Beyond conflict: kinship theory of intragenomic conflict predicts individual variation in altruistic behavior

Studies of the genetic basis of behavioral variation have emphasized gene cooperation within networks, often overlooking gene conflicts. The Kinship Theory of Intragenomic Conflict (KTIC) proposes that conflicts can occur within genes when parent-specific alleles have different strategies for maximizing reproductive fitness. Here, we test a prediction of the KTIC – that selection should favor alleles which promote “altruistic” behaviors that support the reproductive fitness of kin. In honey bee (Apis mellifera) colonies, workers act altruistically when tending to the queen by performing a “retinue” behavior, distributing the queen’s mandibular pheromone (QMP) throughout the hive. Workers exposed to QMP do not activate their ovaries, ensuring they care for the queen’s brood instead of competing to lay unfertilized eggs. Thus, the KTIC predicts that response to QMP should be favored by the maternal genome. Using a reciprocal cross design, we tested for parent-of-origin effects on the workers’ 1) responsiveness to QMP, 2) ovary activation, and 3) brain transcriptome. We hypothesized that QMP-responsive workers have smaller and less active ovaries, influenced by the workers’ parent-of-origin. With an allele-specific transcriptomic analysis, we tested whether QMP-responsive workers show enriched maternal allele-biased gene expression compared to QMP-unresponsive workers. Finally, we explored how parent-of-origin gene expression patterns are associated with overall gene expression patterns and regulatory networks. We report evidence in support of the KTIC for the retinue behavior and associated conflicts within gene networks. Our study provides new insights into the genetic basis of behavior and the potential for behavioral variation influenced by intragenomic conflict.

[1]  Azusa Inoue Noncanonical imprinting: intergenerational epigenetic inheritance mediated by Polycomb complexes. , 2022, Current opinion in genetics & development.

[2]  G. Amdam,et al.  Resolving the zinc binding capacity of honey bee vitellogenin and locating its putative binding sites , 2022, Insect molecular biology.

[3]  David M Dormagen,et al.  Behavioral variation across the days and lives of honey bees , 2022, iScience.

[4]  E. Duncan,et al.  Phenotypic Plasticity: What Has DNA Methylation Got to Do with It? , 2022, Insects.

[5]  G. Kelsey,et al.  Features and mechanisms of canonical and noncanonical genomic imprinting , 2021, Genes & development.

[6]  A. Toth,et al.  The honey bee genome-- what has it been good for? , 2021 .

[7]  L. O’Connell,et al.  Social boldness correlates with brain gene expression in male green anoles , 2021, Hormones and Behavior.

[8]  Beryl M. Jones,et al.  Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks , 2020, eLife.

[9]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[10]  C. Grozinger,et al.  Tissue‐specific transcription patterns support the kinship theory of intragenomic conflict in honey bees (Apis mellifera) , 2020, Molecular ecology.

[11]  Mingyao Li,et al.  Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data , 2020, bioRxiv.

[12]  B. Taylor,et al.  The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp , 2020, Nature Communications.

[13]  Beryl M. Jones,et al.  Behavior-related gene regulatory networks: A new level of organization in the brain , 2020, Proceedings of the National Academy of Sciences.

[14]  S. Yi,et al.  Lineage and Parent-of-Origin Effects in DNA Methylation of Honey Bees (Apis mellifera) Revealed by Reciprocal Crosses and Whole-Genome Bisulfite Sequencing , 2020, Genome biology and evolution.

[15]  Kitty Lo,et al.  Paternally‐biased gene expression follows kin‐selected predictions in female honey bee embryos , 2020, Molecular ecology.

[16]  Rachel E. Moore,et al.  Delta-Notch Signaling: The Long and the Short of a Neuron’s Influence on Progenitor Fates , 2020, Journal of developmental biology.

[17]  D. Gordon,et al.  Gene expression variation in the brains of harvester ant foragers is associated with collective behavior , 2020, Communications Biology.

[18]  Eamonn B. Mallon,et al.  Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression , 2020, bioRxiv.

[19]  C. Köhler,et al.  Genomic imprinting in plants—revisiting existing models , 2020, Genes & development.

[20]  Luisa F. Pallares,et al.  The structure of behavioral variation within a genotype , 2019, bioRxiv.

[21]  E. V. Kovalenko,et al.  The Drosophila nuclear receptors EcR and ERR jointly regulate the expression of genes involved in carbohydrate metabolism. , 2019, Insect biochemistry and molecular biology.

[22]  Stephen S. Gisselbrecht,et al.  A Comprehensive Drosophila melanogaster Transcription Factor Interactome , 2019, Cell reports.

[23]  G. Robinson,et al.  Honey bee neurogenomic responses to affiliative and agonistic social interactions , 2018, Genes, brain, and behavior.

[24]  G. Robinson,et al.  A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds , 2018, bioRxiv.

[25]  A. Brockmann,et al.  Egr-1: A Candidate Transcription Factor Involved in Molecular Processes Underlying Time-Memory , 2018, Front. Psychol..

[26]  C. Pirk,et al.  Reproductive parasitism by worker honey bees suppressed by queens through regulation of worker mandibular secretions , 2018, Scientific Reports.

[27]  R. Crewe,et al.  Reproductive parasitism by worker honey bees suppressed by queens through regulation of worker mandibular secretions , 2018, Scientific Reports.

[28]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[29]  S. Fahrbach,et al.  Queen mandibular pheromone modulates hemolymph ecdysteroid titers in adult Apis mellifera workers , 2018, Apidologie.

[30]  P. Georgiev,et al.  Drosophila DNA-Binding Proteins in Polycomb Repression , 2018 .

[31]  A. Gardner,et al.  The meaning of intragenomic conflict , 2017, Nature Ecology & Evolution.

[32]  H. Bourbon,et al.  Genome Regulation by Polycomb and Trithorax: 70 Years and Counting , 2017, Cell.

[33]  Eamonn B. Mallon,et al.  Do social insects support Haig's kin theory for the evolution of genomic imprinting? , 2017, Epigenetics.

[34]  M. Beekman,et al.  Paternal effects on Apis mellifera capensis worker ovary size , 2017, Apidologie.

[35]  E. Duncan,et al.  Notch signalling mediates reproductive constraint in the adult worker honeybee , 2016, Nature Communications.

[36]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[37]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.

[38]  R. Feil,et al.  Regulatory links between imprinted genes: evolutionary predictions and consequences , 2016, Proceedings of the Royal Society B: Biological Sciences.

[39]  D. Zilberman,et al.  Evolution and function of genomic imprinting in plants , 2015, Genes & development.

[40]  D. Gordon From division of labor to the collective behavior of social insects , 2015, Behavioral Ecology and Sociobiology.

[41]  G. Robinson,et al.  Laboratory Assay of Brood Care for Quantitative Analyses of Individual Differences in Honey Bee (Apis mellifera) Affiliative Behavior , 2015, PloS one.

[42]  T. Shinoda,et al.  Molecular basis of juvenile hormone signaling. , 2015, Current opinion in insect science.

[43]  Vladimir B. Bajic,et al.  Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera , 2015, Scientific Reports.

[44]  Matthew E. Hudson,et al.  Genomic signatures of evolutionary transitions from solitary to group living , 2015, Science.

[45]  Sarah D. Kocher,et al.  A Search for Parent-of-Origin Effects on Honey Bee Gene Expression , 2015, G3: Genes, Genomes, Genetics.

[46]  J. Godwin,et al.  Characterizing the neurotranscriptomic states in alternative stress coping styles , 2015, BMC Genomics.

[47]  K. Nicolaides,et al.  The role and interaction of imprinted genes in human fetal growth , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

[48]  E. Dubois,et al.  A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation , 2015, Genome research.

[49]  D. G. Pinheiro,et al.  Developmental regulation of ecdysone receptor (EcR) and EcR-controlled gene expression during pharate-adult development of honeybees (Apis mellifera) , 2014, Front. Genet..

[50]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[51]  Y. Le Conte,et al.  Queen and young larval pheromones impact nursing and reproductive physiology of honey bee (Apis mellifera) workers , 2014, Behavioral Ecology and Sociobiology.

[52]  Raphaël Jeanson,et al.  Interindividual variability in social insects – proximate causes and ultimate consequences , 2014, Biological reviews of the Cambridge Philosophical Society.

[53]  A. Bourke Hamilton's rule and the causes of social evolution , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[54]  A. Clark,et al.  Using next-generation RNA sequencing to identify imprinted genes , 2014, Heredity.

[55]  D. Gordon The Ecology of Collective Behavior , 2014, PLoS biology.

[56]  G. Robinson,et al.  Activity-dependent gene expression in honey bee mushroom bodies in response to orientation flight , 2013, Journal of Experimental Biology.

[57]  S. Foster,et al.  Behavioural plasticity and evolution , 2013, Animal Behaviour.

[58]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[59]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[60]  S. Cobey,et al.  Standard methods for instrumental insemination of Apis mellifera queens , 2013 .

[61]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[62]  Timothy E. Reddy,et al.  Effects of sequence variation on differential allelic transcription factor occupancy and gene expression , 2012, Genome research.

[63]  Sarah D. Kocher,et al.  Cooperation, Conflict, and the Evolution of Queen Pheromones , 2011, Journal of Chemical Ecology.

[64]  K. Ingram,et al.  Differential regulation of the foraging gene associated with task behaviors in harvester ants , 2011, BMC Ecology.

[65]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[66]  E. Birney,et al.  Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans , 2010, Science.

[67]  Francis L W Ratnieks,et al.  The evolution of extreme altruism and inequality in insect societies , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.

[68]  S. Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[69]  C. Grozinger,et al.  Dissecting the role of Kr‐h1 brain gene expression in foraging behavior in honey bees (Apis mellifera) , 2008, Insect molecular biology.

[70]  K. Hartfelder,et al.  Identification of a juvenile hormone esterase-like gene in the honey bee, Apis mellifera L.--expression analysis and functional assays. , 2008, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[71]  G. Robinson,et al.  Endocrine modulation of a pheromone-responsive gene in the honey bee brain , 2007, Journal of Comparative Physiology A.

[72]  K. Hartfelder,et al.  Ovariole number—a predictor of differential reproductive success among worker subfamilies in queenless honeybee (Apis mellifera L.) colonies , 2006, Behavioral Ecology and Sociobiology.

[73]  M. Gho,et al.  Lethal Giant Larvae Controls the Localization of Notch-Signaling Regulators Numb, Neuralized, and Sanpodo in Drosophila Sensory-Organ Precursor Cells , 2005, Current Biology.

[74]  G. Robinson,et al.  Gene Expression Profiles in the Brain Predict Behavior in Individual Honey Bees , 2003, Science.

[75]  D. Queller Theory of genomic imprinting conflict in social insects , 2003, BMC Evolutionary Biology.

[76]  M. Winston,et al.  New components of the honey bee (Apis mellifera L.) queen retinue pheromone , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[77]  D. Haig The Kinship Theory of Genomic Imprinting , 2000 .

[78]  G. Robinson,et al.  Queen mandibular gland pheromone influences worker honey bee (Apis mellifera L.) foraging ontogeny and juvenile hormone titers. , 1998, Journal of insect physiology.

[79]  D. Haig Intragenomic conflict and the evolution of eusociality. , 1992, Journal of theoretical biology.

[80]  Choongrak Kim,et al.  Exact Properties of Some Exact Test Statistics for Comparing Two Binomial Proportions , 1990 .

[81]  T. D. Seely Queen substance dispersal by messenger workers in honeybee colonies , 1979, Behavioral Ecology and Sociobiology.

[82]  G. Pertea,et al.  GFF Utilities: GffRead and GffCompare. , 2020, F1000Research.

[83]  R. Schmidt Spirit of the hive , 2011 .

[84]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[85]  L. Connor Queen Rearing Essentials , 2009 .

[86]  M. Winston,et al.  Variation in worker response to honey bee (Apis mellifera L.) queen mandibular pheromone (Hymenoptera: Apidae) , 2005, Journal of Insect Behavior.

[87]  M. Bartolomei,et al.  Genomic imprinting in mammals. , 1997, Annual review of genetics.

[88]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[89]  R. Currie,et al.  Drifting behaviour of drone honey bees (Apis mellifera L.) in commercial apiaries , 1991 .

[90]  Alexander S. Mikheyev,et al.  Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns , 2015, eLife.