Payne, J. L. & Wagner, A. The causes of evolvability and their evolution. Nat. Rev. Genet. 20, 24–38 (2019).
Google Scholar
Fragata, I., Blanckaert, A., Dias Louro, M. A., Liberles, D. A. & Bank, C. Evolution in the light of fitness landscape theory. Trends Ecol. Evol. 34, 69–82 (2019).
Kondrashov, D. A. & Kondrashov, F. A. Topological features of rugged fitness landscapes in sequence space. Trends Genet. 31, 24–33 (2015).
Google Scholar
Gros, P.-A., Le Nagard, H. & Tenaillon, O. The evolution of epistasis and its links with genetic robustness, complexity and drift in a phenotypic model of adaptation. Genetics 182, 277–293 (2009).
Google Scholar
Weinreich, D. M., Delaney, N. F., Depristo, M. A. & Hartl, D. L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770), 111–114 (2006).
Google Scholar
da Silva, J., Coetzer, M., Nedellec, R., Pastore, C. & Mosier, D. E. Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185, 293–303 (2010).
Schenk, M. F., Szendro, I. G., Salverda, M. L. M., Krug, J. & de Visser, J. A. G. M. Patterns of Epistasis between beneficial mutations in an antibiotic resistance gene. Mol. Biol. Evol. 30, 1779–1787 (2013).
Google Scholar
O’Maille, P. E. et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat. Chem. Biol. 4, 617–623 (2008).
Ortlund, E. A., Bridgham, J. T., Redinbo, M. R. & Thornton, J. W. Crystal structure of an ancient protein: Evolution by conformational epistasis. Science 317, 1544–1548 (2007).
Google Scholar
Iwasa, Y., Michor, F. & Nowak, M. A. Stochastic tunnels in evolutionary dynamics. Genetics 166, 1571–1579 (2004).
Barton, N. H. Sewall wright on evolution in Mendelian populations and the “shifting balance”. Genetics 202, 3–4 (2016).
Zheng, J., Payne, J. L. & Wagner, A. Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks. Science 365(6451), 347–353 (2019).
Google Scholar
Paaby, A. B. & Rockman, M. V. Cryptic genetic variation: Evolution’s hidden substrate. Nat. Rev. Genet. 15, 247–258 (2014).
Google Scholar
Zheng, J., Guo, N. & Wagner, A. Selection enhances protein evolvability by increasing mutational robustness and foldability. Science 370(6521), eabb5962 (2020).
Google Scholar
Dolan, P. T., Whitfield, Z. J. & Andino, R. Mechanisms and concepts in RNA virus population dynamics and evolution. Annu. Rev. Virol. 5, 69–92 (2018).
Google Scholar
Sanjuán, R. & Domingo-Calap, P. Genetic diversity and evolution of viral populations. Encycl. Virol. https://doi.org/10.1016/B978-0-12-809633-8.20958-8 (2021).
Google Scholar
Sanjuán, R. & Domingo-Calap, P. Mechanisms of viral mutation. Cell. Mol. Life Sci. 73, 4433–4448 (2016).
Makimaa, H., Ingle, H. & Baldridge, M. T. Enteric viral co-infections: Pathogenesis and perspective. Viruses 12, 904 (2020).
Google Scholar
Kim, K. W. et al. Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing. Sci. Rep. 11, 3934 (2021).
Google Scholar
Kumar, N., Sharma, S., Barua, S., Tripathi, B. N. & Rouse, B. T. Virological and immunological outcomes of coinfections. Clin. Microbiol. Rev. 31, e00111-e117 (2018).
Google Scholar
Sanjuán, R. Collective infectious units in viruses. Trends Microbiol. 25, 402–412 (2017).
Altan-Bonnet, N., Perales, C. & Domingo, E. Extracellular vesicles: Vehicles of en bloc viral transmission. Virus Res. 265, 143–149 (2019).
Google Scholar
Feng, Z. et al. A pathogenic picornavirus acquires an envelope by hijacking cellular membranes. Nature 496, 367–371 (2013).
Google Scholar
Chen, Y.-H. et al. Phosphatidylserine vesicles enable efficient en bloc transmission of enteroviruses. Cell 160, 619–630 (2015).
Google Scholar
Santiana, M. et al. Vesicle-cloaked virus clusters are optimal units for inter-organismal viral transmission. Cell Host. Microbe. 24, 208-220.e8 (2018).
Google Scholar
Arantes, T. S. et al. The large marseillevirus explores different entry pathways by forming giant infectious vesicles. J. Virol. 90, 5246–5255 (2016).
Google Scholar
Slack, J. & Arif, B. M. The baculoviruses occlusion-derived virus: Virion structure and function. Adv. Virus Res. 69, 99–165 (2007).
Google Scholar
Usmani, S. M. et al. Direct visualization of HIV-enhancing endogenous amyloid fibrils in human semen. Nat. Commun. 5, 3508 (2014).
Google Scholar
Cuevas, J. M., Durán-Moreno, M. & Sanjuán, R. Multi-virion infectious units arise from free viral particles in an enveloped virus. Nat. Microbiol. 2, 17078 (2017).
Google Scholar
Sanjuán, R. (2021) The social life of viruses. Annu. Rev. Virol. 8, null
Kauffman, S. A. & Weinberger, E. D. The NK model of rugged fitness landscapes and its application to maturation of the immune response. J. Theor. Biol. 141, 211–245 (1989).
Google Scholar
Vignuzzi, M. & López, C. B. Defective viral genomes are key drivers of the virus-host interaction. Nat. Microbiol. 4, 1075–1087 (2019).
Google Scholar
Rezelj, V. V., Levi, L. I. & Vignuzzi, M. The defective component of viral populations. Curr. Opin. Virol. 33, 74–80 (2018).
Sanjuán, R. & Thoulouze, M.-I. Why viruses sometimes disperse in groups†. Virus. Evol. https://doi.org/10.1093/ve/vez025 (2019).
Google Scholar
Bourke, A. F. G. The validity and value of inclusive fitness theory. Proc. Biol. Sci. 278, 3313–3320 (2011).
Frank, S. A. Natural selection. VII. History and interpretation of kin selection theory. J. Evol. Biol. 26, 1151–1184 (2013).
Google Scholar
Lehtonen, J. Multilevel selection in kin selection language. Trends Ecol. Evol. 31, 752–762 (2016).
Nowak, M. A. & Sigmund, K. Evolutionary dynamics of biological games. Science 303(5659), 793–799 (2004).
Google Scholar
Nowak, M. A. Five rules for the evolution of cooperation. Science 314, 1560–1563 (2006).
Google Scholar
Perc, M. & Szolnoki, A. Coevolutionary games—A mini review. Biosystems 99, 109–125 (2010).
West, S. A., Griffin, A. S. & Gardner, A. Evolutionary explanations for cooperation. Curr. Biol. 17, R661–R672 (2007).
Google Scholar
Fletcher, J. A. & Doebeli, M. A simple and general explanation for the evolution of altruism. Proc. Royal Soc. B 276, 13–19 (2009).
Bourke, A. F. G. Hamilton’s rule and the causes of social evolution. Philos. Trans. R Soc. Lond. B Biol. Sci. 369, 20130362 (2014).
Kuzdzal-Fick, J. J., Fox, S. A., Strassmann, J. E. & Queller, D. C. High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium. Science 334(6062), 1548–1551 (2011).
Google Scholar
Obolski, U. et al. With a little help from my friends: Cooperation can accelerate the rate of adaptive valley crossing. BMC Evol. Biol. 17, 143 (2017).
Shirogane, Y., Watanabe, S. & Yanagi, Y. Cooperation between different variants: A unique potential for virus evolution. Virus Res. 264, 68–73 (2019).
Google Scholar
Andino, R. & Domingo, E. Viral quasispecies. Virology 479–480, 46–51 (2015).
Bagheri, H. C. Unresolved boundaries of evolutionary theory and the question of how inheritance systems evolve: 75 years of debate on the evolution of dominance. J. Exp. Zool. B Mol. Dev. Evol. 306, 329–359 (2006).
Agrawal, A. F. & Whitlock, M. C. Inferences about the distribution of dominance drawn from yeast gene knockout data. Genetics 187, 553–566 (2011).
Google Scholar
Huber, C. D., Durvasula, A., Hancock, A. M. & Lohmueller, K. E. Gene expression drives the evolution of dominance. Nat. Commun. 9, 2750 (2018).
Google Scholar
Madlung, A. Polyploidy and its effect on evolutionary success: Old questions revisited with new tools. Heredity 110, 99–104 (2013).
Google Scholar
Zeyl, C. Experimental studies on ploidy evolution in yeast. FEMS Microbiol. Lett. 233, 187–192 (2004).
Google Scholar
Kanade, V. Evolution with recombination. In 2011 IEEE 52nd Annual Symposium on Foundations of Computer Science (pp. 837–846). IEEE.
Qi, Y., Hou, Z., Yin, M., Sun, H. & Huang, J. An immune multi-objective optimization algorithm with differential evolution inspired recombination. Appl. Soft. Comput. 29, 395–410 (2015).
Otto, S. P. The evolutionary consequences of polyploidy. Cell 131, 452–462 (2007).
Google Scholar
Freeling, M. & Thomas, B. C. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16, 805–814 (2006).
Google Scholar
Lynch, M. & Conery, J. S. The origins of genome complexity. Science 302, 1401–1404 (2003).
Google Scholar
Lynch, M. & Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459–473 (2000).
Google Scholar
García-Arriaza, J., Manrubia, S. C., Toja, M., Domingo, E. & Escarmís, C. Evolutionary transition toward defective RNAs that are infectious by complementation. J. Virol. 78, 11678–11685 (2004).
Murcia, P. R. et al. Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathog. 8(5), e1002730 (2012).
Google Scholar
Bennett, G. M. & Moran, N. A. Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole. PNAS 112, 10169–10176 (2015).
Google Scholar