Phylogenetic Relationships of Tilia (Malvaceae) Inferred from Multiple Nuclear Loci and Plastid Genomes

Premise of research. Tilia L. is a Eurasian–eastern North American disjunct plant genus with great economic and ecological importance. However, a robust phylogeny has not been established with a comprehensive taxon sampling and a large amount of data. Methodology. We obtained DNA sequences of plastomes and multiple nuclear loci using the anchored hybrid enrichment technique and next-generation sequencing technology. Orthologous nuclear loci were inferred using tree-based methods. Phylogenetic analyses were performed using maximum parsimony, Bayesian, and coalescence-based species tree methods. Parentages of polyploids were inferred from the nuclear and plastid phylogenies. Pivotal results. Craigia yunnanensis W.W.Smith & W.E.Evans is sister to Tilia, within which T. endochrysea Hand.-Mazz., endemic to southern China, is the earliest-diverging lineage, followed by the European species T. platyphyllos Scop. The European T. cordata Mill. and eastern Asian T. amurensis Rupr. and T. kiusiana Makino & Shirasawa form a clade, while the North American T. americana L. is most closely related to the eastern and western Asian species complex including T. chingiana Hu & Cheng, T. mandshurica Maxim., T. oliveri Szyszyl., and western Asian T. tomentosa Moench. Significant incongruence exists between nuclear and plastid phylogenies. Conclusions. Our phylogenetic results suggest that there are six distinctive lineages or species complexes in the genus, (1) T. endochrysea; (2) T. platyphyllos; (3) T. kiusiana; (4) T. cordata and T. amurensis; (5) T. chingiana, T. miqueliana, and T. oliveri; and (6) T. tomentosa and T. americana. They may be divided into two sections (Trichophilyra and Tilia) and three subsections (Tilia, Lindnera, and Trabeculares). The prevalent incongruence between nuclear and plastid phylogenies confirms the importance of ancient hybridization and introgression in the evolutionary history of the genus. Polyploid species in Eurasia and their corresponding diploid parental lineages may have formed a hybrid swarm in the region.