Temperature preference biases parental genome retention during hybrid evolution

Interspecific hybridization can introduce genetic variation that aids in adaptation to new or changing environments. Here we investigate how the environment, and more specifically temperature, interacts with hybrid genomes to alter parental genome representation over time. We evolved Saccharomyces cerevisiae x Saccharomyces uvarum hybrids in nutrient-limited continuous culture at 15°C for 200 generations. In comparison to previous evolution experiments at 30°C, we identified a number of temperature specific responses, including the loss of the S. cerevisiae allele in favor of the cryotolerant S. uvarum allele for several portions of the hybrid genome. In particular, we discovered a genotype by environment interaction in the form of a reciprocal loss of heterozygosity event on chromosome XIII. Which species haplotype is lost or maintained is dependent on the parental species temperature preference and the temperature at which the hybrid was evolved. We show that a large contribution to this directionality is due to temperature sensitivity at a single locus, the high affinity phosphate transporter PHO84. This work helps shape our understanding of what forces impact genome evolution after hybridization, and how environmental conditions may favor or disfavor hybrids over time.


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Comparative genomics of thousands of plants, animals, and fungi has revealed that 26 portions of genomes from many species are derived from interspecific hybridization, indicating 27 that hybridization occurs frequently in nature. However, the influence of processes such as 28 selection, drift, and/or the presence or absence of backcrossing to a parental population on hybrid 29 genome composition in incipient hybrids remains largely unknown. In some cases, hybrids will 30 persist with both parental genomes in fairly equal proportions as new hybrid species or lineages, 31 while in other instances, hybrid genomes will become biased towards one parent sub-genome 32 over time [1][2][3][4][5][6][7][8][9]. Untangling the genetic and environmental factors that lead to these outcomes is 33 a burgeoning field. 34 Some hybrid genotypes will be unfit due to genetic hybrid incompatibilities or cytotype x S. uvarum hybrids have been isolated from fermentation environments [55,59]. 72 We previously evolved S. cerevisiae x S. uvarum hybrids in the laboratory in several 73 nutrient-limited environments at the preferred growth temperature of S. cerevisiae [60]. We 74 frequently observed a phenomenon known as loss of heterozygosity (LOH) in these evolved 75 hybrids, in which an allele from one species is lost while the other species' allele is maintained. 76 The outcome of such events is the homogenization of the hybrid genome at certain loci, and 77 represents a way in which a hybrid genome may become biased toward one parent's sub- 78 genome. This type of mutation can occur due to gene conversion or break induced repair, and as 79 previously noted, has also been observed in organisms including S. pastorianus, pathogenic 80 hybrid yeast, and hybrid plants, but its role in adaptation has been unclear [47,61,62]. We used 81 genetic manipulation and competitive fitness assays to show that a particular set of LOH events 82 was the result of selection on the loss of the S. uvarum allele and amplification of the S. 83 cerevisiae allele at the high affinity phosphate transporter PHO84 in phosphate limited 84 conditions. By empirically demonstrating that LOH can be the product of selection, we 85 illuminated how an underappreciated mutation class can underlie adaptive hybrid phenotypes.

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This prior study illuminated how the environment (differences in nutrient availability) 87 can bias a hybrid genome towards one parent sub-genome. Due to many examples of genotype 88 by temperature interaction in hybrids across many taxa, and in particular difference in species 89 temperature preference in our hybrids, we speculated that temperature is an important 90 environmental modifier which may influence parental sub-genome representation in hybrids.

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Temperature can perturb fundamentally all physiological, developmental, and ecological 92 processes, and as such, temperature is an essential factor in determining species distribution and 93 biodiversity at temporal and spatial scales [63][64][65]. We hypothesized that in S. cerevisiae x S. 94 uvarum hybrids, S. cerevisiae alleles may be favored at warmer temperatures, whereas S. uvarum 95 alleles may be preferred at colder temperatures, giving the hybrid an expanded capacity to adapt.

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To test how temperature influences hybrid genome composition over time, we evolved the same 97 interspecific hybrid yeast in the laboratory at 15°C for 200 generations. In comparing laboratory 98 evolution at 15°C and 30°C, we present evidence that temperature can indeed bias hybrid 99 genome composition towards one parental sub-genome, and we focus on a reciprocal LOH event 100 at the PHO84 locus. We show that which species' allele is lost or maintained at this locus is 101 dependent on the parental species' temperature preference and the temperature at which the  Loss of S. cerevisiae alleles in cold evolved hybrids 118 We detected large scale copy number variants in our cold evolved populations, including 119 whole and partial chromosome aneuploidy and loss of heterozygosity ( Table 1; Tables S1-S2; 120 Figures S1-S7). Previously, in hybrids evolved at 30°C, we observed more LOH events in which 121 the S. uvarum allele was lost (5/9 LOH events), and found a significant preference for S. 122 cerevisiae partial and whole chromosome amplification [60]. In contrast, in hybrids evolved at 123 15°C, we observe 6/6 LOH events in which the S. cerevisiae allele is lost and the S. uvarum 124 allele is maintained, suggestive of a S. uvarum cold temperature benefit. While our sample sizes 125 are modest, together these results indicate that temperature can determine hybrid genomic 126 composition in the generations following a hybridization event.    Figure 1A). The directionality of this LOH event is the opposite outcome of our 155 observations of hybrids evolved at 30° C, in which the S. cerevisiae allele was amplified and the 156 S. uvarum allele was lost in this same region (3/6 populations, Figure 1A). The direction of 157 resolution of these LOH events thus appears to be modulated by temperature.    showing the opposite trend, and some clones having similar fitness at both temperatures (Table   238 2). It thus appears that temperature specific antagonistic pleiotropy, in which a clone has high 239 fitness at one temperature and low fitness at the other temperature, is relatively rare, with the    shifted from its optimal environment, and a difference in the size of the adaptive space available.

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There was no overlap in genes with variants identified in datasets from 15°C and 30°C. 268 We suspect that the low growth temperature is a selective pressure for both the hybrids 269 and the parental populations, and we did observe mutations in two genes (BNA7 and OTU1) that  Figure S8). 294 Most mutations were heterozygous, but within several lineages, we observed evidence of a LOH 295 event that caused the TPK2 mutation to become homozygous. Clones bearing a homozygous 296 mutation in TPK2 showed a faster flocculation phenotype than their heterozygous counterparts. 297 We similarly observed one lineage with a mutation causing a pre-mature stop and subsequent 298 LOH in SFL1, whose isolated clones displayed a robust flocculation phenotype. We suspect that 299 our previous lack of detection is likely due to the well-established genetic differences in the show that temperature can influence parental representation in a hybrid genome. We find a 306 variety of mutations whose annotated function is associated with temperature or nutrient 307 limitation, including both previously described and novel genes. Most notably, we discover a 308 temperature and species specific gene by environment interaction in hybrids, which empirically 309 demonstrates that temperature influences hybrid genome evolution.

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Growth temperature appears to be one of the most definitive phenotypic differences preferences and potentially environment specific incompatibilities.

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More broadly, through the lens of PHO84, we establish LOH as an important molecular 348 mechanism in hybrid adaptation, but we also demonstrate that this mutation type has fitness 349 tradeoffs. The selection of a particular species allele may confer a fitness advantage in a given

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The variants were then filtered using bcftools/1.5 for quality scores above 10 and read depth   Figure S1. Copy number plots of cold-evolved hybrids populations.