Molecular Phylogenetics and Evolution最新文献

{"title":"Novel island species elucidate a species complex of Neotropical crocodiles","authors":"Jose Avila-Cervantes ,&nbsp;Pierre Charruau ,&nbsp;J. Rogelio Cedeño-Vázquez ,&nbsp;Hoai-Nam Bui ,&nbsp;Miryam Venegas-Anaya ,&nbsp;Marta Vargas ,&nbsp;Marco A. López-Luna ,&nbsp;Héctor González-Cortés ,&nbsp;David A. Macías-Díaz ,&nbsp;Jonathan S. Pérez-Flores ,&nbsp;Gabriel Barrios-Quiroz ,&nbsp;J. Miguel Salazar ,&nbsp;W. Owen McMillan ,&nbsp;Hans C.E. Larsson","doi":"10.1016/j.ympev.2025.108341","DOIUrl":"10.1016/j.ympev.2025.108341","url":null,"abstract":"<div><div>The evolutionary history of Neotropical crocodiles has remained elusive. They inhabit a broad geographic range with populations spanning from coastal, inland, and insular locations. Using a selection of natural insular, coastal, and one inland population of <em>C. acutus</em>, coastal <em>C. moreletii</em>, and the single surviving population of <em>C. rhombifer</em>, we discovered a remarkable genetic diversity for the group. Moreover, geometric morphometric results of skull shapes shows that these crocodylus species span a morphological cline. We recovered a high genetic differentiation between <em>C. moreletii</em>, <em>C. rhombifer</em>, and five clusters of <em>C. acutus</em>. The genetic and geographic differences among the <em>C. acutus</em> clusters were used to suggest these may be a species complex. Several ecological, morphological and genetics traits are identified in the well-studied populations from Banco Chinchorro and Cozumel islands off the Mexican Yucatan Peninsula to support discrete species designations for these populations. This work suggests the presence of rapid, recent evolution of several cryptic <em>Crocodylus</em> species throughout the Neotropics.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108341"},"PeriodicalIF":3.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143739269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes – with particular focus on Hymenocoleus Robbr.","authors":"Lovisa Thilén ,&nbsp;Olivier Lachenaud ,&nbsp;Olle Thureborn ,&nbsp;Sylvain G. Razafimandimbison ,&nbsp;Catarina Rydin","doi":"10.1016/j.ympev.2025.108338","DOIUrl":"10.1016/j.ympev.2025.108338","url":null,"abstract":"<div><div>Members of the tribe Palicoureeae of the coffee family (Rubiaceae) have a complex taxonomic history and have been the focus of few modern systematic studies. The tribe comprises about 1,100 tropical species in ten genera. To investigate phylogeny, we used a target capture approach and the angiosperm-wide Angiosperms353 bait set to produce genomic data for a representative taxon sample of Palicoureeae, with particular focus on the African genus <em>Hymenocoleus</em>. Using coalescent-based inference methods, we find that <em>Puffia gerrardii</em> (recently separated from <em>Geophila</em>) is sister to <em>Hymenocoleus</em>. The deepest split in <em>Hymenocoleus</em> is highly affected by incomplete lineage sorting, possibly as a consequence of rapid speciation during the early evolution of the clade. Remaining interspecific relationships in <em>Hymenocoleus</em> could be confidently resolved and while Robbrecht’s traditional infrageneric classification scheme based on floral features is not supported as reflecting evolution in the group, we find that several other features do, e.g. characters of pyrenes and involucral cups. Although not free of challenges, a strong advantage with our analytical approach is that gene tree heterogeneity can be taken into account. Including flanking regions yielded data sets that had the strongest power to reject polytomies and produced less gene tree error, resulting in species trees with higher normalised quartet scores and higher average support compared to trees inferred only from exon data. Presumably paralogous loci are often filtered out prior to species tree estimation but we find that they may contribute important phylogenetic information when using an inference method that actively accounts for them.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"208 ","pages":"Article 108338"},"PeriodicalIF":3.6,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756155","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":"Phylogenetic relationships and species composition of host community influence the transmission of coronaviruses in sympatric bats","authors":"Chen Zhang ,&nbsp;Hao Gu ,&nbsp;Jie Peng ,&nbsp;Biao He ,&nbsp;Yuhang Liu ,&nbsp;Xiaomin Yan ,&nbsp;Jiang Feng ,&nbsp;Ying Liu","doi":"10.1016/j.ympev.2025.108343","DOIUrl":"10.1016/j.ympev.2025.108343","url":null,"abstract":"<div><div>Since the emergence of Severe Acute Respiratory Syndrome (SARS) in 2002, bats have been recognized as important reservoirs of diverse coronaviruses (CoVs). Despite extensive research on the broad geographic transmission of bat CoVs, there is a notable gap in understanding the transmission dynamics within sympatric bat communities. Using a phylogeographic Bayesian statistical framework, we examined CoV transmission patterns and their determinants in a region where four bat roosting caves coexist and CoVs circulate persistently. Our findings reveal that two subgenera of CoVs, α-CoVs and β-CoVs dominate different bat caves at varying times. Notably, β-CoVs show more frequent cross-species transmission events among the dominant reservoir hosts, bats of Rhinolophidae. Phylogenetic distance between host species emerges as the key influence factor of viral cross-species transmission, whereas cohabitation duration and the number of hosts sharing caves do not significantly influence viral transmission. In addition, we emphasize that the compositional similarity of species in the roosting caves is critical for the inter-cave transmission of bat-CoVs, rather than the distance between cave. These results provide novel insights into the complex transmission dynamics of bat CoVs within sympatric bat communities.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108343"},"PeriodicalIF":3.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Explosion of goby fish diversity at the Eocene-Oligocene transition","authors":"W. Tyler McCraney ,&nbsp;Christine E. Thacker ,&nbsp;Brant C. Faircloth ,&nbsp;Richard C. Harrington ,&nbsp;Thomas J. Near ,&nbsp;Michael E. Alfaro","doi":"10.1016/j.ympev.2025.108342","DOIUrl":"10.1016/j.ympev.2025.108342","url":null,"abstract":"<div><div>A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34–33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (<em>Acanthomorpha</em>: <em>Percomorpha</em>: <em>Gobiiformes</em>) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of <em>Apogonidae</em> and <em>Gobioidei</em> to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108342"},"PeriodicalIF":3.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143726295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mixed, not stirred: Genomic data confirm the first case of interspecific hybridization in planarian triclads (Platyhelminthes: Tricladida) and raise questions about a possibly novel form of hybrid speciation","authors":"Daniel Dols-Serrate ,&nbsp;Longhua Guo ,&nbsp;Leonid Kruglyak ,&nbsp;Marta Riutort","doi":"10.1016/j.ympev.2025.108339","DOIUrl":"10.1016/j.ympev.2025.108339","url":null,"abstract":"<div><div>Speciation is a complex process where many evolutionary forces interplay. The Mediterranean is acknowledged as one of the most relevant biodiverse areas in the Palearctic region and researchers have long studied the species inhabiting it to pursue the goals of evolutionary biology. Here, we study a complex of freshwater flatworm species of the genus <em>Dugesia</em> from Corsica and Sardinia using restriction site-associated DNA sequencing (specifically, 3RAD) data to unravel their evolutionary history and tackle the processes driving it. We assess the phylogenetic relationships and population structure within the group and evaluate new species boundaries using multispecies coalescent approaches. Furthermore, we offer insights into the environmental niche model of the group and use said model to guide our sampling efforts and collect and present molecular evidence for the first time of <em>Dugesia leporii</em> specimens, endemic from Sardinia last spotted in 1999. Our results indicate that paleoclimatic conditions rather than microplate tectonic dynamics were likely an important driver of diversification for the Corso-Sardinian group. Furthermore, our results warrant the taxonomic re-evaluation of the group as eight primary species candidates are established based on molecular data. Our study also reveals the first case of interspecific natural hybridization reported in Dugesiidae and, to our knowledge, in Tricladida. Finally, we discuss how this hybridization might constitute a new form of hybrid speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108339"},"PeriodicalIF":3.6,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712283","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":"Whole genome sequencing and phylogenetic analyses of the Sillaginidae family fish","authors":"Qi Liu ,&nbsp;Weihua Mao ,&nbsp;Yiting Wang ,&nbsp;Jiaguang Xiao ,&nbsp;Shilpi Saha ,&nbsp;Tianxiang Gao ,&nbsp;Fei Liu","doi":"10.1016/j.ympev.2025.108340","DOIUrl":"10.1016/j.ympev.2025.108340","url":null,"abstract":"<div><div>For a long time, the taxonomic study of the Sillaginidae family of fish has been relatively slow, leaving the evolutionary relationships among species unclear. Previous research has mainly relied on morphological characteristics, with molecular studies limited primarily to mitochondrial genomics, including analyses of gene fragments and whole mitochondrial genomic sequence. This approach resulted in less precise and comprehensive species identification. In this study, we employed high-depth whole-genome sequencing (WGS) and genome surveys on 13 specimens representing 9 species of Sillaginidae fish collected from the wild. Our analysis included a thorough genomic survey and the assembly of draft genomes for each specimen. The genome sizes of Sillaginidae species are highly similar, ranging from 511.71 Mb to 578.27 Mb, with most individuals exhibiting repeat sequences content below 34.69 %. After the genome draft assembly of each sample, we identified conserved genes and shared consistent sequences among individuals and constructed a species phylogenetic tree based on these data. The results revealed that <em>Sillago ingenua</em> occupies the basal branch, followed by <em>S. maculata</em> and <em>S. aeolus</em>, then <em>Sillaginopsis panijus</em>, <em>S. japonica</em> and <em>S. asiatica</em>, and finally <em>S. nigrofasciata</em> and <em>S.</em> cf. <em>sihama</em>. Subsequently, we validated the phylogenetic tree using genome-wide single nucleotide variations, and the results were highly consistent. This research provides, for the first time, a whole-genome perspective on the evolutionary relationships among Sillaginidae species, offering valuable insights into their taxonomy and historical evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108340"},"PeriodicalIF":3.6,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702272","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":"Inferring inter-phylum gene transfer events from unique genes detected in Parageobacillus thermoglucosidasius","authors":"A. Cuecas ,&nbsp;J.A. Delgado ,&nbsp;J.M. Gonzalez","doi":"10.1016/j.ympev.2025.108329","DOIUrl":"10.1016/j.ympev.2025.108329","url":null,"abstract":"<div><div>A pan-genome includes the complete pool of genes of a species including those recently acquired. The new additions of genetic material to a genome are frequently linked to horizontal gene transfer (HGT) processes and can confer adaptive advantages improving the recipient functional response and growth. Previous studies have reported that <em>Parageobacillus</em> have frequent DNA exchange mainly with other members of the phylum Bacillota sharing similar environments. Nevertheless, the occurrence of transfer events between phylogenetically distant microorganisms is scarcely known. In this work, based on the pan-genome of <em>Parageobacillus thermoglucosidasius</em>, we detected a number of unique genes within the species which were used to carry out BLAST searches to find out similar genes in distant bacteria taxa. We aimed to infer potential inter-phylum HGT events. Results suggested genetic exchanges among different phyla. Among them Actinomycetota, Pseudomonadota and the Bacteroidota/Chlorobiota group were the dominant observed phyla. Those HGT events frequently involved ATP binding cassette transporters, enzymes of the C metabolism and transcriptional regulators. Based on the frequency of these genes within specific phyla, directional HGT events could be proposed. A dominant origin of the suggested HGT events could be within the Bacillota. This exploratory analysis indicates that Bacillota are frequent exporters of DNA both within the phylum and to phylogenetically distant groups. Long-distance HGT can assist to better understand microbial evolution, the relevance of HGT processes within the prokaryotes and the genomic plasticity of microorganisms.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108329"},"PeriodicalIF":3.6,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic and morphological evidence supports the reinstatement of the bamboo genus Clavinodum from Oligostachyum (Poaceae: Bambusoideae)","authors":"Zheng-Yang Niu ,&nbsp;Zhi-Xian Zhang ,&nbsp;Zhuo-Yu Cai ,&nbsp;Yi-Hua Tong ,&nbsp;Si-Jin Zeng ,&nbsp;Sean W. Graham ,&nbsp;Nian-He Xia","doi":"10.1016/j.ympev.2025.108327","DOIUrl":"10.1016/j.ympev.2025.108327","url":null,"abstract":"<div><div>One of the most intractable problems in bamboo systematics concerns the three-branched bamboos of tribe Arundinarieae (Poaceae: Bambusoideae), which are collectively characterized by having three branches per mid-culm node. Previous phylogenetic studies based on double-digest restriction-site associated DNA sequencing (ddRAD-seq) data confirmed that <em>Oligostachyum</em>, a member of this group, is non-monophyletic, and in particular that <em>Oligostachyum oedogonatum</em> is a problematic species deserving further attention, as it appears to be morphologically and phylogenetically distinct from the other three-branched bamboos. Here we aim to define and confirm the phylogenetic position of <em>O. oedogonatum</em>, by including representatives from across its geographic range. We also provide new insights into the overall phylogeny of the three-branched bamboos and closely related genera, using multiple phylogenomic datasets. While a plastid genome-based tree is very poorly supported, phylogenies inferred using two sets of conserved nuclear genes and single nucleotide polymorphism (SNP) data yield generally well-supported and congruent topologies using coalescent-based approaches. The tree inferred from the largest concatenated gene set is the most dissimilar to other inferences. The nuclear-based data sets all recover a major clade that includes all of the three-branched bamboos and four other genera, which can be distinguished from related taxa due to their possession of three stigmas per floret and leptomorph rhizomes. Notably, eight <em>O. oedogonatum</em> samples form a clade that is distantly related to other members of <em>Oligostachyum</em>, including the type species of the genus (<em>Oligostachyum sulcatum</em>). Population genetic approaches and multi-species coalescent-based analysis of the nuclear data sets imply that seven of these populations can be treated as a single species, <em>O. oedogonatum</em>, but that one population from Jinggangshan is likely an intergeneric hybrid between <em>O. oedogonatum</em> and <em>Pleioblastus</em>. Morphologically, <em>O. oedogonatum</em> differs from all other three-branched bamboos, in having strongly asymmetrically swollen supra-nodal ridges, a laterally compressed spikelet, and rachilla segments that disarticulate readily below fertile florets. Because of its morphological distinctiveness and molecular phylogenetic position, we propose that this taxon should be reinstated as <em>Clavinodum oedogonatum</em>. We provide a new description for this monotypic genus here.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108327"},"PeriodicalIF":3.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genotyping-by-sequencing elucidates the species limits of Ukrainian taxa within Veronica subg. Pseudolysimachium","authors":"Mareike Daubert ,&nbsp;Marie Hoensbroech ,&nbsp;Zoya M. Tsymbalyuk ,&nbsp;Christoph Nehrke ,&nbsp;Sergei L. Mosyakin ,&nbsp;Dirk C. Albach","doi":"10.1016/j.ympev.2025.108328","DOIUrl":"10.1016/j.ympev.2025.108328","url":null,"abstract":"<div><div>The subgenus <em>Veronica</em> subg. <em>Pseudolysimachium</em> contains mostly species occurring in natural and seminatural grasslands throughout Eurasia and is characterized by one of the highest diversification rates within <em>Veronica</em>, making it difficult to outline species boundaries, especially in taxa from its diversity hotspots. To resolve species limits among its Ukrainian members, the European diversity hotspot of the group, we combine evidence from GBS, niche modeling, palynology and morphometrics and compare the climatic niches of three closely related species.</div><div>We confirm that <em>Veronica maeotica</em> and <em>V.<!--> <!-->steppacea</em> are distinct species. Both taxa, even though previously largely ignored, represent independent lineages in the phylogeny and are characterized each by a unique combination of morphological traits. <em>Veronica steppacea</em> is adapted to a drier, more continental climate than its closest relative, <em>V.<!--> <!-->barrelieri</em>, highlighting the importance of the zonality of the Eurasian steppe belt in shaping the diversity of the subgenus. <em>Veronica<!--> <!-->incana</em> is split into two geographically distinct clades, providing evidence that plants with a cobwebby indumentum arose twice within the subgenus. Two other Ukrainian taxa, <em>V.<!--> <!-->gryniana</em> and <em>V.<!--> <!-->incana</em> subsp.<em> <!-->hololeuca</em>, may be of hybrid origin.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108328"},"PeriodicalIF":3.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny, species delimitation, and biogeographical history of Bredia","authors":"Jin-Hong Dai ,&nbsp;Ren-Chao Zhou ,&nbsp;Ying Liu","doi":"10.1016/j.ympev.2025.108326","DOIUrl":"10.1016/j.ympev.2025.108326","url":null,"abstract":"<div><div>Species delimitation in plants is sometimes challenging due to morphological convergence, interspecific gene flow, and historically limited sampling. <em>Bredia</em> Blume as currently defined comprises 27 species and has been resolved as monophyletic in previous phylogenomic studies. However, relationships among several major lineages in the genus remain elusive, and the species boundaries of some problematic taxa have not been tested. In this study, we employed comprehensive taxon sampling and reconstructed the phylogeny of <em>Bredia</em> using single-copy orthologs (SCOs), genomic single nucleotide polymorphisms (SNPs), and whole plastomes. The species tree derived from SCOs provided the highest resolution, strongly supporting all interspecific relationships. We identified instances of morphological convergence and potential hybridization/introgression within groups of interest and discussed species limits based on monophyly, genetic divergence, and morphological diagnosability. Using this robust phylogeny, we inferred divergence times and biogeographical history for <em>Bredia</em>. The genus originated in the Yunnan-Myanmar-Thailand Border region and the Beibu Gulf region during the middle Miocene, initially adapting to karst habitats. Over time, certain lineages shifted to non-karst environments. One such lineage migrated to the southeastern part of the Eastern Asiatic Kingdom in the late Miocene, where it rapidly diversified forming several major lineages. Subsequently, a mainland lineage reached Taiwan via a land bridge between the late Pliocene and the early Pleistocene and diversified in the region, eventually spreading to the Ryukyu Islands in the middle Pleistocene.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"207 ","pages":"Article 108326"},"PeriodicalIF":3.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639871","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}