Impact of environmental (pH) change in a model aquatic herbivore: from genes to populations
Abstract
Organisms are subjected to a variety of environmental stressors in which they must respond in order to survive and reproduce. While some individuals are able to adjust to these stressors and live to produce offspring and propagate their genes, others do not and are extirpated. Although it is known that organisms can respond to environmental stress, the underlying physiological and genetic mechanisms are often not well understood. Elucidating the evolutionary responses of organisms to environmental gradients is important, especially in light of increasing anthropogenic changes to our environment. In this dissertation, I looked at the acidification and alkalization of three North American lakes (Frenchman, Hill, Madison). In particular, I was interested in the underlying genetic response (evolution) of populations of the keystone aquatic zooplankter, Daphnia pulicaria, to the pH gradient found in these three lakes. In Chapter one, I used ecological genetic tools to determine local adaptation of the model organism, D. pulicaria, across a pH gradient in three North American lakes. I predicted there would be genetic differentiation and local adaptation among the three Daphnia populations. I genotyped individuals, which were used to determine genetic structure of the three populations. To test for signatures of local adaptation, a survivorship experiment across a pH gradient under common garden conditions was performed. In Chapter two, I was interested in determining candidate genes that may be involved in acid-base regulation in D. pulicaria. Previous studies have shown that carbonic anhydrases (CAs), a family of zinc metallo-enzymes, are responsible for acid-base regulation in many organisms. Through the use of phylogenetic tools, Chapter two attempted to find homologous CA isoforms in Daphnia that are implicated in acid-base regulation in closely related aquatic taxa. In Chapter three, I characterized the three isoforms of α-CAs found in Chapter two (CA1, CA2, and CA5). In addition, under common garden conditions, I investigated the differential expression of those CAs from D. pulicaria clones isolated from three North American lakes that exhibit a pH gradient. Finally, in Chapter four, I investigated the processes which affect genetic variation: neutral processes (i.e. genetic drift) versus natural selection (i.e. positive, purifying selection). I predicted that there will be evidence of selection at variants of these three CA loci and that specific CA genotypes will convey a fitness advantage via differential survivorship across a pH gradient. Populations were analyzed using population genetic tools. Further, five distinct CA genotypes were chosen for a common garden pH survival experiment to determine differential survivorship across a pH gradient. In summary, I identified three CAs that were homologous to CAs found to be implicated in acid-base regulation in other aquatic organisms. These isoforms were well-conserved across taxa and I found evidence that CA1 was differentially-expressed across a pH gradient and that CA5 was always up-regulated in the Frenchman population regardless of pH. In addition, I found evidence that D. pulicaria populations were locally adapted to native pH conditions and that sequence variation in the three CA isoforms are implicated in adaptive responses to pH environment in these populations. While, this dissertation provides support that CAs are involved in acid-base regulation in Daphnia, further study is warranted. In particular, RNA-seq experiments could implicate additional genes that are involved in acid-base regulation. In addition, protein structure analysis and activity assays of the CA isoforms and their variants could provide additional evidence to their role in acid-base regulation.
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