Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of Saccharomyces cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak x vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak, and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.

物种内，对不同生态位的差异化适应可限制基因流，并推动种群分化。然而在部分情形下，生态位间的界限会瓦解，形成兼具两种环境特征的混合生态位。我们此前曾报道，葡萄园与橡树土壤间的差异构成了一道生态屏障，限制了酿酒酵母（Saccharomyces cerevisiae）不同谱系间的基因交流。葡萄园分离株可耐受与葡萄相关的胁迫，而北美橡树菌株则对冻融循环具有极强的耐受性。本研究从威斯康星州的樱桃树中分离得到酿酒酵母菌株，该生境兼具葡萄园的特征（如高糖浓度）与频繁的冻融循环。基因组测序结果显示，所分离的菌株具有高度杂合性，且是橡树谱系与葡萄园谱系近期杂交产生的后代。我们发现，这些杂交菌株在部分性状上与葡萄园菌株表型相似，而在另一些性状上则更接近橡树菌株。樱桃树来源菌株在樱桃汁中生长能力格外优异，这提示它们已适应了这一特定生态位。我们对樱桃树、橡树及葡萄园来源的菌株开展了转录组谱分析，结果显示，这些樱桃树来源的杂交菌株的基因表达模式依基因集不同，可呈现类似葡萄园菌株或类似橡树菌株的特征；在部分案例中，其表达模式与共同的胁迫耐受特性相关联。对这些天然杂交菌株的等位基因特异性表达分析表明，功能调控基因集存在协同的顺式调控进化。本研究结果提示，这两种谱系的杂交或许为菌株在这一独特生态位中存活繁衍提供了遗传解决方案。