1
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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2
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Wyatt CDR, Bentley MA, Taylor D, Favreau E, Brock RE, Taylor BA, Bell E, Leadbeater E, Sumner S. Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps. Nat Commun 2023; 14:1046. [PMID: 36828829 PMCID: PMC9958023 DOI: 10.1038/s41467-023-36456-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/31/2023] [Indexed: 02/26/2023] Open
Abstract
A key mechanistic hypothesis for the evolution of division of labour in social insects is that a shared set of genes co-opted from a common solitary ancestral ground plan (a genetic toolkit for sociality) regulates caste differentiation across levels of social complexity. Using brain transcriptome data from nine species of vespid wasps, we test for overlap in differentially expressed caste genes and use machine learning models to predict castes using different gene sets. We find evidence of a shared genetic toolkit across species representing different levels of social complexity. We also find evidence of additional fine-scale differences in predictive gene sets, functional enrichment and rates of gene evolution that are related to level of social complexity, lineage and of colony founding. These results suggest that the concept of a shared genetic toolkit for sociality may be too simplistic to fully describe the process of the major transition to sociality.
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Affiliation(s)
- Christopher Douglas Robert Wyatt
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK.
| | - Michael Andrew Bentley
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Daisy Taylor
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Emeline Favreau
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Ryan Edward Brock
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Benjamin Aaron Taylor
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Emily Bell
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Ellouise Leadbeater
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK.
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3
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Favreau E, Geist KS, Wyatt CDR, Toth AL, Sumner S, Rehan SM. Co-expression Gene Networks and Machine-learning Algorithms Unveil a Core Genetic Toolkit for Reproductive Division of Labour in Rudimentary Insect Societies. Genome Biol Evol 2022; 15:6926469. [PMID: 36527688 PMCID: PMC9830183 DOI: 10.1093/gbe/evac174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
The evolution of eusociality requires that individuals forgo some or all their own reproduction to assist the reproduction of others in their group, such as a primary egg-laying queen. A major open question is how genes and genetic pathways sculpt the evolution of eusociality, especially in rudimentary forms of sociality-those with smaller cooperative nests when compared with species such as honeybees that possess large societies. We lack comprehensive comparative studies examining shared patterns and processes across multiple social lineages. Here we examine the mechanisms of molecular convergence across two lineages of bees and wasps exhibiting such rudimentary societies. These societies consist of few individuals and their life histories range from facultative to obligately social. Using six species across four independent origins of sociality, we conduct a comparative meta-analysis of publicly available transcriptomes. Standard methods detected little similarity in patterns of differential gene expression in brain transcriptomes among reproductive and non-reproductive individuals across species. By contrast, both supervised machine learning and consensus co-expression network approaches uncovered sets of genes with conserved expression patterns among reproductive and non-reproductive phenotypes across species. These sets overlap substantially, and may comprise a shared genetic "toolkit" for sociality across the distantly related taxa of bees and wasps and independently evolved lineages of sociality. We also found many lineage-specific genes and co-expression modules associated with social phenotypes and possible signatures of shared life-history traits. These results reveal how taxon-specific molecular mechanisms complement a core toolkit of molecular processes in sculpting traits related to the evolution of eusociality.
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Affiliation(s)
| | | | - Christopher D R Wyatt
- Department of Genetics, Environment, Evolution, University College London, London WC1E 6BT, United Kingdom
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4
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Tong C, Avilés L, Rayor LS, Mikheyev AS, Linksvayer TA. Genomic signatures of recent convergent transitions to social life in spiders. Nat Commun 2022; 13:6967. [PMID: 36414623 PMCID: PMC9681848 DOI: 10.1038/s41467-022-34446-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Leticia Avilés
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Linda S Rayor
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander S Mikheyev
- Evolutionary Genomics Group, Research School of Biology, Australian National University, Canberra, 0200, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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5
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Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proc Natl Acad Sci U S A 2022; 119:2110361119. [PMID: 35042774 PMCID: PMC8785959 DOI: 10.1073/pnas.2110361119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
Gene duplication is a major source of evolutionary innovation and is associated with the increases in biological complexity and adaptive radiation. Termites are model social organisms characterized by a sophisticated caste system. We analyzed the genome of the Japanese subterranean termite, an ecologically and economically important insect acting as a destructive pest. The analyses revealed the significance of gene duplication in social evolution. Gene duplication associated with caste-biased gene expression was prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity, and defense, and they were often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome, and methylome of the Japanese subterranean termite Reticulitermes speratus. Our analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression was prevalent in the R. speratus genome. The duplicated genes comprised diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense), and a novel class of termite lineage–specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but their expression patterns were highly variable, exhibiting caste biases. Some of the assayed duplicated genes were expressed in caste-specific organs, such as the accessory glands of the queen ovary and the frontal glands of soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization conferring caste-specialized functions.
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6
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Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. Sci Rep 2021; 11:3654. [PMID: 33574391 PMCID: PMC7878513 DOI: 10.1038/s41598-020-75432-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/05/2020] [Indexed: 01/30/2023] Open
Abstract
A striking feature of advanced insect societies is the existence of workers that forgo reproduction. Two broad types of workers exist in eusocial bees: nurses who care for their young siblings and the queen, and foragers who guard the nest and forage for food. Comparisons between these two worker subcastes have been performed in honeybees, but data from other bees are scarce. To understand whether similar molecular mechanisms are involved in nurse-forager differences across distinct species, we compared gene expression and DNA methylation profiles between nurses and foragers of the buff-tailed bumblebee Bombus terrestris and the stingless bee Tetragonisca angustula. These datasets were then compared to previous findings from honeybees. Our analyses revealed that although the expression pattern of genes is often species-specific, many of the biological processes and molecular pathways involved are common. Moreover, the correlation between gene expression and DNA methylation was dependent on the nucleotide context, and non-CG methylation appeared to be a relevant factor in the behavioral changes of the workers. In summary, task specialization in worker bees is characterized by a plastic and mosaic molecular pattern, with species-specific mechanisms acting upon broad common pathways across species.
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7
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Collins DH, Wirén A, Labédan M, Smith M, Prince DC, Mohorianu I, Dalmay T, Bourke AFG. Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees. Mol Ecol 2021; 30:718-735. [PMID: 33238067 PMCID: PMC7898649 DOI: 10.1111/mec.15752] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022]
Abstract
The queen‐worker caste system of eusocial insects represents a prime example of developmental polyphenism (environmentally‐induced phenotypic polymorphism) and is intrinsic to the evolution of advanced eusociality. However, the comparative molecular basis of larval caste determination and subsequent differentiation in the eusocial Hymenoptera remains poorly known. To address this issue within bees, we profiled caste‐associated gene expression in female larvae of the intermediately eusocial bumblebee Bombus terrestris. In B. terrestris, female larvae experience a queen‐dependent period during which their caste fate as adults is determined followed by a nutrition‐sensitive period also potentially affecting caste fate but for which the evidence is weaker. We used mRNA‐seq and qRT‐PCR validation to isolate genes differentially expressed between each caste pathway in larvae at developmental stages before and after each of these periods. We show that differences in gene expression between caste pathways are small in totipotent larvae, then peak after the queen‐dependent period. Relatively few novel (i.e., taxonomically‐restricted) genes were differentially expressed between castes, though novel genes were significantly enriched in late‐instar larvae in the worker pathway. We compared sets of caste‐associated genes in B. terrestris with those reported from the advanced eusocial honeybee, Apis mellifera, and found significant but relatively low levels of overlap of gene lists between the two species. These results suggest both the existence of low numbers of shared toolkit genes and substantial divergence in caste‐associated genes between Bombus and the advanced eusocial Apis since their last common eusocial ancestor.
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Affiliation(s)
- David H Collins
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Anders Wirén
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marjorie Labédan
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michael Smith
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - David C Prince
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Jeffrey Cheah Biomedical Centre, WT-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich, UK
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8
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Harrison MC, Chernyshova AM, Thompson GJ. No obvious transcriptome-wide signature of indirect selection in termites. J Evol Biol 2020; 34:403-415. [PMID: 33290587 DOI: 10.1111/jeb.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 11/26/2022]
Abstract
The evolution of sterile helper castes in social insects implies selection on genes that underlie variation in this nonreproductive phenotype. These focal genes confer no direct fitness and are presumed to evolve through indirect fitness effects on the helper's reproducing relatives. This separation of a gene's phenotypic effect on one caste and its fitness effect on another suggests that genes for this and other forms of reproductive altruism are buffered from selection and will thus evolve closer to the neutral rate than genes directly selected for selfish reproduction. We test this hypothesis by comparing the strength of selection at loci associated in their expression with reproductive versus sterile castes in termites. Specifically, we gather caste-biased gene expression data from four termite transcriptomes and measure the global dN/dS ratio across gene sets and phylogenetic lineages. We find that the majority of examined orthologous gene groups show patterns of nucleotide substitution that are consistent with strong purifying selection and display little evidence for distinct signatures of direct versus indirect selection in reproductive and sterile castes. For one particular species (Reticulitermes flavipes), the strength of purifying selection is relaxed in a reproductive nymph-biased gene set, which opposes the nearly neutral idea. In other species, the synonymous rate (dS) alone was often found to be the highest in the sterile worker caste, suggesting a more subtle signature of indirect selection or an altogether different relationship between caste-biased expression and rates of molecular evolution.
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Affiliation(s)
- Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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9
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Holland JG, Bloch G. The Complexity of Social Complexity: A Quantitative Multidimensional Approach for Studies of Social Organization. Am Nat 2020; 196:525-540. [PMID: 33064587 DOI: 10.1086/710957] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractThe rapid increase in "big data" during the postgenomic era makes it crucial to appropriately measure the level of social complexity in comparative studies. We argue that commonly used qualitative classifications lump together species showing a broad range of social complexity and falsely imply that social evolution always progresses along a single linear stepwise trajectory that can be deduced from comparing extant species. To illustrate this point, we compared widely used social complexity measures in "primitively eusocial" bumble bees with "advanced eusocial" stingless bees, honey bees, and attine ants. We find that a single species can have both higher and lower levels of complexity compared with other taxa, depending on the social trait measured. We propose that measuring the complexity of individual social traits switches focus from semantic discussions and offers several directions for progress. First, quantitative social traits can be correlated with molecular, developmental, and physiological processes within and across lineages of social animals. This approach is particularly promising for identifying processes that influence or have been affected by social evolution. Second, key social complexity traits can be combined into multidimensional lineage-specific quantitative indices, enabling fine-scale comparison across species that are currently bundled within the same level of social complexity.
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10
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Kapheim KM, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, Ben-Shahar Y. Brain microRNAs among social and solitary bees. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200517. [PMID: 32874647 PMCID: PMC7428247 DOI: 10.1098/rsos.200517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
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Affiliation(s)
- Karen M. Kapheim
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
- Author for correspondence: Karen M. Kapheim e-mail:
| | - Beryl M. Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eirik Søvik
- Department of Science and Mathematics, Volda University College, 6100 Volda, Norway
| | - Eckart Stolle
- Centre of Molecular Biodiversity Research, Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Guy Bloch
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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11
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Linksvayer TA, Johnson BR. Re-thinking the social ladder approach for elucidating the evolution and molecular basis of insect societies. CURRENT OPINION IN INSECT SCIENCE 2019; 34:123-129. [PMID: 31401545 DOI: 10.1016/j.cois.2019.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/21/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
The evolution of large insect societies is a major evolutionary transition that occurred in the long-extinct ancestors of termites, ants, corbiculate bees, and vespid wasps. Researchers have long used 'social ladder thinking': assuming progressive stepwise phenotypic evolution and asserting that extant species with simple societies (e.g. some halictid bees) represent the ancestors of species with complex societies, and thus provide insight into general early steps of eusocial evolution. We discuss how this is inconsistent with data and modern evolutionary 'tree thinking'. Phylogenetic comparative methods with broad sampling provide the best means to make rigorous inferences about ancestral traits and evolutionary transitions that occurred within each lineage, and to determine whether consistent phenotypic and genomic changes occurred across independent lineages.
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Affiliation(s)
| | - Brian R Johnson
- Department of Entomology and Nematology, University of California Davis, United States
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12
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Cini A, Sumner S, Cervo R. Inquiline social parasites as tools to unlock the secrets of insect sociality. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180193. [PMID: 30967091 PMCID: PMC6388031 DOI: 10.1098/rstb.2018.0193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2018] [Indexed: 01/07/2023] Open
Abstract
Insect societies play a crucial role in the functioning of most ecosystems and have fascinated both scientists and the lay public for centuries. Despite the long history of study, we are still far from understanding how insect societies have evolved and how social cohesion in their colonies is maintained. Here we suggest inquiline social parasites of insect societies as an under-exploited experimental tool for understanding sociality. We draw on examples from obligate inquiline (permanent) social parasites in wasps, ants and bees to illustrate how these parasites may allow us to better understand societies and learn more about the evolution and functioning of insect societies. We highlight three main features of these social parasite-host systems-namely, close phylogenetic relationships, strong selective pressures arising from coevolution and multiple independent origins-that make inquiline social parasites particularly suited for this aim; we propose a conceptual comparative framework that considers trait losses, gains and modifications in social parasite-host systems. We give examples of how this framework can reveal the more elusive secrets of sociality by focusing on two cornerstones of sociality: communication and reproductive division of labour. Together with social parasites in other taxonomic groups, such as cuckoos in birds, social parasitism has a great potential to reveal the mechanisms and evolution of complex social groups. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
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Affiliation(s)
- Alessandro Cini
- Centre for Biodiversity and Environment Research, University College London, Gower Street, London WC1E 6BT, UK
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano, 6, 50019 Sesto Fiorentino, Italy
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, University College London, Gower Street, London WC1E 6BT, UK
| | - Rita Cervo
- Dipartimento di Biologia, Università degli Studi di Firenze, Via Madonna del Piano, 6, 50019 Sesto Fiorentino, Italy
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13
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Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. Life (Basel) 2018; 9:life9010002. [PMID: 30583535 PMCID: PMC6463014 DOI: 10.3390/life9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 01/03/2023] Open
Abstract
Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus–Fusarium euwallaceae and Xyleborus glabratus–Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.
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14
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Kocher SD. A toolkit for caste differentiation. Nat Ecol Evol 2018; 2:1689-1690. [DOI: 10.1038/s41559-018-0705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Qiu B, Larsen RS, Chang NC, Wang J, Boomsma JJ, Zhang G. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat Ecol Evol 2018; 2:1782-1791. [PMID: 30349091 PMCID: PMC6217981 DOI: 10.1038/s41559-018-0689-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
Specialized queens and life-time unmated workers evolved once in the common ancestor of all ants, but whether caste development across ants continues to be at least partly regulated by a single core set of genes remains obscure. We analysed brain transcriptomes from five ant species (three subfamilies) and reconstructed the origins of genes with caste-biased expression. Ancient genes predating the Neoptera were more likely to regulate gyne (virgin queen) phenotypes, while caste differentiation roles of younger, ant-lineage-specific genes varied. Transcriptome profiling showed that the ancestral network for caste-specific gene-regulation has been maintained, but that signatures of common ancestry are obscured by later modifications. Adjusting for such differences, we identified a core gene-set that: 1. consistently displayed similar directions and degrees of caste-differentiated expression, and 2. have mostly not been reported as being involved in caste differentiation. These core regulatory genes exist in the genomes of ant species that secondarily lost the queen caste, but expression differences for reproductive and sterile workers are minor and similar to social paper wasps that lack differentiated castes. Many caste-biased ant genes have caste-differentiated expression in honeybees, but directions of caste bias were uncorrelated, as expected when permanent castes evolved independently in both lineages.
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Affiliation(s)
- Bitao Qiu
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Stenbak Larsen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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16
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Alleman A, Feldmeyer B, Foitzik S. Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes. Sci Rep 2018; 8:1951. [PMID: 29386535 PMCID: PMC5792630 DOI: 10.1038/s41598-018-20262-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/15/2018] [Indexed: 01/08/2023] Open
Abstract
The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure. We are the first to confirm this at the molecular level, revealing that slavemaking species exhibit a wider variety of genes with species-specific patterns of expression within their raiding phenotypes, whereas expression similarity is commonly found during the non-raiding phenotype. Host species response to slavemaker aggression, however, is indicated by strong changes in the expression of a relatively few number genes. Additionally, the expression of individual genes such as Acyl-CoA-Delta(11) desaturase and Trypsin-7 is strongly associated with the raiding phenotype of all three slavemaking species. Here, we provide novel insight into the gene expression patterns associated with raiding and nest defense behavior in Temnothorax ants, suggesting lineage-specific evolutionary patterns among both slavemakers and hosts.
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Affiliation(s)
- Austin Alleman
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany.
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Johannes von Müller Weg 6, Mainz, 55128, Germany
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17
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Wu T, Dhami GK, Thompson GJ. Soldier‐biased gene expression in a subterranean termite implies functional specialization of the defensive caste. Evol Dev 2017; 20:3-16. [DOI: 10.1111/ede.12243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Tian Wu
- Biology DepartmentWestern UniversityLondonOntarioCanada
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18
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Warner MR, Mikheyev AS, Linksvayer TA. Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers. Mol Biol Evol 2017; 34:1780-1787. [PMID: 28419349 PMCID: PMC5455959 DOI: 10.1093/molbev/msx123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Kin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes experienced reduced selection compared with genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also experienced reduced selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
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19
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Chau LM, Goodisman MAD. Gene duplication and the evolution of phenotypic diversity in insect societies. Evolution 2017; 71:2871-2884. [PMID: 28875541 DOI: 10.1111/evo.13356] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 12/16/2022]
Abstract
Gene duplication is an important evolutionary process thought to facilitate the evolution of phenotypic diversity. We investigated if gene duplication was associated with the evolution of phenotypic differences in a highly social insect, the honeybee Apis mellifera. We hypothesized that the genetic redundancy provided by gene duplication could promote the evolution of social and sexual phenotypes associated with advanced societies. We found a positive correlation between sociality and rate of gene duplications across the Apoidea, indicating that gene duplication may be associated with sociality. We also discovered that genes showing biased expression between A. mellifera alternative phenotypes tended to be found more frequently than expected among duplicated genes than singletons. Moreover, duplicated genes had higher levels of caste-, sex-, behavior-, and tissue-biased expression compared to singletons, as expected if gene duplication facilitated phenotypic differentiation. We also found that duplicated genes were maintained in the A. mellifera genome through the processes of conservation, neofunctionalization, and specialization, but not subfunctionalization. Overall, we conclude that gene duplication may have facilitated the evolution of social and sexual phenotypes, as well as tissue differentiation. Thus this study further supports the idea that gene duplication allows species to evolve an increased range of phenotypic diversity.
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Affiliation(s)
- Linh M Chau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Michael A D Goodisman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332
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20
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Abstract
The study of insect social behavior has offered tremendous insight into the molecular mechanisms mediating behavioral and phenotypic plasticity. Genomic applications to the study of eusocial insect species, in particular, have led to several hypotheses for the processes underlying the molecular evolution of behavior. Advances in understanding the genetic control of social organization have also been made, suggesting an important role for supergenes in the evolution of divergent behavioral phenotypes. Intensive study of social phenotypes across species has revealed that behavior and caste are controlled by an interaction between genetic and environmentally mediated effects and, further, that gene expression and regulation mediate plastic responses to environmental signals. However, several key methodological flaws that are hindering progress in the study of insect social behavior remain. After reviewing the current state of knowledge, we outline ongoing challenges in experimental design that remain to be overcome in order to advance the field.
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Affiliation(s)
- Chelsea A Weitekamp
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
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21
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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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22
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Collins DH, Mohorianu I, Beckers M, Moulton V, Dalmay T, Bourke AFG. MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect. Sci Rep 2017; 7:45674. [PMID: 28361900 PMCID: PMC5374498 DOI: 10.1038/srep45674] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/02/2017] [Indexed: 01/08/2023] Open
Abstract
In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically arise via environmental influences. A fundamental challenge is to understand how a single genome can thereby produce alternative phenotypes. A powerful approach is to compare the molecular basis of caste determination and differentiation along the evolutionary trajectory between primitively and advanced eusocial species, which have, respectively, relatively undifferentiated and strongly differentiated adult castes. In the advanced eusocial honeybee, Apis mellifera, studies suggest that microRNAs (miRNAs) play an important role in the molecular basis of caste determination and differentiation. To investigate how miRNAs affect caste in eusocial evolution, we used deep sequencing and Northern blots to isolate caste-associated miRNAs in the primitively eusocial bumblebee Bombus terrestris. We found that the miRNAs Bte-miR-6001-5p and -3p are more highly expressed in queen- than in worker-destined late-instar larvae. These are the first caste-associated miRNAs from outside advanced eusocial Hymenoptera, so providing evidence for caste-associated miRNAs occurring relatively early in eusocial evolution. Moreover, we found little evidence that miRNAs previously shown to be associated with caste in A. mellifera were differentially expressed across caste pathways in B. terrestris, suggesting that, in eusocial evolution, the caste-associated role of individual miRNAs is not conserved.
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Affiliation(s)
- David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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23
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Toth AL, Rehan SM. Molecular Evolution of Insect Sociality: An Eco-Evo-Devo Perspective. ANNUAL REVIEW OF ENTOMOLOGY 2017; 62:419-442. [PMID: 27912247 DOI: 10.1146/annurev-ento-031616-035601] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes. Despite this proliferation of ideas, there has been little synthesis, even though these ideas are not mutually exclusive and may in fact be complementary. We review available data on molecular evolution of insect sociality and highlight key biotic and abiotic factors influencing social insect genomes. We then suggest both phylogenetic and ecological evolutionary developmental biology (eco-evo-devo) perspectives for a more synthetic view of molecular evolution in insect societies.
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Affiliation(s)
- Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011;
- Department of Entomology, Iowa State University, Ames, Iowa 50011
| | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire 03824;
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24
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McKenzie SK, Fetter-Pruneda I, Ruta V, Kronauer DJC. Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication. Proc Natl Acad Sci U S A 2016; 113:14091-14096. [PMID: 27911792 PMCID: PMC5150400 DOI: 10.1073/pnas.1610800113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A major aim of sociogenomic research is to uncover common principles in the molecular evolution of sociality. This endeavor has been hampered by the small number of specific genes currently known to function in social behavior. Here we provide several lines of evidence suggesting that ants have evolved a large and novel clade of odorant receptor (OR) genes to perceive hydrocarbon-based pheromones, arguably the most important signals in ant communication. This genomic expansion is also mirrored in the ant brain via a corresponding expansion of a specific cluster of glomeruli in the antennal lobe. We show that in the clonal raider ant, hydrocarbon-sensitive basiconic sensilla are found only on the ventral surface of the female antennal club. Correspondingly, nearly all genes in a clade of 180 ORs within the 9-exon subfamily of ORs are expressed exclusively in females and are highly enriched in expression in the ventral half of the antennal club. Furthermore, we found that across species and sexes, the number of 9-exon ORs expressed in antennae is tightly correlated with the number of glomeruli in the antennal lobe region innervated by odorant receptor neurons from basiconic sensilla. Evolutionary analyses show that this clade underwent a striking gene expansion in the ancestors of all ants and slower but continued expansion in extant ant lineages. This evidence suggests that ants have evolved a large clade of genes to support pheromone perception and that gene duplications have played an important role in the molecular evolution of ant communication.
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Affiliation(s)
- Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065;
| | - Ingrid Fetter-Pruneda
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065
| | - Vanessa Ruta
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY 10065
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065
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25
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Linksvayer TA, Wade MJ. Theoretical Predictions for Sociogenomic Data: The Effects of Kin Selection and Sex-Limited Expression on the Evolution of Social Insect Genomes. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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26
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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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27
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Standage DS, Berens AJ, Glastad KM, Severin AJ, Brendel VP, Toth AL. Genome, transcriptome and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylation system in a social insect. Mol Ecol 2016; 25:1769-84. [PMID: 26859767 DOI: 10.1111/mec.13578] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 01/04/2023]
Abstract
Comparative genomics of social insects has been intensely pursued in recent years with the goal of providing insights into the evolution of social behaviour and its underlying genomic and epigenomic basis. However, the comparative approach has been hampered by a paucity of data on some of the most informative social forms (e.g. incipiently and primitively social) and taxa (especially members of the wasp family Vespidae) for studying social evolution. Here, we provide a draft genome of the primitively eusocial model insect Polistes dominula, accompanied by analysis of caste-related transcriptome and methylome sequence data for adult queens and workers. Polistes dominula possesses a fairly typical hymenopteran genome, but shows very low genomewide GC content and some evidence of reduced genome size. We found numerous caste-related differences in gene expression, with evidence that both conserved and novel genes are related to caste differences. Most strikingly, these -omics data reveal a major reduction in one of the major epigenetic mechanisms that has been previously suggested to be important for caste differences in social insects: DNA methylation. Along with a conspicuous loss of a key gene associated with environmentally responsive DNA methylation (the de novo DNA methyltransferase Dnmt3), these wasps have greatly reduced genomewide methylation to almost zero. In addition to providing a valuable resource for comparative analysis of social insect evolution, our integrative -omics data for this important behavioural and evolutionary model system call into question the general importance of DNA methylation in caste differences and evolution in social insects.
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Affiliation(s)
- Daniel S Standage
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Ali J Berens
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew J Severin
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.,Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.,School of Informatics and Computing, Indiana University, Bloomington, IN, 47405, USA
| | - Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.,Department of Entomology, Iowa State University, Ames, IA, 50011, USA
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28
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Morandin C, Tin MMY, Abril S, Gómez C, Pontieri L, Schiøtt M, Sundström L, Tsuji K, Pedersen JS, Helanterä H, Mikheyev AS. Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol 2016; 17:43. [PMID: 26951146 PMCID: PMC4780134 DOI: 10.1186/s13059-016-0902-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species. RESULTS Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another. CONCLUSIONS These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland.
| | - Mandy M Y Tin
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Crisanto Gómez
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Luigi Pontieri
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Jes Søe Pedersen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, 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.
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29
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30
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31
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Amsalem E, Galbraith DA, Cnaani J, Teal PEA, Grozinger CM. Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens. Mol Ecol 2015; 24:5596-615. [PMID: 26453894 DOI: 10.1111/mec.13410] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 02/02/2023]
Abstract
Diapause is the key adaptation allowing insects to survive unfavourable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species and are hypothesized to be regulated by a conserved suite of genes (a 'toolkit'). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens, we examined the physiological and transcriptomic changes associated with diapause and CO2 treatment, which causes queens to bypass diapause. We performed comparative analyses with genes previously identified to be associated with diapause in the Dipteran Sarcophaga crassipalpis and with caste differentiation in bumble bees. As in Diptera, diapause in bumble bees is associated with physiological and transcriptional changes related to nutrient storage, stress resistance and core metabolic pathways. There is a significant overlap, both at the level of transcript and gene ontology, between the genetic mechanisms mediating diapause in B. terrestris and S. crassipalpis, reaffirming the existence of a conserved insect diapause genetic toolkit. However, a substantial proportion (10%) of the differentially regulated transcripts in diapausing queens have no clear orthologs in other species, and key players regulating diapause in Diptera (juvenile hormone and vitellogenin) appear to have distinct functions in bumble bees. We also found a substantial overlap between genes related to caste determination and diapause in bumble bees. Thus, our studies demonstrate an intriguing interplay between pathways underpinning adaptation to environmental extremes and the evolution of sociality in insects.
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Affiliation(s)
- Etya Amsalem
- Department of Entomology, Center for Pollinator Research, Center for Chemical Ecology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - David A Galbraith
- Department of Entomology, Center for Pollinator Research, Center for Chemical Ecology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Peter E A Teal
- Chemistry Research Unit, US Department of Agriculture, 1600-1700 SW, 23rd Drive, Gainesville, FL, 32608, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Center for Chemical Ecology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
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32
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Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies. Proc Natl Acad Sci U S A 2015; 112:13970-5. [PMID: 26483466 DOI: 10.1073/pnas.1515937112] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.
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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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Cini A, Patalano S, Segonds-Pichon A, Busby GBJ, Cervo R, Sumner S. Social parasitism and the molecular basis of phenotypic evolution. Front Genet 2015; 6:32. [PMID: 25741361 PMCID: PMC4332356 DOI: 10.3389/fgene.2015.00032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/23/2015] [Indexed: 11/21/2022] Open
Abstract
Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization.
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Affiliation(s)
- Alessandro Cini
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Solenn Patalano
- Institute of Zoology, Zoological Society of LondonLondon, UK
- The Babraham Institute, Babraham Research Campus – CambridgeCambridge, UK
| | | | - George B. J. Busby
- Institute of Zoology, Zoological Society of LondonLondon, UK
- Wellcome Trust Centre for Human GeneticsOxford, UK
| | - Rita Cervo
- Dipartimento di Biologia, Università di FirenzeFirenze, Italy
| | - Seirian Sumner
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Biological Sciences, University of BristolBristol, UK
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Mikheyev AS, Linksvayer TA. Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns. eLife 2015; 4:e04775. [PMID: 25621766 PMCID: PMC4383337 DOI: 10.7554/elife.04775] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/23/2015] [Indexed: 11/24/2022] Open
Abstract
Studies of the genetic basis and evolution of complex social behavior emphasize
either conserved or novel genes. To begin to reconcile these perspectives, we studied
how the evolutionary conservation of genes associated with social behavior depends on
regulatory context, and whether genes associated with social behavior exist in
distinct regulatory and evolutionary contexts. We identified modules of co-expressed
genes associated with age-based division of labor between nurses and foragers in the
ant Monomorium pharaonis, and we studied the relationship between
molecular evolution, connectivity, and expression. Highly connected and expressed
genes were more evolutionarily conserved, as expected. However, compared to the rest
of the genome, forager-upregulated genes were much more highly connected and
conserved, while nurse-upregulated genes were less connected and more evolutionarily
labile. Our results indicate that the genetic architecture of social behavior
includes both highly connected and conserved components as well as loosely connected
and evolutionarily labile components. DOI:http://dx.doi.org/10.7554/eLife.04775.001 Animal species vary widely in their degree of social behavior. Some species live
solitarily, and others, such as ants and humans, form large societies. Many
researchers have tried to understand the genetic changes underlying the evolution of
social behavior. Some researchers suggest that it involves recycling existing genes
that also have other conserved functions. Others propose that the evolution of social
behavior involves completely new genes that are not found in related but solitary
species. Ants are one of the best-studied social animals. An established colony can contain
many 1000s of individuals that live and work together and perform different roles.
The queen's job is to lay eggs, while the worker ants do everything else,
including collecting food, caring for the young, and protecting the colony. In some
species of ant—including the pharaoh ant—a worker's role changes
as it ages. Younger workers tend to stay in the nest and nurse the brood, while older
workers tend to leave the nest and forage for food. Mikheyev and Linksvayer asked: which genes are responsible for this age-based
division of labor? And how did this aspect of social behavior evolve? First, after
observing pharaoh ants from two colonies set up in the laboratory, they confirmed
that workers nursing the brood were on average almost a week younger than those seen
collecting food. Next Mikheyev and Linksvayer identified which genes were expressed
in ants of different ages, or ants engaged in different tasks. Specific sets of genes
were expressed more (or ‘up-regulated’) in nurse workers, while others
were up-regulated in foraging workers. Mikheyev and Linksvayer then investigated how rapidly these genes had evolved by
comparing them to related genes found in other social insects (fire ants and honey
bees). They also determined the ‘connectivity’ of these genes by asking
how many other genes showed similar expression patterns. In many organisms, how
rapidly a gene evolves depends on how tightly connected its expression is to the
expression of other genes; highly connected genes evolve more slowly. The genes that were expressed more in the older foraging workers were both more
highly connected and more evolutionarily conserved in the other social insects. Genes
that were up-regulated in the younger nurse workers were more loosely connected and
rapidly evolving. Mikheyev and Linksvayer's findings show that the evolution of social behavior
in animals involves both new genes, which tend to be loosely connected, and conserved
genes, which tend to be more highly connected. DOI:http://dx.doi.org/10.7554/eLife.04775.002
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Affiliation(s)
- Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
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Molodtsova D, Harpur BA, Kent CF, Seevananthan K, Zayed A. Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviors. Front Genet 2014; 5:431. [PMID: 25566318 PMCID: PMC4275039 DOI: 10.3389/fgene.2014.00431] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/21/2014] [Indexed: 11/13/2022] Open
Abstract
It is increasingly apparent that genes and networks that influence complex behavior are evolutionary conserved, which is paradoxical considering that behavior is labile over evolutionary timescales. How does adaptive change in behavior arise if behavior is controlled by conserved, pleiotropic, and likely evolutionary constrained genes? Pleiotropy and connectedness are known to constrain the general rate of protein evolution, prompting some to suggest that the evolution of complex traits, including behavior, is fuelled by regulatory sequence evolution. However, we seldom have data on the strength of selection on mutations in coding and regulatory sequences, and this hinders our ability to study how pleiotropy influences coding and regulatory sequence evolution. Here we use population genomics to estimate the strength of selection on coding and regulatory mutations for a transcriptional regulatory network that influences complex behavior of honey bees. We found that replacement mutations in highly connected transcription factors and target genes experience significantly stronger negative selection relative to weakly connected transcription factors and targets. Adaptively evolving proteins were significantly more likely to reside at the periphery of the regulatory network, while proteins with signs of negative selection were near the core of the network. Interestingly, connectedness and network structure had minimal influence on the strength of selection on putative regulatory sequences for both transcription factors and their targets. Our study indicates that adaptive evolution of complex behavior can arise because of positive selection on protein-coding mutations in peripheral genes, and on regulatory sequence mutations in both transcription factors and their targets throughout the network.
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Affiliation(s)
| | - Brock A Harpur
- Department of Biology, York University Toronto, ON, Canada
| | - Clement F Kent
- Department of Biology, York University Toronto, ON, Canada
| | | | - Amro Zayed
- Department of Biology, York University Toronto, ON, Canada
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Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. Proc Natl Acad Sci U S A 2014; 111:17929-34. [PMID: 25453090 DOI: 10.1073/pnas.1420369111] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.
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Jasper WC, Linksvayer TA, Atallah J, Friedman D, Chiu JC, Johnson BR. Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees. Mol Biol Evol 2014; 32:334-46. [PMID: 25351750 DOI: 10.1093/molbev/msu292] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolution of novel phenotypes in the adult organism is unclear. Here, we conduct ten RNA-Seq experiments across both novel and conserved tissues in the honey bee to determine to what extent postdevelopmental novelty is based on changes to the coding regions of genes. We make several discoveries. First, we show that with respect to novel physiological functions in the adult animal, positively selected tissue-specific genes of high expression underlie novelty by conferring specialized cellular functions. Such genes are often, but not always taxonomically restricted genes (TRGs). We further show that positively selected genes, whether TRGs or conserved genes, are the least connected genes within gene expression networks. Overall, this work suggests that the evo-devo paradigm is limited, and that the evolution of novelty, postdevelopment, follows additional rules. Specifically, evo-devo stresses that high network connectedness (repeated use of the same gene in many contexts) constrains coding sequence change as it would lead to negative pleiotropic effects. Here, we show that in the adult animal, the converse is true: Genes with low network connectedness (TRGs and tissue-specific conserved genes) underlie novel phenotypes by rapidly changing coding sequence to perform new-specialized functions.
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Affiliation(s)
| | | | - Joel Atallah
- Department of Evolution and Ecology, University of California-Davis
| | - Daniel Friedman
- Department of Evolution and Ecology, University of California-Davis
| | - Joanna C Chiu
- Department of Entomology, University of California-Davis
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39
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Zuk M, Balenger SL. Behavioral ecology and genomics: new directions, or just a more detailed map? Behav Ecol 2014. [DOI: 10.1093/beheco/aru172] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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