Molecular Phylogenetics and Evolution最新文献

{"title":"Resolving taxonomic uncertainties in ailiid catfishes (Siluriformes: Ailiidae) using Genome-Scale data","authors":"Jash Hang Limbu ,&nbsp;Dipak Rajbanshi ,&nbsp;Jiantao Hu ,&nbsp;Laxman Khanal ,&nbsp;Chenhong Li","doi":"10.1016/j.ympev.2025.108384","DOIUrl":"10.1016/j.ympev.2025.108384","url":null,"abstract":"<div><div>The Ailiidae family, endemic to South and Southeast Asia, comprises diverse freshwater catfish inhabiting major river basins across the region. Evolutionary relationships and taxonomic classification within Ailiidae family remain contentious. Here, we resolve these uncertainties using phylogenomic data from 29 specimens representing 11 species and six of the seven recognized genera, supplemented by two outgroup taxa<!--> <!-->(<em>Pachypterus atherinoides</em> <!-->and<!--> <em>P. acutirostris</em>). Hybridization target enrichment and high-throughput sequencing yielded 4,434 single-copy nuclear coding loci. After trimming loci with more than 50 % missing taxa, 2,102 loci, totaling 505,110 bp, were used for phylogenomic analyses. The results confirm monophyly of all studied genera (<em>Ailia</em>, <em>Ailiichthys</em>, <em>Clupisoma</em>, <em>Eutropiichthys</em>, <em>Silonia</em> and <em>Laides</em>), after the reclassification of <em>Clupisoma montanum</em> and <em>C. sinense</em> into the genus <em>Laides,</em> based on concordant molecular, morphological and meristic evidence. Notably, <em>Ailia coila</em> and <em>Ailiichthys punctata</em> formed an early diverging clade, sister to remaining Ailiidae. Furthermore, our results corroborate that the genera <em>Eutropiichthys</em> <!-->and<!--> <em>Silonia</em> <!-->represent distinct lineages within Ailiidae, warranting their formal retention in the family. Divergence dating estimated the most recent common ancestor of Ailiidae arose during the Pleistocene, with a median age of 2.1 million years ago (95 % HPD: 3.34–1.0 Ma). Biogeographic reconstructions identified the Ganges–Brahmaputra River basin (South Asia) as the center of origin for Ailiidae, followed by dispersal to the Irrawaddy–Salween, Pahang and Indus River basins. Pleistocene climatic fluctuations, tectonic uplift and changes in sea-level may have influenced the dispersal of Ailiidae catfishes. These geological events restructured river systems and exposed land bridges, allowing movement across previously isolated basins. Paleo-river connections between the major drainages of South and Southeast Asia likely facilitated multiple events of vicariance and dispersal, driving diversification within the Ailiidae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108384"},"PeriodicalIF":3.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the drivers of speciation in Alpine Noccaea (Brassicaceae) reveal an evolution predominantly shaped by geography.","authors":"Camille Voisin, Philippe Choler, Camille Vacher, Christophe Perrier, Julien Renaud, Delphine Rioux, Florian C Boucher","doi":"10.1016/j.ympev.2025.108381","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108381","url":null,"abstract":"<p><p>The process of species delimitation, defined as the act of recognising biologically meaningful taxonomic units, enables the detection of overall biodiversity and the exploration of speciation processes. Given the complex nature of the origin of biodiversity, a significant number of cryptic Alpine plant groups exhibit ambiguity regarding their phylogenetic relationships and species circumscription. In this study, we attempt to apply the principles of integrative taxonomy to a complex of cryptic alpine plants from the genus Noccaea, which are often described as substrate specialists. We benefited from an extensive sampling across the Alps combined with high-throughput genotyping to apply a modern and standardised method of species delimitation. We find that the Noccaea rotundifolia complex is represented by five species within the Alps, which exhibit a restricted geographic distribution. Four of these species diverged approximately 350 ka ago (259-429), indicating a recent diversification. Instead of recognizing species with different substrate affinities, as done by current taxonomy, we rather find that the most widespread species are substrate generalists but with allopatric distributions. Our findings indicate that N. rotundifolia is growing exclusively in the west of the well-known biogeographic barrier of the Aosta Valley. N. corymbosa is found to grow between the Aosta Valley barrier and the Lake Como one. N. cepaeifolia, in turn, is observed in the eastern Alps, separated by the Brenner valley. Overall, this study provides a detailed systematic review, supporting the pivotal role of the recognized Alpine biogeographic barriers, in shaping species distribution and speciation.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108381"},"PeriodicalIF":3.6,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into the phylogeny and evolutionary history of scale insects (Hemiptera: Coccoidea): Resolving family-level relationships.","authors":"Jun Deng, Xianghao Weng, Wentao Ma, Lin Zhang, Chen Wang, Qingsong Zhou, Jiangtao Zhang, Xubo Wang, Xiaolei Huang","doi":"10.1016/j.ympev.2025.108383","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108383","url":null,"abstract":"<p><p>Scale insects (Hemiptera: Coccoidea), comprising archaeococcoids and neococcoids, represent the fourth largest superfamily within the order Hemiptera and are recognized as significant agricultural and forestry pests. Despite the increasing availability of insect genomic data, systematic phylogenetic studies of scale insects at the family level have been limited due to challenges in specimen collection, identification, and sequencing. In this study, we sequenced the genomes of 46 species representing 20 families and integrated this data with publicly available sequences to encompass 22 families, representing 95% of Coccoidea taxa. Notably, 14 of these families are sequenced for the first time. This work establishes a robust phylogenetic framework for scale insects. Our findings clarified the phylogenetic relationships of archaeococcoids, confirming Matsucoccidae as the most primitive extant group of scale insects and identifying Putoidae as a transitional lineage between archaeococcoids and neococcoids. We further demonstrated that Xenococcidae belongs to the neococcoids, distinct from Pseudococcidae, and revealed that Coccidae form a paraphyletic group, with Aclerdidae nested within Coccidae. Using MCMCTree analysis, we estimated the divergence times of various Coccoidea families and proposed a comprehensive evolutionary framework for scale insects. This study addresses key gaps in the phylogenetic and evolutionary understanding of Coccoidea, providing a valuable genomic resource and advancing our knowledge of their phylogeny and evolutionary history.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108383"},"PeriodicalIF":3.6,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring genome architecture as a source of phylogenetic characters for resolving the apulmonate arachnid polytomy","authors":"Benjamin C. Klementz ,&nbsp;Siddharth S. Kulkarni ,&nbsp;Kaitlyn M. Abshire ,&nbsp;Prashant P. Sharma","doi":"10.1016/j.ympev.2025.108380","DOIUrl":"10.1016/j.ympev.2025.108380","url":null,"abstract":"<div><div>Chromosome-level genome assemblies are powerful tools for identifying the presence of rare genomic changes that can overcome phylogenetically intractable problems. Chelicerata, the sister group to the remaining arthropods, harbors a soft polytomy at the base of an internal node named Euchelicerata, which is variably resolved across phylogenomic studies. As a result, seven orders, comprising horseshoe crabs and six apulmonate arachnid lineages, exhibit highly unstable placements from one study to the next, typically with maximal nodal support. Here, we analyzed recently released chromosome-level genomes of two of these orders, Opiliones (harvestmen) and Solifugae (camel spiders). We show that both Opiliones and Solifugae exhibit an unduplicated genome condition, as inferred from analysis of gene clusters, microRNAs, and macrosynteny. These results are congruent with phylogenomic studies that have refuted traditional morphological placements of Opiliones and Solifugae as close relatives of orders within Arachnopulmonata, a subset of six arachnid orders that are united by a shared whole genome duplication. Additionally, we examine irreversible chromosome fusion-with-mixing events as potential sources of phylogenetic data. We show that while fusion and mixing events are common in apulmonate arachnids, multiple mixing events support incompatible unrooted tree topologies. These results suggest that fusion and mixing events have evolved convergently in the chelicerate tree of life, particularly for extant lineages with a small number of chromosomes. Overall, our findings demonstrate that broader sampling of chelicerate genomes and establishment of genomic resources for key missing orders are essential to unlocking the potential of rare genomic changes as phylogenetic data sources.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108380"},"PeriodicalIF":3.6,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disentangling the evolutionary history of terrestrial planarians through phylogenomics","authors":"Lisandra Benítez-Álvarez ,&nbsp;Nuria Escudero ,&nbsp;Judit Salces-Ortiz ,&nbsp;Iñaki Rojo ,&nbsp;Fernando Ángel Fernández-Álvarez ,&nbsp;Eduardo Mateos ,&nbsp;Fernando Carbayo ,&nbsp;Rosa Fernández","doi":"10.1016/j.ympev.2025.108371","DOIUrl":"10.1016/j.ympev.2025.108371","url":null,"abstract":"<div><div>Triclads (Platyhelminthes, Tricladida) are found in marine, freshwater, and terrestrial habitats worldwide except Antarctica. Terrestrial planarians are grouped into the family Geoplanidae, which is subdivided into the subfamilies Geoplaninae, Bipaliinae, Rhynchodeminae, and Microplaninae. Some of these subfamilies result from taxonomic rearrangements based on molecular phylogenies inferred from a few molecular markers. However, the diagnosis of Rhynchodeminae was not aligned with the morphology of all its representatives. While the subfamilies are recovered as monophyletic in recent molecular phylogenies, robust hypotheses regarding the relationships between them remain unknown. In this study, we employ for the first time a phylogenomic framework to investigate the evolutionary relationships among the subfamilies, starting by obtaining the first transcriptomes for 15 species of terrestrial planarians. A total of 16 different datasets, comprising nearly two thousand single-copy genes inferred from transcriptomic data, were analyzed using various phylogenetic inference methods. We recovered, for the first time, a well-supported topology of phylogenetic relationships among Geoplanidae subfamilies, positioning Bipaliinae and Microplaninae as a clade sister to Rhynchodeminae + Geoplaninae. Internal relationships within the genus <em>Microplana</em> were not supported in our analyses. The subfamily Rhynchodeminae, represented in our phylogeny by species from the tribes Rhynchodemini and Caenoplanini, is re-diagnosed to align with previous taxonomic rearrangements. This study not only represents a significant step forward in the phylogenetic resolution of Geoplanidae but also provides important insights into the broader evolutionary dynamics shaping land planarian diversity.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108371"},"PeriodicalIF":3.6,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards the next generation of species delimitation methods: an overview of machine learning applications","authors":"Matheus M.A. Salles,&nbsp;Fabricius M.C.B. Domingos","doi":"10.1016/j.ympev.2025.108368","DOIUrl":"10.1016/j.ympev.2025.108368","url":null,"abstract":"<div><div>Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, whether based on morphological, molecular, or other types of data. In the case of methods based on DNA sequences, most of them are rooted in the coalescent theory. However, coalescence-based models have limitations, for instance regarding complex evolutionary scenarios and large datasets. In this context, machine learning (ML) can be considered as a promising analytical tool, and provides an effective way to explore dataset structures when species-level divergences are hypothesized. In this review, we examine the use of ML in species delimitation and provide an overview and critical appraisal of existing workflows. We also provide simple explanations on how the main types of ML approaches operate, which should help uninitiated researchers and students interested in the field. Our review suggests that while current ML methods designed to infer species limits are analytically powerful, they also present specific limitations and should not be considered as definitive alternatives to coalescent methods for species delimitation. Future ML enterprises to delimit species should consider the constraints related to the use of simulated data, as in other model-based methods relying on simulations. Conversely, the flexibility of ML algorithms offers a significant advantage by enabling the analysis of diverse data types (e.g., genetic and phenotypic) and handling large datasets effectively. We also propose best practices for the use of ML methods in species delimitation, offering insights into potential future applications. We expect that the proposed guidelines will be useful for enhancing the accessibility, effectiveness, and objectivity of ML in species delimitation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108368"},"PeriodicalIF":3.6,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic analyses revealed a new lineage of house mouse (Mus musculus) in Gyirong Basin of Xizang Autonomous Region, China","authors":"Yingjie Chen ,&nbsp;Rongguo Wang ,&nbsp;Zhongxu Zhu ,&nbsp;Naresh Subedi ,&nbsp;Xuelong Jiang ,&nbsp;Meidong Jing ,&nbsp;Ling Huang","doi":"10.1016/j.ympev.2025.108370","DOIUrl":"10.1016/j.ympev.2025.108370","url":null,"abstract":"<div><div>In the present study, we collected 20 individuals and 12 individuals of wild mice from the Gyirong Basin of Xizang Autonomous Region in China and Sudurpashchim in Nepal. Phylogeny and genetic structure inferred from different types of genomic markers suggest that these samples all belong to <em>Mus musculus</em>, among which individuals from Gyirong Basin represent a new genomic lineage (named as <em>M. m. gyirongus</em>), and samples from Sudurpashchim represent an intermediate population between the central population and <em>M. m. castaneus</em>. <em>M. m. gyirongus</em>, along with <em>M. m. domesticus</em> and <em>M. m. musculus</em>, differentiated from the central population compactly during ∼ 272,000–251,000 years ago in the interglacial period. Three lineages all experienced continuous population decline before ∼ 70,000 years ago. Then, they underwent population fluctuations at different periods that might have been impacted by climate changes, migration history, and human activities. Genes related to the structure and function of neural synapses, reproduction and development, regulation of cell cycle and carcinogenesis, and immune response have undergone positive selection in the genome of <em>M. m. gyirongus</em>. The discovery of <em>M. m. gyirongus</em> not only helps us to better understand the evolutionary history of <em>M. musculus</em>, but also provides new regional resources for breeding novel laboratory mouse strains.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"209 ","pages":"Article 108370"},"PeriodicalIF":3.6,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary dynamics and codon bias analysis of canine circovirus: Insights into global spread and host adaptability","authors":"Gen Li ,&nbsp;Rongqi Liu ,&nbsp;Yongyi Chen ,&nbsp;Huixian Liang ,&nbsp;Yinyi Liang ,&nbsp;Xin Li ,&nbsp;Yankun Ke ,&nbsp;Bowen Lin ,&nbsp;Jianfeng Zhong ,&nbsp;Xiaofeng Guo ,&nbsp;Jun Che ,&nbsp;Jun Luo","doi":"10.1016/j.ympev.2025.108369","DOIUrl":"10.1016/j.ympev.2025.108369","url":null,"abstract":"<div><div>Circoviruses are relatively new pathogens, and new circoviruses are constantly being discovered, with a growing range of hosts. Recently, canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and dissemination of CanineCV were fragmented. Here, when conducting a metagenomic analysis of shelter dogs, we identified a canine circovirus positivity rate of 32.4% and obtained three new viral strains. Furthermore, we integrated publicly available viral sequences and employed multiple bioinformatic software tools to analyze the evolution, codon usage bias, recombination, origin, spatiotemporal distribution and host adaptability of CanineCV. In this study, CanineCV could be divided into five distinct phylogenetic clades, named as China-I, China-II, Cosmopolitan, EA, and SEA clades. The extensive inter-clade recombination was observed, which plays an important role in viral evolution, while based on existing sequence information, CanineCV most likely originated in Norway from <em>Vulpes vulpes</em> in 1950.7. Notably, CanineCV exhibits greater adaptability to human hosts compared to previously documented hosts, as indicated by host adaptability indices, suggesting that this virus may possess zoonotic potential. In summary, our study elucidates the phylogeography and evolutionary dynamics of CanineCV and underscores the importance of investigating its potential for zoonotic transmission.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"209 ","pages":"Article 108369"},"PeriodicalIF":3.6,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143916223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the potential of Angiosperms353 markers for species identification of Eastern Mediterranean orchids","authors":"Bastien Anthoons ,&nbsp;Margaretha A. Veltman ,&nbsp;Spyros Tsiftsis ,&nbsp;Barbara Gravendeel ,&nbsp;Andreas D. Drouzas ,&nbsp;Hugo de Boer ,&nbsp;Panagiotis Madesis","doi":"10.1016/j.ympev.2025.108360","DOIUrl":"10.1016/j.ympev.2025.108360","url":null,"abstract":"<div><div>Tuberous orchids are ecologically vulnerable species, threatened by a range of environmental pressures such as overharvesting, grazing and land use change. Conservation efforts require accurate species identification, but are impeded by limited phylogenetic resolution of traditional genetic markers, which is exacerbated by widespread taxonomic conflict regarding the classification of orchids. Target enrichment holds promise to resolve both these challenges by offering a large set of nuclear loci with which to increase phylogenetic resolution and evaluate competing species models.</div><div>Here, we evaluate the effectiveness of the Angiosperms353 markers for distinguishing over 50 tuberous orchid species native to Greece and we explore the possibility of narrowing these markers to a smaller set that could function as a minimal probe set. Our methodology consists of a three-tiered approach: 1) generating a species-level phylogeny using all Angiosperms353 loci with sufficient target recovery, 2) evaluating competing species models based on “splitter” and “lumper” classifications through Bayes Factor species delimitation, and 3) ranking the potential of Angiosperms353 loci to discriminate representatives of lineages with different divergence times based on their phylogenetic informativeness. While the inferred multi-species coalescent phylogeny had overall high support, Bayes Factor delimitation revealed mixed outcomes, favouring splitting in <em>Serapias</em>, while favouring splitting in basal clades and lumping in more recently diverged clades in <em>Ophrys</em>. A molecular clock analysis of <em>Ophrys</em> confirms rapid and recent radiation in clades marked by phylogenetic uncertainty, suggesting the need for additional loci to fully resolve this genus. Finally, we found 30 loci to be highly phylogenetically informative across four epochs of <em>Orchidinae</em> evolution; we suggest these are promising candidates for future marker development. Our findings enhance the Plant Tree of Life (PAFTOL) by contributing additional phylogenomic data for species that were previously underrepresented in trees built with these markers, while shedding light on the ongoing “splitter”-vs-“lumper” debate and offering new directions for species identification of tuberous orchids, a group with distinct taxonomic and conservation challenges.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"209 ","pages":"Article 108360"},"PeriodicalIF":3.6,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)","authors":"Dan-Hui Liu ,&nbsp;Quan-Ru Liu ,&nbsp;Komiljon Sh. Tojibaev ,&nbsp;Alexander P. Sukhorukov ,&nbsp;Hafiz Muhammad Wariss ,&nbsp;Yue Zhao ,&nbsp;Lei Yang ,&nbsp;Wen-Jun Li","doi":"10.1016/j.ympev.2025.108361","DOIUrl":"10.1016/j.ympev.2025.108361","url":null,"abstract":"<div><div>The application of omics data serves as a powerful tool for investigating the roles of incomplete lineage sorting (ILS) and hybridization in shaping genomic diversity, offering deeper insights into complex evolutionary processes. In this study, we utilized deep genome sequencing data from 76 individuals of <em>Lappula</em> and its closely allied genera, collected from China and Central Asia. By employing the HybPiper and Easy353 pipelines, we recovered 262–279 single-copy nuclear genes (SCNs) and 352–353 Angiosperms353 genes, respectively. We analyzed multiple datasets, including complete chloroplast genomes and a filtered set of 475 SCNs, to conduct phylogenetic analyses using both concatenated and coalescent-based methods. Furthermore, we employed Quartet Sampling (QS), coalescent simulations, MSCquartets, HyDe, and reticulate network analyses to investigate the sources of phylogenetic discordance. Our results confirm that <em>Lappula</em> is polyphyletic, with <em>L. mogoltavica</em> clustering with <em>Pseudolappula sinaica</em> and forming a sister relationship with other taxa included in this study. Additionally, three <em>Lepechiniella</em> taxa nested within distinct clades of <em>Lappula</em>. Significant gene tree discordance was observed at several nodes within <em>Lappula</em>. Coalescent simulations and hybrid detection analyses suggest that both ILS and hybridization contribute to these discrepancies. Flow cytometry (FCM) analyses confirmed the presence of both diploid and tetraploid taxa within <em>Lappula</em>. Phylogenetic network analyses further revealed that Clades IV and VII likely originated through hybridization, with the tetraploids in Clade IV arising from two independent hybridization events. Additionally, the “ghost lineage” identified as sister to <em>Lappula redowskii</em> serves as one of the donors in allopolyploidization. In conclusion, our study provides new insights into the deep phylogenetic relationships of Asian <em>Lappula</em> and its closely allied genera, contributing to a more comprehensive understanding of the evolution and diversification of <em>Lappula</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108361"},"PeriodicalIF":3.6,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}