1
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Belcher LJ, Dewar AE, Hao C, Katz Z, Ghoul M, West SA. SOCfinder: a genomic tool for identifying social genes in bacteria. Microb Genom 2023; 9:001171. [PMID: 38117204 PMCID: PMC10763506 DOI: 10.1099/mgen.0.001171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023] Open
Abstract
Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [1] code for an extracellular protein [2], have a cooperative functional annotation, or [3] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa and B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder.
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Affiliation(s)
| | - Anna E. Dewar
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Zohar Katz
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Stuart A. West
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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2
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Belcher LJ, Dewar AE, Hao C, Ghoul M, West SA. Signatures of kin selection in a natural population of the bacteria Bacillus subtilis. Evol Lett 2023; 7:315-330. [PMID: 37829498 PMCID: PMC10565896 DOI: 10.1093/evlett/qrad029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/14/2023] [Accepted: 07/07/2023] [Indexed: 10/14/2023] Open
Abstract
Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.
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Affiliation(s)
| | - Anna E Dewar
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Chunhui Hao
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Melanie Ghoul
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Stuart A West
- Department of Biology, University of Oxford, Oxford, United Kingdom
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3
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Barkdull M, Moreau CS. Worker Reproduction and Caste Polymorphism Impact Genome Evolution and Social Genes Across the Ants. Genome Biol Evol 2023; 15:evad095. [PMID: 37243539 PMCID: PMC10287540 DOI: 10.1093/gbe/evad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Eusocial insects are characterized by several traits, including reproductive division of labor and caste polymorphisms, which likely modulate genome evolution. Concomitantly, evolution may act on specific genes and pathways underlying these novel, sociality-associated phenotypes. Reproductive division of labor should increase the magnitude of genetic drift and reduce the efficacy of selection by reducing effective population size. Caste polymorphism has been associated with relaxed selection and may facilitate directional selection on caste-specific genes. Here, we use comparative analyses of 22 ant genomes to test how reproductive division of labor and worker polymorphism influence positive selection and selection intensity across the genome. Our results demonstrate that worker reproductive capacity is associated with a reduction in the degree of relaxed selection but is not associated with any significant change to positive selection. We find decreases in positive selection in species with polymorphic workers, but no increase in the degree of relaxed selection. Finally, we explore evolutionary patterns in specific candidate genes associated with our focal traits in eusocial insects. Two oocyte patterning genes previously implicated in worker sterility evolve under intensified selection in species with reproductive workers. Behavioral caste genes generally experience relaxed selection associated with worker polymorphism, whereas vestigial and spalt, both associated with soldier development in Pheidole ants, experience intensified selection in worker polymorphic species. These findings expand our understanding of the genetic mechanisms underlying elaborations of sociality. The impacts of reproductive division of labor and caste polymorphisms on specific genes illuminate those genes' roles in generating complex eusocial phenotypes.
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Affiliation(s)
- Megan Barkdull
- Department of Ecology & Evolutionary Biology, Cornell University
| | - Corrie S Moreau
- Department of Ecology & Evolutionary Biology, Cornell University
- Department of Entomology, Cornell University
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4
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Du M, Bernstein R, Hoppe A, Bienefeld K. Consequences of incorrect genetic parameter estimates for single-trait and multi-trait genetic evaluations in honeybees. J Anim Breed Genet 2022; 139:666-678. [PMID: 35775281 DOI: 10.1111/jbg.12728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/10/2022] [Indexed: 12/01/2022]
Abstract
Genetic and residual variances of traits are important input parameters for best linear unbiased prediction (BLUP) breeding value estimation. In honeybees, estimates of these variances are often associated with large standard errors, entailing a risk to perform genetic evaluations under wrong premises. The consequences hereof have not been sufficiently studied. In particular, there are no adequate investigations on this topic accounting for multi-trait selection or genetic peculiarities of the honeybee. We performed simulation studies and explored the consequences of selection for honeybee populations with a broad range of true and assumed genetic parameters. We found that in single-trait evaluations, the response to selection was barely compromised by assuming erroneous parameters, so that reductions in genetic progress after 20 years never exceeded 21%. Phenotypic selection appeared inferior to BLUP selection, particularly under low heritabilities. Parameter choices for genetic evaluation had great effects on inbreeding development. By wrongly assuming high heritabilities, inbreeding rates were reduced by up to 74%. When parallel selection was performed for two traits, the right choice of genetic parameters appeared considerably more crucial as several incorrect premises yielded inadvertent negative selection for one of the traits. This phenomenon occurred in multiple constellations in which the selection traits expressed a negative genetic correlation. It was not reflected in the estimated breeding values. Our results indicate that breeding efforts heavily rely on detailed knowledge on genetic parameters, particularly when multi-trait selection is performed. Thus, considerable effort should be invested into precise parameter estimations.
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Affiliation(s)
- Manuel Du
- Institute for Bee Research Hohen Neuendorf, Hohen Neuendorf, Germany
| | - Richard Bernstein
- Institute for Bee Research Hohen Neuendorf, Hohen Neuendorf, Germany
| | - Andreas Hoppe
- Institute for Bee Research Hohen Neuendorf, Hohen Neuendorf, Germany
| | - Kaspar Bienefeld
- Institute for Bee Research Hohen Neuendorf, Hohen Neuendorf, Germany
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5
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Kin selection for cooperation in natural bacterial populations. Proc Natl Acad Sci U S A 2022; 119:2119070119. [PMID: 35193981 PMCID: PMC8892524 DOI: 10.1073/pnas.2119070119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/03/2023] Open
Abstract
Bacteria secrete many molecules outside the cell, where they provide benefits to other cells. One potential reason for producing these “public goods” is that they benefit closely related cells that share the gene for cooperation (kin selection). While many laboratory studies have supported this hypothesis, there is a lack of evidence that kin selection favors cooperation in natural populations. We examined bacterial genomes from the environment and used population genetics theory to analyze the DNA sequences. Our analyses suggest that public goods cooperation has indeed been favored by kin selection in natural populations. Bacteria produce a range of molecules that are secreted from the cell and can provide a benefit to the local population of cells. Laboratory experiments have suggested that these “public goods” molecules represent a form of cooperation, favored because they benefit closely related cells (kin selection). However, there is a relative lack of data demonstrating kin selection for cooperation in natural populations of bacteria. We used molecular population genetics to test for signatures of kin selection at the genomic level in natural populations of the opportunistic pathogen Pseudomonas aeruginosa. We found consistent evidence from multiple traits that genes controlling putatively cooperative traits have higher polymorphism and greater divergence and are more likely to harbor deleterious mutations relative to genes controlling putatively private traits, which are expressed at similar rates. These patterns suggest that cooperative traits are controlled by kin selection, and we estimate that the relatedness for social interactions in P. aeruginosa is r = 0.84. More generally, our results demonstrate how molecular population genetics can be used to study the evolution of cooperation in natural populations.
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6
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Differential Selection on Caste-Associated Genes in a Subterranean Termite. INSECTS 2022; 13:insects13030224. [PMID: 35323522 PMCID: PMC8955789 DOI: 10.3390/insects13030224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
Abstract
Analyzing the information-rich content of RNA can help uncover genetic events associated with social insect castes or other social polymorphisms. Here, we exploit a series of cDNA libraries previously derived from whole-body tissue of different castes as well as from three behaviourally distinct populations of the Eastern subterranean termite Reticulitermes flavipes. We found that the number (~0.5 M) of single nucleotide variants (SNVs) was roughly equal between nymph, worker and soldier caste libraries, but dN/dS (ratio of nonsynonymous to synonymous substitutions) analysis suggested that some of these variants confer a caste-specific advantage. Specifically, the dN/dS ratio was high (~4.3) for genes expressed in the defensively specialized soldier caste, relative to genes expressed by other castes (~1.7−1.8) and regardless of the North American population (Toronto, Raleigh, Boston) from which the castes were sampled. The populations, meanwhile, did show a large difference in SNV count but not in the manner expected from known demographic and behavioural differences; the highly invasive unicolonial population from Toronto was not the least diverse and did not show any other unique substitution patterns, suggesting any past bottleneck associated with invasion or with current unicoloniality has become obscured at the RNA level. Our study raises two important hypotheses relevant to termite sociobiology. First, the positive selection (dN/dS > 1) inferred for soldier-biased genes is presumably indirect and of the type mediated through kin selection, and second, the behavioural changes that accompany some social insect urban invasions (i.e., ‘unicoloniality’) may be detached from the loss-of-diversity expected from invasion bottlenecks.
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7
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Kistler T, Basso B, Phocas F. A simulation study of a honeybee breeding scheme accounting for polyandry, direct and maternal effects on colony performance. Genet Sel Evol 2021; 53:71. [PMID: 34496761 PMCID: PMC8425095 DOI: 10.1186/s12711-021-00665-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Efficient breeding programs are difficult to implement in honeybees due to their biological specificities (polyandry and haplo-diploidy) and complexity of the traits of interest, with performances being measured at the colony scale and resulting from the joint effects of tens of thousands of workers (called direct effects) and of the queen (called maternal effects). We implemented a Monte Carlo simulation program of a breeding plan designed specifically for Apis mellifera's populations to assess the impact of polyandry versus monoandry on colony performance, inbreeding level and genetic gain depending on the individual selection strategy considered, i.e. complete mass selection or within-family (maternal lines) selection. We simulated several scenarios with different parameter setups by varying initial genetic variances and correlations between direct and maternal effects, the selection strategy and the polyandry level. Selection was performed on colony phenotypes. RESULTS All scenarios showed strong increases in direct breeding values of queens after 20 years of selection. Monoandry led to significantly higher direct than maternal genetic gains, especially when a negative correlation between direct and maternal effects was simulated. However, the relative increase in these genetic gains depended also on their initial genetic variability and on the selection strategy. When polyandry was simulated, the results were very similar with either 8 or 16 drones mated to each queen. Across scenarios, polyandrous mating resulted in equivalent or higher gains in performance than monoandrous mating, but with considerably lower inbreeding rates. Mass selection conferred a ~ 20% increase in performance compared to within-family selection, but was also accompanied by a strong increase in inbreeding levels (25 to 50% higher). CONCLUSIONS Our study is the first to compare the long-term effects of polyandrous versus monoandrous mating in honeybee breeding. The latter is an emergent strategy to improve specific traits, such as resistance to varroa, which can be difficult or expensive to phenotype. However, if used during several generations in a closed population, monoandrous mating increases the inbreeding level of queens much more than polyandrous mating, which is a strong limitation of this strategy.
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Affiliation(s)
- Tristan Kistler
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Benjamin Basso
- INRAE, UR 406 Abeilles et Environnement, 84914, Avignon, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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8
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Schrader L, Winter M, Errbii M, Delabie J, Oettler J, Gadau J. Inhibition of HSP90 causes morphological variation in the invasive ant
Cardiocondyla obscurior. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:333-340. [DOI: 10.1002/jez.b.23035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/16/2023]
Affiliation(s)
- Lukas Schrader
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Miles Winter
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Jacques Delabie
- Laboratório de Mirmecologia Cocoa Research Center‐CEPLAC & UESC‐DCAA Itabuna Bahia Brazil
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie University of Regensburg Regensburg Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity University of Münster Münster Germany
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9
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Harrison MC, Chernyshova AM, Thompson GJ. No obvious transcriptome-wide signature of indirect selection in termites. J Evol Biol 2020; 34:403-415. [PMID: 33290587 DOI: 10.1111/jeb.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/16/2020] [Accepted: 11/30/2020] [Indexed: 11/26/2022]
Abstract
The evolution of sterile helper castes in social insects implies selection on genes that underlie variation in this nonreproductive phenotype. These focal genes confer no direct fitness and are presumed to evolve through indirect fitness effects on the helper's reproducing relatives. This separation of a gene's phenotypic effect on one caste and its fitness effect on another suggests that genes for this and other forms of reproductive altruism are buffered from selection and will thus evolve closer to the neutral rate than genes directly selected for selfish reproduction. We test this hypothesis by comparing the strength of selection at loci associated in their expression with reproductive versus sterile castes in termites. Specifically, we gather caste-biased gene expression data from four termite transcriptomes and measure the global dN/dS ratio across gene sets and phylogenetic lineages. We find that the majority of examined orthologous gene groups show patterns of nucleotide substitution that are consistent with strong purifying selection and display little evidence for distinct signatures of direct versus indirect selection in reproductive and sterile castes. For one particular species (Reticulitermes flavipes), the strength of purifying selection is relaxed in a reproductive nymph-biased gene set, which opposes the nearly neutral idea. In other species, the synonymous rate (dS) alone was often found to be the highest in the sterile worker caste, suggesting a more subtle signature of indirect selection or an altogether different relationship between caste-biased expression and rates of molecular evolution.
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Affiliation(s)
- Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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10
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Friedman DA, Johnson BR, Linksvayer TA. Distributed physiology and the molecular basis of social life in eusocial insects. Horm Behav 2020; 122:104757. [PMID: 32305342 DOI: 10.1016/j.yhbeh.2020.104757] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/24/2022]
Abstract
The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single multicellular organism. In the colonial (eusocial) insects such as ants, bees, and termites, molecular and behavioral responses of interacting nestmates are tightly linked, and key physiological processes are regulated at the scale of the colony. Such colony-level physiological processes regulate nestmate physiology in a distributed fashion, through various social communication mechanisms. As a result of physiological decentralization over evolutionary time, organismal mechanisms, for example related to pheromone detection, hormone signaling, and neural signaling pathways, are deployed in novel contexts to influence nestmate and colony traits. Here we explore how functional genomic, physiological, and behavioral studies can benefit from considering the traits of eusocial insects in this light. We highlight functional genomic work exploring how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages. We also consider similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and make specific hypotheses regarding the physiology of eusocial taxa. Integrating theoretical models of distributed systems with empirical functional genomics approaches will be useful in addressing fundamental questions related to the evolution of eusociality and collective behavior in natural systems.
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Affiliation(s)
- D A Friedman
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America.
| | - B R Johnson
- University of California, Davis, Department of Entomology, Davis, CA 95616, United States of America
| | - T A Linksvayer
- University of Pennsylvania, Department of Biology, Pennsylvania, PA 19104, United States of America
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11
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Medial Cortical Structures Mediate Implicit Trustworthiness Judgments about Kin Faces, but Not Familiar Faces: A Brief Report. PSYCH 2019. [DOI: 10.3390/psych1010037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human kin recognition activates substrates of the extended facial processing network, notably the right-hemisphere structures involved in self-face recognition and posterior medial cortical substrates. To understand the mechanisms underlying prosociality toward kin faces in comparison to other familiar faces, we investigated the neural correlates of implicit trustworthiness ratings to faces of actual kin and personal friends, controlling for activation to distracter faces. When controlling for activation associated with unknown faces, trustworthiness ratings of faces of kin, compared to friends, were associated with increased activation in the dorsal anterior cingulate cortex, posterior cingulate, and precuneous. On the other hand, trustworthiness ratings of friend faces, relative to kin faces, were associated with the lateral occipital gyrus and insular cortex. Trustworthiness ratings for unknown faces were only associated with activation in the fusiform gyrus. These findings suggest that we should employ medial cortical substrates known to be part of the self-other network when making implicit social judgements about kin, but not other classes of facial stimuli.
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12
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Conditional expression explains molecular evolution of social genes in a microbe. Nat Commun 2019; 10:3284. [PMID: 31337766 PMCID: PMC6650454 DOI: 10.1038/s41467-019-11237-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 06/25/2019] [Indexed: 12/30/2022] Open
Abstract
Conflict is thought to play a critical role in the evolution of social interactions by promoting diversity or driving accelerated evolution. However, despite our sophisticated understanding of how conflict shapes social traits, we have limited knowledge of how it impacts molecular evolution across the underlying social genes. Here we address this problem by analyzing the genome-wide impact of social interactions using genome sequences from 67 Dictyostelium discoideum strains. We find that social genes tend to exhibit enhanced polymorphism and accelerated evolution. However, these patterns are not consistent with conflict driven processes, but instead reflect relaxed purifying selection. This pattern is most likely explained by the conditional nature of social interactions, whereby selection on genes expressed only in social interactions is diluted by generations of inactivity. This dilution of selection by inactivity enhances the role of drift, leading to increased polymorphism and accelerated evolution, which we call the Red King process.
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13
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Warner MR, Mikheyev AS, Linksvayer TA. Transcriptomic basis and evolution of the ant nurse-larval social interactome. PLoS Genet 2019; 15:e1008156. [PMID: 31107868 PMCID: PMC6544314 DOI: 10.1371/journal.pgen.1008156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/31/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Development is often strongly regulated by interactions among close relatives, but the underlying molecular mechanisms are largely unknown. In eusocial insects, interactions between caregiving worker nurses and larvae regulate larval development and resultant adult phenotypes. Here, we begin to characterize the social interactome regulating ant larval development by collecting and sequencing the transcriptomes of interacting nurses and larvae across time. We find that the majority of nurse and larval transcriptomes exhibit parallel expression dynamics across larval development. We leverage this widespread nurse-larva gene co-expression to infer putative social gene regulatory networks acting between nurses and larvae. Genes with the strongest inferred social effects tend to be peripheral elements of within-tissue regulatory networks and are often known to encode secreted proteins. This includes interesting candidates such as the nurse-expressed giant-lens, which may influence larval epidermal growth factor signaling, a pathway known to influence various aspects of insect development. Finally, we find that genes with the strongest signatures of social regulation tend to experience relaxed selective constraint and are evolutionarily young. Overall, our study provides a first glimpse into the molecular and evolutionary features of the social mechanisms that regulate all aspects of social life.
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Affiliation(s)
- Michael R. Warner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alexander S. Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Timothy A. Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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14
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15
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Faragalla KM, Chernyshova AM, Gallo AJ, Thompson GJ. From gene list to gene network: Recognizing functional connections that regulate behavioral traits. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:317-329. [DOI: 10.1002/jez.b.22829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 09/10/2018] [Indexed: 12/27/2022]
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16
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Favreau E, Martínez-Ruiz C, Rodrigues Santiago L, Hammond RL, Wurm Y. Genes and genomic processes underpinning the social lives of ants. CURRENT OPINION IN INSECT SCIENCE 2018; 25:83-90. [PMID: 29602366 DOI: 10.1016/j.cois.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 05/06/2023]
Abstract
The >15000 ant species are all highly social and show great variation in colony organization, complexity and behavior. The mechanisms by which such sociality evolved, as well as those underpinning the elaboration of ant societies since their ∼140 million year old common ancestor, have long been pondered. Here, we review recent insights generated using various genomic approaches. This includes understanding the molecular mechanisms underlying caste differentiation and the diversity of social structures, studying the impact of eusociality on genomic evolutionary rates, and investigating gene expression changes associated with differences in lifespan between castes. Furthermore, functional studies involving RNAi and CRISPR have recently been successfully applied to ants, opening the door to exciting research that promises to revolutionize the understanding of the evolution and diversification of social living.
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Affiliation(s)
- Emeline Favreau
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Carlos Martínez-Ruiz
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Leandro Rodrigues Santiago
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert L Hammond
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom.
| | - Yannick Wurm
- Organismal Biology Department, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom.
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17
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Ghoul M, Andersen SB, West SA. Sociomics: Using Omic Approaches to Understand Social Evolution. Trends Genet 2017; 33:408-419. [PMID: 28506494 DOI: 10.1016/j.tig.2017.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
All of life is social, from genes cooperating to form organisms, to animals cooperating to form societies. Omic approaches offer exceptional opportunities to solve major outstanding problems in the study of how sociality evolves. First, omics can be used to clarify the extent and form of sociality in natural populations. This is especially useful in species where it is difficult to study social traits in natural populations, such as bacteria and other microbes. Second, omics can be used to examine the consequences of sociality for genome evolution and gene expression. This is especially useful in cases where there is clear variation in the level of sociality, such as the social insects. Major tasks for the future are to apply these approaches to a wider range of non-model organisms, and to move from exploratory analyses to the testing of evolutionary theory.
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Affiliation(s)
- Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| | - Sandra B Andersen
- Langone Medical Center, New York University, 423 East 23rd Street, New York, NY 10010, USA.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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18
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Barker JL, Bronstein JL, Friesen ML, Jones EI, Reeve HK, Zink AG, Frederickson ME. Synthesizing perspectives on the evolution of cooperation within and between species. Evolution 2017; 71:814-825. [PMID: 28071790 DOI: 10.1111/evo.13174] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 12/24/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
Cooperation is widespread both within and between species, but are intraspecific and interspecific cooperation fundamentally similar or qualitatively different phenomena? This review evaluates this question, necessary for a general understanding of the evolution of cooperation. First, we outline three advantages of cooperation relative to noncooperation (acquisition of otherwise inaccessible goods and services, more efficient acquisition of resources, and buffering against variability), and predict when individuals should cooperate with a conspecific versus a heterospecific partner to obtain these advantages. Second, we highlight five axes along which heterospecific and conspecific partners may differ: relatedness and fitness feedbacks, competition and resource use, resource-generation abilities, relative evolutionary rates, and asymmetric strategy sets and outside options. Along all of these axes, certain asymmetries between partners are more common in, but not exclusive to, cooperation between species, especially complementary resource use and production. We conclude that cooperation within and between species share many fundamental qualities, and that differences between the two systems are explained by the various asymmetries between partners. Consideration of the parallels between intra- and interspecific cooperation facilitates application of well-studied topics in one system to the other, such as direct benefits within species and kin-selected cooperation between species, generating promising directions for future research.
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Affiliation(s)
- Jessica L Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721.,Current Address: Aarhus Institute of Advanced Studies, Aarhus University, 8000, Aarhus C, Denmark
| | - Judith L Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
| | - Emily I Jones
- Department of BioSciences, Rice University, Houston, Texas, 77005
| | - H Kern Reeve
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, 14853
| | - Andrew G Zink
- Department of Biology, San Francisco State University, San Francisco, California, 94132
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
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Cunningham CB, Badgett MJ, Meagher RB, Orlando R, Moore AJ. Ethological principles predict the neuropeptides co-opted to influence parenting. Nat Commun 2017; 8:14225. [PMID: 28145404 PMCID: PMC5296637 DOI: 10.1038/ncomms14225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/08/2016] [Indexed: 01/29/2023] Open
Abstract
Ethologists predicted that parental care evolves by modifying behavioural precursors in the asocial ancestor. As a corollary, we predict that the evolved mechanistic changes reside in genetic pathways underlying these traits. Here we test our hypothesis in female burying beetles, Nicrophorus vespilloides, an insect where caring adults regurgitate food to begging, dependent offspring. We quantify neuropeptide abundance in brains collected from three behavioural states: solitary virgins, individuals actively parenting or post-parenting solitary adults and quantify 133 peptides belonging to 18 neuropeptides. Eight neuropeptides differ in abundance in one or more states, with increased abundance during parenting in seven. None of these eight neuropeptides have been associated with parental care previously, but all have roles in predicted behavioural precursors for parenting. Our study supports the hypothesis that predictable traits and pathways are targets of selection during the evolution of parenting and suggests additional candidate neuropeptides to study in the context of parenting.
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Affiliation(s)
| | - Majors J. Badgett
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Richard B. Meagher
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Ron Orlando
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Allen J. Moore
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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