The Phylogeny and Evolutionary Structure of the Genus Lilium
Prepared by Bret Hansen — Lilium Species Foundation (2025 Edition)
Preface
This document represents an evolving synthesis of modern molecular research, classical taxonomy, and field observation surrounding the genus Lilium. It is intended for educational use only, integrating current genomic data with morphological and ecological context. The information presented reflects the best available understanding as of 2025 but remains subject to revision as new phylogenetic evidence emerges.
Introduction
The genus Lilium comprises approximately 100 recognized species distributed across the Northern Hemisphere—from the temperate woodlands of Europe and the Caucasus to the subtropical mountains of East Asia and the diverse habitats of North America. Long celebrated for their horticultural value and symbolic importance, lilies also provide a remarkable window into plant evolution.
Molecular studies have revealed that Lilium represents a complex radiation of lineages shaped by geography, pollinator specialization, and climatic oscillation. Plastome and nuclear analyses now recognize several well-supported sections, each corresponding to distinct biogeographic centers: Martagon (Eurasia), Pseudolirium (North America), Liriotypus (Europe–Caucasus), Archelirion (Japan), Sinomartagon (East Asia), Leucolirion (continental and insular trumpet lilies), and Daurolirion (Siberia–northern Asia).
These sections capture both deep-time divergences dating to the Miocene and more recent radiations shaped by Pleistocene climate cycles and mountain uplift. Molecular studies using plastid (cpDNA) and nuclear (ITS, GISH, RADseq) data have illuminated the complex interplay between isolation, hybridization, and adaptation that defines the genus. Though morphologically diverse—ranging from pendent Turk’s-cap lilies to outward-facing trumpets—all Lilium share a common genomic architecture and characteristic bulb morphology.
Together, the lilies of the world form one of the most geographically and ecologically versatile lineages of the monocot order Liliales. The genus is an evolutionary bridge connecting Eurasian and American floras, a record of continental drift and biotic interchange preserved in living color.
Composite Phylogenetic Topology of the Genus Lilium
Genus LILIUM (simplified)
│
├─ Section MARTAGON (Eurasian Turk’s-cap lilies)
│
├─ Section LIRIOTYPUS (European–Caucasian lilies)
│
├─ Section PSEUDOLIRIUM (North American lilies)
│
├─ Section SINOMARTAGON (Eastern Asiatic lilies)
│
├─ Section ARCHELIRION (Oriental lilies)
│
├─ Section LEUCOLIRION (Trumpet lilies of China, Ryukyu, and Philippines)
│
└─ Section DAUROLIRION (Siberian steppe lilies; basal lineage)
This mor ecomplete bipartite structure of the genus suggests an ancient boreal ancestor that radiated west and east during Miocene climatic oscillations, followed by repeated alpine isolation and trans-Beringian dispersal.
┌── Section Liriotypus
│ (Mediterranean–Caucasian lilies)
│ e.g., L. candidum, L. chalcedonicum, L. monadelphum
│
┌───────┤
│ └── Section Martagon
│ (Eurasian woodland lilies)
│ e.g., L. martagon, L. hansonii, L. tsingtauense
│
│
┌────────┤ GROUP A: Eurasian / East Asian Lineage
│ │
│ ├── Section Archelirion
│ │ (Oriental lilies of Japan)
│ │ e.g., L. auratum, L. speciosum, L. japonicum
│ │
│ └── Northern Sinomartagon Complex
│ (Northeast Asian & continental species)
│ e.g., L. lancifolium, L. leichtlinii, L. davidii, L. maculatum
│
│
────────────┤
│
│ ┌── Section Leucolirion (subsection 6a)
│ │ Continental Trumpet Lilies
│ │ e.g., L. regale, L. leucanthum, L. sargentiae
│ │
│ ├── Section Leucolirion (subsection 6b)
│ │ Island Trumpet Lilies
│ │ e.g., L. longiflorum, L. formosanum, L. philippinense
│ │
│ GROUP B: Hengduan–Himalayan / North American Lineage
│ │
│ ├── Sino-Himalayan Sinomartagon Complex
│ │ (Alpine and high-montane species)
│ │ e.g., L. nanum, L. wardii, L. saccatum, L. souliei
│ │
│ ├── Section Pseudolirium
│ │ (North American lilies)
│ │ e.g., L. columbianum, L. pardalinum, L. superbum, L. pyrophilum
│ │
│ └── Transitional Himalayan Line
│ (Bridge species between Sinomartagon and Leucolirion)
│ e.g., L. puerense, L. anhuiense
│
│
└── Outgroups / Basal taxa:
Fritillaria karelinii (sister genus)
Nomocharis-like lilies (embedded within Lilium in plastome data)
This composite topology integrates plastome data (Duan et al. 2022; Kim et al. 2019; Zhou et al. 2024) with classical morphology (Comber 1949; Stearn 1950). It demonstrates a Eurasian–American dichotomy (Groups A & B) that mirrors Miocene biogeography. Repeated evolution of floral forms (trumpet, Turk’s-cap, campanulate) under different pollination pressures.The biggest change is the breakdown of the old “Sinomartagon” section into distinct northern (A) and southern clades (B). The isolation of Leucolirion island forms as an insular radiation tied to Pleistocene land bridges. Represnting a clear maternal lineage connection from wild trumpet and Oriental species to modern hybrid cultivars
Section I — Martagon (Eurasian Turk’s-cap Lilies)
Section Martagon represents one of the most ancient lineages in the genus, occupying a broad zone from central Europe across Siberia into northeastern Asia. The group is characterized by nodding, reflexed flowers (“Turk’s-cap” form), whorled leaves, and early spring emergence—traits associated with cold temperate forest ecologies. Molecular phylogenies identify Martagon as a basal branch within the Eurasian complex, sister to Sinomartagon and Liriotypus.
ASCII Topology of Section Martagon
Section MARTAGON
│
├─ Group A: Western & Central Eurasian Core
│ ├── L. martagon (Europe, W. Siberia)
│ ├── L. hansonii (Korea, NE China, Japan)
│ └── L. tsingtauense (Manchuria; small, orange-flowered form)
│
├─ Group B: Northeastern & Altaic Lineage
│ ├── L. medeoloides (Japan to Kuriles)
│ └── L. distichum (NE Asia; Manchuria to Primorye)
│
└─ Transitional/Derived Forms
├── L. callosum (SE Asia; borderline with Sinomartagon)
└── L. cernuum (Manchuria; morphologically variable)
Summary
Martagon lilies likely diverged during the early Miocene, coinciding with Eurasian forest expansion. Their persistence across glacial–interglacial cycles suggests strong adaptation to cold and partial shade. Chromosome counts (2n=24) and low plastome divergence indicate long-term stability. The reflexed flower form and subtle fragrance point to pollination by crepuscular moths and long-tongued bees, an ancient ecological pairing that later diversified in Asia.
Section II — Pseudolirium (North American Lilies)
Section Pseudolirium encompasses the entire North American radiation of true lilies, the only New World clade within the genus Lilium. Plastome and nuclear data confirm the group’s strong monophyly, separating it cleanly from all Eurasian sections. Its members have adapted to nearly every ecological niche across the continent, from alpine meadows to coastal dunes and swampy savannas.
ASCII Topology of Section Pseudolirium
Section PSEUDOLIRIUM (North American Lilies)
│
├─ Group A: Pacific Northwest & Northern Rockies Lineage
│ ├── L. columbianum
│ ├── L. washingtonianum
│ ├── L. kelleyanum
│ ├── L. parvum
│ └── L. humboldtii
│
├─ Group B: California Coastal & Serpentine Endemics
│ ├── L. pardalinum complex
│ │ ├── ssp. pardalinum
│ │ ├── ssp. vollmeri
│ │ ├── ssp. pitkinense
│ │ └── natural hybrids with L. parvum and L. humboldtii
│ ├── L. occidentale
│ ├── L. maritimum
│ ├── L. bolanderi
│ └── L. parryi
│
├─ Group C: Eastern & Southeastern Wetland Lineage
│ ├── L. superbum
│ ├── L. pyrophilum
│ ├── L. michauxii
│ ├── L. iridollae
│ └── L. canadense
│
└─ Transitional / Outlier taxa
├── L. wigginsii
└── Hybrid swarms (L. pardalinum × L. parvum, L. humboldtii × L. parryi, L.occidentalle x columbianium & kellogii, L. bolanderi x L. rubencens)
Summary
The Pseudolirium lineage radiated from western montane ancestors during the late Miocene–Pliocene, spreading eastward as climates diversified. Hybridization is common, producing blurred species boundaries in the western complex. Pollination shifted from butterflies and bees toward hummingbirds in coastal species, a unique case of convergent evolution within Lilium. Horticulturally, this section contributed vital genetics to the Bellingham and San Gabriel hybrids, providing vivid pigmentation and resilience.
Section III — Liriotypus (European–Caucasian Lilies)
Section Liriotypus encompasses the Mediterranean–Caucasian clade of Lilium, extending from the Balkans through the Caucasus into western Asia. These lilies exhibit upright or nodding scarlet-orange flowers, often unspotted or faintly marked, with bright pigmentation and strong diurnal pollinator syndromes. Molecular phylogenies define Liriotypus as the westernmost lineage of Lilium, sister to Martagon.
ASCII Topology of Section Liriotypus
Section LIRIOTYPUS
│
├─ Eastern–Caucasian Group
│ ├── L. monadelphum
│ ├── L. szovitsianum
│ ├── L. kesselringianum
│ └── L. ledebourii
│
├─ Western–Mediterranean Group
│ ├── L. chalcedonicum
│ ├── L. albanicum
│ ├── L. carniolicum
│ ├── L. jankae
│ └── L. bulbiferum
│
└─ Outgroup / Transitional
├── L. pyrenaicum
├── L. bosniacum
└── L. ponticum
Summary
Liriotypus species represent the ancestral western pollination model, defined by strong coloration, upright habit, and day-active butterfly and bee pollination. Molecular data suggest moderate gene flow with Martagon in the Caucasus. Phylogenetically, this section anchors the western Eurasian lilies, forming a bridge between Europe’s ancient flora and Asia’s later radiations.
Section IV — Archelirion (Oriental Lilies)
Section Archelirion includes the famed Oriental lilies of Japan and adjacent regions, representing a lineage of large, fragrant, and vividly patterned species. The name derives from arche (“overarching”) and lirion (“lily”), referring to the grand floral form. Molecular evidence links Archelirion to Leucolirion, but its members form a discrete island radiation.
ASCII Topology of Section Archelirion
Section ARCHELIRION (Oriental Lilies)
│
├─ Clade A: Continental Core
│ ├── L. speciosum
│ └── L. auratum
│
├─ Clade B: Southern Island Lineage
│ ├── L. longiflorum
│ ├── L. nobilissimum
│ ├── L. ukeyuri
│ └── L. alexandrae
│
└─ Clade C: Northern Highland Forms
├── L. japonicum
└── L. rubellum
Summary
The Archelirion lilies epitomize the “Oriental” type—broad, heavily spotted flowers with strong fragrance and hybridization potential. These species likely arose through insular speciation across Japan’s mountainous archipelago. Their genetics show close affinity to Leucolirion island species, suggesting periodic introgression during Pleistocene land-bridge phases.
Section V — Sinomartagon (Asiatic Section)
The most species-rich section of Lilium, Sinomartagon encompasses a broad range of East Asian lilies, from the Himalayas to Korea and Japan. Its diversity spans upright, outward, and pendent floral forms, reflecting major pollination and ecological transitions.
ASCII Topology of Section Sinomartagon
Section SINOMARTAGON (Asiatic Lilies)
│
├─ Clade 5a: Northern Continental Group
│ ├── L. davidii
│ ├── L. lancifolium
│ ├── L. leichtlinii
│ └── L. concolor
│
├─ Clade 5b: Central Chinese / Himalayan
│ ├── L. nanum
│ ├── L. wardii
│ ├── L. lophophorum
│ ├── L. souliei
│ ├── L. amoenum
│ └── L. bakerianum
│
├─ Clade 5c: Southeastern Montane
│ ├── L. matangense
│ ├── L. huidongense
│ ├── L. jinfushanense
│ └── L. medogense
│
└─ Clade 5d: Northeastern Asian Outliers
├── L. pensylvanicum
└── L. dauricum
Summary
Plastome and ITS data reveal Sinomartagon is not fully monophyletic—its species occupy multiple plastid clades (VIII and IX), showing gene flow with adjacent sections. The group displays remarkable morphological plasticity, from small alpine bell-forms to tall, showy meadow lilies. Ecologically, Sinomartagon links the cool temperate flora of Siberia with subtropical Chinese mountain systems, embodying the genus’s evolutionary dynamism.
Section VI — Leucolirion (Trumpet Lilies of China, Ryukyu Islands, and the Philippines)
Section Leucolirion comprises the trumpet-flowered lilies—species with large, funnel-shaped blossoms and strong fragrance, inhabiting river valleys, scree slopes, and subtropical coasts. It bridges the continental mountains of western China and the island arcs of the western Pacific. Phylogenomic data separate Leucolirion into two primary lineages: a continental “6a” group and an insular “6b” radiation.
ASCII Topology of Section Leucolirion
Section LEUCOLIRION (Trumpet Lilies)
│
├─ Group 6a: Continental Trumpet Core
│ ├── L. regale
│ ├── L. leucanthum
│ ├── L. sulphureum
│ └── L. sargentiae
│
├─ Group 6b: Island Trumpet Lineage
│ ├── L. longiflorum
│ ├── L. formosanum
│ ├── L. nobilissimum
│ ├── L. philippinense
│ ├── L. alexandrae
│ └── L. ukeyuri
│
└─ Transitional / Himalayan–Southern Line
├── L. anhuiense
└── L. puerense
Summary
The continental Leucolirion lilies of Sichuan–Yunnan form the ancestral backbone of the trumpet lineage—large, white, and powerfully fragrant species adapted to arid valleys and rocky slopes. In contrast, the insular “Island Trumpet Lineage” radiated through the Ryukyu–Taiwan–Philippines arc, producing smaller, narrower-flowered species tolerant of humidity and coastal exposure. Molecular studies confirm at least two plastome lineages and ongoing introgression with Archelirion.
Horticulturally, Leucolirion supplied the maternal genomes of modern Longiflorum and Aurelian hybrids, conferring vigor, heat tolerance, and floral elegance. The section’s history reflects the shifting boundaries of land and sea during the Pleistocene, its lilies embody both continental endurance and island adaptation.
Section VII — Daurolirion (Siberian Steppe Lilies)
The smallest and most ancient branch of Lilium, Daurolirion contains cold-hardy, early-flowering species of the Siberian and Mongolian steppes. Its members are distinctive for their compact stature, grassy leaves, and upright, unspotted orange or yellow flowers—adaptations to short seasons and high sunlight.
ASCII Topology of Section Daurolirion
Section DAUROLIRION
│
├── L. dauricum
├── L. pensylvanicum
├── L. callosum
└── L. cernuum
Summary
Once included within Sinomartagon, molecular data now confirm Daurolirion as a basal sister to the main Eurasian complex, diverging approximately 15–18 million years ago. Its members are among the hardiest lilies known, persisting across permafrost margins and arid steppes. The section bridges the gap between ancient temperate forest lilies and the cold-adapted flora of northern Asia, marking the genus’s ecological frontier.
Synthesis and Evolutionary Overview
The genus Lilium represents a case study in continental radiation—its diversification mirrors the tectonic and climatic evolution of the Northern Hemisphere. Each section traces a unique trajectory shaped by isolation, climate, and pollination ecology:
-
Western Eurasia (Liriotypus & Martagon): basal diurnal syndromes, butterfly and bee pollination, stable temperate ancestry.
-
Eastern Asia (Sinomartagon & Archelirion): explosive diversification under monsoon climate; shift to nocturnal and moth pollination.
-
North America (Pseudolirium): adaptive radiation across forest, desert, and swamp ecosystems following a Miocene migration via Beringia.
-
Tibet–China Axis (Leucolirion & Daurolirion): trumpet-flowered adaptations to high altitude, strong fragrance, and cold desiccation.
Molecular studies (e.g., Duan et al. 2022; Zhou et al. 2024) reveal that hybridization and chloroplast capture have been pervasive throughout the genus, blurring strict sectional boundaries. Yet the broad structure, seven coherent biogeographic sections, remains robust. Together, they encapsulate over 20 million years of plant evolution, where geography and pollination forged one of botany’s most elegant lineages.
Concluding Remarks
Modern genomics has transformed our understanding of Lilium. Where 19th-century taxonomy relied on tepal color and form, today’s molecular phylogenies reveal a dynamic picture of divergence, convergence, and migration. The lilies’ journey—from Mediterranean slopes to Himalayan passes, from Pacific rainforests to Appalachian bogs, stands as a living chronicle of adaptation and survival.
Though the genus has inspired countless horticultural hybrids, the wild species remain the foundation of all lily diversity. Preserving these species and their habitats ensures not only the survival of genetic heritage but also the continuity of one of the planet’s most storied and beautiful genera.
Works cited
Comber, H. F. “A New Classification of the Genus Lilium.” Lily Yearbook (Royal Horticultural Society) 13 (1949): 86–105.
Stearn, W. T. A Handbook of the Genus Lilium. London: Royal Horticultural Society, 1950.
Nishikawa, T. et al. “Phylogenetic Analysis of the Genus Lilium Based on ITS Sequences.” Theoretical and Applied Genetics 102 (2001): 870–880.
Gao, Y. D., et al. “Phylogeny and Biogeography of Lilium Based on Complete Plastid Genomes.” Frontiers in Plant Science 13 (2022): 865606.
Duan, Y., et al. “Molecular Phylogeny and Biogeography of Lilium.” Botanical Journal of the Linnean Society 199 (2022): 323–341.
Kim, J. S., et al. “Plastome Evolution and Systematics in the Genus Lilium.” Plant Diversity 41 (2019): 281–293.
Zhou, T. et al. “Phylogenomic Insights into the Evolutionary History of Lilium and Related Genera.” Frontiers in Plant Science 15 (2024): 2403410.
Liang, S. Y. “New Species of Lilium from China.” Acta Phytotaxonomica Sinica 23 (1985): 392.
Wilson, E. H. The Lily of China. London: Methuen, 1919.
Douglas, D. A., et al. “Molecular Systematics of North American Lilies.” American Journal of Botany 98 (2011): 139–15