Molecular Phylogenetics and Evolution最新文献

{"title":"Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes.","authors":"Justin M Bernstein, Yannick Z Francioli, Drew R Schield, Richard H Adams, Blair W Perry, Keaka Farleigh, Cara F Smith, Jesse M Meik, Stephen P Mackessy, Todd A Castoe","doi":"10.1016/j.ympev.2025.108309","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108309","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"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}

{"title":"The big, the small and the weird: A phylogenomic analysis of extant Priapulida","authors":"Jan Raeker ,&nbsp;Arianna Lord ,&nbsp;María Herranz ,&nbsp;Gonzalo Giribet ,&nbsp;Katrine Worsaae ,&nbsp;Andreas Schmidt-Rhaesa","doi":"10.1016/j.ympev.2025.108297","DOIUrl":"10.1016/j.ympev.2025.108297","url":null,"abstract":"<div><div>Priapulida is a small phylum of 22 described species that are divided into two size classes (microscopic and macroscopic), distinguished by adult and larval morphology. Most priapulidans are rare or live in inaccessible habitats, and freshly collected material for molecular studies is difficult to obtain. With this study, we for the first time aim to resolve the phylogeny of extant Priapulida using transcriptomic, genomic, and morphological data. We analyze six newly assembled transcriptomes alongside existing data, covering seven species and four genera. Additionally, we include genomic data from museum-preserved species, adding another genus via low-coverage genome sequencing. Conserved regions from these data produce a combined phylogenomic tree, augmented by morphological data to suggest positions for the rare taxa <em>Acanthopriapulus</em> and <em>Maccabeus</em>. Our findings show that the microscopic <em>Meiopriapulus</em> consistently groups as a sister taxon to other priapulidans and not with <em>Tubiluchus</em>, as suggested in previous studies. <em>Maccabeus</em>, which exhibits both size-class characteristics, is the sister taxon to all the macroscopic species, while <em>Acanthopriapulus</em> is a sister taxon to <em>Priapulus</em>, but molecular data are needed to support their suggested positions. Ancestral state reconstruction suggests that small body size, lack of caudal appendages, and internal fertilization are ancestral traits for Priapulida. This supports the derived evolution of macroscopic size and other traits in the group, aligning with its microscopic sister groups Kinorhyncha and Loricifera. Due to the diversity of priapulidans and the unique morphologies of some species, further fossil studies and potential discoveries of priapulidan microfossils are essential to fully understand the evolutionary history of this phylum.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108297"},"PeriodicalIF":3.6,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069943","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":"Genomic insights into the biogeography and evolution of Galápagos iguanas","authors":"Cecilia Paradiso ,&nbsp;Paolo Gratton ,&nbsp;Emiliano Trucchi ,&nbsp;Julia López-Delgado ,&nbsp;Marco Gargano ,&nbsp;Lorenzo Garizio ,&nbsp;Ian M. Carr ,&nbsp;Giuliano Colosimo ,&nbsp;Christian Sevilla ,&nbsp;Mark E. Welch ,&nbsp;Mohd Firdaus-Raih ,&nbsp;Mohd Noor Mat-Isa ,&nbsp;Simon J. Goodman ,&nbsp;Gabriele Gentile","doi":"10.1016/j.ympev.2025.108294","DOIUrl":"10.1016/j.ympev.2025.108294","url":null,"abstract":"<div><div>Galápagos iguanas are a monophyletic group endemic to the Galápagos archipelago, comprising the marine iguana <em>Amblyrhynchus cristatus</em> and three species of land iguanas: <em>Conolophus subcristatus</em>, <em>C. pallidus</em> and <em>C. marthae</em>. The biogeographic history of the land species in relation to their current distributions remains uncertain, in particular the origins of <em>C. marthae</em>, which is restricted to a small area of the northern part of Isabela Island. The classification of <em>C. pallidus</em> as a separate species has also been debated.</div><div>We analyzed DNA sequences (RADseq) to reconstruct demographic histories of selected local populations of all Galápagos iguana species and estimate their divergence times within a multispecies coalescent framework. Our results indicate an early date for the colonization of Galápagos by iguanas, relative to island formation, at <em>ca.</em> 10 Mya, and support a recent split of <em>C. marthae</em> via allopatric speciation, after the emergence of Isabela Island, at <em>ca.</em> 0.57 Mya. We find contrasting demographic histories in <em>C. marthae</em> and the syntopic population of <em>C. subcristatus,</em> suggesting competitive interaction between these species. We also confirm that the divergence of <em>C. pallidus</em> from <em>C. subcristatus</em> is recent (0.09 Mya) and close in time to the split between populations of <em>C. subcristatus</em> from different islands. Our genetic data support recent census estimates indicating a relatively small current effective population size (<em>N</em>_e) in all the studied populations. Our findings shed light on the evolutionary history of Galápagos iguanas and emphasize the need for targeted conservation strategies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108294"},"PeriodicalIF":3.6,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069909","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":"Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea)","authors":"Bo-Cheng Wang ,&nbsp;Ming-Luen Jeng ,&nbsp;Jing-Fu Tsai ,&nbsp;Li-Wei Wu","doi":"10.1016/j.ympev.2025.108292","DOIUrl":"10.1016/j.ympev.2025.108292","url":null,"abstract":"<div><div>Taiwan, a relatively young continental island, harbors a high proportion of endemic phasmids, reflecting its unique evolutionary history. However, a comprehensive phylogenetic framework to clarify these phasmids is still lacking. In this study, we sequenced ten of eleven valid genera and two undescribed species of Taiwanese phasmids (total 16 species) using the genome-skimming approach. We also integrated these sequences with public databases to create two aligned datasets: one comprising 92 taxa (mitogenomes) and the other 606 taxa (seven nuclear and mitochondrial genes), enabling us to examine their phylogenetic relationships using longer sequences and more samples. Our analyses show that Taiwanese phasmids should be categorized into six families, with a revised number of genera to 13. Furthermore, four species require taxonomic treatments: namely <em>Micadina honei</em> (Günther, 1940) comb. nov., <em>Micadina truncatum</em> (<span><span>Shiraki, 1935</span></span>) comb. nov., <em>Otraleus okunii</em> (<span><span>Shiraki, 1935</span></span>) comb. nov., and <em>Ramulus granulatus</em> (<span><span>Shiraki, 1935</span></span>) syn. nov. now recognized as <em>Ramulus artemis</em> (<span><span>Westwood, 1859</span></span>). While some Taiwanese genera exhibit polyphyletic relationships, our findings highlight the importance of taxon sampling, particularly for type species in resolving these systematic issues. The genome-skimming approach has proven to be an excellent method for producing comparable sequence datasets, facilitating the investigation of highly diverse insects, even when samples are old, small, or have highly fragmented DNAs.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108292"},"PeriodicalIF":3.6,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048628","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":"Unravelling phylogenetic relationships within the genus Lispe (Diptera: Muscidae) through genome-assisted and de novo analyses of RAD-seq data","authors":"Kinga Walczak ,&nbsp;Marcin Piwczyński ,&nbsp;Thomas Pape ,&nbsp;Nikolas P. Johnston ,&nbsp;James F. Wallman ,&nbsp;Krzysztof Szpila ,&nbsp;Andrzej Grzywacz","doi":"10.1016/j.ympev.2025.108291","DOIUrl":"10.1016/j.ympev.2025.108291","url":null,"abstract":"<div><div><em>Lispe</em> represents a species-rich genus within the family Muscidae. The current subdivision of <em>Lispe</em> species into species groups is based mainly on adult morphology and ecology, with the only available phylogenetic study based on three molecular markers. Nonetheless, certain species groups remain unclear and the relationships and composition of these groups are still unresolved. This study employs restriction-site associated DNA sequencing (RAD-seq) with both reference-based and <em>de novo</em> reads assembly approaches to investigate relationships within <em>Lispe</em>. To apply a reference-based approach we utilised Oxford Nanopore Technologies (ONT) long read sequencing to assemble a draft genome of <em>L</em>. <em>tentaculata</em>. We evaluated various assemblers for ONT reads of <em>L</em>. <em>tentaculata</em> in order to demonstrate the highest effectiveness in terms of completeness and assembly quality. The resulting phylogenetic trees topologies are well supported and present a consistent division into three main clades: 1) the <em>palposa</em>-, <em>rigida</em>- and <em>caesia</em>-groups, 2) the <em>nicobarensis</em>-, <em>nivalis</em>-, <em>scalaris</em>- and <em>tentaculata</em>-groups and 3) the <em>longicollis</em>-, <em>desjardinsii</em>-, <em>uliginosa</em>- and <em>kowarzi</em>-groups. The primary discrepancy between topologies obtained under our various analytical approaches is the relationship between the <em>leucospila</em>-group and all other ingroup taxa, being a sister taxon either to all remaining <em>Lispe</em> or to a clade consisting of the <em>longicollis</em>-, <em>desjardinsii</em>-, <em>uliginosa</em>- and <em>kowarzi</em>-groups. <em>Lispe polonaise</em>, included for the first time in a molecular phylogenetic analysis, is nested within the <em>caesia</em>-group. Similarly, <em>L</em>. <em>capensis</em> and the hitherto unassigned <em>L</em>. <em>mirabilis</em> belong to the <em>tentaculata</em>-group. Our study confirms the validity of the 14 species groups currently recognised in the genus <em>Lispe</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108291"},"PeriodicalIF":3.6,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061242","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 analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution","authors":"Zhen Yang ,&nbsp;Lisong Liang ,&nbsp;Weibo Xiang ,&nbsp;Qiong Wu ,&nbsp;Lujun Wang ,&nbsp;Qinghua Ma","doi":"10.1016/j.ympev.2025.108293","DOIUrl":"10.1016/j.ympev.2025.108293","url":null,"abstract":"<div><div>Phylogenomic analyses have shown that reticulate evolution greatly affects the accuracy of phylogenetic inferences, and thus may challenge the authority of bifurcating phylogenetic trees. In this study, we re-evaluated the phylogenetic backbone of the genus <em>Corylus</em> based on complete taxon sampling and genomic data. We assembled 581 single-copy nuclear genes and whole plastomes from 64 genome resequencing datasets to elucidate the reticulate relationships within <em>Corylus</em>. Nuclear coalescent and concatenation phylogenies revealed identical and fully supported backbone, clarifying the sisterhood between sect. <em>Acanthochlamys</em> and sect. <em>Siphonochlamys</em> as well as the phylogenetic position of <em>C. fargesii</em> and <em>C. wangii</em>, which have yet been addressed in previous phylogenetic studies. However, the monophyly of <em>C. jacquemontii</em> and <em>C. kwechowensis</em> and the distinction between <em>C. ferox</em> and <em>C. ferox</em> var. <em>thibetica</em> were not supported. Gene trees-species tree conflicts and cytonuclear discordance were identified, with multiple evidences supporting that hybridization/introgression, coupled with incomplete lineage sorting, have led to substantial phylogenetic incongruence in <em>Corylus</em>. Moreover, typical geographical clustering rather than strict monophyletic pattern in plastome phylogeny implies chloroplast capture within <em>Corylus</em> and offers evidence of cytoplasmic introgression. Overall, this study provides a robust phylogenomic backbone for <em>Corylus</em> and unravels that reticulate evolution can greatly shape taxonomic revision.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108293"},"PeriodicalIF":3.6,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143043512","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}