Molecular Phylogenetics and Evolution最新文献

{"title":"Phylogeny and evolutionary history of the tribe Scymnini Mulsant, 1846 (Coleoptera: Coccinellidae) based on a multi-locus dataset, with emphasis on the Asian lineage","authors":"Weidong Huang ,&nbsp;Jiamin Zhuang ,&nbsp;Xinyue Liang ,&nbsp;Wenjing Li ,&nbsp;Xingmin Wang ,&nbsp;Xiaosheng Chen","doi":"10.1016/j.ympev.2025.108504","DOIUrl":"10.1016/j.ympev.2025.108504","url":null,"abstract":"<div><div>The tribe Scymnini Mulsant, 1846 (Coleoptera: Coccinellidae) is a species-rich and ecologically diverse group widely recognized for its role as a biocontrol agent against homopterous insects, including aphids, psyllids, mealybugs, and whiteflies. However, the phylogenetic relationships within Scymnini and their evolutionary history remain poorly understood. We present what is, to our knowledge, the first most taxonomically comprehensive molecular phylogeny of the tribe to date, with emphasis on the Asian lineage, aiming to establish a framework for future studies on this ecologically significant insect group. Phylogenetic trees were inferred using maximum likelihood and Bayesian approaches based on five nuclear and three mitochondrial markers, comprising a total of 4,935 bp. The ingroup included 94 Scymnini taxa, complemented by 40 outgroup species representing diverse coccinellid subfamilies and tribes, to test the phylogenetic relationships among Asian Scymnini. Our results indicate that the Asian Scymnini is paraphyletic, with <em>Axinoscymnus</em>, <em>Slipinskiscymnus</em>, and <em>Clitostethus</em> forming a distinct clade separate from the main Asian Scymnini lineage. Despite this, the analysis strongly supports the monophyly of these genera, along with <em>Nephus</em>, <em>Sasajiscymnus</em>, <em>Nephaspis</em>, and <em>Horniolus</em>. Additionally, the Asian <em>Scymnus</em> was recovered as paraphyletic, as two species of the subgenus <em>Scymnus</em> (<em>Orthoscymnus</em>) Canepari formed a well-supported clade distinct from the main <em>Scymnus</em> lineage. Molecular dating based on fossil record suggests that generic diversification within the Asian Scymnini occurred between the Paleocene and Miocene, while the common ancestor of Coccinellidae dates back to the Early Cretaceous, approximately 143 Ma. Our results provide a novel phylogenetic framework for revising Scymnini classification and offer new insights into its evolutionary history, with broader implications for understanding Coccinellidae phylogeny.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108504"},"PeriodicalIF":3.6,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145618279","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":"Leaping between branches: Hybridisation and the tangled evolutionary history of true lemurs","authors":"Giacomo Mercuri ,&nbsp;Giovanni Merici ,&nbsp;Kyle Kai-How Farh ,&nbsp;Lukas F.K. Kuderna ,&nbsp;Jeffrey Rogers ,&nbsp;Tomàs Marques-Bonet ,&nbsp;Giuseppe Donati ,&nbsp;Riccardo Percudani ,&nbsp;Cristian Capelli","doi":"10.1016/j.ympev.2025.108503","DOIUrl":"10.1016/j.ympev.2025.108503","url":null,"abstract":"<div><div>The true lemurs (genus <em>Eulemur</em>) are a genetically diverse and spatially widespread group of species inhabiting most of Madagascar’s forests. Including 12 recognized species, the genus can be divided into four major evolutionary groups: <em>E. rubriventer</em>, <em>E. mongoz</em>, the <em>Brown Lemur Species Complex (BLSC),</em> and the <em>coronatus-macaco-flavifrons complex</em> (CMFC), although monophyly for the CMFC is not always supported. Recent genome-based studies highlighted topological and chronological differences between nuclear and mitochondrial phylogenies of true lemurs, which could be explained by events of hybridisation. In order to reconstruct the evolutionary history of the genus, we test for gene-flow between <em>Eulemur</em> clades using a set of whole genome sequences representative of the diversity of the genus. Events of hybridization among true lemurs clades were identified, explaining discordances between mitochondrial and nuclear phylogenies and providing the context for mito-nuclear co-evolution, which we detected for <em>E. rubriventer.</em> Overall, by directly testing for hybridization among <em>Eulemur</em> species, we developed an evolutionary model that deepens our understanding of the unique and complex history of the genus <em>Eulemur</em>, and sets it as a starting point for future research.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108503"},"PeriodicalIF":3.6,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145618280","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":"Multiple origins, singular success: genomic evidence for past recurrent hybridization in Chenopodium album s. str. (Amaranthaceae)","authors":"Bohumil Mandák ,&nbsp;Farzaneh Habibi ,&nbsp;Dijana Čortan ,&nbsp;Alexander Belyayev ,&nbsp;David E. Jarvis ,&nbsp;Eric N. Jellen ,&nbsp;Peter J. Maughan ,&nbsp;Sergei L. Mosyakin ,&nbsp;Pertti Uotila ,&nbsp;Karol Krak","doi":"10.1016/j.ympev.2025.108500","DOIUrl":"10.1016/j.ympev.2025.108500","url":null,"abstract":"<div><div>Polyploidy, particularly allopolyploidy resulting from interspecific hybridization followed by chromosome duplication, plays a key role in plant diversification and ecological success. <em>Chenopodium album</em> s. str. is one of the world’s most widespread and morphologically variable weeds, yet the timing and mechanism of its origin as an allohexaploid (2n = 6x = 54) remained unresolved. Using RADseq data, this study investigated the origin of ‘BBCCDD’ allohexaploid <em>C. album</em> s. str. and closely related hexaploid taxa by analyzing their relationship to putative diploid progenitors with the ‘BB’ genome (<em>C. ficifolium</em>, <em>C. suecicum</em>, <em>C. ucrainicum</em>) and tetraploid species with the ‘CCDD’ subgenomic combination (<em>C. betaceum</em>, <em>C. glaucophyllum</em>, <em>C. novopokrovskyanum</em>, <em>C. striatiforme</em>). The genomic sequences were mapped to the chromosome-scale reference genome of <em>C. formosanum</em>, a closely related allohexaploid. Results reveal that <em>C. album</em> s. str. does not genetically align with contemporary diploid or tetraploid taxa, suggesting its origin from extinct ancestors rather than ongoing hybridization. Both its ‘BB’ and ‘CCDD’ subgenomes show higher or comparable number of genetic lineages, respectively, than its extant di- and tetraploid relatives, implying conservation of ancestral variation in the allohexaploid. Furthermore, 16 distinct subgenomic combinations were identified within <em>C. album</em> s. str., confirming its polytopic and repeated origin across geographic regions. This explains the remarkable morphological and ecological plasticity observed across its range. This research underscores <em>C. album</em> s. str. as an ancient, stabilized, and globally invasive polyploid, shaped by multiple hybridization events and fixed heterozygosity, offering parallels with other polyploid species such as <em>Triticum/Aegilops</em> complex.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108500"},"PeriodicalIF":3.6,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145530423","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":"Different expansion events of the actin and tubulin gene families within spirotrichean ciliates (Alveolate, Ciliophora)","authors":"Hua Su,&nbsp;Zengyu Song,&nbsp;Guoling Chai,&nbsp;Fangfang He,&nbsp;Yize Li,&nbsp;Yuxuan Qian,&nbsp;Xuefen Lu,&nbsp;Qi Zhang,&nbsp;Zhenzhen Yi","doi":"10.1016/j.ympev.2025.108489","DOIUrl":"10.1016/j.ympev.2025.108489","url":null,"abstract":"<div><div>Actin and tubulin are important components of eukaryotic cytoskeletons that participate in many fundamental cellular processes. As unicellular eukaryotes with abundant cytoskeletons, ciliates offer an excellent model for exploring the origin and evolution of these two gene families. Nonetheless, it remains unclear whether the evolutionary relationships between actin and tubulin subfamilies are consistent across closely related species. Additionally, previous studies inferred the evolutionary patterns of these gene families using different methods, therefore, evaluating the consistency of their results is necessary. Here, we analyzed the evolutionary histories of cytoskeletal subfamilies ActI, ActII, and β-Tub in spirotrichean ciliates based on PCR products and omics data. The results showed: (1) Early PCR-based Sanger sequencing provided valuable insights into evolutionary patterns of ciliate gene families, but primer biases may have limited coverage to certain gene family members. Omics data, though potentially incomplete for some species, offer a more comprehensive approach for future evolutionary studies by minimizing primer biases. (2) Actin and tubulin gene subfamilies exhibited distinct evolutionary patterns, with their histories diverging even within the same species. Expansions of different subfamilies occurred independently in various ancestral groups, and divergent evolutionary patterns between gene families may be associated their distinct biological functions. (3) Subfamilies ActI and ActII underwent different lineag-specific expansion events across spirotrichean groups. ActI expanded at least twice in Euplotia but not in other groups, whereas Euplotia and Hypotrichia each underwent a single ActII expansion. Collectively, these findings provided important insights into the complex evolutionary patterns of eukaryotic cytoskeletons.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108489"},"PeriodicalIF":3.6,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145427268","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":"Synchronous Miocene radiations and geographic-dependent diversification of pantropical Xylopia (Annonaceae)","authors":"Francis J. Nge ,&nbsp;David M. Johnson ,&nbsp;Nancy A. Murray ,&nbsp;Laura Holzmeyer ,&nbsp;Keegan Floyd ,&nbsp;Gregory Stull ,&nbsp;Vincent R.C. Soule ,&nbsp;Pierre Sepulchre ,&nbsp;Delphine Tardif ,&nbsp;Carlos Rodrigues-Vaz ,&nbsp;Thomas L.P. Couvreur","doi":"10.1016/j.ympev.2025.108485","DOIUrl":"10.1016/j.ympev.2025.108485","url":null,"abstract":"<div><h3>Aim</h3><div>The evolutionary drivers of hyperdiversity in tropical rain forests are complex and multifaceted. We used the pantropical <em>Xylopia</em> (Annonaceae) genus to address the diversification of rain forest lineages through time, across different regions, and into novel non-rain forest habitats with a comparative phylogenetic approach.</div></div><div><h3>Location</h3><div>Global (pantropical).</div></div><div><h3>Methods</h3><div>We generated a time-calibrated phylogeny of <em>Xylopia</em> using hybrid capture sequence data, including 88% (168/191 spp.) of species within the genus. Diversification analyses were conducted to test for the presence of rate heterogeneity (BAMM, ClaDS, CoMET) and environmental-dependent (RPANDA), geographic-dependent, and habitat dependent (GeoHiSSE) diversification in <em>Xylopia.</em></div></div><div><h3>Results</h3><div>Significant diversification rate heterogeneity was detected along the backbone of the core <em>Xylopia</em> clade, leading to near synchronous radiations across tropical regions globally in the Miocene, with higher diversification rates in Africa, Central America, and Madagascar, and lower rates in Australia + New Guinea. Transitions from rain forest to subhumid habitats led to lower diversification rates, whereas transitions to ultramafic habitats lead to higher rates. Regional diversification models indicate sea-level changes as an important driver for Asian, Australian, Pacific, and Neotropical clades and regional temperature changes as the main diversification driver for an African clade of <em>Xylopia</em>.</div></div><div><h3>Main conclusions</h3><div>Our study shows that despite synchronous radiations across regions, different regional environmental drivers have affected the diversification of <em>Xylopia</em> across tropical regions globally. A noteworthy example includes radiations of all five Malagasy clades <em>c.</em> 7 Ma coinciding with the establishment of heavy seasonal rainfall linked with the Indian monsoon. The diversification dynamics of rain forests are complex and heterogenous, with different clade-dependent and region-dependent environmental drivers.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108485"},"PeriodicalIF":3.6,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145427272","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 of Amazonian squirrel monkeys (Saimiri: Primates, Cebidae)","authors":"Michelle P. Mercês ,&nbsp;Hazel Byrne ,&nbsp;Natalie Finnegan ,&nbsp;Maria L. Harada ,&nbsp;Fernanda P. Paim ,&nbsp;Felipe E. Silva ,&nbsp;Anita Stone ,&nbsp;Marcela G.M. Lima ,&nbsp;Anthony B. Rylands ,&nbsp;José de Sousa e Silva Júnior ,&nbsp;Jessica W. Lynch","doi":"10.1016/j.ympev.2025.108487","DOIUrl":"10.1016/j.ympev.2025.108487","url":null,"abstract":"<div><div>Phylogenetic relationships among squirrel monkeys (genus <em>Saimiri</em>) are still poorly resolved. Morphology-based taxonomies range from two to 12 taxa, while molecular phylogenies have recovered up to 17 different lineages. The last species account lists 11 taxa: <em>Saimiri boliviensis boliviensis</em>, <em>S. boliviensis peruviensis</em>, <em>S. vanzolinii</em>, <em>S. oerstedii oerstedii</em>, <em>S. oerstedii citrinellus</em>, <em>S. sciureus</em>, <em>S. collinsi</em>, <em>S. cassiquiarensis, S. albigena</em>, <em>S. macrodon</em> and <em>S. ustus</em>. Here we gathered a phylogenomic dataset for <em>Saimiri</em> using <em>double digest</em> restriction-site associated DNA sequencing (ddRadseq) to construct a phylogeny for squirrel monkeys in Amazonia. All the phylogenomic analyses strongly supported the division of the genus in two main clades, corresponding to the Gothic- and Roman-arch groups based on morphology, and provided strong support for five major lineages: <em>S. boliviensis</em> + <em>S. vanzolinii</em>; <em>S. ustus</em>; <em>S. cassiquiariensis</em>; <em>S. macrodon</em>; and <em>S. sciureus</em> + <em>S. collinsi</em>. Structure analyses showed evidence for population clusters based on geography within these lineages, but also shared ancestry across clusters, and Dsuite analyses showed evidence for gene flow across the Gothic species. Our time-calibrated tree confirmed that the diversification of Amazonian <em>Saimiri</em> occurred during the Pleistocene.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108487"},"PeriodicalIF":3.6,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145427274","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":"Harnessing transposable elements: A new frontier in insect systematics","authors":"Shiyu Du ,&nbsp;Feng Zhang","doi":"10.1016/j.ympev.2025.108486","DOIUrl":"10.1016/j.ympev.2025.108486","url":null,"abstract":"<div><div>Insect genomes are largely composed of non-coding repetitive sequences, often exceeding 50 % of the total genomic content; these are also known as transposable elements (TEs). The increasing availability of extensive insect genomes, facilitated by advancements in sequencing technology, has made it feasible to explore the potential of TEs in insect systematics. Exhibiting varying degrees of differentiation across taxonomic levels, insect TEs may serve as informative characters for species-level analyses. This study focused on the Drosophiloidea as a case to evaluate the potential of TEs as phylogenetic markers and for insect phylogeny. We identified 2,390 species-specific TE families using genomes from 128 species and quantified their copy numbers in each species. Subsequently, we constructed phylogenetic trees based on the presence/absence (0/1 coding) of these TEs using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference methods. Comparison with the recognized phylogeny showed incongruences in overall topology, especially at higher levels (suprageneric), where TE-based trees recovered about 51–55.8 % of nodes consistent with the phylogeny. At lower levels (infrageneric), TEs recovered monophyly in 54.5–68.2 % of nodes. Given the limitations of tree-based methods in resolving the relationships of species, we performed clustering analysis on normalized and dimensionally reduced TE copy numbers, which revealed that TEs can effectively distinguish closely related species. Furthermore, by considering the phylogenetic signal strength of TEs, we found that phylogenetic trees constructed using TEs with higher RI values (&gt;0.5) exhibited the smallest normalized Robinson-Foulds distances to known phylogenies (0.379–0.408), indicating that accounting for phylogenetic signal may improve inference accuracy. Notably, we observed no significant difference (<em>p</em>-values = 0.7425) in the performance of TEs between genomes generated by next-generation and third-generation sequencing platforms. Clustering analysis of different TE types (including LTR, SINE, LINE, RC, DNA, and Unknown) indicated that all types provide comparable resolution for species delimitation. Overall, TEs show greater utility at lower taxonomic levels, particularly for species delimitation. This study provides insights into the use of genome-wide TE features for insect systematics, contributing to a better understanding of their application in phylogenetic and taxonomic studies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108486"},"PeriodicalIF":3.6,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145398587","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":"Museomics resolves 200 years of taxonomic uncertainty: Strix pulsatrix Wied, 1820 (Strigiformes, Strigidae) is a valid species","authors":"Sergio D. Bolívar-Leguizamón ,&nbsp;Aline Henrique Corrêa ,&nbsp;Glayson Ariel Bencke ,&nbsp;Luís F. Silveira","doi":"10.1016/j.ympev.2025.108488","DOIUrl":"10.1016/j.ympev.2025.108488","url":null,"abstract":"<div><div>The identification of valid species is central to biology, and genetic data have been essential in uncovering new taxonomic units across groups. For polytypic taxa, genetics helps distinguish valid units from natural variation. <em>Pulsatrix perspicillata</em> (Spectacled Owl) is a widespread polytypic species with six recognized subspecies. We used genetic data and museomics techniques to: (i) test the validity of <em>Strix pulsatrix</em> <span><span>Wied, 1820</span></span> (=<em>Pulsatrix perspicillata pulsatrix</em>) as a species distinct from <em>Pulsatrix perspicillata</em>; and (ii) estimate the phylogenetic relationships and divergence times within the genus <em>Pulsatrix</em> Kaup, 1848. We conducted population structure and phylogenetic analyses using SNPs matrices and alignments of Ultraconserved Elements (UCEs) from 16 individuals of <em>Pulsatrix</em> spp., including four historical samples of <em>P. p. pulsatrix</em>. Additionally, we sequenced the mtDNA-ND2 gene from 38 samples representing all known <em>Pulsatrix</em> species to further elucidate phylogenetic relationships and estimate divergence times. Our results indicate that <em>Pulsatrix perspicillata pulsatrix</em> represents an independent lineage from <em>P. perspicillata</em>, as supported by its reciprocal monophyly and distinct population structure. UCE analyses also grouped <em>P. koeniswaldiana</em> (Tawny-browed Owl) and <em>P. melanota</em> (Band-bellied Owl) into a distinct cluster. Phylogenetic analyses based on both UCEs and mtDNA-ND2 sequences support the monophyly of the genus <em>Pulsatrix</em>. <em>Pulsatrix koeniswaldiana</em> and <em>P. melanota</em> form a monophyletic group that is sister to <em>P. perspicillata</em>. <em>Pulsatrix</em> diverged in the Late Miocene and diversified in the Pliocene-Quaternary. The evolutionary history of <em>Pulsatrix</em> appears to have been influenced by (a) the final phase of the Andean uplift and (b) climatic oscillations during the Pleistocene. <em>Pulsatrix p. pulsatrix</em> shows genetic divergence consistent with a species-level split from <em>P. perspicillata</em>, and we henceforth recognize it as <em>Pulsatrix pulsatrix</em> (<span><span>Wied, 1820</span></span>). We recommend future studies to assess its current distribution and inform the development of conservation strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"215 ","pages":"Article 108488"},"PeriodicalIF":3.6,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145403004","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 framework, biogeography and character evolution of the genus Campylotropis (Fabaceae, Papilionoideae)","authors":"Li-Sha Jiang ,&nbsp;Yu Feng ,&nbsp;Jun-Yi Zhang ,&nbsp;Xiong Li ,&nbsp;Min Liao ,&nbsp;Heng-Ning Deng ,&nbsp;Qi Yu ,&nbsp;Bo Xu","doi":"10.1016/j.ympev.2025.108484","DOIUrl":"10.1016/j.ympev.2025.108484","url":null,"abstract":"<div><div>The shrub genus <em>Campylotropis</em> (Fabaceae, trib. Desmodieae, subtrib. Lespedezinae) encompasses approximately 40 species, predominantly distributed across temperate and subtropical East Asia, with its diversity centered in the Hengduan Mountains and southern China. Historical constraints in sampling and methodological approaches have long obscured its evolutionary history and species relationships. This study provides the most comprehensive phylogenomic analysis of <em>Campylotropis</em> to date, incorporating 91 samples representing 40 taxa. Leveraging sequence data from 77 plastid genes and 1,233 single-copy nuclear genes (SCGs), we reconstructed the genus’s phylogenomic framework, estimated divergence times, inferred ancestral area distributions, and traced the evolution of key morphological traits. Our results robustly confirm the monophyly of <em>Campylotropis</em>, distinguishing it from allied genera. We delineated six well-supported clades within the genus and resolved previously unresolved relationships. The conflicts between nuclear and chloroplast phylogenies highlight a complex evolutionary history, likely influenced by chloroplast capture and incomplete lineage sorting (ILS) during rapid radiation. We found that global climate change and tectonic activities since the late Miocene likely shaped lineage diversification, with Quaternary climate oscillations potentially triggering rapid radiation within the genus. Ancestral area reconstruction suggests that <em>Campylotropis</em> originated in the Hengduan Mountains and southern China before dispersing swiftly across adjacent East Asian regions. By integrating extensive sampling with nuclear genomic data, this study elucidates the evolutionary history of <em>Campylotropis</em> and enhances our understanding of diversification processes in biodiversity hotspots.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108484"},"PeriodicalIF":3.6,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145416753","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 “Genomic and phenotypic characterization of Thermosynechococcus-like strains reveals eight species within the genus Thermosynechococcus and a novel genus Parathermosynechococcus gen. nov.”. [Mol. Phylogenet. Evol. 197 (2024) 108094]","authors":"Jie Tang ,&nbsp;Ying Jiang ,&nbsp;Zhe Hu ,&nbsp;Huizhen Zhou ,&nbsp;Dawei You ,&nbsp;Maurycy Daroch","doi":"10.1016/j.ympev.2025.108479","DOIUrl":"10.1016/j.ympev.2025.108479","url":null,"abstract":"","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108479"},"PeriodicalIF":3.6,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356843","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}