Adaptations to environmental changes typically take very long periods of time to occur following genetic variation created by random mutations in DNA. Many environments on earth today are changing so quickly, though, that these changes have the potential to outpace many organisms’ ability to naturally adapt to their new environments. This could be especially true for slow growing trees that have long life cycles and are unable to move in response to unfavorable environmental conditions, like drought, extreme temperatures, or even asynchrony between flowering and the emergence of pollinating insects.
This situation raises the question, “How do you respond to rapid change in your local environment if you are not physically able to move to more favorable conditions?”
UMCES researcher, Paul Gugger, is conducting research in a novel area of science called epigenetics, which studies modifications to DNA that do not involve changes to the underlying DNA sequence and may affect gene expression and adaptation. He is using epigenetics to try to improve understanding of how a species of oak tree may be able to adapt to rapid environmental change.
It is commonly assumed that heritable adaptation in plants and animals occurs only through genetic mutation, but that may not always be the case. Plants and animals can influence the expression of their genes through a process called DNA methylation, which represents an additional source of heritable variation comprising one area of epigenetics (“on top of” genetics). DNA methylation occurs when methyl (CH3) groups are added to DNA molecules. The addition of these methyl groups can change how a gene is expressed in an organism, but it does not actually change that organism’s genetic sequence. In fact, methylation is reversible. Methylation can occur rapidly relative to genetic change from DNA mutation and it can also be inherited, and therefore passed down to future generations.
With the development of state-of-the-art genome sequencing techniques, scientists are able to detect the existence of the methyl groups in DNA and more importantly, relate this methylation to specific genes within a sequence to better identify and understand the adaptive functions that might be influenced by this phenomenon.
The valley oak (Quercus lobata) is a species of oak that grows in the Central Valley and other smaller valleys in California. It is considered to be an important keystone species by providing habitat to many other species in these ecosystems. It is a slow growing tree that prefers mild, wet winters and hot dry summers. Projected climate change in this region of California could see warming air temperatures along with increased drought frequency, which could adversely affect the valley oak as it requires large amounts of water to survive.
Gugger’s work is investigating whether DNA methylation could be a short-term strategy through which plants can respond to climate change and whether it might be a mechanism through which long-lived trees may respond to rapidly changing environmental conditions.
Gugger and colleagues first approached these questions by looking at how DNA methylation varies in nature in relation to climate gradients along the landscape, which allows them to test whether methylation might be involved in current adaptations to the different environmental conditions that oaks face in different parts of their distribution. To that end, they extracted DNA from leaves collected at almost 60 sites throughout valley oak’s distribution, which exist along a natural climate gradient (map at right). Using the DNA, they were able to identify where methylation occurs along the genome sequences in relation to genes and where methylation varies among individuals in nature. These variable sites, called single-methylation variants or SMVs, might reflect different adaptations of valley oak populations to the different environments they inhabit within California.
Through a variety of statistical tests, Gugger and colleagues identified 43 climate-associated SMVs for which climate was significantly associated with DNA methylation levels. They then sought to understand the potential functions of the genomic regions with these interesting methylation patterns. This is where having a draft genome sequence for the valley oak was so critical. Through some of his other work (https://valleyoak.ucla.edu/), Gugger was able to identify the genomic context of these 43 climate-associated SMVs and showed that several occur in or near genes that have known involvement in plant response to environment.
Gugger’s results provide some of the first evidence to suggest a potential role for DNA methylation in improving oak adaptability to environmental change. DNA methylation, therefore, may be a mechanism for plants to respond to environmental changes, and may lead to local adaptation in natural populations of trees. These results suggest implications for other tree species in other regions of the country, including in Maryland. Further study is needed to investigate the importance of methylation in other natural ecology and evolutionary contexts. For example, one fragment, called scaffold20751.233xx was associated with maximum temperature and is located near a gene involved in valley oak’s response to dehydration. The map to the left shows the methylation levels per sample (black and white pie charts) in relation to mean maximum temperature (background color gradient). The darker pie charts indicate higher levels of SMV’s in this particular fragment in the areas that are experiencing the highest maximum temperatures. Oaks found along the coastline, where the ocean may provide a moderating effect on temperature, showed the lowest level of SMV’s associated with this particular fragment, while oaks located in areas with some of the highest maximum temperatures showed some of the highest levels of SMV’s.