Molecular Phylogenetics and Evolution最新文献

{"title":"Mitochondrial genome and ultraconserved elements reveal a species complex within the Central American brocket deer Mazama temama (Artiodactyla: Cervidae)","authors":"Luis A. Escobedo-Morales ,&nbsp;Susette Castañeda-Rico ,&nbsp;Salvador Mandujano ,&nbsp;Livia León-Paniagua ,&nbsp;Enrique Martínez-Meyer ,&nbsp;Jesús E. Maldonado","doi":"10.1016/j.ympev.2025.108400","DOIUrl":"10.1016/j.ympev.2025.108400","url":null,"abstract":"<div><div>Mazama temama (Kerr, 1792) is a neotropical deer with a wide distribution across the humid forests from Mexico through Colombia. While three subspecies are currently recognized based on morphological and pelage coloration, the presence of a phylogeographic structure is unknown, and recent debates suggest the possibility of it being a species complex. Here, we conduct phylogenetic analyses, explore demographic history, and perform species delimitation analyses using genome-wide ultraconserved elements (UCE) and the whole mitochondrial genome sequenced from museum specimens. Our results reveal three well-supported lineages within M. temama. Based on the mitochondrial dataset, these lineages diverged from the sister clade formed by other Mazama species 2.3 million years ago. The northernmost lineage diverged from southern Central America around 1.2 and 1.4 million years ago, as the UCE and mitochondrial datasets indicated, respectively. The ancestral small population size and Late Pleistocene dispersal patterns contributed to an isolation-by-distance scenario. We propose that M. temama represents a species complex divided by ecological barriers. Consequently, we recommend recognizing three separate species: M. temama (Kerr, 1792) for populations from Mexico to Honduras, M. reperticia Goldman, 1913 for populations from Nicaragua to Panama, and M. zetta Thomas, 1913 for populations in Colombia and Ecuador, limited by the northern Andean Cordillera.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108400"},"PeriodicalIF":3.6,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144481820","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":"Phylogeny of the species-rich pantropical genus Zanthoxylum (Rutaceae) based on hybrid capture.","authors":"Lee Ping Ang, Salvatore Tomasello, Jun Wen, Marc S Appelhans","doi":"10.1016/j.ympev.2025.108398","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108398","url":null,"abstract":"<p><p>Pantropical regions possess the highest biodiversity on earth yet detailed systematic studies involving pantropical genera often pose significant challenges due to the extensive need for intercontinental sampling. Zanthoxylum, a genus comprising 225 species within the family Rutaceae, provides an excellent model for such studies due to its distribution on most continents and tropical archipelagos. Despite the genus' economic significance, no phylogenetic study with a comprehensive taxon sampling has been conducted. Previous research using Sanger sequencing failed to resolve key questions regarding the genus. To resolve these questions, this study employs the hybrid capture method to: (1) conduct a comprehensive phylogenetic analysis of Zanthoxylum; (2) evaluate Engler's and Reynel's sectional classifications; (3) explore the evolution of the homochlamydeous flower character in section Zanthoxylum; (4) test the monophyly of several species, particularly those with a wide distribution; and (5) to assess hybridization and incomplete lineage sorting in Zanthoxylum. Our analyses resolved Zanthoxylum as monophyletic with four clades centred on different biogeographical regions. Sections Tobinia, Pterota and Zanthoxylum are monophyletic and section Blackburnia and section Macqueria each proved to be polyphyletic. Zanthoxylum s.str. is only monophyletic if Z. clava-herculis and Z. nitidum with heterochlamydeous flowers are placed in it. The separation of Zanthoxylum s.str. into section Sinensis and section Zanthoxylum is not supported. Section Macqueria is highly polyphyletic and spread across three main clades, while section Pterota and section Tobinia are each monophyletic. The widespread Z. asiaticum sampled throughout its distribution from Madagascar and tropical Africa to tropical Asia was found to be monophyletic, representing its own isolated clade within Zanthoxylum. A sectional classification synopsis for Zanthoxylum is provided except that future taxonomic work for section Macqueria is necessary. Quartet sampling suggests incomplete lineage sorting and hybridization within Zanthoxylum.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108398"},"PeriodicalIF":3.6,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into wheatgrass: unravelling genetic diversity, population structure, and evolutionary dynamics in Pseudoroegneria species","authors":"Yuanyuan Ji ,&nbsp;Nadeem Khan ,&nbsp;Raju Chaudhary ,&nbsp;Sampath Perumal ,&nbsp;Zhengping Wang ,&nbsp;Pierre Hucl ,&nbsp;Bill Biligetu ,&nbsp;Andrew G. Sharpe ,&nbsp;Lingling Jin","doi":"10.1016/j.ympev.2025.108397","DOIUrl":"10.1016/j.ympev.2025.108397","url":null,"abstract":"<div><div><em>Pseudoroegneria</em> species are outcrossing perennial grasses with significant ecological and agricultural value due to its resilience in challenging environmental conditions in the temperate regions. Understanding the extent and pattern of genetic diversity and population structure is essential for the breeding improvement and conservation of these species. In the current research, we analyzed genomic variations of 145 genotypes representing seven species (<em>P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata</em>) from major global lineages, using genotyping-by-sequencing. Different metrics including nucleotide diversity, observed heterozygosity, and Tajima’s D were used to evaluate genetic diversity among populations revealing significant variation among species, with <em>P. stipifolia</em> exhibiting the highest diversity and <em>P. spicata</em> the lowest. Population structure analyses, including principal component analysis, admixture inference, and phylogenetic reconstruction, identified six distinct genetic clusters, with <em>P. spicata</em> (a North American species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutionary history of Eurasian <em>Pseudoroegneria</em> species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, and <em>f</em>-branch statistics confirmed close relationships among <em>P. spicata</em>, <em>P. libanotica</em>, and <em>P. tauri</em>, with evidence of unidirectional gene flow between <em>P. stipifolia</em>, <em>P. geniculata</em>, and <em>P. strigosa</em>. These findings highlight the importance of high genetic variation in the <em>P. stipifolia</em> population, suggesting its potential to be a reservoir of valuable alleles for resilient genotypes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108397"},"PeriodicalIF":3.6,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487243","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 insights into historical biogeography and species delimitation of African Ampelocissus (Vitaceae).","authors":"Romer Narindra Rabarijaona, Jin-Ren Yu, Zhi-Yong Tang, Rindra Manasoa Ranaivoson, Russell L Barrett, Mijoro Rakotoarinivo, Bing Liu, Yi-Chen You, Samaila S Yaradua, Romeo Gbiribou, Jun Wen, Zhi-Duan Chen, Li-Min Lu","doi":"10.1016/j.ympev.2025.108388","DOIUrl":"10.1016/j.ympev.2025.108388","url":null,"abstract":"<p><p>Ampelocissus Planch. (Vitaceae) comprises c. 95 currently recognized species that are distributed across tropical and subtropical regions in Asia, Australia, continental Africa, Madagascar, and Central America. Ampelocissus has attracted extensive attention for its close relationship with the economically important grape genus Vitis L. Despite their widespread use as food and medicinal plants, only two species have IUCN conservation status. The circumscription of several African species remains unclear due to a lack of integrative molecular and morphological studies. In this study, we conduct a comprehensive investigation of the phylogeny, biogeography, and morphological evolution of Ampelocissus using phylogenomic data with expanded taxon sampling, particularly from Africa. Our phylogenetic analyses resolve four major clades, supporting traditionally defined sections within Ampelocissus. African species of Ampelocissus are shown to be non-monophyletic, forming two lineages with distinct inflorescence types: the paniculate lineage and the cymose lineage. However, each lineage includes species from both Africa and Asia. Our biogeographic reconstruction suggests that African Ampelocissus lineages may have originated in Asia during the Eocene and supports at least two independent dispersal events from Asia to continental Africa and one from Asia to Madagascar. We further demonstrate that inflorescence type, flower-stalk, and tendril-associated inflorescences are well conserved across the phylogeny and serve as key taxonomic characteristics. Finally, we revisit the taxonomy of some controversial African Ampelocissus species and describe three new taxa from Madagascar, integrating molecular, morphological, and geographic evidence.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108388"},"PeriodicalIF":3.6,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337288","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":"Metagenomic analyses reveal three supergroups of Wolbachia in a single genus of feather-feeding lice (Penenirmus)","authors":"Ember B. Clodfelter ,&nbsp;Jorge Doña ,&nbsp;Kimberly K.O. Walden ,&nbsp;Kevin P. Johnson","doi":"10.1016/j.ympev.2025.108387","DOIUrl":"10.1016/j.ympev.2025.108387","url":null,"abstract":"<div><div>Insects with nutritionally limited diets often harbor bacterial endosymbionts that supplement their nutritional requirements. However, not all interactions between bacteria and insects are mutually beneficial. <em>Wolbachia</em> is a genus of bacteria that frequently causes cytoplasmic incompatibility and other reproductive parasitic effects on many of its arthropod hosts. In nematodes and some insects, however, <em>Wolbachia</em> is a nutritional mutualist. A lineage of <em>Wolbachia</em> closely related to mutualist strains has previously been identified in parasitic lice, including the louse genus <em>Penenirmus</em> (Ischnocera), which specializes in feeding on feathers. In this study, we used genome-resolved metagenomics to examine the diversity of <em>Wolbachia</em> across the genus <em>Penenirmus</em>, with a focus on evidence of long term associations with their hosts, which could indicate a mutualistic relationship. Phylogenomic analysis of over 100 genes from <em>Wolbachia</em> provided a well-resolved phylogeny of this bacterial genus. Across diverse species of the louse genus <em>Penenirmus,</em> genome-resolved metagenomic assemblies of <em>Wolbachia</em> from these insects revealed the presence of three different supergroups (B, F, and V). Supergroup V had not previously been known from lice. Cophylogenetic analysis revealed significant congruence between the <em>Wolbachia</em> and louse trees, although some branches showed incongruence.</div><div>The <em>Wolbachia</em> in <em>Penenirmus</em> species from supergroups F and B showed evidence of potential mutualism by having long branches, cophylogenetic congruence with their louse hosts, and comparatively smaller genome sizes. Long branch attraction may be affecting the phylogenetic position of two lineages of <em>Wolbachia</em>, but the relative position of all other samples was comparatively stable.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108387"},"PeriodicalIF":3.6,"publicationDate":"2025-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318789","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":"Discordance between phylogenomic methods in Near Eastern mountain newts (Neurergus, Salamandridae)","authors":"Stephanie Koster ,&nbsp;Robin Polanen ,&nbsp;Aziz Avcı ,&nbsp;Sergé Bogaerts ,&nbsp;Emin Bozkurt ,&nbsp;Forough Goudarzi ,&nbsp;Mahmoud-Reza Hemami ,&nbsp;Kurtuluş Olgun ,&nbsp;Frank Pasmans ,&nbsp;Sebastian Steinfartz ,&nbsp;Nazan Üzüm ,&nbsp;Manon de Visser ,&nbsp;James France ,&nbsp;Anagnostis Theodoropoulos ,&nbsp;Ben Wielstra","doi":"10.1016/j.ympev.2025.108386","DOIUrl":"10.1016/j.ympev.2025.108386","url":null,"abstract":"<div><div>Target enrichment by sequence capture allows researchers to collect genome-wide sequence data, suitable to re-evaluate complex systematic and taxonomic cases. The family Salamandridae is rife with rapid, successive speciation events, introgression and incomplete lineage sorting: factors that complicate the inferring of phylogenetic relationships and species boundaries. Phylogenetic relationships among, and the (sub)species status of, the taxa comprising the newt genus <em>Neurergus</em> are not fully resolved. We perform target enrichment by sequence capture to obtain ca. 7 k nuclear DNA markers, and conduct concatenated analysis with RAxML, gene-tree summary analysis in ASTRAL, and species tree estimation in SNAPPER, and investigate admixture between populations and genetic introgression with ADMIXTURE and Dsuite. We observe discordance between analyses pertaining to the placement of <em>N. crocatus</em>. We consider the placement of <em>N. crocatus</em> as sister to <em>N. derjugini</em> sensu lato in SNAPPER, instead of to <em>N</em>. <em>kaiseri</em> + <em>N</em>. <em>derjugini</em> sensu lato as in RAxML and ASTRAL, to be an artifact of introgression, as backed up by our Dsuite analysis. We show that <em>N. strauchii barani</em> and <em>N. strauchii munzurensis</em>, often treated as distinct species, are deeply nested within <em>N. strauchii</em> sensu stricto and should not be treated as species. Keeping them as subspecies would render the nominotypical subspecies as polyphyletic. Furthermore, we confirm that <em>N. derjugini microspilotus</em> should not be considered a distinct species, but as a subspecies of <em>N. derjugini</em> sensu lato. We consistently recover the northern and southern lineages of <em>N. kaiseri</em> as distinct genetic groups with geographically restricted admixture and recommend that these are treated as two distinct species. Our study highlights the strength of target enrichment by sequence capture in resolving systematic and taxonomic questions in taxa with a history of genetic admixture and introgression.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108386"},"PeriodicalIF":3.6,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144310893","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":"Phylogeny and evolutionary history of alpine alkali grasses (Poaceae: Puccinellia) within the subtribe Coleanthinae","authors":"Anna Wróbel ,&nbsp;Ewelina Klichowska ,&nbsp;Marcin Nobis","doi":"10.1016/j.ympev.2025.108385","DOIUrl":"10.1016/j.ympev.2025.108385","url":null,"abstract":"<div><div>Alkali grasses (Poaceae: <em>Puccinellia</em>) are a widely-distributed and species-rich group that has developed tolerance to alkaline and/or saline conditions. With more than 100 species, the genus is the largest in the subtribe Coleanthinae and is characterized by the ubiquity of polyploidy and hybridization. Despite large taxonomic and ecological diversity, the evolutionary history of alkali grasses and the emergence of their high-mountain diversity remain poorly understood. In this study, we combined genomic data (DArTseq), nuclear ribosomal, and chloroplast markers to shed more light on the origins of alpine alkali grasses within the subtribe Coleanthinae. Using a global perspective, we found that the alpine species of the Pan-Tibetan Highlands emerged at different timescales along the evolutionary history of <em>Puccinellia</em>. Particularly, our results revealed that two high-alpine species, <em>P. pamirica</em> and <em>P. subspicata</em>, are resolved near the backbone of the infrageneric diversification of alkali grasses and remain closely related to multiple arctic species. Our integrative approach suggests a key role of cold-tolerance during the early stages of evolutionary radiation of the genus and highlights the importance of the Pleistocene climate oscillations for speciation in alkali grasses.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108385"},"PeriodicalIF":3.6,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295467","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":"Integrating morphology, ecology, and genomics: Unraveling the population genetic and evolution within the Rosa graciliflora complex","authors":"Jia Miao ,&nbsp;Liang-Ying Li ,&nbsp;Zhen-Long Liang ,&nbsp;Yu Feng ,&nbsp;Cheng Zhang ,&nbsp;Shi-Qi Li ,&nbsp;Heng-Ning Deng ,&nbsp;Jian Ru ,&nbsp;Zhong-Yu Tang ,&nbsp;Xin-Fen Gao","doi":"10.1016/j.ympev.2025.108382","DOIUrl":"10.1016/j.ympev.2025.108382","url":null,"abstract":"<div><div>Species delimitation in recently diverged lineages presents significant challenges in plant systematics, particularly in the genus <em>Rosa</em>, where recent radiation, incomplete lineage sorting, and frequent hybridization have created intricate evolutionary patterns. This study presents a comprehensive investigation of a monophyletic complex comprising <em>R. graciliflora</em>, <em>R. tibetica</em>, and <em>R. tsinlingensis</em>, integrating morphological, ecological, and genomic approaches. Morphological analysis of 392 specimens revealed substantial interspecific trait overlap without distinct morphological boundaries, while ecological niche analysis demonstrated significant habitat overlap, both challenging the current taxonomic classification. Phylogenetic analysis, population genetic structure analysis, and principal component analysis (PCA) based on genome-wide SNP data from 190 individuals across 26 populations did not support the monophyly of these three traditionally recognized species, indicating low genetic differentiation and extensively interwoven genetic backgrounds. Population genetic structure primarily reflected geographical distribution patterns, with genetic differentiation mainly driven by geographic distance and environmental factors. Significant gene flow was detected among adjacent populations. Selective sweep analysis identified key genes associated with flower color and flowering time. Correlation analysis suggested that solar radiation is a crucial environmental factor influencing leaflet number and flower color variation. Based on these findings, we propose treating <em>R. tsinlingensis</em> and <em>R. tibetica</em> as synonyms of <em>R. graciliflora</em>. Our findings underscore the limitations of morphological classification in reflecting the genetic and ecological diversity within the <em>R. graciliflora</em> complex, highlighting the importance of multidimensional data in understanding plant evolution and biodiversity conservation in the face of changing environments.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108382"},"PeriodicalIF":3.6,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236065","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":"Resolving taxonomic uncertainties in ailiid catfishes (Siluriformes: Ailiidae) using Genome-Scale data","authors":"Jash Hang Limbu ,&nbsp;Dipak Rajbanshi ,&nbsp;Jiantao Hu ,&nbsp;Laxman Khanal ,&nbsp;Chenhong Li","doi":"10.1016/j.ympev.2025.108384","DOIUrl":"10.1016/j.ympev.2025.108384","url":null,"abstract":"<div><div>The Ailiidae family, endemic to South and Southeast Asia, comprises diverse freshwater catfish inhabiting major river basins across the region. Evolutionary relationships and taxonomic classification within Ailiidae family remain contentious. Here, we resolve these uncertainties using phylogenomic data from 29 specimens representing 11 species and six of the seven recognized genera, supplemented by two outgroup taxa<!--> <!-->(<em>Pachypterus atherinoides</em> <!-->and<!--> <em>P. acutirostris</em>). Hybridization target enrichment and high-throughput sequencing yielded 4,434 single-copy nuclear coding loci. After trimming loci with more than 50 % missing taxa, 2,102 loci, totaling 505,110 bp, were used for phylogenomic analyses. The results confirm monophyly of all studied genera (<em>Ailia</em>, <em>Ailiichthys</em>, <em>Clupisoma</em>, <em>Eutropiichthys</em>, <em>Silonia</em> and <em>Laides</em>), after the reclassification of <em>Clupisoma montanum</em> and <em>C. sinense</em> into the genus <em>Laides,</em> based on concordant molecular, morphological and meristic evidence. Notably, <em>Ailia coila</em> and <em>Ailiichthys punctata</em> formed an early diverging clade, sister to remaining Ailiidae. Furthermore, our results corroborate that the genera <em>Eutropiichthys</em> <!-->and<!--> <em>Silonia</em> <!-->represent distinct lineages within Ailiidae, warranting their formal retention in the family. Divergence dating estimated the most recent common ancestor of Ailiidae arose during the Pleistocene, with a median age of 2.1 million years ago (95 % HPD: 3.34–1.0 Ma). Biogeographic reconstructions identified the Ganges–Brahmaputra River basin (South Asia) as the center of origin for Ailiidae, followed by dispersal to the Irrawaddy–Salween, Pahang and Indus River basins. Pleistocene climatic fluctuations, tectonic uplift and changes in sea-level may have influenced the dispersal of Ailiidae catfishes. These geological events restructured river systems and exposed land bridges, allowing movement across previously isolated basins. Paleo-river connections between the major drainages of South and Southeast Asia likely facilitated multiple events of vicariance and dispersal, driving diversification within the Ailiidae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"210 ","pages":"Article 108384"},"PeriodicalIF":3.6,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the drivers of speciation in Alpine Noccaea (Brassicaceae) reveal an evolution predominantly shaped by geography","authors":"Camille Voisin ,&nbsp;Philippe Choler ,&nbsp;Camille Vacher ,&nbsp;Christophe Perrier ,&nbsp;Julien Renaud ,&nbsp;Delphine Rioux ,&nbsp;Florian C. Boucher","doi":"10.1016/j.ympev.2025.108381","DOIUrl":"10.1016/j.ympev.2025.108381","url":null,"abstract":"<div><div>The process of species delimitation, defined as the act of recognising biologically meaningful taxonomic units, enables the detection of overall biodiversity and the exploration of speciation processes. Given the complex nature of the origin of biodiversity, a significant number of cryptic Alpine plant groups exhibit ambiguity regarding their phylogenetic relationships and species circumscription. In this study, we attempt to apply the principles of integrative taxonomy to a complex of cryptic alpine plants from the genus <em>Noccaea,</em> which are often described as substrate specialists. We benefited from an extensive sampling across the Alps combined with high-throughput genotyping to apply a modern and standardised method of species delimitation. We find that the <em>Noccaea rotundifolia</em> complex is represented by five species within the Alps, which exhibit a restricted geographic distribution. Four of these species diverged approximately 350 ka ago (259–429), indicating a recent diversification. Instead of recognizing species with different substrate affinities, as done by current taxonomy, we rather find that the most widespread species are substrate generalists but with allopatric distributions. Our findings indicate that <em>N. rotundifolia</em> is growing exclusively in the west of the well-known biogeographic barrier of the Aosta Valley. <em>N. corymbosa</em> is found to grow between the Aosta Valley barrier and the Lake Como one. <em>N. cepaeifolia</em>, in turn, is observed in the eastern Alps, separated by the Brenner valley. Overall, this study provides a detailed systematic review, supporting the pivotal role of the recognized Alpine biogeographic barriers, in shaping species distribution and speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108381"},"PeriodicalIF":3.6,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144210375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}