Molecular Phylogenetics and Evolution最新文献

{"title":"Algae-to-host horizontal gene transfer in Paramecium bursaria is associated with host adaptation during endosymbiosis.","authors":"Lei Yang, Deyu Wei, Yuan Li, Xiao Chen","doi":"10.1016/j.ympev.2026.108726","DOIUrl":"10.1016/j.ympev.2026.108726","url":null,"abstract":"<p><p>Paramecium bursaria maintains a stable endosymbiosis with green algae, yet the evolutionary consequences of this association remain unclear. Here, we screened the host genome for algal-derived horizontally transferred genes (HTGs) using a lineage-aware workflow designed to detect horizontal gene transfer (HGT) between two defined lineages. We identified 16 candidate HTGs, including four putative newly transferred genes and 12 homologous transferred genes, most of which were functionally associated with redox homeostasis and metabolism. Five HTGs showed symbiosis-dependent expression. RNAi knockdown of GH32s and SATs reduced host proliferation, total cell area, and motility, while GH32s knockdown also reduced endosymbiont load. Duplication patterns suggest that most transfers may have occurred after the P. bursaria lineage diverged from the sampled Paramecium species but before its lineage-specific whole-genome duplication (WGD). The HTGs also showed host-associated shifts in GC content and gene length, while representative HTGs retained conserved domains and functional motifs. Together, our results support algae-to-host HGT in P. bursaria and suggest that some transferred genes may contribute to metabolic integration during endosymbiosis.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108726"},"PeriodicalIF":4.0,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851721","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":"Corrigendum to \"Reticulate evolution, introgression, and recent diversification in Epimedium sect. Macroceras\" [Molecul. Phylog. Evol. 223 (2026) 108646].","authors":"Emi Kusatake, Momoka Konishi, Shuto Tomokuni, Yosuke Yanagi, Shungo Kariyama, Takehito Itoh, Atsushi Toyoda, Seung-Chul Kim, Makiko Mimura","doi":"10.1016/j.ympev.2026.108713","DOIUrl":"10.1016/j.ympev.2026.108713","url":null,"abstract":"","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108713"},"PeriodicalIF":4.0,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148762510","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":"Introgression shapes the genomic conflict landscape of Malus, providing evidence for a reticulate backbone in a woody crop lineage.","authors":"Xiao-Ya Li, Zhao-Qian Niu, Ya-Wen Zheng, Jue-Lin Huang, Dai-Kun Ma, Jia-Xin Huang, Qiang Hao, Ti-Cao Zhang, Si-Yu Xie, Chao Xu, Bin-Bin Liu","doi":"10.1016/j.ympev.2026.108702","DOIUrl":"10.1016/j.ympev.2026.108702","url":null,"abstract":"<p><p>Phylogenomic discordance is widespread across plants, but its evolutionary significance is often obscured when conflict is treated primarily as analytical noise rather than as evidence of underlying processes. In woody lineages in particular, incomplete lineage sorting, introgression, and genome duplication can interact over long timescales to produce complex genomic histories that are not adequately summarized by a strictly bifurcating tree. Here, we use Malus as a model woody genus to investigate how these processes structure conflict across a genus-scale, accession-based phylogenomic framework. Using broad taxon sampling, hundreds of nuclear loci, plastid genomes, and genome-wide SNP summaries, we reconstruct a robust nuclear backbone for sampled Malus lineages and evaluate where discordance is concentrated and which processes best explain it. Nuclear analyses resolve eight major clades, whereas conflict is non-random and localized to recurrent hotspots rather than evenly distributed across the tree. Cytonuclear discordance is similarly concentrated, especially around Clade H, represented by sampled accessions of M. tschonoskii, where localized plastid-nuclear disagreement is consistent with candidate plastid capture or organellar introgression. Multiple complementary analyses further indicate that the strongest conflict is not explained by ILS alone, but instead reflects lineage-structured introgression, while polyploid complexes represent additional localized sources of evolutionary complexity. Together, these results provide evidence for a reticulate genomic backbone in Malus and show how integrating nuclear, plastid, and genome-wide conflict analyses can help distinguish background discordance from process-specific signals in woody plant radiations. Several lineage-level reticulation hypotheses identified here should now be tested with broader population-level sampling and curated reference accessions.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108702"},"PeriodicalIF":4.0,"publicationDate":"2026-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148702930","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 and evolution of the Lauraceae based on targeted capture data.","authors":"Zhi Yang, Yuyu Ye, Francis J Nge, Bing Liu, Yong Yang","doi":"10.1016/j.ympev.2026.108735","DOIUrl":"https://doi.org/10.1016/j.ympev.2026.108735","url":null,"abstract":"<p><p>The family Lauraceae, a hyper-diverse magnoliid family comprising approximately 63 genera and over 3,000 species, plays a key ecological role in tropical and subtropical forests. Yet deep relationships among its nine tribes remain unresolved, likely due to limited sampling and complex evolutionary processes such as incomplete lineage sorting (ILS) and gene flow. To address these challenges, we generated datasets of 255 single-copy nuclear genes and chloroplast genomes using a newly designed Lauraceae-specific probe set, achieving the most comprehensive genus-level sampling (84%) to date. Phylogenomic analyses reconstructed a robust nuclear tree, which resolved the Neocinnamomeae as sister to the Caryodaphnopsideae and revealed pronounced gene tree conflict and pervasive cytonuclear discordance. To investigate the evolutionary processes underlying these patterns, comprehensive analyses were conducted. The results indicate that conflicting nuclear gene trees reflect the combined effects of ILS, gene tree estimation error, and gene flow, with ILS dominating across the core Lauraceae, whereas cytonuclear discordance is primarily driven by extensive gene flow. Diversification analyses further indicate that episodes of rapid lineage accumulation coincide with major gene flow events, suggesting a potential role of gene flow in the diversification of Lauraceae. Overall, this study provides a robust nuclear phylogenomic framework for Lauraceae and demonstrates that gene flow had profound effects on its evolutionary history, shedding light on the contribution of gene flow to the diversification of hyper-diverse tropical plant lineages.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108735"},"PeriodicalIF":4.0,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148898316","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":"Paralogous evolution of the ITS2 region in Xiphophorus.","authors":"Kang Du, Manfred Schartl, Gabriel A Preising, Yuan Lu, Matthias Wolf, Dunja K Lamatsch","doi":"10.1016/j.ympev.2026.108725","DOIUrl":"10.1016/j.ympev.2026.108725","url":null,"abstract":"<p><p>Ribosomal ITS2 is widely used in phylogenetic studies, yet its multigene organization and potential paralogy can obscure true species relationships. This proof-of-concept study investigates whether ITS2 sequences derived from long-read genomic data in multiple Xiphophorus species primarily reflect orthologous history or are shaped by ancient and local duplications. Phylogenetic analyses reveal two major, reciprocally mirroring ITS2 clades that represent long-standing paralogous rDNA lineages rather than simple allelic variants. The two paralogons show strong asymmetry in copy retention and loss for the majority of the species analyzed in this study. Exceptionally some other species are confined to one paralogon group and exhibit alternating ITS2 variants consistent with persistent ancestral polymorphism. A striking copy number imbalance in X. variatus, combined with its phylogenetic incongruence relative to the established species tree, is best explained by historical rDNA introgression followed by biased concerted evolution that nearly erased one paralogous copy. Despite incomplete homogenization, heterogeneous evolutionary rates, and occasional long-branch artifacts, the recovered paralog-specific topologies largely recapitulate the accepted Xiphophorus species phylogeny, indicating that ITS2 retains a robust organismal signal while also recording episodes of introgression and differential paralog evolution. These results demonstrate that explicit recognition of ITS2 paralogs can both improve phylogenetic interpretation and open avenues for future sequence-structure-based analyses of rDNA evolution and genus-level systematics in Xiphophorus.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108725"},"PeriodicalIF":4.0,"publicationDate":"2026-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148860552","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":"Gradual evolutionary trajectories of mitochondrion-related organelles in anaerobic SLAMP ciliates (Eukaryota, Alveolata).","authors":"Jia Li, Changyu Zhu, Guoling Chai, Fangfang He, Zengyu Song, Zhicheng Chen, Miaoying Chen, Zhenzhen Yi","doi":"10.1016/j.ympev.2026.108721","DOIUrl":"10.1016/j.ympev.2026.108721","url":null,"abstract":"<p><p>Ciliates are an excellent model for studying convergent transitions from mitochondria to mitochondrion-related organelles (MROs) in protists. Despite our growing knowledge of adaptive evolution in ciliate MROs, the progressive evolutionary trajectories within anaerobic ciliate lineages and the MRO metabolisms of facultatively anaerobic ciliates remain unexplored. In this study, we predicted MRO metabolisms of eight species within the anaerobic monophyletic APM (Armophorea, Parablepharismea, Muranotrichea) clade and a facultative anaerobe from its sister class Spirotrichea. Our main results are as follows: (1) During their adaptation to anaerobic environments, the MRO electron transfer chain (ETC) components and their associated functions have been progressively lost in the APM clade. (2) The MRO of the last common ancestor of Armophorea likely possesses complexes Ⅰ, Ⅱ, and Ⅴ, but lacks functional complexes Ⅲ and Ⅳ. Subsequently, during their adaptation to anaerobic environments, the armophorean lineage has further lost complex Ⅴ in the order Clevelandellida and Metopida. (3) In the MRO of the facultatively anaerobic ciliate Heterodeviata sinica, complexes Ⅲ and Ⅳ are absent, and alternative oxidases (AOX) play a key role in adaptation to fluctuating dissolved oxygen levels. (4) The fused [FeFe]-hydrogenase appears to have been acquired by the last common ancestor of ciliates through horizontal gene transfer (HGT), followed by multiple independent losses. Our results provide insights into the progressive adaptations of anaerobic ciliates to the low-oxygen environments.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108721"},"PeriodicalIF":4.0,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148857738","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 deceitful claw: Erection of Synonyx gen. Nov. and Synonyxidae fam. Nov. in Hypsibioidea (Eutardigrada: Parachela).","authors":"Pritam K Dey, Napat Emdee, Piotr Gąsiorek, Alejandro López-López, Łukasz Michalczyk","doi":"10.1016/j.ympev.2026.108692","DOIUrl":"https://doi.org/10.1016/j.ympev.2026.108692","url":null,"abstract":"<p><p>Claws are strongly sclerotised elements of tardigrade exoskeleton of a great phylogenetic and taxonomic importance. Although several general claw curvatures and anatomies can be distinguished within Eutardigrada, some more subtle differences in claw architecture have evaded the attention of taxonomists and have caused profound errors in species classification. Our study exposes a particularly deceitful morphotype and has widespread consequences for parachelan systematics, affecting two of the three major superfamilies in the order. Specifically, we analysed integratively 26 populations representing the Ursulinius cameruni complex from India and multiple locations in Australasia. Our genetic and morphological analyses demonstrate that this evolutionary lineage does not belong in Isohypsibioidea, but in Hypsibioidea. Moreover, some other taxa previously classified in different hypsibioid families are transferred to the new lineage. Specifically, Synonyxidae fam. nov. and Synonyxgen. nov. are established to accommodate the unique claw and cuticular morphotype of the Ursulinius cameruni complex. Also, Synonyx panjurliisp. nov., the type species for the new genus, is described from India, and two further hypsibioidean species are transferred from other genera to Synonyxgen. nov.: S. antonovaecomb. nov. (formerly Hypsibiidae: Hypsibius) and S. gibbosuscomb. nov. (formerly Acutuncidae: Mixibius). All these systematic changes clearly reflect the difficulties associated with a proper interpretation of claw structure in this peculiar phylogenetic linage. The evolution of Synonyxidae fam. nov. in Hypsibioidea is discussed in detail. Additionally, we elaborate on the taxonomic status and composition of Mixibius.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108692"},"PeriodicalIF":4.0,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148537423","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":"Out of North Africa: Evolution and biogeography of Afro-Arabian dwarf tarantulas (Theraphosidae, Ischnocolinae)","authors":"Jan Korba,&nbsp;Vera Opatova","doi":"10.1016/j.ympev.2026.108559","DOIUrl":"10.1016/j.ympev.2026.108559","url":null,"abstract":"<div><div>Large-scale vicariant events are expected to create congruent phylogeographic patterns among unrelated taxa. A continental-wide disjunction displayed by unrelated plant taxa across Afro-Arabia (the RAND flora pattern) has been traditionally explained as a consequence of late Miocene aridification of the region and the formation of the Sahara Desert. We implement genomic data (UCE), divergence time estimation and biogeographic analyses to uncover the origins of RAND pattern distribution in dwarf tarantula genus <em>Ischnocolus</em> <span><span>Ausserer, 1871</span></span>. The results suggest that the disjunct distribution of <em>Ischnocolus</em> resulted from ecological vicariance driven by the Middle Miocene climate cooling, predating the timing of the aridification of the region. Our results thus bring evidence of phylogeographic discordance of the RAND pattern origins among different taxa. Conserved lifestyle and the preference for humid environments among the early diverging <em>Ischnocolus</em> lineages also suggest that dispersal across Afro-Arabia was likely catalyzed by interspecific competitive exclusion. Subsequent lifestyle switches, that enabled the dwarf tarantulas to successfully colonize dry environments, evolved repeatedly in the group’s evolution. Additionally, we delimit the boundaries of the genus <em>Ischnocolus</em> and assess its position within the tarantula phylogeny. As a consequence, we revalidate the genus <em>Luphocemus</em> Denis, 1960, which is endemic to North Africa.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108559"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146137692","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":"Limitations of molecular dating using constant birth–death rate priors in deep time reflected in Brachiopoda evolution","authors":"Luyan Li ,&nbsp;Joëlle Barido-Sottani ,&nbsp;Daniele Silvestro","doi":"10.1016/j.ympev.2026.108557","DOIUrl":"10.1016/j.ympev.2026.108557","url":null,"abstract":"<div><div>Molecular dating often struggles to align with fossil records when divergence times are estimated in deep evolutionary history, particularly during the Palaeozoic era. This discrepancy may arise because of the assumptions embedded in constant birth–death rate priors, which oversimplify complex evolutionary dynamics and remain the default setting in most analyses. In the present study, we tested the impact of different models and priors on phylogenetic inference on a dataset of Rhynchonellata (Brachiopoda), and explored whether the divergence times inferred from molecular clocks and fossils can be reconciled. In particular, we addressed rate heterogeneity, that is, variation in speciation (λ) and extinction (μ) rates over time, in divergence time estimation by incorporating the birth–death rates inferred independently from fossil occurrence data as rate priors and calibration points. These were reviewed using Marshall’s temporal calibration method and ancestral state reconstruction. We showed that using the birth–death skyline model as a tree prior significantly reduces the gap between age estimates. Furthermore, to assess the generality of these patterns beyond a deeply diverging clade, we conducted a robustness check using Lingulidae, a comparatively young, re-diversified lineage, and determined that skyline models also produced divergence-time estimates more consistent with those inferred from the fossil record in this dataset. Overall, we showed that using a constant birth–death rate prior, which ignores rate heterogeneity, can affect the accuracy of the resulting phylogenetic trees. Our results revealed that when the lineages used for molecular dating persisted through the Cambrian explosion, Ordovician extinction, and Permian-Triassic (P-T) boundary, caution should be implemented in the interpretation of phylogenetic inferences as the data from molecular alignments alone and standard model assumptions may not reflect the significant shifts in diversification dynamics that occurred during these time periods. These findings highlight the inadequacy of constant birth–death rate priors in the presence of rate heterogeneity across deep time, thus limiting their reliability for studying lineages with complex evolutionary histories. Our analyses showed that informative priors from independent analyses of the fossil occurrences can improve the quality of molecular clock analyses, indicating the requirement of more flexible models to improve the precision of molecular dating in deep-time research.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108557"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159503","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":"Structural dynamics of chloroplast genome in Paphiopedilum (Orchidaceae): in response to natural hybridization","authors":"Xue-Ying Wei ,&nbsp;Ai-Qun Hu ,&nbsp;Jin Zhou ,&nbsp;Jiang-Ping Shu ,&nbsp;Wei-Yue Sun ,&nbsp;Li-Qiang Li ,&nbsp;Jian-Wen Shao ,&nbsp;Hui Wang ,&nbsp;Yue-Hong Yan","doi":"10.1016/j.ympev.2025.108521","DOIUrl":"10.1016/j.ympev.2025.108521","url":null,"abstract":"<div><div>Chloroplast genomes, once considered highly conserved, have been shown to exhibit significant structural variations, though the underlying mechanisms remain unclear. In this study, we investigated the chloroplast genome structure of eight populations comprising 76 individuals of <em>Paphiopedilum barbigerum</em>, <em>P. helenae</em>, and <em>P. vejvarutianum</em>. By using chloroplast genome sequences and 15,924 nuclear SNP loci, we conducted analyses and validations of chloroplast genome structural recombination and natural hybridization. Our key findings include the following: (1) Structural variations in the chloroplast genomes were found to be stable and heritable across populations. (2) In <em>P. barbigerum</em>, populations exhibiting structural variation contained an unidentified insertion sequence in the SSC region, which was associated with a significant reduction in GC content within this region. (3) The presence of non-LTR retrotransposons suggests their potential role in the expansion and contraction of the IR region in <em>Paphiopedilum</em>, with this chloroplast variation potentially linked to natural hybridization events. (4) The incongruent phylogenetic relationships, gene flow and gene introgression among <em>P. barbigerum</em>, <em>P. helenae</em>, and <em>P. vejvarutianum</em> point to a history of hybridization within these species. Our study proposes that both transposon activity and hybridization play crucial roles in driving chloroplast structural variations. For the first time, the structural variations of chloroplasts have been linked to transposons and natural hybridization, breaking the traditional stereotype of chloroplasts being highly conserved. This discovery enhances our understanding of how natural hybridization contributes to species formation and provides a basis for exploring the evolutionary mechanisms of chloroplast genomes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"218 ","pages":"Article 108521"},"PeriodicalIF":3.6,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745409","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}