The tree of life is a foundational concept for the biological sciences. Over the last few decades, herculean efforts by researchers have dramatically increased the available data with which we can better understand the structure and the processes that shape evolutionary relationships. However, despite these advances, new challenges have emerged. Here, I describe several projects that aim to better reconstruct a more complete view of the complexity underlying phylogenies. Specifically, I demonstrate the extensive genome conflict present in virtually all genomic datasets. Furthermore, despite this conflict, we can address several fundamental questions about macroevolution. Primarily, I will focus on the evolution of the plant clade, Caryophyllales, that include cacti, carnivores, ice plants, cushion plants, and other ecologically diverse taxa. I will also describe some of the limits to our ability to reconstruct the phylogenetic past, despite our enormous efforts.