Premise of research. Tilia 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 is sister to Tilia, within which T. endochrysea endemic to southern China is the earliest lineage diverging followed by the European species T. platyphyllos. The European T. cordata and eastern Asian T. amurensis and T. kiusiana form a clade, while the North American T. americana is most closely related to the eastern and western Asian species complex including T. chingiana, T. mandshurica, T. oliver, and western Asian T. tomentosa. 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 including 1) T. endochrysea, 2) T. platyphyllos, 3) T. kiusiana, 4) T. cordata and T. amurensis, 5) T. chingiana, T. miqueliana, 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 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.

Anchored hybrid enrichment method was used to generate the data and the data set has been processed.