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Du S, Tihelka E, Yu D, Chen WJ, Bu Y, Cai C, Engel MS, Luan YX, Zhang F. Revisiting the four Hexapoda classes: Protura as the sister group to all other hexapods. Proc Natl Acad Sci U S A 2024; 121:e2408775121. [PMID: 39298489 DOI: 10.1073/pnas.2408775121] [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: 05/02/2024] [Accepted: 08/21/2024] [Indexed: 09/21/2024] Open
Abstract
Insects represent the most diverse animal group, yet previous phylogenetic analyses based on morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod lineages-the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura)-have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialization. We addressed this issue by sampling all hexapod orders and experimenting with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage ("Protura-sister") and Collembola as a sister group to Diplura, a clade corresponding to the original composition of Entognatha, and characterized by the shared possession of internal muscles in the antennal flagellum. The previously recognized 'Elliplura' hypothesis is recovered only under the site-homogeneous substitution models with partial supermatrices. Our cross-validation analysis shows that the site-heterogeneous CAT-GTR model, which recovers "Protura-sister," fits significantly better than homogeneous models. Furthermore, the morphologically unusual Protura are also supported as the earliest-diverging hexapod lineage by other lines of evidence, such as mitogenomes, comparative embryology, and sperm morphology, which produced results similar to those in this study. Our backbone phylogeny of hexapods will facilitate the exploration of the underpinnings of hexapod terrestrialization and megadiversity.
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Affiliation(s)
- Shiyu Du
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Daoyuan Yu
- Department of Ecology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wan-Jun Chen
- Mammoth (Shenzhen) Education Technology Co. Ltd, Shenzhen 518000, China
| | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai 200041, China
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Michael S Engel
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
- Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
| | - Yun-Xia Luan
- Guangdong Provincial Key Laboratory of Insect Development Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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2
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Shin S, Baker AJ, Enk J, McKenna DD, Foquet B, Vandergast AG, Weissman DB, Song H. Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales. Sci Rep 2024; 14:21377. [PMID: 39271747 PMCID: PMC11399444 DOI: 10.1038/s41598-024-72622-6] [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: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.
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Affiliation(s)
- Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Austin J Baker
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
- Entomology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Duane D McKenna
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Bert Foquet
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Amy G Vandergast
- San Diego Field Station, Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - David B Weissman
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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3
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Oliveira IDS. An updated world checklist of velvet worms (Onychophora) with notes on nomenclature and status of names. Zookeys 2023; 1184:133-260. [PMID: 38023768 PMCID: PMC10680090 DOI: 10.3897/zookeys.1184.107286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 12/01/2023] Open
Abstract
More than a decade has passed since the publication of the only world checklist available for Onychophora. During this period, numerous nomenclatural acts and taxonomic changes have been suggested within the group and a wealth of novel data has been published on many taxa. Herein, the up-to-date taxonomic scenario within Onychophora is presented, with appraisal of name status. This checklist covers both extant (Peripatidae and Peripatopsidae) and fossil taxa, and each species is accompanied by information on synonyms, type designation, holotype location, type locality, and language of original description. Additional remarks include nomenclatural inconsistencies, synonymizations, name misspellings, conflicting collecting event data, availability of taxonomically informative molecular data, etc. According to the data, 237 species are currently assigned to Onychophora: 140 of Peripatopsidae, 92 of Peripatidae, and five fossil species with unclear relationship to extant taxa. Since the previous checklist, 37 species have been added to Onychophora, representing an increase of 18.5% in the diversity described for the group. Yet, taxonomic descriptions seem slow-paced, with an average of 3.6 onychophoran species being described annually. From the taxonomic standpoint, 216 species are valid, although many of them require morphological revision and molecular characterization; 21 species exhibit major taxonomic ambiguities and have been regarded as nomina dubia. Recurrent taxonomic issues identified in the literature include inaccurate collecting event data, doubtful taxonomic assignment of molecular sequences, and non-observance of nomenclatural rules. These and other taxonomic aspects are addressed herein in the light of the directives established by the International Code of Zoological Nomenclature.
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Affiliation(s)
- Ivo de Sena Oliveira
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, D-34132, Kassel, GermanyUniversity of KasselKasselGermany
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antônio Carlos 6627, 31270-901, Belo Horizonte, Minas Gerais, BrazilUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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4
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Li X, Li H, Yang Z, Wu Y, Zhang M. Exploring objective feature sets in constructing the evolution relationship of animal genome sequences. BMC Genomics 2023; 24:634. [PMID: 37872534 PMCID: PMC10594854 DOI: 10.1186/s12864-023-09747-x] [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: 08/07/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences. RESULT Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage. CONCLUSION Our study provides objective feature sets in constructing evolution relationships at the genomic level.
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Affiliation(s)
- Xiaolong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hong Li
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.
| | - Zhenhua Yang
- School of Economics and Management, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Yuan Wu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Mengchuan Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China
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5
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Van Damme K, Cornetti L, Fields PD, Ebert D. Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution. Syst Biol 2021; 71:777-787. [PMID: 34850935 PMCID: PMC9203061 DOI: 10.1093/sysbio/syab094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]
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Affiliation(s)
- Kay Van Damme
- Centre for Academic Heritage and Archives & Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Tvärminne Zoological Station (TZS), University of Helsinki, J.A. Palménin tie 260, Hanko, Finland
| | - Luca Cornetti
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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6
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Kohli M, Letsch H, Greve C, Béthoux O, Deregnaucourt I, Liu S, Zhou X, Donath A, Mayer C, Podsiadlowski L, Gunkel S, Machida R, Niehuis O, Rust J, Wappler T, Yu X, Misof B, Ware J. Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. iScience 2021; 24:103324. [PMID: 34805787 PMCID: PMC8586788 DOI: 10.1016/j.isci.2021.103324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/14/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.
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Affiliation(s)
- Manpreet Kohli
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Harald Letsch
- Department for Animal Biodiversity, Universität Wien, Vienna, Austria
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Olivier Béthoux
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Isabelle Deregnaucourt
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Shanlin Liu
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Simon Gunkel
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano, Japan
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Jes Rust
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Torsten Wappler
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Xin Yu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Jessica Ware
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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7
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Yan L, Pape T, Meusemann K, Kutty SN, Meier R, Bayless KM, Zhang D. Monophyletic blowflies revealed by phylogenomics. BMC Biol 2021; 19:230. [PMID: 34706743 PMCID: PMC8555136 DOI: 10.1186/s12915-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/23/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. RESULTS We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. CONCLUSIONS Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.
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Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Karen Meusemann
- Evolutionary Biology & Ecology, University of Freiburg, Freiburg, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
- Department of Entomology, California Academy of Sciences, San Francisco, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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9
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Yan L, Buenaventura E, Pape T, Narayanan Kutty S, Bayless KM, Zhang D. A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae). Cladistics 2021; 37:540-558. [PMID: 34570937 DOI: 10.1111/cla.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 11/28/2022] Open
Abstract
The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life-history, we inferred a backbone phylogeny based on transcriptomic data from 26 sarcophagid species covering all three subfamilies plus 15 outgroups. The phylogeny was inferred using maximum parsimony and maximum likelihood methods based on a series of supermatrices, one set with overall information content improved by MARE (2290 loci), one set with 100% gene coverage for all included species (587 loci), and the last set including mitochondrial and nuclear genes (589 loci) and additional taxa. In order to obtain a more detailed hypothesis, we utilized the supertree approach to combine results from the present study with previously published hypotheses. This resulted supertree covers 84 of the one hundred currently recognized sarcophagid genera and formed the basis for the ancestral state reconstructions. The monophyletic Sarcophagidae is well-supported as sister to {Mystacinobiidae + Oestridae}, and relationships at the subfamily level are inferred as {Sarcophaginae, (Paramacronychiinae + Miltogramminae)}. The Sarcophagidae and each subfamily originated in the Americas, with Sarcophaginae diversifying mainly in the Neotropics, whereas the major radiation of both Miltogramminae and Paramacronychiinae occurred in the Palaearctic. Sarcosaprophagy is reconstructed as the ancestral larval feeding habit of the family Sarcophagidae and each subfamily. The ancestral sarcophagid larva probably utilized dead invertebrates as food, and the food spectrum expanded together with the diversification of breeding strategies. Particularly, kleptoparasitism in Miltogramminae is derived from sarcosaprophagy and may be seen as having derived from the breeding biology of 'lower' miltogrammines, the larvae of which feed on buried vertebrate carrion.
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Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Eliana Buenaventura
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, 10115, Germany
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543, Singapore.,Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, 2601, Australia.,Department of Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
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10
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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11
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Beutel RG, Friedrich F, Economo EP. Patterns of morphological simplification and innovation in the megadiverse Holometabola (Insecta). Cladistics 2021; 38:227-245. [DOI: 10.1111/cla.12483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rolf Georg Beutel
- Entomology Group Institut für Zoologie und Evolutionsforschung Friedrich‐Schiller‐Universität Jena Erbertstrasse 1 Jena D‐07743 Germany
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
| | - Frank Friedrich
- Institut für Zoologie Universität Hamburg Martin‐Luther‐King‐Platz 3 Hamburg D‐20146 Germany
| | - Evan P. Economo
- Biodiversity and Biocomplexity Unit Okinawa Institute of Science and Technology Graduate University 1919‐1 Tancha, Onna‐son Kunigami‐gun Okinawa 904‐0495 Japan
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12
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Dittrich K, Wipfler B. A review of the hexapod tracheal system with a focus on the apterygote groups. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 63:101072. [PMID: 34098323 DOI: 10.1016/j.asd.2021.101072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Respiratory systems are key innovations for the radiation of terrestrial arthropods. It is therefore surprising that there is still a considerable lack of knowledge. In this review of the available information on tracheal systems of hexapods (with a focus on the apterygote lineages Protura, Collembola, Diplura, Archaeognatha and Zygentoma), we summarize available data on the spiracles (number, position and morphology), the shape and variability of tracheal branching patterns including anastomoses, the tracheal fine structure and the respiratory proteins. The available data are strongly fragmented, and information for most subgroups is missing. In various cases, individual observations for one species account for the knowledge of the entire order. The available data show that there are strong differences between but also within apterygote orders. We conclude that the available data are insufficient to derive detailed conclusions on the hexapod ground plan and outline the possible evolutionary scenarios for the tracheal system in this group.
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Affiliation(s)
- Kathleen Dittrich
- Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
| | - Benjamin Wipfler
- Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
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13
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Yu DN, Yu PP, Zhang LP, Storey KB, Gao XY, Zhang JY. Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations. PeerJ 2021; 9:e11402. [PMID: 34221707 PMCID: PMC8231340 DOI: 10.7717/peerj.11402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera. METHODS Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups. RESULTS Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.
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Affiliation(s)
- Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Pan-Pan Yu
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Le-Ping Zhang
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Xin-Yan Gao
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
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14
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Huang K, Wang J, Huang J, Zhang S, Vogler AP, Liu Q, Li Y, Yang M, Li Y, Zhou X. Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects. Front Microbiol 2021; 12:633075. [PMID: 34239504 PMCID: PMC8260032 DOI: 10.3389/fmicb.2021.633075] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/14/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.
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Affiliation(s)
- Kuanguan Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Jie Wang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Junhao Huang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Shouke Zhang
- Department of Forestry Protection, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London Silwood Park, Ascot, United Kingdom
| | - Quanquan Liu
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Yongchun Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Maowei Yang
- Institute of Forestry Investigation and Planning of Guangning, Guangning, China
| | - You Li
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, United States
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15
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Takezaki N. Resolving the Early Divergence Pattern of Teleost Fish Using Genome-Scale Data. Genome Biol Evol 2021; 13:6178791. [PMID: 33739405 PMCID: PMC8103497 DOI: 10.1093/gbe/evab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Regarding the phylogenetic relationship of the three primary groups of teleost fishes, Osteoglossomorpha (bonytongues and others), Elopomorpha (eels and relatives), Clupeocephala (the remaining teleost fish), early morphological studies hypothesized the first divergence of Osteoglossomorpha, whereas the recent prevailing view is the first divergence of Elopomorpha. Molecular studies supported all the possible relationships of the three primary groups. This study analyzed genome-scale data from four previous studies: 1) 412 genes from 12 species, 2) 772 genes from 15 species, 3) 1,062 genes from 30 species, and 4) 491 UCE loci from 27 species. The effects of the species, loci, and models used on the constructed tree topologies were investigated. In the analyses of the data sets (1)–(3), although the first divergence of Clupeocephala that left the other two groups in a sister relationship was supported by concatenated sequences and gene trees of all the species and genes, the first divergence of Elopomorpha among the three groups was supported using species and/or genes with low divergence of sequence and amino-acid frequencies. This result corresponded to that of the UCE data set (4), whose sequence divergence was low, which supported the first divergence of Elopomorpha with high statistical significance. The increase in accuracy of the phylogenetic construction by using species and genes with low sequence divergence was predicted by a phylogenetic informativeness approach and confirmed by computer simulation. These results supported that Elopomorpha was the first basal group of teleost fish to have diverged, consistent with the prevailing view of recent morphological studies.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Mikicho, Kitagun, Kagawa, Japan
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16
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Krieger J, Hörnig MK, Kenning M, Hansson BS, Harzsch S. More than one way to smell ashore - Evolution of the olfactory pathway in terrestrial malacostracan crustaceans. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101022. [PMID: 33385761 DOI: 10.1016/j.asd.2020.101022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Crustaceans provide a fascinating opportunity for studying adaptations to a terrestrial lifestyle because within this group, the conquest of land has occurred at least ten times convergently. The evolutionary transition from water to land demands various morphological and physiological adaptations of tissues and organs including the sensory and nervous system. In this review, we aim to compare the brain architecture between selected terrestrial and closely related marine representatives of the crustacean taxa Amphipoda, Isopoda, Brachyura, and Anomala with an emphasis on the elements of the olfactory pathway including receptor molecules. Our comparison of neuroanatomical structures between terrestrial members and their close aquatic relatives suggests that during the convergent evolution of terrestrial life-styles, the elements of the olfactory pathway were subject to different morphological transformations. In terrestrial anomalans (Coenobitidae), the elements of the primary olfactory pathway (antennules and olfactory lobes) are in general considerably enlarged whereas they are smaller in terrestrial brachyurans compared to their aquatic relatives. Studies on the repertoire of receptor molecules in Coenobitidae do not point to specific terrestrial adaptations but suggest that perireceptor events - processes in the receptor environment before the stimuli bind - may play an important role for aerial olfaction in this group. In terrestrial members of amphipods (Amphipoda: Talitridae) as well as of isopods (Isopoda: Oniscidea), however, the antennules and olfactory sensilla (aesthetascs) are largely reduced and miniaturized. Consequently, their primary olfactory processing centers are suggested to have been lost during the evolution of a life on land. Nevertheless, in terrestrial Peracarida, the (second) antennae as well as their associated tritocerebral processing structures are presumed to compensate for this loss or rather considerable reduction of the (deutocerebral) primary olfactory pathway. We conclude that after the evolutionary transition from water to land, it is not trivial for arthropods to establish aerial olfaction. If we consider insects as an ingroup of Crustacea, then the Coenobitidae and Insecta may be seen as the most successful crustacean representatives in this respect.
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Affiliation(s)
- Jakob Krieger
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Marie K Hörnig
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Matthes Kenning
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
| | - Bill S Hansson
- Max-Planck-Institute for Chemical Ecology, Department of Evolutionary Neuroethology, 07745, Jena, Germany.
| | - Steffen Harzsch
- University of Greifswald, Zoological Institute and Museum, Cytology and Evolutionary Biology, 17489, Greifswald, Germany.
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17
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Wang J, Chen X, He F, Song X, Huang S, Yue W, Chen Y, Su Z, Wang C. Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:443-454. [PMID: 33346084 PMCID: PMC8242267 DOI: 10.1016/j.gpb.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/04/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Funan He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yipei Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
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18
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Jeong JH, Kim H, Ryu S, Kim W. The First Pycnogonid Draft Genome of Nymphon striatum. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.554164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Katz AD. Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of "Universal" Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock. Genes (Basel) 2020; 11:genes11101172. [PMID: 33036318 PMCID: PMC7600954 DOI: 10.3390/genes11101172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 01/04/2023] Open
Abstract
Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.
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Affiliation(s)
- Aron D. Katz
- Engineer Research Development Center, 2902 Newmark Dr., Champaign, IL 61826, USA;
- Department of Entomology, University of Illinois at Urbana-Champaign, 320 Morrill Hall, 505 South Goodwin Ave., Urbana, IL 61801, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, 1816 South Oak Street, Champaign, IL 61820, USA
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20
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Huang W, Xie X, Peng F, Liang X, Wang X, Chen X. Optimizing the widely used nuclear protein-coding gene primers in beetle phylogenies and their application in the genus Sasajiscymnus Vandenberg (Coleoptera: Coccinellidae). Ecol Evol 2020; 10:7731-7738. [PMID: 32760560 PMCID: PMC7391345 DOI: 10.1002/ece3.6497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 11/26/2022] Open
Abstract
Advances in genomic biology and the increasing availability of genomic resources allow developing hundreds of nuclear protein-coding (NPC) markers, which can be used in phylogenetic research. However, for low taxonomic levels, it may be more practical to select a handful of suitable molecular loci for phylogenetic inference. Unfortunately, the presence of degenerate primers of NPC markers can be a major impediment, as the amplification success rate is low and they tend to amplify nontargeted regions. In this study, we optimized five NPC fragments widely used in beetle phylogenetics (i.e., two parts of carbamoyl-phosphate synthetase: CADXM and CADMC, Topoisomerase, Wingless and Pepck) by reducing the degenerate site of primers and the length of target genes slightly. These five NPC fragments and 6 other molecular loci were amplified to test the monophyly of the coccinellid genus Sasajiscymnus Vandenberg. The analysis of our molecular data set clearly supported the genus Sasajiscymnus may be monophyletic but confirmation with an extended sampling is required. A fossil-calibrated chronogram was generated by BEAST, indicating an origin of the genus at the end of the Cretaceous (77.87 Myr). Furthermore, a phylogenetic informativeness profile was generated to compare the phylogenetic properties of each gene more explicitly. The results showed that COI provides the strongest phylogenetic signal among all the genes, but Pepck, Topoisomerase, CADXM and CADMC are also relatively informative. Our results provide insight into the evolution of the genus Sasajiscymnus, and also enrich the molecular data resources for further study.
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Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic CollegeGuangzhouChina
| | - Feng Peng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xingmin Wang
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmDepartment of Forest ProtectionCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Bio‐Pesticide Innovation and Application, Guangdong ProvinceEngineering Research Center of BiocontrolMinistry of Education and Guangdong ProvinceGuangzhouChina
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21
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Dunoyer LA, Seifert AW, Van Cleve J. Evolutionary bedfellows: Reconstructing the ancestral state of autotomy and regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:94-115. [PMID: 32558244 DOI: 10.1002/jez.b.22974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 11/11/2022]
Abstract
Some form of regeneration occurs in all lifeforms and extends from single-cell organisms to humans. The degree to which regenerative ability is distributed across different taxa, however, is harder to ascertain given the potential for phylogenetic constraint or inertia, and adaptive processes to shape this pattern. Here, we examine the phylogenetic history of regeneration in two groups where the trait has been well-studied: arthropods and reptiles. Because autotomy is often present alongside regeneration in these groups, we performed ancestral state reconstructions for both traits to more precisely assess the timing of their origins and the degree to which these traits coevolve. Using an ancestral trait reconstruction, we find that autotomy and regeneration were present at the base of the arthropod and reptile trees. We also find that when autotomy is lost it does not re-evolve easily. Lastly, we find that the distribution of regeneration is intimately connected to autotomy with the association being stronger in reptiles than in arthropods. Although these patterns suggest that decoupling autotomy and regeneration at a broad phylogenetic scale may be difficult, the available data provides useful insight into their entanglement. Ultimately, our reconstructions provide the important groundwork to explore how selection may have played a role during the loss of regeneration in specific lineages.
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Affiliation(s)
- Luc A Dunoyer
- Department of Biology, University of Kentucky, Lexington, Kentucky.,Department of Life Sciences, Wake Technical Community College, Raleigh, North Carolina
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, Kentucky
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
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Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
- Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
- Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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23
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Kozma MT, Ngo-Vu H, Wong YY, Shukla NS, Pawar SD, Senatore A, Schmidt M, Derby CD. Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins. PLoS One 2020; 15:e0230266. [PMID: 32163507 PMCID: PMC7067487 DOI: 10.1371/journal.pone.0230266] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
Crustaceans express genes for at least three classes of putative chemosensory proteins. These are: Ionotropic Receptors (IRs), derived from the heterotetrameric ionotropic glutamate receptors (iGluRs); Transient Receptor Potential (TRP) channels, a diverse set of sensor-channels that include several families of chemoreceptor channels; and Gustatory Receptor Like receptors (GRLs), ionotropic receptors that are homologues of Gustatory Receptors (GRs) of insects and are expressed sparingly in most crustaceans so far studied. IRs are typically numerically the most dominant of these receptor proteins in crustaceans and include two classes: co-receptor IRs, which are necessary for making a functional receptor-channel; and tuning IRs, whose specific combination in the IR subunits in the heterotetramer confers chemical specificity. Previous work showed that the transcriptomes from two major chemosensory organs-the lateral flagellum of the antennule (LF) and the tips of the legs (dactyls)-of the Caribbean spiny lobster Panulirus argus express four co-receptor IRs and over 100 tuning IRs. In this paper, we examined and compared the transcriptomes from the LF and dactyls of P. argus and three other decapod crustaceans-the clawed lobster Homarus americanus, red swamp crayfish Procambarus clarkii, and the blue crab Callinectes sapidus. Each species has at least ca. 100 to 250 IRs, 1 to 4 GRLs, and ca. 15 TRP channels including those shown to be involved in chemoreception in other species. The IRs show different degrees of phylogenetic conservation: some are arthropod-conserved, others are pancrustacean-conserved, others appear to be crustacean-conserved, and some appear to be species-specific. Many IRs appear to be more highly expressed in the LF than dactyl. Our results show that decapod crustaceans express an abundance of genes for chemoreceptor proteins of different types, phylogenetic conservation, and expression patterns. An understanding of their functional roles awaits determining their expression patterns in individual chemosensory neurons and the central projections of those neurons.
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Affiliation(s)
- Mihika T. Kozma
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Hanh Ngo-Vu
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Yuen Yan Wong
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Neal S. Shukla
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Shrikant D. Pawar
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Manfred Schmidt
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Charles D. Derby
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
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24
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Noah KE, Hao J, Li L, Sun X, Foley B, Yang Q, Xia X. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates. Evol Bioinform Online 2020; 16:1176934320903735. [PMID: 32076367 PMCID: PMC7003163 DOI: 10.1177/1176934320903735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 01/04/2023] Open
Abstract
Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such "big data" sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new "principled" codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.
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Affiliation(s)
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Luyan Li
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoyan Sun
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Qun Yang
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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25
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Trebels B, Dippel S, Schaaf M, Balakrishnan K, Wimmer EA, Schachtner J. Adult neurogenesis in the mushroom bodies of red flour beetles (Tribolium castaneum, HERBST) is influenced by the olfactory environment. Sci Rep 2020; 10:1090. [PMID: 31974446 PMCID: PMC6978414 DOI: 10.1038/s41598-020-57639-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
Several studies showed adult persisting neurogenesis in insects, including the red flour beetle Tribolium castaneum, while it is absent in honeybees, carpenter ants, and vinegar flies. In our study, we focus on cell proliferation in the adult mushroom bodies of T. castaneum. We reliably labelled the progenies of the adult persisting mushroom body neuroblasts and determined the proliferation rate under several olfactory conditions within the first week after adult eclosion. We found at least two phases of Kenyon cell proliferation in the early adult beetle. Our results suggest that the generation of Kenyon cells during the first three days after adult eclosion is mainly genetically predetermined and a continuation of the developmental processes (nature), whereas from day four on proliferation seems to be mainly dependent on the odour environment (nurture). Considering that the mushroom bodies are linked to learning and memory, neurogenesis in the mushroom bodies is part of the remodelling of neuronal circuits leading to the adaption to the environment and optimization of behaviour.
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Affiliation(s)
- Björn Trebels
- Philipps-University Marburg, Department of Biology, Animal Physiology, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany
| | - Stefan Dippel
- Philipps-University Marburg, Department of Biology, Animal Physiology, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany
| | - Magdalina Schaaf
- Philipps-University Marburg, Department of Biology, Animal Physiology, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany
| | - Karthi Balakrishnan
- Department of Forest Zoology and Forest Conservation, Georg-August-University Göttingen, Büsgen-Institute, Büsgenweg 3, Göttingen, 37077, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, Georg-August-University Göttingen, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, GZMB, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, Göttingen, 37077, Germany
| | - Joachim Schachtner
- Philipps-University Marburg, Department of Biology, Animal Physiology, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany.
- Clausthal University of Technology, Adolph-Roemer-Str. 2a, 38678, Clausthal-Zellerfeld, Germany.
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26
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Nolan ED, Santibáñez-López CE, Sharma PP. Developmental gene expression as a phylogenetic data class: support for the monophyly of Arachnopulmonata. Dev Genes Evol 2020; 230:137-153. [PMID: 31927629 DOI: 10.1007/s00427-019-00644-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/10/2019] [Indexed: 01/01/2023]
Abstract
Despite application of genome-scale datasets, the phylogenetic placement of scorpions within arachnids remains contentious between two different phylogenetic data classes. Paleontologists continue to recover scorpions in a basally branching position, partly owing to their morphological similarity to extinct marine orders like Eurypterida (sea scorpions). Phylogenomic datasets consistently recover scorpions in a derived position, as the sister group of Tetrapulmonata (a clade of arachnids that includes spiders). To adjudicate between these hypotheses using a rare genomic change (RGC), we leveraged the recent discovery of ancient paralogy in spiders and scorpions to assess phylogenetic placement. We identified homologs of four transcription factors required for appendage patterning (dachshund, homothorax, extradenticle, and optomotor blind) in arthropods that are known to be duplicated in spiders. Using genomic resources for a spider, a scorpion, and a harvestman, we conducted gene tree analyses and assayed expression patterns of scorpion gene duplicates. Here we show that scorpions, like spiders, retain two copies of all four transcription factors, whereas arachnid orders like mites and harvestmen bear a single copy. A survey of embryonic expression patterns of the scorpion paralogs closely matches those of their spider counterparts, with one paralog consistently retaining the putatively ancestral pattern found in the harvestman, as well as the mite, and/or other outgroups. These data comprise a rare genomic change in chelicerate phylogeny supporting the inference of a distal placement of scorpions. Beyond demonstrating the diagnostic power of developmental genetic data as a phylogenetic data class, a derived placement of scorpions within the arachnids, together with an array of stem-group Paleozoic scorpions that occupied marine habitats, effectively rules out a scenario of a single colonization of terrestrial habitat within Chelicerata, even in tree topologies contrived to recover the monophyly of Arachnida.
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Affiliation(s)
- Erik D Nolan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Developmental Biology, Washington University of St. Louis, St. Louis, MO, 63110, USA
| | - Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biology, Eastern Connecticut State University, 83 Windham Street, Willimantic, CT, 06266, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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27
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Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, Niehuis O, Szucsich NU, Zdobnov EM. The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. Genome Biol Evol 2020; 12:3534-3549. [PMID: 31778187 PMCID: PMC6938034 DOI: 10.1093/gbe/evz260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Felipe A Simao
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Marco A Gabaglio
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany
| | | | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
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28
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Ballesteros JA, Santibáñez López CE, Kováč Ľ, Gavish-Regev E, Sharma PP. Ordered phylogenomic subsampling enables diagnosis of systematic errors in the placement of the enigmatic arachnid order Palpigradi. Proc Biol Sci 2019; 286:20192426. [PMID: 31847768 PMCID: PMC6939912 DOI: 10.1098/rspb.2019.2426] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 11/18/2019] [Indexed: 11/12/2022] Open
Abstract
The miniaturized arachnid order Palpigradi has ambiguous phylogenetic affinities owing to its odd combination of plesiomorphic and derived morphological traits. This lineage has never been sampled in phylogenomic datasets because of the small body size and fragility of most species, a sampling gap of immediate concern to recent disputes over arachnid monophyly. To redress this gap, we sampled a population of the cave-inhabiting species Eukoenenia spelaea from Slovakia and inferred its placement in the phylogeny of Chelicerata using dense phylogenomic matrices of up to 1450 loci, drawn from high-quality transcriptomic libraries and complete genomes. The complete matrix included exemplars of all extant orders of Chelicerata. Analyses of the complete matrix recovered palpigrades as the sister group of the long-branch order Parasitiformes (ticks) with high support. However, sequential deletion of long-branch taxa revealed that the position of palpigrades is prone to topological instability. Phylogenomic subsampling approaches that maximized taxon or dataset completeness recovered palpigrades as the sister group of camel spiders (Solifugae), with modest support. While this relationship is congruent with the location and architecture of the coxal glands, a long-forgotten character system that opens in the pedipalpal segments only in palpigrades and solifuges, we show that nodal support values in concatenated supermatrices can mask high levels of underlying topological conflict in the placement of the enigmatic Palpigradi.
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Affiliation(s)
- Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI, USA
| | | | - Ľubomír Kováč
- Department of Zoology, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Košice, Slovakia
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI, USA
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29
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Naumann B, Reip HS, Akkari N, Neubert D, Hammel JU. Inside the head of a cybertype – three-dimensional reconstruction of the head muscles of Ommatoiulus avatar (Diplopoda: Juliformia: Julidae) reveals insights into the feeding movements of Juliformia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe origin and diversification of the arthropod head is one of the major topics in the field of evolutionary morphology of Arthropoda. Among the major arthropod groups, Myriapoda and, more precisely Diplopoda, are generally poorly studied regarding their head anatomy. However, this group is of pivotal importance to understand the evolutionary functional morphology of the arthropod head. In this study, we investigate the complete musculoskeletal system of the diplopod head with a detailed description of the cephalic anatomy of the recently described species Ommatoiulus avatar. The comparison of our data with the literature on the few other species available show that the morphology of the musculoskeletal system within Juliformia, a subgroup of the Diplopoda, is relatively conservative. Using video recordings of the feeding movements in addition to the anatomical data, we revise the mechanism of the mandibular movements in Juliformia. There was a controversy whether mandibular abduction is an active process, facilitated by contraction of an abductor muscle, or if it is a passive process, mediated by tentorial and gnathochilarial movements not involving a direct abduction by muscular contraction. We show that mandibular abduction in Ommatoiulus is an active movement involving the contraction of an abductor muscle. This is similar to the mandibular abduction in other arthropod groups.
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Affiliation(s)
- Benjamin Naumann
- Institute of Zoology and Evolutionary Research, Friedrich-Schiller-University, Jena, Germany
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Hans S Reip
- Department of Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Nesrine Akkari
- 3rd Zoological Department, Natural History Museum Vienna, Vienna, Austria
| | - David Neubert
- Institute of Zoology and Evolutionary Research, Friedrich-Schiller-University, Jena, Germany
| | - Jörg U Hammel
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, Geesthacht, Germany
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30
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Simon S, Letsch H, Bank S, Buckley TR, Donath A, Liu S, Machida R, Meusemann K, Misof B, Podsiadlowski L, Zhou X, Wipfler B, Bradler S. Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00345] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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31
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Hamilton CA, St Laurent RA, Dexter K, Kitching IJ, Breinholt JW, Zwick A, Timmermans MJTN, Barber JR, Kawahara AY. Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives. BMC Evol Biol 2019; 19:182. [PMID: 31533606 PMCID: PMC6751749 DOI: 10.1186/s12862-019-1505-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 03/13/2023] Open
Abstract
BACKGROUND Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. RESULTS The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). CONCLUSIONS Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
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Affiliation(s)
- C A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844, USA.
| | - R A St Laurent
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - K Dexter
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - I J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - J W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- RAPiD Genomics, 747 SW 2nd Avenue #314, Gainesville, FL, 32601, USA
| | - A Zwick
- Australian National Insect Collection, CSIRO, Clunies Ross St, Acton, ACT, Canberra, 2601, Australia
| | - M J T N Timmermans
- Department of Natural Sciences, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - J R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725, USA
| | - A Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
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Tilbury MA, McCarthy S, Domagalska M, Ederth T, Power AM, Wall JG. The expression and characterization of recombinant cp19k barnacle cement protein from Pollicipes pollicipes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190205. [PMID: 31495308 DOI: 10.1098/rstb.2019.0205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Adhesive proteins of barnacle cement have potential as environmentally friendly adhesives owing to their ability to adhere to various substrates in aqueous environments. By understanding the taxonomic breath of barnacles with different lifestyles, we may uncover commonalities in adhesives produced by these specialized organisms. The 19 kDa cement protein (cp19k) of the stalked barnacle Pollicipes pollicipes was expressed in Escherichia coli BL21 to investigate its adhesive properties. Initial expression of hexahistidine-tagged protein (rPpolcp19k-his) yielded low levels of insoluble protein. Co-overproduction of E. coli molecular chaperones GroEL-GroES and trigger factor (TF) increased soluble protein yields, although TF co-purified with the target protein (TF-rPpolcp19k-his). Surface coat analysis revealed high levels of adsorption of the TF-rPpolcp19k-his complex and of purified E. coli TF on both hydrophobic and hydrophilic surfaces, while low levels of adsorption were observed for rPpolcp19k-his. Tag-free rPpolcp19k protein also exhibited low adsorption compared to fibrinogen and Cell-Tak controls on hydrophobic, neutral hydrophilic and charged self-assembled monolayers under surface plasmon resonance assay conditions designed to mimic the barnacle cement gland or seawater. Because rPpolcp19k protein displays low adhesive capability, this protein is suggested to confer the ability to self-assemble into a plaque within the barnacle cement complex. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.
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Affiliation(s)
- Maura A Tilbury
- Microbiology, School of Natural Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Centre for Research in Medical Devices (CÚRAM), School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sean McCarthy
- Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Magdalena Domagalska
- Microbiology, School of Natural Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Thomas Ederth
- Division of Molecular Physics, IFM, Linköping University, 581 83 Linköping, Sweden
| | - Anne Marie Power
- Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - J Gerard Wall
- Microbiology, School of Natural Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Centre for Research in Medical Devices (CÚRAM), School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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Richards ZT, Carvajal JI, Wallace CC, Wilson NG. Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae. Mar Genomics 2019; 50:100703. [PMID: 31466869 DOI: 10.1016/j.margen.2019.100703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/16/2019] [Indexed: 01/17/2023]
Abstract
The genus Alveopora is a scleractinian coral taxon whose phylogenetic classification has recently changed from the family Poritidae to Acroporidae. This change, which was made based on single-locus genetic data, has led to uncertainty about the placement of Alveopora and the ability for deep evolutionary relationships in these groups to be accurately recovered and represented by limited genetic datasets. We sought to characterize the higher-level position of Alveopora using newly available transcriptome data to confirm its placement within Acroporidae and resolve its closest ancestor. Here we present an analysis of a new 2031 gene dataset that confirms the placement of Alveopora within Acroporidae corroborating other single-locus (COI, 16S and ITS) analyses and a mitogenome dataset. We also resolve the position of Alveopora as sister to the genus Montipora. This has allowed the re-interpretation of morphology, and a rediagnosis of the family Acroporidae and the genus Alveopora.
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Affiliation(s)
- Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6012, Australia; Department of Aquatic Zoology, Western Australian Museum, Kew Street, Welshpool, WA, 6106, Australia.
| | - Jose I Carvajal
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia
| | - Carden C Wallace
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, Queensland 4101, Australia
| | - Nerida G Wilson
- Molecular Systematics Unit, Western Australian Museum, Kew Street, Welshpool, WA 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
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Phylogenomics of the longitarsal Colossendeidae: The evolutionary history of an Antarctic sea spider radiation. Mol Phylogenet Evol 2019; 136:206-214. [PMID: 31002869 DOI: 10.1016/j.ympev.2019.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 11/20/2022]
Abstract
Sea spiders (Pycnogonida) constitute a group of marine benthic arthropods that has a particularly high species diversity in the Southern Ocean. The "longitarsal" group of the sea spider family Colossendeidae is especially abundant in this region. However, this group also includes some representatives from other oceans, which raises the question where the group originates from. Therefore, we here investigated the phylogeny of the group with a hybrid enrichment approach that yielded a dataset of 1607 genes and over one million base pairs. We obtained a well-resolved phylogeny of the group, which is mostly consistent with morphological data. The data support an Antarctic origin of the longitarsal Colossendeidae and multiple dispersal events to other regions, which occurred at different timescales. This scenario is consistent with evidence found in other groups of marine invertebrates and highlights the role of the Southern Ocean as a source for non-Antarctic biota, especially of the deep sea. Our results suggest an initially slow rate of diversification followed by a more rapid radiation possibly correlated with the mid-Miocene cooling of Antarctica, similar to what is found in other taxa.
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Carapelli A, Bu Y, Chen WJ, Nardi F, Leo C, Frati F, Luan YX. Going Deeper into High and Low Phylogenetic Relationships of Protura. Genes (Basel) 2019; 10:E292. [PMID: 30974866 PMCID: PMC6523364 DOI: 10.3390/genes10040292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022] Open
Abstract
Proturans are small, wingless, soil-dwelling arthropods, generally associated with the early diversification of Hexapoda. Their bizarre morphology, together with conflicting results of molecular studies, has nevertheless made their classification ambiguous. Furthermore, their limited dispersal capability (due to the primarily absence of wings) and their euedaphic lifestyle have greatly complicated species-level identification. Mitochondrial and nuclear markers have been applied herein to investigate and summarize proturan systematics at different hierarchical levels. Two new mitochondrial genomes are described and included in a phylum-level phylogenetic analysis, but the position of Protura could not be resolved with confidence due to an accelerated rate of substitution and extensive gene rearrangements. Mitochondrial and nuclear loci were also applied in order to revise the intra-class systematics, recovering three proturan orders and most of the families/subfamilies included as monophyletic, with the exception of the subfamily Acerentominae. At the species level, most morphologically described species were confirmed using molecular markers, with some exceptions, and the advantages of including nuclear, as well as mitochondrial, markers and morphology are discussed. At all levels, an enlarged taxon sampling and the integration of data from different sources may be of significant help in solving open questions that still persist on the evolutionary history of Protura.
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Affiliation(s)
- Antonio Carapelli
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun Bu
- Natural History Research Center, Shanghai Natural History Museum, Shanghai Science & Technology Museum, Shanghai 200041, China.
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Wan-Jun Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Chiara Leo
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Francesco Frati
- Department of Life Sciences, University of Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Yun-Xia Luan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Ballesteros JA, Sharma PP. A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error. Syst Biol 2019; 68:896-917. [DOI: 10.1093/sysbio/syz011] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 02/10/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractHorseshoe crabs (Xiphosura) are traditionally regarded as sister group to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We re-evaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic data set to date, expanding outgroup sampling, and including data from whole genome sequencing projects. In spite of uncertainty in the placement of some arachnid clades, all analyses show Xiphosura consistently nested within Arachnida as the sister group to Ricinulei (hooded tick spiders). It is apparent that the radiation of arachnids is an old one and occurred over a brief period of time, resulting in several consecutive short internodes, and thus is a potential case for the confounding effects of incomplete lineage sorting (ILS). We simulated coalescent gene trees to explore the effects of increasing levels of ILS on the placement of horseshoe crabs. In addition, common sources of systematic error were evaluated, as well as the effects of fast-evolving partitions and the dynamics of problematic long branch orders. Our results indicated that the placement of horseshoe crabs cannot be explained by missing data, compositional biases, saturation, or ILS. Interrogation of the phylogenetic signal showed that the majority of loci favor the derived placement of Xiphosura over a monophyletic Arachnida. Our analyses support the inference that horseshoe crabs represent a group of aquatic arachnids, comparable to aquatic mites, breaking a long-standing paradigm in chelicerate evolution and altering previous interpretations of the ancestral transition to the terrestrial habitat. Future studies testing chelicerate relationships should approach the task with a sampling strategy where the monophyly of Arachnida is not held as the premise.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Sharma PP. Integrating morphology and phylogenomics supports a terrestrial origin of insect flight. Proc Natl Acad Sci U S A 2019; 116:2796-2798. [PMID: 30696764 PMCID: PMC6386717 DOI: 10.1073/pnas.1822087116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706
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Rocha M, Antas P, Castro LFC, Campos A, Vasconcelos V, Pereira F, Cunha I. Comparative Analysis of the Adhesive Proteins of the Adult Stalked Goose Barnacle Pollicipes pollicipes (Cirripedia: Pedunculata). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:38-51. [PMID: 30413912 DOI: 10.1007/s10126-018-9856-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/14/2018] [Indexed: 06/08/2023]
Abstract
Adhesion in barnacles is still poorly understood. The cement gland secretes an insoluble multi-protein complex, which adheres very strongly to a variety of substrates in the presence of water. This adhesion mechanism is bioinspiring for the engineering of new adhesive materials, but to replicate this adhesive system, the genes coding for the cement constitutive proteins must be identified and elucidated, and their products characterised. Here, the complete sequences of three cement protein (CP) genes (CP-100K, CP-52K, and CP-19K) isolated from the cement gland of the stalked barnacle Pollicipes pollicipes (order Scalpelliformes) were obtained using RACE PCR. The three genes were compared to the 23 other acorn barnacle CP genes so far sequenced (order Sessilia) to determine common and differential patterns and molecular properties, since the adhesives of both orders have visibly different characteristics. A shotgun proteomic analysis was performed on the cement, excreted at the membranous base of specimens, where the products of the three genes sequenced in the gland were identified, validating their function as CPs. A principal component analysis (PCA) was performed, to cluster CPs into groups with similar amino acid composition. This analysis uncovered three CP groups, each characterised by similar residue composition, features in secondary structure, and some biochemical properties, including isoelectric point and residue accessibility to solvents. The similarity among proteins in each defined group was low despite comparable amino acid composition. PCA can identify putative adhesive proteins from NGS transcriptomic data regardless of their low homology. This analysis did not highlight significant differences in residue composition between homologous acorn and stalked barnacle CPs. The characteristics responsible for the structural differences between the cement of stalked and acorn barnacles are described, and the presence of nanostructures, such as repetitive homologous domains and low complexity regions, and repetitive β-sheets are discussed relatively to self-assembly and adhesion.
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Affiliation(s)
- Miguel Rocha
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Paulo Antas
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Alexandre Campos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Vítor Vasconcelos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Filipe Pereira
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Isabel Cunha
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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Savojardo C, Luchetti A, Martelli PL, Casadio R, Mantovani B. Draft genomes and genomic divergence of two
Lepidurus
tadpole shrimp species (Crustacea, Branchiopoda, Notostraca). Mol Ecol Resour 2018; 19:235-244. [DOI: 10.1111/1755-0998.12952] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/18/2018] [Accepted: 09/24/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology University of Bologna Bologna Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology University of Bologna Bologna Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology University of Bologna Bologna Italy
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
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Schwentner M, Richter S, Rogers DC, Giribet G. Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics. Proc Biol Sci 2018; 285:20181524. [PMID: 30135168 PMCID: PMC6125901 DOI: 10.1098/rspb.2018.1524] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding the evolution of Tetraconata or Pancrustacea-the clade that includes crustaceans and insects-requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.
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Affiliation(s)
- Martin Schwentner
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Centrum of Natural History, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Stefan Richter
- Allgemeine und Spezielle Zoologie, Universität Rostock, Universitätsplatz 2, 18055 Rostock, Germany
| | - D Christopher Rogers
- Kansas Biological Survey, Kansas University, Higuchi Hall, 2101 Constant Avenue, Lawrence, KS 66047, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Pizarro D, Divakar PK, Grewe F, Leavitt SD, Huang JP, Dal Grande F, Schmitt I, Wedin M, Crespo A, Lumbsch HT. Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi. FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0407-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Freitas L, Mello B, Schrago CG. Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda. J Evol Biol 2018; 31:1623-1631. [PMID: 30058265 DOI: 10.1111/jeb.13355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time. Here, we investigated the performance of the MSC for a phylogenomic data set of hexapods compiled by Misof et al. (2014, Science 346:763). Our analysis recovered the monophyly of most insect orders, and major phylogenetic relationships were in agreement with current insect systematics. We identified, however, some evolutionary associations that were consistently problematic. Most noticeable, Hexapod monophyly was disrupted by the sister group relationship between the remiped crustacean and Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea were found to be phylogenetically unstable. We show that these controversial phylogenetic arrangements were also poorly supported by previous analyses, and therefore, we evaluated their robustness to stochastic errors from sampling sites and terminals, confirming standing problems in hexapod phylogeny in the genomics age.
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Affiliation(s)
- Lucas Freitas
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Sayyari E, Whitfield JB, Mirarab S. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol 2018; 34:3279-3291. [PMID: 29029241 DOI: 10.1093/molbev/msx261] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Species tree reconstruction from genome-wide data is increasingly being attempted, in most cases using a two-step approach of first estimating individual gene trees and then summarizing them to obtain a species tree. The accuracy of this approach, which promises to account for gene tree discordance, depends on the quality of the inferred gene trees. At the same time, phylogenomic and phylotranscriptomic analyses typically use involved bioinformatics pipelines for data preparation. Errors and shortcomings resulting from these preprocessing steps may impact the species tree analyses at the other end of the pipeline. In this article, we first show that the presence of fragmentary data for some species in a gene alignment, as often seen on real data, can result in substantial deterioration of gene trees, and as a result, the species tree. We then investigate a simple filtering strategy where individual fragmentary sequences are removed from individual genes but the rest of the gene is retained. Both in simulations and by reanalyzing a large insect phylotranscriptomic data set, we show the effectiveness of this simple filtering strategy.
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Affiliation(s)
- Erfan Sayyari
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
| | | | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA
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Simon S, Blanke A, Meusemann K. Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:328-338. [PMID: 29763650 DOI: 10.1016/j.asd.2018.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Alexander Blanke
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany; Medical and Biological Engineering Research Group, School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Hull, UK
| | - Karen Meusemann
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg (Brsg.), Germany; Center of Molecular Biodiversity Research (ZMB), Zoological Research Museum A. Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany.
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Cai YY, Gao YJ, Zhang LP, Yu DN, Storey KB, Zhang JY. The mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) and the phylogeny of Ephemeroptera in Pterygota. Mitochondrial DNA B Resour 2018; 3:577-579. [PMID: 33474248 PMCID: PMC7799546 DOI: 10.1080/23802359.2018.1467239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022] Open
Abstract
The phylogenetic relationship between Ephemeroptera (mayflies) and Odonata (dragonflies and damselflies) remains hotly debated in the insect evolution community. We sequenced the complete mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) to discuss the phylogenetic relationship of Palaeoptera. The mitochondrial genome of Caenis sp. is a circular molecule of 15,254 bp in length containing 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), which showed the typical insect mitochondrial gene arrangement. In BI and ML phylogenetic trees using 71 species of 12 orders, our results support the Ephemeroptera as the basal group of winged insects.
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Affiliation(s)
- Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Ya-Jie Gao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | | | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
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Freese HM, Sikorski J, Bunk B, Scheuner C, Meier-Kolthoff JP, Spröer C, Gram L, Overmann J. Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter. Genome Biol Evol 2018; 9:3297-3311. [PMID: 29194520 PMCID: PMC5730936 DOI: 10.1093/gbe/evx249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists.
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Affiliation(s)
- Heike M Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Lone Gram
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,Institute of Microbiology, University Braunschweig, Germany
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49
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Godwin RL, Opatova V, Garrison NL, Hamilton CA, Bond JE. Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901. Mol Phylogenet Evol 2018; 126:303-313. [PMID: 29656103 DOI: 10.1016/j.ympev.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/08/2018] [Accepted: 04/06/2018] [Indexed: 02/08/2023]
Abstract
The mygalomorph family Ctenizidae has a world-wide distribution and currently contains nine genera and 135 species. However, the monophyly of this group has long been questioned on both morphological and molecular grounds. Here, we use Anchored Hybrid Enrichment (AHE) to gather hundreds of loci from across the genome for reconstructing the phylogenetic relationships among the nine genera and test the monophyly of the family. We also reconstruct the possible ancestral ranges of the most inclusive clade recovered. Using AHE, we generate a supermatrix of 565 loci and 115,209 bp for 27 individuals. For the first time, analyses using all nine genera produce results definitively establishing the non-monophyly of Ctenizidae. A lineage formed exclusively by representatives of South African Stasimopus was placed as the sister group to the remaining taxa in the tree, and the Mediterranean Cteniza and Cyrtocarenum were recovered with high support as sister to exemplars of Euctenizidae, Migidae, and Idiopidae. All the remaining genera-Bothriocyrtum, Conothele, Cyclocosmia, Hebestatis, Latouchia, and Ummidia-share a common ancestor. Based on these results, we formally elevate this clade to the level of family. Our results definitively establish both the non-monophyly of the Ctenizidae and non-validity of the subfamilies Ummidiinae and Ctenizinae. In order to establish the placement of the remaining three ctenizid genera, Cteniza, Cyrtocarenum, and Stasimopus, thorough analyses within the context of a complete mygalomorph phylogenetic framework are needed. We formally describe the family Halonoproctidae Pocock 1901 and infer that the family's most recent common ancestor was likely distributed in western North America and Asia.
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Affiliation(s)
- Rebecca L Godwin
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Vera Opatova
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Nicole L Garrison
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
| | - Chris A Hamilton
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.
| | - Jason E Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL, 36849, USA.
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