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Barkdull M, Moreau CS. Worker Reproduction and Caste Polymorphism Impact Genome Evolution and Social Genes Across the Ants. Genome Biol Evol 2023; 15:evad095. [PMID: 37243539 PMCID: PMC10287540 DOI: 10.1093/gbe/evad095] [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: 08/01/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Eusocial insects are characterized by several traits, including reproductive division of labor and caste polymorphisms, which likely modulate genome evolution. Concomitantly, evolution may act on specific genes and pathways underlying these novel, sociality-associated phenotypes. Reproductive division of labor should increase the magnitude of genetic drift and reduce the efficacy of selection by reducing effective population size. Caste polymorphism has been associated with relaxed selection and may facilitate directional selection on caste-specific genes. Here, we use comparative analyses of 22 ant genomes to test how reproductive division of labor and worker polymorphism influence positive selection and selection intensity across the genome. Our results demonstrate that worker reproductive capacity is associated with a reduction in the degree of relaxed selection but is not associated with any significant change to positive selection. We find decreases in positive selection in species with polymorphic workers, but no increase in the degree of relaxed selection. Finally, we explore evolutionary patterns in specific candidate genes associated with our focal traits in eusocial insects. Two oocyte patterning genes previously implicated in worker sterility evolve under intensified selection in species with reproductive workers. Behavioral caste genes generally experience relaxed selection associated with worker polymorphism, whereas vestigial and spalt, both associated with soldier development in Pheidole ants, experience intensified selection in worker polymorphic species. These findings expand our understanding of the genetic mechanisms underlying elaborations of sociality. The impacts of reproductive division of labor and caste polymorphisms on specific genes illuminate those genes' roles in generating complex eusocial phenotypes.
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Affiliation(s)
- Megan Barkdull
- Department of Ecology & Evolutionary Biology, Cornell University
| | - Corrie S Moreau
- Department of Ecology & Evolutionary Biology, Cornell University
- Department of Entomology, Cornell University
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2
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Suzuki RH, Hanada T, Hayashi Y, Shigenobu S, Maekawa K, Hojo MK. Gene expression profiles of chemosensory genes of termite soldier and worker antennae. INSECT MOLECULAR BIOLOGY 2023. [PMID: 37017304 DOI: 10.1111/imb.12841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
Termites have an elaborate social system that involves cooperation and division of labour among colony members. Although this social system is regulated by chemical signals produced in the colony, it remains unclear how these signals are perceived by other members. Signal transduction is well known to be triggered by the reception of odorant molecules by some binding proteins in the antennae, after which, a signal is transmitted to chemosensory receptors. However, there is insufficient information on the role of chemosensory genes involved in signal transduction in termites. Here, we identified the genes involved in chemosensory reception in the termite Reticulitermes speratus and performed a genome-wide comparative transcriptome analysis of worker and soldier antennae. First, we identified 31 odorant-binding proteins (OBPs), and three chemosensory protein A (CheA) from the genome data. Thereafter, we performed RNA sequencing to compare the expression levels of OBPs, CheAs, and previously identified chemosensory receptor genes between worker and soldier antennae. There were no receptor genes with significant differences in expression between castes. However, the expression levels of three non-receptor odorant-detection/binding proteins (OBP, CheA, and Sensory neuron membrane protein) were significantly different between castes. Real-time qPCR (RT-qPCR) analysis using antennae and other head parts confirmed that these genes were highly expressed in soldier antennae. Finally, independent RT-qPCR analysis showed that the expression patterns of these genes were altered in soldiers from different social contexts. Present results suggest that gene expression levels of some non-receptors are affected by both castes and behavioural interactions among colony members in termites.
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Affiliation(s)
- Ryohei H Suzuki
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - Takumi Hanada
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | | | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | | | - Masaru K Hojo
- School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
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3
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Marriott C, Bae P, Chebib J. Deterministic Response Threshold Models of Reproductive Division of Labor Are More Robust Than Probabilistic Models in Artificial Ants. ARTIFICIAL LIFE 2022; 28:264-286. [PMID: 35727996 DOI: 10.1162/artl_a_00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We implement an agent-based simulation of the response threshold model of reproductive division of labor. Ants in our simulation must perform two tasks in their environment: forage and reproduce. The colony is capable of allocating ant resources to these roles using different division of labor strategies via genetic architectures and plasticity mechanisms. We find that the deterministic allocation strategy of the response threshold model is more robust than the probabilistic allocation strategy. The deterministic allocation strategy is also capable of evolving complex solutions to colony problems like niche construction and recovery from the loss of the breeding caste. In addition, plasticity mechanisms had both positive and negative influence on the emergence of reproductive division of labor. The combination of plasticity mechanisms has an additive and sometimes emergent impact.
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Affiliation(s)
- Chris Marriott
- University of Washington, School of Engineering and Technology.
| | - Peter Bae
- University of Washington, School of Engineering and Technology
| | - Jobran Chebib
- University of Edinburgh, Institute of Evolutionary Biology
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4
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Nouhaud P, Beresford J, Kulmuni J. Assembly of a hybrid Formica aquilonia × F. polyctena ant genome from a haploid male. J Hered 2022; 113:353-359. [PMID: 35394540 PMCID: PMC9270870 DOI: 10.1093/jhered/esac019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Abstract
Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here, we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ~60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenopteran BUSCOs and was pseudo-scaffolded using the assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one-third of the genome consists of repeats, and 17 426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.
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Affiliation(s)
- Pierre Nouhaud
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Jack Beresford
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Jonna Kulmuni
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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5
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Abouheif E. My road to the ants: A model clade for eco-evo-devo. Curr Top Dev Biol 2022; 147:231-290. [PMID: 35337451 DOI: 10.1016/bs.ctdb.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter is the story of how I pioneered ants as a system for studying eco-evo-devo, a field that integrates developmental biology with ecology and evolutionary biology. One aim of eco-evo-devo is to understand how the interactions between genes and their environments during development facilitates the origin and evolution of novel phenotypes. In a series of six parts, I review some of the key discoveries from my lab on how novel worker caste systems in ants--soldiers and supersoldiers--originated and evolved. I also discuss some of the ideas that emerged from these discoveries, including the role that polyphenisms, hidden developmental potentials, and rudimentary organs play in facilitating developmental and evolutionary change. As superorganisms, I argue that ants are uniquely positioned to reveal types of variation that are often difficult to observe in nature. In doing so, they have the potential to transform our view of biology and provide new perspectives in medicine, agriculture, and biodiversity conservation. With my story I hope to inspire the next generation of biologists to continue exploring the unknown regions of phenotypic space to solve some of our most pressing societal challenges.
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Affiliation(s)
- Ehab Abouheif
- Department of Biology, McGill University, Montreal, QC, Canada.
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6
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Chang H, Lee DH. Positive Eusocial Impacts on Ants by Taurine Derivatives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1370:425-432. [DOI: 10.1007/978-3-030-93337-1_40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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Schmid-Hempel P. Sociality and parasite transmission. Behav Ecol Sociobiol 2021; 75:156. [PMID: 34720348 PMCID: PMC8540878 DOI: 10.1007/s00265-021-03092-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022]
Abstract
Parasites and their social hosts form many different relationships. But what kind of selection regimes are important? A look at the parameters that determine fitness of the two parties suggests that social hosts differ from solitary ones primarily in the structure of transmission pathways. Because transmission is, both, the physical encounter of a new host and infecting it, several different elements determine parasite transmission success. These include spatial distance, genetic distance, or the temporal and ecological niche overlaps. Combing these elements into a ‘generalized transmission distance’ that determines parasite fitness aids in the identification of the critical steps. For example, short-distance transmission to genetically similar hosts within the social group is the most frequent process under sociality. Therefore, spatio-genetical distances are the main driver of parasite fitness. Vice versa, the generalized distance identifies the critical host defences. In this case, host defences should be primarily selected to defend against the within-group spread of an infection, especially among closely related group members.
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Affiliation(s)
- Paul Schmid-Hempel
- Institute of Integrative Biology (IBZ), ETH Zürich, ETH-Zentrum CHN, Universitätstrasse 16, CH-8092 Zürich, Switzerland
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8
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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9
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Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O. The genomic basis of evolutionary differentiation among honey bees. Genome Res 2021; 31:1203-1215. [PMID: 33947700 PMCID: PMC8256857 DOI: 10.1101/gr.272310.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
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Affiliation(s)
- Bertrand Fouks
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California 95161, USA
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Hung N Nguyen
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jacob Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Daniel Ence
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Katharina J Hoff
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Stefanie Nachweide
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Lars Romoth
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Mario Stanke
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | | | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nikolaus Koeniger
- Department of Behavioral Physiology and Sociobiology (Zoology II), University of Würzburg, 97074 Würzburg, Germany
| | - Panuwan Chantawannakul
- Environmental Science Research Center (ESRC) and Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gene E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christine G Elsik
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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10
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Gilbert C, Peccoud J, Cordaux R. Transposable Elements and the Evolution of Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:355-372. [PMID: 32931312 DOI: 10.1146/annurev-ento-070720-074650] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France;
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
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11
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Muñoz-Valencia V, Kähkönen K, Montoya-Lerma J, Díaz F. Characterization of a New Set of Microsatellite Markers Suggests Polygyny and Polyandry in Atta cephalotes (Hymenoptera: Formicidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:3021-3027. [PMID: 32964936 DOI: 10.1093/jee/toaa200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 06/11/2023]
Abstract
The leaf-cutting ant, Atta cephalotes L. (1758), is a major herbivore with great economic impact in the Neotropics. Because of its broad range and human-mediated dissemination, the ecology of this ant has received considerable attention; however, questions concerning its population genetics, dispersal, and social structure remain unexplored. Here, we aimed to identify and provide information on molecular and statistical performance of a suite of polymorphic microsatellite markers for A. cephalotes while demonstrating their utility for further genetic studies. We designed primer sequences targeting thousands of microsatellite loci and then screened 30 of these for amplification and polymorphism. Fifteen of these loci were selected and used to evaluate their polymorphism using 74 ants sampled from 15 different nests of the same location. This set of 15 loci exhibited variation of 2-20 alleles, with a mean heterozygosity of 0.57. All loci followed Hardy-Weinberg expectations with no evidence of linkage disequilibrium, while two loci showed evidence of null alleles. Our preliminary analysis suggested substantial nest differentiation with no population viscosity within the sampled location, as well as colonies with multiple queens (polygyny) and paternity (polyandry). Our newly identified microsatellites have proven to be highly informative to investigate gene flow, social structure and reproduction of this key agricultural pest.
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Affiliation(s)
- Vanessa Muñoz-Valencia
- Grupo de Ecología de Agroecosistemas y Hábitats Naturales, Department of Biology, Faculty of Natural Science, Universidad del Valle, Meléndez campus, Cali, Colombia
| | - Kirsi Kähkönen
- Organismal and Evolutionary Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - James Montoya-Lerma
- Grupo de Ecología de Agroecosistemas y Hábitats Naturales, Department of Biology, Faculty of Natural Science, Universidad del Valle, Meléndez campus, Cali, Colombia
| | - Fernando Díaz
- Department of Entomology, University of Arizona, Tucson, Arizona
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12
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Sharanowski BJ, Ridenbaugh RD, Piekarski PK, Broad GR, Burke GR, Deans AR, Lemmon AR, Moriarty Lemmon EC, Diehl GJ, Whitfield JB, Hines HM. Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization. Mol Phylogenet Evol 2020; 156:107023. [PMID: 33253830 DOI: 10.1016/j.ympev.2020.107023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/26/2022]
Abstract
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
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Affiliation(s)
| | - Ryan D Ridenbaugh
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Patrick K Piekarski
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA; Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Gavin R Broad
- Department of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30606, USA
| | - Andrew R Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Gloria J Diehl
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61801, USA
| | - Heather M Hines
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802; Department of Biology, Pennsylvania State University, University Park, PA, 16802
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13
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Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts. Emerg Top Life Sci 2020; 4:59-76. [PMID: 32558901 DOI: 10.1042/etls20190069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/14/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.
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14
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Ramalho MDO, Martins C, Morini MSC, Bueno OC. What Can the Bacterial Community of Atta sexdens (Linnaeus, 1758) Tell Us about the Habitats in Which This Ant Species Evolves? INSECTS 2020; 11:E332. [PMID: 32481532 PMCID: PMC7349130 DOI: 10.3390/insects11060332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022]
Abstract
Studies of bacterial communities can reveal the evolutionary significance of symbiotic interactions between hosts and their associated bacteria, as well as identify environmental factors that may influence host biology. Atta sexdens is an ant species native to Brazil that can act as an agricultural pest due to its intense behavior of cutting plants. Despite being extensively studied, certain aspects of the general biology of this species remain unclear, such as the evolutionary implications of the symbiotic relationships it forms with bacteria. Using high-throughput amplicon sequencing of 16S rRNA genes, we compared for the first time the bacterial community of A. sexdens (whole ant workers) populations according to the habitat (natural versus agricultural) and geographical location. Our results revealed that the bacterial community associated with A. sexdens is mainly influenced by the geographical location, and secondarily by the differences in habitat. Also, the bacterial community associated with citrus differed significantly from the other communities due to the presence of Tsukamurella. In conclusion, our study suggests that environmental shifts may influence the bacterial diversity found in A. sexdens.
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Affiliation(s)
- Manuela de Oliveira Ramalho
- Centro de Estudos de Insetos Sociais—CEIS, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil;
- Department of Entomology, Cornell University, 129 Garden Ave, Ithaca, NY 14850, USA
| | - Cintia Martins
- Campus Ministro Reis Velloso, Universidade Federal do Piauí, Av. São Sebastião, 2819, Parnaíba, Piauí 64202-020, Brazil;
| | - Maria Santina Castro Morini
- Núcleo de Ciências Ambientais, Universidade de Mogi das Cruzes, Av. Dr. Cândido Xavier de Almeida e Souza, 200, Centro Cívico, Mogi das Cruzes 08780-911, SP, Brazil;
| | - Odair Correa Bueno
- Centro de Estudos de Insetos Sociais—CEIS, Instituto de Biociências, Universidade Estadual Paulista, UNESP, Campus Rio Claro, Avenida 24A, 1515, Bela Vista, Rio Claro 13506-900, SP, Brazil;
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15
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Complex Evolutionary History of Mboumar, a Mariner Element Widely Represented in Ant Genomes. Sci Rep 2020; 10:2610. [PMID: 32054918 PMCID: PMC7018970 DOI: 10.1038/s41598-020-59422-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Mboumar-9 is an active mariner-transposable element previously isolated in the ant Messor bouvieri. In this work, a mariner-like element, Mboumar, isolated from 22 species of ants, is analyzed. These species belong to nine different subfamilies, including Leptanillinae, the most primitive ant subfamily, and Myrmicinae and Formicidae, the most derived ones. Consequently, Mboumar-like elements seem to be well-represented in ant genomes. The phylogenetic tree drawn for mariner elements is highly inconsistent with the phylogeny of host ants, with almost identical elements found in clearly distant species and, on the contrary, more variable elements in closely related species. The inconsistency between the two phylogenetic trees indicates that these transposable elements have evolved independently from the speciation events of the ants that host them. Besides, we found closer genetic relationships among elements than among their host ants. We also found potential coding copies with an uninterrupted open reading frame of 345 aa in 11 species. The putative transposase codified by them showed a high sequence identity with the active Mboumar-9 transposase. The results of selection tests suggest the intervention of purifying selection in the evolution of these elements. Overall, our study suggests a complex evolutionary history of the Mboumar-like mariner in ants, with important participation of horizontal transfer events. We also suggest that the evolutionary dynamics of Mboumar-like elements can be influenced by the genetic system of their host ants, which are eusocial insects with a haplodiploid genetic system.
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16
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Kurafeiski JD, Pinto P, Bornberg-Bauer E. Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding. Genome Biol Evol 2019; 11:406-414. [PMID: 30597011 PMCID: PMC6370388 DOI: 10.1093/gbe/evy269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2018] [Indexed: 01/25/2023] Open
Abstract
Transcriptional regulation is crucial for all biological processes and well investigated at the molecular level for a wide range of organisms. However, it is quite unclear how innovations, such as the activity of a novel regulatory element, evolve. In the case of transcription factor (TF) binding, both a novel TF and a novel-binding site would need to evolve concertedly. Since promiscuous functions have recently been identified as important intermediate steps in creating novel specific functions in many areas such as enzyme evolution and protein-protein interactions, we ask here how promiscuous binding of TFs to TF-binding sites (TFBSs) affects the robustness and evolvability of this tightly regulated system. Specifically, we investigate the binding behavior of several hundred TFs from different species at unprecedented breadth. Our results illustrate multiple aspects of TF-binding interactions, ranging from correlations between the strength of the interaction bond and specificity, to preferences regarding TFBS nucleotide composition in relation to both domains and binding specificity. We identified a subset of high A/T binding motifs. Motifs in this subset had many functionally neutral one-error mutants, and were bound by multiple different binding domains. Our results indicate that, especially for some TF-TFBS associations, low binding specificity confers high degrees of evolvability, that is that few mutations facilitate rapid changes in transcriptional regulation, in particular for large and old TF families. In this study we identify binding motifs exhibiting behavior indicating high evolutionary potential for innovations in transcriptional regulation.
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Affiliation(s)
| | - Paulo Pinto
- Molecular Evolution and Bioinformatics, University of Muenster, Germany
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17
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Allen ML, Rhoades JH, Sparks ME, Grodowitz MJ. Differential Gene Expression in Red Imported Fire Ant ( Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages. INSECTS 2018; 9:E185. [PMID: 30563147 PMCID: PMC6315859 DOI: 10.3390/insects9040185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022]
Abstract
Solenopsis invicta Buren is an invasive ant species that has been introduced to multiple continents. One such area, the southern United States, has a history of multiple control projects using chemical pesticides over varying ranges, often resulting in non-target effects across trophic levels. With the advent of next generation sequencing and RNAi technology, novel investigations and new control methods are possible. A robust genome-guided transcriptome assembly was used to investigate gene expression differences between S. invicta larvae and pupae. These life stages differ in many physiological processes; of special importance is the vital role of S. invicta larvae as the colonies' "communal gut". Differentially expressed transcripts were identified related to many important physiological processes, including digestion, development, cell regulation and hormone signaling. This dataset provides essential developmental knowledge that reveals the dramatic changes in gene expression associated with social insect life stage roles, and can be leveraged using RNAi to develop effective control methods.
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Affiliation(s)
- Margaret L Allen
- USDA-ARS Biological Control of Pests Research Unit, National Biological Control Laboratory, Stoneville, MS 38776, USA.
| | - Joshua H Rhoades
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA.
| | - Michael E Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD 20705, USA.
| | - Michael J Grodowitz
- USDA-ARS Biological Control of Pests Research Unit, National Biological Control Laboratory, Stoneville, MS 38776, USA.
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18
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Jia LY, Chen L, Keller L, Wang J, Xiao JH, Huang DW. Doublesex Evolution Is Correlated with Social Complexity in Ants. Genome Biol Evol 2018; 10:3230-3242. [PMID: 30476039 PMCID: PMC6300070 DOI: 10.1093/gbe/evy250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
The Dmrt (doublesex and mab-3-related transcription factor) genes are transcription factors crucial for sex determination and sexual differentiation. In some social insects, doublesex (dsx) exhibits widespread caste-specific expression across different tissues and developmental stages and has been suggested as a candidate gene for regulating division of labor in social insects. We therefore conducted a molecular evolution analysis of the Dmrt gene family in 20 ants. We found that the insect-specific oligomerization domain of DSX, oligomerization domain 2, was absent in all ants, except for the two phylogenetically basal ant species (Ponerinae), whose social structure and organization resemble the presumed ancestral condition in ants. Phylogenetic reconstruction and selection analysis revealed that dsx evolved faster than the other three members of the Dmrt family. We found evidence for positive selection for dsx in the ant subfamilies with more advanced social organization (Myrmicinae and Formicinae), but not in the Ponerinae. Furthermore, we detected expression of two Dmrt genes, dsx and DMRT11E, in adult ants, and found a clear male-biased expression pattern of dsx in most species for which data are available. Interestingly, we did not detect male-biased expression of dsx in the two ant species that possess a genetic caste determination system. These results possibly suggest an association between the evolution of dsx and social organization as well as reproductive division of labor in ants.
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Affiliation(s)
- Ling-Yi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Laurent Keller
- Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jin-Hua Xiao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Da-Wei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Nankai University, Tianjin, China
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19
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20
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Opachaloemphan C, Yan H, Leibholz A, Desplan C, Reinberg D. Recent Advances in Behavioral (Epi)Genetics in Eusocial Insects. Annu Rev Genet 2018; 52:489-510. [PMID: 30208294 DOI: 10.1146/annurev-genet-120116-024456] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eusocial insects live in societies in which distinct family members serve specific roles in maintaining the colony and advancing the reproductive ability of a few select individuals. Given the genetic similarity of all colony members, the diversity of morphologies and behaviors is surprising. Social communication relies on pheromones and olfaction, as shown by mutants of orco, the universal odorant receptor coreceptor, and through electrophysiological analysis of neuronal responses to pheromones. Additionally, neurohormonal factors and epigenetic regulators play a key role in caste-specific behavior, such as foraging and caste switching. These studies start to allow an understanding of the molecular mechanisms underlying social behavior and provide a technological foundation for future studies of eusocial insects. In this review, we highlight recent findings in eusocial insects that advance our understanding of genetic and epigenetic regulations of social behavior and provide perspectives on future studies using cutting-edge technologies.
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Affiliation(s)
- Comzit Opachaloemphan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; ,
| | - Hua Yan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; , .,Department of Biology, University of Florida, Gainesville, Florida 32611, USA; .,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | | | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA; ,
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; , .,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
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21
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Liutkevičiūtė Z, Gil-Mansilla E, Eder T, Casillas-Pérez B, Di Giglio MG, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber CW. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. FASEB J 2018; 32:fj201800443. [PMID: 29939785 PMCID: PMC6174076 DOI: 10.1096/fj.201800443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/04/2018] [Indexed: 01/12/2023]
Abstract
Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.-Liutkevičiūtė, Z., Gil-Mansilla, E., Eder, T., Casillas-Pérez, B., Di Giglio, M. G., Muratspahić, E., Grebien, F., Rattei, T., Muttenthaler, M., Cremer, S., Gruber, C. W. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity.
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Affiliation(s)
- Zita Liutkevičiūtė
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Esther Gil-Mansilla
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Thomas Eder
- Division of Computational Systems Biology (CUBE), Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | | | | | - Edin Muratspahić
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology (CUBE), Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Sylvia Cremer
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Christian W. Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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22
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Glastad KM, Arsenault SV, Vertacnik KL, Geib SM, Kay S, Danforth BN, Rehan SM, Linnen CR, Kocher SD, Hunt BG. Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera. Genome Biol Evol 2018; 9:1687-1698. [PMID: 28854636 PMCID: PMC5522706 DOI: 10.1093/gbe/evx128] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/12/2022] Open
Abstract
Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing so, we generated new DNA methylomes for three species of interest, including one solitary and one facultatively eusocial halictid bee and a sawfly. We demonstrate that the strength of correlation between CpG content and DNA methylation varies widely among hymenopteran taxa, highlighting shortcomings in the utility of CpG content as a proxy for DNA methylation in comparative studies of taxa with sparse DNA methylomes. We observed strikingly high levels of DNA methylation in the sawfly relative to other investigated hymenopterans. Analyses of molecular evolution suggest the relatively distinct sawfly DNA methylome may be associated with positive selection on functional DNMT3 domains. Sawflies are an outgroup to all ants, bees, and wasps, and no sawfly species are eusocial. We find no evidence that either global expansions or variation within individual ortholog groups in DNA methylation are consistently associated with the evolution of social behavior.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania
| | | | | | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Sasha Kay
- Department of Entomology, University of Georgia
| | | | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire
| | | | - Sarah D Kocher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
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HsTRPA of the Red Imported Fire Ant, Solenopsis invicta, Functions as a Nocisensor and Uncovers the Evolutionary Plasticity of HsTRPA Channels. eNeuro 2018; 5:eN-NWR-0327-17. [PMID: 29445768 PMCID: PMC5810042 DOI: 10.1523/eneuro.0327-17.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/14/2018] [Accepted: 01/18/2018] [Indexed: 12/29/2022] Open
Abstract
Solenopsis invicta, the red imported fire ant, represents one of the most devastating invasive species. To understand their sensory physiology, we identified and characterized their Hymenoptera-specific (Hs) TRPA channel, SiHsTRPA. Consistent with the sensory functions of SiHsTRPA, it is activated by heat, an electrophile, and an insect repellent. Nevertheless, SiHsTRPA does not respond to most of the honey bee ortholog (AmHsTRPA)-activating compounds. The jewel wasp ortholog (NvHsTRPA) is activated by these compounds even though it outgroups both AmHsTRPA and SiHsTRPA. Characterization of AmHsTRPA/SiHsTRPA chimeric channels revealed that the amino acids in the N terminus, as well as ankyrin repeat 2 (AR2) of AmHsTRPA, are essential for the response to camphor. Furthermore, amino acids in ARs 3 and 5–7 were specifically required for the response to diallyl disulfide. Thus, amino acid substitutions in the corresponding domains of SiHsTRPA during evolution would be responsible for the loss of chemical sensitivity. SiHsTRPA-activating compounds repel red imported fire ants, suggesting that SiHsTRPA functions as a sensor for noxious compounds. SiHsTRPA represents an example of the species-specific modulation of orthologous TRPA channel properties by amino acid substitutions in multiple domains, and SiHsTRPA-activating compounds could be used to develop a method for controlling red imported fire ants.
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Hemimetabolous genomes reveal molecular basis of termite eusociality. Nat Ecol Evol 2018; 2:557-566. [PMID: 29403074 PMCID: PMC6482461 DOI: 10.1038/s41559-017-0459-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022]
Abstract
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
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Favreau E, Martínez-Ruiz C, Rodrigues Santiago L, Hammond RL, Wurm Y. Genes and genomic processes underpinning the social lives of ants. CURRENT OPINION IN INSECT SCIENCE 2018; 25:83-90. [PMID: 29602366 DOI: 10.1016/j.cois.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 05/06/2023]
Abstract
The >15000 ant species are all highly social and show great variation in colony organization, complexity and behavior. The mechanisms by which such sociality evolved, as well as those underpinning the elaboration of ant societies since their ∼140 million year old common ancestor, have long been pondered. Here, we review recent insights generated using various genomic approaches. This includes understanding the molecular mechanisms underlying caste differentiation and the diversity of social structures, studying the impact of eusociality on genomic evolutionary rates, and investigating gene expression changes associated with differences in lifespan between castes. Furthermore, functional studies involving RNAi and CRISPR have recently been successfully applied to ants, opening the door to exciting research that promises to revolutionize the understanding of the evolution and diversification of social living.
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Affiliation(s)
- Emeline Favreau
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Carlos Martínez-Ruiz
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Leandro Rodrigues Santiago
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert L Hammond
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom.
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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Pennell TM, Holman L, Morrow EH, Field J. Building a new research framework for social evolution: intralocus caste antagonism. Biol Rev Camb Philos Soc 2018; 93:1251-1268. [PMID: 29341390 PMCID: PMC5896731 DOI: 10.1111/brv.12394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 12/06/2017] [Accepted: 12/18/2017] [Indexed: 01/02/2023]
Abstract
The breeding and non‐breeding ‘castes’ of eusocial insects provide a striking example of role‐specific selection, where each caste maximises fitness through different morphological, behavioural and physiological trait values. Typically, queens are long‐lived egg‐layers, while workers are short‐lived, largely sterile foragers. Remarkably, the two castes are nevertheless produced by the same genome. The existence of inter‐caste genetic correlations is a neglected consequence of this shared genome, potentially hindering the evolution of caste dimorphism: alleles that increase the productivity of queens may decrease the productivity of workers and vice versa, such that each caste is prevented from reaching optimal trait values. A likely consequence of this ‘intralocus caste antagonism’ should be the maintenance of genetic variation for fitness and maladaptation within castes (termed ‘caste load’), analogous to the result of intralocus sexual antagonism. The aim of this review is to create a research framework for understanding caste antagonism, drawing in part upon conceptual similarities with sexual antagonism. By reviewing both the social insect and sexual antagonism literature, we highlight the current empirical evidence for caste antagonism, discuss social systems of interest, how antagonism might be resolved, and challenges for future research. We also introduce the idea that sexual and caste antagonism could interact, creating a three‐way antagonism over gene expression. This includes unpacking the implications of haplodiploidy for the outcome of this complex interaction.
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Affiliation(s)
- Tanya M Pennell
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Luke Holman
- School of Biosciences, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Edward H Morrow
- Evolution Behaviour and Environment Group, School of Life Sciences, University of Sussex, Falmer, East Sussex, BN1 9QG, UK
| | - Jeremy Field
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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27
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Yang L, Lin Z, Fang Q, Wang J, Yan Z, Zou Z, Song Q, Ye G. The genomic and transcriptomic analyses of serine proteases and their homologs in an endoparasitoid, Pteromalus puparum. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:56-68. [PMID: 28713011 DOI: 10.1016/j.dci.2017.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
In insects, serine proteases (SPs) and serine protease homologs (SPHs) constitute a large family of proteins involved in multiple physiological processes such as digestion, development, and immunity. Here we identified 145 SPs and 38 SPHs in the genome of an endoparasitoid, Pteromalus puparum. Gene duplication and tandem repeats were observed in this large SPs/SPHs family. We then analyzed the expression profiles of SP/SPH genes in response to different microbial infections (Gram-positive bacterium Micrococcus luteus, Gram-negative bacterium Escherichia coli, and entomopathogenic fungus Beauveria bassiana), as well as in different developmental stages and tissues. Some SPs/SPHs also displayed distinct expression patterns in venom gland, suggesting their specific physiological functions as venom proteins. Our finding lays groundwork for further research of SPs and SPHs expressed in the venom glands.
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Affiliation(s)
- Lei Yang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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28
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Dhaygude K, Trontti K, Paviala J, Morandin C, Wheat C, Sundström L, Helanterä H. Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta. PeerJ 2017; 5:e3998. [PMID: 29177112 PMCID: PMC5701548 DOI: 10.7717/peerj.3998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.
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Affiliation(s)
- Kishor Dhaygude
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kalevi Trontti
- Department of Biosciences, Neurogenomics Laboratory, University of Helsinki, Helsinki, Finland
| | - Jenni Paviala
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Christopher Wheat
- Department of Zoology Ecology, Stockholm University, Stockholm, Sweden
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
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29
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Qiu GH, Yang X, Zheng X, Huang C. The eukaryotic genome is structurally and functionally more like a social insect colony than a book. Epigenomics 2017; 9:1469-1483. [PMID: 28972397 DOI: 10.2217/epi-2017-0059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.
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Affiliation(s)
- Guo-Hua Qiu
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xiaoyan Yang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Xintian Zheng
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
| | - Cuiqin Huang
- Fujian Provincial Key Laboratory for the Prevention & Control of Animal Infectious Diseases & Biotechnology, College of Life Sciences, Longyan University, Longyan 364012, Fujian, PR China
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30
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Withee JR, Rehan SM. Social Aggression, Experience, and Brain Gene Expression in a Subsocial Bee. Integr Comp Biol 2017; 57:640-648. [DOI: 10.1093/icb/icx005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Jacob R. Withee
- Department of Biological Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824, USA
| | - Sandra M. Rehan
- Department of Biological Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824, USA
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31
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Simone-Finstrom M. Social Immunity and the Superorganism: Behavioral Defenses Protecting Honey Bee Colonies from Pathogens and Parasites. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/0005772x.2017.1307800] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Morandin C, Mikheyev AS, Pedersen JS, Helanterä H. Evolutionary constraints shape caste-specific gene expression across 15 ant species. Evolution 2017; 71:1273-1284. [PMID: 28262920 DOI: 10.1111/evo.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Jes Søe Pedersen
- Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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33
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Yue Y, Hou S, Wang X, Zhan L, Cao G, Li G, Shi Y, Zhang P, Hong W, Lin H, Liu B, Shi F, Yang Y, Jin Y. Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing. RNA Biol 2017; 14:1399-1410. [PMID: 28277933 DOI: 10.1080/15476286.2017.1294308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.
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Affiliation(s)
- Yuan Yue
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Shouqing Hou
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Xiu Wang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China.,b Institute of Ecology, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Leilei Zhan
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guozheng Cao
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guoli Li
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yang Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Peng Zhang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Weiling Hong
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Hao Lin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Baoping Liu
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Feng Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yun Yang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yongfeng Jin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
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Korb J. Why do social insect queens live so long? Approaches to unravel the sociality-aging puzzle. CURRENT OPINION IN INSECT SCIENCE 2016; 16:104-107. [PMID: 27720043 DOI: 10.1016/j.cois.2016.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/02/2016] [Accepted: 06/07/2016] [Indexed: 05/25/2023]
Abstract
Social insects are characterized by an apparent reshaping of the fecundity/longevity trade-off with sociality. Currently, we have only sketchy information about the potential underlying causes and mechanisms of aging and senescence which in addition are restricted to few model insect organisms (mainly the fruit fly Drosophila melanogaster and the honey bee Apis mellifera). How can we gain a more thorough understanding how sociality shapes senescence and the fecundity/longevity trade-off? By reviewing available literature, I propose a comparative approach that offers the opportunity to gain fundamental insights into uncovering the basis for this life history trade-off and its reshaping with sociality.
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Affiliation(s)
- Judith Korb
- Evolutionary Biology & Ecology, University of Freiburg, Germany.
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35
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36
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Rehan SM, Glastad KM, Lawson SP, Hunt BG. The Genome and Methylome of a Subsocial Small Carpenter Bee, Ceratina calcarata. Genome Biol Evol 2016; 8:1401-10. [PMID: 27048475 PMCID: PMC4898796 DOI: 10.1093/gbe/evw079] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2016] [Indexed: 12/14/2022] Open
Abstract
Understanding the evolution of animal societies, considered to be a major transition in evolution, is a key topic in evolutionary biology. Recently, new gateways for understanding social evolution have opened up due to advances in genomics, allowing for unprecedented opportunities in studying social behavior on a molecular level. In particular, highly eusocial insect species (caste-containing societies with nonreproductives that care for siblings) have taken center stage in studies of the molecular evolution of sociality. Despite advances in genomic studies of both solitary and eusocial insects, we still lack genomic resources for early insect societies. To study the genetic basis of social traits requires comparison of genomes from a diversity of organisms ranging from solitary to complex social forms. Here we present the genome of a subsocial bee, Ceratina calcarata This study begins to address the types of genomic changes associated with the earliest origins of simple sociality using the small carpenter bee. Genes associated with lipid transport and DNA recombination have undergone positive selection in C. calcarata relative to other bee lineages. Furthermore, we provide the first methylome of a noneusocial bee. Ceratina calcarata contains the complete enzymatic toolkit for DNA methylation. As in the honey bee and many other holometabolous insects, DNA methylation is targeted to exons. The addition of this genome allows for new lines of research into the genetic and epigenetic precursors to complex social behaviors.
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Affiliation(s)
- Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham
| | | | - Sarah P Lawson
- Department of Biological Sciences, University of New Hampshire, Durham
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37
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Abstract
Many exciting studies have begun to elucidate the genetics of the morphological and physiological diversity of ants, but as yet few studies have investigated the genetics of ant behavior directly. Ant genomes are marked by extreme rates of gene turnover, especially in gene families related to olfactory communication, such as the synthesis of cuticular hydrocarbons and the perception of environmental semiochemicals. Transcriptomic and epigenetic differences are apparent between reproductive and sterile females, males and females, and workers that differ in body size. Quantitative genetic approaches suggest heritability of task performance, and population genetic studies indicate a genetic association with reproductive status in some species. Gene expression is associated with behavior including foraging, response to queens attempting to join a colony, circadian patterns of task performance, and age-related changes of task. Ant behavioral genetics needs further investigation of the feedback between individual-level physiological changes and socially mediated responses to environmental conditions.
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Affiliation(s)
- D A Friedman
- Department of Biology, Stanford University, Stanford, California 94305-5020;
| | - D M Gordon
- Department of Biology, Stanford University, Stanford, California 94305-5020;
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38
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Stanton-Geddes J, Nguyen A, Chick L, Vincent J, Vangala M, Dunn RR, Ellison AM, Sanders NJ, Gotelli NJ, Cahan SH. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species. BMC Genomics 2016; 17:171. [PMID: 26934985 PMCID: PMC4776372 DOI: 10.1186/s12864-016-2466-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/12/2016] [Indexed: 12/03/2022] Open
Abstract
Background The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism’s transcriptome measured across an experimental gradient. We characterized thermal reactionomes of two common ant species in the eastern U.S, the northern cool-climate Aphaenogaster picea and the southern warm-climate Aphaenogaster carolinensis, across 12 temperatures that spanned their entire thermal breadth. Results We found that at least 2 % of all genes changed expression with temperature. The majority of upregulation was specific to exposure to low temperatures. The cool-adapted A. picea induced expression of more genes in response to extreme temperatures than did A. carolinensis, consistent with the enhanced response hypothesis. In contrast, under high temperatures the warm-adapted A. carolinensis downregulated many of the genes upregulated in A. picea, and required more extreme temperatures to induce down-regulation in gene expression, consistent with the tolerance hypothesis. We found no evidence for a trade-off between constitutive and inducible gene expression as predicted by the genetic assimilation hypothesis. Conclusions These results suggest that increases in upper thermal limits may require an evolutionary shift in response mechanism away from damage repair toward tolerance and prevention. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2466-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Stanton-Geddes
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA. .,Data Scientist, Dealer.com, 1 Howard St, Burlington, VT, 05401, USA.
| | - Andrew Nguyen
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Lacy Chick
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - James Vincent
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Mahesh Vangala
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Robert R Dunn
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Aaron M Ellison
- Harvard Forest, Harvard University, Petersham, MA, 01336, USA
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Nicholas J Gotelli
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
| | - Sara Helms Cahan
- Department of Biology, University of Vermont, Burlington, VT, 05405, USA
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Genetic architecture of key social trait differs significantly between primitive and advanced eusocial species. Proc Natl Acad Sci U S A 2015; 112:13755-6. [PMID: 26518508 DOI: 10.1073/pnas.1519065112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Cunningham CB, Ji L, Wiberg RAW, Shelton J, McKinney EC, Parker DJ, Meagher RB, Benowitz KM, Roy-Zokan EM, Ritchie MG, Brown SJ, Schmitz RJ, Moore AJ. The Genome and Methylome of a Beetle with Complex Social Behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biol Evol 2015; 7:3383-96. [PMID: 26454014 PMCID: PMC4700941 DOI: 10.1093/gbe/evv194] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis. The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.
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Affiliation(s)
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia
| | - R Axel W Wiberg
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Jennifer Shelton
- Division of Biology & Bioinformatics Center & Arthropod Genomics Center, Kansas State University
| | | | - Darren J Parker
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | | | | | | | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, United Kingdom
| | - Susan J Brown
- Division of Biology & Bioinformatics Center & Arthropod Genomics Center, Kansas State University
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Smith CR, Helms Cahan S, Kemena C, Brady SG, Yang W, Bornberg-Bauer E, Eriksson T, Gadau J, Helmkampf M, Gotzek D, Okamoto Miyakawa M, Suarez AV, Mikheyev A. How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites. Mol Biol Evol 2015; 32:2919-31. [PMID: 26226984 PMCID: PMC4651238 DOI: 10.1093/molbev/msv165] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A central goal of biology is to uncover the genetic basis for the origin of new
phenotypes. A particularly effective approach is to examine the genomic
architecture of species that have secondarily lost a phenotype with respect to
their close relatives. In the eusocial Hymenoptera, queens and workers have
divergent phenotypes that may be produced via either expression of alternative
sets of caste-specific genes and pathways or differences in expression patterns
of a shared set of multifunctional genes. To distinguish between these two
hypotheses, we investigated how secondary loss of the worker phenotype in
workerless ant social parasites impacted genome evolution across two independent
origins of social parasitism in the ant genera Pogonomyrmex and
Vollenhovia. We sequenced the genomes of three social
parasites and their most-closely related eusocial host species and compared gene
losses in social parasites with gene expression differences between host queens
and workers. Virtually all annotated genes were expressed to some degree in both
castes of the host, with most shifting in queen-worker bias across developmental
stages. As a result, despite >1 My of divergence from the last common
ancestor that had workers, the social parasites showed strikingly little
evidence of gene loss, damaging mutations, or shifts in selection regime
resulting from loss of the worker caste. This suggests that regulatory changes
within a multifunctional genome, rather than sequence differences, have played a
predominant role in the evolution of social parasitism, and perhaps also in the
many gains and losses of phenotypes in the social insects.
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Affiliation(s)
| | | | - Carsten Kemena
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC
| | - Wei Yang
- Department of Computer Science, University of Illinois Urbana-Champaign
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfälische Wilhems-Universität Münster, Münster, Germany
| | - Ti Eriksson
- School of Life Sciences, Arizona State University
| | | | | | - Dietrich Gotzek
- Department of Entomology, University of Georgia Department of Animal Biology, University of Illinois Urbana-Champaign
| | - Misato Okamoto Miyakawa
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Andrew V Suarez
- Department of Animal Biology, University of Illinois Urbana-Champaign Department of Entomology, University of Illinois Urbana-Champaign
| | - Alexander Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
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Palomeque T, Sanllorente O, Maside X, Vela J, Mora P, Torres MI, Periquet G, Lorite P. Evolutionary history of the Azteca-like mariner transposons and their host ants. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2015. [PMID: 26195134 DOI: 10.1007/s00114-015-1294-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Three different complete mariner elements were found in the genome of the ant Tapinoma nigerrimum. One (Tnigmar-Mr) was interrupted by a 900-bp insertion that corresponded to an incomplete member of a fourth mariner element, called Azteca. In this work, we isolate and characterize full-length Tnigmar-Az elements in T. nigerrimum. The purpose of this study is to clarify the evolutionary history of Azteca elements and their hosts as well as the possible existence of horizontal transfer processes. For this, Azteca-like elements were also retrieved from the available sequences of various ant genomes, representing four different ant subfamilies: Dolichoderinae, Formicinae, Myrmicinae, and Ponerinae. The tree topology resulting for the Azteca-like elements bore very little resemblance to that of their respective hosts. The pervasive presence of Azteca-like elements in all ant genomes, together with the observation that extant copies are usually younger than the genomes that host them, could be explained either by lineage sorting or by recent horizontal transfer of active elements. However, the finding of closer genetic relationships between elements than between the ants that host them is consistent with the latter scenario. This is clearly observed in Sinvmar-Az, Tnigmar-Az, Acepmar-Az, and Cflomar-Az elements, suggesting the existence of horizontal transfer processes. On the contrary, some elements displayed more divergence than did the hosts harboring them. This may reflect either further horizontal transfer events or random lineage sorting.
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Affiliation(s)
- Teresa Palomeque
- Departamento de Biología Experimental, Universidad de Jaén, 23071, Jaén, Spain
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43
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Rehan SM, Toth AL. Climbing the social ladder: the molecular evolution of sociality. Trends Ecol Evol 2015; 30:426-33. [PMID: 26051561 DOI: 10.1016/j.tree.2015.05.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/24/2022]
Abstract
Genomic tools are allowing us to dissect the roles of genes and genetic architecture in social evolution, and eusocial insects are excellent models. Numerous hypotheses for molecular evolution of eusociality have been proposed, ranging from regulatory shifts in 'old' genes to rapid evolution of 'new' genes. A broad model to explain this major transition in evolution has been lacking. We provide a synthetic framework centered on the idea that different evolutionary processes dominate during different transitional stages, beginning with changes in gene regulation and culminating in novel genes later on. By considering multiple mechanisms as we 'climb the social ladder', we can test whether the transitions from solitary to simple sociality to complex sociality represent incremental changes or genetic revolutions.
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Affiliation(s)
- Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Amy L Toth
- Department of Evolution, Ecology, and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
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44
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Barribeau SM, Sadd BM, du Plessis L, Brown MJF, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, Erler S, Evans J, Helbing S, Karaus E, Lattorff HMG, Marxer M, Meeus I, Näpflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse RM, Yu N, Zdobnov EM, Schmid-Hempel P. A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol 2015; 16:83. [PMID: 25908406 PMCID: PMC4408586 DOI: 10.1186/s13059-015-0628-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees and other sequenced social insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain this depauperate immune repertoire. Here, based on full genome sequences, we describe the immune repertoire of two ecologically and commercially important bumblebee species that diverged approximately 18 million years ago, the North American Bombus impatiens and European Bombus terrestris. Results We find that the immune systems of these bumblebees, two species of honeybee, and a solitary leafcutting bee, are strikingly similar. Transcriptional assays confirm the expression of many of these genes in an immunological context and more strongly in young queens than males, affirming Bateman’s principle of greater investment in female immunity. We find evidence of positive selection in genes encoding antiviral responses, components of the Toll and JAK/STAT pathways, and serine protease inhibitors in both social and solitary bees. Finally, we detect many genes across pathways that differ in selection between bumblebees and honeybees, or between the social and solitary clades. Conclusions The similarity in immune complement across a gradient of sociality suggests that a reduced immune repertoire predates the evolution of sociality in bees. The differences in selection on immune genes likely reflect divergent pressures exerted by parasites across social contexts. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0628-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Ben M Sadd
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA.
| | - Louis du Plessis
- Theoretical Biology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland. .,Computational Evolution, Department of Biosystems Science and Evolution, ETH Zürich, 4058, Basel, Switzerland. .,Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland.
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, London, TW20 0EX, UK.
| | - Severine D Buechel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Kaat Cappelle
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - James C Carolan
- Maynooth University Department of Biology, Maynooth University, Maynooth, Kildare, Ireland.
| | - Olivier Christiaens
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Thomas J Colgan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, 2, Ireland. .,School of Biological and Chemical Sciences, Queen Mary University of London, E1 41NS, London, UK.
| | - Silvio Erler
- Department of Apiculture and Sericulture, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Cluj-Napoca, 400372, Romania. .,Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany.
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, 20705, USA.
| | - Sophie Helbing
- Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany.
| | - Elke Karaus
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - H Michael G Lattorff
- Institut für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06120, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany. .,Institut für Biologie, Tierphysiologie, Martin-Luther-Universität Halle-Wittenberg, Wittenberg, 06099, Germany.
| | - Monika Marxer
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Ivan Meeus
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Kathrin Näpflin
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Jinzhi Niu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium. .,College of Plant Protection, Southwest University, Chongqing, 400716, PR China.
| | - Regula Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium. .,College of Plant Protection, Southwest University, Chongqing, 400716, PR China.
| | - Robert M Waterhouse
- Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland. .,Department of Genetic Medicine and Development, University of Geneva Medical School, 1211, Geneva, Switzerland. .,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Na Yu
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.
| | - Evgeny M Zdobnov
- Swiss Institute of Bioinformatics, 1211, Lausanne, Switzerland. .,Department of Genetic Medicine and Development, University of Geneva Medical School, 1211, Geneva, Switzerland.
| | - Paul Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.
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45
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Biewer M, Schlesinger F, Hasselmann M. The evolutionary dynamics of major regulators for sexual development among Hymenoptera species. Front Genet 2015; 6:124. [PMID: 25914717 PMCID: PMC4392698 DOI: 10.3389/fgene.2015.00124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/16/2015] [Indexed: 11/28/2022] Open
Abstract
All hymenopteran species, such as bees, wasps and ants, are characterized by the common principle of haplodiploid sex determination in which haploid males arise from unfertilized eggs and females from fertilized eggs. The underlying molecular mechanism has been studied in detail in the western honey bee Apis mellifera, in which the gene complementary sex determiner (csd) acts as primary signal of the sex determining pathway, initiating female development by csd-heterozygotes. Csd arose from gene duplication of the feminizer (fem) gene, a transformer (tra) ortholog, and mediates in conjunction with transformer2 (tra2) sex-specific splicing of fem. Comparative molecular analyses identified fem/tra and its downstream target doublesex (dsx) as conserved unit within the sex determining pathway of holometabolous insects. In this study, we aim to examine evolutionary differences among these key regulators. Our main hypothesis is that sex determining key regulators in Hymenoptera species show signs of coevolution within single phylogenetic lineages. We take advantage of several newly sequenced genomes of bee species to test this hypothesis using bioinformatic approaches. We found evidences that duplications of fem are restricted to certain bee lineages and notable amino acid differences of tra2 between Apis and non-Apis species propose structural changes in Tra2 protein affecting co-regulatory function on target genes. These findings may help to gain deeper insights into the ancestral mode of hymenopteran sex determination and support the common view of the remarkable evolutionary flexibility in this regulatory pathway.
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Affiliation(s)
- Matthias Biewer
- Population Genetics of Social Insects, Institute of Genetics, University of Cologne Cologne, Germany ; Livestock Population Genomics Group, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
| | - Francisca Schlesinger
- Population Genetics of Social Insects, Institute of Genetics, University of Cologne Cologne, Germany ; Institute of Bee Research Hohen Neuendorf, Germany
| | - Martin Hasselmann
- Population Genetics of Social Insects, Institute of Genetics, University of Cologne Cologne, Germany ; Livestock Population Genomics Group, Institute of Animal Science, University of Hohenheim Stuttgart, Germany
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46
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Korb J, Poulsen M, Hu H, Li C, Boomsma JJ, Zhang G, Liebig J. A genomic comparison of two termites with different social complexity. Front Genet 2015; 6:9. [PMID: 25788900 PMCID: PMC4348803 DOI: 10.3389/fgene.2015.00009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/09/2015] [Indexed: 11/15/2022] Open
Abstract
The termites evolved eusociality and complex societies before the ants, but have been studied much less. The recent publication of the first two termite genomes provides a unique comparative opportunity, particularly because the sequenced termites represent opposite ends of the social complexity spectrum. Zootermopsis nevadensis has simple colonies with totipotent workers that can develop into all castes (dispersing reproductives, nest-inheriting replacement reproductives, and soldiers). In contrast, the fungus-growing termite Macrotermes natalensis belongs to the higher termites and has very large and complex societies with morphologically distinct castes that are life-time sterile. Here we compare key characteristics of genomic architecture, focusing on genes involved in communication, immune defenses, mating biology and symbiosis that were likely important in termite social evolution. We discuss these in relation to what is known about these genes in the ants and outline hypothesis for further testing.
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Affiliation(s)
- Judith Korb
- Department of Evolutionary Biology and Ecology, Institute of Biology I, University of FreiburgFreiburg, Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
| | - Haofu Hu
- China National Genebank, BGI-ShenzhenShenzhen, China
| | - Cai Li
- China National Genebank, BGI-ShenzhenShenzhen, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of CopenhagenCopenhagen, Denmark
| | - Jacobus J. Boomsma
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, Centre for Social Evolution, University of CopenhagenCopenhagen, Denmark
- China National Genebank, BGI-ShenzhenShenzhen, China
| | - Jürgen Liebig
- School of Life Sciences, Arizona State UniversityTempe, AZ, USA
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47
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Helanterä H, d'Ettorre P. A comparative study of egg recognition signature mixtures in Formica ants. Evolution 2015; 69:520-9. [PMID: 25545864 DOI: 10.1111/evo.12590] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 12/04/2014] [Indexed: 11/28/2022]
Abstract
Processing of information from the environment, such as assessing group membership in social contexts, is a major determinant of inclusive fitness. For social insects, recognizing brood origin is crucial for inclusive fitness in many contexts, such as social parasitism and kin conflicts within colonies. Whether a recognition signature is informative in kin conflicts depends on the extent of a genetic contribution into the cues. We investigated colony- and matriline-specific variation in egg surface hydrocarbons in seven species of Formica ants. We show that chemical variance is distributed similarly to genetic variation, suggesting a significant genetic contribution to eggs odors in the genus. Significant among matriline components, and significant correlations between chemical and genetic similarity among individuals also indicate kin informative egg odors in several species. We suggest that egg odor surface variation could play a large role in within colony conflicts, and that a comparative method can reveal novel insight into communication of identity.
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Affiliation(s)
- Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Bioscience, University of Helsinki, Helsinki, Finland; Tvärminne Zoological Station, University of Helsinki, Helsinki, Finland.
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48
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Ross L, Blackmon H, Lorite P, Gokhman VE, Hardy NB. Recombination, chromosome number and eusociality in the Hymenoptera. J Evol Biol 2015; 28:105-16. [PMID: 25382409 PMCID: PMC4328152 DOI: 10.1111/jeb.12543] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 02/05/2023]
Abstract
Extraordinarily high rates of recombination have been observed in some eusocial species. The most popular explanation is that increased recombination increases genetic variation among workers, which in turn increases colony performance, for example by increasing parasite resistance. However, support for the generality of higher recombination rates among eusocial organisms remains weak, due to low sample size and a lack of phylogenetic independence of observations. Recombination rate, although difficult to measure directly, is correlated with chromosome number. As predicted, several authors have noted that chromosome numbers are higher among the eusocial species of Hymenoptera (ants, bees and wasps). Here, we present a formal comparative analysis of karyotype data from 1567 species of Hymenoptera. Contrary to earlier studies, we find no evidence for an absolute difference between chromosome number in eusocial and solitary species of Hymenoptera. However, we find support for an increased rate of chromosome number change in eusocial taxa. We show that among eusocial taxa colony size is able to explain some of the variation in chromosome number: intermediate-sized colonies have more chromosomes than those that are either very small or very large. However, we were unable to detect effects of a number of other colony characteristics predicted to affect recombination rate - including colony relatedness and caste number. Taken together, our results support the view that a eusocial lifestyle has led to variable selection pressure for increased recombination rates, but that identifying the factors contributing to this variable selection will require further theoretical and empirical effort.
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Affiliation(s)
- L Ross
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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49
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Park D, Jung JW, Choi BS, Jayakodi M, Lee J, Lim J, Yu Y, Choi YS, Lee ML, Park Y, Choi IY, Yang TJ, Edwards OR, Nah G, Kwon HW. Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. BMC Genomics 2015; 16:1. [PMID: 25553907 PMCID: PMC4326529 DOI: 10.1186/1471-2164-16-1] [Citation(s) in RCA: 448] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/02/2014] [Indexed: 12/03/2022] Open
Abstract
Background The honey bee is an important model system for increasing understanding of molecular and neural mechanisms underlying social behaviors relevant to the agricultural industry and basic science. The western honey bee, Apis mellifera, has served as a model species, and its genome sequence has been published. In contrast, the genome of the Asian honey bee, Apis cerana, has not yet been sequenced. A. cerana has been raised in Asian countries for thousands of years and has brought considerable economic benefits to the apicultural industry. A cerana has divergent biological traits compared to A. mellifera and it has played a key role in maintaining biodiversity in eastern and southern Asia. Here we report the first whole genome sequence of A. cerana. Results Using de novo assembly methods, we produced a 238 Mbp draft of the A. cerana genome and generated 10,651 genes. A.cerana-specific genes were analyzed to better understand the novel characteristics of this honey bee species. Seventy-two percent of the A. cerana-specific genes had more than one GO term, and 1,696 enzymes were categorized into 125 pathways. Genes involved in chemoreception and immunity were carefully identified and compared to those from other sequenced insect models. These included 10 gustatory receptors, 119 odorant receptors, 10 ionotropic receptors, and 160 immune-related genes. Conclusions This first report of the whole genome sequence of A. cerana provides resources for comparative sociogenomics, especially in the field of social insect communication. These important tools will contribute to a better understanding of the complex behaviors and natural biology of the Asian honey bee and to anticipate its future evolutionary trajectory. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-16-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Gyoungju Nah
- Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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50
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Transposable element islands facilitate adaptation to novel environments in an invasive species. Nat Commun 2014; 5:5495. [PMID: 25510865 PMCID: PMC4284661 DOI: 10.1038/ncomms6495] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 10/06/2014] [Indexed: 01/20/2023] Open
Abstract
Adaptation requires genetic variation, but founder populations are generally genetically depleted. Here we sequence two populations of an inbred ant that diverge in phenotype to determine how variability is generated. Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. A non-random distribution of gene families, larvae/adult specific gene expression and signs of differential methylation in TE islands indicate intragenomic differences in regulation, evolutionary rates and coalescent effective population size. Our study reveals a tripartite interplay between TEs, life history and adaptation in an invasive species. Genetic variation is key to species evolution. Here the authors sequence two phenotypically distinct populations of the ant Cardiocondyla obscurior, and find accumulations of transposable elements correlating with genetic variation that may have a role in differentiation, adaptation and speciation.
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