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  • Review Article
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Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents

Key Points

  • Developmental symbiosis and developmental plasticity contribute in numerous ways to animal evolution

  • Symbionts help to generate organs and maintain species-specific interactions with their animal hosts.

  • Symbionts provide selectable variation and can generate the conditions for reproductive isolation

  • Symbionts may have promoted major evolutionary transitions such as multicellularity

  • Plasticity allows the integration of the organism into its environment, changing development to account for predators, conspecifics, diet and temperature.

  • Plasticity provides the raw material for genetic accommodation and niche construction.

  • Plasticity can both help and harm populations experiencing stresses such as global climate change.

Abstract

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

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Figure 1: Milestones towards a new vision for the central importance of symbiotic interactions as being fundamental to all aspects of animal biology.

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References

  1. Gilbert, S. F. & Epel, D. Ecological Developmental Biology: Integrating Epigenetics, Medicine and Evolution (Sinauer Associates Inc., 2008).

    Google Scholar 

  2. Abouheif, E. et al. Eco-evo-devo: the time has come. Adv. Exp. Med. Biol. 781, 107–125 (2014).

    PubMed  Google Scholar 

  3. McFall-Ngai, M. J. Unseen forces: the influence of bacteria on animal development. Dev. Biol. 242, 1–14 (2002).

    CAS  PubMed  Google Scholar 

  4. Gilbert, S. F., Sapp, J. & Tauber, A. I. A symbiotic view of life: we have never been individuals. Q. Rev. Biol. 87, 325–341 (2012).

    PubMed  Google Scholar 

  5. McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl Acad. Sci. USA 110, 3229–3236 (2013). A review of animal evolution and of how the emergence and expansion of the human microbiome project has reshaped our thinking about how microorganisms control host health, not only as pathogens, but also as symbionts.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Tsuchida, T. et al. Symbiotic bacterium modifies aphid body color. Science 330, 1102–1104 (2010).

    CAS  PubMed  Google Scholar 

  7. Oliver, K. M., Degnan, P. H., Hunter, M. S. & Moran, N. A. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325, 992–994 (2009). This paper provides evidence that symbionts and hosts function together for selection.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Dunbar, H. E., Wilson, A. C., Ferguson, N. R. & Moran, N. A. Aphid thermal tolerance is governed by a point mutation in bacterial symbionts. PLoS Biol. 5, e96 (2007).

    PubMed  PubMed Central  Google Scholar 

  9. Moran, N. A. & Yun, Y. Experimental replacement of an obligate insect symbiont. Proc. Natl Acad. Sci. USA 112, 2093–2096 (2015). First experimental demonstration of the strong effect of symbiont genotype on host ecology.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Sharon, G. et al. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 107, 20051–20056 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Brucker, R. M. & Bordenstein, S. R. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science 341, 667–669 (2013). This study shows that symbionts can have crucial evolutionary roles in providing barriers that keep related species separate. Complex interactions that have evolved between host genes and the microbiome may be responsible for mediating this effect.

    CAS  PubMed  Google Scholar 

  12. West-Eberhard, M. J. Developmental Plasticity and Evolution (Oxford Univ. Press, 2003). A groundbreaking synthesis, demonstrating the importance of plasticity to evolution and showing that genes can often be followers, not leaders, of the phenotype.

    Google Scholar 

  13. Bradshaw, W. E. & Zani, P. A. & Holzapfel, C. M. Adaptation to temperate climates. Evolution 58, 1748–1762 (2004).

    PubMed  Google Scholar 

  14. Charmantier, A. et al. Adaptive phenotypic plasticity in response to climate change in a wild bird population. Science 320, 800–803 (2008).

    CAS  PubMed  Google Scholar 

  15. Odling-Smee, F. J., Laland, K. N. & Feldman, M. W. Niche Construction: The Neglected Process in Evolution (Princeton Univ. Press, 2003).

    Google Scholar 

  16. Waddington, C. H. Genetic assimilation of an acquired character. Evolution 7, 118–126 (1953). The seminal paper demonstrating genetic assimilation in a laboratory population; it shows that selection can fix environmentally induced traits into the genome.

    Google Scholar 

  17. Suzuki, Y. & Nijhout, H. F. Evolution of a polyphenism by genetic accommodation. Science 311, 650–652 (2006). This paper demonstrates the process of genetic accommodation in the laboratory, uncovering the hormonal mechanisms that evolved to produce the differentially sensitive lineages, and suggests that cryptic genetic variation is sufficient to explain the process.

    CAS  PubMed  Google Scholar 

  18. Margulis, L. Symbiosis in Cell Evolution (W. H. Freeman, 1981).

    Google Scholar 

  19. Wagner, G. P., Kin, K., Muglia, L. & Pavlicev, M. Evolution of mammalian pregnancy and the origin of the decidual stromal cell. Int. J. Dev. Biol. 58, 117–126 (2014).

    CAS  PubMed  Google Scholar 

  20. Lynch, V. J. et al. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep. 10, 551–561 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Dayel, M. J. et al. Cell differentiation and morphogenesis in the colony-forming choanoflagellate Salpingoeca rosetta. Dev. Biol. 357, 73–82 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Alegado, R. A. & King, N. Bacterial influences on animal origins. Cold Spring Harb. Perspect. Biol. 6, a016162 (2014).

    PubMed  PubMed Central  Google Scholar 

  23. Standen, E. M., Du, T. Y. & Larsson, H. C. Developmental plasticity and the origin of tetrapods. Nature 513, 54–58 (2014).

    CAS  PubMed  Google Scholar 

  24. Herman, J. J. et al. How stable “should” epigenetic modification be? Insights from adaptive plasticity and bet hedging. Evolution 68, 632–643 (2014).

    PubMed  Google Scholar 

  25. Heard, E. & Martienssen, R. A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157, 95–109 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Dias, B. G. & Ressler, K. J. Prental olfactory experiences influences behavior and neural structure in subsequent generations. Nat. Neurosci. 17, 89–96 (2014).

    CAS  PubMed  Google Scholar 

  27. Gilbert, S. F. & Epel, D. Ecological Developmental Biology: The Environmental Regulation of Development, Health, and Evolution (Sinauer Associates Inc., 2015). This book attempts to integrate developmental symbiosis, developmental plasticity, environmental epigenesis and teratology into evolutionary biology.

    Google Scholar 

  28. Rosenberg, E., Koren, O., Reshef, L., Efrony, R. & Zilber-Rosenberg, I. The role of microorganisms in coral health, disease and evolution. Nat. Rev. Microbiol. 5, 355–362 (2007).

    CAS  PubMed  Google Scholar 

  29. Bosch, T. C. & McFall-Ngai, M. Metaorganisms as the new frontier. Zoology 114, 185–190 (2011).

    PubMed  Google Scholar 

  30. Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Erwin, D. H. & Valentine, J. W. The Cambrian Explosion: The Construction of Animal Biodiversity (Roberts and Co., 2013).

    Google Scholar 

  32. Franzenburg, S. et al. Distinct antimicrobial tissue activity shapes host species-specific bacterial associations. Proc. Natl Acad. Sci. USA 110, E3730–E3738 (2013). This paper provides evidence that in the early branching metazoan Hydra spp., specialized AMPs partly regulate phylosymbiosis across related species.

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Ochman, H. et al. Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8, e1000546 (2010).

    PubMed  PubMed Central  Google Scholar 

  34. Hadfield, M. G. Biofilms and marine invertebrate larvae: what bacteria produce that larvae use to choose settlement sites. Ann. Rev. Mar. Sci. 3, 453–470 (2011).

    PubMed  Google Scholar 

  35. Hoerauf, A. Mansonella perstans — the importance of an endosymbiont. N. Engl. J. Med. 361, 1502–1504 (2008).

    Google Scholar 

  36. Dedeine, F. et al. Removing symbiotic Wolbachia specifically inhibits oogenesis in a parasitic wasp. Proc. Natl Acad. Sci. USA 98, 6247–6252 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Waterman, R. J. & Bidartando, M. I. Deception above, deception below: linking pollination and mycorrhizal biology of orchids. J. Exp. Bot. 59, 1085–1096 (2008).

    CAS  PubMed  Google Scholar 

  38. Landmann, F., Foster, J. M., Michalski, M. L., Slatko, B. E. & Sullivan, W. Coevolution between an endosymbiont and its nematode host: Wolbachia asymmetric posterior localization and AP polarity establishment. PLoS Negl. Trop. Dis. 8, e3096 (2014).

    PubMed  PubMed Central  Google Scholar 

  39. Umesaki, Y. Immunohistochemical and biochemical demonstration of the change in glycolipid composition of the intestinal epithelial cell surface in mice in relation to epithelial cell differentiation and bacterial association. J. Histochem. Cytochem. 32, 299–304 (1984).

    CAS  PubMed  Google Scholar 

  40. Stappenbeck, T. S., Hooper, L. V. & Gordon, J. I. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl Acad. Sci. USA 99, 15451–15455 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Hooper, L. V. & Gordon, J. I. Commensal host–bacterial relationships in the gut. Science 292, 1115–1118 (2001). References 40 and 41 demonstrate that symbionts induce normal gene expression and organogenesis in vertebrate hosts.

    CAS  PubMed  Google Scholar 

  42. Rawls, J. F., Samuel, B. S. & Gordon, J. I. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl Acad. Sci. USA 101, 4596–4601 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Bates, J. M. et al. Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev. Biol. 297, 374–386 (2006).

    CAS  PubMed  Google Scholar 

  44. Rawls, J. F., Mahowald, M. A., Ley, R. E. & Gordon, J. I. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127, 423–433 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. McFall-Ngai, M. J. & Ruby, E. G. Symbiont recognition and subsequent morphogenesis as early events in an animal–bacterial mutualism. Science. 254, 1491–1494 (1991).

    CAS  PubMed  Google Scholar 

  46. Altura, M. A. et al. The first engagement of partners in the Euprymna scolopes–Vibrio fischeri symbiosis is a two-step process initiated by a few environmental symbiont cells. Environ. Microbiol. 15, 2937–2950 (2013).

    PubMed  PubMed Central  Google Scholar 

  47. Kremer, N. et al. Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization. Cell Host Microbe 14, 183–194 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Koropatnick, T. A. et al. Microbial factor-mediated development in a host–bacterial mutualism. Science 306, 1186–1188 (2004).

    CAS  PubMed  Google Scholar 

  49. Dobber, R., Hertogh-Huijbregts, A., Rozing, J., Bottomly, K. & Nagelkerken, L. The involvement of the intestinal microflora in the expansion of CD4+ T cells with a naive phenotype in the periphery. Dev. Immunol. 2, 141–150 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. O'Hara, A. M. & Shanahan, F. The gut flora as a forgotten organ. EMBO Rep. 7, 688–693 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Kieper, W. C. et al. Recent immune status determines the source of antigens that drive homeostatic T cell expansion. J. Immunol. 174, 3158–3163 (2005).

    CAS  PubMed  Google Scholar 

  52. Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107–118 (2005).

    CAS  PubMed  Google Scholar 

  53. Mazmanian, S. K., Round, J. L. & Kasper, D. L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620–625 (2008).

    CAS  PubMed  Google Scholar 

  54. Ardeshir, A. et al. Breast-fed and bottle-fed infant rhesus macaques develop distinct gut microbiotas and immune systems. Sci. Transl Med. 6, 252ra120 (2014).

    PubMed  PubMed Central  Google Scholar 

  55. Jeon, S. G. et al. Probiotic Bifidobacterium breve induces IL10producing Tr1 cells in the colon. PLoS Pathog. 8, e1002714 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Chu, H. & Mazmanian, S. K. Innate immune recognition of the microbiota promotes host–microbial symbiosis. Nat. Immunol. 14, 668–675 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Khosravi, A. et al. Gut microbiota promote hematopoiesis to control bacterial infection. Cell Host Microbe 15, 374–381 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Bevins, C. L. & Salzman, N. H. The potter's wheel: the host's role in sculpting its microbiota. Cell. Mol. Life Sci. 68, 3675–3685 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Franzenburg, S. et al. Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. ISME J. 7, 781–790 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Cullen, T. W. et al. Gut microbiota. Antimicrobial peptide resilience of prominent gut commensals during inflammation. Science 347, 170–175 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Zasloff, M. Antimicrobial peptides of multicellular organisms. Nature 415, 389–395 (2002).

    CAS  PubMed  Google Scholar 

  62. Salzman, N. H., Ghosh, D., Huttner, K. M., Paterson, Y. & Bevins, C. L. Protection against enteric salmonellosis in transgenic mice expressing a human intestinal defensin. Nature 422, 522–526 (2003).

    CAS  PubMed  Google Scholar 

  63. Oh, J. et al. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Res. 23, 2103–2114 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Bosch, T. C. Rethinking the role of immunity: lessons from Hydra. Trends Immunol. 35, 495–502 (2014).

    CAS  PubMed  Google Scholar 

  65. Tauber, A. I. Expanding immunology: defense versus ecological perspectives. Perspect. Biol. Med. 51, 270–284 (2008).

    Google Scholar 

  66. Shen, W. et al. Adaptive immunity to murine skin commensals. Proc. Natl Acad. Sci. USA 111, E2977–E2986 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. McFall-Ngai, M. Adaptive immunity: care for the community. Nature 445, 153 (2007).

    CAS  PubMed  Google Scholar 

  68. Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J. & Relman, D. A. The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255–1262 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Hooper, L. V., Littman, D. R. & Macpherson, A. J. Interactions between the microbiota and the immune system. Science 336, 1268–1273 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Wikoff, W. R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl Acad. Sci. USA 106, 698–703 (2009).

    Google Scholar 

  71. Lyte, M. Probiotics function mechanistically as delivery vehicles for neuroactive compounds: microbial endocrinology in the design and use of probiotics. Bioessays 33, 574–581 (2011).

    CAS  PubMed  Google Scholar 

  72. Yano, J. M. et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell 161, 264–276 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Sudo, N. et al. Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. J. Physiol. 558, 263–275 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Diaz Heijtz, R. et al. Normal gut microbiota modulates brain development and behavior. Proc. Natl Acad. Sci. USA 108, 3047–3052 (2011).

    PubMed  Google Scholar 

  75. Mayer, E. A. et al. Gut microbes and the brain: paradigm shift in neuroscience. J. Neurosci. 34, 15490–15496 (2014).

    PubMed  PubMed Central  Google Scholar 

  76. Clarke, G. et al. The microbiome–gut–brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol. Psychiatry 18, 666–673 (2013).

    CAS  PubMed  Google Scholar 

  77. Theis, K. R. et al. Symbiotic bacteria appear to mediate hyena social odors. Proc. Natl Acad. Sci. USA 110, 19832–19837 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Bravo, J. A. et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc. Natl Acad. Sci. USA 108, 16050–16055 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Ezenwa, V. O., Gerardo, N. M., Inouye, D. W., Medina, M. & Xavier, J. B. Animal behavior and the microbiome. Science 338, 198–199 (2012).

    CAS  PubMed  Google Scholar 

  80. Desbonnet, L., Clarke, G., Shanahan, F., Dinan, T. G. & Cryan, J. F. Microbiota is essential for social development in the mouse. Mol. Psychiatry 19, 146–148 (2014).

    CAS  PubMed  Google Scholar 

  81. Hsiao, E. Y. et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155, 1451–1463 (2013). Evidence that gut symbionts help to regulate crucial behaviours in mammals and may ameliorate mental illness.

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Moran, N. A., McCutcheon, J. P. & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42, 165–190 (2008).

    CAS  PubMed  Google Scholar 

  83. Gilbert, S. F. et al. Codevelopment and symbiosis: taking the heat for the big guy. Phil. Trans. R. Soc. B 365, 371–378 (2010).

    Google Scholar 

  84. Bordenstein, S. R. in Insect Symbiosis (eds Bourtzis, K. & Miller, T. A.) 283–304 (CRC Press, 2003).

    Google Scholar 

  85. Zilber-Rosenberg, I. & Rosenberg, E. Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32, 723–735 (2008).

    CAS  PubMed  Google Scholar 

  86. Brucker, R. M. & Bordenstein, S. R. Speciation by symbiosis. Trends Ecol. Evol. 27, 443–451 (2012).

    PubMed  Google Scholar 

  87. Alegado, R. A. et al. A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals. eLife 1, e00013 (2012).

    PubMed  PubMed Central  Google Scholar 

  88. Cornelis, G. et al. Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials. Proc. Natl Acad. Sci. USA 112, E487–E496 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Brucker, R. M. & Bordenstein, S. R. Response to Comment on “The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia”. Science. 345, 1011 (2014).

    CAS  PubMed  Google Scholar 

  90. Price, T. D., Qvarnström, A. & Irwin, D. E. The role of phenotypic plasticity in driving genetic evolution. Proc. Biol. Sci. 270, 1433–1440 (2003). This review shows that moderate levels of plasticity are optimal in permitting population survival in novel environments, whereas high levels of plasticity may inhibit genetic change when plastic responses place the population close to an adaptive peak.

    PubMed  PubMed Central  Google Scholar 

  91. Sultan, S. in Transformations of Lamarckism: From Subtle Fluids to Molecular Biology (eds Gissis, S. & Jablonka, E.) 193–203 (MIT Press, 2011).

    Google Scholar 

  92. Wright, S. Evolution in Mendelian populations. Genetics 16, 97–159 (1931).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Laland, K. et al. Does evolutionary theory need a rethink? Nature 514, 161–164 (2014).

    CAS  PubMed  Google Scholar 

  94. Snell-Rood, E. C. An overview of the evolutionary causes and consequences of behavioural plasticity. Animal Behav. 85, 1004–1011 (2013).

    Google Scholar 

  95. Baldwin, J. M. A new factor in evolution. Am. Naturalist 30, 441–451 (1896).

    Google Scholar 

  96. Schmalhausen, I. I. Factors of Evolution: The Theory of Stabilizing Selection (Blakiston Co., 1949).

    Google Scholar 

  97. Bateson, P. The return of the whole organism. J. Biosci. 30, 31–39 (2005).

    PubMed  Google Scholar 

  98. Gibson, G. & Hogness, D. S. Effect of polymorphism in the Drosophila regulatory gene Ultrabithorax on homeotic stability. Science 271, 200–203 (1996). This study demonstrates that environmental sensitivity or canalization can be altered in a population by selection on regulatory loci.

    CAS  PubMed  Google Scholar 

  99. Kaneko, K. Symbiotic sympatric speciation: consequence of interaction-driven phenotype differentiation through developmental plasticity. Popul. Ecol. 44, 71–85 (2002).

    Google Scholar 

  100. Behara, N. & Nanjundiah, V. Phenotypic plasticity can potentiate rapid evolutionary change. J. Theor. Biol. 226, 177–184 (2004).

    Google Scholar 

  101. Lande, R. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation. J. Exp. Evol. 22, 1435–1446 (2009).

    Google Scholar 

  102. Frisch, D. et al. A millennial scale chronicle of evolutionary responses to cultural eutrophication in Daphnia. Ecol. Lett. 17, 360–368 (2014).

    PubMed  Google Scholar 

  103. Ledón-Rettig, C. C., Pfennig, D. W., Chunco, A. J. & Dworkin, I. Cryptic genetic variation in natural populations: a predictive framework. Integr. Comp. Biol. 54, 783–793 (2014).

    PubMed  Google Scholar 

  104. Gomez-Mestre, I. & Buchholz, D. R. Developmental plasticity mirrors differences among taxa in spadefoot toads linking plasticity and diversity. Proc. Natl Acad. Sci. USA 103, 19021–19026 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Aubret, F. & Shine, R. Genetic assimilation and the postcolonization erosion of phenotypic plasticity in island tiger snakes. Curr. Biol. 19, 1932–1936 (2009).

    CAS  PubMed  Google Scholar 

  106. Scoville, A. G. & Pfrender, M. E. Phenotypic plasticity facilitates recurrent rapid adaptation to introduced predators. Proc. Natl Acad. Sci. USA 107, 4260–4263 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. McGuigan, K., Nishimura, N., Currey, M., Hurwit, D. & Cresko, W. A. Cryptic genetic variation and body size evolution in threespine stickleback. Evolution 65, 1203–1211 (2011).

    PubMed  Google Scholar 

  108. Moczek, A. P. et al. The role of developmental plasticity in evolutionary innovation. Proc. Biol. Sci. 278, 2705–2713 (2011).

    PubMed  PubMed Central  Google Scholar 

  109. Scheiner, S. M. Genetics and evolution of phenotypic plasticity. Annu. Rev. Ecol. Systemat. 24, 35–68 (1993).

    Google Scholar 

  110. Abouheif, E. & Wray, G. A. Evolution of the gene network underlying wing polyphenism in ants. Science 297, 249–252 (2002).

    CAS  PubMed  Google Scholar 

  111. Snell-Rood, E. C. & Moczek, A. P. Insulin signaling as a mechanism underlying developmental plasticity: the role of FOXO in a nutritional polyphenism. PLoS ONE 7, e34857 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Snell-Rood, E. C. et al. Developmental decoupling of alternative phenotypes: insights from the transcriptomes of hiorn-polyphenic beetles. Evolution 65, 231–245 (2011).

    PubMed  Google Scholar 

  113. Kijimoto, T., Moczek, A. P. & Andrews, J. Diversification of doublesex function underlies morph-, sex-, and species-specific development of beetle horns. Proc. Natl Acad. Sci. USA 109, 20526–20531 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  114. Moczek, A. P. & Kijimoto, T. Development and evolution of insect polyphenisms: novel insights through the study of sex determination mechanisms. Curr. Opin. Insect Sci. 1, 52–58 (2014).

    PubMed  Google Scholar 

  115. Ragsdale, E. J., Müller, M. R., Rödelsperger, C. & Sommer, R. J. A developmental switch coupled to the evolution of plasticity acts through a sulfatase. Cell 155, 922–933 (2013).

    CAS  PubMed  Google Scholar 

  116. Susoy, V. et al. Rapid diversification associated with a macroevolutionary pulse of developmental plasticity. eLife 4, e05463 (2015).

    PubMed Central  Google Scholar 

  117. Snell-Rood, E. C., Van Dyken, J. D., Cruickshank, T., Wade, M. J. & Moczek, A. P. Toward a population genetic framework for developmental evolution: the costs, limits, and consequences of phenotypic plasticity. Bioessays 32, 71–81 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Van Dyken, J. D. & Wade, M. J. The genetic signature of conditional expression. Genetics 84, 557–570 (2010). This paper models the effects of conditional expression on sequence polymorphism, connecting the spatial and temporal frequency of environments inducing gene expression with standing genetic variation.

    Google Scholar 

  119. Cruickshank, T. & Wade, M. J. Microevolutionary support for a developmental hourglass: gene expression patterns shape sequence variation and divergence in Drosophila. Evol. Dev. 10, 583–590 (2008).

    PubMed  Google Scholar 

  120. Kijimoto, T. et al. The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region. Proc. Biol. Sci. 281, 20142084 (2014).

    PubMed  PubMed Central  Google Scholar 

  121. Day, T. & Bonduriansky, R. A unified approach to the evolutionary consequences of genetic and nongenetic inheritance. Am. Naturalist 178, E18–E36 (2011).

    Google Scholar 

  122. Lewontin, R. C. in Evolution from Molecules to Men (ed. Bendall, D. S.) 273–285 (Cambridge University Press, 1983).

    Google Scholar 

  123. Callahan, B. J., Fukami, T. & Fisher, D. S. Rapid evolution of adaptive niche construction in experimental microbial populations. Evolution 68, 3307–3316 (2014).

    PubMed  Google Scholar 

  124. Saltz, J. B. & Nuzhdin, S. V. Genetic variation in niche construction: implications for development and evolutionary genetics. Trends Ecol. Evol. 29, 8–14 (2014).

    PubMed  Google Scholar 

  125. Hansen, J. et al. Assessing “dangerous climate change”: required reduction of carbon emissions to protect young people, future generations and nature. PLoS ONE 8, e81648 (2013).

    PubMed  PubMed Central  Google Scholar 

  126. National Research Council. Advancing the Science of Climate Change (The National Academies Press, 2010).

  127. Santidrián Tomillo, P. et al. Climate driven egg and hatchling mortality threatens survival of eastern Pacific leatherback turtles. PLoS ONE 7, e37602 (2012).

    PubMed  PubMed Central  Google Scholar 

  128. Santidrián Tomillo, P., Genovart, M., Paladino, F. V., Spotila, J. R. & Oro, D. Climate change overruns resilience conferred by temperature-dependent sex determination in sea turtles and threatens their survival. Glob. Chang. Biol. 21, 2980–2988 (2015).

    PubMed  Google Scholar 

  129. Telemeco, R. S. et al. Extreme developmental temperatures result in morphological abnormalities in painted turtles (Chrysemys picta): a climate change perspective. Integr. Zool. 8, 197–208 (2013).

    PubMed  Google Scholar 

  130. Hawkes, L. A., Broderick, A. C., Godfrey, M. H. & Godley, B. J. Climate change and marine turtles. Endang. Sp. Res. 7, 137–154 (2009).

    Google Scholar 

  131. Telemeco, R. S. & Abbott, K. C., & Janzen, F. J. Modeling the effects of climate change-induced shifts in reproductive phenology on temperature-dependent traits. Am. Naturalist 181, 637–648 (2013).

    Google Scholar 

  132. Rafferty, N. E. et al. Phenological overlap of interactibg species in a changing climate: an assessment of available approaches. Ecol. Evol. 3, 3183–3193 (2013).

    PubMed  PubMed Central  Google Scholar 

  133. Rafferty, N. E. & Ives, A. R. Pollinator effectiveness varies with experimental shifts in flowering time. Ecology 93, 803–814 (2012).

    PubMed  Google Scholar 

  134. Bartomeus, I. et al. Biodiversity ensures plant-pollinator phonological synchrony against climate change. Ecol. Lett. 16, 1331–1338 (2013).

    PubMed  Google Scholar 

  135. Van Valen, L. M. A new evolutionary law. Evol. Theory 1, 1–30 (1973).

    Google Scholar 

  136. Tauber, A. I. Reframing developmental biology and building evolutionary theory's new synthesis. Perspect. Biol. Med. 53, 257–270 (2010).

    PubMed  Google Scholar 

  137. Pigliucci, M. & Muller, G. B. Evolution — The Extended Synthesis (MIT Press, 2010).

    Google Scholar 

  138. Gilbert, S. F. A holobiont birth narrative: the epigenetic transmission of the human microbiome. Front. Genet. 5, 282 (2014).

    PubMed  PubMed Central  Google Scholar 

  139. Jiménez, E. et al. Is meconium from healthy newborns actually sterile? Res. Microbiol. 159, 187–193 (2008).

    PubMed  Google Scholar 

  140. Aagaard, K. et al. The placenta harbors a unique microbiome. Sci. Transl Med. 6, 237ra265 (2014).

    Google Scholar 

  141. Ley, R. E., Peterson, D. A. & Gordon, J. I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837–848 (2006).

    CAS  PubMed  Google Scholar 

  142. Makino, H. et al. Mother-toinfant transmission of intestinal bifidobacterial strains has an impact on the early development of vaginally delivered infant's microbiota. PLoS ONE 8, e78331 (2013).

    PubMed  PubMed Central  Google Scholar 

  143. Guarner, F. & Malagelada, J. R. Role of bacteria in experimental colitis. Best Pract. Res. Clin. Gastroenterol. 17, 793–804 (2003).

    CAS  PubMed  Google Scholar 

  144. Jakobsson, H. E. et al. Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut 63, 559–566 (2014).

    CAS  PubMed  Google Scholar 

  145. Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426–529 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  146. Bohnhoff, M., Drake, B. L. & Miller, C. P. The effect of an antibiotic on the susceptibility of the mouse's intestinal tract to Salmonella infection. Antibiot. Annu. 3, 453–455 (1955).

    PubMed  Google Scholar 

  147. Buffie, C. G. & Pamer, E. G. Microbiota-mediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol. 13, 790–801 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. Fraune, S. et al. Bacteria–bacteria interactions within the microbiota of the ancestral metazoan Hydra contribute to fungal resistance. ISME J. 9, 1543–1556 (2014).

    PubMed  PubMed Central  Google Scholar 

  149. Harris, R. N. et al. Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus. ISME J. 3, 818–824 (2009).

    CAS  PubMed  Google Scholar 

  150. Becker, M. H. & Harris, R. N. Cutaneous bacteria of the redback salamander prevent morbidity associated with a lethal disease. PLoS ONE 5, e10957 (2010).

    PubMed  PubMed Central  Google Scholar 

  151. Becker, M. H. et al. The bacterially produced metabolite violacein is associated with survival of amphibians infected with a lethal fungus. Appl. Environ. Microbiol. 75, 6635–6638 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  152. Pang, I. K., Ichinohe, T. & Iwasaki, A. IL1R signaling in dendritic cells replaces pattern-recognition receptors in promoting CD8+ T cell responses to influenza A virus. Nat. Immunol. 14, 246–253 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  153. Pickard, J. M. et al. Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness. Nature 514, 638–641 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  154. Cordaux, R. et al. Evidence for a new feminizing Wolbachia strain in the isopod Armadillidium vulgare: evolutionary implications. Heredity 93, 78–84 (2004).

    CAS  PubMed  Google Scholar 

  155. Williams, J. B. & Lee, R. E. Jr. Plant senescence cues entry into diapause in the gall fly Eurosta solidaginis: resulting metabolic depression is critical for water conservation. J. Exp. Biol. 208, 4437–4444 (2005).

    PubMed  Google Scholar 

  156. Odling-Smee, J. et al. Niche construction theory: a practical guide for ecologists. Q. Rev. Biol. 88, 4–28 (2013).

    PubMed  Google Scholar 

  157. Raz, G. & Jablonka, E. Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity. Q. Rev. Bio 84, 131–176 (2009).

    Google Scholar 

  158. Cubas, P., Vincent, C. & Coen, E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161 (1999).

    CAS  PubMed  Google Scholar 

  159. Paaby, A. B. & Rockman, M. V. Cryptic genetic variation: evolution's hidden substrate. Nat. Rev. Genet. 15, 247–258 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  160. Bergman, A. & Siegal, M. L. Evolutionary capacitance as a general feature of complex gene networks. Nature 424, 549–552 (2003).

    CAS  PubMed  Google Scholar 

  161. Ledón-Rettig, C. C., Pfennig, D. W. & Crespi, E. J. Diet and hormonal manipulation reveal cryptic genetic variation: implications for the evolution of novel feeding strategies. Proc. Biol. Sci. 277, 3569–3578 (2010).

    PubMed  PubMed Central  Google Scholar 

  162. Rutherford, S. L. & Lindquist, S. Hsp90 as a capacitor for morphological evolution. Nature 396, 336–342 (1998). A seminal paper providing a mechanism for buffering, which can lead to the accumulation of genetic variation that is neutral under typical environmental conditions, but phenotypically expressed under stressful or novel environmental conditions.

    CAS  PubMed  Google Scholar 

  163. Sangster, T. A. et al. Hsp90 affects the expression of genetic variation and developmental stability in quantitative traits. Proc. Natl Acad. Sci. USA 105, 2963–2968 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  164. Sangster, T. A. et al. Hsp90buffered genetic variation is common in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 105, 2969–2974 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  165. Rohner, N. et al. Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish. Science 342, 1372–1375 (2014).

    Google Scholar 

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Acknowledgements

S.F.G. is supported by National Science Federation (NSF) grant IOS 145177 and by a Swarthmore College faculty research award. T.C.G.B. is supported by grants from the Deutsche Forschungsgemeinschaft (DFG) and by the DFG Cluster of Excellence Inflammation at Interfaces. C.L.R is supported by NSF grants IOS 1120209 and IOS 1256689.

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Glossary

Ecological evolutionary developmental biology

(Eco-Evo-Devo). The scientific programme that incorporates the rules governing the interactions between an organism's genes, development and environment into evolutionary theory.

Reproductive isolation

The phenomenon whereby members of two potentially interbreeding populations are prevented from producing viable or fertile hybrid offspring.

Holobionts

The eukaryotic organism (host) plus its persistent symbionts. The cow, for instance, is a combination of the mammalian body plus the symbionts, the enzymes of which allow it to digest grasses, and so on.

Microbiomes

The totality of microorganisms and their collective genetic material present in or on the body of a macroscopic host organism or in another environment.

Germ-free mice

Mice bred in sterile facilities with no contact with microorganisms.

Chemotaxis

The movement of an entity such as a cell along a gradient of chemical concentration towards the source of the chemical.

Gnotobiotic

A condition when the investigator knows all of the microorganisms in the host. Germ-free mice are often called gnotobiotic. Gnotobiotic animals are born in aseptic conditions and immediately transferred to an isolation area where all incoming air, food and water is sterilized.

Extragenetic inheritance

Mechanisms of inherited variation that are not derived from nucleic acid composition variants in the parent.

Epialleles

DNA sequences that are identical by nucleic acid composition but may differ in their secondary modifications such as DNA methylation, histone acetylation or methylation, or chromatin context. Also known as epimutations when they differ from wildtype.

Genotype-by-environment interactions

Processes wherein different genotypes respond to environmental variation in different ways.

Choanoflagellate

A group of unicellular and colonial flagellates that are thought to be the sister group of multicellular animals.

Genetic assimilation

A subset of genetic accommodation, whereby a trait induced by the environment becomes part of the genetic repertoire of the organism.

Bithorax

When the third thoracic segment of a fly becomes a repeat of the second thoracic segment, creating two sets of wings.

Polyphenism

The phenomenon when the same genotype can give rise to two or more distinct functional phenotypes.

Modern synthesis

Also called the neo-Darwin synthesis, this model of evolution reconciles natural selection with Mendelian genetics.

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Gilbert, S., Bosch, T. & Ledón-Rettig, C. Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents. Nat Rev Genet 16, 611–622 (2015). https://doi.org/10.1038/nrg3982

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