Molecular Phylogenetics and Evolution最新文献

{"title":"Harmony in diversity: Reorganizing the families within the order Pseudomonadales","authors":"José David Flores-Félix ,&nbsp;Paula García-Fraile ,&nbsp;Zaki Saati-Santamaría","doi":"10.1016/j.ympev.2025.108321","DOIUrl":"10.1016/j.ympev.2025.108321","url":null,"abstract":"<div><div>An accurate and coherent bacterial taxonomy is essential for studying the ecological aspects of microorganisms and for understanding microbial communities and their dynamics. The order <em>Pseudomonadales</em> is of particular importance in biological research due to its ability to interact with eukaryotic hosts, including taxa of clinical relevance (e.g.: <em>Pseudomonas</em>, <em>Moraxella</em>, <em>Acinetobacter</em>), or due to its functions in soil and water ecosystems. Despite their relevance, we have identified several inconsistencies in the organisation of genera within families in this order. Here, we perform comprehensive phylogenetic and phylogenomic analyses to reorganise these taxa. Average amino acid identity (AAI) values shared within and between families support our reclassifications. We propose seven new families, including new ecologically relevant families (e.g.: <em>Oceanobacteraceae</em> fam. nov.), as well as several taxonomic emendations. Our results also support the inclusion of <em>Cellvibrionales</em> and <em>Oceanospirillales</em> within <em>Pseudomonadales</em>. This revised organisation provides a robust delineation of these taxa into families, characterised by AAI values ranging from 60% to 77%. AAI distances between families are predominantly below 60%. This reclassification contributes to establishment of a more reliable taxonomic framework within <em>Gammaproteobacteria</em>, providing the basis for a more comprehensive understanding of their evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108321"},"PeriodicalIF":3.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562949","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":"Diversity, Phylogeny, and historical biogeography of the genus Coccocarpia (lichenized Ascomycota: Peltigerales) in the tropics","authors":"Luis Fernando Coca ,&nbsp;H.Thorsten Lumbsch ,&nbsp;Joel A. Mercado-Díaz ,&nbsp;Todd J. Widhelm ,&nbsp;Bernard Goffinet ,&nbsp;Paul Kirika ,&nbsp;Robert Lücking","doi":"10.1016/j.ympev.2025.108312","DOIUrl":"10.1016/j.ympev.2025.108312","url":null,"abstract":"<div><div><em>Coccocarpia</em> Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, <em>C</em>. <em>erythroxyli</em>, <em>C</em>. <em>palmicola</em>, and <em>C</em>. <em>pellita</em>, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, <em>RPB2</em>), <em>Coccocarpia</em> was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, <em>Coccocarpia</em> may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. <em>Coccocarpia</em> likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the <em>epiphylla</em> and <em>stellata</em> clades.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108312"},"PeriodicalIF":3.6,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143494693","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 distribution and types of Multicopper oxidases in Basidiomycota fungi","authors":"Gonzalo Molpeceres,&nbsp;Pablo Aza,&nbsp;Iván Ayuso-Fernández,&nbsp;Guillermo Padilla,&nbsp;Francisco Javier Ruiz-Dueñas,&nbsp;Susana Camarero","doi":"10.1016/j.ympev.2025.108310","DOIUrl":"10.1016/j.ympev.2025.108310","url":null,"abstract":"<div><div>Multicopper oxidases (MCOs) comprise different types of enzymes widely distributed in nature with quite diverse functions. Laccases are the most interesting MCOs from a biotechnological point of view, particularly those secreted by ligninolytic Basidiomycota fungi due to their versatility to oxidize lignin and a variety of aromatic substrates. The term “laccase” has been broadly (but sometimes erroneously) applied due to their low sequence homology and some overlapping activities with other MCO groups.</div><div>We examined the distribution and phylogenetic relationships of MCOs in Basidiomycota fungi aiming to provide a complete and precise picture of the different MCO types across the division, including fungal orders phylogenetically distant from those typically studied. The phylogenetic tree revealed eight clusters of MCOs, each sharing common sequence/structural features. With this information we classified the MCOs in eight groups and described their distinctive amino acid residues. These eight MCO types are: laccases (LAC), ferroxidases (FOX), laccase-ferroxidases (LAC-FOX), ascorbate oxidases (AO), fungal pigment MCOs, and three new groups of laccase-like enzymes or “atypical laccases” related to but different from laccases sensu stricto, namely novel laccases (NLAC), new MCO (NMCO) and new laccases with potential ferroxidase activity (NLF). Additionally, several MCOs already described in the literature were reclassified into the updated groups.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108310"},"PeriodicalIF":3.6,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143494746","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":"Study of epiphytic non-geniculate coralline algae Reveals an Evolutionarily significant Genus, Pseudoderma gen. nov. (Lithophylloideae, Corallinophycidae)","authors":"Shu-Heng Yan ,&nbsp;Xu-Lei Wang ,&nbsp;Zhong-Min Sun ,&nbsp;Bang-Mei Xia ,&nbsp;Wen-Hui Gu ,&nbsp;Guang-Ce Wang","doi":"10.1016/j.ympev.2025.108313","DOIUrl":"10.1016/j.ympev.2025.108313","url":null,"abstract":"<div><div>Epiphytic non-geniculate coralline algae (ENCA) are distributed broadly, while limited research on their diversity has constrained our understanding of their ecological roles in marine environments, and impeded a comprehensive understanding of coralline algae. In this study, the diversity and ecological characteristics of ENCA epiphytic on 113 red macroalgal specimens collected from coastal China were examined. Three species delimitation algorithms revealed 24 primary species hypotheses (PSH), of which 22 were corroborated through phylogenetic analysis based on the <em>psb</em>A gene. Further multi-gene concatenated phylogenetic analyses and morpho-anatomical assessments revealed a new genus within Lithophylloideae, <em>Pseudoderma gen. nov.</em>, which is closely related to the genus <em>Titanoderma</em> and exhibits morphological similarities. A hypothesis concerning the growth patterns was proposed to elucidate the morphological differences among <em>Titanoderma</em>, <em>Lithophyllum</em>, and <em>Pseudoderma</em>: the presence or absence of hypothallial palisade cells indicated distinct thallus thickening patterns, either dominated by elongation of the hypothallial cells or by division of the perithallial cells. These processes resulted in fast-growing thin-crust thalli or longer-lasting thick-crust thalli, adapted to epiphytic or epilithic lifestyles, respectively. <em>Pseudoderma</em> included at least six new taxa, and <em>Pseudoderma sinicarum</em> sp. <em>nov.</em>, was designated as the holotype species of this genus. In conclusion, this study has underscored the unexpected biodiversity of ENCA, and the identification of the novel genus <em>Pseudoderma</em> from ENCA groups carried significant evolutionary implications for enhancing our understanding of coralline algae systematics.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108313"},"PeriodicalIF":3.6,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143494703","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":"Copepod phylogenomics supports Canuelloida as a valid order separate from Harpacticoida","authors":"James P. Bernot ,&nbsp;Sahar Khodami ,&nbsp;Jens Boyen ,&nbsp;Marleen De Troch ,&nbsp;Geoffrey A. Boxshall ,&nbsp;Pedro Martínez Arbizu","doi":"10.1016/j.ympev.2025.108311","DOIUrl":"10.1016/j.ympev.2025.108311","url":null,"abstract":"<div><div>Copepods are small crustaceans that are ubiquitous in aquatic environments. They are particularly abundant in marine and freshwater plankton, marine sediments, and as parasites or commensals of other aquatic organisms. Despite their abundance and importance, phylogenetic relationships among copepods are poorly resolved. The validity of higher-level taxa, including several orders, has continued to be controversial throughout the 21st century. This study has two main goals: first, to use phylogenomic data to assess relationships among the four major copepod orders: Calanoida, Cyclopoida, Harpacticoida, and Siphonostomatoida, which together include more than 98 % of copepod species diversity, and second, to test the validity of the recently proposed order Canuelloida. Towards these goals, we sampled 28 copepod transcriptomes and genomes spanning 20 families and 5 orders, including the first transcriptome of a representative of Canuelloida. We identified 2,527 single copy protein coding genes comprising 939,460 amino acid (aa) positions and 530,269 informative sites. All phylogenetic analyses support a monophyletic Podoplea (i.e., the superorder comprising all copepod orders except for Calanoida and Platycopioida) with Calanoida as its sister taxon. We find robust support across all methods for Canuelloida as a distinct order separate from the traditionally recognized Harpacticoida (Oligoarthra). Contrary to several recent studies of smaller sets of nuclear genes or mitochondrial genomes, we recover Cyclopoida and Harpacticoida as sister taxa and find that gene tree discordance analysis rejects the alternative topologies. Transcriptomic data are promising for resolving the backbone of the copepod phylogeny but collecting and sequencing the nearly 15,000 species of copepods, many of which are infrequently encountered and less than 1 mm in size, remains a major hurdle.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108311"},"PeriodicalIF":3.6,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143477260","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":"Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes","authors":"Justin M. Bernstein ,&nbsp;Yannick Z. Francioli ,&nbsp;Drew R. Schield ,&nbsp;Richard H. Adams ,&nbsp;Blair W. Perry ,&nbsp;Keaka Farleigh ,&nbsp;Cara F. Smith ,&nbsp;Jesse M. Meik ,&nbsp;Stephen P. Mackessy ,&nbsp;Todd A. Castoe","doi":"10.1016/j.ympev.2025.108309","DOIUrl":"10.1016/j.ympev.2025.108309","url":null,"abstract":"<div><div>Species tree inference is often assumed to be more accurate as datasets increase in size, with whole genomes representing the best-case-scenario for estimating a single, most-likely speciation history with high confidence. However, genomes may harbor a complex mixture of evolutionary histories among loci, which amplifies the opportunity for model misspecification and impacts phylogenetic inference. Accordingly, multiple distinct and well-supported phylogenetic trees are often recovered from genome-scale data, and approaches for biologically interpreting these distinct signatures are a major challenge for evolutionary biology in the age of genomics. Here, we analyze 32 whole genomes of nine taxa and two outgroups from the Western Rattlesnake species complex. Using concordance factors, topology weighting, and concatenated and species tree analyses with a chromosome-level reference genome, we characterize the distribution of phylogenetic signal across the genomic landscape. We find that concatenated and species tree analyses of autosomes, the Z (sex) chromosome, and mitochondrial genome yield distinct, yet strongly supported phylogenies. Analyses of site-specific likelihoods show additional patterns consistent with rampant model misspecification, a likely consequence of several evolutionary processes. Together, our results suggest that a combination of historic and recent introgression, along with natural selection, recombination rate variation, and cytonuclear co-evolution of nuclear-encoded mitochondrial genes, underlie genome-wide variation in phylogenetic signal. Our results highlight both the power and complexity of interpreting whole genomes in a phylogenetic context and illustrate how patterns of phylogenetic discordance can reveal the impacts of different evolutionary processes that contribute to genome-wide variation in phylogenetic signal.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108309"},"PeriodicalIF":3.6,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411718","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, morphological and acoustic data support a revised taxonomy of the lissodelphinine dolphin subfamily","authors":"Anders Galatius ,&nbsp;Carl Christian Kinze ,&nbsp;Morten Tange Olsen ,&nbsp;Jakob Tougaard ,&nbsp;Dietrich Gotzek ,&nbsp;Michael R. McGowen","doi":"10.1016/j.ympev.2025.108299","DOIUrl":"10.1016/j.ympev.2025.108299","url":null,"abstract":"<div><div>The dolphin genus <em>Lagenorhynchus</em> has included six species of dolphins characterized by short, wide rostra. Genetic analyses have consistently found the genus to be polyphyletic with four of the species being included in the subfamily Lissodelphininae. A recent paper synthesized available molecular, morphological and acoustic evidence to support a taxonomic revision of the genus, assigning <em>L. obliquidens, L. obscurus, L. australis</em> and <em>L. cruciger</em> to the genus <em>Sagmatias</em> within Lissodelphiniae. Here, we add new phylogenomic data to a previously analyzed dataset including over 3000 nuclear genes and complete mitochondrial genomes and reevaluate morphological and acoustic evidence for the phylogenetic relationships among the Lissodelphininae. We find strong molecular evidence that <em>L. australis</em> and <em>L. cruciger</em> are more closely related to the four members of the genus <em>Cephalorhynchus</em> than they are to <em>L. obliquidens</em> and <em>L. obscurus.</em> Independently of the molecular data, the available morphological and acoustic evidence supports these relationships. As a consequence, to achieve monophyletic taxonomic units, we propose inclusion of <em>L. australis</em> and <em>L. cruciger</em> in <em>Cephalorhynchus</em>. As <em>Sagmatias australis</em> is the type species of <em>Sagmatias,</em> which now falls in synonymy with <em>Cephalorhynchus</em>, and as there is no previous available generic name for <em>L. obliquidens</em> and <em>L. obscurus,</em> we propose a new genus for these two species, <em>Aethalodelphis,</em> meaning sooty or dusky dolphin.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108299"},"PeriodicalIF":3.6,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366945","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":"Comparative phylogeography of four lizard taxa within an oceanic island","authors":"Theodora Antoniou ,&nbsp;Andreas C. Dimitriou ,&nbsp;Emmanouela Karameta ,&nbsp;Aglaia Antoniou ,&nbsp;Nikos Poulakakis ,&nbsp;Spyros Sfenthourakis","doi":"10.1016/j.ympev.2025.108295","DOIUrl":"10.1016/j.ympev.2025.108295","url":null,"abstract":"<div><div>Comparative phylogeography aims to detect common patterns of differentiation among taxa attributed to the same geological or environmental barriers and, thus, find shared drivers of genomic splits and landscape features that explain patterns of occurrence and genetic diversity. Following this approach, this work focuses on four endemic lizard taxa, namely <em>Acanthodactylus schreiberi schreiberi, Ophisops elegans schlueteri, Phoenicolacerta troodica,</em> and <em>Laudakia cypriaca,</em> that co-occur in Cyprus, an isolated island of the Mediterranean. In an attempt to discern possible effects of the geological and ecological history of the region on diversity patterns along the lineages under study, samples were collected from all parts of Cyprus, and phylogenetic reconstructions, species delimitation analyses, and biogeographic comparisons were conducted at both genetic and genomic levels (Sanger and ddRAD sequencing data, respectively) for all four taxa. The derived phylogenomic relationships provide evidence of a strong genetic structure within the island that agrees with the geographical origins of each population. A rare case of an island-to-mainland dispersal event is confirmed for one of the focal taxa, making it one of the few documented cases of this type. Estimated diversification times during the Miocene reflect the timing of the first arrival on the island, while further diversification seems to have been strongly affected by the Pleistocene oscillations.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108295"},"PeriodicalIF":3.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolution of wasp mimicry and biogeography in the genus Temnostoma (Diptera: Syrphidae)","authors":"Jiří Hadrava ,&nbsp;Jan Klečka ,&nbsp;Kevin Moran ,&nbsp;Irena Klečková ,&nbsp;Scott Kelso ,&nbsp;Claudia Etzbauer ,&nbsp;Jeffrey H. Skevington ,&nbsp;Ximo Mengual","doi":"10.1016/j.ympev.2025.108298","DOIUrl":"10.1016/j.ympev.2025.108298","url":null,"abstract":"<div><div>One of the most remarkable examples of Batesian mimicry occurs in the genus <em>Temnostoma</em> Le Peletier &amp; Audinet-Serville, 1828 (Diptera: Syrphidae). Adults of this genus have an overall resemblance to hymenopterans combined with behavioural mimicry (they move the fore legs in front of the head mimicking hymenopteran antennae). While some species of <em>Temnostoma</em> are considered highly accurate mimics of social wasps, other species have a darker colour pattern and are rather relatively poor yellowjacket mimics. Both colour phenotypes are widespread through the Holarctic. Here, we infer for the first time the evolutionary history of the genus with special focus on the evolution of mimicry and biogeography.</div><div>With material covering 75 % of known species of <em>Temnostoma</em> and both colour phenotypes from each biogeographical region, we inferred a molecular phylogeny based on six molecular markers (mitochondrial protein-coding COI gene, nuclear 28 s rRNA gene, and four nuclear protein-coding genes: AATS, CK1, TULP, and RBP-15). Using Bayesian inference, we obtained a highly resolved phylogenetic tree supporting the monophyly of the genus <em>Temnostoma</em> as a sister group of genus <em>Takaomyia</em> Hervé-Bazin, 1914. Within <em>Temnostoma</em>, <em>Te. daochus</em> and <em>Te. barberi</em> (two Nearctic species with strikingly different mimicry patterns) were found to be closely related to each other and together form a lineage sister to the rest of the genus.</div><div>Our results suggest that the behavioural mimicry of wasp antennae is a plesiomorphic state inherited from a common ancestor that includes the genera <em>Temnostoma</em> and <em>Takaomyia</em>. Within <em>Temnostoma</em>, the dark colour pattern (poor yellowjacket mimicry) appears to be an ancestral state and highly accurate social wasp mimicry has appeared two times independently within the genus. In some species inhabiting northern parts of the Holarctic, secondary darkening and consequent degradation of the yellowjacket mimicry appeared. This indicates high evolutionary plasticity and ongoing selection pressure on morphological characters related to mimicry in hover flies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108298"},"PeriodicalIF":3.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143081478","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":"Historical biogeography of the Mugil cephalus species complex and its rapid global colonization","authors":"Philipp Thieme ,&nbsp;Celine Reisser ,&nbsp;Corinne Bouvier ,&nbsp;Fabien Rieuvilleneuve ,&nbsp;Philippe Béarez ,&nbsp;Richard R. Coleman ,&nbsp;Jean Jubrice Anissa Volanandiana ,&nbsp;Esmeralda Pereira ,&nbsp;Mauro Nirchio–Tursellino ,&nbsp;María Inés Roldán ,&nbsp;Sandra Heras ,&nbsp;Nathalia Tirado-Sánchez ,&nbsp;Eric Pulis ,&nbsp;Fabien Leprieur ,&nbsp;Jean-Dominique Durand","doi":"10.1016/j.ympev.2025.108296","DOIUrl":"10.1016/j.ympev.2025.108296","url":null,"abstract":"<div><div>Our understanding of speciation processes in marine environments remains very limited and the role of different reproductive barriers are still debated. While physical barriers were considered important drivers causing reproductive isolation, recent studies highlight the importance of climatic and hydrological changes creating unsuitable habitat conditions as factors promoting population isolation. Although speciation in marine fishes has been investigated from different perspectives, these studies often have a limited geographical extant. Therefore, data on speciation within widely distributed species are largely lacking. Species complexes offer valuable opportunities to study the initial stages of speciation. Herein we study speciation within the <em>Mugil cephalus</em> species complex (MCSC) which presents a unique opportunity due to its circumglobal distribution.</div><div>We used a whole-genome shotgun analysis approach to identify SNPs among the 16 species within the MCSC. We inferred the phylogenetic relationships within the species complex followed by a time-calibration analysis. Subsequently, we estimated the ancestral ranges within the species complex to explore their biogeographical history.</div><div>Herein, we present a fully resolved and well-supported phylogeny of the MCSC. Its origin is dated at around 3.79 Ma after which two main clades emerged: one comprising all West Atlantic and East Pacific species and the other all East Atlantic and Indo-Pacific species. Rapid dispersal following an initial founder colonization from the West to the East Atlantic led to the population of all major realms worldwide in less than 2 Myr. Physical and climatic barriers heavily impacted the ancestral distribution ranges within the MCSC and triggered the onset of speciation.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108296"},"PeriodicalIF":3.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069912","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}