Date of Award
Doctor of Philosophy (PhD)
Arms races involve bouts of reciprocal co-adaptation to a social environment. We have a strong sense for how arms races drive the evolution of genes in purely antagonistic contexts, such as host-pathogen or predator-prey. In these systems, conflict that produces arms races between two parties results in positive selection – the fixation of adaptive alleles between species – for both parties. However, we do not have an equal sense for how arms races during cooperative enterprises shape genic evolution. If we assume that arms races affect genic evolution similarly regardless of context – antagonistic or cooperative – then we would expect a signature of positive selection as a hallmark of arms races that have occurred between otherwise cooperating parties. This dissertation attempted to test this prediction using two different systems, within-family conflicts in the plant genus Arabidopsis and between-clone conflicts in the social amoeba Dictyostelium discoideum. In Chapter 1, I introduce conflict and cooperation, how arms races drive positive selection, and my study systems in more detail. Because two of my chapters have already been published, they can be found under List of Publications. In Paper I, I used sets of genes predicted by theory to be involved in within-family conflicts over maternal resource allotment to the developing seed. I tested whether these genes exhibited the telltale signature of an arms race as predicted. I found evidence that strongly supports a mother-offspring conflict scenario: genes enriched in the maternal seed coat and endosperm show elevated rates of adaptation relative to the embryo. This supports mother-offspring conflict because, as the intermediate provisioning tissue for the embryo, the endosperm is predicted to be the seed compartment in conflict with the mother plant, not the embryo. Further, I find that genes enriched in nutrient transfer tissues show elevated rates of adaptation relative to those enriched in non-transfer tissues. This further supports a mother-offspring conflict scenario over maternal resource allocation. I rule out other competing hypotheses including selection for smaller seed size in the A. thaliana lineage. In Chapter 2, I continue to focus on within-family conflict over maternal resource allocation in seeds, this time using genes that have parent-of-origin biased expression (imprinting). The kinship theory of imprinting predicts that imprinted genes are in conflict with the mother plant over maternal resource allotment. Given the coincident mother-offspring conflict over maternal resource allocation I found in Paper I, I test whether imprinted genes experience a selection pressure distinct from that. I test the prediction that an arms race between mother plant and imprinted genes has driven positive selection of genes – here imprinted genes only. If test if the signatures I find are significantly greater than that of the background tissues. I find that imprinted genes show higher rates of adaptive evolution than their background tissues. This suggests that the selection pressure on imprinted genes is specific to their imprinting status. Further, my results are consistent with a conflict scenario over maternal resource allocation. In Paper II, I switched systems to the social amoeba D. discoideum to test whether between-individual conflicts during asexual fruiting body development could lead to arms races. Using genes identified by my collaborator, I tested whether genes differentially expressed during chimeric mixing showed evidence of an arms race. We would expect a possible arms race during chimeric mixing in order to suppress cheating, or the disproportionate contribution of one genotype to spore at the expense of the other genotype that goes into sterile stalk. Consistent with an arms race scenario, I found that genes differentially expressed – both up- and down-regulated – during chimeric mixing had higher rates of adaptive evolution when compared to the genomic background. This suggests that these genes may be important in the wild for facultative strategies to prevent exploitation by other genotypes. Overall, these studies examined the effect of conflict in the context of cooperation on genic evolution: is it the same as we see with pure antagonism? This answer is that it appears to be. Not only can we use these kinds of methods to test theory about conflict genes in a robust way, but we can also use these methods to confirm the genes we identify are relevant to our organism in the wild. The latter is especially powerful for organisms like microbes or plants where observing social conflicts is not necessarily as straightforward as in animals. Further, these results suggest a strong role for kin conflict in seed development that has been largely understudied. It is the hope that this dissertation sparks a new set of kin conflict questions for researchers interested in both the proximate and ultimate factors affecting seed development.
Chair and Committee
David Queller Joan Strassmann
Justin Fay, Jonathan Myers, Kenneth Olsen,
Geist, Katherine Sylvia, "Genomic Signatures of Conflict and Cooperation in Plants and Social Amoebae" (2019). Arts & Sciences Electronic Theses and Dissertations. 1903.