Investigating whether epistasis constrained Threonine Deaminase 2’s novel function evolution in Solanaceae, and how selfing affects transposable element dynamics in Ipomoea

Abstract

Gene duplication is one of the primary sources of new genes in evolution, and, on rare occasions, novel functions can arise from newly duplicated genes. Much attention has been paid to the evolutionary mechanisms of novelty through gene duplication, which could take from dozens of years to dozens of millions of years. However, it remains understudied what factors could prolong this process. One possible explanation for a prolonged process generating novel functions in a copy is that the novel function needs many additive substitutions to occur. Alternatively, the number of function-switching substitutions could be few, but their effects are epistatic and require other neutral permissive substitutions to be fixed by drift first, which could take a long time. A third possibility is that selection pressure on the novel function temporarily fluctuates, and the novel function could be lost through maladaptive substitution accumulation when selection is relaxed, requiring more substitutions to leverage the effects of these maladaptive substitutions when selection resumes. In the first part of my dissertation, I examine the relative contributions of these constraining factors, especially epistasis, to the prolonged adaptive evolution of Threonine Deaminase copy 2 (TD2) in the family Solanaceae. TD2 in tomato (TD2S) is reported to have evolved a novel function over 30-50 million years of adaptive evolution following duplication. The novel function constitutes two aspects that are considered adaptive: 1) having a higher catalytic efficiency, and 2) being resistant to protease. To test whether epistasis prolongs TD2S’s evolution of catalytic efficiency, I identify three key substitutions that could significantly enhance its catalytic efficiency and examine whether their effects depend on the presence of other substitutions. To test whether epistasis prolongs TD2S’s evolution of protease resistance, I divide its sequence into three segments and design a dozen chimeric constructs by fusing one or two segments of TD2 with two or one segments of TD1, which is non-resistant. I quantitatively examine their protease resistance and ask whether any segment of TD2 could confer resistance regardless of the presence of other segments in the chimeric constructs. I find that epistasis, especially high-order epistasis, is involved in TD2S’s evolution in both catalytic efficiency and protease resistance. I then compare the temporal patterns of when key substitutions and potential permissive and epistatic resistance-enhancing substitutions occur in the phylogeny. I find that this pattern matches the expectation of adaptive evolution constrained by epistasis, as earlier data suggests. I also find that fluctuating selection may have constrained TD2S’s resistance evolution, but of less importance than epistasis. Together, these results suggest that epistasis and potential fluctuating selection prolonged TD2S’s adaptive evolution.The transition from outcrossing to selfing is one of the most important evolutionary transitions in plants, which is well studied to be accompanied by changes in various phenotypic traits and genomic features. Many theoretical studies have predicted how these traits and features would change after the transition, and many empirical studies have verified most of these predictions. Among genomic features, one that is less studied and is expected to behave differently under different models when the transition occurs is transposable elements (TEs). The two major models on how a transition from outcrossing to selfing affects TEs’ dynamics are 1) the ectopic recombination model and 2) the deleterious insertion model. The first model predicts that selfers will have more TE in their genomes than their closely related outcrossers, because increased homozygosity in selfers could reduce TE-induced ectopic recombination. The second model predicts that selfers will have less TE than outcrossers because selfers have smaller genomes and stronger background selection, which will help purge deleterious TEs more quickly. In the second part of my dissertation, I examine which model better describes the TE differences in the predominantly selfing species Ipomoea lacunosa (LAC) and its closely related predominantly outcrossing species I. trifida (TRIF). To do so, I annotated the TE content, identified all LTR-RT elements, and calculated the average TE-gene distance and insertion age of all intact LTR-RTs in the two genomes. I find that LAC has higher TE content, fewer solo-LTRs, and shorter average distance to genes than TRIF. These results suggest that the ectopic recombination model, not the deleterious insertion model, better describes changes in TE activity in LAC than TRIF.