In this thesis, I investigate the evolution of betalains in Caryophyllales. Betalains are a group of red and yellow pigments, which in plants occur only in the order Caryophyllales. Here, betalains replace the otherwise ubiquitous anthocyanin pigments, and the two pigment types appear mutually exclusive. Some lineages of Caryophyllales maintain anthocyanins, and the distribution of the two pigments with respect to relationships within the order suggests a complex evolutionary history, that allows for the possibility of repeated convergent shifts from anthocyanin to betalain pigmentation.

First, I begin by framing my thesis with a review of the concepts of convergence and parallelism, including the connection between these terms and concepts of adaptation and constraint. I then discuss convergence at the level of molecular sequence data, and explore ideas of convergence at multiple hierarchies and their integration in the evolution of complex traits.

Second, I conduct a reanalysis of the evolution of betalains, using the latest phylogenomic hypothesis of Caryophyllales relationships and up to date pigmentation data. I show that these data support up to four origins of betalains. I re-examine the phylogeny of DODA, a key gene in the betalain biosynthesis pathway, and show that the distribution of betalain-related enzyme activity is consistent with multiple origins of high activity following repeated gene duplications, consistent with inferred origins of betalains. I argue that multiple transitions to high activity in this enzyme have facilitated multiple origins of betalain pigmentation.

Third, given this scenario, I assess the molecular signal for convergent evolution in DODA lineage. I reconstruct ancestral sequences and show that experimental testing of their activity supports multiple origins of high activity. I infer historical substitutions and show that a complex history of convergent molecular evolution has occurred, across multiple branches of the gene tree and in different order depending on origin. I support my findings with a suite of statistical methods and discuss how these approaches differ and how they can be used to interrogate betalain evolutionary history.

Fourth, I explore convergence at the level of genome structure. I sequence and assemble three new Caryophyllales genomes with long reads. Two key genes of the betalain pathway are clustered in the Beta vulgaris genome, and I use comparative genomics to explore the evolutionary history of this clustering. Strikingly, I show that a pattern dispersed synteny of betalain-implicated DODA paralogues, has occurred multiple times via different mechanisms. I discuss the potential significance of this finding with respect to syntenic evolution and the evolution of betalains.

Finally, I use comparative expression to explore betalain origins. I design pigment induction experiments in diverse taxa representing multiple origins and measure associated gene expression with RNA-seq. I interrogate these data with coexpression techniques and provide new insights into comparative gene networks and betalain regulation.