From Hybridization to Evolution: Unraveling the Genetic Mysteries of Yeast Hybrids

Written by: Artemiza Martinez, Biological Science, Lehigh University

Ever heard of a mule? These intriguing hybrids result from the unconventional mating of a horse and a donkey. They are fascinating examples that challenge our understanding of species boundaries. Biologists traditionally define species based on an organism’s ability to mate and produce viable offspring. But what happens when these boundaries blur and two species can interbreed? Typically, hybridization leads to less fertile offspring, reducing the chances of passing genetic material between species. However, in some rare cases, the genetic combination can produce a viable and fertile hybrid capable of adapting rapidly to new environmental conditions. This phenomenon introduces a novel mechanism of speciation (Runemark et al. 2019; Herrera and Garcia-Bertrand 2023).

While the mule serves as a classic example of hybrids, our exploration of species boundaries transcends scales, delving into the realm of yeast–those tiny unicellular microorganisms that belong to the fungal kingdom.

Despite their diminutive size, yeast adhere to the same species definitions applied to larger animals. In the Lang Lab, we study a group of yeast in the genus Saccharomyces. The best-known species, Saccharomyces cerevisiae (S. cerevisiae), commonly known as “the sugar fungus of beer,”  has lived alongside humans for over 9,000 years (Duan et al. 2018). Yeast has a remarkable ability to fuel fermentation, not only shaping the flavors of bread, wine, and beer (Gallone et al. 2016, 2019; Lahue et al. 2020) but also playing an indispensable role in antibiotic production and bioremediation (Tullio 2022). Most importantly, this yeast helps us answer complex questions about cell biology and genetics (Botstein and Fink 2011) (see Figure 1).

Figure 1. Two species of Saccharomyces yeast under 100X magnification. A) The common brewer’s yeast S. cerevisiae.  B) wild yeast S. paradoxus. Although both species look very similar morphologically, their genomes differ by approximately 15%. C) Example of a hybrid between S. cerevisiae and S. paradoxus, showing a distinct morphology different from either parent.

The remarkable genetic diversity among yeast species is truly astonishing, with genomes differing by 15% to 35% across the genus Saccharomyces (Morales and Dujon 2012). To put this into perspective, the genetic differences between S. cerevisiae and S. paradoxus, the two most closely related species, are similar to the genetic differences between humans and mice (Dujon 2006). Despite this wide genetic divergence, scientists have confirmed the remarkable ability of yeast species, especially the Saccharomyces species, to interbreed in controlled laboratory settings and in diverse natural and fermentation environments (Bendixsen et al. 2021). This recurrent mating has prompted scientists to delve deeply into the mysteries of these hybrids.

The specific combination of genes inherited from parent species can significantly influence the hybrid’s characteristics, adaptability, and overall performance. But what are these genetic combinations that make one hybrid more suitable than another?

In a cell, protein-protein interactions need to fit together perfectly to function correctly, much like jigsaw puzzle. If the pieces belong to the same picture, they all match and complete the picture. However, mixing pieces from different puzzles often results in many pieces that do not fit together, leaving the picture incomplete (see Figure 2). In hybrid cells, proteins from each parent species are suddenly required to work together, despite having evolved independently. This can lead to significant mismatches in protein interactions, causing cellular processes to fail and reducing the hybrid’s viability (Maheshwari and Barbash 2011). Through evolution, beneficial mutations can further optimize these interactions, gradually improving the hybrid’s overall performance. On the other hand, in rare hybrid crosses, some protein interactions might actually be beneficial, exhibit improved or superior performance compared to their parents —a phenomenon known as hybrid vigor (Chen, Z. J. 2013). This process of adaptation and the occasional advantageous interaction underscore the complexity and potential of hybrid organism.

Figure 2. Illustration depicting the interaction between proteins as pieces of a jigsaw puzzle. A) Two proteins from the same species fit together perfectly. B) In a hybrid, proteins from different species most of the time fail to interact correctly. C) Over time, mutations may arise in the hybrid, improving protein interactions and enhancing the hybrid’s cellular function.

In this research, we focus on identifying the regions of the hybrid genome where beneficial mutations occur. By studying these areas, we can understand which proteins are more likely to face negative or positive interactions, providing valuable insights into the mechanisms of hybrid adaptation.

To address our research questions, we conducted crosses between two yeast species, S. cerevisiae and S. paradoxus. Normally, this cross would be mostly infertile, but by applying advanced molecular biology techniques, we successfully increased their fertility (Bozdag et al. 2019). This process yielded viable hybrid progeny, each with a unique combination of genes from both parent species. We then characterized these hybrids by measuring  their growth rates and by sequencing their entire genomes.

Many of these hybrids grew very slowly, suggesting that their genetic combinations were not favorable. To investigate how these hybrids might adapt and improve over time, we use a technique called experimental evolution  (Kawecki et al.  2012). By evolving these hybrids, we expect beneficial mutations to arise, improving protein interactions and consequently enhancing their growth. This approach enables us to observe the specific mutations that drive adaptation and gain a deeper understanding of the genetic mechanisms behind hybrid improvement.

Experimental evolution is a powerful tool for identifying evolved genetic interactions. This approach is like a time machine in the laboratory. It involves the continuous reproduction of yeast over many generations under controlled conditions. We leverage this technique by simultaneously evolving hundreds of hybrid populations. Using automated liquid-handling robotics, we perform daily dilutions from saturated yeast cultures into fresh media, allowing the yeast to keep dividing without interruption (Martínez and Lang 2023) (see Figure 3). Yeast has a short generation time, dividing approximately every two hours, yielding over 3,600 generations in just one year! This rapid generation time makes yeast an ideal model organism for studying evolutionary processes.

At regular intervals, we assess the adaptation capacity of our hybrid yeast by comparing their fitness to their ancestors’ and parental species. We sequence their DNA to identify advantageous mutations. By studying multiple populations evolving in parallel, we can determine whether they follow similar evolutionary paths or diverge in their adaptation processes. Currently, we have evolved multiple hybrids over thousands of generations and observed rapid adaptations, resulting in improved growth compared to their ancestor. We are investigating which specific mutations drive these adaptations and their broader impact on our understanding of hybrid biology and evolution.

Figure 3. Liquid-handling robotics performing parallel serial dilutions of hybrid yeast populations within a controlled environment. The robot conducts serial dilutions using a 96-well plate, with each well containing an independent population. This setup allows us to evolve hundreds of populations in parallel, providing a high-throughput method to study evolutionary processes.

Our exploration of yeast genetic diversity not only sheds light on their remarkable evolutionary adaptability, but also has broader implications for understanding hybrid adaptation in more complex organisms, like the mule. Just as the mule demonstrates exceptional traits from both horses and donkeys—such as their superior strength and endurance—our yeast hybrids reveal the potential within genetic combinations and adaptation of hybrid genomes. So, the next time you marvel at the unique characteristics of a mule or other hybrids, remember the secret is their unusual genetic combinations.

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