This week’s BEACON Researchers at Work post is by MSU graduate student Carlos Anderson.
This blog post is a follow up to one I wrote last year about my research on speciation with digital organisms. One of my projects tested the hypothesis that compensatory adaptation—an evolutionary process in which secondary mutations can reduce the negative effects of accumulated deleterious mutations—causes hybrid inviability between populations, a form of reproductive isolation that may lead to speciation. Using digital organisms, I showed that hybrids between compensated populations inherited combinations of deleterious and compensatory mutations that turned out to be incompatible in the hybrid. This incompatibility arose because the full combination of deleterious and compensatory mutations from either parent were not always present in the hybrid, causing a mismatch between deleterious and compensatory mutations.
Over the past year, I have been working on complementing my digital work with biological organisms, specifically, the budding yeast. Yeast are unicellular fungi, known primarily for their use in brewing and baking, but have also been used extensively in scientific research. Using common techniques in yeast genetics, I deleted certain genes from yeast that caused their growth rate to slow down, simulating the effects of deleterious mutations. Currently, I am allowing populations of yeast with these deleterious mutations to evolve separately, so that each population acquires compensatory mutations independently of other such populations. After 500 generations (they are currently at around 50), I will hybridize different populations and measure the growth rate of the hybrids. If I find that hybrids are less fit than their parents, I will also be able to tease apart the interactions between deleterious or compensatory mutations that cause incompatibilities. If I find such incompatibilities, this work would not only show that reproductive isolation can form via compensatory adaptation, but it would also support the utility of digital organisms in evolutionary research.
In another study using digital organisms, I tested whether speciation could proceed in the face of migration between populations. I also tested whether differences in environments between populations promoted or constrained speciation. I found that when the environments were different, reproductive isolation developed even at high migration rates of 10%. When the environments were the same, however, even a 1% migration prevented reproductive isolation. The reason was that when the environments were the same, any beneficial mutations in one population that were transferred to the other population through migration were also adaptive in the other population. This caused both populations to adapt similarly, preventing reproductive isolation between them.
Since those experiments, I have added two variables that may affect reproductive isolation: dimensionality and type of hybridization. Dimensionality describes the number of selective pressures in an environment. It has been hypothesized that adaptation to multiple selective pressures may increase divergence between populations, and thus increase the probability of genetic incompatibilities. To test this hypothesis, I evolved populations under both low and high dimensionality, where the environments could be the same or different between the populations (as in the previous experiments). I found that, indeed, populations that adapted to a highly dimensional environment produced hybrids that were less fit than hybrids produced by populations adapted to few dimensions.
The other variable I added was the type of hybridization. Originally, hybrids were created by exchanging a single, contiguous region of a random size from the parental genomes. Thus, hybrids often inherited complete sets of tightly-linked co-adapted genetic regions from each parent, hiding potential incompatibilities between populations. In an attempt to expose these co-adapted genetic regions, I implemented a hybridization method in which every site of the genome could potentially recombine, thereby increasing the number of recombination break points. Whereas with the original hybridization method populations that adapted to similar environments did not form as strong reproductive isolation as populations that adapted to different environments (when there was no migration between populations), the new hybridization method caused both treatments—same environments and different environments—to show similar levels of reproductive isolation. These results show that genetic incompatibilities can form even when populations adapt to the same environment.
Finally, using digital organisms I explored a hypothesis related to the formation of genetic incompatibilities. As I have discussed, when a population becomes geographically divided into two, each population evolves independently of the other, so that genetic incompatibilities may form. Genetic incompatibilities may cause hybrids to be inviable, which is a form of reproductive isolation (i.e., speciation). One theoretical prediction of this process posits that the number of genetic incompatibilities involving two alleles should increase quadratically through time (the so-called “snowball effect”). This prediction is very difficult to test with biological organisms because a lot of genetic manipulations would have to be performed. Using digital organisms, I tested the snowball effect and found that pairwise incompatibilities do increase quadratically through time. But I also found the presence of “buffer” alleles in hybrids that lessened the fitness effect of these incompatibilities, showing that more complex interactions may explain hybrid inviability.
Overall, my research opens the exciting possibility that speciation can form through complex genetic incompatibilities, some of which may be due to compensatory adaptation, regardless of the environmental differences (or lack of) between populations. My next project is to examine more closely compensatory adaptation itself. I will test how population size, mutation rate, and the initial fitness effect of deleterious mutations affect the rate of compensatory adaptation (versus reversion). Knowledge of the effects of these factors on compensation is not only relevant to my research on speciation, but also relevant to broader topics where compensation is important, such as the recovery of endangered species and the fight against antibiotic resistance.
For more information about Carlos’ work, you can contact him at carlosja at msu dot edu.