Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Abstract

Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe. We sequenced 45 Liliaceae plastomes and combined them with publicly available data (for a total of 139 plastomes) to explore the systematics, origin, divergence, and evolution of Lilieae. Our taxon sampling covers all ten sections of Lilium, all Cardiocrinum species, three Notholirion species, and major phylogenetic clades of Fritillaria. Our phylogenetic analysis confirms the monophyly of major sections/subgenera of Lilium and Fritillaria with strong support. We dated the origin of Lilieae to the Eocene, with genera and species radiations inferred to have occurred in the Miocene. The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau (QTP): the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe. Ancestral-state reconstructions of the bulb component number (including bulblets and scales) show a strong correlation with the genus-level phylogenetic diversity in Lilieae. They also predict that the most recent common ancestor of Lilieae had bulbs with numerous bulblets. Based on these observations, we predicted that climatic oscillations associated with the QTP uplift played an important role in the evolution of the Lilieae bulb. Our findings provide a well-supported picture of evolutionary relationships and a useful framework for understanding the pathway of bulb evolution within Lilieae, contributing to a better understanding of the evolutionary history of lilies.

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

“…We observed L. brownii of Comber’s Archelirion far from the other two species of Archelirion ) L. japonicum and L. speciosum ( and close to the two species of Leucolirion ( L. formosanum and L. longiflorum ). Similarly, Li et al 9 classified L. brownii alongside L. formosanum and L. longiflorum in a genus-level study of the Liliaceae family's evolution. As our results warn, and with the help of ITS-dataset classification 92 , 93 , now with the approval of cp genome-based classification, L. brownii can be moved from the Archelirion to the Leucolirion.…”

“…Liliaceae contains 15 genera and around 900 species 7 . The family’s classification has shifted significantly as a result of modern molecular phylogenetic analysis 1 , 8 , 9 . Lilium is a genus in Liliaceae, which contains circa 100 species 10 .…”

The phylogeny of Seseli (Apiaceae, Apioideae): insights from molecular and morphological data

“…Plastomes have been widely used in studying the phylogeny of Apiaceae, Ranunculaceae Juss., Saxifragaceae Juss., Allium L., Liliaceae Juss., etc. [27][28][29][30][31][32][33][34][35][36][37]. However, there has been no study on the phylogeny of Seseli based on plastomes and therefore there is ample opportunity to investigate phylogenetic and taxonomic issues of Seseli using plastomes.…”

Evidence from Phylogenomics and Morphology Provide Insights into the Phylogeny, Plastome Evolution, and Taxonomy of Kitagawia

“…These characteristics have led to their widespread use in analyses of phylogenetic relationships [ 38 , 39 , 40 ]. Plastome sequences can effectively improve the support and resolution of phylogenies at the generic level and beyond [ 41 , 42 , 43 , 44 , 45 , 46 ]. In particular, the plastome-based phylogeny performed by Liu et al [ 47 ] constructed a robust phylogenetic framework for Peucedanum sensu lato and provided a valuable reference to our investigation of Kitagawia .…”