Molecular Phylogenetics and Evolution最新文献

{"title":"An integrated framework for evolution of ciliated protists (Protista, Ciliophora) from the perspective of comparative genomics","authors":"Yuexin Wang ,&nbsp;Didi Jin ,&nbsp;Xiaopeng Hou ,&nbsp;Khaled A.S. Al-Rasheid ,&nbsp;Chen Shao ,&nbsp;Tengteng Zhang","doi":"10.1016/j.ympev.2025.108468","DOIUrl":"10.1016/j.ympev.2025.108468","url":null,"abstract":"<div><div>Early-branching eukaryotes are associated with the early branching events during eukaryogenesis. Understanding their genomic diversity and evolution can provide insights into the origin and speciation of eukaryotes. Ciliated protists (ciliates) are a group of early-branching unicellular eukaryotes with a high biodiversity, making them excellent models for evolutionary studies. However, their genomic diversity and evolution remain insufficiently understood. In this study, the comparative genomic and phylogenomic analyses were conducted using well-annotated macronuclear genomes from 16 bulk-cultured ciliates across four major classes. Our results indicate that: a) ciliates exhibit significant genomic diversity, with genome sizes ranging from 18.4 Mb to 117.1 Mb, extensive stop codon rearrangements, and tens of thousands of nanochromosomes in Spirotrichea and Litostomatea, reflecting dynamic genome architecture and adaptive evolution; b) gene family expansions highlight divergent evolutionary trajectories among ciliate classes, with Heterotrichea enhancing cell division capacity and Spirotrichea focusing on signal transduction; c) phylogenetic and structural analyses of meiosis related zinc finger protein and calcium channel related calmodulin gene families indicate that they predate the divergence of ciliates with functional diversification; d) anaerobic <em>Entodinium caudatum</em> retains abundant ubiquitin-related genes, while halotolerant <em>Fabrea salina</em> enriches anaphase-promoting complex cofactors (a crucial E3 ubiquitin ligase), suggesting that the encystment might be enhanced for both species. In summary, we systematically investigated the genomic landscape of ciliates to broaden our understanding of the genomic diversity and evolutionary patterns of ciliates.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108468"},"PeriodicalIF":3.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145014485","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":"Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes)","authors":"Jing Zhao ,&nbsp;Hong Yu ,&nbsp;Carl J. Rothfels ,&nbsp;Jian-Jun Yang ,&nbsp;Shao-Li Fang ,&nbsp;Zhao-Rong He ,&nbsp;Li-Bing Zhang ,&nbsp;Xin-Mao Zhou","doi":"10.1016/j.ympev.2025.108454","DOIUrl":"10.1016/j.ympev.2025.108454","url":null,"abstract":"<div><div>The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships “true tree” based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108454"},"PeriodicalIF":3.6,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145008676","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":"Untangling intergeneric mito-nuclear discordance: evidence for ancient introgression in two vole genera, Clethrionomys and Alticola (Rodentia, Cricetidae)","authors":"Ivan A. Dvoyashov ,&nbsp;Semyon Yu. Bodrov ,&nbsp;Tatyana V. Petrova ,&nbsp;Nataliya I. Abramson","doi":"10.1016/j.ympev.2025.108459","DOIUrl":"10.1016/j.ympev.2025.108459","url":null,"abstract":"<div><div>Cases of intergeneric introgression have been poorly studied. That is why the mito–nuclear discordance in the tribe Clethrionomyini has been confusing and attracted our special attention. The phylogenetic position of the subgenus <em>Aschizomys</em> of rock voles (<em>Alticola</em>) has long been debated: a discussion that has resurfaced after early phylogenetic studies on cytochrome <em>b</em> placed <em>Aschizomys</em> with <em>Clethrionomys</em> (red-backed voles). Subsequent studies based on multiple nuclear markers support the monophyly of rock voles but have left unresolved whether the observed mito–nuclear discordance has resulted from intergeneric introgression or other factors, such as the retention of ancestral polymorphisms. Here, we compiled existing divergence time estimates for transcriptomic and mitochondrial data of both genera and demonstrated that both factors affect the mitochondrial phylogeny of <em>Aschizomys</em>. We then investigated potential traces of nuclear intergeneric introgression corresponding to mitochondrial signals using transcriptomic and quaddRAD sequencing datasets. Despite applying multiple introgression detection approaches, we did not find convincing evidence of nuclear intergeneric introgression. Nonetheless, certain tests produced conflicting outcomes, highlighting potential methodological sensitivities or complex evolutionary signals. Our study represents the first genome-wide investigation of mito–nuclear discordance between <em>Clethrionomys</em> and <em>Alticola</em>, thus contributing to a broader understanding of evolutionary processes in these rodents.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108459"},"PeriodicalIF":3.6,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145004701","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":"Integrative taxonomy reveals Parakaliella harimensis (Pilsbry, 1901) as a distinct East Asian Euconulus species with deep genetic structure","authors":"Sara Kafimola ,&nbsp;Veronika Horsáková ,&nbsp;Markéta Nováková ,&nbsp;Eva Mikulášková ,&nbsp;Kazuki Kimura ,&nbsp;Stefan Meng ,&nbsp;Jan Divíšek ,&nbsp;Jeffrey C. Nekola ,&nbsp;Michal Horsák","doi":"10.1016/j.ympev.2025.108460","DOIUrl":"10.1016/j.ympev.2025.108460","url":null,"abstract":"<div><div>The remarkable phenotypic plasticity of land snail shells often results in convergent evolution, leading to frequent taxonomic misidentifications and non-monophyletic classifications. The taxonomy of the Holarctic micro land snails related to <em>Euconulus fulvus</em> has been particularly challenging to resolve. This study integrates mitochondrial and nuclear DNA phylogenetics, geometric morphometrics, and climate suitability modeling to clarify the phylogenetic and taxonomic status of an East Asian lineage within this group. We confirm that this lineage represents a distinct and previously misclassified species, <em>Euconulus harimensis</em>, which was formerly placed within the genus <em>Parakaliella</em>. While standard mtDNA and nDNA markers showed this evolutionary lineage as polyphyletic, two newly developed nuclear markers (ZN507 and TEP1) resolved the lineage, except for one individual, within a single robust clade of <em>E. harimensis</em>. Geometric morphometric analyses revealed significant differences in shell shape, which, along with unique shell microsculpture, further support its taxonomic separation. Although <em>E. harimensis</em> possesses the smallest distribution range of all related species, it exhibits the highest intraspecific genetic diversity. The models of suitable climatic conditions for both the present and the Last Glacial Maximum showed no major shifts, suggesting high climatic stability of the species range during the Pleistocene. This, along with other palaeobiogeographic factors, may have contributed to the unexpectedly high intraspecific genetic diversity of this species despite its limited range. Our findings provide new insights into the evolutionary processes that shape land snail inter- and intraspecific diversity, with implications for their taxonomy, which has often relied on shell morphology only. Additionally, phylogenetic analysis based on the new markers sheds novel light on the taxonomy and evolution of <em>E. fulvus</em> and <em>E. alderi</em>, highlighting the need for further taxonomic research.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108460"},"PeriodicalIF":3.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002074","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":"Contrasting diversification patterns across wood rushes from Luzula sect. Luzula (Juncaceae) revealed by 3RAD genome-wide sequencing","authors":"Carolina Carrizo García ,&nbsp;Valentin Heimer ,&nbsp;Peter Schönswetter ,&nbsp;Claudio Varotto ,&nbsp;Božo Frajman ,&nbsp;Mingai Li","doi":"10.1016/j.ympev.2025.108455","DOIUrl":"10.1016/j.ympev.2025.108455","url":null,"abstract":"<div><div>Among the different mechanisms triggering diversification processes, chromosomal rearrangements that generate karyotypic changes are common in plants. <em>Luzula</em> (Juncaceae) is among the few angiosperm genera with holocentric chromosomes, which can undergo chromosome fission (agmatoploidy) or fusion (symploidy), resulting in karyotypes with different chromosome numbers and sizes. In this study, 3RAD genome-wide sequencing data and plastid sequences were used to explore evolutionary trends and patterns of genetic diversification among diploid taxa of <em>Luzula</em> sect. <em>Luzula</em> centred in the European Alpine System. In addition, we inferred its phylogenetic relationships to other closely related sections, of which several proved to be non-monophyletic. The species of <em>Luzula</em> sect. <em>Luzula</em> are segregated into three lineages, which show contrasting patterns regarding bifurcated branching, reticulation, and levels of coancestry as a result of different evolutionary histories. Agmatoploid species are found in two of these clades, displaying different karyotypes, while the third lineage comprises only <em>L. campestris</em>. Based on a molecular dating reconstruction, at least two putatively independent transitions towards agmatoploidy are estimated, which have occurred between the mid- and late Pleistocene in <em>Luzula sect. Luzula</em>. In addition, several trans-continental migrations, e.g. between Europe and Africa, were inferred. This study provides a new perspective on the complexity of diversification among wood rushes, which may serve as a basis for future exploration of the occurrence of agmatoploidy and its role in species diversification.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108455"},"PeriodicalIF":3.6,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002049","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":"Complex reticulation in backbone subfamily relationships in Leguminosae","authors":"Jacob S. Stai ,&nbsp;Warren Cardinal-McTeague ,&nbsp;Anne Bruneau ,&nbsp;Steven B. Cannon","doi":"10.1016/j.ympev.2025.108438","DOIUrl":"10.1016/j.ympev.2025.108438","url":null,"abstract":"<div><div>Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies – Cercidoideae, Dialioideae, and Caesalpinioideae – bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the genera <em>Cercis</em> and <em>Poeppigia</em> apparently unduplicated descendants of one of the parental lineages. In Caesalpinioideae, the hybridization appears to involve a member of the Papilionoideae lineage, and some other lineage, potentially extinct. Several independent lines of evidence converged on a single backbone hypothesis and the above hypotheses of reticulate evolution: phylogenies calculated from both superalignments and from multi-tree coalescent-based analyses; concordance factor analysis of the set of gene family alignments and topologies; and direct inference of reticulation events via maximum pseudo-likelihood implemented by PhyloNet.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108438"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994775","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":"The evolutionary history of insect-associated xinmoviruses","authors":"Luis Hernández-Pelegrín","doi":"10.1016/j.ympev.2025.108453","DOIUrl":"10.1016/j.ympev.2025.108453","url":null,"abstract":"<div><div>Viruses are ubiquitous biological entities that shape host evolution and ecosystem dynamics. Among them, negative-sense single-stranded RNA (−ssRNA) viruses form a diverse group that includes well-characterized vertebrate pathogens and an expanding repertoire of invertebrate-infecting viruses. Recent advances in high-throughput sequencing have revealed numerous insect-associated −ssRNA viruses, reshaping our understanding of their diversity, transmission, and ecological significance.</div><div>This study identified 22 novel xinmoviruses, expanding the known host range of this viral family to include Lepidoptera and Plecoptera for the first time. Additionally, xinmovirus-derived non-retroviral endogenous viral elements (nrEVEs) were identified in multiple insect lineages, expanding previous findings that were limited to mosquitoes. Phylogenetic analysis of the <em>Xinmoviridae</em> family revealed host-driven evolutionary patterns with potential cross-order transmission events. Similarly, nrEVEs provided evidence of specific viral-host interactions, with nrEVEs showing greater similarity to exogenous viruses infecting the same insect order and, in some cases, the same insect species.</div><div>Together, these findings significantly expand the known diversity and evolutionary landscape of xinmoviruses. By uncovering new hosts, viral lineages, and genomic integrations, this study provides a more comprehensive framework for understanding their ecological distribution, transmission dynamics, and potential biological functions.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108453"},"PeriodicalIF":3.6,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994762","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":"Diversification in Amazonian Hypocnemis antbirds (Aves: Thamnophilidae) inferred from Ultraconserved Elements (UCEs)","authors":"Áurea Cronemberger ,&nbsp;Camila C. Ribas ,&nbsp;Alexandre Aleixo","doi":"10.1016/j.ympev.2025.108456","DOIUrl":"10.1016/j.ympev.2025.108456","url":null,"abstract":"<div><div>Warbling antbirds consist of an avian genus (<em>Hypocnemis</em>) with a wide distribution, confined to the Amazon basin, and whose true diversity and evolutionary history remain poorly understood. Here, we used sequences of 2,222 Ultra-conserved Elements (UCEs) and 30 exons loci from 58 specimens belonging to all currently recognized <em>Hypocnemis</em> species and all but one subspecies to infer phylogenies, population structure, interspecific limits, and the genus’ biogeographic history. A consensus of phylogenies, networks, and phylogeographic structure analyses recovered up to thirteen independent evolutionary units within the genus, which currently has eight named species. Except for one case, these lineages corroborate currently recognized taxa; based on our analyses, we propose the recognition of two additional species in the genus: <em>H. implicata</em> and <em>H. ochraceiventris</em>. From a biogeographic perspective, our estimated scenarios indicate separation of the two main <em>Hypocnemis</em> lineages during the Miocene, subsequent concentration of Pliocene splits in western and northern Amazonia, and more recent Pleistocene diversification in the southeastern part of the basin. Lineage relationships in the southeastern group are complex, and support a pattern whereby lineages in close contact on the Brazilian shield are not each other’s closest relatives. This pattern challenges simplistic biogeographic interpretations and suggests that independent range-expansion and admixture events, local extinction, and even behavioral attributes under strong divergent selection, may be coupled with vicariant scenarios.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108456"},"PeriodicalIF":3.6,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933764","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":"A single widespread species or multiple narrow endemics: a search for boundaries within the Piper amalago complex (Piperaceae)","authors":"James Smith ,&nbsp;Cara Hastings ,&nbsp;Christopher Davidson ,&nbsp;Sven Buerki ,&nbsp;Stephen Novak ,&nbsp;Allan Bornstein","doi":"10.1016/j.ympev.2025.108457","DOIUrl":"10.1016/j.ympev.2025.108457","url":null,"abstract":"<div><div>The delimitation of species boundaries has been a constant challenge to the fields of systematics, natural history, and conservation biology. Subtle and minor morphological differences in a widespread species complex make delimiting species boundaries particularly difficult. High throughput targeted sequencing of hundreds of loci has allowed researchers to obtain improved insights into evolutionary processes and resolved previously ambiguous phylogenetic relationships. <em>Piper amalago</em> (subgenus <em>Gonistum</em>) is morphologically similar to, and geographically overlaps with, many other Neotropical <em>Piper</em> species that have narrow restricted distributions, or occur as narrow endemics. Taxonomists have debated whether morphological differences between <em>P. amalago</em> and other similar species merit distinct species status or if these taxa represent a single widespread species exhibiting extensive intraspecific variation. Recent molecular analyses demonstrated that <em>P. amalago</em> is paraphyletic with morphologically similar species, notably <em>P. martensianum</em>, but these findings lack phylogenetic support. This study investigates the phylogenetic relationships of <em>P. amalago</em> and several closely related species using multiple DNA sequences, and seeks to determine whether species can be delimited on the basis of phylogenetic, geographical, and morphological information. The Angiosperms353 bait set was used to retrieve nuclear genes to build maximum likelihood and multispecies coalescent phylogenetic hypotheses. Available DNA sequence data are consistent with the presence of a single, monophyletic, widespread species complex, with considerable morphological variation and some geographic structure. While the drivers of the morphological variation within this complex are not yet fully understood, we have a better understanding of evolutionary relationships and species boundaries within <em>Piper</em>, a giant genus.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108457"},"PeriodicalIF":3.6,"publicationDate":"2025-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144933763","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":"Genome-based phylogenetics and species delimitation for the narrowly distributed Pachyhynobius salamander (Caudata: Hynobiidae) reveal cryptic biodiversity","authors":"Yongxuan Xiao ,&nbsp;Tingli Hu ,&nbsp;Suxin Shi ,&nbsp;Hui Wang ,&nbsp;Caiwen Zhang ,&nbsp;Dapeng Pang ,&nbsp;Yinfan Cai ,&nbsp;Tao Pan ,&nbsp;Pablo Orozco-terWengel ,&nbsp;Baowei Zhang","doi":"10.1016/j.ympev.2025.108458","DOIUrl":"10.1016/j.ympev.2025.108458","url":null,"abstract":"<div><div>Species delimitation is a challenging issue in taxonomy, especially in the absence of clear diagnostic morphological characters, a particular problem for cryptic species. In recent years, the rapid development of high-throughput sequencing technologies, when combined with genomic species delimitation methods such as the multispecies coalescent, has significantly improved the ability to resolve cryptic species. However, traditional methods like Bayesian phylogenetics and phylogeography often result in over-splitting due to their failure to fully consider factors such as gene flow. This study focuses on the genus <em>Pachyhynobius</em>, endemic to China, utilizing specific-locus amplified fragment sequencing technology to construct a high-quality nuclear genome SNP dataset. Systematic genomics combined with various species delimitation methods that incorporate the genealogical differentiation index and the isolation by distance model for geographic information was used to systematically evaluate the species boundaries of this genus. The results show that <em>Pachyhynobius</em> consists of four genetically independent, geographically disjunct lineages with deep genetic differentiation occurring over millions of years. Although these lineages have relatively close geographic distributions, long-term ecological niche conservatism and the sky island effect may be key driving forces responsible for their continued isolation and independent evolutionary paths. Multi-method species delimitation analysis further provides a comprehensive evaluation of the potentially distinct genetic lineages within the group, identifying them as potential cryptic species. Although new species have not yet been formally named, the evidence provided offers a new example for understanding the identification and evolutionary mechanisms of cryptic species in geographically restricted habitats.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108458"},"PeriodicalIF":3.6,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144926744","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}