Lilium brunneum represents a newly discovered and described lily species with a limited distribution in isolated alpine regions of north-western Yunnan, China. The recognition of this new species as a distinct entity is supported by both morphological and molecular data. Furthermore, the investigation of this region, identified as a ‘hotspot’ due to its high diversity and endemicity within the genus Lilium, is anticipated to provide greater insight into the processes of speciation and the maintenance of species boundaries in this genus. Further fieldwork aimed at exploring these regions is expected to discover additional new species and therefore warrants special attention and resources.

Hengduan Mountains, Liliaceae, Lilium brunneum, Lilium souliei complex, new species

The southwestern region of China, which encompasses the Hengduan Mountains and the Tibetan Plateau, is renowned for its numerous mountain ranges. Amongst these, the Hengduan Mountains and Eastern Himalaya Mountain ranges are recognised as two of the world’s biodiversity hotspots (Marchese 2015; Yu et al. 2020). Over an extended period, beginning in the late Miocene, the Hengduan Mountains experienced complex orogeny, notably characterised by rapid uplift, resulting in a highly rugged terrain and significant environmental heterogeneity (Wang et al. 2012). This diverse ecological landscape has led to the region being described as a cradle of evolution due to its remarkable biodiversity (Lu et al. 2018). While these mountainous regions provide favorable conditions for the survival of wildlife, their remote and rugged nature poses challenges to exploration efforts. The extensive expanse of unexplored regions presents opportunities for discovering previously unidentified or unrecognised species, largely due to a lack of investigation and sampling.

The genus Lilium L., a prominent member of the monocot family Liliaceae, comprises approximately 123 species (POWO 2024; WFO 2025). This genus consists of non-climbing, bulbous herbaceous plants (Peruzzi 2016) and is distributed across mid to high latitudes of the Northern Hemisphere (Liang and Tamura 2000; Skinner 2002). Extant species are primarily concentrated in temperate regions of the Northern Hemisphere, while East Asia hosts a notably greater diversity of Lilium species compared to Central Asia, Europe and North America (Gong et al. 2017; Dhiman et al. 2020). The Hengduan Mountains and the Himalayas are considered to be the central distribution area of Lilium (De Jong 1974; Du et al. 2014, 2017). However, the taxonomic status of several species in the Hengduan Mountain region remains unclear and requires clarification.

In our previous studies focusing on this region – particularly upon members of the former genus Nomocharis Franchet – we discovered that campanulate-flowered species, such as Lilium souliei (Franch.) Sealy, and its close relatives, are nested within the Nomocharis-clade (Gao et al. 2013b, 2015; Yuan and Gao 2024). This finding reveals unexpected relationships given the significant differences in phenotypic characteristics. These alpine lilies, characterised by their dwarf habit and bell-shaped, nodding flowers, include L. souliei, L. saccatum S.Yun Liang, L. medogense S.Yun Liang, L. paradoxum Stearn and L. georgei (W.E. Evans) Sealy. Several of these species were only described in the last century, with few records existing other than the type specimens, resulting in potential taxonomic confusion within this group. Consequently, we will refer to this group as the L. souliei complex for brevity.

According to field records accumulated and verified by the authors, the L. souliei complex is distributed from north-western Yunnan Province to south-eastern Tibet, traversing the Hengduan and extending into the Eastern Himalaya Mountain ranges (Dhiman et al. 2020). Amongst these, L. souliei has the broadest distribution, thriving in alpine grass and shrub habitats at elevations of 2800–4000 m above sea level (Wu et al. 2012), primarily in the central part of the Hengduan Mountains. L. saccatum is predominantly found in the shrub and grassland slopes of the Eastern Himalaya at approximately 3900 m (Liang 1987). In contrast, L. paradoxum and L. medogense exhibit much narrower distributions. L. paradoxum is endemic to southeastern Tibet, with limited populations at around 3500 m (Stearn 1956), while L. medogense is confined to alpine wetland habitats around 3600 m (Liang 1985) in Motuo (Medog) County, Xizang, China (Fig. 1).

Figure 1. 

Morphological characteristics and geographic distribution of the Lilium souliei complex. (L. georgei, http://specimens.kew.org/herbarium/K003949823).

With further investigations in the Hengduan Mountains and surrounding areas, coupled with advancements in molecular phylogenetics, we recognise that this is an opportune time to clarify the status of several monophyletic yet taxonomically ambiguous lily groups in the region. In this context, the L. souliei complex serves as an exemplary focus for detailed investigation and taxonomic revision. Through a comprehensive review of the literature and examination of herbarium specimens, the author, Gao, proposes that L. georgei (W.E. Evans) Sealy, first discovered by George Forrest in 1924 along the Myanmar-China border (Sealy 1950), also belongs to this complex.

In the summers of 2023 and 2024, the authors undertook two consecutive field trips to the remote areas of the Gaoligong Mountains in Yunnan (mid to southern part of the Hengduan Mountains), aiming to rediscover this lily and collect additional information and materials since no records exist beyond those documented by Forrest. Unfortunately, L. georgei was not located, as access to the type locality is currently restricted; however, a new species belonging to this group was discovered and is described in this paper.

In the present study, we utilise both morphological and molecular data to elucidate the status and phylogenetic position of the putative new species by comparing its morphology with that of closely related taxa. Simultaneously, this study aims to provide a more informative overview of the L. souliei complex, highlighting distinguishing characteristics amongst species and clarifying geographic distribution patterns. We hope this research will illuminate the diversity of lilies in the Hengduan Mountains and adjacent areas, contributing to and enriching the catalogue of the genus Lilium.

The overall size of Lilium brunneum is significantly smaller when compared to L. medogense and L. paradoxum. Based on specimen measurements, the average plant height and corolla width for L. medogense are 45.6 cm and 5.6 cm, respectively, while those of L. paradoxum are 40.5 cm and 5.5 cm. In contrast, L. brunneum displays a distinctly shorter average plant height of 22.3 cm and a corolla width of only 2.0 cm (Table 1, rows 5 and 9). Notably, the former two species can be easily distinguished within the L. souliei complex owing to their significantly larger sizes compared to the other members. Furthermore, both species exhibit whorled leaves (typically 3–5 whorls), a characteristic absent in the remaining members of the complex. Specifically, L. medogense is distinguished by its bright yellow flowers, making it particularly prominent amongst the complex, as the other members typically present more or less purplish hues. Consequently, these two species were not included in further fine-scale comparisons below, as they cannot be confused with the other members of the complex.

Regarding the remaining members, L. brunneum exhibits several distinguishing characteristics when compared to L. souliei, L. saccatum and L. georgei. Principal Component Analysis (PCA) based on morphological measurements from multiple individuals demonstrates clear boundaries between these species (Fig. 4). As a predominant member within the complex, L. souliei is positioned in the upper-left quadrant and displays wide morphological variation (Fig. 4), likely associated with its extensive geographic distribution (Fig. 1) facilitating a broad range of variations in response to niche diversity. In comparison to L. brunneum, L. souliei is characterised by longer pedicels (measured from the flower base to the bract, Fig. 3D), a greater distance between the filaments and ovary (Fig. 3G) and purple-coloured tepals. The PCA plot indicates a complete lack of overlap between L. brunneum and L. georgei (Fig. 4). Although the collection sites for L. brunneum are geographically closest to those of L. georgei (Fig. 1), the latter possesses a larger habit, particularly in flower size (Fig. 5B, Table 1), and exhibits more striking colouration, as is noted in the description on the collection label of L. georgei, where Forrest wrote: ‘flowers that are soft blue-purple throughout, deepest on the exterior’ (G. Forrest 24772, https://data.rbge.org.uk/herb/E00381818). These differences collectively support the clear delineation of these two species.

While L. brunneum is situated closest to L. saccatum in the PCA plot, they remain distinctly isolated without any overlap (Fig. 4). The principal components contributing to this separation are primarily flower organ size (e.g. dimensions O). A detailed comparison between L. saccatum and L. brunneum can also be found in Table 1 and Suppl. material 1. In addition to these differences, L. brunneum exhibits lighter-coloured outer tepal bases (Figs 2C, 3C) and features a pale green style (Fig. 3F), whereas the style of L. saccatum is dark purplish-black (Fig. 3H). Notably, their geographic distributions are not connected with, but rather widely separated from, that of L. souliei (Fig. 1).

The molecular phylogenetic analysis also supports the distinct status of the new species. While the nuclear ITS region has certain limitations due to its relatively short length (approximately 630 bp), it remains sufficient for species delimitation, although it lacks the resolution needed to clarify detailed relationships amongst selected taxa (Yao et al. 2010; Zhang et al. 2022). In the ITS phylogenetic tree, L. medogense, L. saccatum, L. paradoxum, L. souliei, L. brunneum and L. yapingense Y.D. Gao & X.J. He constitute a robustly supported clade (PP = 0.97, BS = 92%, Fig. 6). As previously mentioned, this clade contains several parallel sub-clades due to insufficient informative sites; however, the separation of each recognised species remains clear. Amongst these species, individuals from the two populations of L. brunneum form a distinct clade that is allied with L. souliei, L. yapingense and a clade consisting of L. paradoxum, L. medogense and L. saccatum (Fig. 6). The convergence of the latter three species is supported by considerable evidence (PP = 0.95, BS = 80%), suggesting a closer relationship compared to the other members. The clustering of L. yapingense within this clade indicates that this dwarf lily, characterised by its whitish to pinkish campanulate flowers, as described by Gao et al. (2013a), may share a common ancestry with the members of the L. souliei complex.

In the chloroplast phylogenetic inferences, the tree topologies generated by Bayesian inference (BI) and maximum likelihood (ML) are congruent. The chloroplast consensus tree demonstrates that the two populations of L. brunneum cluster together, forming a sister clade to L. paradoxum, with moderate support; this confidence significantly increases upon the inclusion of L. saccatum (PP = 0.99, BS = 80%, Fig. 7). Moreover, all members of the L. souliei complex are found clustered within the same clade with robust support (PP = 0.99, BS = 100%); however, two species from the former genus Nomocharis are also included and positioned as sisters to L. souliei. Consequently, under chloroplast phylogenetic analysis, the complex is not monophyletic, revealing incongruence between nuclear ITS and plastid genome data.

According to prior research, such incongruences are common within the genus Lilium and the most plausible explanation may involve genetic introgression, with the chloroplast tree providing a more accurate reflection of geographic relationships (Gao et al. 2013b, 2015). For instance, L. souliei, which encompasses the broadest distribution range within the complex, overlaps geographically with L. apertum Franch. and L. saluenense (Balf. f.) S.Y. Liang, which are sister species on the chloroplast tree, receiving strong support (PP = 1.00, BS = 100%). Similarly, although L. taliense Franch. is classified within the Sinomartagon-clade in the nuclear ITS phylogeny, it clusters with species from the Nomocharis-clade in the chloroplast tree due to sympatric distributions, likely resulting from introgression via interspecific hybridisation. In fact, Lilium species distributed throughout the Hengduan Mountains region have been consistently found clustered within a single clade in both previous and current plastid-based phylogenetic trees (Gao et al. 2015; Duan et al. 2022; Yuan and Gao 2024). This pattern suggests that substantial gene flow has occurred or is ongoing amongst these species within this biodiversity hotspot.

While gene flow can be detected amongst species that are partially sympatric and distributed in the Hengduan Mountains, it is unexpected that several sympatric Lilium species exhibit no evidence of gene exchange. For example, the new species coexists with L. yapingense, which, according to the nuclear phylogeny, is quite closely related to the entire L. souliei complex. However, there is no evidence of interaction between them at the chloroplast genome level, which is unexpected, as introgression would typically be anticipated in such cases. Comparative studies on three gradient-distributed lilies in the same region have shown asymmetric gene flow amongst species, with shared chloroplast genome types (Gao et al. 2020). Although L. brunneum is found near to L. yapingense, they appear to lack gene exchange, as evidenced by the intact nature of their chloroplast genomes in the plastid phylogenetic tree, a surprising observation considering that they share the same locality and blooming period. The latter aspect has been identified as a critical factor influencing the isolation of gene exchanges amongst lilies (Gao et al. 2020; Feng et al. 2025). This scenario indicates the presence of unknown mechanisms that prevent hybridisation amongst these species, which are likely associated with the high levels of endemism observed in this region.

Further examples of this phenomenon can also be observed within the complex itself. While the distribution ranges of L. saccatum and L. medogense are geographically proximate (Fig. 1), their phylogenetic relationship is relatively distant. L. saccatum thrives in shrubby grasslands on mountain slopes at elevations exceeding 3600 m, whereas L. medogense is found in fissured clearings at the edges of alpine wetlands interspersed with fir forests at lower elevations. This ecological disparity may suggest the presence of isolating mechanisms beyond niche diversification and habitat isolation; for instance, differences in floral structures potentially driven by their respective pollinator assemblages (Levin 1978; Baack et al. 2015; Liu et al. 2019) may contribute to the maintenance of species boundaries, thereby restricting gene flow amongst these sympatric lilies and further enhancing biodiversity and endemism within the Hengduan Mountains region.

In conclusion, both morphological and molecular evidence confirm that L. brunneum is a distinct new species. This finding enhances our understanding of L. souliei and its closely related species, further enriching the catalog of lilies in the Hengduan Mountains region. Additionally, this research contributes to our understanding of species boundaries and the mechanisms contributing to the high levels of endemism observed in this area. Future efforts, including field studies, systematic research with additional data (such as population-level research utilising next-generation sequencing) and analyses of niche diversity, are needed to elucidate the possible undetected species, their origins and the mechanisms maintaining species boundaries.

The authors express their gratitude to Professor Xin-Fen Gao, Dr. Wen-Bin Ju, Mr. Heng-Ning Deng, Jun-Yi Zhang and Ms. Yu-Mei Yuan of the Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Associate Professor Pan Li from Zhejiang University for their invaluable assistance with sample collection. Special thanks are given to Mr. Melvyn Herbert for his contributions to material collection and linguistic refinement of the manuscript.