The field of phylogenetics is drastically changing with the increased use of multi-locus and genomic data. A major challenge with this expansion is that conflicting genealogical histories often exist in different genes, and the answer is not as simple as increasing the amount of data. These differing gene histories can cause gene tree discordance that occurs when phylogenies obtained from individual gene trees differ among themselves and from the species tree, potentially leading to incongruent tree topologies. Underlying discordance and uncertainty are constantly seen in phylogenomic studies and are repeatedly explained as results of biological processes including gene flow, incomplete lineage sorting (ILS), or paralogous sequence duplication and loss. The North American endemic genus Packera Á. Löve & D. Löve (Asteraceae) is estimated to have about 64 species and varieties and is known to be complicated by hybridization, polyploidy, and reticulation, making resolving evolutionary relationships in the group complex. Previous phylogenomic work on the group has shown that there are high levels of underlying discordance, with only 49% of the gene trees represented in the final species tree, and the remaining 51% of the gene trees show differing evolutionary relationships. Additionally, 51% of internal nodes were not highly supported. Thus, to obtain a better understanding of potential gene flow and its effect on Packera, we investigated the causes and consequences of nuclear discordance, including evolutionary processes of ILS and gene flow, to understand how they influence the phylogenetic patterns seen in Packera. To do this, we compared the topology and support values of Packera phylogenies resulting from the normal paralog selection processes defined by HybPiper, along with other paralog selection or pruning methods. We then investigated whether pruning the paralogs instead of performing a selection process affected the topology and support of our phylogeny. To investigate hybridization and its effect on the species relationships in our tree, we used likelihood methods to infer phylogenetic networks to find any evidence of gene flow among species lineages in this complicated genus. We anticipate this work will provide further insight into how underlying biological processes can influence species relationships and levels of discordance within phylogenomic studies.