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Hellemans S, Rocha MM, Wang M, Romero Arias J, Aanen DK, Bagnères AG, Buček A, Carrijo TF, Chouvenc T, Cuezzo C, Constantini JP, Constantino R, Dedeine F, Deligne J, Eggleton P, Evans TA, Hanus R, Harrison MC, Harry M, Josens G, Jouault C, Kalleshwaraswamy CM, Kaymak E, Korb J, Lee CY, Legendre F, Li HF, Lo N, Lu T, Matsuura K, Maekawa K, McMahon DP, Mizumoto N, Oliveira DE, Poulsen M, Sillam-Dussès D, Su NY, Tokuda G, Vargo EL, Ware JL, Šobotník J, Scheffrahn RH, Cancello E, Roisin Y, Engel MS, Bourguignon T. Genomic data provide insights into the classification of extant termites. Nat Commun 2024; 15:6724. [PMID: 39112457 PMCID: PMC11306793 DOI: 10.1038/s41467-024-51028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements analyzed as concatenated matrices or within the multi-species coalescence framework. Our classification is further supported by analyses controlling for rogue loci and taxa, and topological tests. We show that the Neoisoptera are composed of seven family-level monophyletic lineages, including the Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae Holmgren, raised from subfamilial rank. The species-rich Termitidae are composed of 18 subfamily-level monophyletic lineages, including the new subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae, Neocapritermitinae, Protohamitermitinae, and Promirotermitinae; and the revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and Mirocapritermitinae Kemner. Building an updated taxonomic classification on the foundation of unambiguously supported monophyletic lineages makes it highly resilient to potential destabilization caused by the future availability of novel phylogenetic markers and methods. The taxonomic stability is further guaranteed by the modularity of the new termite classification, designed to accommodate as-yet undescribed species with uncertain affinities to the herein delimited monophyletic lineages in the form of new families or subfamilies.
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Affiliation(s)
- Simon Hellemans
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan.
- Evolutionary Biology and Ecology, Université libre de Bruxelles, Brussels, Belgium.
| | - Mauricio M Rocha
- Museu de Zoologia da Universidade de São Paulo, Ipiranga, São Paulo/SP, Brazil
| | - Menglin Wang
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Johanna Romero Arias
- Evolutionary Biology and Ecology, Université libre de Bruxelles, Brussels, Belgium
| | - Duur K Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | | | - Aleš Buček
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Thomas Chouvenc
- University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Davie, Florida, USA
| | - Carolina Cuezzo
- Museu de Zoologia da Universidade de São Paulo, Ipiranga, São Paulo/SP, Brazil
| | - Joice P Constantini
- Museu de Zoologia da Universidade de São Paulo, Ipiranga, São Paulo/SP, Brazil
| | | | - Franck Dedeine
- Institut de Recherche sur la Biologie de l'Insecte, UMR 7261, CNRS / Université de Tours, Faculté des Sciences et Techniques, Parc Grandmont, Tours, France
| | - Jean Deligne
- Royal Museum for Central Africa, Entomology, Tervuren, Belgium
- Département de Biologie des Organismes, Université libre de Bruxelles, Brussels, Belgium
| | - Paul Eggleton
- Department of Life Sciences, Natural History Museum, London, UK
| | - Theodore A Evans
- School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Robert Hanus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster. Hüfferstrasße 1, Münster, Germany
| | - Myriam Harry
- UMR Evolution, Génomes, Comportement, Ecologie (EGCE), IDEEV, Université Paris Saclay-CNRS-IRD, 12 route 128, Gif-sur-Yvette, France
| | - Guy Josens
- Département de Biologie des Organismes, Université libre de Bruxelles, Brussels, Belgium
| | - Corentin Jouault
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, Muséum national d'Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, Paris, France
- Géosciences Rennes (UMR 6118), Université de Rennes, CNRS, Rennes, France
- Institut des Sciences de l'Évolution de Montpellier (UMR 5554), Université de Montpellier, CNRS, F-, Montpellier, France
| | - Chicknayakanahalli M Kalleshwaraswamy
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
- Department of Entomology, Keladi Shivappa Nayaka University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Esra Kaymak
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Judith Korb
- Evolutionary Biology & Ecology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany & Charles Darwin University, Darwin, Australia
| | - Chow-Yang Lee
- Department of Entomology, University of California, Riverside, CA, USA
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, Muséum national d'Histoire naturelle (MNHN), CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, Paris, France
| | - Hou-Feng Li
- Department of Entomology, National Chung Hsing University, Taichug, Taiwan
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Kiyoto Maekawa
- Faculty of Science, Academic Assembly, University of Toyama, Toyama, Japan
| | - Dino P McMahon
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Department for Materials and the Environment, BAM Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Nobuaki Mizumoto
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
- Department of Entomology & Plant Pathology, Auburn University, Auburn, AL, USA
| | - Danilo E Oliveira
- Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá, PA, Brazil
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen East, Denmark
| | - David Sillam-Dussès
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology, LEEC, UR 4443, Villetaneuse, France
| | - Nan-Yao Su
- University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Davie, Florida, USA
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, Japan
| | - Edward L Vargo
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Jessica L Ware
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Jan Šobotník
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Rudolf H Scheffrahn
- University of Florida, Fort Lauderdale Research and Education Center, 3205 College Avenue, Davie, Florida, USA
| | - Eliana Cancello
- Museu de Zoologia da Universidade de São Paulo, Ipiranga, São Paulo/SP, Brazil
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université libre de Bruxelles, Brussels, Belgium
| | - Michael S Engel
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Perú
- Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 14, Perú
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan.
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
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Schwaha T, Decker SH, Baranyi C, Saadi AJ. Rediscovering the unusual, solitary bryozoan Monobryozoon ambulans Remane, 1936: first molecular and new morphological data clarify its phylogenetic position. Front Zool 2024; 21:5. [PMID: 38443908 PMCID: PMC10913646 DOI: 10.1186/s12983-024-00527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND One of the most peculiar groups of the mostly colonial phylum Bryozoa is the taxon Monobryozoon, whose name already implies non-colonial members of the phylum. Its peculiarity and highly unusual lifestyle as a meiobenthic clade living on sand grains has fascinated many biologists. In particular its systematic relationship to other bryozoans remains a mystery. Despite numerous searches for M. ambulans in its type locality Helgoland, a locality with a long-lasting marine station and tradition of numerous courses and workshops, it has never been reencountered until today. Here we report the first observations of this almost mythical species, Monobryozoon ambulans. RESULTS For the first time since 1938, we present new modern, morphological analyses of this species as well as the first ever molecular data. Our detailed morphological analysis confirms most previous descriptions, but also ascertains the presence of special ambulatory polymorphic zooids. We consider these as bud anlagen that ultimately consecutively separate from the animal rendering it pseudo-colonial. The remaining morphological data show strong ties to alcyonidioidean ctenostome bryozoans. Our morphological data is in accordance with the phylogenomic analysis, which clusters it with species of Alcyonidium as a sister group to multiporate ctenostomes. Divergence time estimation and ancestral state reconstruction recover the solitary state of M. ambulans as a derived character that probably evolved in the Late Cretaceous. In this study, we also provide the entire mitogenome of M. ambulans, which-despite the momentary lack of comparable data-provides important data of a unique and rare species for comparative aspects in the future. CONCLUSIONS We were able to provide first sequence data and modern morphological data for the unique bryozoan, M. ambulans, which are both supporting an alcyonidioidean relationship within ctenostome bryozoans.
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Affiliation(s)
- Thomas Schwaha
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria.
| | - Sebastian H Decker
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Christian Baranyi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
| | - Ahmed J Saadi
- Department of Evolutionary Biology, University of Vienna, Schlachthausgasse 43, 1030, Vienna, Austria
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Li YD, Engel MS, Tihelka E, Cai C. Phylogenomics of weevils revisited: data curation and modelling compositional heterogeneity. Biol Lett 2023; 19:20230307. [PMID: 37727076 PMCID: PMC10509570 DOI: 10.1098/rsbl.2023.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023] Open
Abstract
Weevils represent one of the most prolific radiations of beetles and the most diverse group of herbivores on land. The phylogeny of weevils (Curculionoidea) has received extensive attention, and a largely satisfactory framework for their interfamilial relationships has been established. However, a recent phylogenomic study of Curculionoidea based on anchored hybrid enrichment (AHE) data yielded an abnormal placement for the family Belidae (strongly supported as sister to Nemonychidae + Anthribidae). Here we reanalyse the genome-scale AHE data for Curculionoidea using various models of molecular evolution and data filtering methods to mitigate anticipated systematic errors and reduce compositional heterogeneity. When analysed with the infinite mixture model CAT-GTR or using appropriately filtered datasets, Belidae are always recovered as sister to the clade (Attelabidae, (Caridae, (Brentidae, Curculionidae))), which is congruent with studies based on morphology and other sources of molecular data. Although the relationships of the 'higher Curculionidae' remain challenging to resolve, we provide a consistent and robust backbone phylogeny of weevils. Our extensive analyses emphasize the significance of data curation and modelling across-site compositional heterogeneity in phylogenomic studies.
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Affiliation(s)
- Yan-Da Li
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Michael S. Engel
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
| | - Erik Tihelka
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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Struck TH, Golombek A, Hoesel C, Dimitrov D, Elgetany AH. Mitochondrial Genome Evolution in Annelida-A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution. Syst Biol 2023; 72:925-945. [PMID: 37083277 PMCID: PMC10405356 DOI: 10.1093/sysbio/syad023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/22/2023] Open
Abstract
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
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Affiliation(s)
- Torsten H Struck
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Anja Golombek
- Centre of Molecular Biodiversity Research, Zoological Research Museum Alexander KoenigBonn 53113, Germany
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Christoph Hoesel
- FB05 Biology/Chemistry; University of Osnabrück, Osnabrück 49069, Germany
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Asmaa Haris Elgetany
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
- Zoology Department, Faculty of Science, Damietta University, New Damietta, Central zone, 34517, Egypt
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