Benjamen Kline

Benjamen Kline

Mar 21, 2022

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Genetic Panel Recipe: Part 2

Now that genetic sequences have been submitted for the panel I am designing, I thought it might be a good time to talk through what parts of the genome we are targeting to answer our research questions. As a reminder, the primary research objective of this project is to examine the underlying genetic variation that enables populations adapt to thermal stress. In order to do this, we will examine both neutral and adaptive genetic variation in brook trout across the native species range.

Genetic variation broadly describes the differences in DNA sequence among individuals or among populations. More specifically, the differences in alleles and allele frequencies that often occur as a result of genetic recombination or mutations. There are two types of genetic variation that we often focus on in conservation genomics: neutral and adaptive genetic variation. Both forms of genetic variation can be useful for answering questions about the natural world; however, they tell us different things.

Neutral genetic variation refers to changes in the DNA sequence that do not have an effect on the fitness of survival of the organism. As such, neutral genetic variation is also not effected by evolution. Changes in neutral genetic variation are frequently the product of processes such as mutation, migration, and drift. Studying the neutral genetic variation of an organism or a population can help us as scientists to understand how these processes occur across the landscape. Understanding neutral genetic variation can help us differentiate individuals from unique populations at the genetic level. It can also tell us how many genetically distinct individuals there are in a population and provide a proxy for what we refer to as the "effective" population size. Using neutral genetic variation, we can understand how the genetic structure of populations may have changed through space and time.

Adaptive genetic variation refers to genetic variation that is directly linked to the fitness of an organism or populations. Adaptive genetic variation can tell us about the "adaptive" or evolutionary potential of a population or species. This type of genetic variation is under the influence of natural selection and is heritable from one generation to the next. Quantifying adaptive genetic variation in wild populations can tell us more about how organisms may respond in persist when environmental conditions change. Populations or individuals that have a high degree of adaptive genetic variation in response in changing environmental conditions are likely to be buffered from the effects of changing conditions, whereas individuals with low adaptive genetic variation may not be as well suited to survive in unfavorable environments.

By quantifying both neutral and adaptive genetic variation across the species range, we will be able to better understand how populations of brook trout will respond to climate change. By examining neutral genetic variation, we can designate genetically distinct populations, quantify effective population size, and examine immigration and emigration of genotypes between populations. Looking at adaptive variation can tell us which populations of brook trout we might expect to survive high levels of thermal stress, and which populations may be at greatest risk of decline in response to climate change. By combining this information into a single genetic panel, we can provide a practical tool to scientists and managers to improve conservation of this iconic coldwater species.

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About This Project

Freshwater fish account for a quarter of the world’s vertebrate species and are critical to maintaining healthy ecosystems and supporting local communities. However, freshwater fish remain one of the most vulnerable taxa to climate change, with over 1/3 of species threatened with extinction. How will fish adapt and survive in response to climate change? We are attempting to answer this question by examining the underlying genetic variation that enables populations adapt to thermal stress.

Blast off!

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