bioRxiv preprint doi: https://doi.org/10.1101/602201; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Role of host genetic diversity for susceptibility-to-infection in 2 the evolution of virulence of a plant virus 3 4 Rubén González,1 Anamarija Butković,1 and Santiago F. Elena1,2,* 5 6 1Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 7 46980 Paterna, València, Spain 8 2The Santa Fe Institute, Santa Fe, NM 87501, USA 9 *Corresponding author: E-mail: [email protected] 10 1 bioRxiv preprint doi: https://doi.org/10.1101/602201; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 11 Abstract 12 Predicting viral emergence is difficult due to the stochastic nature of the underlying 13 processes and the many factors that govern pathogen evolution. Environmental factors 14 affecting the host, the pathogen and the interaction between both are key in emergence. 15 In particular, infectious disease dynamics are affected by spatiotemporal heterogeneity in 16 their environments. A broad knowledge of these factors will allow better estimating 17 where and when viral emergence is more likely to occur. Here we investigate how the 18 population structure for susceptibility-to-infection genes of the plant Arabidopsis 19 thaliana shapes the evolution of Turnip mosaic virus (TuMV). For doing so we have 20 evolved TuMV lineages in two radically different host population structures: (i) multiple 21 genetically homogeneous A. thaliana subpopulations and (ii) a single maximally 22 genetically heterogeneous population. We found faster adaptation of TuMV to 23 homogeneous than to heterogeneous host populations. However, viruses evolved in 24 heterogeneous host populations were more pathogenic and infectious than viruses 25 evolved in the homogeneous population. Furthermore, the viruses evolved in 26 homogeneous populations showed stronger signatures of local specialization than viruses 27 evolved in heterogeneous populations. These results illustrate how the genetic diversity 28 of hosts in an experimental ecosystem favors the evolution of virulence of a pathogen. 29 30 Key words: evolution of virulence, experimental evolution, infection matrix, host 31 population structure, Potyvirus, resistance to infection, virus evolution 32 2 bioRxiv preprint doi: https://doi.org/10.1101/602201; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 33 1. Introduction 34 Since the term “emerging infectious disease” was coined in the mid-1900s, its definition 35 has evolved (Rosenthal et al. 2015). Woolhouse and Dye (2001) enunciated the most 36 comprehensive definition of an emerging infectious disease as one “whose incidence is 37 increasing following its first introduction into a new host population or whose incidence 38 is increasing in an existing host population as a result of long-term changes in its 39 underlying epidemiology”. Engering et al. (2013) rephrased this definition and suggested 40 that emergence events can be classified into three groups: (i) viruses showing up in a 41 novel host, (ii) mutant viral strains displaying novel traits in the same host, and (iii) 42 already known viral diseases spreading out in a new geographic area. Following these 43 definitions, viral emergence is usually associated to cross-species transmission but it can 44 actually occur with or without species jump (Di Giallonardo and Holmes 2015). 45 The emergence and re-emergence of viruses cause serious threatening to public 46 health (Morens and Fauci 2013) and are responsible for large yield losses in crops that 47 compromise food security (Vurro et al. 2010). Gaining knowledge on the principles that 48 govern viral emergence would allow to predict when and where such events are more 49 likely to happen. Achieving an accurate prediction of the emergence of viral diseases is 50 a challenging task, because emergence is governed by multiple and diverse factors that 51 remain poorly understood or completely unknown. Predictions will become even more 52 difficult under the ongoing climate change that will favor the conditions for development 53 and dispersal of the virus’ vectors (Garrett et al. 2006; Baylis 2017). 54 The spectrum of disease severity can be attributed to heterogeneity in virus virulence 55 or in host factors; the two are not necessarily independent explanations and they may 56 actually complement and/or interact each other. A problem faced by viruses is that host 57 populations consist of individuals that had different degrees of susceptibility to infection 3 bioRxiv preprint doi: https://doi.org/10.1101/602201; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 58 (Schmid-Hempel and Koella 1994; Pfennig 2001). Therefore, adaptive changes 59 improving viral fitness in one host may be selected against, or be neutral, in an alternative 60 one. Genetic variability in susceptibility of hosts and infectiousness of viruses have been 61 well studied in animals and plants (Schmid-Hempel and Koella 1994; Altizer et al. 2006; 62 Brown and Tellier 2011; Anttila et al. 2015; Parrat et al. 2016). Variability within host 63 populations can arise from nonrandom spatial distributions of genotypes: social groups 64 of animals are more closely related to each other than to other members of the population, 65 and plant crops are generally cultivated as genetically homogeneous plots. These 66 situations facilitate virus transmission among genetically similar host genotypes. Spatial 67 structure and local migration predict evolution of less aggressive exploitation in 68 horizontally transmitted parasites (reviewed in Parrat et al. (2016)). For example, Boots 69 and Mealor (2007) observed that Plodia interpunctella granulosis virus (PiGV) evolved 70 in spatially-structured lepidopteran host populations become less virulent than the one 71 maintained in well mixed host populations. More recently, Berngruber et al. (2015) 72 showed that a latent l bacteriophage won competition against a virulent one in a spatially- 73 structured host populations but lost in well mixed populations. In a natural context, it has 74 been observed that virulent Linum marginale fungi were more frequent in highly resistant 75 Melampsora lini plant populations whereas avirulent pathogens dominated susceptible 76 populations (Thrall and Burdon 2003; Thrall et al. 2012). Similar results were observed 77 in laboratory evolution experiments with the pathosystem Arabidopsis thaliana - Tobacco 78 etch virus (TEV): a negative association between plant natural accessions permissiveness 79 to infection and TEV virulence was evolved (Hillung et al. 2014). Finally, host 80 population structure also promotes coexistence of hosts and parasites by creating refugia 81 due to limited dispersal of viruses; increased dispersal makes coexistence less stable 82 (Brockhurst et al. 2006). 4 bioRxiv preprint doi: https://doi.org/10.1101/602201; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 83 The role of host population heterogeneity has also received quite a lot of attention 84 from theoreticians (e.g., Comins et al. 1992; Gandon et al. 1996; Boots and Sasaki 1999, 85 2002; Gandon and Michalakis 2002; Tellier and Brown 2011), resulting in a number of 86 interesting predictions that in many instances have not been properly tested 87 experimentally. One of the most tantalizing predictions is that in the absence of host 88 heterogeneity, parasites must evolve toward a host exploitation strategy that maximizes 89 transmission with low virulence (Haraguchi and Sasaki 2000; Regoes et al. 2000; 90 Rodríguez and Torres-Sorando 2001; Ganusov et al. 2002; Gandon 2004; Lively 2010; 91 Moreno-Gámez et al. 2013). However, in the context of emerging diseases, right after 92 the spill-over of the new pathogen into the heterogeneous host population and prior to 93 adaptive evolution to take place, Yates et al. (2006) showed that host heterogeneity has a 94 small effect in the probability of establishing the disease. Very recently, Chabas et al. 95 (2018) showed that evolutionary emergence is more likely to occur when the host 96 population contains intermediate levels of resistant hosts, confirming this prediction using 97 different phages and bacterial hosts with different alterations in the CRISPR/Cas immune 98 systems that conferred the cells with different levels of resistance. 99 In this study we use experimental evolution to explore the effect of host population 100 structure for genes involved in susceptibility to infection in the evolution of 101 infectiousness and virulence of a plant virus; in particular, we want to explore the extent 102 to which host heterogeneity determines the rate of evolution of these two fitness-related 103 traits. According to the above theoretical predictions and experimental observations in 104 other pathosystems, we expect the virus infectiousness and virulence to evolve to lower 105 levels in genetically homogeneous host populations, but at a faster rate, than in maximally 106 genetically diverse host populations.