Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes).

The advent of high-throughput genomic sequencing has provided unprecedented access to genome-scale data. This deluge of data has yielded new insights into phylogenetic relationships across the tree of life. However, incongruent results arising from different data partitions or from the use of different analyses have often been overlooked or insufficiently explored. In this study, we analyze the transcriptomes and plastomes of Selaginellaceae, an important land plant lineage and an ideal system to thoroughly explore phylogenomic incongruence. We aimed to reconstruct the most likely phylogenetic relationships in Selaginaceae and to examine the underlying causes of incongruence using various tests. Our major findings include: (1) phylogenomic incongruence in Selaginellaceae is quite common; (2) some plastid genes did not evolve as a linked unit, different from what is generally thought in vascular plants; (3) quantifying phylogenetic signal across different sites and genes that cause significant incongruence is necessary in phylogenomic analysis; (4) cytonuclear discordance and gene-tree conflict can be explained by incomplete lineage sorting, hybridization, and unique plastome traits; and (5) the most likely relationships "true tree" based on different datasets and phylogenetic analyses within Selaginellaceae are (Selaginoidoideae, (Boreoselaginelloideae, (Gymnogynoideae, (Sinoselaginelloideae, (Pulvinielloideae, (Lycopodioidoideae + Selaginelloideae))))). The data-analysis workflows established here might offer a framework for future phylogenomic studies for other complicated lineages.