Molecular Phylogenetics and Evolution最新文献

{"title":"Phylogenomics insights into the evolution of pronotal leaf mimicry in Hierodulinae (Mantodea: Mantidae)","authors":"Xiao-Dong Xu ,&nbsp;Chen-Yang Shen ,&nbsp;Kenneth B. Storey ,&nbsp;Dan-Na Yu ,&nbsp;Yue Ma ,&nbsp;Jia-Yong Zhang","doi":"10.1016/j.ympev.2025.108475","DOIUrl":"10.1016/j.ympev.2025.108475","url":null,"abstract":"<div><div>The evolutionary relationships within the mantid subfamily Hierodulinae remain contentious, particularly concerning the morphological diversity and classification of species with leaf-like pronotum, which are broad and flattened thoracic structures. Traditionally regarded as a defining characteristic of the genus <em>Rhombodera</em>, specifically as a specialized pronotal trait, mitochondrial phylogenomics has cast doubt on this assumption, suggesting potential homoplasy. In this study, we generated 30 high-quality transcriptomes of Hierodulinae and established the first Mantodea-specific orthologous database (Mantodea_odb) to identify universal single-copy orthologues (USCOs) for phylogenomic inference. By integrating genomic and transcriptomic data, we reconstructed well-supported phylogenetic trees using both maximum likelihood and coalescent-based approaches, which provided the framework to assess evolutionary patterns of morphological traits. Divergence time estimation and ancestral state reconstruction suggested that the leaf-like pronotum evolved independently on multiple occasions within Hierodulinae, corresponding temporally to the late Paleogene to early Neogene (Oligocene-Miocene transition, ca. 20–23 Ma). Notably, our molecular phylogeny exhibits a strong correlation with distinct clades delineated by male genital morphology, thereby resolving longstanding taxonomic inconsistencies. These findings reveal decoupled evolutionary patterns between homoplastic pronotal traits and conserved genital morphology in Hierodulinae, showcasing how phylogenomics can discriminate between convergent and conserved traits.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108475"},"PeriodicalIF":3.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253892","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":"Spider nest-retreat origin, diversification, and architectural plasticity link to historical and current temperature fluctuations","authors":"Rui Zhong ,&nbsp;Jian Chang ,&nbsp;Yunhe Wang ,&nbsp;Haixin Zhang ,&nbsp;Yu Peng ,&nbsp;Ingi Agnarsson ,&nbsp;Jie Liu","doi":"10.1016/j.ympev.2025.108478","DOIUrl":"10.1016/j.ympev.2025.108478","url":null,"abstract":"<div><div>Ongoing climate change mandates improved understanding of how temperature fluctuations influence organismal evolution and behavior. Detritus-based nest-retreats in spiders have originated multiple times in parallel—hypothesized to be an adaptive response to climatic fluctuations. We investigated the potential role of climate change in shaping the evolution of nest-retreats over geological timescales, and the short-term effect of temperature on the morphology and energy investment of nest-retreats in <em>Campanicola campanulata</em> (Theridiidae). Phylogenetic analyses reconstruct twelve origins of nest-retreats, first appearing in the Eocene, and diversifying during the Late Cenozoic Icehouse period. Spiders respond to experimentally lowered temperatures by making larger nest-retreats, indicating a direct impact of temperature on retreat architecture. Our results for the first time affirm the thermoregulatory function of spider nests and suggest that temperature impacts nest-retreats across both evolutionary and ecological timescales. Nest-retreat spiders can serve as a model to study the origins of thermoregulatory nest-building in animals and how it may be impacted by ongoing climate change.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108478"},"PeriodicalIF":3.6,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253890","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":"Incomplete lineage sorting, hybridization and polyploidization blurred phylogenetic relationships of gentians from the Qinghai-Tibetan Plateau","authors":"Shan-Shan Sun ,&nbsp;Shu-Han Xu ,&nbsp;Wen-Jie Yi ,&nbsp;Shi-Long Chen ,&nbsp;Pan Li ,&nbsp;Daiki Takahashi ,&nbsp;Harue Abe ,&nbsp;Xiao-Lei Ma ,&nbsp;Peng-Cheng Fu","doi":"10.1016/j.ympev.2025.108476","DOIUrl":"10.1016/j.ympev.2025.108476","url":null,"abstract":"<div><div>Resolving evolutionary relationships among species undergoing radiation is challenging. <em>Gentiana</em> is a species-rich genus with a sub-cosmopolitan distribution, in which several sections have undergone recent radiation. In this study, we reassessed the phylogeny of <em>Gentiana</em> with particular focus on the controversial section <em>Kudoa</em>, and elucidated the complex phylogenetic relationship as well as their underlying causes in this section. Combining with a large number of single-copy orthologous genes and complete chloroplast genome sequences, we revised the delimitation of sections <em>Kudoa</em> and <em>Isomeria</em>, and proposed a new section <em>Uniflorae</em>. Our results suggested that <em>G. yakushimensis</em>, one of the most controversial species in <em>Gentiana</em>, should be transferred from section <em>Kudoa</em> to <em>Pneumonanthe</em>. The revised section <em>Kudoa</em> comprised two morphologically distinct series, and was composed of five genetic clades, with one clade corresponding to series <em>Verticilatae</em>. Although the backbone of <em>Kudoa</em> phylogeny was clear, current genetic data were insufficient to clarify species boundaries for several species. Evidence from single-copy orthologous genes and genome-wide SNPs revealed widespread hybridization against a background of extensive incomplete lineage sorting (ILS) in section <em>Kudoa</em>, accounting for the gene tree discordance. Genome size data indicated that tetraploids occurred in three out of the five clades, demonstrating that polyploidization further complicated the phylogeny of section <em>Kudoa</em>. In summary, <em>Gentiana</em> comprises 14 sections under our revised classification, and ILS, hybridization and polyploidization collectively contributed to the phylogenetic ambiguity of section <em>Kudoa</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108476"},"PeriodicalIF":3.6,"publicationDate":"2025-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145246028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics of an early-branching clade of Orthocladiinae (Diptera: Chironomidae)","authors":"Hai-Feng Xu ,&nbsp;Zhi-Chao Zhang ,&nbsp;Dan Zhang ,&nbsp;Viktor Baranov ,&nbsp;Chen-Hong Li ,&nbsp;Xiao-Long Lin","doi":"10.1016/j.ympev.2025.108477","DOIUrl":"10.1016/j.ympev.2025.108477","url":null,"abstract":"<div><div>The early-branching clade of Orthocladiinae and Prodiamesinae represent ancient, highly diverse, and ecologically adaptable key groups within Chironomidae (Diptera). Their larvae are widely distributed in freshwater ecosystems and serve as core bioindicators for water quality monitoring. However, due to historically incomplete geographical sampling and insufficient resolution of molecular markers, the taxonomic status of Prodiamesinae and the phylogenetic relationships among several problematic genera within the early-branching clade of Orthocladiinae have remained unresolved. This study systematically selected representative species from Prodiamesinae and the early-branching clade of Orthocladiinae to construct a highly confident molecular phylogenetic framework using universal single-copy orthologous nuclear genomic data. Key findings include: Prodiamesinae should be subsumed within Orthocladiinae, forming a sister group with <em>Propsilocerus</em> and treated as a synonym of Orthocladiinae (= Prodiamesinae <strong>syn. n.</strong>); the phylogenetic relationships among the early-branching clade of Orthocladiinae have been conclusively resolved; the origin of Orthocladiinae <em>sensu lato</em> (including Prodiamesinae and the early-branching clade of Orthocladiinae) dates back to the Early-Middle Jurassic (<em>ca.</em> 199–165 million years ago). These results reshape the higher-level classification system of Chironomidae, providing a reliable taxonomic foundation and evolutionary framework for future studies.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108477"},"PeriodicalIF":3.6,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214482","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":"Overwater dispersal from a single source island shaped the diversity of green anole lizards (Anolis carolinensis subgroup)","authors":"Javier Torres ,&nbsp;R. Graham Reynolds ,&nbsp;Kin Onn Chan ,&nbsp;Paul Hime ,&nbsp;Richard E. Glor","doi":"10.1016/j.ympev.2025.108474","DOIUrl":"10.1016/j.ympev.2025.108474","url":null,"abstract":"<div><div>The Cuban green anoles, members of the <em>Anolis carolinensis</em> species complex, are among the most successful colonizing lineages of anole lizards in the Caribbean. We use ddRAD and Sanger sequence data to clarify the evolutionary relationships among all members of the <em>A. carolinensis</em> species complex (generally called Cuban green anoles), demarcate species boundaries, and explain the geographic origins of this key group of highly dispersive anoles. This study supports the “Out of Cuba” hypothesis involving six or seven independent colonization events from a Cuban source with one possible island-to-island dispersal event between the Cayman Islands and Navassa. Independent colonization events occurred from three main clades delimited by western, central, and eastern Cuba. West Cuban lineages dispersed twice—to the Cay Sal Bank (Bahamas) and to Florida. Central Cuban lineages dispersed twice—to the Bahamas archipelago and the Bay Islands (Honduras), respectively, with the latter seemingly owing to human assistance. East Cuban lineages colonized the Bahamas archipelago once as well as Little Cayman and Navassa, although it is unclear if all these colonizations occurred directly from Cuba. We recommend continued recognition of all species in the complex except <em>A. fairchildi—</em>which we consider a subspecies of <em>A. porcatus</em>—for a total of 8 species in this group: <em>A. allisoni</em>, <em>A. brunneus</em>, <em>A. carolinensis</em>, <em>A. longiceps</em>, <em>A. maynardii</em>, <em>A. porcatus</em>, <em>A. smaragdinus</em>, and <em>A. torresfundorai</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108474"},"PeriodicalIF":3.6,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145208511","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":"Trends in substitution models of protein evolution for phylogenetic inference","authors":"David Ferreiro,&nbsp;Elena Pazos,&nbsp;Miguel Arenas","doi":"10.1016/j.ympev.2025.108473","DOIUrl":"10.1016/j.ympev.2025.108473","url":null,"abstract":"<div><div>Substitution models of protein evolution describe the rates of evolutionary change among amino acids and are essential for a variety of evolutionary studies, including the reconstruction of phylogenetic histories and ancestral sequences, among others. The earliest substitution models of protein evolution are based on empirical protein sequences and, despite their unrealistic assumptions, are still routinely used in protein phylogenetics. Next, the incorporation of additional parameters that inform about evolutionary constraints on protein stability and protein function provided a significant increase in the accuracy of the modeling. However, despite the wide variety of substitution models of protein evolution that were presented, only a small subset has been implemented in evolutionary frameworks of practical use in phylogenetics. Here, we overview general trends in the development and application of substitution models of protein evolution, including their theoretical fundamentals, goals, areas for improvement, and implementation in phylogenetic frameworks. We also provide detailed practical examples of phylogenetic inference using advanced structurally constrained substitution models.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108473"},"PeriodicalIF":3.6,"publicationDate":"2025-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145194074","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":"Hybridization and incomplete lineage sorting characterize the evolutionary history of two East Asian clades of Stewartia (Theaceae)","authors":"Han-Yang Lin ,&nbsp;Miao Sun ,&nbsp;Jian-Jun Jin ,&nbsp;Cheng-Xin Fu ,&nbsp;Douglas E. Soltis ,&nbsp;Pamela S. Soltis ,&nbsp;Yun-Peng Zhao","doi":"10.1016/j.ympev.2025.108472","DOIUrl":"10.1016/j.ympev.2025.108472","url":null,"abstract":"<div><div>Reticulate evolution and recalcitrant phylogenetic relationships are common in the East Asian evergreen broad-leaved forests (EA-EBLFs),. Hybridization and incomplete lineage sorting (ILS) can both occur during diversification of these forests, yet the extent of ILS has often been overlooked. Among floristic elements in the EA-EBLFs, plant genera that are disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) provide an excellent system to explore the magnitude of hybridization and ILS after vicariance and long-distance dispersal. Here, we investigated the evolutionary history of <em>Stewartia</em> L. (Theaceae), one of the EA-ENA disjuncts whose major members inhabit the EA-EBLFs (ca. 20 spp. in EA vs. two spp. in ENA) using target enrichment sequence data obtained from Angiosperms353. Based on nearly complete taxon sampling, we recovered two <em>Stewartia</em> clades (the EA deciduous and evergreen clades) in the EA-EBLFs. Our estimates indicate that these two clades started to diversify in the late Miocene, and the evergreen clade showed a higher diversification rate than the deciduous clade. The SNaQ and NANUQ analyses detected hybridization signals within both clades, primarily involving <em>S. serrata</em> and <em>S. tonkinensis</em>, respectively. In addition, the QuIBL analysis revealed co-occurring introgression and ILS in 98/105 and 318/360 tested triplets (Δ BIC &lt; − 10) in the deciduous and evergreen clades, respectively. The Phytop analysis further supported ILS as the primary source of gene-tree discordance. Our study reveals complex phylogenetic and evolutionary patterns in EA-EBLF endemics and highlights the importance of hybridization and ILS in this region.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108472"},"PeriodicalIF":3.6,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145093139","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 reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand","authors":"Weixuan Ning ,&nbsp;Heidi M. Meudt ,&nbsp;Antoine N. Nicolas ,&nbsp;Gregory M. Plunkett ,&nbsp;Peter B. Heenan ,&nbsp;William G. Lee ,&nbsp;Jennifer A. Tate","doi":"10.1016/j.ympev.2025.108469","DOIUrl":"10.1016/j.ympev.2025.108469","url":null,"abstract":"<div><div>Genera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in <em>Azorella</em> (Apiaceae) sections <em>Schizeilema</em> and <em>Stilbocarpa</em> that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6<em>x</em> and 10<em>x</em>), and assess the biogeography of the New Zealand <em>Azorella</em> species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two <em>Azorella</em> sections in New Zealand likely resulted from different biogeographic events from South America − one to the subantarctic islands (section <em>Stilbocarpa</em>) and a second to the South Island (section <em>Schizeilema</em>). In addition, within section <em>Schizeilema</em>, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand <em>Azorella</em> and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108469"},"PeriodicalIF":3.6,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082656","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":"Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes","authors":"Mabodiba M. Maake ,&nbsp;Chrizelle W. Beukes ,&nbsp;Magriet A. van der Nest ,&nbsp;Juanita R. Avontuur ,&nbsp;Esther K. Muema ,&nbsp;Tomasz Stępkowski ,&nbsp;Stephanus N. Venter ,&nbsp;Emma T. Steenkamp","doi":"10.1016/j.ympev.2025.108471","DOIUrl":"10.1016/j.ympev.2025.108471","url":null,"abstract":"<div><div>Given that several, mainly endemic South African Genisteae genera occupy basal positions in legume phylogenetic trees, this region of Africa is considered a primaeval centre of diversification of this legume tribe. Despite the importance of South Africa in Genisteae evolution, almost all studies have focused on rhizobia nodulating Genisteae in their centres of diversity in either the Mediterranean Basin or the Americas. Therefore, this study aimed to identify and characterize rhizobial strains associated with <em>Argyrolobium</em> species native to areas of the Grassland biome associated with the Great Escarpment, which dominates the subcontinent’s eastern landscape, and compare these to bradyrhizobia nodulating Genisteae in other centres of diversity. Phylogenetic analyses of five housekeeping genes (<em>dnaK, glnII, gyrB, recA,</em> and <em>rpoB</em>) separated the 18 <em>Bradyrhizobium</em> strains examined into five well-supported groups. Three of these were conspecific with <em>B. arachidis</em>, <em>B. brasilense/B. australafricanum</em> and <em>B. ivorense</em>, while the remaining two appeared to be new to science. After confirming their novelty using Average Nucleotide Identity, a metric for genome relatedness, and certain phenotypic traits, we recognized them as novel species for which we proposed the names <em>B. spitzkopense</em> sp. nov. (Arg816^Ts) and <em>B. mpumalangense</em> sp. nov. (Arg237L^Ts). Phylogenetic analyses of <em>nodA</em> gene sequences showed that about half of the strains examined, irrespective of their species identity, harboured alleles known only from the Grassland biome along the Great Escarpment that were previously detected in <em>Bradyrhizobium</em> strains nodulating Crotalarieae endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique <em>nodA</em> alleles typically encode the <em>nodH</em> gene, the product of which adds a sulfate moiety to the Nod factor (the signalling molecule for establishing the nitrogen-fixing symbiosis). The remaining strains had <em>nodA</em> alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, the genomes of these other strains lacked <em>nodH</em> but encoded <em>nodZ</em>, the gene involved in the fucosylation of the Nod factor. Our findings, therefore, showed that the root nodules of Genisteae (and its sister tribe Crotalarieae) native to the Grassland biome along the Great Escarpment are often related <em>Bradyrhizobium</em> strains that are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108471"},"PeriodicalIF":3.6,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145076650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics and the falsification of shearwater species (Puffinus mauretanicus, P. yelkouan) hypotheses: a comment on Ferrer Obiol et al. (2023)","authors":"George Sangster ,&nbsp;Meritxell Genovart ,&nbsp;Tim Guilford ,&nbsp;Daniel Oro ,&nbsp;Maite Louzao ,&nbsp;M. de L. Brooke ,&nbsp;José Manuel Arcos","doi":"10.1016/j.ympev.2025.108470","DOIUrl":"10.1016/j.ympev.2025.108470","url":null,"abstract":"<div><div><span><span>Ferrer Obiol et al. (2023)</span></span> applied double digest restriction-site associated sequencing (ddRAD-seq) data to delimit species in North Atlantic and Mediterranean <em>Puffinus</em> shearwaters. These authors concluded that the Balearic/Yelkouan shearwaters (<em>P. mauretanicus</em>/<em>P. yelkouan</em>) sister-species pair comprised a single species based on analyses of ddRAD-seq data and a very brief and deficient review of other evidence. While it is clear that reduced representation genomic data are often suitable for the discovery and documentation of species and their relationships, the issue of whether such data are sufficient to <em>falsify</em> hypotheses of species taxa has received only limited attention so far. Here, we note that detection of species in phylogenomic analyses based on reduced representation sequencing methods will be problematic if species differences are only found in a small portion of the genome (so-called ‘genomic islands of differentiation’), as has been documented in multiple case studies. This means that genomic differences between some species may only be detected if (i) entire genomes are sequenced, and (ii) a formal search for islands of differentiation is conducted. Valid species may be overlooked in reduced representation approaches, such as ddRAD sequencing. Consequently, an apparent lack of overall phylogenomic divergence (e.g. lack of reciprocal monophyly, low genome-wide <em>F</em>_ST) should not be used by taxonomists as evidence that such taxa are not valid species. We conclude that the apparent lack of divergence in the ddRAD-seq data of <span><span>Ferrer Obiol et al. (2023)</span></span> does not represent credible evidence that <em>P. mauretanicus</em> and <em>P. yelkouan</em> are conspecific. In addition, we show that the authors misrepresented other available taxonomic data, failing to properly follow an integrative approach.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"214 ","pages":"Article 108470"},"PeriodicalIF":3.6,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071309","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}