1
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Ewart KM, Ho SYW, Chowdhury AA, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc Biol Sci 2024; 291:20232439. [PMID: 38772424 DOI: 10.1098/rspb.2023.2439] [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: 10/30/2023] [Accepted: 05/02/2024] [Indexed: 05/23/2024] Open
Abstract
Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we analysed nine genomes, including newly sequenced genomes from three non-eusocial cockroaches. Using a phylogenomic approach, we found that termite genomes have experienced lower rates of synonymous substitutions than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of non-synonymous substitutions in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24-31% of the genes analysed) compared with the latter (2-4%). We infer that this is due to reductions in effective population size, rather than gene-specific effects (e.g. indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging of deleterious alleles at the colony level. Additionally, we identified genomic adaptations that may underpin caste differentiation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Frederick R Jaya
- Ecology & Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Okinawa International University, Okinawa, Japan
| | - Juno Bennett
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Harley A Rose
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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2
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Pyenson BC, Rehan SM. Gene regulation supporting sociality shared across lineages and variation in complexity. Genome 2024; 67:99-108. [PMID: 38096504 DOI: 10.1139/gen-2023-0054] [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] [Indexed: 01/25/2024]
Abstract
Across evolutionary lineages, insects vary in social complexity, from those that exhibit extended parental care to those with elaborate divisions of labor. Here, we synthesize the sociogenomic resources from hundreds of species to describe common gene regulatory mechanisms in insects that regulate social organization across phylogeny and levels of social complexity. Different social phenotypes expressed by insects can be linked to the organization of co-expressing gene networks and features of the epigenetic landscape. Insect sociality also stems from processes like the emergence of parental care and the decoupling of ancestral genetic programs. One underexplored avenue is how variation in a group's social environment affects the gene expression of individuals. Additionally, an experimental reduction of gene expression would demonstrate how the activity of specific genes contributes to insect social phenotypes. While tissue specificity provides greater localization of the gene expression underlying social complexity, emerging transcriptomic analysis of insect brains at the cellular level provides even greater resolution to understand the molecular basis of social insect evolution.
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Affiliation(s)
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
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3
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Lin S, Elsner D, Ams L, Korb J, Rosengaus R. A genetic toolkit underlying the queen phenotype in termites with totipotent workers. Sci Rep 2024; 14:2214. [PMID: 38278833 PMCID: PMC10817970 DOI: 10.1038/s41598-024-51772-7] [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: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Social insect castes (e.g., queens, workers) are prime examples of phenotypic plasticity (i.e., different phenotypes arising from the same genotype). Yet, the mechanisms that give rise to highly fertile, long-lived queens versus non-reproducing, short-lived workers are not well understood. Recently, a module of co-expressed genes has been identified that characterizes queens compared to workers of the termite Cryptotermes secundus (Kalotermitidae): the Queen Central Module (QCM). We tested whether the QCM is shared in termite species, in which queens gradually develop via early larval and late larval instars, the latter functioning as totipotent workers (linear development). Similar as in C. secundus, gene expression profiles revealed an enrichment of QCM genes in Zootermopsis angusticollis queens, a species from another termite family (Archotermopsidae). The expression of these QCM genes became gradually enriched during development from early larval instars via workers to queens. Thus, our results support the hypothesis of a conserved genetic toolkit that characterizes termite queens with gradual linear development. Our data also imply a strong caste-specific tissue specificity with the QCM signal being restricted to head-prothorax tissues in termite queens. This tissue-specific expression of key aging-related genes might have facilitated the evolution of a long lifespan in termite queens.
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Affiliation(s)
- Silu Lin
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Daniel Elsner
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Leon Ams
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Judith Korb
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany.
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina Campus, Darwin, NT, 0909, Australia.
| | - Rebeca Rosengaus
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, 02115, USA.
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4
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Taylor BA, Taylor D, Bodrug‐Schepers A, Câmara Ferreira F, Stralis‐Pavese N, Himmelbauer H, Guigó R, Reuter M, Sumner S. Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp. Mol Ecol 2024; 33:e17217. [PMID: 38014715 PMCID: PMC10953455 DOI: 10.1111/mec.17217] [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: 04/27/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Social insect reproductives and non-reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes in obligately social taxa such as honey bees, while relatively few studies have addressed the molecular correlates of reproductive differentiation in species in which the division of reproductive labour is established only in plastic dominance hierarchies. To address this knowledge gap, we generate the first genome for any stenogastrine wasp and analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social species Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive 'queues' exhibited by social colonies of this species, we show that reproductive division of labour in this species is associated with transcriptomic signatures that are more subtle and variable than those observed in social taxa in which colony living has become obligate; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that genes associated with reproductive division of labour overlap to some extent with those underlying division of labour in the separate polistine origin of wasp sociality but only explain a small portion of overall variation in this trait. These results indicate that broad patterns of within-colony transcriptomic differentiation in this species are similar to those in Polistinae but offer little support for the existence of a strongly conserved 'toolkit' for sociality.
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Affiliation(s)
- Benjamin A. Taylor
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Daisy Taylor
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Nancy Stralis‐Pavese
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Roderic Guigó
- Centre for Genomic RegulationBarcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
| | - Max Reuter
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
- Centre for Life's Origins and EvolutionUniversity College LondonLondonUK
| | - Seirian Sumner
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
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5
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Yin Z, Ding G, Xue Y, Yu X, Dong J, Huang J, Ma J, He F. A postmeiotically bifurcated roadmap of honeybee spermatogenesis marked by phylogenetically restricted genes. PLoS Genet 2023; 19:e1011081. [PMID: 38048317 PMCID: PMC10721206 DOI: 10.1371/journal.pgen.1011081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/14/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
Haploid males of hymenopteran species produce gametes through an abortive meiosis I followed by meiosis II that can either be symmetric or asymmetric in different species. Thus, one spermatocyte could give rise to two spermatids with either equal or unequal amounts of cytoplasm. It is currently unknown what molecular features accompany these postmeiotic sperm cells especially in species with asymmetric meiosis II such as bees. Here we present testis single-cell RNA sequencing datasets from the honeybee (Apis mellifera) drones of 3 and 14 days after emergence (3d and 14d). We show that, while 3d testes exhibit active, ongoing spermatogenesis, 14d testes only have late-stage spermatids. We identify a postmeiotic bifurcation in the transcriptional roadmap during spermatogenesis, with cells progressing toward the annotated spermatids (SPT) and small spermatids (sSPT), respectively. Despite an overall similarity in their transcriptomic profiles, sSPTs express the fewest genes and the least RNA content among all the sperm cell types. Intriguingly, sSPTs exhibit a relatively high expression level for Hymenoptera-restricted genes and a high mutation load, suggesting that the special meiosis II during spermatogenesis in the honeybee is accompanied by phylogenetically young gene activities.
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Affiliation(s)
- Zhiyong Yin
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guiling Ding
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingdi Xue
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xianghui Yu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiaxing Huang
- State Key Laboratory of Resource Insects, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Ma
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Feng He
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
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6
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Goekoop R, de Kleijn R. Hierarchical network structure as the source of hierarchical dynamics (power-law frequency spectra) in living and non-living systems: How state-trait continua (body plans, personalities) emerge from first principles in biophysics. Neurosci Biobehav Rev 2023; 154:105402. [PMID: 37741517 DOI: 10.1016/j.neubiorev.2023.105402] [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: 06/22/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Living systems are hierarchical control systems that display a small world network structure. In such structures, many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a 'power-law' cluster size distribution (a mereology). Just like their structure, the dynamics of living systems shows fractal-like qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' (treble) that are nested within lower frequencies or 'traits' (bass), producing a power-law frequency spectrum that is known as a 'state-trait continuum' in the behavioral sciences. Here, we argue that the power-law dynamics of living systems results from their power-law network structure: organisms 'vertically encode' the deep spatiotemporal structure of their (anticipated) environments, to the effect that many small clusters near the base of the hierarchy produce high frequency signal changes and fewer larger clusters at its top produce ultra-low frequencies. Such ultra-low frequencies exert a tonic regulatory pressure that produces morphological as well as behavioral traits (i.e., body plans and personalities). Nested-modular structure causes higher frequencies to be embedded within lower frequencies, producing a power-law state-trait continuum. At the heart of such dynamics lies the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.q., earthquakes, stock market fluctuations). Since hierarchical structure produces hierarchical dynamics, the development and collapse of hierarchical structure (e.g., during maturation and disease) should leave specific traces in system dynamics (shifts in lower frequencies, i.e. morphological and behavioral traits) that may serve as early warning signs to system failure. The applications of this idea range from (bio)physics and phylogenesis to ontogenesis and clinical medicine.
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Affiliation(s)
- R Goekoop
- Free University Amsterdam, Department of Behavioral and Movement Sciences, Parnassia Academy, Parnassia Group, PsyQ, Department of Anxiety Disorders, Early Detection and Intervention Team (EDIT), Lijnbaan 4, 2512VA The Hague, the Netherlands.
| | - R de Kleijn
- Faculty of Social and Behavioral Sciences, Department of Cognitive Psychology, Pieter de la Courtgebouw, Postbus 9555, 2300 RB Leiden, the Netherlands
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7
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Lacy KD, Kronauer DJC. Evolution: How sweat bees gained and lost eusociality. Curr Biol 2023; 33:R770-R773. [PMID: 37490864 DOI: 10.1016/j.cub.2023.05.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Eusocial insects divide labor between reproductive and non-reproductive individuals. The molecular mechanisms underlying the evolution of these castes have remained mysterious. A comparative genomic study of sweat bees points to a familiar factor as a regulator of behavioral specialization: juvenile hormone.
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Affiliation(s)
- Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA.
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8
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Toga K, Bono H. Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites. Int J Mol Sci 2023; 24:ijms24098353. [PMID: 37176060 PMCID: PMC10179490 DOI: 10.3390/ijms24098353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Eusociality in insects has evolved independently many times. One of the most notable characteristics of eusociality is the reproductive division of labor. In social insects, the reproductive division of labor is accomplished by queens and workers. Transcriptome analyses of queens and workers have been conducted for various eusocial species. However, the genes that regulate the reproductive division of labor across all or multiple eusocial species have not yet been fully elucidated. Therefore, we conducted a meta-analysis using publicly available RNA-sequencing data from four major groups of social insects. In this meta-analysis, we collected 258 pairs (queen vs. worker) of RNA-sequencing data from 34 eusocial species. The meta-analysis identified a total of 20 genes that were differentially expressed in queens or workers. Out of these, 12 genes have not previously been reported to be involved in the reproductive division of labor. Functional annotation of these 20 genes in other organisms revealed that they could be regulators of behaviors and physiological states related to the reproductive division of labor. These 20 genes, revealed using massive datasets of numerous eusocial insects, may be key regulators of the reproductive division of labor.
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Affiliation(s)
- Kouhei Toga
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
| | - Hidemasa Bono
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
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9
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Orr SE, Goodisman MA. Social insect transcriptomics and the molecular basis of caste diversity. CURRENT OPINION IN INSECT SCIENCE 2023; 57:101040. [PMID: 37105497 DOI: 10.1016/j.cois.2023.101040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Studies of gene expression provide fundamentally important information on the molecular mechanisms underlying variation in phenotype. Recent technological advances have allowed for the robust study of gene expression through analysis of whole transcriptomes. Here, we review current advances in social insect transcriptomics and discuss their implications in understanding phenotypic diversity. Recent transcriptomic studies provide detailed inventories of the genes involved in producing distinct phenotypes in social species. These investigations have identified key genes and networks involved in producing distinct social insect castes. Nevertheless, questions concerning the evolution of gene expression patterns remain. We suggest a path forward for studying gene expression in future studies of biological systems.
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Affiliation(s)
- Sarah E Orr
- School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA
| | - Michael Ad Goodisman
- School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, USA.
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10
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Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. Nat Ecol Evol 2023; 7:557-569. [PMID: 36941345 DOI: 10.1038/s41559-023-02001-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023]
Abstract
Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.
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Affiliation(s)
- Beryl M Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Benjamin E R Rubin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Callum J Kingwell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Z Yan Wang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Karen M Kapheim
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biology, Utah State University, Logan, UT, USA
| | - Eli S Wyman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Per A Adastra
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Liu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - S RaElle Jackson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shawn M Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Matthew J McBride
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Nikki Van Dorp
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mauricio Fernández Otárola
- Biodiversity and Tropical Ecology Research Center (CIBET) and School of Biology, University of Costa Rica, San José, Costa Rica
| | - Melanie Pham
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Schraiber
- Department of Biology, Temple University, Philadelphia, PA, USA
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Fernando Villanea
- Department of Biology, Temple University, Philadelphia, PA, USA
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Robert J Paxton
- Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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11
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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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12
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Smith CR. Sexual dimorphism as a facilitator of worker caste evolution in ants. Ecol Evol 2023; 13:e9825. [PMID: 36818531 PMCID: PMC9929627 DOI: 10.1002/ece3.9825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/17/2023] Open
Abstract
Ant societies are primarily composed of females, whereby labor is divided into reproductive, or queen, and non-reproductive, or worker, castes. Workers and reproductive queens can differ greatly in behavior, longevity, physiology, and morphology, but queen-worker differences are usually modest relative to the differences in males. Males are short-lived, typically do not provide the colony with labor, often look like a different species, and only occur seasonally. It is these differences that have historically led to their neglect in social insect research, but also why they may facilitate novel phenotypic variation - by increasing the phenotypic variability that is available for selection. In this study, worker variation in multivariate size-shape space paralleled male-queen variation. As worker variation increased within species, so did sexual variation. Across species in two independent genera, using head width as a proxy for body size, sexual size dimorphism correlated with worker polymorphism regardless of whether the ancestral condition was large or small worker/sexual dimorphism. Mounting molecular data support the hypothesis that queen-worker caste determination has co-opted many genes/pathways from sex determination. The molecular evidence, coupled with the observations from this study, leads to the hypothesis that sexual selection and selection on colony-level traits are non-independent, and that sexual dimorphism may even have facilitated the evolution of the distinct worker caste.
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13
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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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14
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Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism. Sci Rep 2022; 12:20771. [PMID: 36456708 PMCID: PMC9715534 DOI: 10.1038/s41598-022-25132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Distyly, a floral dimorphism associated with heteromorphic self-incompatibility and controlled by the S-locus supergene, evolved independently multiple times. Comparative analyses of the first transcriptome atlas for the main distyly model, Primula veris, with other distylous species produced the following findings. A set of 53 constitutively expressed genes in P. veris did not include any of the housekeeping genes commonly used to normalize gene expression in qPCR experiments. The S-locus gene CYPT acquired its role in controlling style elongation via a change in expression profile. Comparison of genes differentially expressed between floral morphs revealed that brassinosteroids and auxin are the main hormones controlling style elongation in P. veris and Fagopyrum esculentum, respectively. Furthermore, shared biochemical pathways might underlie the expression of distyly in the distantly related P. veris, F. esculentum and Turnera subulata, suggesting a degree of correspondence between evolutionary convergence at phenotypic and molecular levels. Finally, we provide the first evidence supporting the previously proposed hypothesis that distyly supergenes of distantly related species evolved via the recruitment of genes related to the phytochrome-interacting factor (PIF) signaling network. To conclude, this is the first study that discovered homologous genes involved in the control of distyly in distantly related taxa.
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15
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Forni G, Mikheyev AS, Luchetti A, Mantovani B. Gene transcriptional profiles in gonads of Bacillus taxa (Phasmida) with different cytological mechanisms of automictic parthenogenesis. ZOOLOGICAL LETTERS 2022; 8:14. [PMID: 36435814 PMCID: PMC9701443 DOI: 10.1186/s40851-022-00197-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The evolution of automixis - i.e., meiotic parthenogenesis - requires several features, including ploidy restoration after meiosis and maintenance of fertility. Characterizing the relative contribution of novel versus pre-existing genes and the similarities in their expression and sequence evolution is fundamental to understand the evolution of reproductive novelties. Here we identify gonads-biased genes in two Bacillus automictic stick-insects and compare their expression profile and sequence evolution with a bisexual congeneric species. The two parthenogens restore ploidy through different cytological mechanisms: in Bacillus atticus, nuclei derived from the first meiotic division fuse to restore a diploid egg nucleus, while in Bacillus rossius, diploidization occurs in some cells of the haploid blastula through anaphase restitution. Parthenogens' gonads transcriptional program is found to be largely assembled from genes that were already present before the establishment of automixis. The three species transcriptional profiles largely reflect their phyletic relationships, yet we identify a shared core of genes with gonad-biased patterns of expression in parthenogens which are either male gonads-biased in the sexual species or are not differentially expressed there. At the sequence level, just a handful of gonads-biased genes were inferred to have undergone instances of positive selection exclusively in the parthenogen species. This work is the first to explore the molecular underpinnings of automixis in a comparative framework: it delineates how reproductive novelties can be sustained by genes whose origin precedes the establishment of the novelty itself and shows that different meiotic mechanisms of reproduction can be associated with a shared molecular ground plan.
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Affiliation(s)
- Giobbe Forni
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
- Dip. Scienze Agrarie e Ambientali, University of Milano, Milano, Italy
| | - Alexander S Mikheyev
- Australian National University, ACT, Canberra, 2600, Australia
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Andrea Luchetti
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy.
| | - Barbara Mantovani
- Dip. Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, 40126, Bologna, Italy
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16
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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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17
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Rosvall KA. Evolutionary endocrinology and the problem of Darwin's tangled bank. Horm Behav 2022; 146:105246. [PMID: 36029721 DOI: 10.1016/j.yhbeh.2022.105246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/20/2022] [Accepted: 08/10/2022] [Indexed: 11/04/2022]
Abstract
Like Darwin's tangled bank of biodiversity, the endocrine mechanisms that give rise to phenotypic diversity also exhibit nearly endless forms. This tangled bank of mechanistic diversity can prove problematic as we seek general principles on the role of endocrine mechanisms in phenotypic evolution. A key unresolved question is therefore: to what degree are specific endocrine mechanisms re-used to bring about replicated phenotypic evolution? Related areas of inquiry are booming in molecular ecology, but behavioral traits are underrepresented in this literature. Here, I leverage the rich comparative tradition in evolutionary endocrinology to evaluate whether and how certain mechanisms may be repeated hotspots of behavioral evolutionary change. At one extreme, mechanisms may be parallel, such that evolution repeatedly uses the same gene or pathway to arrive at multiple independent (or, convergent) origins of a particular behavioral trait. At the other extreme, the building blocks of behavior may be unique, such that outwardly similar phenotypes are generated via lineage-specific mechanisms. This review synthesizes existing case studies, phylogenetic analyses, and experimental evolutionary research on mechanistic parallelism in animal behavior. These examples show that the endocrine building blocks of behavior have some elements of parallelism across replicated evolutionary events. However, support for parallelism is variable among studies, at least some of which relates to the level of complexity at which we consider sameness (i.e. pathway vs. gene level). Moving forward, we need continued experimentation and better testing of neutral models to understand whether, how - and critically, why - mechanism A is used in one lineage and mechanism B is used in another. We also need continued growth of large-scale comparative analyses, especially those that can evaluate which endocrine parameters are more or less likely to undergo parallel evolution alongside specific behavioral traits. These efforts will ultimately deepen understanding of how and why hormone-mediated behaviors are constructed the way that they are.
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Affiliation(s)
- Kimberly A Rosvall
- Indiana University, Bloomington, USA; Department of Biology, USA; Center for the Integrative Study of Animal Behavior, USA.
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18
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Qiu B, Dai X, Li P, Larsen RS, Li R, Price AL, Ding G, Texada MJ, Zhang X, Zuo D, Gao Q, Jiang W, Wen T, Pontieri L, Guo C, Rewitz K, Li Q, Liu W, Boomsma JJ, Zhang G. Canalized gene expression during development mediates caste differentiation in ants. Nat Ecol Evol 2022; 6:1753-1765. [PMID: 36192540 PMCID: PMC9630140 DOI: 10.1038/s41559-022-01884-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/12/2022] [Indexed: 11/30/2022]
Abstract
Ant colonies are higher-level organisms consisting of specialized reproductive and non-reproductive individuals that differentiate early in development, similar to germ-soma segregation in bilateral Metazoa. Analogous to diverging cell lines, developmental differentiation of individual ants has often been considered in epigenetic terms but the sets of genes that determine caste phenotypes throughout larval and pupal development remain unknown. Here, we reconstruct the individual developmental trajectories of two ant species, Monomorium pharaonis and Acromyrmex echinatior, after obtaining >1,400 whole-genome transcriptomes. Using a new backward prediction algorithm, we show that caste phenotypes can be accurately predicted by genome-wide transcriptome profiling. We find that caste differentiation is increasingly canalized from early development onwards, particularly in germline individuals (gynes/queens) and that the juvenile hormone signalling pathway plays a key role in this process by regulating body mass divergence between castes. We quantified gene-specific canalization levels and found that canalized genes with gyne/queen-biased expression were enriched for ovary and wing functions while canalized genes with worker-biased expression were enriched in brain and behavioural functions. Suppression in gyne larvae of Freja, a highly canalized gyne-biased ovary gene, disturbed pupal development by inducing non-adaptive intermediate phenotypes between gynes and workers. Our results are consistent with natural selection actively maintaining canalized caste phenotypes while securing robustness in the life cycle ontogeny of ant colonies.
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Affiliation(s)
- Bitao Qiu
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xueqin Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | - Rasmus Stenbak Larsen
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ruyan Li
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alivia Lee Price
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guo Ding
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Michael James Texada
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiafang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Dashuang Zuo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qionghua Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | | | | | - Luigi Pontieri
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Kim Rewitz
- Section for Cell and Neurobiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jacobus J Boomsma
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, China.
- Women's Hospital, School of Medicine, Zhejiang University, Shangcheng District, Hangzhou, China.
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19
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Berger J, Legendre F, Zelosko KM, Harrison MC, Grandcolas P, Bornberg-Bauer E, Fouks B. Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression. Genes (Basel) 2022; 13:1948. [PMID: 36360186 PMCID: PMC9689775 DOI: 10.3390/genes13111948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2023] Open
Abstract
(1) Unravelling the molecular basis underlying major evolutionary transitions can shed light on how complex phenotypes arise. The evolution of eusociality, a major evolutionary transition, has been demonstrated to be accompanied by enhanced gene regulation. Numerous pieces of evidence suggest the major impact of transposon insertion on gene regulation and its role in adaptive evolution. Transposons have been shown to be play a role in gene duplication involved in the eusocial transition in termites. However, evidence of the molecular basis underlying the eusocial transition in Blattodea remains scarce. Could transposons have facilitated the eusocial transition in termites through shifts of gene expression? (2) Using available cockroach and termite genomes and transcriptomes, we investigated if transposons insert more frequently in genes with differential expression in queens and workers and if those genes could be linked to specific functions essential for eusocial transition. (3) The insertion rate of transposons differs among differentially expressed genes and displays opposite trends between termites and cockroaches. The functions of termite transposon-rich queen- and worker-biased genes are related to reproduction and ageing and behaviour and gene expression, respectively. (4) Our study provides further evidence on the role of transposons in the evolution of eusociality, potentially through shifts in gene expression.
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Affiliation(s)
- Juliette Berger
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Kevin-Markus Zelosko
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
| | - Mark C. Harrison
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
| | - Philippe Grandcolas
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
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20
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Traniello JF, Linksvayer TA, Coto ZN. Social complexity and brain evolution: insights from ant neuroarchitecture and genomics. CURRENT OPINION IN INSECT SCIENCE 2022; 53:100962. [PMID: 36028191 DOI: 10.1016/j.cois.2022.100962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/02/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Brain evolution is hypothesized to be driven by requirements to adaptively respond to environmental cues and social signals. Diverse models describe how sociality may have influenced eusocial insect-brain evolution, but specific impacts of social organization and other selective forces on brain architecture have been difficult to distinguish. Here, we evaluate predictions derived from and/or inferences made by models of social organization concerning the effects of individual and collective behavior on brain size, structure, and function using results of neuroanatomical and genomic studies. In contrast to the predictions of some models, we find that worker brains in socially complex species have great behavioral and cognitive capacity. We also find that colony size, the evolution of worker physical castes, and task specialization affect brain size and mosaicism, supporting the idea that sensory, processing and motor requirements for behavioral performance select for adaptive allometries of functionally specialized brain centers. We review available transcriptomic and comparative genomic studies seeking to elucidate the molecular pathways functionally associated with social life and the genetic changes that occurred during the evolution of social complexity. We discuss ways forward, using comparative neuroanatomy, transcriptomics, and comparative genomics, to distinguish among multiple alternative explanations for the relationship between the evolution of neural systems and social complexity.
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Affiliation(s)
- James Fa Traniello
- Department of Biology, Boston University, Boston, MA, USA; Graduate Program in Neuroscience, Boston University, Boston, MA, USA.
| | | | - Zachary N Coto
- Department of Biology, Boston University, Boston, MA, USA
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21
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Wójcik Ł, Chęć M, Skowronek P, Grabowski M, Persona K, Strachecka A. Do the different life history strategies of ants and honeybees determine fat body morphology? ARTHROPOD STRUCTURE & DEVELOPMENT 2022; 69:101186. [PMID: 35696737 DOI: 10.1016/j.asd.2022.101186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/22/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
The separation of two sister groups such as ants and bees in the Cretaceous involved the development of distinctive characteristics to occupy separate ecological niches. From the point of view of biology and ecology, it is important to see how different life history strategies affect the physiology of these insects. The fat body is the most metabolically important tissue in the organism of each insect. Therefore, we conducted a comparative analysis of the morphological image of the subcuticular fat body in different localisation/segments in Formica (Seviformica) cinerea and Apis mellifera mellifera foragers, because of the similarity of their functions in colonies. We observed that the fat bodies of ants and bees were composed of the same cell types: trophocytes and oenocytes. However, in each of the segments, the fat body cells in ants were bigger and there were fewer of them in comparison with bees. The dorsal part of the fat body of ants had a bilayer structure, where the outer layer was formed by binucleated oenocytes. Binucleated oenocytes were also found in the inner layer near the heart and tracheole. In bees, the fat body was unilayered and the trophocytes and oenocytes were present side by side. The similarities and, in particular, the differences in the structure of the fat body are the adaptation of these sister groups to life in a diverse environment.
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Affiliation(s)
- Łukasz Wójcik
- Department of Invertebrate Ecophysiology and Experimental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
| | - Magdalena Chęć
- Department of Cell Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033, Lublin, Poland
| | - Patrycja Skowronek
- Department of Invertebrate Ecophysiology and Experimental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Marcin Grabowski
- Department of Invertebrate Ecophysiology and Experimental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Kamil Persona
- Department of Invertebrate Ecophysiology and Experimental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
| | - Aneta Strachecka
- Department of Invertebrate Ecophysiology and Experimental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland
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22
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Yu CN, Kuo CY, Lin HC, Su YC. Foraging Payoffs Change With Group Size in Kin and Non-kin Groups of an Argyrodinae Kleptoparasitic Spider, Argyrodes miniaceus. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.813777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Evolutionary transitions from solitary to group-living are ubiquitous in animal systems. While the fitness consequences of group size changes are often investigated, the long-standing debate on whether kinship is a prerequisite of sociality is still ongoing. In the current study, we used kleptoparasitic spiders Argyrodes miniaceus (subfamily Argyrodinae, Theridiidae) as a model system to assess the role of group size on the foraging payoffs of kin and non-kin groups. We set up laboratory-manipulated kin and non-kin foraging groups and used feeding occurrence and duration as proxies for foraging benefits and feeding latency and the number of host attacks as estimates of foraging costs. Compared to solitary individuals, feeding durations of successfully fed individuals in groups was not significantly different from that of solitary foragers in both kin and non-kin groups. The occurrences of feeding decreased significantly in group sizes two and above, in non-kin groups, and in group sizes three and above, in kin groups. In kin groups, groups size two had significantly shorter feeding latencies compared to other group sizes, even though feeding duration did not change systematically with group size. Similarly, the number of attacks from the hosts were highest in non-kin groups with more than two individuals and in kin groups with more than three individuals. The juxtaposition of kin and non-kin group showed that A. miniaceus enjoyed the highest foraging payoffs when being solitary or in small groups (group size two). However, host attacks appeared to hamper feeding occurrences in kin groups, which was not observed in non-kin groups. Our results contrast sharply with the feeding benefits of kinship recorded in kin-based groups of sub-social species present in related subfamilies in the Theridiidae.
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23
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Ding G, Gao Q, Chen J, Zhao J, Zhang G, Liu W. Validation of Potential Reference Genes for Real-Time qPCR Analysis in Pharaoh Ant, Monomorium pharaonis (Hymenoptera: Formicidae). Front Physiol 2022; 13:852357. [PMID: 35295570 PMCID: PMC8919206 DOI: 10.3389/fphys.2022.852357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Ants are highly diverse social insects living in colonies consisted of up to millions of individuals with reproductive division of labors. Due to the interests in disclosing the genetic and epigenetic regulation mechanisms underlying the distinct developmental trajectories between castes and division of labor in colonies, many ant species have recently been established as laboratory models for evolutionary development and social behavior studies. These functional studies often request a precise quantification of the relative gene expression level, which relies on a stably expressed reference genes for normalization. A core set of reliable reference genes for this purpose however has not been established yet in ants. In the present study, we tested the expression patterns and amplification efficiencies of 12 abundantly expressed candidate genes in Monomorium pharaonis, one of the few ant species that are suitable for laboratory rearing and experimentation. We quantified the expression levels of these genes by RT-qPCR in seven different conditions: embryo development, sexual development, worker development, adult phenotypes, tissues, and two abiotic manipulative treatments in pharaoh ant. Finally, five genes, elongation factor-1 alpha (EF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), TATA-box-binding protein (TATA), tubulin gamma-2 chain-like (TBLg2), heat shock protein 67B2-like (HSP67) were found to be the most stable reference genes across seven conditions. We also identified the most stable reference genes applicable for each distinct condition and the optimal number of reference genes entailed were evaluated. Our study validates reliable reference genes for RT-qPCR analysis which lays the foundation for future studies in pharaoh ant.
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Affiliation(s)
- Guo Ding
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- BGI-Shenzhen, Shenzhen, China
| | - Qionghua Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Jun Chen
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jie Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Guojie Zhang,
| | - Weiwei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Weiwei Liu,
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24
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Das B, de Bekker C. Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor. BMC Genomics 2022; 23:57. [PMID: 35033027 PMCID: PMC8760764 DOI: 10.1186/s12864-021-08282-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 12/19/2022] Open
Abstract
Background Circadian clocks allow organisms to anticipate daily fluctuations in their environment by driving rhythms in physiology and behavior. Inter-organismal differences in daily rhythms, called chronotypes, exist and can shift with age. In ants, age, caste-related behavior and chronotype appear to be linked. Brood-tending nurse ants are usually younger individuals and show “around-the-clock” activity. With age or in the absence of brood, nurses transition into foraging ants that show daily rhythms in activity. Ants can adaptively shift between these behavioral castes and caste-associated chronotypes depending on social context. We investigated how changes in daily gene expression could be contributing to such behavioral plasticity in Camponotus floridanus carpenter ants by combining time-course behavioral assays and RNA-Sequencing of forager and nurse brains. Results We found that nurse brains have three times fewer 24 h oscillating genes than foragers. However, several hundred genes that oscillated every 24 h in forager brains showed robust 8 h oscillations in nurses, including the core clock genes Period and Shaggy. These differentially rhythmic genes consisted of several components of the circadian entrainment and output pathway, including genes said to be involved in regulating insect locomotory behavior. We also found that Vitellogenin, known to regulate division of labor in social insects, showed robust 24 h oscillations in nurse brains but not in foragers. Finally, we found significant overlap between genes differentially expressed between the two ant castes and genes that show ultradian rhythms in daily expression. Conclusion This study provides a first look at the chronobiological differences in gene expression between forager and nurse ant brains. This endeavor allowed us to identify a putative molecular mechanism underlying plastic timekeeping: several components of the ant circadian clock and its output can seemingly oscillate at different harmonics of the circadian rhythm. We propose that such chronobiological plasticity has evolved to allow for distinct regulatory networks that underlie behavioral castes, while supporting swift caste transitions in response to colony demands. Behavioral division of labor is common among social insects. The links between chronobiological and behavioral plasticity that we found in C. floridanus, thus, likely represent a more general phenomenon that warrants further investigation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08282-x.
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Affiliation(s)
- Biplabendu Das
- Department of Biology, College of Sciences, University of Central Florida, Orlando, FL, 32816, USA. .,Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, 32816, USA.
| | - Charissa de Bekker
- Department of Biology, College of Sciences, University of Central Florida, Orlando, FL, 32816, USA. .,Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL, 32816, USA.
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25
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Abstract
Many species have separate haploid and diploid phases. Theory predicts that each phase should experience the effects of evolutionary forces (like selection) differently. In the haploid phase, all fitness-affecting alleles are exposed to selection, whereas in the diploid phase, those same alleles can be masked by homologous alleles. This predicts that selection acting on genes expressed in haploids should be more effective than diploid-biased genes. Unfortunately, in arrhenotokous species, this prediction can be confounded with the effects of sex-specific expression, as haploids are usually reproductive males. Theory posits that, when accounting for ploidal- and sex-specific expression, selection should be equally efficient on haploid- and diploid-biased genes relative to constitutive genes. Here, we used a multiomic approach in honey bees to quantify the evolutionary rates of haploid-biased genes and test the relative effects of sexual- and haploid-expression on molecular evolution. We found that 16% of the honey bee’s protein-coding genome is highly expressed in haploid tissue. When accounting for ploidy and sex, haploid- and diploid-biased genes evolve at a lower rate than expected, indicating that they experience strong negative selection. However, the rate of molecular evolution of haploid-biased genes was higher than diploid-based genes. Genes associated with sperm storage are a clear exception to this trend with evidence of strong positive selection. Our results provide an important empirical test of theory outlining how selection acts on genes expressed in arrhenotokous species. We propose the haploid life history stage affects genome-wide patterns of diversity and divergence because of both sexual and haploid selection.
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Affiliation(s)
| | - Amy L. Dapper
- Department of Biological Sciences, Mississippi State University, 219 Harned Hall, 295 Lee Blvd, Mississippi State, Mississippi 39762, USA
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26
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Strachecka A, Olszewski K, Kuszewska K, Chobotow J, Wójcik Ł, Paleolog J, Woyciechowski M. Segmentation of the subcuticular fat body in Apis mellifera females with different reproductive potentials. Sci Rep 2021; 11:13887. [PMID: 34230567 PMCID: PMC8260796 DOI: 10.1038/s41598-021-93357-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2021] [Indexed: 11/08/2022] Open
Abstract
Evolution has created different castes of females in eusocial haplodiploids. The difference between them lies in their functions and vulnerability but above all in their reproductive potentials. Honeybee queens are highly fertile. On the other hand, the workers are facultatively sterile. However, rebel workers, i.e. workers that develop in a queenless colony, reproduce more often than normal workers. As a result, the fat body of these bees, which apart from acting as the energy reserve, is also the site of numerous metabolic processes, had to specialize in different functions perfected over millions of years of eusocial evolution. Assuming that the variety of functions manifests itself in the pleomorphic structure of the fat body cells, we predicted that also different parts of the fat body, e.g. from different segments of the abdomen, contain different sets of cells. Such differences could be expected between queens, rebels and normal workers, i.e. females with dramatically different reproductive potentials. We confirmed all these expectations. Although all bees had the same types of cells, their proportion and segmental character corresponded with the caste reproductive potential and physiological characteristics shaped in the evolutionary process. The females with an increased reproductive potential were characterized by the presence of oenocytes in the third tergite and high concentrations of compounds responsible for energy reserves, like glucose, glycogen and triglycerides. Queens had very large trophocytes, especially in the third tergite. Only in workers did we observe intercellular spaces in all the segments of the fat body, as well as high protein concentrations-especially in the sternite. As expected, the rebels combined many features of the queens and normal workers, what with other findings can help understand the ways that led to the origin of different castes in females of eusocial Hymenoptera.
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Affiliation(s)
- Aneta Strachecka
- Department of Zoology and Animal Ecology, University of Life Sciences in Lublin, Lublin, Poland.
| | - Krzysztof Olszewski
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Karolina Kuszewska
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Jacek Chobotow
- Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Łukasz Wójcik
- Department of Zoology and Animal Ecology, University of Life Sciences in Lublin, Lublin, Poland
| | - Jerzy Paleolog
- Department of Zoology and Animal Ecology, University of Life Sciences in Lublin, Lublin, Poland
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27
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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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28
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Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci U S A 2021; 118:e2025051118. [PMID: 34099551 PMCID: PMC8214670 DOI: 10.1073/pnas.2025051118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite progress uncovering the genomic underpinnings of sociality, much less is known about how social living affects the genome. In different insect lineages, for example, eusocial species show both positive and negative associations between genome size and structure, highlighting the dynamic nature of the genome. Here, we explore the relationship between sociality and genome architecture in Synalpheus snapping shrimps that exhibit multiple origins of eusociality and extreme interspecific variation in genome size. Our goal is to determine whether eusociality leads to an accumulation of repetitive elements and an increase in genome size, presumably due to reduced effective population sizes resulting from a reproductive division of labor, or whether an initial accumulation of repetitive elements leads to larger genomes and independently promotes the evolution of eusociality through adaptive evolution. Using phylogenetically informed analyses, we find that eusocial species have larger genomes with more transposable elements (TEs) and microsatellite repeats than noneusocial species. Interestingly, different TE subclasses contribute to the accumulation in different species. Phylogenetic path analysis testing alternative causal relationships between sociality and genome architecture is most consistent with the hypothesis that TEs modulate the relationship between sociality and genome architecture. Although eusociality appears to influence TE accumulation, ancestral state reconstruction suggests moderate TE abundances in ancestral species could have fueled the initial transitions to eusociality. Ultimately, we highlight a complex and dynamic relationship between genome and social evolution, demonstrating that sociality can influence the evolution of the genome, likely through changes in demography related to patterns of reproductive skew.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027;
- Department of Biological Sciences, State University of New York College at Old Westbury, Old Westbury, NY 11568
| | - Stephen E Harris
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
- Department of Biology, State University of New York Purchase College, Purchase, NY 10577
| | | | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS B2Y 4A2, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dustin R Rubenstein
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027
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29
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Pinto BJ, Weis JJ, Gamble T, Ode PJ, Paul R, Zaspel JM. A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae). J Hered 2021; 112:558-564. [PMID: 34043785 DOI: 10.1093/jhered/esab032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae. Among this under-studied group are braconid wasps in the genus Cotesia; a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing technologies, including Oxford Nanopore, whole-genome shotgun sequencing, and 3-D chromatin contact information (Hi-C). Our assembly is one of the most contiguous, complete, and publicly available hymenopteran genomes, represented by 3,355 scaffolds with a scaffold N50 of ~28Mb and a BUSCO score of ~99%. Given the genome sizes found in closely related species, our genome assembly was ~50% larger than expected, which was apparently induced by runaway amplification of three types of repetitive elements: simple repeats, Long Terminal Repeats (LTRs), and Long Interspersed Nuclear Elements (LINEs). This assembly is another step forward for genomics across this hyper-diverse, yet understudied, order of insects. The assembled genomic data and metadata files are publicly available via Figshare (https://doi.org/10.6084/m9.figshare.13010549).
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Affiliation(s)
- Brendan J Pinto
- Department of Integrative Biology, University of Texas at Austin, TX, USA.,Milwaukee Public Museum, Milwaukee, WI, USA
| | | | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.,Bell Museum of Natural History, University of Minnesota, St Paul, MN, USA
| | - Paul J Ode
- Colorado State University, Ft. Collins, CO, USA
| | - Ryan Paul
- Colorado State University, Ft. Collins, CO, USA
| | - Jennifer M Zaspel
- Milwaukee Public Museum, Milwaukee, WI, USA.,Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
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30
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Monroy Kuhn JM, Meusemann K, Korb J. Disentangling the aging gene expression network of termite queens. BMC Genomics 2021; 22:339. [PMID: 33975542 PMCID: PMC8114706 DOI: 10.1186/s12864-021-07649-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ants and some bees) can live from a few years to decades. This makes social insects promising models in aging research providing insights into how a long reproductive life can be achieved. Yet, aging studies on social insect reproductives are hampered by a lack of quantitative data on age-dependent survival and time series analyses that cover the whole lifespan of such long-lived individuals. We studied aging in queens of the drywood termite Cryptotermes secundus by determining survival probabilities over a period of 15 years and performed transcriptome analyses for queens of known age that covered their whole lifespan. Results The maximum lifespan of C. secundus queens was 13 years, with a median maximum longevity of 11.0 years. Time course and co-expression network analyses of gene expression patterns over time indicated a non-gradual aging pattern. It was characterized by networks of genes that became differentially expressed only late in life, namely after ten years, which associates well with the median maximum lifespan for queens. These old-age gene networks reflect processes of physiological upheaval. We detected strong signs of stress, decline, defense and repair at the transcriptional level of epigenetic control as well as at the post-transcriptional level with changes in transposable element activity and the proteostasis network. The latter depicts an upregulation of protein degradation, together with protein synthesis and protein folding, processes which are often down-regulated in old animals. The simultaneous upregulation of protein synthesis and autophagy is indicative of a stress-response mediated by the transcription factor cnc, a homolog of human nrf genes. Conclusions Our results show non-linear senescence with a rather sudden physiological upheaval at old-age. Most importantly, they point to a re-wiring in the proteostasis network and stress as part of the aging process of social insect queens, shortly before queens die. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07649-4.
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Affiliation(s)
- José Manuel Monroy Kuhn
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany. .,Computational Discovery Research, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, D-85764, Neuherberg, Germany.
| | - Karen Meusemann
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT 2601, Canberra, Australia
| | - Judith Korb
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.
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31
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Korb J, Heinze J. Ageing and sociality: why, when and how does sociality change ageing patterns? Philos Trans R Soc Lond B Biol Sci 2021; 376:20190727. [PMID: 33678019 PMCID: PMC7938171 DOI: 10.1098/rstb.2019.0727] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 02/07/2023] Open
Abstract
Individual lifespans vary tremendously between and also within species, but the proximate and ultimate causes of different ageing speeds are still not well understood. Sociality appears to be associated with the evolution of greater longevity and probably also with a larger plasticity of the shape and pace of ageing. For example, reproductives of several termites and ants reach lifespans that surpass those of their non-reproductive nestmates by one or two decades. In this issue, 15 papers explore the interrelations between sociality and individual longevity in both, group-living vertebrates and social insects. Here, we briefly give an overview of the contents of the various contributions, including theoretical and comparative studies, and we explore the similarities and dissimilarities in proximate mechanisms underlying ageing among taxa, with particular emphasis on nutrient-sensing pathways and, in insects, juvenile hormone. These studies point to an underestimated role of more downstream processes. We highlight the need for reliable transcriptomic markers of ageing and a comprehensive ageing theory of social animals, which includes the reproductive potential of workers, and considers the fact that social insect queens reach maturity only after a prolonged period of producing non-reproductive workers. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'
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Affiliation(s)
- Judith Korb
- Department of Evolutionary Biology and Ecology, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
| | - Jürgen Heinze
- Department of Zoology/Evolutionary Biology, University of Regensburg, Universitätsstraße, 93040 Regensburg, Germany
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32
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Korb J, Meusemann K, Aumer D, Bernadou A, Elsner D, Feldmeyer B, Foitzik S, Heinze J, Libbrecht R, Lin S, Majoe M, Monroy Kuhn JM, Nehring V, Negroni MA, Paxton RJ, Séguret AC, Stoldt M, Flatt T. Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190728. [PMID: 33678016 PMCID: PMC7938167 DOI: 10.1098/rstb.2019.0728] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
The exceptional longevity of social insect queens despite their lifelong high fecundity remains poorly understood in ageing biology. To gain insights into the mechanisms that might underlie ageing in social insects, we compared gene expression patterns between young and old castes (both queens and workers) across different lineages of social insects (two termite, two bee and two ant species). After global analyses, we paid particular attention to genes of the insulin/insulin-like growth factor 1 signalling (IIS)/target of rapamycin (TOR)/juvenile hormone (JH) network, which is well known to regulate lifespan and the trade-off between reproduction and somatic maintenance in solitary insects. Our results reveal a major role of the downstream components and target genes of this network (e.g. JH signalling, vitellogenins, major royal jelly proteins and immune genes) in affecting ageing and the caste-specific physiology of social insects, but an apparently lesser role of the upstream IIS/TOR signalling components. Together with a growing appreciation of the importance of such downstream targets, this leads us to propose the TI-J-LiFe (TOR/IIS-JH-Lifespan and Fecundity) network as a conceptual framework for understanding the mechanisms of ageing and fecundity in social insects and beyond. This article is part of the theme issue 'Ageing and sociality: why, when and how does sociality change ageing patterns?'
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Affiliation(s)
- Judith Korb
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
| | - Karen Meusemann
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Canberra, Acton 2601, Australia
| | - Denise Aumer
- Developmental Zoology, Molecular Ecology Research Group, Hoher Weg 4, D-06099 Halle (Saale), Germany
| | - Abel Bernadou
- Zoology/Evolutionary Biology, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Daniel Elsner
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Senckenberg, Georg-Voigt-Straße 14-16, D-60325 Frankfurt, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
| | - Jürgen Heinze
- Zoology/Evolutionary Biology, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
| | - Silu Lin
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
| | - Megha Majoe
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
| | - José Manuel Monroy Kuhn
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
| | - Volker Nehring
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
| | - Matteo A. Negroni
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
| | - Robert J. Paxton
- Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
| | - Alice C. Séguret
- Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48149 Münster, Germany
| | - Marah Stoldt
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - the So-Long consortium
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Hauptstraße 1, D-79104 Freiburg (Breisgau), Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Canberra, Acton 2601, Australia
- Developmental Zoology, Molecular Ecology Research Group, Hoher Weg 4, D-06099 Halle (Saale), Germany
- Zoology/Evolutionary Biology, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Senckenberg, Georg-Voigt-Straße 14-16, D-60325 Frankfurt, Germany
- Institute of Organismic and Molecular Evolution (IOME), Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, D-55128 Mainz, Germany
- Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle, Germany
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, 48149 Münster, Germany
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
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33
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Lin S, Werle J, Korb J. Transcriptomic analyses of the termite, Cryptotermes secundus, reveal a gene network underlying a long lifespan and high fecundity. Commun Biol 2021; 4:384. [PMID: 33753888 PMCID: PMC7985136 DOI: 10.1038/s42003-021-01892-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Organisms are typically characterized by a trade-off between fecundity and longevity. Notable exceptions are social insects. In insect colonies, the reproducing caste (queens) outlive their non-reproducing nestmate workers by orders of magnitude and realize fecundities and lifespans unparalleled among insects. How this is achieved is not understood. Here, we identified a single module of co-expressed genes that characterized queens in the termite species Cryptotermes secundus. It encompassed genes from all essential pathways known to be involved in life-history regulation in solitary model organisms. By manipulating its endocrine component, we tested the recent hypothesis that re-wiring along the nutrient-sensing/endocrine/fecundity axis can account for the reversal of the fecundity/longevity trade-off in social insect queens. Our data from termites do not support this hypothesis. However, they revealed striking links to social communication that offer new avenues to understand the re-modelling of the fecundity/longevity trade-off in social insects.
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Affiliation(s)
- Silu Lin
- grid.5963.9Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Jana Werle
- grid.5963.9Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Judith Korb
- grid.5963.9Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
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34
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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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35
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Age-related division of labor occurs in ants at the earliest stages of colony initiation. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-02974-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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36
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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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37
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Wang M, Liu Y, Wen T, Liu W, Gao Q, Zhao J, Xiong Z, Wang Z, Jiang W, Yu Y, Wu L, Yuan Y, Wei X, Xu J, Cheng M, Zhang P, Li P, Hou Y, Yang H, Zhang G, Li Q, Liu C, Liu L. Chromatin accessibility and transcriptome landscapes of Monomorium pharaonis brain. Sci Data 2020; 7:217. [PMID: 32641764 PMCID: PMC7343836 DOI: 10.1038/s41597-020-0556-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022] Open
Abstract
The emergence of social organization (eusociality) is a major event in insect evolution. Although previous studies have investigated the mechanisms underlying caste differentiation and social behavior of eusocial insects including ants and honeybees, the molecular circuits governing sociality in these insects remain obscure. In this study, we profiled the transcriptome and chromatin accessibility of brain tissues in three Monomorium pharaonis ant castes: queens (including mature and un-mated queens), males and workers. We provide a comprehensive dataset including 16 RNA-sequencing and 16 assay for transposase accessible chromatin (ATAC)-sequencing profiles. We also demonstrate strong reproducibility of the datasets and have identified specific genes and open chromatin regions in the genome that may be associated with the social function of these castes. Our data will be a valuable resource for further studies of insect behaviour, particularly the role of brain in the control of eusociality.
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Affiliation(s)
- Mingyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yang Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Tinggang Wen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Weiwei Liu
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institution of Zoology, Chinese Academy of Science, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kunming, 650223, China
| | - Qionghua Gao
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institution of Zoology, Chinese Academy of Science, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kunming, 650223, China
| | - Jie Zhao
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institution of Zoology, Chinese Academy of Science, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kunming, 650223, China
| | - Zijun Xiong
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wei Jiang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yeya Yu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI College, Zhengzhou University, Zhengzhou, 450000, China
| | - Liang Wu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Yuan
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaoyu Wei
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jiangshan Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mengnan Cheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Pei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Panyi Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Huanming Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310013, China
| | - Guojie Zhang
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
- State Key Laboratory of Genetic Resource and Evolution, Kunming Institution of Zoology, Chinese Academy of Science, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kunming, 650223, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Qiye Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Gene Bank, BGI-Shenzhen, Shenzhen, 518120, China.
- Shenzhen Bay Laboratory, Shenzhen, 518083, China.
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38
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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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39
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Cunningham CB. Functional genomics of parental care of insects. Horm Behav 2020; 122:104756. [PMID: 32353447 DOI: 10.1016/j.yhbeh.2020.104756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022]
Abstract
Parental care was likely the first step most lineages made towards sociality. However, the molecular mechanisms that generate parental care are not broadly characterized. Insects are important as an evolutionary independent group from classic models of parental care, such as, house mice. They provide an opportunity to test the generality of our understanding. With this review, I survey the functional genomics of parental care of insects, summarize several recent advances in the broader framework for studying and understanding parental care, and finish with suggested priorities for further research. Although there are too few studies to draw definitive conclusions, I argue that natural selection appears to be rewiring existing gene networks to produce parental care, that the epigenetic mechanisms influencing parental care are not well understood, and, as an interesting early consensus, that genes strongly associated with carer/offspring interactions appear biased towards proteins that are secreted. I summarize the studies that have functionally validate candidate genes and highlight the increasing need to perform this work. I finish with arguments for both conceptual and practical changes moving forward. I argue that future work can increase the use of predictive frameworks, broaden its definition of conservation of mechanism to gene networks rather than single genes, and increase the use of more established comparative methods. I further highlight the practical considerations of standardizing analyses and reporting, increasing the sampling of both carers and offspring, better characterizing gene regulatory networks, better characterizing taxonomically restricted genes and any consistent role they have underpinning parental care, and using factorial designs to disentangle the influence of multiple variables on the expression of parental care.
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40
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Friedman DA, Johnson BR, Linksvayer TA. Distributed physiology and the molecular basis of social life in eusocial insects. Horm Behav 2020; 122:104757. [PMID: 32305342 DOI: 10.1016/j.yhbeh.2020.104757] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single multicellular organism. In the colonial (eusocial) insects such as ants, bees, and termites, molecular and behavioral responses of interacting nestmates are tightly linked, and key physiological processes are regulated at the scale of the colony. Such colony-level physiological processes regulate nestmate physiology in a distributed fashion, through various social communication mechanisms. As a result of physiological decentralization over evolutionary time, organismal mechanisms, for example related to pheromone detection, hormone signaling, and neural signaling pathways, are deployed in novel contexts to influence nestmate and colony traits. Here we explore how functional genomic, physiological, and behavioral studies can benefit from considering the traits of eusocial insects in this light. We highlight functional genomic work exploring how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages. We also consider similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and make specific hypotheses regarding the physiology of eusocial taxa. Integrating theoretical models of distributed systems with empirical functional genomics approaches will be useful in addressing fundamental questions related to the evolution of eusociality and collective behavior in natural systems.
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Affiliation(s)
- D A Friedman
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America.
| | - B R Johnson
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America
| | - T A Linksvayer
- University of Pennsylvania, Department of Biology, Pennsylvania, PA 19104, United States of America
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41
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A Single Gene Causes Thelytokous Parthenogenesis, the Defining Feature of the Cape Honeybee Apis mellifera capensis. Curr Biol 2020; 30:2248-2259.e6. [DOI: 10.1016/j.cub.2020.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/05/2020] [Accepted: 04/15/2020] [Indexed: 02/01/2023]
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42
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Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A 2020; 117:13615-13625. [PMID: 32471944 PMCID: PMC7306772 DOI: 10.1073/pnas.2000344117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Developmental processes are an important source of phenotypic variation, but the extent to which this variation contributes to evolutionary change is unknown. We used integrative genomic analyses to explore the relationship between developmental and social plasticity in a bee species that can adopt either a social or solitary lifestyle. We find genes regulating this social flexibility also regulate development, and positive selection on these genes is influenced by their function during development. This suggests that developmental plasticity may influence the evolution of sociality. Our additional finding of genetic variants linked to differences in social behavior sheds light on how phenotypic variation derived from development may become encoded into the genome, and thus contribute to evolutionary change. Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality.
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43
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Tong C, Najm GM, Pinter-Wollman N, Pruitt JN, Linksvayer TA. Comparative Genomics Identifies Putative Signatures of Sociality in Spiders. Genome Biol Evol 2020; 12:122-133. [PMID: 31960912 PMCID: PMC7108510 DOI: 10.1093/gbe/evaa007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 12/15/2022] Open
Abstract
Comparative genomics has begun to elucidate the genomic basis of social life in insects, but insight into the genomic basis of spider sociality has lagged behind. To begin, to characterize genomic signatures associated with the evolution of social life in spiders, we performed one of the first spider comparative genomics studies including five solitary species and two social species, representing two independent origins of sociality in the genus Stegodyphus. We found that the two social spider species had a large expansion of gene families associated with transport and metabolic processes and an elevated genome-wide rate of molecular evolution compared with the five solitary spider species. Genes that were rapidly evolving in the two social species relative to the five solitary species were enriched for transport, behavior, and immune functions, whereas genes that were rapidly evolving in the solitary species were enriched for energy metabolism processes. Most rapidly evolving genes in the social species Stegodyphus dumicola were broadly expressed across four tissues and enriched for transport functions, but 12 rapidly evolving genes showed brain-specific expression and were enriched for social behavioral processes. Altogether, our study identifies putative genomic signatures and potential candidate genes associated with spider sociality. These results indicate that future spider comparative genomic studies, including broader sampling and additional independent origins of sociality, can further clarify the genomic causes and consequences of social life.
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Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania
| | - Gabriella M Najm
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Noa Pinter-Wollman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Jonathan N Pruitt
- Department of Psychology, Neurobiology & Behaviour, McMaster University, Hamilton, Ontario, Canada
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Abstract
Neuroscience has a long, rich history in embracing unusual animals for research. Over the past several decades, there has been a technology-driven bottleneck in the species used for neuroscience research. However, an oncoming wave of technologies applicable to many animals hold promise for enabling researchers to address challenging scientific questions that cannot be solved using traditional laboratory animals. Here, we discuss how leveraging the convergent evolution of physiological or behavioral phenotypes can empower research mapping genotype to phenotype interactions. We present two case studies using electric fish and poison frogs and discuss how comparative work can teach us about evolutionary constraint and flexibility at various levels of biological organization. We also offer advice on the potential and pitfalls of establishing novel model systems in neuroscience research. Finally, we end with a discussion on the use of charismatic animals in neuroscience research and their utility in public outreach. Overall, we argue that convergent evolution frameworks can help identify generalizable principles of neuroscience.
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Affiliation(s)
- Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
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45
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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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