Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article

Degree

Doctor of Philosophy

Program

Biology

Supervisor

Keyghobadi, Nusha

Abstract

Genetic diversity represents a population’s evolutionary potential, as well as its demographic and evolutionary history. Advances in DNA sequencing have allowed the development of new and potentially powerful methods to quantify this diversity. However, when using these methods best practices for sampling populations and analyzing data are still being developed. Furthermore, while effects of the landscape on spatial patterns of genetic variation have received considerable attention, we have a poorer understanding of how genetic diversity changes as a result of temporal variation in environmental and demographic variables. Here, I take advantage of advances in DNA sequencing to investigate genetic diversity at single nucleotide polymorphisms (SNPs) across space and time in a model system of the butterfly, Parnassius smintheus.

I used double digest restriction site associated DNA sequencing to genotype SNPs in P. smintheus from populations in Alberta, Canada. To develop recommendations for analyzing data, I tested the effect of varying the maximum amount of missing data (and therefore the number of SNPs) on common population genetic analyses. Most analyses were robust to varying amounts of missing data, except for population assignment tests where larger datasets (with more missing data) revealed higher-resolution population structure. I also examined the effect of sample size on the same set of analyses, finding that some (e.g., estimation of genetic differentiation) required as few as five individuals per population, while others (e.g., population assignment) required at least 15.

I used the SNP dataset to investigate factors shaping patterns of genetic diversity at different spatial scales and across time. At a larger spatial scale but a single time point, both weather (snow depth and mean minimum temperatures) and land cover (the distance between meadow patches) predicted genetic diversity and differentiation. At a smaller spatial but longer temporal scale, I used a smaller SNP dataset to show that genetic diversity is lost over repeated demographic bottlenecks driven by winter weather, and subsequently recovered through gene flow. My work contributes to understanding how genetic diversity is shaped in natural populations, and points to the importance of both land cover and weather (and specifically, variability in weather) to this process.

Summary for Lay Audience

Genetic diversity describes differences in DNA sequence among individuals of the same population or even between species. In principle, it is this diversity that allows populations to adapt over time when their environment changes. Understanding what factors influence the diversity of natural populations is a central question for both evolutionary biology and for conservation biology (where preserving genetic diversity of endangered populations is a key goal).

I used a new way to measure DNA sequence differences among individuals to assess genetic diversity and to ask what ecological factors are important for maintaining that diversity in the Rocky Mountain Apollo butterfly (Parnassius smintheus). This method allows thousands of genetic differences to be identified across an individual’s genome. Because this method is new and there are few established guidelines relative to older methods, I tested different ways to process my data. I looked at how to choose which genetic differences to include, as well as how many individuals to sample from each population to get accurate results. I found that compared to some older methods of measuring genetic differences, I was able to sample fewer individuals per population.

I then used the DNA sequence differences I had identified to look at what environmental factors affect genetic diversity in populations from the Rocky Mountains of western Alberta. I found that populations that experience less snow and more extreme winter temperatures have lower genetic diversity. This occurs because these conditions can lead to dramatic reductions in population size, which in turn reduce genetic diversity. Populations surrounded by more forest, as opposed to meadows, also have lower genetic diversity and are more genetically different from other populations. This is because forest limits how easily the butterflies can move among populations.

My work provides real-life evidence of how weather and climate, the physical landscape, and changes in population size are expected to affect a population’s genetic diversity. Since climate change will lead to both increased weather extremes and increased forest cover in mountain landscapes, it is likely to result in losses of genetic diversity from populations of the Rocky Mountain Apollo.

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