like S. undulata and S. obscura. Such findings emphasize the role of genomic structure and evolution in ecological adaptation control among Siniperca species (Chen et al., 2020; Zhang et al., 2022; Jiang et al., 2023).
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 56 3 Phylogenetic Reconstruction and Analytical Methods 3.1 Sample collection and genome data construction strategies Phylogenetic reconstruction must be done with cautious broad sampling, in which all aspects of taxonomic and geographic diversity of Siniperca species are covered. Multiple samples have been enabled to generate genome-scale data through next-generation sequencing and significantly improved the resolution and power of phylogenetic inference. Approaches entail whole-genome sequencing, enrichment of targeted nuclear coding regions, and strict sequencing quality control of the data to limit errors and achieve maximum coverage (Young and Gillung, 2019; Dissanayake, 2020). 3.2 Identification and alignment of single-copy orthologous genes A critical part of phylogenomics is the identification of single-copy orthologous genes, excellent markers for making inferences about evolution. The process is eased by bioinformatic pipelines that clip gene families so that only those that occur as single copies in every sampled taxon remain. High-quality multiple sequence alignments are then generated within these genes, as the quality of the alignments directly impacts the validity of resulting phylogenetic analysis (Young and Gillung, 2019; Dissanayake, 2020). 3.3 Phylogenetic tree construction and divergence time estimation Phylogenetic trees are also constructed using a number of methods, including maximum likelihood, Bayesian inference, and distance-based approaches. Maximum likelihood and Bayesian methods are applied as they are more precise, especially with genome-scale data, though it is computationally costly. RAxML and IQ-TREE are some of the programs used in tree estimation. Divergence time estimation applies molecular clock models and fossil calibrations to infer divergence timing, putting observed patterns into a background of evolution (Horiike, 2016; Kendall et al., 2018; Young and Gillung, 2019). 3.4 Topological interpretation and taxonomic implications of phylogenetic results Phylogenetic tree topology analysis is the driving force to the realization of evolutionary relationships and to taxonomic recast direction. Well-supported phylogenomic frameworks will resolve past evolutionary disputes, define species limits, and reveal diversification patterns. Phylogenetic results combined with morphological and ecological information enable improved species delimitation and can uncover new taxa or recast those previously recorded. Methodological integrity, including artefact detection and control and model violation, is crucial for ensuring reliability in taxonomic conclusions ( Young and Gillung, 2019; Struck et al., 2023). 4 Comparative Genomics and Detection of Adaptive Evolution Signals 4.1 Gene family expansion/contraction analysis and functional enrichment In Siniperca species, comparative genomics has been used successfully to interpret gene family expansions and contractions—those significant signatures of adaptive evolution. Scientists have found extensive expansions of gene families involved in immune response, sensory perception (e.g., vision and smell), and energy metabolism. These tendencies are most probably adaptations to the predatory life style, environmental heterogeneity, and enhanced prey detection ability in a range of aquatic habitats. Functional enrichment analyses have revealed that the gene families are overrepresented in biological processes such as immune defense, nutrient acquisition, and responding to environmental stimuli, suggesting that gene family evolution is closely linked with ecological specialization and evolutionary innovation (Steffansson et al., 2004; Regev et al., 2015; Csilléry et al., 2018). 4.2 Screening of positively selected genes and identification of rapidly evolving regions Since Siniperca differentiated into various species, certain genes have undergone strong positive selection in adapting to the evolutional environment. Identification of such genes is typically achieved by estimating the nonsynonymous to synonymous substitution ratio (dN/dS) and site-specific evolutionary models. Advances such as Bayesian inference and machine learning techniques such as convolution neural networks and transfer learning have improved the identification of rapidly evolving genomic regions. These approaches are especially powerful in Siniperca to detect candidate genes for the polygenic traits of feeding behavior, aggressiveness, and temperature tolerance where scientists can detect recent positive selection even in polygenic trait scenarios (Csilléry et al., 2018; Lartillot et al., 2020; DeGiorgio et al., 2025).
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 57 4.3 Candidate genes related to environmental adaptation and their biological functions Most of the candidate genes uncovered by positive selection analysis or gene family evolution analysis in Siniperca are involved in key functions of environmental adaptation, including immune regulation, sensory perception (especially olfaction and vision), reproduction, and stress response. These functions are critical for Siniperca species to adapt to freshwater systems with fluctuating thermal, oxygen, and feeding regimes. Functional enrichment and annotation analysis also connect these genes to important adaptive characters such as disease resistance, prey specialization, and environmental stress tolerance and shed light on their ecological functions in evolutionary divergence (Ellegren, 2008; Csilléry et al., 2018; Salazar-Tortosa et al., 2023). 4.4 Convergent evolution at the genomic level and inter-species ecological comparisons Comparative genomic analysis between Siniperca and other freshwater fish have found examples of convergent evolution—where unrelated lineages develop the same characters or gene changes independently under the same environmental pressures. For example, conserved signatures of selection have been detected across species in genes that are associated with visual receptors, mucosal immunity, and metabolism. Comparisons of gene regulatory networks and adaptive loci among taxa may uncover convergent adaptive strategies and the level of regulatory and functional convergence (Figure 2). Such studies improve our understanding of Siniperca species and other species adapting to similar hydrology and temperature environments, and reveals the genomic foundation of convergent phenotypes (Regev et al., 2015; Csilléry et al., 2018). Figure 2 Genomic structure and sequence information of the Sinipercagenus (Adopted from Liang et al., 2019) 5 Analysis of Adaptive Evolutionary Mechanisms at the Genomic Level 5.1 Selective pressures from ecological factors such as temperature, water environment, and diet Siniperca members are dispersed in diverse freshwater ecosystems throughout China and possess impressive ecological adaptations to temperature, water quality, and diet. Siniperca members vary from subtropical low-oxygen water to cold oxygen-rich rivers in northern China and possess physiological and metabolic distinctions. Genomic analysis indicates that metabolic genes underwent rapid evolutionary rates, allegedly an adaptation to their carnivorous diet as well as environmental sensitivity (Han, 2024). Ecological stresses such as temperature fluctuations, fluctuating dissolved oxygen, and nutrient differences apparently have exerted positive pressure on energy metabolism genes, oxidative stress response genes, and nutrient uptake genes (Huang, 2020; Bafna et al., 2021). Aside from that, adaptive evolution can also be facilitated through events of gene loss to prefer against duplicative functions in new habitats, a process that occurs within aquatic and flying mammals but which also might be promoted to Sinipercaspecies (Langer et al., 2018).
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 58 5.2 Adaptive evolutionary pathways of systems involving metabolism, immunity, and sensory functions At the advanced freshwater ecosystem level, Siniperca species have signatures of adaptive evolution in immunity and metabolism genes. Regions of positive selection are generally enriched in pathogen recognition, mucosal immunity, and antimicrobial peptide production genes, suggesting that such systems are largely the primary targets of long-term selective pressure. Siniperca spp. are predatory fish. also exhibit adaptive evolution of metabolic enzymes for detoxification and energy use (Huang, 2020; Slodkowicz and Goldman, 2020). Genes that regulate sensory function-especially those that deal with smell and sight-exhibit species-specific divergences as well as rapid evolution. This is likely because of adaptation to different water turbidity and prey detection processes. 5.3 Association analysis between phenotypic variation and gene function variation Siniperca species exhibit intense phenotypic variability in body size, head morphology, coloration, and aggression. How the genetic basis for such traits is established is a cornerstone question in evolutionary genomics. Recent advancements in statistical models such as the phenotype-genotype branch-site model (PG-BSM) and evolution-guided regression models have enabled correlation of some genetic change with phenotypic evolution (Wang and Chen, 2024). In Siniperca, these approaches allow one to identify codon replacements or gene loss events for traits such as pyloric caeca formation and feeding behavior, giving strong evidence on how genetic divergence is involved in ecological specialization (Youssef et al., 2019; Huang, 2020). 5.4 Integration of molecular mechanisms with morphological and ecological adaptation Integrating phylogenetic histories with protein structure information and ecological data throws additional light on Siniperca species adaptive evolution. Positively selected sites are clustered in functionally key regions of proteins—catalytic domains and signal interfaces, for example—indicates their involvement in trait development. These molecular adaptations must be accompanied by morphological traits such as jaw morphology, dentition, and feeding mode. Synthesis studies that integrate genomic data, behavioral ecology, physiological performance, and environmental characteristics reveals how Siniperca species achieve ecological success and drive lineage diversification through molecular innovation (Slodkowicz and Goldman, 2020; Tong et al., 2023). 6 Scientific Significance and Application Prospects of the Research 6.1 Contributions to fish phylogeny and evolutionary biology This research contributes to fish phylogeny knowledge by applying genomic and phylogenetic methods to explain Siniperca evolutionary relationships. Based on high-throughput sequencing and comparative genomics, the study provides insight into Siniperca adaptive evolution, speciation, and diversification and contributes to overall evolutionary biology by providing an account of mechanisms of ecological adaptation and lineage divergence in freshwater fishes. The integration of genomic data into evolutionary research is an indication of the increasing scientific trend in utilizing the ability of new technology to explore complex biological questions better, hence accelerating the advancement of science and widening the boundaries of evolutionary science (Konieczny, 2023). 6.2 Providing a genomic basis for conservation and precision breeding of Siniperca species Evolutionary information and genomic data generated by this study form a sound foundation for conservation of Siniperca species. Genetic diversity, population genetic structure, and detection of adaptive loci in the study enable the development of site-based conservation practices for maintaining genetic integrity and potential adaptation in nature populations. Besides, identification of key genes and markers for desirable traits enables precision breeding to be possible through broodstock selection for optimal growth, disease resistance, and environmental adaptability. The uses are consistent with current and future trajectories of genetic DNA testing and genomic assessment in resource management and sustainable aquaculture (Shi, 2024). 6.3 Application potential of genomic information in trait improvement and environmental adaptation assessment Genomic information gained from this research have great potential for Siniperca aquaculture enhancement in traits. With the linkage of genetic markers with desirable economic traits, i.e., growth rate, feed conversion, and resistance to stress, marker-assisted selection can be utilized by breeders to speed up genetic progress. Besides, the
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 59 ability to assess and estimate adaptive genetic variation improves the possibility of predicting and estimating the environmental fitness of culture stocks, promoting the development of resilient aquaculture systems in the shadows of a changing environment. The use of genomic information within these fields mirrors larger trends in science research, where new technologies and new modes of analysis are propelling limits of innovation and utilitarian applications in industry and conservation alike (Konieczny, 2023; Shi, 2024). 7 Challenges and Strategic Recommendations 7.1 Limitations in genome data coverage and representativeness Current studies of Siniperca spp. are severely handicapped by inadequate coverage and representativeness of genome data. Most genomic studies sample only a small number of species or populations, whose scope in attempting to cover the complete scope of genetic diversity and adaptive variation necessary in order to make robust evolutionary and functional inference is limited. This lack of whole-genome resources also restrains finding key genes for important traits and adaptation and thereby reduces breeding and conservation program efficiency (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024; Shao et al., 2025). 7.2 Constraints in phylogenetic and functional analysis models Phylogenetic and functional analysis platforms of Siniperca tend to be limited by reliance on a small number of genetic markers or a single-omics that are unable to produce good resolution to distinguish between genetically close species or to uncover complex evolutionary relationships. In addition, the incomplete reference databases and restricted experimental verification reduce gene function annotation and adaptive mechanisms understanding precision (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024). 7.3 Necessity of multi-omics integration and fine-scale functional validation One of the emerging requirements is to utilize multi-omics approaches including genomics, transcriptomics, proteomics, and metabolomics to respond to Siniperca biology in an integrated manner. Multi-omics can be used in combination to reveal the molecular basis of attributes like growth, immunity, and environment adaptation at different levels of biology. However, sophisticated high-resolution functional verification such as gene editing and physiological assays is underdeveloped, while uses of omics information are limited to aquaculture and conservation (Guo et al., 2018; Xiao et al., 2020; Zhong et al., 2022; Bao et al., 2024; Shao et al., 2025). 7.4 Future research suggestions: integration of functional experiments, physiological validation, and ecological simulation Future research should expand the number of genome sequencing study objects to more Siniperca species and populations, thus ensuring broader data representativeness and coverage. Evolution and use of advanced phylogenetic and functional analysis models, supported by improved reference databases, will help in more accurate evolutionary and functional inference. Incorporation of multi-omics data with functional assays, physiological validation, and ecological modeling will provide an integrated picture of trait development and environmental acclimatization, eventually leading to precision breeding, sustainable aquaculture, and effective conservation planning for Siniperca spp. (Guo et al., 2018; Xiao et al., 2020; Bao et al., 2024; Zhong et al., 2022; Shao et al., 2025). 8 Concluding Remarks Recent advances in large-scale genomic sequencing and phylogenetic analysis have enabled Siniperca phylogeny to be reconstructed more confidently. High-throughput sequencing of thousands of nuclear coding sequences and comprehensive analyses have confirmed the monophyly of Sinipercidae, supporting classification into two genera, Siniperca and Coreoperca. Notably, Siniperca scherzeri was identified as the most basal taxon, and well-defined Siniperca clades were delineated, providing unequivocal support to the validity of several contentious species and clarifying relationships that had hitherto remained ambiguous due to limited morphological differentiation. Genomic analysis has revealed widespread signals of adaptive evolution in Siniperca, particularly in genes associated with predatory feeding, growth, and environmental adaptation. Positive selection scans revealed sudden evolution in feeding behavior, aggressiveness, and physiological traits such as euryhalinity and pyloric caeca
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 54-62 http://ecoevopublisher.com/index.php/ijmec 60 formation. Genome-wide association analysis also detected SNPs and candidate genes for economically important traits such as growth, muscle, and bone development, thus leaving a molecular legacy of adaptation and trait evolution in Siniperca. Together with high-quality genome assemblies, phylogenetic analysis, and functional genomics, they provide new insights into Siniperca breeding and conservation. Genomic resources facilitate accurate species identification, genetic diversity inference, and marker-assisted selection breeding in aquaculture. Population history and adaptive evolution guide conservation management, and adaptive evolution genes involved in growth and adaptation aid precision breeding and environmental adaptability. These improvements collectively enhance the Siniperca species' ecological adaptation and sustainable use research. Acknowledgments Thanks to the animal research team for their support and help in data collection and data collection. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Bafna V., Zhou D., Stobdan T., Iranmehr A., Kryazhimskiy S., Haddad G., and Zhao H., 2021, Multiple mechanisms drive genomic adaptation to extreme O₂ levels in Drosophila melanogaster, Nature Communications, 12: 997. https://doi.org/10.1038/s41467-021-21281-6 Bao L., Peng J., Tuo Y., Fang H., and Chu W., 2024, Research progress on nutritional requirements and formulated feeds for Siniperca: a comprehensive review, Fishes, 9(12): 487. https://doi.org/10.3390/fishes9120487 Chen J., Lin L., Han L., Li G., Liu X., Huang C., Zhang Z., Bi S., Liang J., Li H., Zhang Y., Liu S., Yi H., Sun J., Wei X., and Chen Q., 2024, Morphological characteristics, genetic diversity, and microsatellite analysis of the progenies (F1, F2, and backcross descendant) of Siniperca chuatsi and Siniperca scherzeri, Aquaculture Research, 2024(1): 6672569. https://doi.org/10.1155/2024/6672569 Chen X., Zhang Z., Yin Z., Li J., He S., Tang S., Xu J., Lv L., Dou Y., Li L., Liang X., Cai W., Zhang Y., Kuhl H., Wuertz S., and Tao Y., 2020, Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding, Communications Biology, 3: 361. https://doi.org/10.1038/s42003-020-1094-y Csilléry K., Rodríguez-Verdugo A., Guillaume F., and Rellstab C., 2018, Detecting the genomic signal of polygenic adaptation and the role of epistasis in evolution, Molecular Ecology, 27: 606-612. https://doi.org/10.1111/mec.14499 DeGiorgio M., Santos A., Arnab S., and Fumagalli M., 2025, Efficient detection and characterization of targets of natural selection using transfer learning, Molecular Biology and Evolution, 42(5): msaf094. https://doi.org/10.1093/molbev/msaf094 Dissanayake A., 2020, Applied aspects of methods to infer phylogenetic relationships amongst fungi, Mycosphere, 11: 2652-2676. https://doi.org/10.5943/mycosphere/11/1/18 Ellegren H., 2008, Comparative genomics and the study of evolution by natural selection, Molecular Ecology, 17(21): 4586-4596. https://doi.org/10.1111/j.1365-294X.2008.03954.x Guo C., Zhang T., Li Z., Beauchamp D., Li W., Hicks B., Liu J., and Lin M., 2018, Impacts of hatchery-reared mandarin fish Siniperca chuatsi stocking on wild fish community and water quality in a shallow Yangtze lake, Scientific Reports, 8: 11481. https://doi.org/10.1038/s41598-018-29758-z Han Y.P., 2024, Population genomics of primates: diversity, structure, and evolutionary dynamics, International Journal of Molecular Evolution and Biodiversity, 14(3): 108-119. https://doi.org/10.5376/ijmeb.2024.14.0014 Horiike T., 2016, An introduction to molecular phylogenetic analysis, Robotics and Autonomous Systems, 4: 36-45. https://doi.org/10.7831/RAS.4.36-45 Huang Y., 2020, Dissecting genomic determinants of positive selection with an evolution-guided regression model, Molecular Biology and Evolution, 39(1): msab291. https://doi.org/10.1093/molbev/msab291 Jiang J., Zhao J., Lu L., and Li C., 2023, Comparative genomics revealed drastic gene difference in two small Chinese perches, Siniperca undulata and S. obscura, G3: Genes|Genomes|Genetics, 13(7): jkad101. https://doi.org/10.1093/g3journal/jkad101
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International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 63-73 http://ecoevopublisher.com/index.php/ijmec 63 Research Insight Open Access Research on Biological Control Technologies and Mechanism Analysis of Common Pests and Diseases inChrysanthemum morifolium(Hangbaiju) Jianli Lu 1, Chuchu Liu 2 1 Traditional Chinese Medicine Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China 2 Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: chuchu.liu@@cuixi.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2 doi: 10.5376/ijmec.2025.15.0007 Received: 26 Jan., 2025 Accepted: 28 Feb., 2025 Published: 15 Mar., 2025 Copyright © 2025 Lu and Liu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Lu J.L., and Liu C.C., 2025, Research on biological control technologies and mechanism analysis of common pests and diseases in Chrysanthemum morifolium (Hangbaiju), International Journal of Molecular Ecology and Conservation, 15(2): 63-73 (doi: 10.5376/ijmec.2025.15.0007) Abstract Chrysanthemum morifolium pest and disease control is ushering in a green transformation, and biological control technology has become a key solution due to its environmentally friendly characteristics. This study comprehensively sorted out the current mainstream biological control systems, covering multiple dimensions such as microbial antagonism, natural enemy regulation, botanical pesticides and ecological management, deeply analyzed their mechanisms of action and evaluated their application prospects. In the field of microbial control, Bacillus subtilis and Trichoderma harzianum have shown excellent disease inhibition capabilities. These beneficial microorganisms work through a dual mechanism: on the one hand, they secrete antimicrobial active substances to directly inhibit pathogens, and on the other hand, they activate the plant's own immune defense system. Natural enemy insects such as ladybugs and lacewings have built a natural pest control network, which has a significant control effect on common pests such as aphids and red spiders. In terms of botanical pesticides, natural ingredients such as matrine and tea tree essential oil have attracted much attention due to their broad-spectrum antibacterial and insect repellent properties. Field practice has confirmed that the integration of multiple biological control methods can produce a synergistic effect and achieve a win-win situation of economic benefits and ecological protection. This study not only provides a systematic solution for the green production of chrysanthemum, but also provides a practical example for promoting sustainable agricultural development. Keywords Chrysanthemum morifolium; Biological control; Microbial agents; Natural enemy insects; Plant-derived pesticides 1 Introduction Chrysanthemum morifolium is an important economic crop with medicinal, edible and ornamental value. Its cultivation process is often plagued by various diseases and pests (Sha et al., 2023; Lyu et al., 2024). Although traditional chemical control is effective, it has caused a series of environmental and ecological problems: increased pest resistance, destruction of beneficial biological communities and hidden dangers to agricultural product safety (Xu et al., 2021). More seriously, non-point source pollution caused by pesticide residues is threatening the stability of agricultural ecosystems (Chen et al., 2018), which has prompted researchers to turn to more sustainable green control strategies. Biological control technology has shown unique advantages. Bacillus siamensis can effectively inhibit leaf spot caused by Nigrospora oryzae (Sha et al., 2023); volatile terpenes released by Chrysanthemum morifolium itself build an indirect defense network by attracting natural enemies (Xu et al., 2021). These control measures based on ecological interactions not only avoid the negative impact of chemical pesticides, but also maintain farmland biodiversity. This study will systematically sort out the latest progress in biological control of Chrysanthemum morifolium, focusing on analyzing the synergistic mechanism of antagonistic microorganisms, natural enemy insects and plant-derived active substances. This study will also evaluate the field performance of different biological control factors to provide a scientific basis for the establishment of an efficient and environmentally friendly pest and disease management system, and help the sustainable development of the Chrysanthemum morifoliumindustry.
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 63-73 http://ecoevopublisher.com/index.php/ijmec 64 2 Overview of Common Pests and Diseases in Hangbaiju 2.1 Major diseases Chrysanthemum morifoliumis threatened by a variety of fungal diseases during cultivation. Powdery mildew is a typical airborne disease, and its typical symptoms are the formation of white powdery spots on leaves and stems. The disease is particularly rampant under warm and dry conditions, seriously affecting the normal growth and development of plants by interfering with photosynthesis and inducing leaf deformities. Fusarium oxysporum is caused by the soil-borne pathogen Fusarium oxysporum, which invades the root system and destroys the vascular system, resulting in characteristic leaf yellowing and wilting symptoms. The pathogen can be spread through soil, irrigation water and diseased residues, causing dwarfing or even death of plants in the field. Studies have shown that biochar improvement can effectively reduce the number of Fusarium oxysporum in the soil (Chen et al., 2018). Leaf spot is another important disease with a complex pathogenic composition, including Epicoccum sorghinum and Nigrospora oryzae. The disease initially manifests as scattered necrotic spots, which merge into large brown-black patches as the disease progresses, eventually causing the leaves to curl and necrotize. High temperature and high humidity environments significantly increase the severity of the disease, posing a serious threat to yield (Chen et al., 2020; Sha et al., 2023). 2.2 Major pests During the cultivation of Chrysanthemum morifolium, two typical pests often attack it. Aphids, as a representative of piercing-sucking pests, continuously suck the plant sap, causing leaf curling and growth stagnation. At the same time, as a virus transmission medium, they aggravate the degree of damage (Ji-Shuang, 2007). Its population grows exponentially under 15~25 ℃ conditions, with explosive damage characteristics. Red spiders show a different damage pattern. This type of tiny mite pest destroys leaf mesophyll cells through its mouth needle, causing characteristic chlorotic spots, and in severe cases, causing leaves to scorch and fall off (Srikumar et al., 2015). It is worth noting that this pest has dual damage characteristics: in addition to damage to the aboveground part, its root infection can form typical root nodules, significantly inhibiting the absorption of water and nutrients by seedlings, causing plant development stunting. A dry environment above 28℃ is particularly conducive to the rapid proliferation of its population, and the damage is particularly prominent in facility cultivation. 2.3 Damage mechanisms of pests and diseases Various pests and diseases interfere with the normal physiological functions of Chrysanthemum morifolium through different pathways. After Fusarium oxysporum infects the plant, it selectively destroys the vascular system, blocks the transport of water and mineral nutrients, and eventually causes systemic wilting of the plant. Leaf spot disease directly damages the mesophyll tissue, significantly reducing the chlorophyll content and photosynthetic efficiency. Field observations showed that the affected plants showed typical apical wilting (Figure 1A) and leaf yellowing (Figure 1B), and the lesions showed characteristic brown necrosis (Figure 1C, Figure 1D), which directly reflected the severity of the disease. The harm of piercing-sucking pests should not be ignored. Aphids not only cause malnutrition of plants by continuously sucking phloem sap, but also act as virus carriers to cause complex infection. Red spiders aggravate the water imbalance and metabolic disorder of plants by destroying the mesophyll cell structure. These biological stress factors work together to inhibit the growth and development of Chrysanthemum morifoliumfrom multiple levels, ultimately leading to a significant decrease in yield and quality (Chen et al., 2020; Sha et al., 2023). Establishing a targeted prevention and control system is of great significance to ensuring the sustainable development of the Chrysanthemum morifoliumindustry. 3 Biological Control Technologies for Hangbaiju Pests and Diseases 3.1 Microbial control Microbial control, as an important means of green control of Chrysanthemum morifolium diseases, has shown unique advantages. Bacillus siamensis D65 showed significant inhibitory effects on Nigrospora oryzae, the
International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.2, 63-73 http://ecoevopublisher.com/index.php/ijmec 65 pathogen of leaf spot disease (Sha et al., 2023). The strain directly inhibits the growth of pathogens by secreting antimicrobial substances, and may activate the plant defense system at the same time, with a dual control mechanism. Figure 1 Symptoms of disease inC. morifoliumand pathogenicity test (Adopted from Chen et al., 2018) Image caption: (A) Field symptoms; (B) Diseased branches near the top of the chrysanthemum; (C,D) Symptoms of leaf spot disease; (E) Leaf 5 days after inoculation with sterile PDA plug; (F) Leaf 5 days after artificial inoculation; (G) Branch before inoculation; (H) Branch 7 days after inoculation (Adopted from Chen et al., 2018) Bacillus bacteria have broad application prospects in plant disease control. Studies have shown that B. siamensis D65 exhibits broad-spectrum antagonistic activity against a variety of plant pathogenic fungi, which provides a scientific basis for its application in the comprehensive control of Chrysanthemum morifolium diseases. In addition, soil improvement measures such as biochar application can effectively reduce the population density of Fusarium oxysporum (Chen et al., 2018). This strategy of controlling soil-borne diseases by regulating soil microbial communities provides a new idea for the ecological control of Chrysanthemum morifoliumwilt. Microbial pesticides are gradually replacing traditional chemical pesticides. The discovery and application of highly effective antagonistic strains such as B. siamensis D65 marks a new stage in the control of Chrysanthemum morifoliumdiseases dominated by microbial regulation (Sha et al., 2023). This type of biological agent not only has significant control effects, but is also environmentally friendly and not prone to inducing drug resistance, which meets the requirements of sustainable development of modern agriculture. 3.2 Natural enemy insect control Predatory natural enemies such as ladybugs and lacewings have shown significant effects in the control of aphids in Chrysanthemum morifolium. These natural enemies can effectively control the density of aphid populations and reduce the degree of plant damage through direct predation (Zhang et al., 2019). Although there are few studies on the application of predatory mites on Chrysanthemum morifolium, their successful practice in integrated pest management provides a reference for their application. 3.3 Plant-derived pesticides and natural product control Botanical pesticides are widely valued for their natural insecticidal activity and are gradually becoming a sustainable alternative to synthetic chemical pesticides. Although no plant extracts specifically for Chrysanthemum morifolium have been clearly applied to pest control, the potential of botanical substances in
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