Packera discordance

To obtain a better understanding of potential gene flow and its effect on genus Packera A. Love & D. Love (Asteraceae), 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.