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Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts.
Ecology and Evolution ( IF 2.3 ) Pub Date : 2020-06-02 , DOI: 10.1002/ece3.6208 Roberto F Nespolo 1, 2, 3 , Jaiber J Solano-Iguaran 1 , Rocío Paleo-López 1 , Julian F Quintero-Galvis 1 , Francisco A Cubillos 3, 4 , Francisco Bozinovic 2
Ecology and Evolution ( IF 2.3 ) Pub Date : 2020-06-02 , DOI: 10.1002/ece3.6208 Roberto F Nespolo 1, 2, 3 , Jaiber J Solano-Iguaran 1 , Rocío Paleo-López 1 , Julian F Quintero-Galvis 1 , Francisco A Cubillos 3, 4 , Francisco Bozinovic 2
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The capacity of some yeasts to extract energy from single sugars, generating CO2 and ethanol (=fermentation), even in the presence of oxygen, is known as the Crabtree effect. This phenomenon represents an important adaptation as it allowed the utilization of the ecological niche given by modern fruits, an abundant source of food that emerged in the terrestrial environment in the Cretaceous. However, identifying the evolutionary events that triggered fermentative capacity in Crabtree‐positive species is challenging, as microorganisms do not leave fossil evidence. Thus, key innovations should be inferred based only on traits measured under culture conditions. Here, we reanalyzed data from a common garden experiment where several proxies of fermentative capacity were recorded in Crabtree‐positive and Crabtree‐negative species, representing yeast phylogenetic diversity. In particular, we applied the “lasso‐OU” algorithm which detects points of adaptive shifts, using traits that are proxies of fermentative performance. We tested whether multiple events or a single event explains the actual fermentative capacity of yeasts. According to the lasso‐OU procedure, evolutionary changes in the three proxies of fermentative capacity that we considered (i.e., glycerol production, ethanol yield, and respiratory quotient) are consistent with a single evolutionary episode (a whole‐genomic duplication, WGD), instead of a series of small genomic rearrangements. Thus, the WGD appears as the key event behind the diversification of fermentative yeasts, which by increasing gene dosage, and maximized their capacity of energy extraction for exploiting the new ecological niche provided by single sugars.
中文翻译：
性能、基因组重排和适应性进化的特征：发酵酵母的教训。
一些酵母即使在有氧的情况下也能从单糖中提取能量，产生CO 2和乙醇（=发酵），这被称为克拉布特里效应。这种现象代表了一种重要的适应，因为它允许利用现代水果所提供的生态位，这是白垩纪陆地环境中出现的丰富食物来源。然而，识别触发克拉布特里阳性物种发酵能力的进化事件具有挑战性，因为微生物不会留下化石证据。因此，关键创新应该仅根据在文化条件下测量的特征来推断。在这里，我们重新分析了一个常见花园实验的数据，其中在 Crabtree 阳性和 Crabtree 阴性物种中记录了几个发酵能力的指标，代表了酵母系统发育的多样性。特别是，我们应用了“lasso-OU”算法，该算法使用发酵性能的代理特征来检测自适应转变点。我们测试了多个事件或单个事件是否可以解释酵母的实际发酵能力。根据lasso-OU程序，我们考虑的三个发酵能力指标（即甘油产量、乙醇产量和呼吸商）的进化变化与单一进化事件（全基因组重复，WGD）一致，而不是一系列小的基因组重排。因此，WGD 似乎是发酵酵母多样化背后的关键事件，发酵酵母通过增加基因剂量，最大化其能量提取能力，以开发单糖提供的新生态位。
更新日期：2020-06-26
中文翻译：
性能、基因组重排和适应性进化的特征：发酵酵母的教训。
一些酵母即使在有氧的情况下也能从单糖中提取能量，产生CO 2和乙醇（=发酵），这被称为克拉布特里效应。这种现象代表了一种重要的适应，因为它允许利用现代水果所提供的生态位，这是白垩纪陆地环境中出现的丰富食物来源。然而，识别触发克拉布特里阳性物种发酵能力的进化事件具有挑战性，因为微生物不会留下化石证据。因此，关键创新应该仅根据在文化条件下测量的特征来推断。在这里，我们重新分析了一个常见花园实验的数据，其中在 Crabtree 阳性和 Crabtree 阴性物种中记录了几个发酵能力的指标，代表了酵母系统发育的多样性。特别是，我们应用了“lasso-OU”算法，该算法使用发酵性能的代理特征来检测自适应转变点。我们测试了多个事件或单个事件是否可以解释酵母的实际发酵能力。根据lasso-OU程序，我们考虑的三个发酵能力指标（即甘油产量、乙醇产量和呼吸商）的进化变化与单一进化事件（全基因组重复，WGD）一致，而不是一系列小的基因组重排。因此，WGD 似乎是发酵酵母多样化背后的关键事件，发酵酵母通过增加基因剂量，最大化其能量提取能力，以开发单糖提供的新生态位。
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