Molecular Phylogenetics and Evolution最新文献

{"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}

{"title":"An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group","authors":"Tomáš Pánek ,&nbsp;Alexander K. Tice ,&nbsp;Pia Corre ,&nbsp;Pavla Hrubá ,&nbsp;David Žihala ,&nbsp;Ryoma Kamikawa ,&nbsp;Euki Yazaki ,&nbsp;Takashi Shiratori ,&nbsp;Keitaro Kume ,&nbsp;Tetsuo Hashimoto ,&nbsp;Ken-ichiro Ishida ,&nbsp;Miluše Hradilová ,&nbsp;Jeffrey D. Silberman ,&nbsp;Andrew Roger ,&nbsp;Yuji Inagaki ,&nbsp;Marek Eliáš ,&nbsp;Matthew W. Brown ,&nbsp;Ivan Čepička","doi":"10.1016/j.ympev.2025.108289","DOIUrl":"10.1016/j.ympev.2025.108289","url":null,"abstract":"<div><div>The phylum Heterolobosea Page and Blanton, 1985 is a group of eukaryotes that contains heterotrophic flagellates, amoebae, and amoeboflagellates, including the infamous brain-eating amoeba <em>Naegleria fowleri</em>. In this study, we investigate the deep evolutionary history of Heterolobosea by generating and analyzing transcriptome data from 16 diverse isolates and combine this with previously published data in a comprehensive phylogenomic analysis. This dataset has representation of all but one of the major lineages classified here as orders. Our phylogenomic analyses recovered a robustly supported phylogeny of Heterolobosea providing a phylogenetic framework for understanding their evolutionary history. Based on the newly recovered relationships, we revised the classification of Heterolobosea to the family level. We describe two new classes (Eutetramitea cl. nov. and Selenaionea cl. nov) and one new order (Naegleriida ord. nov.), and provide a new delimitation of the largest family of Heterolobosea, Vahlkampfiidae Jollos, 1917. Unexpectedly, we unveiled the first two cases of genetic code alterations in the group: UAG as a glutamine codon in the nuclear genome of <em>Dactylomonas venusta</em> and UGA encoding tryptophan in the mitochondrial genome of <em>Neovahlkampfia damariscottae</em>. In addition, analysis of the genome of the latter species confirmed its inability to make flagella, whereas we identified hallmark flagellum-specific genes in most other heteroloboseans not previously observed to form flagellates, suggesting that the loss of flagella in Heterolobosea is much rarer than generally thought. Finally, we define the first autapomorphy of the subphylum Pharyngomonada, represented by a fusion of two key genes for peroxisomal β-oxidation enzymes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108289"},"PeriodicalIF":3.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017121","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 species delimitation in the Lepidophyma sylvaticum complex (Squamata: Xantusiidae) using ddRADseq and morphological data","authors":"José Daniel Lara-Tufiño ,&nbsp;Rubi Nelsi Meza-Lázaro ,&nbsp;Adrián Nieto-Montes de Oca","doi":"10.1016/j.ympev.2025.108288","DOIUrl":"10.1016/j.ympev.2025.108288","url":null,"abstract":"<div><div>The <em>Lepidophyma sylvaticum</em> complex occurs from west-central Nuevo León to the Sierra de Chiconquiaco in central Veracruz, Mexico. Morphological studies have revealed population groups that are “moderately divergent from each other” within the complex. In addition, a molecular phylogenetic study found <em>L. sylvaticum</em> to be strongly structured and paraphyletic with respect to <em>L. micropholis</em>. We used ddRADseq and morphological data to evaluate the phylogenetic relationships and species boundaries within the complex. Phylogenetic analyses performed using both concatenation and coalescent methods estimated the same well-supported tree, composed of five allopatric, strongly supported lineages of <em>L. sylvaticum</em> (from Nuevo León [NL]; Sierra de Álvarez, San Luis Potosí [ASLP]; southeastern San Luis Potosí, Querétaro, Hidalgo, and northwestern Veracruz [HSQV]; Tamaulipas [T]; and Puebla and northern Veracruz [PV]) branching off (in that order) from the base of the tree, with <em>L. micropholis</em> as the sister taxon to the last of them. A population genetics analysis revealed one pattern of genetic structure in <em>L. micropholis</em> and three in <em>L. sylvaticum</em>: one in the <em>L. sylvaticum</em> NL and ASLP lineages, another in the <em>L. sylvaticum</em> HSQV and T lineages, and a third in the <em>L. sylvaticum</em> PV lineage. The six lineages identified were genetically distinctive across our phylogenetic and population genetics analyses, and congruent with geography. Species tree and phylogenetic network analyses, considering the six lineages as potentially independent, inferred trees identical to the concatenated tree. Additionally, the phylogenetic network analysis detected a recent introgression event from the <em>L. sylvaticum</em> T lineage into <em>L. micropholis</em>. A time-calibrated tree indicated that the diversification of the complex began in the late Miocene and continued into the Pleistocene. A species delimitation analysis, based on the genealogical divergence index, suggested that the <em>L. sylvaticum</em> NL, ASLP, and PV lineages are independent evolutionary lineages. A morphological analysis showed that <em>L. micropholis</em> and the <em>L. sylvaticum</em> NL and ASLP lineages were distinguishable from each other and from the remaining <em>L. sylvaticum</em> lineages. We conclude that the <em>L. sylvaticum</em> NL and ASLP lineages, the two oldest in the complex, represent independent evolutionary lineages, and propose recognizing the other four lineages as subspecies (historical sublineages) of <em>L. sylvaticum sensu stricto</em>.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108288"},"PeriodicalIF":3.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017129","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":"Comprehensive phylogenetic analysis of newly detected rodent adenoviruses sheds light on ancient host-switches","authors":"Márton Z. Vidovszky ,&nbsp;Győző L. Kaján ,&nbsp;Kinga P. Böszörményi ,&nbsp;Iva I. Podgorski ,&nbsp;Andor Doszpoly ,&nbsp;Mónika Z. Ballmann ,&nbsp;Gergő Mitró ,&nbsp;Gabriella Skoda ,&nbsp;Marije Turk ,&nbsp;Matthijs K. Groothuizen ,&nbsp;Marina Bidin ,&nbsp;Rodinde Hendrickx ,&nbsp;Silvio Hemmi ,&nbsp;László Egyed ,&nbsp;Mária Benkő ,&nbsp;Balázs Harrach","doi":"10.1016/j.ympev.2025.108287","DOIUrl":"10.1016/j.ympev.2025.108287","url":null,"abstract":"<div><div>Here we provide a comprehensive update on the diversity and genetic relatedness of adenoviruses occurring in rodents. Extensive PCR screenings revealed the presence of adenoviral DNA in samples originating from representatives of 17 rodent species from four different suborders of Rodentia. Distinct sequences of 28 different adenoviruses were obtained from the positive samples. Out of these, 20 were from hitherto unknown, putative novel adenoviruses, whereas 6 were variants of previously published murine adenoviruses. Additionally, two known viruses, guinea pig adenovirus 1 and squirrel adenovirus 1 were also detected. By PCR and primer walking, we determined the sequence of a considerable part of the genomic DNA of squirrel adenovirus 1, detected in red squirrel (<em>Sciurus vulgaris</em>) samples from Germany previously. We annotated the almost complete genome sequence of a novel mastadenovirus found by data mining in the bulk data of the Ord’s kangaroo rat (<em>Dipodomys ordii</em>) genome project. We revisited the sequence of the gene of E1B 19 K protein of mouse adenovirus 3. In contrast to the prototype strain, where a truncated version of this gene has been found, in our sample of mouse adenovirus 3, it seemed to be intact. Based on phylogeny reconstructions, all rodent adenoviruses clustered in the genus <em>Mastadenovirus</em>. Interestingly, however, there wasn’t a common monophyletic clade encompassing every adenovirus of rodent origin. Instead, three major lineages were observed. Because two lineages contained viral sequences deduced from samples of three suborders, and one consisted almost exclusively of adenoviruses from the family Muridae, we hypothesize there has been a long-term coevolution with the rodent hosts, as a result of possible ancient host-switch events. Several putative viruses appeared in distinct branches further away from the three clades. Thus, the evolutionary past of the adenoviruses of rodents remains to be studied further.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108287"},"PeriodicalIF":3.6,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017124","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":"Generic delimitation in the Cyphotheca-Plagiopetalum-Sporoxeia clade","authors":"Qi-Yuan Zhuang ,&nbsp;Jin-Hong Dai ,&nbsp;Chun-Yu Zou ,&nbsp;Yan Liu ,&nbsp;Zhi-Yong Yu ,&nbsp;Xin Jiang ,&nbsp;Qiu-Jie Zhou ,&nbsp;Zheng-Ming Zhu ,&nbsp;Wen-Xiang Zhang ,&nbsp;Xi-Bin Guo ,&nbsp;Ren-Chao Zhou ,&nbsp;Ying Liu","doi":"10.1016/j.ympev.2025.108290","DOIUrl":"10.1016/j.ympev.2025.108290","url":null,"abstract":"<div><div>The <em>Cyphotheca</em>-<em>Plagiopetalum</em>-<em>Sporoxeia</em> clade (Sonerileae, Melastomataceae) comprises <em>Cyphotheca</em> Diels, <em>Plagiopetalum</em> Rehder, <em>Sporoxeia</em> W.W.Sm., and some species of the highly polyphyletic <em>Phyllagathis</em> Blume, as well as some undescribed species, which requires taxonomic revision at the generic level. In this study, we expanded taxon sampling of the CPS clade and reconstructed phylogenetic relationships using genomic SNPs and whole plastomes assembled from genome resequencing data. We recognized six subclades in the CPS clade and observed strong cytonuclear incongruences within and among subclades. Gene tree simulation and Patterson’s <em>D</em>-statistic indicated that the conflicting phylogenetic signals were mainly caused by incomplete lineage sorting and hybridization/introgression. Molecular and morphological divergence among species of the CPS clade were evaluated using principal component analysis. Genomic SNP data clearly separated the six subclades, whereas the boundaries of some subclades were obscure in the plots of morphological data. Through reconstruction of morphological characteristics, we found a high level of homoplasy for some characters but also identified potential synapomorphies for the lineages. Based on the results, a revised generic classification is proposed for the CPS clade. Specifically, we expand <em>Cyphotheca</em>, <em>Plagiopetalum</em>, and <em>Sporoxeia</em> to include additional species, and establish three new genera, namely <em>Chiehchenii</em>, <em>Neophyllagathis</em>, and <em>Sporocyphoxeia</em>. A description and a list of species are provided for each of the six genera. Four new species are described.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108290"},"PeriodicalIF":3.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973459","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":"A thorny tale: The origin and diversification of Cirsium (Compositae)","authors":"Lucía D. Moreyra ,&nbsp;Alfonso Susanna ,&nbsp;Juan Antonio Calleja ,&nbsp;Jennifer R. Ackerfield ,&nbsp;Turan Arabacı ,&nbsp;Carme Blanco-Gavaldà ,&nbsp;Christian Brochmann ,&nbsp;Tuncay Dirmenci ,&nbsp;Kazumi Fujikawa ,&nbsp;Mercè Galbany-Casals ,&nbsp;Tiangang Gao ,&nbsp;Abel Gizaw ,&nbsp;Iraj Mehregan ,&nbsp;Roser Vilatersana ,&nbsp;Juan Viruel ,&nbsp;Bayram Yıldız ,&nbsp;Frederik Leliaert ,&nbsp;Alexey P. Seregin ,&nbsp;Cristina Roquet","doi":"10.1016/j.ympev.2025.108285","DOIUrl":"10.1016/j.ympev.2025.108285","url":null,"abstract":"<div><div>Widely distributed plant genera offer insights into biogeographic processes and biodiversity. The Carduus-Cirsium group, with over 600 species in eight genera, is diverse across the Holarctic regions, especially in the Mediterranean Basin, Southwest Asia, Japan, and North America. Despite this diversity, evolutionary and biogeographic processes within the group, particularly for the genus <em>Cirsium</em>, remain underexplored. This study examines the biogeographic history and diversification of the group, focusing on <em>Cirsium</em>, using the largest molecular dataset for the group (299 plants from 251 taxa). Phylogenomic analyses based on 350 nuclear loci, derived from target capture sequencing, revealed highly resolved and consistent phylogenetic trees, with some incongruences likely due to hybridization and incomplete lineage sorting. Ancestral range estimations suggest that the Carduus-Cirsium group originated during the Late Miocene in the Western Palearctic, particularly in the Mediterranean, Eastern Europe, or Southwest Asia. A key dispersal event to tropical eastern Africa around 10.7 million years ago led to the genera Afrocarduus and Afrocirsium, which later diversified in the Afromontane region. The two subgenera of <em>Cirsium</em>—<em>Lophiolepis</em> and <em>Cirsium</em>—began diversifying around 7.2–7.3 million years ago in the Western Palearctic. During the Early Pliocene, diversification rates increased, with both subgenera dispersing to Southwest Asia, where extensive <em>in situ</em> diversification occurred. Rapid radiations in North America and Japan during the Pleistocene were triggered by jump-dispersals events from Asia, likely driven by geographic isolation and ecological specialization. This added further layers of complexity to the already challenging taxonomic classification of <em>Cirsium</em>.Keywords: Biogeography; Carduinae; <em>Cirsium</em>; Diversification; North Hemisphere; Target-enrichment; Taxonomy.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108285"},"PeriodicalIF":3.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)","authors":"Alden C. Dirks ,&nbsp;Andrew S. Methven ,&nbsp;Andrew N. Miller ,&nbsp;Michelle Orozco-Quime ,&nbsp;Sundy Maurice ,&nbsp;Gregory Bonito ,&nbsp;Judson Van Wyk ,&nbsp;Steven Ahrendt ,&nbsp;Alan Kuo ,&nbsp;William Andreopoulos ,&nbsp;Robert Riley ,&nbsp;Anna Lipzen ,&nbsp;Mansi Chovatia ,&nbsp;Emily Savage ,&nbsp;Kerrie Barry ,&nbsp;Igor V. Grigoriev ,&nbsp;Alexander J. Bradshaw ,&nbsp;Francis M. Martin ,&nbsp;A. Elizabeth Arnold ,&nbsp;Timothy Y. James","doi":"10.1016/j.ympev.2025.108286","DOIUrl":"10.1016/j.ympev.2025.108286","url":null,"abstract":"<div><div>Lorchels, also known as false morels (<em>Gyromitra sensu lato</em>), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, <em>Discinaceae</em>, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in <em>Discinaceae</em>. We recognized 10 genera across two tribes: tribe <em>Discineae</em> (<em>Discina</em>, <em>Maublancomyces</em>, <em>Neogyromitra</em>, <em>Piscidiscina</em>, and <em>Pseudodiscina</em>) and tribe <em>Gyromitreae</em> (<em>Gyromitra</em>, <em>Hydnotrya</em>, <em>Paragyromitra</em>, <em>Pseudorhizina</em>, and <em>Pseudoverpa</em>); <em>Piscidiscina</em> was newly erected and 26 new combinations were formalized. <em>Paradiscina melaleuca</em> and <em>Marcelleina donadinii</em> formed their own family-level clade sister to <em>Morchellaceae,</em> which merits further taxonomic study<em>.</em> Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (<em>Hydnotrya</em> spp.), whereas the other <em>Discinaceae</em> genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic—either MAT1-1 or MAT1-2—but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in <em>Gyromitra esculenta</em> strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (<em>Gyromitra</em> and <em>Piscidiscina</em>) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of <em>Geomoriaceae</em> and <em>Helvellaceae</em>—two closely related families with no publicly available genomes—these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"205 ","pages":"Article 108286"},"PeriodicalIF":3.6,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959254","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":"Genome-wide analyses provide insights into genetic variation, phylo- and co-phylogenetic relationships, and biogeography of the entomopathogenic nematode genus Heterorhabditis","authors":"Ricardo A.R. Machado ,&nbsp;Arthur Muller ,&nbsp;Alexandre Hiltmann ,&nbsp;Aashaq Hussain Bhat ,&nbsp;Vladimír Půža ,&nbsp;Antoinette P. Malan ,&nbsp;Carlos Castaneda-Alvarez ,&nbsp;Ernesto San-Blas ,&nbsp;Larry W. Duncan ,&nbsp;David Shapiro-Ilan ,&nbsp;Javad Karimi ,&nbsp;Lalramliana ,&nbsp;Hrang C. Lalramnghaki ,&nbsp;Hugues Baimey","doi":"10.1016/j.ympev.2025.108284","DOIUrl":"10.1016/j.ympev.2025.108284","url":null,"abstract":"<div><div>Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus <em>Heterorhabditis</em>. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus <em>Heterorhabditis</em>. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes. Using the inferred phylogenies, we then investigated co-phylogenetic relationships between <em>Heterorhabditis</em> and their <em>Photorhabdus</em> bacterial symbionts and biogeographical patterns. Robust, well-resolved, and highly congruent phylogenetic relationships were reconstructed using both whole nuclear and mitochondrial genomes. Similarly, whole ribosomal operon sequences proved valuable for phylogenomic reconstructions, though they have limited value to discriminate closely related species. In addition, two mitochondrial genes, the cytochrome <em>c</em> oxidase subunit I (<em>cox-1</em>) and the NADH dehydrogenase subunit 4 (<em>nad-4</em>), and two housekeeping genes, the fanconi-associated nuclease 1 (<em>fan-1</em>) and the serine/threonine-protein phosphatase 4 regulatory subunit 1 (<em>ppfr-1</em>), provided the most robust phylogenetic reconstructions compared to other individual genes. According to our findings, whole nuclear and/or mitochondrial genomes are strongly recommended for reconstructing phylogenetic relationships of the genus <em>Heterorhabditis</em>. If whole nuclear and/or mitochondrial genomes are unavailable, a combination of nuclear and mitochondrial genes can be used as an alternative. Under these circumstances, sequences of multiple conspecific isolates in a genus-wide phylogenetic context should be analyzed to avoid artefactual species over-splitting driven by the high intraspecific sequence divergence of mitochondrial genes and to avoid artefactual species lumping driven by the low interspecific sequence divergence of some nuclear genes. On the other hand, we observed that the genera <em>Heterorhabditis</em> and <em>Photorhabdus</em> exhibit diverse biogeographic patterns, ranging from cosmopolitan species to potentially endemic species, and show high phylogenetic congruence, although host switches have also occurred. Our study contributes to a better understanding of the biodiversity and phylo- and co-phylogenetic relationships of an important group of biological control agents and advances our efforts to develop more tools that are compatible with sustainable and eco-friendly agricultural practices.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"204 ","pages":"Article 108284"},"PeriodicalIF":3.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142959251","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}