Molecular Phylogenetics and Evolution最新文献

{"title":"Phylogeny, species delimitation, and biogeographical history of Bredia.","authors":"Jin-Hong Dai, Ren-Chao Zhou, Ying Liu","doi":"10.1016/j.ympev.2025.108326","DOIUrl":"https://doi.org/10.1016/j.ympev.2025.108326","url":null,"abstract":"<p><p>Species delimitation in plants is sometimes challenging due to morphological convergence, interspecific gene flow, and historically limited sampling. Bredia Blume as currently defined comprises 27 species and has been resolved as monophyletic in previous phylogenomic studies. However, relationships among several major lineages in the genus remain elusive, and the species boundaries of some problematic taxa have not been tested. In this study, we employed comprehensive taxon sampling and reconstructed the phylogeny of Bredia using single-copy orthologs (SCOs), genomic single nucleotide polymorphisms (SNPs), and whole plastomes. The species tree derived from SCOs provided the highest resolution, strongly supporting all interspecific relationships. We identified instances of morphological convergence and potential hybridization/introgression within groups of interest and discussed species limits based on monophyly, genetic divergence, and morphological diagnosability. Using this robust phylogeny, we inferred divergence times and biogeographical history for Bredia. The genus originated in the Yunnan-Myanmar-Thailand Border region and the Beibu Gulf region during the middle Miocene, initially adapting to karst habitats. Over time, certain lineages shifted to non-karst environments. One such lineage migrated to the southeastern part of the Eastern Asiatic Kingdom in the late Miocene, where it rapidly diversified forming several major lineages. Subsequently, a mainland lineage reached Taiwan via a land bridge between the late Pliocene and the early Pleistocene and diversified in the region, eventually spreading to the Ryukyu Islands in the middle Pleistocene.</p>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":" ","pages":"108326"},"PeriodicalIF":3.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic conflict analyses of plastid and mitochondrial genomes of Impatiens (Balsaminaceae) reveal its complex evolutionary history","authors":"Yun-Fen Liang ,&nbsp;Tian-Tian Xue ,&nbsp;Sudhindra R. Gadagkar ,&nbsp;Fei Qin ,&nbsp;Steven B. Janssens ,&nbsp;Sheng-Xiang Yu","doi":"10.1016/j.ympev.2025.108325","DOIUrl":"10.1016/j.ympev.2025.108325","url":null,"abstract":"<div><div><em>Impatiens</em> is among the most diverse angiosperm genera, comprising more than 1000 species. The phylogenetic relationship among sections of <em>Impatiens</em> remains unclear. Plastomes and mitogenomes are useful for resolving problematic relationships in plant phylogenetics; however, conflicts between the organellar genomes have been reported. Here, we reconstructed the phylogeny of <em>Impatiens</em> using concatenated and multispecies coalescent (MSC) methods based on coding and noncoding regions of the plastome and coding regions of the mitogenome from 139 species, representing all major clades in <em>Impatiens</em>. Conflict analyses were conducted to test and visualize the incongruences between the organellar genomes and within the plastome. The analyses supported the monophyly of all subgenera and sections and identified a new clade (clade Longlinensis), but the relationships among these sections are inconsistent. There was incongruence between the organellar genome trees regarding the relationships among sect. <em>Semeiocardium</em>, sect. <em>Racemosae</em> and clade Longlinensis. There was also incongruence within the plastome regarding the relationships among sections <em>Fasciculatae</em>, <em>Impatiens</em>, <em>Tuberosae</em>, <em>Scorpioidae</em>, and <em>Uniflorae</em>. Our results show that incongruence between organellar genomes likely results from the complex evolutionary history of the genus, involving mixed inheritance of organellar genomes and hybridization. The incongruence within the plastome may result from the limited phylogenetic signal in plastome data, which could be due to the rapid radiation between 15.07 and 12.93 Ma. Specific genes and regions that led to such incongruence have been identified. By confirming the monophyly of <em>Impatiens</em> sections and detecting phylogenetic conflicts, this study provides a unique plastid and mitogenomic perspective on <em>Impatiens</em> phylogeny.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108325"},"PeriodicalIF":3.6,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607296","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":"Using phylogenetic data for island biogeography analyses: The DAISIEprep package","authors":"Joshua W. Lambert ,&nbsp;Lizzie Roeble ,&nbsp;Théo Pannetier ,&nbsp;Rampal S. Etienne ,&nbsp;Luis Valente","doi":"10.1016/j.ympev.2025.108324","DOIUrl":"10.1016/j.ympev.2025.108324","url":null,"abstract":"<div><div>New methodologies to infer past evolutionary, ecological and biogeographical processes from molecular phylogenies are rapidly being developed. However, these often employ unfamiliar data structures that may pose a barrier to their use. DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from molecular phylogenetic data across insular assemblages. The method uses an unconventional phylogenetic data structure: instead of considering a single island lineage, it focuses on multiple independent lineages descending from different colonisation events of the island. While analysing phylogenies from this perspective has plenty of potential, this comes with challenges for the user. Here we describe software DAISIEprep, an R package to aid the extraction of data from one or many phylogenetic trees to generate and visualise data in a format interpretable by macroevolutionary and biogeographical inference models. DAISIEprep includes simple algorithms to extract data on island colonists and account for biogeographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when molecular data are not available. The software enables reproducible and user-friendly data extraction, formatting and visualisation of phylogenetic data from island lineages, and will facilitate addressing questions about island evolution, community ecology and anthropogenic impacts in insular systems. The tools presented here will also be useful for researchers who do not plan to use DAISIE but are interested in how to interpret, visualise and analyse phylogenetic datasets of islands species or island-like environments.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108324"},"PeriodicalIF":3.6,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607302","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":"Disconnecting trapdoors: Phylogenomic analyses reveal evolutionary contrasts in trapdoor spiders with intercontinental distribution (Idiopidae, Idiopinae)","authors":"R. Fonseca-Ferreira ,&nbsp;S. Derkarabetian ,&nbsp;M.J.A. Morales ,&nbsp;V. Opatova ,&nbsp;T. Belintani ,&nbsp;R. Lyle ,&nbsp;J.P.L. Guadanucci","doi":"10.1016/j.ympev.2025.108323","DOIUrl":"10.1016/j.ympev.2025.108323","url":null,"abstract":"<div><div>Among Mygalomorphae spiders, the family Idiopidae is the second most diverse, consisting exclusively of trapdoor spiders and is divided into three subfamilies: Arbanitinae, Genysinae, and Idiopinae. The subfamily Idiopinae, distinguished mainly by anterior lateral eyes that project forward, includes 153 species across seven genera, distributed throughout South America, Africa, and parts of Asia. Within this subfamily, the genus <em>Idiops</em> includes the greatest diversity and is the only genus recorded in both the New and Old Worlds. Utilizing a taxon set from the Neotropical and Afrotropical regions, with specimens collected from 1947 to 2021, our study provides the first phylogenomic analysis of the family based on Ultraconserved Elements (UCEs). To assess the monophyly of Idiopinae and <em>Idiops</em>, as well as the relationships among genera within the subfamily, we conducted phylogenetic analyses employing maximum likelihood, Bayesian inference, and coalescent-based methods. The phylogenetic trees reveal that Idiopinae forms a monophyletic lineage, split into two geographically distinct groups: one with African species and the other with Neotropical species. We did not recover monophyly of the genus <em>Idiops</em>; Neotropical <em>Idiops</em> form a monophyletic lineage, while African <em>Idiops</em> species group with <em>Titanidiops</em>, forming a sister lineage to the remaining African Idiopinae. The relationship between the phylogenetic results obtained and the main morphological differences observed among the genera is discussed. Finally, our study challenges the monophyly of Idiopidae by including <em>Neocteniza</em>, which is found to be an independent lineage sister to Ctenizidae and the rest of Idiopidae.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108323"},"PeriodicalIF":3.6,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143598180","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":"Transcriptomic analyses in thirteen Tephritidae species provide insights into the ecological driving force behind odorant receptor evolution","authors":"Emma Persyn ,&nbsp;Pierre-François Duyck ,&nbsp;Marie-Christine François ,&nbsp;Christian Mille ,&nbsp;Vincent Jacob ,&nbsp;Emmanuelle Jacquin-Joly","doi":"10.1016/j.ympev.2025.108322","DOIUrl":"10.1016/j.ympev.2025.108322","url":null,"abstract":"<div><div>The insect olfactory system has evolved while guiding species to specific mating partners, different food sources, and oviposition sites. How species repertoires of odorant receptors (ORs), responsible for the detection of volatile cues, have been shaped by ecologically driven forces remains poorly understood. Due to several host switches back and forth throughout their evolutionary history, fruit flies of the Tephritidae family (Diptera) show highly diverse host preferences, making them good models to address this question. For instance, a comparative analysis of genomic and transcriptomic resources on a large variety of fruit fly species could provide statistical conclusions. Here, we used a RNAseq approach to identify the OR repertoires of thirteen Tephritidae species with different host ranges, namely <em>Bactrocera curvipennis</em>, <em>Bactrocera dorsalis, Bactrocera psidii, Bactrocera tryoni, Bactrocera umbrosa, Bactrocera zonata, Ceratitis capitata</em>, <em>Ceratitis catoirii</em>, <em>Ceratitis quilicii, Dacus ciliatus, Dacus demmerezi, Neoceratitis cyanescens,</em> and <em>Zeugodacus cucurbitae</em>. Manual curation allowed us to annotate 60–80 OR transcripts per species, including the obligatory coreceptor Orco. In total, we reported 698 new OR sequences. Differential expression analyses between antennae and maxillary palps and between the two sexes, performed in three species, revealed some organ- and sex-biased OR expression. Moreover, after adjusting for phylogenetic distance, we found significant correlations between some characteristics of the OR repertoire and species host range: sequences and relative expression level of several ORs were more conserved in polyphagous than in oligophagous species and, in addition, other ORs were found specifically in polyphagous species. Our results provide molecular insights into the ecological driving forces behind Tephritidae OR evolution.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"206 ","pages":"Article 108322"},"PeriodicalIF":3.6,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574500","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":"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}