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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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2
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552006. [PMID: 38014205 PMCID: PMC10680569 DOI: 10.1101/2023.08.04.552006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A. Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robin A. Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F. Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A. Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R. Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C. Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O. Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T. Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M. Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C. Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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Bresnahan ST, Galbraith D, Ma R, Anton K, Rangel J, Grozinger CM. Beyond conflict: Kinship theory of intragenomic conflict predicts individual variation in altruistic behaviour. Mol Ecol 2023; 32:5823-5837. [PMID: 37746895 DOI: 10.1111/mec.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Behavioural variation is essential for animals to adapt to different social and environmental conditions. The Kinship Theory of Intragenomic Conflict (KTIC) predicts that parent-specific alleles can support different behavioural strategies to maximize allele fitness. Previous studies, including in honey bees (Apis mellifera), supported predictions of the KTIC for parent-specific alleles to promote selfish behaviour. Here, we test the KTIC prediction that for altruism-promoting genes (i.e. those that promote behaviours that support the reproductive fitness of kin), the allele with the higher altruism optimum should be selected to be expressed while the other is silenced. In honey bee colonies, workers act altruistically when tending to the queen by performing a 'retinue' behaviour, distributing the queen's mandibular pheromone (QMP) throughout the hive. Workers exposed to QMP do not activate their ovaries, ensuring they care for the queen's brood instead of competing to lay unfertilized eggs. Due to the haplodiploid genetics of honey bees, the KTIC predicts that response to QMP is favoured by the maternal genome. We report evidence for parent-of-origin effects on the retinue response behaviour, ovarian development and gene expression in brains of worker honey bees exposed to QMP, consistent with the KTIC. Additionally, we show enrichment for genes with parent-of-origin expression bias within gene regulatory networks associated with variation in bees' response to QMP. Our study demonstrates that intragenomic conflict can shape diverse social behaviours and influence expression patterns of single genes as well as gene networks.
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Affiliation(s)
- Sean T Bresnahan
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David Galbraith
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rong Ma
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kate Anton
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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5
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Ferguson ST, Bakis I, Edwards ND, Zwiebel LJ. Age and Task Modulate Olfactory Sensitivity in the Florida Carpenter Ant Camponotus floridanus. INSECTS 2023; 14:724. [PMID: 37754692 PMCID: PMC10532128 DOI: 10.3390/insects14090724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023]
Abstract
Age-related changes in behavior and sensory perception have been observed in a wide variety of animal species. In ants and other eusocial insects, workers often progress through an ordered sequence of olfactory-driven behavioral tasks. Notably, these behaviors are plastic, and workers adapt and rapidly switch tasks in response to changing environmental conditions. In the Florida carpenter ant, smaller minors typically perform most of the work needed to maintain the colony, while the larger majors are specialized for nest defense and rarely engage in these routine tasks. Here, we investigate the effects of age and task group on olfactory responses to a series of odorant blends in minor and major worker castes. Consistent with their respective roles within the colony, we observed significant age-associated shifts in the olfactory responses of minors as they transitioned between behavioral states, whereas the responses of majors remained consistently low regardless of age. Furthermore, we have identified a unitary compound, 3-methylindole, which elicited significantly higher responses and behavioral aversion in minor nurses than in similarly aged foragers suggesting that this compound may play an important role in brood care. Taken together, our results suggest that age- and task-associated shifts in olfactory physiology may play a critical role in the social organization of ant colonies.
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Affiliation(s)
| | | | | | - Laurence J. Zwiebel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; (S.T.F.); (I.B.); (N.D.E.)
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6
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Ferguson ST, Bakis I, Edwards ND, Zwiebel LJ. Age and Task Modulate Olfactory Sensitivity in the Florida Carpenter Ant Camponotus floridanus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549561. [PMID: 37503123 PMCID: PMC10370051 DOI: 10.1101/2023.07.18.549561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Age-related changes in behavior and sensory perception have been observed in a wide variety of animal species. In ants and other eusocial insects, workers often progress through an ordered sequence of olfactory-driven behavioral tasks. Notably, these behaviors are plastic, and workers adapt and rapidly switch tasks in response to changing environmental conditions. In the Florida carpenter ant, smaller minors typically perform most of the work needed to maintain the colony while the larger majors are specialized for nest defense and rarely engage in these routine tasks. Here, we investigate the effects of age and task group on olfactory responses to a series of odorant blends in minor and major worker castes. Consistent with their respective roles within the colony, we observed significant age-associated shifts in the olfactory responses of minors as they transitioned between behavioral states, whereas the responses of majors remained consistently low regardless of age. Furthermore, we identified a unitary compound, 3-methylindole, which elicited significantly higher responses and behavioral aversion in minor nurses than in similarly aged foragers suggesting that this compound may play an important role in brood care. Taken together, our results suggest that age- and task-associated shifts in olfactory physiology may play a critical role in the social organization of ant colonies. Simple Summary Florida carpenter ants ( Camponotus floridanus ) live in colonies comprised of thousands of workers. The smallest workers, known as minors, engage in routine tasks such as nursing and foraging while the largest workers, known as majors, are thought to be soldiers specialized for defending the nest. How ant colonies allocate their workforce to address the dynamic and ever-changing needs of the colonies remains an open question in the field, but current evidence suggests that ant social behavior likely results from a combination of genetic/epigenetic, physiological, and systems-level processes. Here, we extend these studies by investigating the role of olfactory sensitivity in regulating ant behavior. Minor workers exhibited significant shifts in olfactory sensitivity and odor coding as they aged and switched tasks. The olfactory sensitivity of majors, however, remained relatively stable as they aged. From these studies, we also identified a single compound, 3-methylindole, which elicited significantly higher olfactory responses and aversive behavior in nurses compared to foragers, suggesting that this chemical may have a role in brood care. Overall, these studies support the hypothesis that changes in olfactory sensitivity play an important role in regulating social behavior in ants.
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7
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Das B, Gordon DM. Biological rhythms and task allocation in ant colonies. CURRENT OPINION IN INSECT SCIENCE 2023:101062. [PMID: 37247773 DOI: 10.1016/j.cois.2023.101062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
Task allocation in ant colonies, mediated by social interactions, regulates which individuals perform each task, and when they are active, in response to the current situation. Many tasks are performed in a daily temporal pattern. An ant's biological clock depends on patterns of gene expression that are regulated using a negative feedback loop which is synchronized to earth's rotation by external cues. An individual's biological clock can shift in response to social cues, and this plasticity contributes to task switching. Daily rhythms in individual ant behavior combine, via interactions within and across task groups, to adjust the collective behavior of colonies. Further work is needed to elucidate how the social cues that lead to task switching influence the molecular mechanisms that generate clock outputs associated with each task, and to investigate the evolution of temporal patterns in task allocation in relation to ecological factors.
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8
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Van Cleve J. Evolutionarily stable strategy analysis and its links to demography and genetics through invasion fitness. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210496. [PMID: 36934754 PMCID: PMC10024993 DOI: 10.1098/rstb.2021.0496] [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: 11/16/2022] [Accepted: 02/07/2023] [Indexed: 03/21/2023] Open
Abstract
Evolutionarily stable strategy (ESS) analysis pioneered by Maynard Smith and Price took off in part because it often does not require explicit assumptions about the genetics and demography of a population in contrast to population genetic models. Though this simplicity is useful, it obscures the degree to which ESS analysis applies to populations with more realistic genetics and demography: for example, how does ESS analysis handle complexities such as kin selection, group selection and variable environments when phenotypes are affected by multiple genes? In this paper, I review the history of the ESS concept and show how early uncertainty about the method lead to important mathematical theory linking ESS analysis to general population genetic models. I use this theory to emphasize the link between ESS analysis and the concept of invasion fitness. I give examples of how invasion fitness can measure kin selection, group selection and the evolution of linked modifier genes in response to variable environments. The ESSs in these examples depend crucially on demographic and genetic parameters, which highlights how ESS analysis will continue to be an important tool in understanding evolutionary patterns as new models address the increasing abundance of genetic and long-term demographic data in natural populations. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.
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Affiliation(s)
- Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
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9
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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: 5] [Impact Index Per Article: 2.5] [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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10
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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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11
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cis-Regulatory changes in locomotor genes are associated with the evolution of burrowing behavior. Cell Rep 2022; 38:110360. [PMID: 35172153 DOI: 10.1016/j.celrep.2022.110360] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits, and some behaviors, is linked to cis-regulatory changes in gene expression. Given this, we compare brain gene expression of two interfertile sister species of Peromyscus mice that show large and heritable differences in burrowing behavior. Species-level differential expression and allele-specific expression in F1 hybrids indicate a preponderance of cis-regulatory divergence, including many genes whose cis-regulation is affected by burrowing behavior. Genes related to locomotor coordination show the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. Furthermore, genetic markers closest to these candidate genes associate with variation in burrow shape in a genetic cross, suggesting an enrichment for loci affecting burrowing behavior near these candidate locomotor genes. Our results provide insight into how cis-regulated gene expression can depend on behavioral context and how this dynamic regulatory divergence between species may contribute to behavioral evolution.
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12
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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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13
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Walsh JT, Garonski A, Jackan C, Linksvayer TA. The Collective Behavior of Ant Groups Depends on Group Genotypic Composition. J Hered 2021; 113:102-108. [PMID: 34634803 DOI: 10.1093/jhered/esab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/06/2021] [Indexed: 11/12/2022] Open
Abstract
Recently, researchers have documented variation between groups in collective behavior. However, how genetic variation within and between groups contributes to population-level variation for collective behavior remains unclear. Understanding how genetic variation of group members relates to group-level phenotypes is evolutionarily important because there is increasing evidence that group-level behavioral variation influences fitness and that the genetic architecture of group-level traits can affect the evolutionary dynamics of traits. Social insects are ideal for studying the complex relationship between individual and group-level variation because they exhibit behavioral variation at multiple scales of organization. To explore how the genetic composition of groups affects collective behavior, we constructed groups of pharaoh ants (Monomorium pharaonis) from 33 genetically distinct colonies of known pedigree. The groups consisted of either all workers from the same single colony or workers from two genetically different colonies, and we assayed the exploration and aggression of the groups. We found that collective exploration, but not aggression, depended on the specific genotypic combination of group members, i.e., we found evidence for genotype-by-genotype epistasis for exploration. Group collective behavior did not depend on the pedigree relatedness between genotypes within groups. Overall, this study highlights that specific combinations of genotypes influence group-level phenotypes, emphasizing the importance of considering nonadditive effects of genotypic interactions between group members.
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Affiliation(s)
- Justin T Walsh
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Garonski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Claire Jackan
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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14
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Gao Q, Xiong Z, Larsen RS, Zhou L, Zhao J, Ding G, Zhao R, Liu C, Ran H, Zhang G. High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis. Gigascience 2020; 9:6034789. [PMID: 33319913 PMCID: PMC7736795 DOI: 10.1093/gigascience/giaa143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.
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Affiliation(s)
- Qionghua Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Rasmus Stenbak Larsen
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Long Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Jie Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guo Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chengyuan Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hao Ran
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
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15
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Muratore IB, Traniello JFA. Fungus-Growing Ants: Models for the Integrative Analysis of Cognition and Brain Evolution. Front Behav Neurosci 2020; 14:599234. [PMID: 33424560 PMCID: PMC7793780 DOI: 10.3389/fnbeh.2020.599234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/23/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - James F. A. Traniello
- Department of Biology, Boston University, Boston, MA, United States
- Graduate Program in Neuroscience, Boston University, Boston, MA, United States
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16
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Bloch NI, Corral‐López A, Buechel SD, Kotrschal A, Kolm N, Mank JE. Different mating contexts lead to extensive rewiring of female brain coexpression networks in the guppy. GENES BRAIN AND BEHAVIOR 2020; 20:e12697. [DOI: 10.1111/gbb.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/10/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Natasha I. Bloch
- Department of Biomedical Engineering Universidad de Los Andes Bogotá D.C. Colombia
| | - Alberto Corral‐López
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
- Department of Genetics, Evolution and Environment University College London UK
| | | | - Alexander Kotrschal
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
- Wageningen University Behavioral Ecology Group Wageningen Netherlands
| | - Niclas Kolm
- Department of Zoology/Ethology Stockholm University Stockholm Sweden
| | - Judith E. Mank
- University of British Columbia Department of Zoology and Biodiversity Research Centre Vancouver Canada
- Department of Genetics, Evolution and Environment University College London UK
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17
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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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18
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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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19
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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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20
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Friedman DA, York RA, Hilliard AT, Gordon DM. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior. Commun Biol 2020; 3:100. [PMID: 32139795 PMCID: PMC7057964 DOI: 10.1038/s42003-020-0813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.
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Affiliation(s)
| | | | | | - Deborah M Gordon
- Stanford University, Department of Biology, Stanford, CA, 94305, USA.
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21
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Fan P, Han B, Hu H, Wei Q, Zhang X, Meng L, Nie J, Tang X, Tian X, Zhang L, Wang L, Li J. Proteome of thymus and spleen reveals that 10-hydroxydec-2-enoic acid could enhance immunity in mice. Expert Opin Ther Targets 2020; 24:267-279. [PMID: 32077781 DOI: 10.1080/14728222.2020.1733529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objectives: 10-hydroxydec-2-enoic acid (10-HDA), a unique component of royal jelly existing only in nature, has the potential to promote human health. Knowledge of 10-HDA in regulating immuno-activity, however, is lacking. The aim of our work is to gain a novel understanding of 10-HDA in promoting immunity.Methods: Immuno-suppressed mice were generated by cyclophosphamide injection, After 10-HDA supplementation to the mice to rescue their immunity, the proteomes of the thymus and spleen were analyzed.Results: The weight of the body, thymus, and spleen in cyclophosphamide-induced mice recovered by 10-HDA indicate its potential role in immuno-organ protection. In the thymus, the enhanced activity of pathways associated with DNA/RNA/protein activities may be critical for T-lymphocyte proliferation/differentiation, and cytotoxicity. In the spleen, the induced pathways involved in DNA/RNA/protein activities, and cell proliferative stimulation suggest their vital role in B-lymphocyte affinity maturation, antigen presentation, and macrophage activity. The up-regulated proteins highly connected in networks modulated by 10-HDA indicate that the mice may evolve tactics to respond to immuno-organ impairment by activating critical physiological processes.Conclusion: Our data constitute a proof-of-concept that 10-HDA is a potential agent to improve immunity in the thymus and spleen and offer a new venue for applying natural products to the therapy for hypoimmunity.
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Affiliation(s)
- Pei Fan
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Bin Han
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Han Hu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Qiaohong Wei
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xufeng Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Lifeng Meng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jing Nie
- Department of Technology, Hunan SJA Laboratory Animal Co., Ltd, Changsha, PR China
| | - Xiaofeng Tang
- Department of Technology, Hunan SJA Laboratory Animal Co., Ltd, Changsha, PR China
| | - Xinyue Tian
- College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Lu Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Liping Wang
- Department of Research & Development, Henan Jianda Bio Sci. & Tech. Co., Ltd, Zhengzhou, PR China
| | - Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
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22
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Araki M, Miyakawa MO, Suzuki T, Miyakawa H. Two insulin‐like peptides may regulate egg production in opposite directions via juvenile hormone signaling in the queenless antPristomyrmex punctatus. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:225-234. [DOI: 10.1002/jez.b.22935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Marina Araki
- Center for Bioscience Research and EducationUtsunomiya UniversityUtsunomiya Tochigi Japan
| | - Misato O. Miyakawa
- Center for Bioscience Research and EducationUtsunomiya UniversityUtsunomiya Tochigi Japan
| | - Tomohiro Suzuki
- Center for Bioscience Research and EducationUtsunomiya UniversityUtsunomiya Tochigi Japan
| | - Hitoshi Miyakawa
- Center for Bioscience Research and EducationUtsunomiya UniversityUtsunomiya Tochigi Japan
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23
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Rubin BER, Jones BM, Hunt BG, Kocher SD. Rate variation in the evolution of non-coding DNA associated with social evolution in bees. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180247. [PMID: 31154980 PMCID: PMC6560270 DOI: 10.1098/rstb.2018.0247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 11/12/2022] Open
Abstract
The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Benjamin E. R. Rubin
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Beryl M. Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Brendan G. Hunt
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Sarah D. Kocher
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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24
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Warner MR, Qiu L, Holmes MJ, Mikheyev AS, Linksvayer TA. Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes. Nat Commun 2019; 10:2651. [PMID: 31201311 PMCID: PMC6570765 DOI: 10.1038/s41467-019-10546-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pharaonis) and honey bees (Apis mellifera), representing two independent origins of eusociality. We identify a substantial shared core of genes upregulated in the abdomens of queen ants and honey bees that also tends to be upregulated in mated female flies, suggesting that these genes are part of a conserved insect reproductive groundplan. Outside of this shared groundplan, few genes are differentially expressed in common. Instead, the majority of the thousands of caste-associated genes are plastically expressed, rapidly evolving, and relatively evolutionarily young. These results emphasize that the recruitment of both highly conserved and lineage-specific genes underlie the convergent evolution of novel traits such as eusociality. Eusocial caste systems have evolved independently multiple times. Here, Warner et al. investigate the amount of shared vs. lineage-specific genes involved in the evolution of caste in pharaoh ants and honey bees by comparing transcriptomes across tissues, developmental stages, and castes.
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Affiliation(s)
| | - Lijun Qiu
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Michael J Holmes
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,School of Life and Environmental Science, University of Sydney, Sydney, 2006, Australia
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,Research School of Biology, Australian National University, Canberra, 0200, Australia
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25
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 DOI: 10.1101/514356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 05/20/2023] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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26
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 PMCID: PMC6544314 DOI: 10.1371/journal.pgen.1008156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R. Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A. Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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27
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Kohlmeier P, Alleman AR, Libbrecht R, Foitzik S, Feldmeyer B. Gene expression is more strongly associated with behavioural specialization than with age or fertility in ant workers. Mol Ecol 2019; 28:658-670. [PMID: 30525254 DOI: 10.1111/mec.14971] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022]
Abstract
The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and more corpulent. Here, we experimentally disentangle behavioural specialization from age and fertility in Temnothorax longispinosus ant workers and analyse how these parameters are linked to whole-body gene expression. A total of 3,644 genes were associated with behavioural specialization which is ten times more than associated with age and 50 times more than associated with fertility. Brood carers were characterized by an upregulation of three Vitellogenin (Vg) genes, one of which, Vg-like A, was the most differentially expressed gene that was recently shown experimentally to control the switch from brood to worker care. The expression of Conventional Vg was unlinked to behavioural specialization, age or fertility, which contrasts to studies on bees and some ants. Diversity in Vg/Vg-like copy number and expression bias across ants supports subfunctionalization of Vg genes and indicates that some regulatory mechanisms of division of labour diverged in different ant lineages. Simulations revealed that our experimental dissociation of co-varying factors reduced transcriptomic noise, suggesting that confounding factors could potentially explain inconsistencies across transcriptomic studies of behavioural specialization in ants. Thus, our study reveals that worker gene expression is mainly linked to the worker's function for the colony and provides novel insights into the evolution of sociality in ants.
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Affiliation(s)
- Philip Kohlmeier
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Austin R Alleman
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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28
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Blaz J, Barrera-Redondo J, Vázquez-Rosas-Landa M, Canedo-Téxon A, Aguirre von Wobeser E, Carrillo D, Stouthamer R, Eskalen A, Villafán E, Alonso-Sánchez A, Lamelas A, Ibarra-Juarez LA, Pérez-Torres CA, Ibarra-Laclette E. Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. Life (Basel) 2018; 9:E2. [PMID: 30583535 PMCID: PMC6463014 DOI: 10.3390/life9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/08/2018] [Accepted: 12/20/2018] [Indexed: 01/03/2023] Open
Abstract
Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus⁻Fusarium euwallaceae and Xyleborus glabratus⁻Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.
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Affiliation(s)
- Jazmín Blaz
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México 04500, Mexico.
| | | | - Anahí Canedo-Téxon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | | | - Daniel Carrillo
- Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA.
| | - Richard Stouthamer
- Department of Plant Pathology, University of California⁻Riverside, Riverside, CA 92521, USA.
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616-8751, USA.
| | - Emanuel Villafán
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
| | - Luis Arturo Ibarra-Juarez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
- Cátedras CONACyT/Instituto de Ecología A.C., Xalapa, Veracruz 91070, Mexico.
| | - Claudia Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
- Cátedras CONACyT/Instituto de Ecología A.C., Xalapa, Veracruz 91070, Mexico.
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, Veracruz 91070, Mexico.
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29
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Kocher SD. A toolkit for caste differentiation. Nat Ecol Evol 2018; 2:1689-1690. [DOI: 10.1038/s41559-018-0705-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Friedman DA, Pilko A, Skowronska-Krawczyk D, Krasinska K, Parker JW, Hirsh J, Gordon DM. The Role of Dopamine in the Collective Regulation of Foraging in Harvester Ants. iScience 2018; 8:283-294. [PMID: 30270022 PMCID: PMC6205345 DOI: 10.1016/j.isci.2018.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/04/2018] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
Colonies of the red harvester ant (Pogonomyrmex barbatus) differ in how they regulate collective foraging activity in response to changes in humidity. We used transcriptomic, physiological, and pharmacological experiments to investigate the molecular basis of this ecologically important variation in collective behavior among colonies. RNA sequencing of forager brain tissue showed an association between colony foraging activity and differential expression of transcripts related to biogenic amine and neurohormonal metabolism and signaling. In field experiments, pharmacological increases in forager brain dopamine titer caused significant increases in foraging activity. Colonies that were naturally most sensitive to humidity were significantly more responsive to the stimulatory effect of exogenous dopamine. In addition, forager brain tissue significantly varied among colonies in biogenic amine content. Neurophysiological variation among colonies associated with individual forager sensitivity to humidity may reflect the heritable molecular variation on which natural selection acts to shape the collective regulation of foraging.
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Affiliation(s)
- Daniel A Friedman
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Anna Pilko
- Department of Chemistry and Biochemistry and the Institute for Quantitative and Computational Biosciences (QCB), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorota Skowronska-Krawczyk
- Shiley Eye Institute, Richard C. Atkinson Lab for Regenerative Ophthalmology, Department of Ophthalmology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karolina Krasinska
- Stanford University Mass Spectrometry, Stanford University, Stanford, CA 94305, USA
| | - Jacqueline W Parker
- Department of Biology, University of Virginia, Charlottesville, Charlottesville, VA 22904, USA
| | - Jay Hirsh
- Department of Biology, University of Virginia, Charlottesville, Charlottesville, VA 22904, USA
| | - Deborah M Gordon
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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31
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Qiu B, Larsen RS, Chang NC, Wang J, Boomsma JJ, Zhang G. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat Ecol Evol 2018; 2:1782-1791. [PMID: 30349091 PMCID: PMC6217981 DOI: 10.1038/s41559-018-0689-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
Specialized queens and life-time unmated workers evolved once in the common ancestor of all ants, but whether caste development across ants continues to be at least partly regulated by a single core set of genes remains obscure. We analysed brain transcriptomes from five ant species (three subfamilies) and reconstructed the origins of genes with caste-biased expression. Ancient genes predating the Neoptera were more likely to regulate gyne (virgin queen) phenotypes, while caste differentiation roles of younger, ant-lineage-specific genes varied. Transcriptome profiling showed that the ancestral network for caste-specific gene-regulation has been maintained, but that signatures of common ancestry are obscured by later modifications. Adjusting for such differences, we identified a core gene-set that: 1. consistently displayed similar directions and degrees of caste-differentiated expression, and 2. have mostly not been reported as being involved in caste differentiation. These core regulatory genes exist in the genomes of ant species that secondarily lost the queen caste, but expression differences for reproductive and sterile workers are minor and similar to social paper wasps that lack differentiated castes. Many caste-biased ant genes have caste-differentiated expression in honeybees, but directions of caste bias were uncorrelated, as expected when permanent castes evolved independently in both lineages.
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Affiliation(s)
- Bitao Qiu
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Stenbak Larsen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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32
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Johnson BR. Taxonomically Restricted Genes Are Fundamental to Biology and Evolution. Front Genet 2018; 9:407. [PMID: 30294344 PMCID: PMC6158316 DOI: 10.3389/fgene.2018.00407] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022] Open
Abstract
Genes limited to particular clades, taxonomically restricted genes (TRGs), are common in all sequenced genomes. TRGs have recently become associated with the evolution of novelty, as numerous studies across the tree of life have now linked expression of TRGs with novel phenotypes. However, TRGs that underlie ancient lineage specific traits have been largely omitted from discussions of the general importance of TRGs. Here it is argued that when all TRGs are considered, it is apparent that TRGs are fundamental to biology and evolution and likely play many complementary roles to the better understood toolkit genes. Genes underlying photosynthesis and skeletons, for example, are examples of commonplace fundamental TRGs. Essentially, although basic cell biology has a highly conserved genetic basis across the tree of life, most major clades also have lineage specific traits central to their biology and these traits are often based on TRGs. In short, toolkit genes underlie what is conserved across organisms, while TRGs define in many cases what is unique. An appreciation of the importance of TRGs will improve our understanding of evolution by triggering the study of neglected topics in which TRGs are of paramount importance.
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Affiliation(s)
- Brian R Johnson
- Department of Entomology and Nematology, Center for Population Biology, University of California, Davis, Davis, CA, United States
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33
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Ant nurse workers exhibit behavioural and transcriptomic signatures of specialization on larval stage. Anim Behav 2018. [DOI: 10.1016/j.anbehav.2018.05.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Favreau E, Martínez-Ruiz C, Rodrigues Santiago L, Hammond RL, Wurm Y. Genes and genomic processes underpinning the social lives of ants. CURRENT OPINION IN INSECT SCIENCE 2018; 25:83-90. [PMID: 29602366 DOI: 10.1016/j.cois.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 05/06/2023]
Abstract
The >15000 ant species are all highly social and show great variation in colony organization, complexity and behavior. The mechanisms by which such sociality evolved, as well as those underpinning the elaboration of ant societies since their ∼140 million year old common ancestor, have long been pondered. Here, we review recent insights generated using various genomic approaches. This includes understanding the molecular mechanisms underlying caste differentiation and the diversity of social structures, studying the impact of eusociality on genomic evolutionary rates, and investigating gene expression changes associated with differences in lifespan between castes. Furthermore, functional studies involving RNAi and CRISPR have recently been successfully applied to ants, opening the door to exciting research that promises to revolutionize the understanding of the evolution and diversification of social living.
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Affiliation(s)
- Emeline Favreau
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Carlos Martínez-Ruiz
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Leandro Rodrigues Santiago
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert L Hammond
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom.
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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35
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Ingram KK, Gordon DM, Friedman DA, Greene M, Kahler J, Peteru S. Context-dependent expression of the foraging gene in field colonies of ants: the interacting roles of age, environment and task. Proc Biol Sci 2017; 283:rspb.2016.0841. [PMID: 27581876 PMCID: PMC5013789 DOI: 10.1098/rspb.2016.0841] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/05/2016] [Indexed: 12/31/2022] Open
Abstract
Task allocation among social insect workers is an ideal framework for studying the molecular mechanisms underlying behavioural plasticity because workers of similar genotype adopt different behavioural phenotypes. Elegant laboratory studies have pioneered this effort, but field studies involving the genetic regulation of task allocation are rare. Here, we investigate the expression of the foraging gene in harvester ant workers from five age- and task-related groups in a natural population, and we experimentally test how exposure to light affects foraging expression in brood workers and foragers. Results from our field study show that the regulation of the foraging gene in harvester ants occurs at two time scales: levels of foraging mRNA are associated with ontogenetic changes over weeks in worker age, location and task, and there are significant daily oscillations in foraging expression in foragers. The temporal dissection of foraging expression reveals that gene expression changes in foragers occur across a scale of hours and the level of expression is predicted by activity rhythms: foragers have high levels of foraging mRNA during daylight hours when they are most active outside the nests. In the experimental study, we find complex interactions in foraging expression between task behaviour and light exposure. Oscillations occur in foragers following experimental exposure to 13 L : 11 D (LD) conditions, but not in brood workers under similar conditions. No significant differences were seen in foraging expression over time in either task in 24 h dark (DD) conditions. Interestingly, the expression of foraging in both undisturbed field and experimentally treated foragers is also significantly correlated with the expression of the circadian clock gene, cycle. Our results provide evidence that the regulation of this gene is context-dependent and associated with both ontogenetic and daily behavioural plasticity in field colonies of harvester ants. Our results underscore the importance of assaying temporal patterns in behavioural gene expression and suggest that gene regulation is an integral mechanism associated with behavioural plasticity in harvester ants.
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Affiliation(s)
- Krista K Ingram
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Deborah M Gordon
- Department of Biology, Stanford University, Gilbert Biological Science Building, Stanford, CA 94305, USA
| | - Daniel A Friedman
- Department of Biology, Stanford University, Gilbert Biological Science Building, Stanford, CA 94305, USA
| | - Michael Greene
- Department of Integrative Biology, University of Colorado, Campus Box 171, PO Box 176634, Denver, CO 80217-3364, USA
| | - John Kahler
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Swetha Peteru
- Department of Geography, Texas A&M University, College Station, TX 77843, USA
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36
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Manfredini F, Romero AE, Pedroso I, Paccanaro A, Sumner S, Brown MJF. Neurogenomic Signatures of Successes and Failures in Life-History Transitions in a Key Insect Pollinator. Genome Biol Evol 2017; 9:3059-3072. [PMID: 29087523 PMCID: PMC5714134 DOI: 10.1093/gbe/evx220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 12/22/2022] Open
Abstract
Life-history transitions require major reprogramming at the behavioral and physiological level. Mating and reproductive maturation are known to trigger changes in gene transcription in reproductive tissues in a wide range of organisms, but we understand little about the molecular consequences of a failure to mate or become reproductively mature, and it is not clear to what extent these processes trigger neural as well as physiological changes. In this study, we examined the molecular processes underpinning the behavioral changes that accompany the major life-history transitions in a key pollinator, the bumblebee Bombus terrestris. We compared neuro-transcription in queens that succeeded or failed in switching from virgin and immature states, to mated and reproductively mature states. Both successes and failures were associated with distinct molecular profiles, illustrating how development during adulthood triggers distinct molecular profiles within a single caste of a eusocial insect. Failures in both mating and reproductive maturation were explained by a general up-regulation of brain gene transcription. We identified 21 genes that were highly connected in a gene coexpression network analysis: nine genes are involved in neural processes and four are regulators of gene expression. This suggests that negotiating life-history transitions involves significant neural processing and reprogramming, and not just changes in physiology. These findings provide novel insights into basic life-history transitions of an insect. Failure to mate or to become reproductively mature is an overlooked component of variation in natural systems, despite its prevalence in many sexually reproducing organisms, and deserves deeper investigation in the future.
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Affiliation(s)
- Fabio Manfredini
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Alfonso E Romero
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Inti Pedroso
- Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile
| | - Alberto Paccanaro
- Department of Computer Science, and Centre for Systems and Synthetic Biology, Royal Holloway University of London, Egham, United Kingdom
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, United Kingdom
- Present address: Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
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37
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Warner MR, Mikheyev AS, Linksvayer TA. Genomic Signature of Kin Selection in an Ant with Obligately Sterile Workers. Mol Biol Evol 2017; 34:1780-1787. [PMID: 28419349 PMCID: PMC5455959 DOI: 10.1093/molbev/msx123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Kin selection is thought to drive the evolution of cooperation and conflict, but the specific genes and genome-wide patterns shaped by kin selection are unknown. We identified thousands of genes associated with the sterile ant worker caste, the archetype of an altruistic phenotype shaped by kin selection, and then used population and comparative genomic approaches to study patterns of molecular evolution at these genes. Consistent with population genetic theoretical predictions, worker-upregulated genes experienced reduced selection compared with genes upregulated in reproductive castes. Worker-upregulated genes included more taxonomically restricted genes, indicating that the worker caste has recruited more novel genes, yet these genes also experienced reduced selection. Our study identifies a putative genomic signature of kin selection and helps to integrate emerging sociogenomic data with longstanding social evolution theory.
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Affiliation(s)
- Michael R Warner
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan
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38
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Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R. Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans. Sci Rep 2017; 7:13547. [PMID: 29051502 PMCID: PMC5648782 DOI: 10.1038/s41598-017-13176-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeng 4, 6708 WE, Wageningen, The Netherlands
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- Biological Sciences Department, NYC College of Technology, City University of New York, 300 Jay Street, Brooklyn, New York, 11201, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Heike Hadrys
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- ITZ, Ecology&Evolution, University of Veterinary Medicine Hanover, Buenteweg 17d, D-30559, Hannover, Germany
- Yale University, Department of Ecology & Evolutionary Biology, 165 Prospect Street, New Haven, CT, 06511, USA
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
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39
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Geffre AC, Liu R, Manfredini F, Beani L, Kathirithamby J, Grozinger CM, Toth AL. Transcriptomics of an extended phenotype: parasite manipulation of wasp social behaviour shifts expression of caste-related genes. Proc Biol Sci 2017; 284:rspb.2017.0029. [PMID: 28404777 DOI: 10.1098/rspb.2017.0029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/13/2017] [Indexed: 01/17/2023] Open
Abstract
Parasites can manipulate host behaviour to increase their own transmission and fitness, but the genomic mechanisms by which parasites manipulate hosts are not well understood. We investigated the relationship between the social paper wasp, Polistes dominula, and its parasite, Xenos vesparum (Insecta: Strepsiptera), to understand the effects of an obligate endoparasitoid on its host's brain transcriptome. Previous research suggests that X. vesparum shifts aspects of host social caste-related behaviour and physiology in ways that benefit the parasitoid. We hypothesized that X. vesparum-infested (stylopized) females would show a shift in caste-related brain gene expression. Specifically, we predicted that stylopized females, who would normally be workers, would show gene expression patterns resembling pre-overwintering queens (gynes), reflecting gyne-like changes in behaviour. We used RNA-sequencing data to characterize patterns of brain gene expression in stylopized females and compared these with those of unstylopized workers and gynes. In support of our hypothesis, we found that stylopized females, despite sharing numerous physiological and life-history characteristics with members of the worker caste, show gyne-shifted brain expression patterns. These data suggest that the parasitoid affects its host by exploiting phenotypic plasticity related to social caste, thus shifting naturally occurring social behaviour in a way that is beneficial to the parasitoid.
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Affiliation(s)
- Amy C Geffre
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Ruolin Liu
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
| | - Fabio Manfredini
- School of Biological Sciences and Centre for Systems and Synthetic Biology, Royal Holloway, University of London, London, UK
| | - Laura Beani
- Department of Biology, University of Florence, Florence, Italy
| | | | - Christina M Grozinger
- Center for Pollinator Research and Department of Entomology, Pennsylvania State University, State College, PA, USA
| | - Amy L Toth
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA .,Department of Entomology, Iowa State University, Ames, IA, USA
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40
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Abstract
The study of insect social behavior has offered tremendous insight into the molecular mechanisms mediating behavioral and phenotypic plasticity. Genomic applications to the study of eusocial insect species, in particular, have led to several hypotheses for the processes underlying the molecular evolution of behavior. Advances in understanding the genetic control of social organization have also been made, suggesting an important role for supergenes in the evolution of divergent behavioral phenotypes. Intensive study of social phenotypes across species has revealed that behavior and caste are controlled by an interaction between genetic and environmentally mediated effects and, further, that gene expression and regulation mediate plastic responses to environmental signals. However, several key methodological flaws that are hindering progress in the study of insect social behavior remain. After reviewing the current state of knowledge, we outline ongoing challenges in experimental design that remain to be overcome in order to advance the field.
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Affiliation(s)
- Chelsea A Weitekamp
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland; ,
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41
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Lucas ER, Romiguier J, Keller L. Gene expression is more strongly influenced by age than caste in the ant Lasius niger. Mol Ecol 2017; 26:5058-5073. [DOI: 10.1111/mec.14256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Eric R. Lucas
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
- Department of Vector Biology; Liverpool School of Tropical Medicine; Liverpool UK
| | - Jonathan Romiguier
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
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42
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Schrader L, Helanterä H, Oettler J. Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior. Mol Biol Evol 2017; 34:535-544. [PMID: 27999112 PMCID: PMC5400372 DOI: 10.1093/molbev/msw240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Plastic gene expression underlies phenotypic plasticity and plastically expressed genes evolve under different selection regimes compared with ubiquitously expressed genes. Social insects are well-suited models to elucidate the evolutionary dynamics of plastic genes for their genetically and environmentally induced discrete polymorphisms. Here, we study the evolution of plastically expressed genes in the ant Cardiocondyla obscurior—a species that produces two discrete male morphs in addition to the typical female polymorphism of workers and queens. Based on individual-level gene expression data from 28 early third instar larvae, we test whether the same evolutionary dynamics that pertain to plastically expressed genes in adults also pertain to genes with plastic expression during development. In order to quantify plasticity of gene expression over multiple contrasts, we develop a novel geometric measure. For genes expressed during development, we show that plasticity of expression is positively correlated with evolutionary rates. We furthermore find a strong correlation between expression plasticity and expression variation within morphs, suggesting a close link between active and passive plasticity of gene expression. Our results support the notion of relaxed selection and neutral processes as important drivers in the evolution of adaptive plasticity.
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Affiliation(s)
- Lukas Schrader
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jan Oettler
- Institut für Zoologie, Universität Regensburg, Regensburg, Germany
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43
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Cunningham CB, VanDenHeuvel K, Khana DB, McKinney EC, Moore AJ. The role of neuropeptide F in a transition to parental care. Biol Lett 2017; 12:rsbl.2016.0158. [PMID: 27095268 DOI: 10.1098/rsbl.2016.0158] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/17/2016] [Indexed: 11/12/2022] Open
Abstract
The genetics of complex social behaviour can be dissected by examining the genetic influences of component pathways, which can be predicted based on expected evolutionary precursors. Here, we examine how gene expression in a pathway that influences the motivation to eat is altered during parental care that involves direct feeding of larvae. We examine the expression of neuropeptide F, and its receptor, in the burying beetle Nicrophorus vespilloides, which feeds pre-digested carrion to its begging larvae. We found that the npf receptor was greatly reduced during active care. Our research provides evidence that feeding behaviour was a likely target during the evolution of parental care in N. vespilloides Moreover, dissecting complex behaviours into ethologically distinct sub-behaviours is a productive way to begin to target the genetic mechanisms involved in the evolution of complex behaviours.
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Affiliation(s)
| | | | - Daven B Khana
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Allen J Moore
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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44
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Morandin C, Mikheyev AS, Pedersen JS, Helanterä H. Evolutionary constraints shape caste-specific gene expression across 15 ant species. Evolution 2017; 71:1273-1284. [PMID: 28262920 DOI: 10.1111/evo.13220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/16/2017] [Indexed: 12/22/2022]
Abstract
Development of polymorphic phenotypes from similar genomes requires gene expression differences. However, little is known about how morph-specific gene expression patterns vary on a broad phylogenetic scale. We hypothesize that evolution of morph-specific gene expression, and consequently morph-specific phenotypic evolution, may be constrained by gene essentiality and the amount of pleiotropic constraints. Here, we use comparative transcriptomics of queen and worker morphs, that is, castes, from 15 ant species to understand the constraints of morph-biased gene expression. In particular, we investigate how measures of evolutionary constraints at the sequence level (expression level, connectivity, and number of gene ontology [GO] terms) correlate with morph-biased expression. Our results show that genes indeed vary in their potential to become morph-biased. The existence of genes that are constrained in becoming caste-biased potentially limits the evolutionary decoupling of the caste phenotypes, that is, it might result in "caste load" occasioning from antagonistic fitness variation, similarly to sexually antagonistic fitness variation between males and females. On the other hand, we suggest that genes under low constraints are released from antagonistic variation and thus more likely to be co-opted for morph specific use. Overall, our results suggest that the factors that affect sequence evolutionary rates and evolution of plastic expression may largely overlap.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan.,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Jes Søe Pedersen
- Centre for Social Evolution, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
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45
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Cunningham CB, Badgett MJ, Meagher RB, Orlando R, Moore AJ. Ethological principles predict the neuropeptides co-opted to influence parenting. Nat Commun 2017; 8:14225. [PMID: 28145404 PMCID: PMC5296637 DOI: 10.1038/ncomms14225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/08/2016] [Indexed: 01/29/2023] Open
Abstract
Ethologists predicted that parental care evolves by modifying behavioural precursors in the asocial ancestor. As a corollary, we predict that the evolved mechanistic changes reside in genetic pathways underlying these traits. Here we test our hypothesis in female burying beetles, Nicrophorus vespilloides, an insect where caring adults regurgitate food to begging, dependent offspring. We quantify neuropeptide abundance in brains collected from three behavioural states: solitary virgins, individuals actively parenting or post-parenting solitary adults and quantify 133 peptides belonging to 18 neuropeptides. Eight neuropeptides differ in abundance in one or more states, with increased abundance during parenting in seven. None of these eight neuropeptides have been associated with parental care previously, but all have roles in predicted behavioural precursors for parenting. Our study supports the hypothesis that predictable traits and pathways are targets of selection during the evolution of parenting and suggests additional candidate neuropeptides to study in the context of parenting.
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Affiliation(s)
| | - Majors J. Badgett
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Richard B. Meagher
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Ron Orlando
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Allen J. Moore
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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46
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Linksvayer TA, Wade MJ. Theoretical Predictions for Sociogenomic Data: The Effects of Kin Selection and Sex-Limited Expression on the Evolution of Social Insect Genomes. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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47
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Babonis LS, Martindale MQ, Ryan JF. Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. BMC Evol Biol 2016; 16:114. [PMID: 27216622 PMCID: PMC4877951 DOI: 10.1186/s12862-016-0683-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone Nematostella vectensis, are the defining apomorphy of the genus Nematostella and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes. RESULTS Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp (Artemia salina) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria (E. coli) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a Nematostella-specific tissue) are enriched in Nematostella-specific genes. CONCLUSIONS Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in N. vectensis, and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that Nematostella-specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA.
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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48
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Camiletti AL, Thompson GJ. Drosophila As a Genetically Tractable Model for Social Insect Behavior. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Abstract
Many exciting studies have begun to elucidate the genetics of the morphological and physiological diversity of ants, but as yet few studies have investigated the genetics of ant behavior directly. Ant genomes are marked by extreme rates of gene turnover, especially in gene families related to olfactory communication, such as the synthesis of cuticular hydrocarbons and the perception of environmental semiochemicals. Transcriptomic and epigenetic differences are apparent between reproductive and sterile females, males and females, and workers that differ in body size. Quantitative genetic approaches suggest heritability of task performance, and population genetic studies indicate a genetic association with reproductive status in some species. Gene expression is associated with behavior including foraging, response to queens attempting to join a colony, circadian patterns of task performance, and age-related changes of task. Ant behavioral genetics needs further investigation of the feedback between individual-level physiological changes and socially mediated responses to environmental conditions.
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Affiliation(s)
- D A Friedman
- Department of Biology, Stanford University, Stanford, California 94305-5020;
| | - D M Gordon
- Department of Biology, Stanford University, Stanford, California 94305-5020;
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50
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Morandin C, Tin MMY, Abril S, Gómez C, Pontieri L, Schiøtt M, Sundström L, Tsuji K, Pedersen JS, Helanterä H, Mikheyev AS. Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants. Genome Biol 2016; 17:43. [PMID: 26951146 PMCID: PMC4780134 DOI: 10.1186/s13059-016-0902-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species. RESULTS Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another. CONCLUSIONS These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.
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Affiliation(s)
- Claire Morandin
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland. .,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland.
| | - Mandy M Y Tin
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan
| | - Sílvia Abril
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Crisanto Gómez
- Department of Environmental Sciences, University of Girona, Campus Montilivi, 17071, Girona, Spain
| | - Luigi Pontieri
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Liselotte Sundström
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Kazuki Tsuji
- Department of Subtropical Agro-Environmental Sciences, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Jes Søe Pedersen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Heikki Helanterä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, FI-10900, Hanko, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, 1919-1 Tancha Onna-son, Kunigami-gun, Okinawa, 904-0412, Japan. .,Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia.
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