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The Genetic Architecture of Hybrid Fitness Under bioRxiv preprint doi: https://doi.org/10.1101/622845; this version posted April 30, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Recombining your way out of trouble: The genetic architecture of hybrid 2 fitness under environmental stress 3 Zebin Zhang1*, Devin P. Bendixsen1*, Thijs Janzen2,3, Arne W. Nolte2,3, Duncan 4 Greig2,4, Rike Stelkens1,2 5 6 7 *These authors contributed equally to the study. 8 9 1Division of Population Genetics, Department of Zoology, Stockholm University, 10 Svante Arrheniusväg 18 B, 106 91 Stockholm, Sweden 11 2Max Planck Institute for Evolutionary Biology, August-Thienemann Straße 2, 24306 12 Plön, Germany 13 3Institute of Biology and Environmental Sciences, University of Oldenburg, Carl-von- 14 Ossietzky-Straße 9-11, 26111 Oldenburg, Germany 15 4The Galton Laboratory, Department of Genetics, Evolution, and Environment, 16 University College London, Gower Street, London WC1E 6BT, United Kingdom 17 18 Corresponding author: Rike Stelkens, Department of Zoology, Stockholm University, 19 Svante Arrheniusväg 18 B, 106 91 Stockholm, Sweden, tel: +46 (0) 816 4223, email: 20 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/622845; this version posted April 30, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 21 Abstract 22 Hybridization between species is a fundamental evolutionary force that can both 23 promote and delay adaptation. There is a deficit in our understanding of the genetic 24 basis of hybrid fitness, especially in non-domesticated organisms. We also know little 25 about how hybrid fitness changes as a function of environmental stress. Here, we 26 made genetically variable F2 hybrid populations from two divergent Saccharomyces 27 yeast species, exposed populations to ten toxins, and sequenced the most resilient 28 hybrids on low coverage using ddRADseq. We expected to find strong negative 29 epistasis and heterozygote advantage in the hybrid genomes. We investigated three 30 aspects of hybridness: 1) hybridity, 2) interspecific heterozygosity, and 3) epistasis 31 (positive or negative associations between non-homologous chromosomes). Linear 32 mixed effect models revealed strong genotype-by-environment interactions with 33 many chromosomes and chromosomal interactions showing species-biased content 34 depending on the environment. Against our predictions, we found extensive selection 35 against heterozygosity such that homozygous allelic combinations from the same 36 species were strongly overrepresented in an otherwise hybrid genomic background. 37 We also observed multiple cases of positive epistasis between chromosomes from 38 opposite species, confirmed by epistasis- and selection-free simulations, which is 39 surprising given the large divergence of the parental species (~15% genome-wide). 40 Together, these results suggest that stress-resilient hybrid genomes can be 41 assembled from the best features of both parents, without paying high costs of 42 negative epistasis across large evolutionary distances. Our findings illustrate the 43 importance of measuring genetic trait architecture in an environmental context when 44 determining the evolutionary potential of hybrid populations. 45 Keywords: Saccharomyces, hybridization, fitness, environmental stress, ddRADseq, 46 heterozygosity, epistasis, genome evolution 2 bioRxiv preprint doi: https://doi.org/10.1101/622845; this version posted April 30, 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. 47 Introduction 48 Populations exposed to gene flow, introgression or hybridization contain vast 49 amounts of genetic variation, sometimes producing phenotypes with more extreme 50 adaptations than found in the parent populations (Shahid, et al. 2008; Stelkens and 51 Seehausen 2009; Pritchard, et al. 2013; Stelkens, Brockhurst, Hurst, Miller, et al. 52 2014; Holzman and Hulsey 2017). The average fitness of hybrid crosses is usually 53 lower than that of non-hybrid crosses due to interspecific incompatibilities or other 54 negative effects, e.g. the break-up and loss of co-adapted beneficial gene complexes 55 for local adaptation (Coyne and Orr 2004). This applies especially to the hybrid 56 offspring of genetically divergent lineages. However, some hybrids show high fitness 57 (Rieseberg, et al. 1999; Dittrich-Reed and Fitzpatrick 2012), which is exploited in 58 agricultural breeding to improve the yield, taste or other desirable traits of cultivars 59 (e.g. Marullo, et al. 2006; Kuczyńska, et al. 2007; Shivaprasad, et al. 2012; Koide, et 60 al. 2019). High hybrid fitness can also be relevant for macroevolutionary dynamics 61 and the generation of biodiversity, when ecologically divergent hybrid phenotypes 62 form their own evolutionary lineage and become reproductively isolated from the 63 parents (Anderson and Stebbins 1954; Lewontin and Birch 1966; Rieseberg, et al. 64 2003; Seehausen 2004; Arnold 2006; Mallet 2007; Nolte and Tautz 2010; Abbott, et 65 al. 2013; Schumer, et al. 2014). 66 Experimental evolution with interspecific hybrids of the budding yeast 67 Sacchromyces spp. has demonstrated that hybrids can colonize new ecological 68 niches (Stelkens, Brockhurst, Hurst and Greig 2014; Stelkens, Brockhurst, Hurst, 69 Miller, et al. 2014), and gain resistance to stress (Greig, et al. 2002; Piotrowski, et al. 70 2012; Dunn, et al. 2013). However, the genetic mechanisms allowing some hybrids 71 to express high fitness phenotypes in the face of negative epistasis between 72 divergent parental genomes are largely unknown, especially in non-domesticated 73 organisms. Also, we know very little about the impact of stressful and deteriorating 74 environmental conditions on the evolutionary potential of hybrid populations, although 3 bioRxiv preprint doi: https://doi.org/10.1101/622845; this version posted April 30, 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. 75 this is becoming increasingly relevant in the face of global environmental change. So 76 far empirical studies of hybrid fitness in an environmental context are scant and the 77 results are mixed. Some found environmental stress to intensify the negative effects 78 of hybridization (Koevoets, et al. 2012; Barreto and Burton 2013), others found hybrid 79 fitness to increase with stress (Edmands and Deimler 2004; Willett 2012; Hwang, et 80 al. 2016b); again others detected no effects of stress on hybrid fitness (Armbruster, 81 et al. 1999). 82 Here, we made genetically highly variable F2 hybrids by crossing two 83 divergent species of Saccharomyces (S. cerevisiae and S. paradoxus). These 84 species have well-sequenced, well-assembled genomes that differ at ~15% of 85 nucleotides genome-wide (Liti, et al. 2009). Due to their large divergence these 86 species produce only ~1% viable F2 hybrid offspring (Hunter, et al. 1996; Boynton, et 87 al. 2018; Rogers, et al. 2018). Because of this, we expected to find strong negative 88 epistasis between genetic material from opposite species and, potentially, 89 heterozygote advantage in the genomes of viable hybrids. We exposed 240 90 populations of these viable F2 hybrids to ten stressful environments containing high 91 concentrations of different toxins (e.g. caffeine, ethanol, lithium acetate; Table S1). At 92 the end of the growth period, we sequenced the genomes of 240 hybrid survivors at 93 low coverage using double digest, restriction-site associated DNA (ddRAD) markers 94 and mapped hybrid genomes to both reference genomes. To identify the genetic and 95 environmental factors shaping hybrid genomes in our experiment, we measured 96 three aspects of ‘hybridness’; 1) hybridity (proportion of hybrid genome mapping to 97 one or other parent species); 2) interspecific heterozygosity (homologous 98 chromosomes from opposite species), and 3) epistasis (positive or negative 99 associations between non-homologous chromosomes from opposite species). 100 Hybridity is a continuous measure, e.g. the proportion of genomic material 101 inherited from one over the other parental species (Gompert and Buerkle 2016), 102 often referred to as hybrid index (Barton and Gale 1993; Buerkle 2005) or admixture 4 bioRxiv preprint doi: https://doi.org/10.1101/622845; this version posted April 30, 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. 103 proportion (Pritchard, et al. 2000; Falush, et al. 2003). Hybridity is useful to place 104 hybrid individuals on a single axis ranging from zero to one with pure parental 105 individuals at opposite ends. However, this simple measure can mask potentially 106 important fitness effects of individual loci (or chromosomes)
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