1
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Stuart SH, Ahmed ACC, Kilikevicius L, Robinson GE. Effects of microRNA-305 knockdown on brain gene expression associated with division of labor in honey bee colonies (Apis mellifera). J Exp Biol 2024; 227:jeb246785. [PMID: 38517067 DOI: 10.1242/jeb.246785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Division of labor in honey bee colonies is based on the behavioral maturation of adult workers that involves a transition from working in the hive to foraging. This behavioral maturation is associated with distinct task-related transcriptomic profiles in the brain and abdominal fat body that are related to multiple regulatory factors including juvenile hormone (JH) and queen mandibular pheromone (QMP). A prominent physiological feature associated with behavioral maturation is a loss of abdominal lipid mass as bees transition to foraging. We used transcriptomic and physiological analyses to study whether microRNAs (miRNAs) are involved in the regulation of division of labor. We first identified two miRNAs that showed patterns of expression associated with behavioral maturation, ame-miR-305-5p and ame-miR-375-3p. We then downregulated the expression of these two miRNAs with sequence-specific antagomirs. Neither ame-miR-305-5p nor ame-miR-375-3p knockdown in the abdomen affected abdominal lipid mass on their own. Similarly, knockdown of ame-miR-305-5p in combination with JH or QMP also did not affect lipid mass. By contrast, ame-miR-305-5p knockdown in the abdomen caused substantial changes in gene expression in the brain. Brain gene expression changes included genes encoding transcription factors previously implicated in behavioral maturation. The results of these functional genomic experiments extend previous correlative associations of microRNAs with honey bee division of labor and point to specific roles for ame-miR-305-5p.
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Affiliation(s)
- Sarai H Stuart
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Amy C Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Kilikevicius
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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2
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Robinson GE, Bliss R, Hudson ME. The genomic case against genetic determinism. PLoS Biol 2024; 22:e3002510. [PMID: 38412239 PMCID: PMC10898719 DOI: 10.1371/journal.pbio.3002510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Animal studies reveal that the molecular wiring of the brain can be altered by heredity, the environment, and their interaction. A deeper molecular understanding of these interactions could be a potent antidote to societal concerns of genetic determinism for human behavior, but this requires a paradigm that extends beyond traditional genome-wide association study (GWAS).
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Affiliation(s)
- Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
- Department of Entomology, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
| | - Rina Bliss
- Department of Sociology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Matthew E. Hudson
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
- Department of Crop Sciences, University of Illinois Urbana Champaign, Urbana, Illinois, United States of America
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3
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Vernier CL, Nguyen LA, Gernat T, Ahmed AC, Chen Z, Robinson GE. Gut microbiota contribute to variations in honey bee foraging intensity. ISME J 2024; 18:wrae030. [PMID: 38412118 PMCID: PMC11008687 DOI: 10.1093/ismejo/wrae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. Although many studies have reported that experimental disruptions to the gut microbial community result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, because of their simple gut microbiota and complex division of labor characterized by colony-level variation in behavioral phenotypes. Although previous studies report correlational differences in gut microbial community associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between European honey bees (Apis mellifera). We found that gut microbial community structure differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in gut microbial community composition were associated with task experience. Moreover, single-microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused effects on foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral trait variation.
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Affiliation(s)
- Cassondra L Vernier
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Lan Anh Nguyen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Tim Gernat
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Amy Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Zhenqing Chen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61810, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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4
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Traniello IM, Bukhari SA, Dibaeinia P, Serrano G, Avalos A, Ahmed AC, Sankey AL, Hernaez M, Sinha S, Zhao SD, Catchen J, Robinson GE. Single-cell dissection of aggression in honeybee colonies. Nat Ecol Evol 2023; 7:1232-1244. [PMID: 37264201 DOI: 10.1038/s41559-023-02090-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Understanding how genotypic variation results in phenotypic variation is especially difficult for collective behaviour because group phenotypes arise from complex interactions among group members. A genome-wide association study identified hundreds of genes associated with colony-level variation in honeybee aggression, many of which also showed strong signals of positive selection, but the influence of these 'colony aggression genes' on brain function was unknown. Here we use single-cell (sc) transcriptomics and gene regulatory network (GRN) analyses to test the hypothesis that genetic variation for colony aggression influences individual differences in brain gene expression and/or gene regulation. We compared soldiers, which respond to territorial intrusion with stinging attacks, and foragers, which do not. Colony environment showed stronger influences on soldier-forager differences in brain gene regulation compared with brain gene expression. GRN plasticity was strongly associated with colony aggression, with larger differences in GRN dynamics detected between soldiers and foragers from more aggressive relative to less aggressive colonies. The regulatory dynamics of subnetworks composed of genes associated with colony aggression genes were more strongly correlated with each other across different cell types and brain regions relative to other genes, especially in brain regions involved with olfaction and vision and multimodal sensory integration, which are known to mediate bee aggression. These results show how group genetics can shape a collective phenotype by modulating individual brain gene regulatory network architecture.
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Affiliation(s)
- Ian M Traniello
- Neuroscience Program, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, USA.
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | | | | | - Guillermo Serrano
- Computational Biology Program, CIMA University of Navarra, Pamplona, Spain
| | - Arian Avalos
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, Agricultural Research Services, United States Department of Agriculture, Baton Rouge, LA, USA
| | - Amy Cash Ahmed
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
| | - Alison L Sankey
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
| | - Mikel Hernaez
- Computational Biology Program, CIMA University of Navarra, Pamplona, Spain
| | - Saurabh Sinha
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Computer Science, UIUC, Urbana, IL, USA
| | - Sihai Dave Zhao
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Statistics, UIUC, Urbana, IL, USA
| | - Julian Catchen
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA
- Department of Evolution, Ecology and Behavior, UIUC, Urbana, IL, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Urbana-Champaign (UIUC), Urbana, IL, USA.
- Carl R Woese Institute for Genomic Biology, UIUC, Urbana, IL, USA.
- Department of Entomology, UIUC, Urbana, IL, USA.
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5
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Shpigler HY, Yaniv A, Gernat T, Robinson GE, Bloch G. The Influences of Illumination Regime on Egg-laying Rhythms of Honey Bee Queens. J Biol Rhythms 2022; 37:609-619. [PMID: 36226630 PMCID: PMC9727117 DOI: 10.1177/07487304221126782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Honey bee queens show extreme fecundity, commonly laying more than a thousand eggs in a single day. It has proven challenging to study the temporal organization of egg-laying behavior because queens are typically active around the clock in the dark cavity of a densely populated nest. To contend with this challenge, we developed two novel methods allowing detailed monitoring of queen activity and egg laying. We first adapted a high-resolution, continuous, tracking system allowing to track the position of barcode-tagged queens in observation hives with colonies foraging outside. We found that the queen is active ~96% of the day with typically no diurnal rhythm. Next, we developed a new laboratory procedure to monitor egg laying at single egg resolution under different light regimes. We found that under constant darkness (DD) and temperature conditions, queens laid eggs with no circadian rhythms. Queen fecundity was severely reduced under constant light (LL). Under a 12:12 illumination regime, queen fecundity was comparable to under constant darkness, with a higher number of eggs during the light phase. These daily rhythms in egg laying continued when these queens were released to DD conditions, suggesting that egg-laying rhythms are influenced by endogenous circadian clocks. These results suggest that honey bee queens are active and lay eggs around the clock with no diurnal rhythms. Light has complex influences on these behaviors, but more studies are needed to determine whether these effects reflect the influence of light directly on the queen or indirectly by affecting workers that interact with the queen.
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Affiliation(s)
- Hagai Y. Shpigler
- Department of Ecology, Evolution, and
Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem, Israel,Carl R. Woese Institute for Genomic
Biology, University of Illinois Urbana–Champaign, Urbana, Illinois, USA,Department of Entomology, Agricultural
Research Organization, The Volcani Center, Rishon LeZion, Israel,Hagai Y. Shpigler,
Department of Entomology, Agricultural Research Organization, The Volcani
Center, Rishon LeZion, Israel; e-mail:
| | - Almog Yaniv
- Department of Ecology, Evolution, and
Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem, Israel
| | - Tim Gernat
- Carl R. Woese Institute for Genomic
Biology, University of Illinois Urbana–Champaign, Urbana, Illinois, USA
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic
Biology, University of Illinois Urbana–Champaign, Urbana, Illinois, USA,Entomology Department, University of
Illinois Urbana–Champaign, Urbana, Illinois, USA,Neuroscience Program, University of
Illinois Urbana–Champaign, Urbana, Illinois, USA
| | - Guy Bloch
- Department of Ecology, Evolution, and
Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University
of Jerusalem, Jerusalem, Israel,Guy Bloch, Department of
Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life
Sciences, The Hebrew University of Jerusalem, Berman 114, Jerusalem 9190401,
Israel; e-mail:
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6
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Abstract
The question of the heritability of behavior has been of long fascination to scientists and the broader public. It is now widely accepted that most behavioral variation has a genetic component, although the degree of genetic influence differs widely across behaviors. Starting with Mendel's remarkable discovery of "inheritance factors," it has become increasingly clear that specific genetic variants that influence behavior can be identified. This goal is not without its challenges: Unlike pea morphology, most natural behavioral variation has a complex genetic architecture. However, we can now apply powerful genome-wide approaches to connect variation in DNA to variation in behavior as well as analyses of behaviorally related variation in brain gene expression, which together have provided insights into both the genetic mechanisms underlying behavior and the dynamic relationship between genes and behavior, respectively, in a wide range of species and for a diversity of behaviors. Here, we focus on two systems to illustrate both of these approaches: the genetic basis of burrowing in deer mice and transcriptomic analyses of division of labor in honey bees. Finally, we discuss the troubled relationship between the field of behavioral genetics and eugenics, which reminds us that we must be cautious about how we discuss and contextualize the connections between genes and behavior, especially in humans.
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Affiliation(s)
- Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
- HHMI, Harvard University, Cambridge, MA 02138
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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7
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Traniello IM, Hamilton AR, Gernat T, Cash-Ahmed AC, Harwood GP, Ray AM, Glavin A, Torres J, Goldenfeld N, Robinson GE. Context-dependent influence of threat on honey bee social network dynamics and brain gene expression. J Exp Biol 2022; 225:jeb243738. [PMID: 35202460 PMCID: PMC9001921 DOI: 10.1242/jeb.243738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/17/2022] [Indexed: 11/20/2022]
Abstract
Adverse social experience affects social structure by modifying the behavior of individuals, but the relationship between an individual's behavioral state and its response to adversity is poorly understood. We leveraged naturally occurring division of labor in honey bees and studied the biological embedding of environmental threat using laboratory assays and automated behavioral tracking of whole colonies. Guard bees showed low intrinsic levels of sociability compared with foragers and nurse bees, but large increases in sociability following exposure to a threat. Threat experience also modified the expression of caregiving-related genes in a brain region called the mushroom bodies. These results demonstrate that the biological embedding of environmental experience depends on an individual's societal role and, in turn, affects its future sociability.
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Affiliation(s)
- Ian M. Traniello
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adam R. Hamilton
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tim Gernat
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, Liepzig D-04109, Germany
| | - Amy C. Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gyan P. Harwood
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Allyson M. Ray
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abigail Glavin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jacob Torres
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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8
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
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9
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Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A 2022; 119:e2115635118. [PMID: 35042800 PMCID: PMC8795548 DOI: 10.1073/pnas.2115635118] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616;
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
| | - Stephen Richards
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Erez Lieberman Aiden
- DNA Zoo and The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030
| | - Miguel L Allende
- Center for Genome Regulation, Universidad de Chile 3425 Santiago, Chile
- Facultad de Ciencias, Universidad de Chile 3425 Santiago, Chile
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Miklós Bálint
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus-Liebig University 35392 Giessen, Germany
| | - Katharine B Barker
- Global Genome Biodiversity Network Secretariat, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara 44121 Ferrara, Italy
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Nicolette D Caperello
- University of California Davis Genome Center, University of California, Davis, CA 95616
| | - Keith Carlson
- The Novim Group, University of California, Santa Barbara, CA 93106
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica 11529 Taipei, Taiwan
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Dalia A Conde
- Conservation Science, Species360 Conservation Science Alliance, Bloomington, MN 55425
- Department of Biology, University of Southern Denmark 5230 Odense M, Denmark
| | - Montserrat Corominas
- Department of Genetics, Microbiology, and Statistics, Universitat de Barcelona 08028 Barcelona, Spain
- Catalan Society for Biology, Institute for Catalan Studies 08001 Barcelona, Spain
| | - Keith A Crandall
- Department of Biostatistics & Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC 20052
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes 111711 Bogotá, Colombia
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - ThankGod E Ebenezer
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Olivier Fedrigo
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Paul Flicek
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, United Kingdom
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen 1350 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology 7491 Trondheim, Norway
| | - Melissa M Goldstein
- Department of Health Policy and Management, George Washington University, Washington, DC 20052
| | - Jennifer Marshall Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
- Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia
| | - Henry T Greely
- Stanford Law School, Stanford University, Stanford, CA 94305
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Kevin J Hackett
- Office of National Programs, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
| | - David Haussler
- Genome Institute, University of California, Santa Cruz, CA 95060
- HHMI, Chevy Chase, MD 20815
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2000, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba 292-0818, Japan
| | | | - Axel Janke
- LOEWE Centre of Translational Biodiversity Genomics, Senckenberg Leibniz Institution for Biodiversity and Earth System Research 60325 Frankfurt am Main, Germany
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- HHMI, Chevy Chase, MD 20815
| | - Warren E Johnson
- Walter Reed Biosystematics Unit, Smithsonian Institution, Suitland, MD 20746
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Jin-Hyoung Kim
- Division of Life Sciences, Korea Polar Research Institute 21990 Incheon, South Korea
| | - W John Kress
- Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics 411-8540 Shizuoka, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research 650-0047 Hyogo, Japan
| | - Mara K N Lawniczak
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | | | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University 752 36 Uppsala, Sweden
| | - Xin Liu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University, Consejo Superior de Investigaciones Cientificas, Parc de Recerca Biomedica de Barcelona 08003 Barcelona, Spain
- Catalan Institute of Research and Advanced Studies 08010 Barcelona, Spain
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona 08193 Barcelona, Spain
| | - Sophie Mazard
- Bioplatforms Australia, Macquarie University, Sydney, NSW 2109, Australia
| | - Jonna A K Mazet
- One Health Institute, University of California Davis, CA 95616
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research 14195 Berlin, Germany
- Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research 10315 Berlin, Germany
| | - Eugene W Myers
- Max Planck Institute for Molecular Cell Biology and Genetics 01307 Dresden, Germany
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Sadye Paez
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
| | - Hyun Park
- Division of Biotechnology, Korea University 02841 Seoul, Korea
| | - Gene E Robinson
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants Associated Unit to Consejo Superior de Investigaciones Cientificas, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona 08193 Bellaterra, Spain
- Laboratoire d'Ecologie Alpine, University Grenoble Alpes, University Savoie Mont Blanc, CNRS 38000 Grenoble, France
| | - Oliver A Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Division of Biology, Department of Evolution, Behavior, and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University 21589 Jeddah, Saudi Arabia
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University 21589 Jeddah, Saudi Arabia
| | - H Bradley Shaffer
- La Kretz Center for California Conservation Science, Institute of Environment and Sustainability, University of California, Los Angeles, CA 90024
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - Timothy M Shank
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
| | - Jacob S Sherkow
- Department of Entomology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- College of Law, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University 224002 Yancheng, China
| | - Leho Tedersoo
- Center of Mycology and Microbiology, University of Tartu 50411 Tartu, Estonia
- College of Science, King Saud University 11451 Riyadh, Saudi Arabia
| | | | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University 710072 Xi'an, China
| | - Xiaofeng Wei
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, Los Angeles, CA 90007
- Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Julia L Wilson
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom
| | - Xun Xu
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Huanming Yang
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Duke Center for Genomic and Computational Biology, Duke University, Durham, NC 27708
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences 650223 Yunnan, China
- BGI-Research, Beijing Genomics Institute-Shenzhen 518083 Shenzhen, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen 2100 Copenhagen, Denmark
- China National Genebank, Beijing Genomics Institute 51803 Shenzhen, China
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10
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Abstract
Animals operate in complex environments, and salient social information is encoded in the nervous system and then processed to initiate adaptive behavior. This encoding involves biological embedding, the process by which social experience affects the brain to influence future behavior. Biological embedding is an important conceptual framework for understanding social decision-making in the brain, as it encompasses multiple levels of organization that regulate how information is encoded and used to modify behavior. The framework we emphasize here is that social stimuli provoke short-term changes in neural activity that lead to changes in gene expression on longer timescales. This process, simplified-neurons are for today and genes are for tomorrow-enables the assessment of the valence of a social interaction, an appropriate and rapid response, and subsequent modification of neural circuitry to change future behavioral inclinations in anticipation of environmental changes. We review recent research on the neural and molecular basis of biological embedding in the context of social interactions, with a special focus on the honeybee.
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Affiliation(s)
- Ian M Traniello
- Neuroscience Program and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
| | - Gene E Robinson
- Neuroscience Program and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA; .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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11
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Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O. The genomic basis of evolutionary differentiation among honey bees. Genome Res 2021; 31:1203-1215. [PMID: 33947700 PMCID: PMC8256857 DOI: 10.1101/gr.272310.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 02/06/2023]
Abstract
In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
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Affiliation(s)
- Bertrand Fouks
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, 48149 Münster, Germany
| | - Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, California 95161, USA
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, New York 10065, USA
| | - Hung N Nguyen
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Jacob Herman
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Daniel Ence
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida 32611, USA
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Katharina J Hoff
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Stefanie Nachweide
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Lars Romoth
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Mario Stanke
- University of Greifswald, Institute for Mathematics and Computer Science, Bioinformatics Group, 17489 Greifswald, Germany
- University of Greifswald, Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | | | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah 84112, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nikolaus Koeniger
- Department of Behavioral Physiology and Sociobiology (Zoology II), University of Würzburg, 97074 Würzburg, Germany
| | - Panuwan Chantawannakul
- Environmental Science Research Center (ESRC) and Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gene E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Christine G Elsik
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina 27403, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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12
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Farahany NA, Robinson GE. The rise and fall of the "warrior gene" defense. Science 2021; 371:1320. [PMID: 33766880 DOI: 10.1126/science.abh4479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Nita A Farahany
- Duke Law School, Durham, NC 27708, USA. .,Duke Initiative for Science & Society, Durham, NC 27708, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.,College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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13
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Chen Z, Traniello IM, Rana S, Cash-Ahmed AC, Sankey AL, Yang C, Robinson GE. Neurodevelopmental and transcriptomic effects of CRISPR/Cas9-induced somatic orco mutation in honey bees. J Neurogenet 2021; 35:320-332. [PMID: 33666542 DOI: 10.1080/01677063.2021.1887173] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In insects, odorant receptors facilitate olfactory communication and require the functionality of the highly conserved co-receptor gene orco. Genome editing studies in a few species of ants and moths have revealed that orco can also have a neurodevelopmental function, in addition to its canonical role in adult olfaction, discovered first in Drosophila melanogaster. To extend this analysis, we determined whether orco mutations also affect the development of the adult brain of the honey bee Apis mellifera, an important model system for social behavior and chemical communication. We used CRISPR/Cas9 to knock out orco and examined anatomical and molecular consequences. To increase efficiency, we coupled embryo microinjection with a laboratory egg collection and in vitro rearing system. This new workflow advances genomic engineering technologies in honey bees by overcoming restrictions associated with field studies. We used Sanger sequencing to quickly select individuals with complete orco knockout for neuroanatomical analyses and later validated and described the mutations with amplicon sequencing. Mutant bees had significantly fewer glomeruli, smaller total volume of all the glomeruli, and higher mean individual glomerulus volume in the antennal lobe compared to wild-type controls. RNA-Sequencing revealed that orco knockout also caused differential expression of hundreds of genes in the antenna, including genes related to neural development and genes encoding odorant receptors. The expression of other types of chemoreceptor genes was generally unaffected, reflecting specificity of CRISPR activity in this study. These results suggest that neurodevelopmental effects of orco are related to specific insect life histories.
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Affiliation(s)
- Zhenqing Chen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ian M Traniello
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Seema Rana
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amy C Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alison L Sankey
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Che Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Biochemistry Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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14
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Abstract
Current risk assessment strategies for honey bees rely heavily upon laboratory tests performed on adult or immature worker bees, but these methods may not accurately capture the effects of agrochemical exposure on honey bee queens. As the sole producer of fertilized eggs inside a honeybee colony, the queen is arguably the most important single member of a functioning colony unit. Therefore, understanding how agrochemicals affect queen health and productivity should be considered a critical aspect of pesticide risk assessment. Here, an adapted method is presented to expose honey bee queens and worker queen attendants to agrochemical stressors administered through a worker diet, followed by tracking egg production in the laboratory and assessing first instar eclosion using a specialized cage, referred to as a Queen Monitoring Cage. To illustrate the method's intended use, results of an experiment in which worker queen attendants were fed diet containing sublethal doses of imidacloprid and effects on queens were monitored are described.
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Affiliation(s)
- Julia D Fine
- Invasive Species and Pollinator Health Research Unit, USDA-ARS;
| | - Kendall M Torres
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Jamilyn Martin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Neuroscience Program, University of Illinois at Urbana-Champaign; Department of Entomology, University of Illinois at Urbana-Champaign
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15
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Jones BM, Rao VD, Gernat T, Jagla T, Cash-Ahmed AC, Rubin BER, Comi TJ, Bhogale S, Husain SS, Blatti C, Middendorf M, Sinha S, Chandrasekaran S, Robinson GE. Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks. eLife 2020; 9:e62850. [PMID: 33350385 PMCID: PMC7755388 DOI: 10.7554/elife.62850] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the regulatory architecture of phenotypic variation is a fundamental goal in biology, but connections between gene regulatory network (GRN) activity and individual differences in behavior are poorly understood. We characterized the molecular basis of behavioral plasticity in queenless honey bee (Apis mellifera) colonies, where individuals engage in both reproductive and non-reproductive behaviors. Using high-throughput behavioral tracking, we discovered these colonies contain a continuum of phenotypes, with some individuals specialized for either egg-laying or foraging and 'generalists' that perform both. Brain gene expression and chromatin accessibility profiles were correlated with behavioral variation, with generalists intermediate in behavior and molecular profiles. Models of brain GRNs constructed for individuals revealed that transcription factor (TF) activity was highly predictive of behavior, and behavior-associated regulatory regions had more TF motifs. These results provide new insights into the important role played by brain GRN plasticity in the regulation of behavior, with implications for social evolution.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Vikyath D Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Department of Physics, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Tim Gernat
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig UniversityLeipzigGermany
| | - Tobias Jagla
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig UniversityLeipzigGermany
| | - Amy C Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Benjamin ER Rubin
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
| | - Troy J Comi
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
| | - Shounak Bhogale
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Syed S Husain
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
| | - Charles Blatti
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig UniversityLeipzigGermany
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of MichiganAnn ArborUnited States
- Center for Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Neuroscience Program, University of Illinois at Urbana–ChampaignUrbanaUnited States
- Department of Entomology, University of Illinois at Urbana–ChampaignUrbanaUnited States
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16
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Shpigler HY, Herb B, Drnevich J, Band M, Robinson GE, Bloch G. Juvenile hormone regulates brain-reproduction tradeoff in bumble bees but not in honey bees. Horm Behav 2020; 126:104844. [PMID: 32860832 DOI: 10.1016/j.yhbeh.2020.104844] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022]
Abstract
Gonadotropic hormones coordinate processes in diverse tissues regulating animal reproductive physiology and behavior. Juvenile hormone (JH) is the ancient and most common gonadotropin in insects, but not in advanced eusocial honey bees and some ants. To start probing the evolutionary basis of this change, we combined endocrine manipulations, transcriptomics, and behavioral analyses to study JH regulated processes in a bumble bee showing a relatively simple level of eusociality. We found that in worker fat body, more JH-regulated genes were up- rather than down-regulated, and enriched for metabolic and biosynthetic pathways. This transcriptomic pattern is consistent with earlier evidence that JH is the major gonadotropin in bumble bees. In the brain, more JH-regulated genes were down- rather than up-regulated and enriched for protein turnover pathways. Brain ribosomal protein gene expression shows a similar trend of downregulation in dominant workers, which naturally have high JH titers. In other species, similar downregulation of protein turnover is found in aging brains or under stress, associated with compromised long-term memory and health. These findings suggest a previously unknown gonadotropin-mediated tradeoff. Analysis of published data reveals no such downregulation of protein turnover pathways in the brain of honey bee workers, which exhibit more complex eusociality and in which JH is not a gonadotropin but rather regulates division of labor. These results suggest that the evolution of complex eusociality in honey bees was associated with modifications in hormonal signalling supporting extended and extremely high fertility while reducing the ancient costs of high gonadotropin titers to the brain.
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Affiliation(s)
- Hagai Y Shpigler
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Brian Herb
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jenny Drnevich
- High-Performance Biological Computing Group, Roy J Carver Biotechnology Center, The University of Illinois at Urbana-Champaign, USA
| | - Mark Band
- Roy J Carver Biotechnology Center, The University of Illinois at Urbana-Champaign, USA; Institute of Evolution, University of Haifa, Israel
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Entomology Department, The University of Illinois at Urbana-Champaign, USA; Neuroscience Program, The University of Illinois at Urbana-Champaign, USA
| | - Guy Bloch
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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17
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Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, Sokolowski MB, Stubbs LJ, Tabe-Bordbar S, Wolfner MF, Robinson GE. Behavior-related gene regulatory networks: A new level of organization in the brain. Proc Natl Acad Sci U S A 2020; 117:23270-23279. [PMID: 32661177 PMCID: PMC7519311 DOI: 10.1073/pnas.1921625117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain-the gene regulatory network (GRN)-that orchestrates expression levels of hundreds to thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial as well as temporal dimensions, across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing inspiration from the rich literature on GRNs related to animal development, comparing and contrasting these two broad classes of GRNs as they relate to their respective phenotypic manifestations. Developmental GRNs also represent a third layer of network biology, playing out over a third timescale, which is believed to play a crucial mediatory role between neuronal networks and behavioral GRNs. We end with a special emphasis on social behavior, discuss whether unique GRN organization and cis-regulatory architecture underlies this special class of behavior, and review literature that suggests an affirmative answer.
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Affiliation(s)
- Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL 61801;
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Beryl M Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Ian M Traniello
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Neuroscience Program, University of Illinois, Urbana-Champaign, IL 61801
| | - Syed A Bukhari
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Informatics Program, University of Illinois, Urbana-Champaign, IL 61820
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109
| | - Paul S Katz
- Department of Biology, University of Massachusetts, Amherst, MA 01003
| | - Jason Keagy
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14260
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Program in Child and Brain Development, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Lisa J Stubbs
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Shayan Tabe-Bordbar
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL 61801
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801;
- Neuroscience Program, University of Illinois, Urbana-Champaign, IL 61801
- Department of Entomology, University of Illinois, Urbana-Champaign, IL 61801
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18
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Mendenhall R, Henderson L, Scott B, Butler L, Turi KN, Greenlee A, Robinson GE, Roberts BW, Rodriguez-Zas SL, Brooks JE, Lleras CL. Involving Urban Single Low-Income African American Mothers in Genomic Research: Giving Voice to How Place Matters in Health Disparities and Prevention Strategies. Fam Med Prim Care Open Access 2020; 4:148. [PMID: 35373191 PMCID: PMC8970351 DOI: 10.29011/2688-7460.100048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article describes the process of using principles from community-based participatory action research to involve low-income, single, African American mothers on the south side of Chicago in genomic research, including as citizen scientists. The South Chicago Black Mothers' Resiliency Project used a mixed methods design to investigate how the stress of living in neighborhoods with high levels of violence affects mothers' mental and physical health. This article seeks to serve as a model for physicians and scholars interested in successfully involving low-income African American mothers in genomic research, and other health-related activities in ways that are culturally sensitive and transformative. The lives of Black mothers who struggle under interlocking systems of oppression that are often hidden from view of most Americans are at the center of this article. Therefore, we provide extensive information about the procedures used to collect the various types of data, the rationale for our procedures, the setting, the responses of mothers in our sample and methodological challenges. This study also has implications for the current COVID-19 pandemic and the need to train a corps of citizen scientists in health and wellness to avoid future extreme loss of life such as the 106,195 lives lost in the United States as of June 1, 2020.
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Affiliation(s)
- Ruby Mendenhall
- Department of Sociology, African American Studies & Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, USA
| | - Loren Henderson
- Department of Sociology and Anthropology, University of Maryland, Baltimore County, USA
| | - Barbara Scott
- Department of Sociology, Northeastern Illinois University, USA
| | - Lisa Butler
- Independent Scholar, Northeastern Illinois University, USA
| | - Kedir N Turi
- Department of Medicine, Vanderbilt University, Nashville, USA
| | - Andrew Greenlee
- Urban and Regional Planning, University of Illinois at Urbana-Champaign, USA
| | - Gene E Robinson
- Institute for Genomic Biology, Integrative Biology, University of Illinois at Urbana-Champaign, USA
| | - Brent W Roberts
- Center for Social and Behavioral Science Psychology, University of Illinois at Urbana-Champaign, USA
| | | | | | - Christy L Lleras
- Human Development & Family Studies, University of Illinois at Urbana-Champaign, USA
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19
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Traniello IM, Bukhari SA, Kevill J, Ahmed AC, Hamilton AR, Naeger NL, Schroeder DC, Robinson GE. Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation. Sci Rep 2020; 10:3101. [PMID: 32080242 PMCID: PMC7033282 DOI: 10.1038/s41598-020-59808-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
Crop pollination by the western honey bee Apis mellifera is vital to agriculture but threatened by alarmingly high levels of colony mortality, especially in Europe and North America. Colony loss is due, in part, to the high viral loads of Deformed wing virus (DWV), transmitted by the ectoparasitic mite Varroa destructor, especially throughout the overwintering period of a honey bee colony. Covert DWV infection is commonplace and has been causally linked to precocious foraging, which itself has been linked to colony loss. Taking advantage of four brain transcriptome studies that unexpectedly revealed evidence of covert DWV-A infection, we set out to explore whether this effect is due to DWV-A mimicking naturally occurring changes in brain gene expression that are associated with behavioral maturation. Consistent with this hypothesis, we found that brain gene expression profiles of DWV-A infected bees resembled those of foragers, even in individuals that were much younger than typical foragers. In addition, brain transcriptional regulatory network analysis revealed a positive association between DWV-A infection and transcription factors previously associated with honey bee foraging behavior. Surprisingly, single-cell RNA-Sequencing implicated glia, not neurons, in this effect; there are relatively few glial cells in the insect brain and they are rarely associated with behavioral plasticity. Covert DWV-A infection also has been linked to impaired learning, which together with precocious foraging can lead to increased occurrence of infected bees from one colony mistakenly entering another colony, especially under crowded modern apiary conditions. These findings provide new insights into the mechanisms by which DWV-A affects honey bee health and colony survival.
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Affiliation(s)
- Ian M Traniello
- Neuroscience Program, University of Illinois at Urbana-Champaign, (UIUC), Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, USA.
| | - Syed Abbas Bukhari
- Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, USA
- Department of Animal Biology, UIUC, Urbana, USA
| | - Jessica Kevill
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Amy Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, USA
| | - Adam R Hamilton
- Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, USA
| | - Nicholas L Naeger
- Department of Entomology, Washington State University, Pullman, WA, USA
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
- School of Biological Sciences, University of Reading, Reading, UK
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Urbana-Champaign, (UIUC), Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, UIUC, Urbana, USA
- Department of Entomology, UIUC, Urbana, USA
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20
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Traniello IM, Chen Z, Bagchi VA, Robinson GE. Valence of social information is encoded in different subpopulations of mushroom body Kenyon cells in the honeybee brain. Proc Biol Sci 2019; 286:20190901. [PMID: 31506059 DOI: 10.1098/rspb.2019.0901] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Over 600 Myr of evolutionary divergence between vertebrates and invertebrates is associated with considerable neuroanatomical variation both across and within these lineages. By contrast, valence encoding is an important behavioural trait that is evolutionarily conserved across vertebrates and invertebrates, and enables individuals to distinguish between positive (potentially beneficial) and negative (potentially harmful) situations. We tested the hypothesis that social interactions of positive and negative valence are modularly encoded in the honeybee brain (i.e. encoded in different cellular subpopulations) as in vertebrate brains. In vertebrates, neural activation patterns are distributed across distinct parts of the brain, suggesting that discrete circuits encode positive or negative stimuli. Evidence for this hypothesis would suggest a deep homology of neural organization between insects and vertebrates for valence encoding, despite vastly different brain sizes. Alternatively, overlapping localization of valenced social information in the brain would imply a 're-use' of circuitry in response to positive and negative social contexts, potentially to overcome the energetic constraints of a tiny brain. We used immediate early gene expression to map positively and negatively valenced social interactions in the brain of the western honeybee Apis mellifera. We found that the valence of a social signal is represented by distinct anatomical subregions of the mushroom bodies, an invertebrate sensory neuropil associated with social behaviour, multimodal sensory integration, learning and memory. Our results suggest that the modularization of valenced social information in the brain is a fundamental property of neuroanatomical organization.
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Affiliation(s)
- Ian M Traniello
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zhenqing Chen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Vikram A Bagchi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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21
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Gadagkar R, Gordon D, Keller L, Michod R, Queller D, Robinson GE, Strassmann J, West-Eberhard MJ. Insights and opportunities in insect social behavior. Curr Opin Insect Sci 2019; 34:ix-xx. [PMID: 31472719 DOI: 10.1016/j.cois.2019.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
| | - Deborah Gordon
- Department of Biology, Stanford University, United States
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Rick Michod
- Department of Ecology and Evolution, University of Arizona, United States
| | - David Queller
- Department of Biology, Washington University in St. Louis, United States
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, and Neuroscience Program, University of Illinois at Urbana-Champaign, United States
| | - Joan Strassmann
- Department of Biology, Washington University in St. Louis, United States
| | - Mary Jane West-Eberhard
- Smithsonian Tropical Research Institute, c/o Escuela de Biologia, Universidad de Costa Rica, Costa Rica
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22
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Hamilton AR, Traniello IM, Ray AM, Caldwell AS, Wickline SA, Robinson GE. Division of labor in honey bees is associated with transcriptional regulatory plasticity in the brain. J Exp Biol 2019; 222:jeb200196. [PMID: 31138635 PMCID: PMC6679348 DOI: 10.1242/jeb.200196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Studies in evolutionary and developmental biology show that relationships between transcription factors (TFs) and their target genes can be altered to result in novel regulatory relationships that generate phenotypic plasticity. We hypothesized that context-dependent shifts in the nervous system associated with behavior may also be linked to changes in TF-target relationships over physiological time scales. We tested this hypothesis using honey bee (Apis mellifera) division of labor as a model system by performing bioinformatic analyses of previously published brain transcriptomic profiles together with new RNAi and behavioral experiments. The bioinformatic analyses identified five TFs that exhibited strong signatures of regulatory plasticity as a function of division of labor. RNAi targeting of one of these TFs (broad complex) and a related TF that did not exhibit plasticity (fushi tarazu transcription factor 1) was administered in conjunction with automated analyses of foraging behavior in the field, laboratory assays of aggression and brood care behavior, and endocrine treatments. The results showed that changes in the regulatory relationships of these TFs were associated with behavioral state, social context and endocrine state. These findings provide the first empirical evidence that TF-target relationships in the brain are altered in conjunction with behavior and social context. They also suggest that one mechanism for this plasticity involves pleiotropic TFs high up in regulatory hierarchies producing behavior-specific transcriptional responses by activating different downstream TFs to induce discrete context-dependent transcriptional cascades. These findings provide new insights into the dynamic nature of the transcriptional regulatory architecture underlying behavior in the brain.
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Affiliation(s)
- Adam R Hamilton
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Ian M Traniello
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Allyson M Ray
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Arminius S Caldwell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
| | - Samuel A Wickline
- Department of Computation and Molecular Biophysics, School of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Champaign-Urbana, Urbana, IL 61801, USA
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23
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Wallberg A, Bunikis I, Pettersson OV, Mosbech MB, Childers AK, Evans JD, Mikheyev AS, Robertson HM, Robinson GE, Webster MT. A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds. BMC Genomics 2019; 20:275. [PMID: 30961563 PMCID: PMC6454739 DOI: 10.1186/s12864-019-5642-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 03/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Olga Vinnere Pettersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mai-Britt Mosbech
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna K Childers
- USDA-ARS Insect Genetics and Biochemistry Research Unit, Fargo, ND, USA.,USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD, USA
| | | | - Hugh M Robertson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Department of Entomology and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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24
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Abstract
For over a century, biologists have proposed a role for phenotypic plasticity in evolution, providing an avenue for adaptation in addition to 'mutation-first' models of evolutionary change. According to the various versions of this idea, the ability of organisms to respond adaptively to their environment through phenotypic plasticity may lead to novel phenotypes that can be screened by natural selection. If these initially environmentally induced phenotypes increase fitness, then genetic accommodation can lead to allele frequency change, influencing the expression of those phenotypes. Despite the long history of 'plasticity-first' models, the importance of genetic accommodation in shaping evolutionary change has remained controversial - it is neither fully embraced nor completely discarded by most evolutionary biologists. We suggest that the lack of acceptance of genetic accommodation in some cases is related to a lack of information on its molecular mechanisms. However, recent reports of epigenetic transgenerational inheritance now provide a plausible mechanism through which genetic accommodation may act, and we review this research here. We also discuss current evidence supporting a role for genetic accommodation in the evolution of eusociality in social insects, which have long been models for studying the influence of the environment on phenotypic variation, and may be particularly good models for testing hypotheses related to genetic accommodation. Finally, we introduce 'eusocial engineering', a method by which novel social phenotypes are first induced by environmental modification and then studied mechanistically to understand how environmentally induced plasticity may lead to heritable changes in social behavior. We believe the time is right to incorporate genetic accommodation into models of the evolution of complex traits, armed with new molecular tools and a better understanding of non-genetic heritable elements.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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25
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Fine JD, Shpigler HY, Ray AM, Beach NJ, Sankey AL, Cash-Ahmed A, Huang ZY, Astrauskaite I, Chao R, Zhao H, Robinson GE. Quantifying the effects of pollen nutrition on honey bee queen egg laying with a new laboratory system. PLoS One 2018; 13:e0203444. [PMID: 30183759 PMCID: PMC6124782 DOI: 10.1371/journal.pone.0203444] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/21/2018] [Indexed: 11/21/2022] Open
Abstract
Honey bee populations have been declining precipitously over the past decade, and multiple causative factors have been identified. Recent research indicates that these frequently co-occurring stressors interact, often in unpredictable ways, therefore it has become important to develop robust methods to assess their effects both in isolation and in combination. Most such efforts focus on honey bee workers, but the state of a colony also depends on the health and productivity of its queen. However, it is much more difficult to quantify the performance of queens relative to workers in the field, and there are no laboratory assays for queen performance. Here, we present a new system to monitor honey bee queen egg laying under laboratory conditions and report the results of experiments showing the effects of pollen nutrition on egg laying. These findings suggest that queen egg laying and worker physiology can be manipulated in this system through pollen nutrition, which is consistent with findings from field colonies. The results generated using this controlled, laboratory-based system suggest that worker physiology controls queen egg laying behavior. Additionally, the quantitative data generated in these experiments highlight the utility of the system for further use as a risk assessment tool.
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Affiliation(s)
- Julia D. Fine
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Hagai Y. Shpigler
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Allyson M. Ray
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Nathanael J. Beach
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Alison L. Sankey
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Amy Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Zachary Y. Huang
- Department of Entomology, Michigan State University, East Lansing, United States of America
| | - Ieva Astrauskaite
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Ran Chao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, United States of America
- LifeFoundry, Inc., Champaign, United States of America
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, United States of America
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, United States of America
- * E-mail:
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26
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Shpigler HY, Saul MC, Murdoch EE, Corona F, Cash-Ahmed AC, Seward CH, Chandrasekaran S, Stubbs LJ, Robinson GE. Honey bee neurogenomic responses to affiliative and agonistic social interactions. Genes Brain Behav 2018; 18:e12509. [PMID: 30094933 DOI: 10.1111/gbb.12509] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/02/2018] [Accepted: 08/02/2018] [Indexed: 12/20/2022]
Abstract
Social interactions can be divided into two categories, affiliative and agonistic. How neurogenomic responses reflect these opposing valences is a central question in the biological embedding of experience. To address this question, we exposed honey bees to a queen larva, which evokes nursing, an affiliative alloparenting interaction, and measured the transcriptomic response of the mushroom body brain region at different times after exposure. Hundreds of genes were differentially expressed at distinct time points, revealing a dynamic temporal patterning of the response. Comparing these results to our previously published research on agonistic aggressive interactions, we found both shared and unique transcriptomic responses to each interaction. The commonly responding gene set was enriched for nuclear receptor signaling, the set specific to nursing was enriched for olfaction and neuron differentiation, and the set enriched for aggression was enriched for cytoskeleton, metabolism, and chromosome organization. Whole brain histone profiling after the affiliative interaction revealed few changes in chromatin accessibility, suggesting that the transcriptomic changes derive from already accessible areas of the genome. Although only one stimulus of each type was studied, we suggest that elements of the observed transcriptomic responses reflect molecular encoding of stimulus valence, thus priming individuals for future encounters. This hypothesis is supported by behavioral analyses showing that bees responding to either the affiliative or agonistic stimulus exhibited a higher probability of repeating the same behavior but a lower probability of performing the opposite behavior. These findings add to our understanding of the biological embedding at the molecular level.
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Affiliation(s)
- Hagai Y Shpigler
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois
| | - Michael C Saul
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois
| | - Emma E Murdoch
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois
| | - Frida Corona
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois
| | - Amy C Cash-Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois
| | - Christopher H Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois.,Department of Cell and Developmental Biology, UIUC, Urbana, Illinois
| | | | - Lisa J Stubbs
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois.,Department of Cell and Developmental Biology, UIUC, Urbana, Illinois.,Neuroscience Program, UIUC, Urbana, Illinois
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign (UIUC), Urbana, Illinois.,Neuroscience Program, UIUC, Urbana, Illinois.,Department of Entomology, UIUC, Urbana, Illinois
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27
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Saul MC, Blatti C, Yang W, Bukhari SA, Shpigler HY, Troy JM, Seward CH, Sloofman L, Chandrasekaran S, Bell AM, Stubbs L, Robinson GE, Zhao SD, Sinha S. Cross-species systems analysis of evolutionary toolkits of neurogenomic response to social challenge. Genes Brain Behav 2018; 18:e12502. [PMID: 29968347 DOI: 10.1111/gbb.12502] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022]
Abstract
Social challenges like territorial intrusions evoke behavioral responses in widely diverging species. Recent work has showed that evolutionary "toolkits"-genes and modules with lineage-specific variations but deep conservation of function-participate in the behavioral response to social challenge. Here, we develop a multispecies computational-experimental approach to characterize such a toolkit at a systems level. Brain transcriptomic responses to social challenge was probed via RNA-seq profiling in three diverged species-honey bees, mice and three-spined stickleback fish-following a common methodology, allowing fair comparisons across species. Data were collected from multiple brain regions and multiple time points after social challenge exposure, achieving anatomical and temporal resolution substantially greater than previous work. We developed statistically rigorous analyses equipped to find homologous functional groups among these species at the levels of individual genes, functional and coexpressed gene modules, and transcription factor subnetworks. We identified six orthogroups involved in response to social challenge, including groups represented by mouse genes Npas4 and Nr4a1, as well as common modulation of systems such as transcriptional regulators, ion channels, G-protein-coupled receptors and synaptic proteins. We also identified conserved coexpression modules enriched for mitochondrial fatty acid metabolism and heat shock that constitute the shared neurogenomic response. Our analysis suggests a toolkit wherein nuclear receptors, interacting with chaperones, induce transcriptional changes in mitochondrial activity, neural cytoarchitecture and synaptic transmission after social challenge. It shows systems-level mechanisms that have been repeatedly co-opted during evolution of analogous behaviors, thus advancing the genetic toolkit concept beyond individual genes.
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Affiliation(s)
- Michael C Saul
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles Blatti
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Wei Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Syed A Bukhari
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Interdisciplinary Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Hagai Y Shpigler
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Ecology, Evolution and Behavior, Hebrew University, Jerusalem, Israel
| | - Joseph M Troy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Interdisciplinary Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Christopher H Seward
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Laura Sloofman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Genetics and Genomic Sciences, Mount Sinai Health System, New York, New York
| | | | - Alison M Bell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Interdisciplinary Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Lisa Stubbs
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Interdisciplinary Informatics Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Sihai D Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois
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28
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Herb BR, Shook MS, Fields CJ, Robinson GE. Defense against territorial intrusion is associated with DNA methylation changes in the honey bee brain. BMC Genomics 2018; 19:216. [PMID: 29580210 PMCID: PMC5870497 DOI: 10.1186/s12864-018-4594-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aggression is influenced by individual variation in temperament as well as behavioral plasticity in response to adversity. DNA methylation is stably maintained over time, but also reversible in response to specific environmental conditions, and may thus be a neuromolecular regulator of both of these processes. A previous study reported DNA methylation differences between aggressive Africanized and gentle European honey bees. We investigated whether threat-induced aggression altered DNA methylation profiles in the honey bee brain in response to a behavioral stimulus (aggression-provoking intruder bee or inert control). We sampled five minutes and two hours after stimulus exposure to examine the effect of time on epigenetic profiles of aggression. RESULTS There were DNA methylation differences between aggressive and control bees for individual cytosine-guanine dinucleotides (CpGs) across the genome. Eighteen individual CpG sites showed significant difference between aggressive and control bees 120 min post stimulus. For clusters of CpGs, we report four genomic regions differentially methylated between aggressive and control bees at the 5-min time point, and 50 regions differentially methylated at the120-minute time point following intruder exposure. Differential methylation occurred at genes involved in neural plasticity, chromatin remodeling and hormone signaling. Additionally, there was a significant overlap of differential methylation with previously published epigenetic differences that distinguish aggressive Africanized and gentle European honey bees, suggesting an evolutionarily conserved use of brain DNA methylation in the regulation of aggression. Lastly, we identified individually statistically suggestive CpGs that as a group were significantly associated with differentially expressed genes underlying aggressive behavior and also co-localize with binding sites of transcription factors involved in neuroplasticity or neurodevelopment. CONCLUSIONS There were DNA methylation differences in the brain associated with response to an intruder. These differences increased in number a few hours after the initial exposure and overlap with previously reported aggression-associated genes and neurobiologically relevant transcription factor binding sites. Many DNA methylation differences that occurred in association with the expression of aggression in real time also exist between Africanized bees and European bees, suggesting an evolutionarily conserved role for epigenetic regulation in aggressive behavior.
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Affiliation(s)
- Brian R Herb
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Molly S Shook
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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29
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Gernat T, Rao VD, Middendorf M, Dankowicz H, Goldenfeld N, Robinson GE. Automated monitoring of behavior reveals bursty interaction patterns and rapid spreading dynamics in honeybee social networks. Proc Natl Acad Sci U S A 2018; 115:1433-1438. [PMID: 29378954 PMCID: PMC5816157 DOI: 10.1073/pnas.1713568115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Social networks mediate the spread of information and disease. The dynamics of spreading depends, among other factors, on the distribution of times between successive contacts in the network. Heavy-tailed (bursty) time distributions are characteristic of human communication networks, including face-to-face contacts and electronic communication via mobile phone calls, email, and internet communities. Burstiness has been cited as a possible cause for slow spreading in these networks relative to a randomized reference network. However, it is not known whether burstiness is an epiphenomenon of human-specific patterns of communication. Moreover, theory predicts that fast, bursty communication networks should also exist. Here, we present a high-throughput technology for automated monitoring of social interactions of individual honeybees and the analysis of a rich and detailed dataset consisting of more than 1.2 million interactions in five honeybee colonies. We find that bees, like humans, also interact in bursts but that spreading is significantly faster than in a randomized reference network and remains so even after an experimental demographic perturbation. Thus, while burstiness may be an intrinsic property of social interactions, it does not always inhibit spreading in real-world communication networks. We anticipate that these results will inform future models of large-scale social organization and information and disease transmission, and may impact health management of threatened honeybee populations.
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Affiliation(s)
- Tim Gernat
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, 04109 Leipzig, Germany
| | - Vikyath D Rao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Martin Middendorf
- Swarm Intelligence and Complex Systems Group, Department of Computer Science, Leipzig University, 04109 Leipzig, Germany
| | - Harry Dankowicz
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nigel Goldenfeld
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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30
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Avalos A, Pan H, Li C, Acevedo-Gonzalez JP, Rendon G, Fields CJ, Brown PJ, Giray T, Robinson GE, Hudson ME, Zhang G. A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee. Nat Commun 2017; 8:1550. [PMID: 29142254 PMCID: PMC5688081 DOI: 10.1038/s41467-017-01800-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Highly aggressive Africanized honeybees (AHB) invaded Puerto Rico (PR) in 1994, displacing gentle European honeybees (EHB) in many locations. Gentle AHB (gAHB), unknown anywhere else in the world, subsequently evolved on the island within a few generations. Here we sequence whole genomes from gAHB and EHB populations, as well as a North American AHB population, a likely source of the founder AHB on PR. We show that gAHB retains high levels of genetic diversity after evolution of gentle behaviour, despite selection on standing variation. We observe multiple genomic loci with significant signatures of selection. Rapid evolution during colonization of novel habitats can generate major changes to characteristics such as morphological or colouration traits, usually controlled by one or more major genetic loci. Here we describe a soft selective sweep, acting at multiple loci across the genome, that occurred during, and may have mediated, the rapid evolution of a behavioural trait. Africanized honey bees (AHB) are notoriously aggressive, but in Puerto Rico they have a ‘gentle’ phenotype. Here, Avalos et al. show that there has been a soft selective sweep at several loci in the Puerto Rican AHB population and suggest a role in the rapid evolution of gentle behaviour.
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Affiliation(s)
- Arian Avalos
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hailin Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Cai Li
- China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | | | - Gloria Rendon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Patrick J Brown
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tugrul Giray
- Departamento de Biología, Universidad de Puerto Rico, Río Piedras, PR, 00931, USA
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Matthew E Hudson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,High-Performance Computing for Biology (HPCBio), Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .,China National Genebank, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China. .,Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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31
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Fischman BJ, Pitts-Singer TL, Robinson GE. Nutritional Regulation of Phenotypic Plasticity in a Solitary Bee (Hymenoptera: Megachilidae). Environ Entomol 2017; 46:1070-1079. [PMID: 28981639 PMCID: PMC5850749 DOI: 10.1093/ee/nvx119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Indexed: 05/16/2023]
Abstract
Phenotypic plasticity involves adaptive responses to predictable environmental fluctuations and may promote evolutionary change. We studied the regulation of phenotypic plasticity in an important agricultural pollinator, the solitary alfalfa leafcutting bee (Megachile rotundata F.). Specifically, we investigated how larval nutrition affects M. rotundata diapause plasticity and how diapause plasticity affects adult female reproductive behavior. Field surveys and laboratory manipulations of aspects of larval diet demonstrated nutritional regulation of M. rotundata diapause plasticity. Manipulation of larval diet quality through the addition of royal jelly, the caste-determining substance of the honey bee Apis mellifera L., increased the probability of diapause in M. rotundata. We also found that larval nutrition and diapause status affected M. rotundata adult female reproductive behavior. Nutritional effects on larval diapause that also impact adult fitness have intriguing implications for the evolution of developmental plasticity in bees. In particular, as the solitary lifestyle of M. rotundata is considered to be the ancestral condition in bees, nutritionally regulated plasticity may have been an ancestral condition in all bees that facilitated the evolution of other forms of phenotypic plasticity, such as the castes of social bees.
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Affiliation(s)
- Brielle J Fischman
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL 61801 ()
- Current address: Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456
| | | | - Gene E Robinson
- Department of Entomology, Neuroscience Program, and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801 ()
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32
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Abstract
E. O. Wilson proposed in Sociobiology that similarities between human and animal societies reflect common mechanistic and evolutionary roots. When introduced in 1975, this controversial hypothesis was beyond science's ability to test. We used genomic analyses to determine whether superficial behavioral similarities in humans and the highly social honey bee reflect common molecular mechanisms. Here, we report that gene expression signatures for individual bees unresponsive to various salient social stimuli are significantly enriched for autism spectrum disorder-related genes. These signatures occur in the mushroom bodies, a high-level integration center of the insect brain. Furthermore, our finding of enrichment was unique to autism spectrum disorders; brain gene expression signatures from other honey bee behaviors do not show this enrichment, nor do datasets from other human behavioral and health conditions. These results demonstrate deep conservation for genes associated with a human social pathology and individual differences in insect social behavior, thus providing an example of how comparative genomics can be used to test sociobiological theory.
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Affiliation(s)
- Hagai Y Shpigler
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Michael C Saul
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Frida Corona
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Lindsey Block
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Amy Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sihai D Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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33
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Naeger NL, Robinson GE. Transcriptomic analysis of instinctive and learned reward-related behaviors in honey bees. ACTA ACUST UNITED AC 2017; 219:3554-3561. [PMID: 27852762 DOI: 10.1242/jeb.144311] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/03/2016] [Indexed: 01/05/2023]
Abstract
We used transcriptomics to compare instinctive and learned, reward-based honey bee behaviors with similar spatio-temporal components: mating flights by males (drones) and time-trained foraging flights by females (workers), respectively. Genome-wide gene expression profiling via RNA sequencing was performed on the mushroom bodies, a region of the brain known for multi-modal sensory integration and responsive to various types of reward. Differentially expressed genes (DEGs) associated with the onset of mating (623 genes) were enriched for the gene ontology (GO) categories of Transcription, Unfolded Protein Binding, Post-embryonic Development, and Neuron Differentiation. DEGs associated with the onset of foraging (473) were enriched for Lipid Transport, Regulation of Programmed Cell Death, and Actin Cytoskeleton Organization. These results demonstrate that there are fundamental molecular differences between similar instinctive and learned behaviors. In addition, there were 166 genes with strong similarities in expression across the two behaviors - a statistically significant overlap in gene expression, also seen in Weighted Gene Co-Expression Network Analysis. This finding indicates that similar instinctive and learned behaviors also share common molecular architecture. This common set of DEGs was enriched for Regulation of RNA Metabolic Process, Transcription Factor Activity, and Response to Ecdysone. These findings provide a starting point for better understanding the relationship between instincts and learned behaviors. In addition, because bees collect food for their colony rather than for themselves, these results also support the idea that altruistic behavior relies, in part, on elements of brain reward systems associated with selfish behavior.
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Affiliation(s)
- Nicholas L Naeger
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA .,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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34
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Affiliation(s)
- Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, and Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL 61801, USA
| | - Andrew B. Barron
- Department of Biological Sciences, Macquarie University, Sydney NSW 2109, Australia
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35
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Jones BM, Kingwell CJ, Wcislo WT, Robinson GE. Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality. Proc Biol Sci 2017; 284:20162228. [PMID: 28053060 PMCID: PMC5247497 DOI: 10.1098/rspb.2016.2228] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
Developmental plasticity may accelerate the evolution of phenotypic novelty through genetic accommodation, but studies of genetic accommodation often lack knowledge of the ancestral state to place selected traits in an evolutionary context. A promising approach for assessing genetic accommodation involves using a comparative framework to ask whether ancestral plasticity is related to the evolution of a particular trait. Bees are an excellent group for such comparisons because caste-based societies (eusociality) have evolved multiple times independently and extant species exhibit different modes of eusociality. We measured brain and abdominal gene expression in a facultatively eusocial bee, Megalopta genalis, and assessed whether plasticity in this species is functionally linked to eusocial traits in other bee lineages. Caste-biased abdominal genes in M. genalis overlapped significantly with caste-biased genes in obligately eusocial bees. Moreover, caste-biased genes in M. genalis overlapped significantly with genes shown to be rapidly evolving in multiple studies of 10 bee species, particularly for genes in the glycolysis pathway and other genes involved in metabolism. These results provide support for the idea that eusociality can evolve via genetic accommodation, with plasticity in facultatively eusocial species like M. genalis providing a substrate for selection during the evolution of caste in obligately eusocial lineages.
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Affiliation(s)
- Beryl M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Callum J Kingwell
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City 20521-9100, Panama
| | - Gene E Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Liu H, Robinson GE, Jakobsson E. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PLoS Comput Biol 2016; 12:e1004921. [PMID: 27359102 PMCID: PMC4928799 DOI: 10.1371/journal.pcbi.1004921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 04/17/2016] [Indexed: 01/11/2023] Open
Abstract
The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for social organization.
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Affiliation(s)
- Hui Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eric Jakobsson
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Southey BR, Zhu P, Carr-Markell MK, Liang ZS, Zayed A, Li R, Robinson GE, Rodriguez-Zas SL. Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing. PLoS One 2016; 11:e0146430. [PMID: 26784945 PMCID: PMC4718678 DOI: 10.1371/journal.pone.0146430] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/15/2015] [Indexed: 12/01/2022] Open
Abstract
Among forager honey bees, scouts seek new resources and return to the colony, enlisting recruits to collect these resources. Differentially expressed genes between these behaviors and genetic variability in scouting phenotypes have been reported. Whole-genome sequencing of 44 Apis mellifera scouts and recruits was undertaken to detect variants and further understand the genetic architecture underlying the behavioral differences between scouts and recruits. The median coverage depth in recruits and scouts was 10.01 and 10.7 X, respectively. Representation of bacterial species among the unmapped reads reflected a more diverse microbiome in scouts than recruits. Overall, 1,412,705 polymorphic positions were analyzed for associations with scouting behavior, and 212 significant (p-value < 0.0001) associations with scouting corresponding to 137 positions were detected. Most frequent putative transcription factor binding sites proximal to significant variants included Broad-complex 4, Broad-complex 1, Hunchback, and CF2-II. Three variants associated with scouting were located within coding regions of ncRNAs including one codon change (LOC102653644) and 2 frameshift indels (LOC102654879 and LOC102655256). Significant variants were also identified on the 5’UTR of membrin, and 3’UTRs of laccase 2 and diacylglycerol kinase theta. The 60 significant variants located within introns corresponded to 39 genes and most of these positions were > 1000 bp apart from each other. A number of these variants were mapped to ncRNA LOC100578102, solute carrier family 12 member 6-like gene, and LOC100576965 (meprin and TRAF-C homology domain containing gene). Functional categories represented among the genes corresponding to significant variants included: neuronal function, exoskeleton, immune response, salivary gland development, and enzymatic food processing. These categories offer a glimpse into the molecular support to the behaviors of scouts and recruits. The level of association between genomic variants and scouting behavior observed in this study may be linked to the honey bee’s genomic plasticity and fluidity of transition between castes.
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Affiliation(s)
- Bruce R. Southey
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ping Zhu
- Biodynamic Optical Imaging Center, College of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Morgan K. Carr-Markell
- School of Integrative Biology, Ecology, Evolution, and Conservation Biology Program, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Zhengzheng S. Liang
- School of Molecular and Cell Biology and Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Amro Zayed
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China and Biodynamic Optical Imaging Center, Peking-Tsinghua Center for Life Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Gene E. Robinson
- Carle Woese Institute for Genomic Biology, Department of Entomology, and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Sandra L. Rodriguez-Zas
- Department of Animal Sciences, Department of Statistics, Neuroscience Program, and Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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38
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Affiliation(s)
- Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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McNeill MS, Kapheim KM, Brockmann A, McGill TAW, Robinson GE. Brain regions and molecular pathways responding to food reward type and value in honey bees. Genes Brain Behav 2016; 15:305-17. [PMID: 26566901 DOI: 10.1111/gbb.12275] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 12/19/2022]
Abstract
The ability of honey bees to evaluate differences in food type and value is crucial for colony success, but these assessments are made by individuals who bring food to the hive, eating little, if any, of it themselves. We tested the hypothesis that responses to food type (pollen or nectar) and value involve different subsets of brain regions, and genes responsive to food. mRNA in situ hybridization of c-jun revealed that brain regions responsive to differences in food type were mostly different from regions responsive to differences in food value, except those dorsal and lateral to the mushroom body calyces, which responded to all three. Transcriptomic profiles of the mushroom bodies generated by RNA sequencing gave the following results: (1) responses to differences in food type or value included a subset of molecular pathways involved in the response to food reward; (2) genes responsive to food reward, food type and food value were enriched for (the Gene Ontology categories) mitochondrial and endoplasmic reticulum activity; (3) genes responsive to only food and food type were enriched for regulation of transcription and translation; and (4) genes responsive to only food and food value were enriched for regulation of neuronal signaling. These results reveal how activities necessary for colony survival are channeled through the reward system of individual honey bees.
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Affiliation(s)
- M S McNeill
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - K M Kapheim
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biology, Utah State University, Logan, UT, USA
| | - A Brockmann
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - T A W McGill
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - G E Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Shpigler HY, Robinson GE. Laboratory Assay of Brood Care for Quantitative Analyses of Individual Differences in Honey Bee (Apis mellifera) Affiliative Behavior. PLoS One 2015; 10:e0143183. [PMID: 26569402 PMCID: PMC4646683 DOI: 10.1371/journal.pone.0143183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/01/2015] [Indexed: 01/18/2023] Open
Abstract
Care of offspring is a form of affiliative behavior that is fundamental to studies of animal social behavior. Insects do not figure prominently in this topic because Drosophila melanogaster and other traditional models show little if any paternal or maternal care. However, the eusocial honey bee exhibits cooperative brood care with larvae receiving intense and continuous care from their adult sisters, but this behavior has not been well studied because a robust quantitative assay does not exist. We present a new laboratory assay that enables quantification of group or individual honey bee brood “nursing behavior” toward a queen larva. In addition to validating the assay, we used it to examine the influence of the age of the larva and the genetic background of the adult bees on nursing performance. This new assay also can be used in the future for mechanistic analyses of eusociality and comparative analyses of affilative behavior with other animals.
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Affiliation(s)
- Hagai Y Shpigler
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United State of America
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United State of America.,Department of Entomology and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United State of America
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Wheeler MM, Ament SA, Rodriguez-Zas SL, Southey B, Robinson GE. Diet and endocrine effects on behavioral maturation-related gene expression in the pars intercerebralis of the honey bee brain. ACTA ACUST UNITED AC 2015; 218:4005-14. [PMID: 26567353 DOI: 10.1242/jeb.119420] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 10/22/2015] [Indexed: 01/05/2023]
Abstract
Nervous and neuroendocrine systems mediate environmental conditions to control a variety of life history traits. Our goal was to provide mechanistic insights as to how neurosecretory signals mediate division of labor in the honey bee (Apis mellifera). Worker division of labor is based on a process of behavioral maturation by individual bees, which involves performing in-hive tasks early in adulthood, then transitioning to foraging for food outside the hive. Social and nutritional cues converge on endocrine factors to regulate behavioral maturation, but whether neurosecretory systems are central to this process is not known. To explore this, we performed transcriptomic profiling of a neurosecretory region of the brain, the pars intercerebralis (PI). We first compared PI transcriptional profiles for bees performing in-hive tasks and bees engaged in foraging. Using these results as a baseline, we then performed manipulative experiments to test whether the PI is responsive to dietary changes and/or changes in juvenile hormone (JH) levels. Results reveal a robust molecular signature of behavioral maturation in the PI, with a subset of gene expression changes consistent with changes elicited by JH treatment. In contrast, dietary changes did not induce transcriptomic changes in the PI consistent with behavioral maturation or JH treatment. Based on these results, we propose a new verbal model of the regulation of division of labor in honey bees in which the relationship between diet and nutritional physiology is attenuated, and in its place is a relationship between social signals and nutritional physiology that is mediated by JH.
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Affiliation(s)
| | - Seth A Ament
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Bruce Southey
- Department of Animal Sciences, UIUC, Urbana, IL 61801, USA
| | - Gene E Robinson
- Department of Entomology, UIUC, Urbana, IL 61801, USA Institute for Genomic Biology, UIUC, Urbana, IL 61801, USA
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Rittschof CC, Coombs CB, Frazier M, Grozinger CM, Robinson GE. Early-life experience affects honey bee aggression and resilience to immune challenge. Sci Rep 2015; 5:15572. [PMID: 26493190 PMCID: PMC4616062 DOI: 10.1038/srep15572] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/29/2015] [Indexed: 11/23/2022] Open
Abstract
Early-life social experiences cause lasting changes in behavior and health for a variety of animals including humans, but it is not well understood how social information ''gets under the skin'' resulting in these effects. Adult honey bees (Apis mellifera) exhibit socially coordinated collective nest defense, providing a model for social modulation of aggressive behavior. Here we report for the first time that a honey bee's early-life social environment has lasting effects on individual aggression: bees that experienced high-aggression environments during pre-adult stages showed increased aggression when they reached adulthood relative to siblings that experienced low-aggression environments, even though all bees were kept in a common environment during adulthood. Unlike other animals including humans however, high-aggression honey bees were more, rather than less, resilient to immune challenge, assessed as neonicotinoid pesticide susceptibility. Moreover, aggression was negatively correlated with ectoparasitic mite presence. In honey bees, early-life social experience has broad effects, but increased aggression is decoupled from negative health outcomes. Because honey bees and humans share aspects of their physiological response to aggressive social encounters, our findings represent a step towards identifying ways to improve individual resiliency. Pre-adult social experience may be crucial to the health of the ecologically threatened honey bee.
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Affiliation(s)
- Clare C. Rittschof
- Carl R. Woese Institute for Genomic Biology, Department of Entomology and Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, 61801
- Department of Entomology, Center for Pollinator Research, The Pennsylvania State University, University Park, PA, 16802
| | - Chelsey B. Coombs
- Department of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801
| | - Maryann Frazier
- Department of Entomology, Center for Pollinator Research, The Pennsylvania State University, University Park, PA, 16802
| | - Christina M. Grozinger
- Department of Entomology, Center for Pollinator Research, The Pennsylvania State University, University Park, PA, 16802
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology and Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, 61801
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Abstract
New genomic tools and resources are now being used to both understand honey bee health and develop tools to better manage it. Here, we describe the use of genomic approaches to identify and characterize bee parasites and pathogens, examine interactions among these parasites and pathogens, between them and their bee hosts, and to identify genetic markers for improved breeding of more resilient bee stocks. We also discuss several new genomic techniques that can be used to more efficiently study, monitor and improve bee health. In the case of using RNAi-based technologies to mitigate diseases in bee populations, we highlight advantages, disadvantages and strategies to reduce risk. The increased use of genomic analytical tools and manipulative technologies has already led to significant advances, and holds great promise for improvements in the health of honey bees and other critical pollinator species.
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Affiliation(s)
- Christina M. Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, PA 16803
| | - Gene E. Robinson
- Department of Entomology, Neuroscience Program, Institute for Genomic Biology, University of Illinois, Urbana-Champaign, 61801
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45
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Liang ZS, Mattila HR, Rodriguez-Zas SL, Southey BR, Seeley TD, Robinson GE. Comparative brain transcriptomic analyses of scouting across distinct behavioural and ecological contexts in honeybees. Proc Biol Sci 2015; 281:rspb.2014.1868. [PMID: 25355476 DOI: 10.1098/rspb.2014.1868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Individual differences in behaviour are often consistent across time and contexts, but it is not clear whether such consistency is reflected at the molecular level. We explored this issue by studying scouting in honeybees in two different behavioural and ecological contexts: finding new sources of floral food resources and finding a new nest site. Brain gene expression profiles in food-source and nest-site scouts showed a significant overlap, despite large expression differences associated with the two different contexts. Class prediction and 'leave-one-out' cross-validation analyses revealed that a bee's role as a scout in either context could be predicted with 92.5% success using 89 genes at minimum. We also found that genes related to four neurotransmitter systems were part of a shared brain molecular signature in both types of scouts, and the two types of scouts were more similar for genes related to glutamate and GABA than catecholamine or acetylcholine signalling. These results indicate that consistent behavioural tendencies across different ecological contexts involve a mixture of similarities and differences in brain gene expression.
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Affiliation(s)
- Zhengzheng S Liang
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Heather R Mattila
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Sandra L Rodriguez-Zas
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Thomas D Seeley
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Gene E Robinson
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Abstract
Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade. This perspective considers the growth of genomics over the next ten years and assesses the computational needs that we will face relative to other "Big Data" activities such as astronomy, YouTube, and Twitter.
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Affiliation(s)
- Zachary D. Stephens
- Coordinated Science Laboratory and Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Skylar Y. Lee
- Coordinated Science Laboratory and Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Faraz Faghri
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Roy H. Campbell
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Chengxiang Zhai
- Carl R. Woese Institute for Genomic Biology & Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Miles J. Efron
- School of Library and Information Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ravishankar Iyer
- Coordinated Science Laboratory and Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Michael C. Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- * E-mail: (MCS); (SS); (GER)
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology & Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MCS); (SS); (GER)
| | - Gene E. Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (MCS); (SS); (GER)
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Khamis AM, Hamilton AR, Medvedeva YA, Alam T, Alam I, Essack M, Umylny B, Jankovic BR, Naeger NL, Suzuki M, Harbers M, Robinson GE, Bajic VB. Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. Sci Rep 2015; 5:11136. [PMID: 26073445 PMCID: PMC4466890 DOI: 10.1038/srep11136] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/01/2015] [Indexed: 12/30/2022] Open
Abstract
Honey bee colonies exhibit an age-related division of labor, with worker bees performing discrete sets of behaviors throughout their lifespan. These behavioral states are associated with distinct brain transcriptomic states, yet little is known about the regulatory mechanisms governing them. We used CAGEscan (a variant of the Cap Analysis of Gene Expression technique) for the first time to characterize the promoter regions of differentially expressed brain genes during two behavioral states (brood care (aka “nursing”) and foraging) and identified transcription factors (TFs) that may govern their expression. More than half of the differentially expressed TFs were associated with motifs enriched in the promoter regions of differentially expressed genes (DEGs), suggesting they are regulators of behavioral state. Strikingly, five TFs (nf-kb, egr, pax6, hairy, and clockwork orange) were predicted to co-regulate nearly half of the genes that were upregulated in foragers. Finally, differences in alternative TSS usage between nurses and foragers were detected upstream of 646 genes, whose functional analysis revealed enrichment for Gene Ontology terms associated with neural function and plasticity. This demonstrates for the first time that alternative TSSs are associated with stable differences in behavior, suggesting they may play a role in organizing behavioral state.
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Affiliation(s)
- Abdullah M Khamis
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Adam R Hamilton
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yulia A Medvedeva
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Tanvir Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Boris Umylny
- Lumenogix Inc., 2935 Rodeo Park Drive East, Santa Fe NM, 87505, USA
| | - Boris R Jankovic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Nicholas L Naeger
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Makoto Suzuki
- DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan
| | - Matthias Harbers
- 1] DNAFORM Inc., Leading Venture Plaza-2, 75-1, Ono-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0046, Japan [2] RIKEN Center for Life Science Technologies, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Gene E Robinson
- Departments of Entomology and Institute for Genomic Biology, Urbana, IL 61801; and Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Vladimir B Bajic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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McNeill MS, Robinson GE. Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus. Insect Mol Biol 2015; 24:377-390. [PMID: 25773289 DOI: 10.1111/imb.12165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Immediate early genes (IEGs) have served as useful markers of brain neuronal activity in mammals, and more recently in insects. The mammalian canonical IEG, c-jun, is part of regulatory pathways conserved in insects and has been shown to be responsive to alarm pheromone in honey bees. We tested whether c-jun was responsive in honey bees to another behaviourally relevant stimulus, sucrose, in order to further identify the brain regions involved in sucrose processing. To identify responsive regions, we developed a new method of voxel-based analysis of c-jun mRNA expression. We found that c-jun is expressed in somata throughout the brain. It was rapidly induced in response to sucrose stimuli, and it responded in somata near the antennal and mechanosensory motor centre, mushroom body calices and lateral protocerebrum, which are known to be involved in sucrose processing. c-jun also responded to sucrose in somata near the lateral suboesophageal ganglion, dorsal optic lobe, ventral optic lobe and dorsal posterior protocerebrum, which had not been previously identified by other methods. These results demonstrate the utility of voxel-based analysis of mRNA expression in the insect brain.
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Affiliation(s)
- M S McNeill
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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49
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Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RFA, Glastad KM, Hunt BG, Goodisman MAD, Hauser F, Grimmelikhuijzen CJP, Pinheiro DG, Nunes FMF, Soares MPM, Tanaka ÉD, Simões ZLP, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science 2015; 348:1139-43. [PMID: 25977371 DOI: 10.1126/science.aaa4788] [Citation(s) in RCA: 235] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/06/2015] [Indexed: 12/14/2022]
Abstract
The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.
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Affiliation(s)
- Karen M Kapheim
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Biology, Utah State University, Logan, UT 84322, USA.
| | - Hailin Pan
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA. Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tanja Magoc
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hugh M Robertson
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Matthew E Hudson
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aarti Venkat
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Brielle J Fischman
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Alvaro Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA. USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel Ence
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA. USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - George D Yocum
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - William P Kemp
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) Red River Valley Agricultural Research Center, Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Jordi Bosch
- Center for Ecological Research and Forestry Applications (CREAF), Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland. Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Eckart Stolle
- Institute of Biology, Department Zoology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 4, D-06099 Halle (Saale), Germany. Queen Mary University of London, School of Biological and Chemical Sciences Organismal Biology Research Group, London E1 4NS, UK
| | - F Bernhard Kraus
- Institute of Biology, Department Zoology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 4, D-06099 Halle (Saale), Germany. Department of Laboratory Medicine, University Hospital Halle, Ernst Grube Strasse 40, D-06120 Halle (Saale), Germany
| | - Sophie Helbing
- Institute of Biology, Department Zoology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 4, D-06099 Halle (Saale), Germany
| | - Robin F A Moritz
- Institute of Biology, Department Zoology, Martin-Luther-University Halle-Wittenberg, Hoher Weg 4, D-06099 Halle (Saale), Germany. German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Karl M Glastad
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA
| | | | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Guariz Pinheiro
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil. Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), 14884-900 Jaboticabal, SP, Brazil
| | - Francis Morais Franco Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Michelle Prioli Miranda Soares
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Érica Donato Tanaka
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Zilá Luz Paulino Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900 Ribeirão Preto, SP, Brazil
| | - Jay D Evans
- USDA-ARS Bee Research Lab, Beltsville, MD 20705 USA
| | - Seth M Barribeau
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Reed M Johnson
- Department of Entomology, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH 44691, USA
| | - Jonathan H Massey
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Martin Hasselmann
- Department of Population Genomics, Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, Germany
| | - Daniel Hamacher
- Department of Population Genomics, Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, Germany
| | - Matthias Biewer
- Department of Population Genomics, Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, Germany
| | - Clement F Kent
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada. Janelia Farm Research Campus, Howard Hughes Medical Institue, Ashburn, VA 20147, USA
| | - Amro Zayed
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Charles Blatti
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saurabh Sinha
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Shawn J Hanrahan
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Sarah D Kocher
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Jun Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong.
| | - Gene E Robinson
- Carl R. WoeseInstitute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center for Advanced Study Professor in Entomology and Neuroscience, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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50
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Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJP, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MMG, Blaxter ML, Bourke AFG, Brown MJF, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FCP, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HMG, Leask M, Lockett GA, Mallon EB, Antonio DSM, Marxer M, Meeus I, Moritz RFA, Nair A, Näpflin K, Nissen I, Niu J, Nunes FMF, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZLP, Soares MPM, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KKO, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol 2015; 16:76. [PMID: 25908251 PMCID: PMC4414376 DOI: 10.1186/s13059-015-0623-3] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/10/2015] [Indexed: 12/25/2022] Open
Abstract
Background The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0623-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ben M Sadd
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA. .,Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Seth M Barribeau
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Guy Bloch
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Dirk C de Graaf
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Peter Dearden
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Christine G Elsik
- Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Jürgen Gadau
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Martin Hasselmann
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany.
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA.
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Eckart Stolle
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Matthias Van Vaerenbergh
- Laboratory of Zoophysiology, Faculty of Sciences, Ghent University, Krijgslaan 281, S2, 9000, Ghent, Belgium.
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Erich Bornberg-Bauer
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Steffen Klasberg
- Westfalian Wilhelms University, Institute of Evolution and Biodiversity, Huefferstrasse 1, 48149, Muenster, Germany.
| | - Anna K Bennett
- Department of Biology, Georgetown University, Washington, DC, 20057, USA.
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Katharina Hoff
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Monica Munoz-Torres
- Department of Biology, Georgetown University, Washington, DC, 20057, USA. .,Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Terence Murphy
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, USA.
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Gro V Amdam
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Martin Beye
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Matthias Biewer
- University of Hohenheim, Institute of Animal Science, Garbenstrasse 17, 70599, Stuttgart, Germany. .,University of Cologne, Institute of Genetics, Cologne, Germany.
| | - Márcia M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Mark L Blaxter
- Institute of Evolutionary Biology and Edinburgh Genomics, The Ashworth Laboratories, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, London, UK.
| | - Severine D Buechel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Rossanah Cameron
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kaat Cappelle
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - James C Carolan
- Maynooth University Department of Biology, Maynooth University, Co, Kildare, Ireland.
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Kate L Ciborowski
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | | | - Thomas J Colgan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
| | - David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Stephanie Dreier
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Louis du Plessis
- Theoretical Biology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,Computational Evolution, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Elizabeth Duncan
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Silvio Erler
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Jay Evans
- USDA-ARS Bee Research Laboratory, Maryland, USA.
| | - Tiago Falcon
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Kevin Flores
- Center for Research in Scientific Computation, North Carolina State University Raleigh, Raleigh, NC, USA.
| | - Flávia C P Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Taro Fuchikawa
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. .,Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
| | - Tanja Gempe
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Sophie Helbing
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Fernanda C Humann
- Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, 15991-502, Matão, Brazil.
| | - Frano Irvine
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Claire E Johnson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Reed M Johnson
- Department of Entomology, The Ohio State University, Wooster, OH, 44791, USA.
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China.
| | - Jonathan H Kidner
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Vasco Koch
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Arian Köhler
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - F Bernhard Kraus
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Laboratory Medicine, University Hospital Halle (Saale), Halle, Germany.
| | - H Michael G Lattorff
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Megan Leask
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | | | - Eamonn B Mallon
- Department of Biology, University of Leicester, Leicester, UK.
| | - David S Marco Antonio
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Monika Marxer
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Robin F A Moritz
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Ajay Nair
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kathrin Näpflin
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Inga Nissen
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Jinzhi Niu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Francis M F Nunes
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, 13565-905, São Carlos, Brazil.
| | | | - Amy Osborne
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Marianne Otte
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany.
| | - Daniel G Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil.
| | - Nina Rossié
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Carolina G Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Regula Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Björn D Schmitt
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Christina Schulte
- Institute of Evolutionary Genetics, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Zilá L P Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, Brazil.
| | - Michelle P M Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14040-900, Ribeirão Preto, Brazil.
| | - Luc Swevers
- Institute of Biosciences & Applications, National Center for Scientific Research Demokritos, Athens, Greece.
| | | | - Florian Wolschin
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Food Science, N-1432, Aas, Norway.
| | - Na Yu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland. .,Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland.
| | - Peshtewani K Aqrawi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kerstin P Blankenburg
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Marcus Coyle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Liezl Francisco
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Matthew E Hudson
- Department of Crop Sciences and Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - LaRonda Jackson
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christie Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Robert Mata
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Tittu Mathew
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Irene F Newsham
- Molecular Genetic Technology Program, School of Health Professions, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 2, Houston, TX, 77025, USA.
| | - Robin Ngo
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Christopher Pham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Nehad Saada
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - DeNard Simmons
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Aarti Venkat
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Griet Debyser
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Bart Devreese
- Laboratory of Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Claire Asher
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Julie Blommaert
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Ariel D Chipman
- Department of Ecology, Evolution, and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Lars Chittka
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Bertrand Fouks
- Institute of Biology, Martin-Luther-University Halle-Wittenberg, Wittenberg, Germany. .,Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27403, USA.
| | - Jisheng Liu
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium. .,School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Meaghan P O'Neill
- Laboratory for Evolution and Development, Genetics Otago and the National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | - Steven E Scherer
- School of Life Sciences, Guangzhou University, Guangzhou, China.
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, Department of Entomology, Neuroscience Program, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Paul Schmid-Hempel
- Experimental Ecology, Institute of Integrative Biology, Eidgenössiche Technische Hochschule (ETH) Zürich, CH-8092, Zürich, Switzerland.
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.
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