Epigenetics

Understanding how populations evolve requires comprehensive knowledge on incredibly complex, synergistic, and cryptic processes, many of which are beyond the scope of current methods and tools. As ecologists, we are often faced with a species that is dispersed across a landscape into small pockets of subpopulations. These subpopulations may have unique adaptations to living in these pockets, and may even have certain physical traits that make them unique (e.g. a unique phenotype). These subtle changes, even between populations of the same species, have a molecular basis in every organism’s DNA. Using genetic techniques, we can identify these molecular signatures across many individuals, and begin to test our ideas about endless ecological and biological questions. These molecular data can be used to infer when populations or species split, even thousands of years ago. We can estimate the genetic health of species, or infer demographic trends like population size…even for events that happened a millennia ago. We can use such data to understand everyday ideas like the history of dog domestication, or apply it to solving the greatest problems in human disease.

The question I am researching isn’t as complex as those posed above. Across the northern parts of North America, Canada Lynx (Lynx canadensis) exist in several different environments. Previous genetic studies have shown that nearly all populations on the mainland are panmictic. Panmixia is the idea that any individual from any location is equally likely to mate with any other individual from any location. The molecular signature behind panmixia is just a very high degree of genetic similarity between all individuals. Several studies have shown that Canada Lynx are nearly genetically identical across the mountains of Alaska, the prairies of Manitoba, and the boreal forests of Québec. However, the island of Newfoundland has its own subpopulation with its own unique genetic diversity. A primary reason why the mainland population is so similar, despite spanning thousands of kilometers, is because Canada Lynx can disperse massive distances to find a mate.

If we only considered the underlying genetic signatures of these populations, we would likely conclude that molecular adaptation plays a minimal role in structuring these populations. But the great diversity of environments that these animals live across suggests that selective pressures should be favoring certain individuals over others in certain environments. Perhaps there are still molecular signatures of differentiation. Perhaps we’re just not looking in the right spots. Maybe these signatures are more subtle, and only modify the underlying DNA without changing the actual sequence of DNA itself.

 

Sample_DistributionThe four geographic locations of Canada Lynx that we are investigating for epigenetic differentiation. Johnson et al., In prep.

Epigenetic modifications do exactly this. Modifications such as DNA methylation modify the structure of DNA without changing the actual underyling sequence. Most importantly, DNA can become methylated due to environmental stressors. Highly publicized studies have shown that activities like smoking can lead to increased methylation throughout the bloodstream, with a quantifiable effect on offspring if occuring while pregnant. DNA methylation can have a direct effect on which genes are expressed. If certain genes are ‘turned off’ due to DNA methylation, direct physical changes can occur including disease and phenotypic change (i.e. physical alteration).

Consequently, we are interested in quantifying genome-wide patterns of methylation in Canada Lynx across these geographic locations. If individuals in different environments have unique signatures of DNA methylation along certain genes, it may explain how Canada Lynx adapt locally to environmental conditions, while their underlying genetic material remains the same. Our goal is to continue the exciting narrative on how our wild populations of Canada Lynx adapt and evolve, using modern high-throughput genetic sequencing and advanced epigenetic techniques.