Phylotranscriptomics reveals conflicts of deep nodes in Saxifragales

Saxifragales comprises 15 families in five well-supported clades: Paeoniaceae, Peridiscaceae, the woody clade, Cynomoriaceae, and the core Saxifragales. Relationships among these groups-particularly the placements of Paeoniaceae and Cynomoriaceae, and family-level relationships within the woody clade-remain uncertain. Here, we analyzed transcriptomes from 88 species (13 families) and plastomes from 14 families (with limited plastid genes retained in the parasitic Cynomoriaceae). Phylogenomic analyses of 1,113 BUSCO single-copy nuclear genes and 78 plastid genes consistently recovered Paeoniaceae as sister to the woody clade (Paeoniaceae + Woody clade, PWC) and supported Cynomoriaceae as sister to the core Saxifragales (Cynomoriaceae + Core Saxifragales, CCS). We detected widespread phylogenetic conflict and cytonuclear discordance, largely driven by pervasive gene flow and, to a lesser extent, incomplete lineage sorting (ILS). Gene tree error contributed to the unstable placement of Cynomoriaceae, while ILS dominated conflicts involving Cercidiphyllaceae. Future work integrating chromosome-level genomes and karyotype evolution may clarify woody clade relationships, and account for horizontal gene transfer in Cynomoriaceae.