Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using...

Phylogenomic discordance is pervasive and cannot always be resolved by increasing the amount of sequencing data alone. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are major contributors to discordance and must be accounted for to avoid misleading evolutionary interpretations. To better understand how these processes influence phylogenetic reconstruction, we conducted a comprehensive phylogenomic study in the complex genus Packera. With over 90 species and varieties, 40% of which exhibit polyploidy, aneuploidy, or other cytological complexities, Packera presents significant challenges for phylogenetic reconstruction. Given these complexities, we assessed different published paralog processing methods on the resulting evolutionary relationships and phylogenetic support of this group. We then applied three of these methods to evaluate their impact on tree topology and our understanding of Packera's evolutionary history by constructing a time-calibrated phylogeny, reconstructing historical biogeography, and testing for ancient reticulation. Phylogenetic outcomes varied based on the paralog processing method used, with no method outperforming others. Our findings highlight the large impact of orthology inference and paralog processing on phylogenomic analyses, particularly in polyploid-rich groups such as Packera, and we offer guidance on methodological impacts along with practical recommendations. We note that gaining a robust understanding of Packera's evolutionary history requires more than computational approaches alone. While technological advancements have greatly expanded our ability to analyze genomic data, effective phylogenomic research still relies on strong taxon sampling and detailed species knowledge. Without careful attention to biological context, phylogenomic studies risk misinterpreting evolutionary history and processes. By integrating genomic results with knowledge of the study system, we can begin to improve the accuracy of evolutionary reconstructions and gain deeper insights into the complex history of plant diversification.