Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Abstract

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Keywords: Asian monsoon; Climatic changes; Distribution range; Evolutionary complexity; Qinghai-Tibet Plateau (QTP); Radiative diversification; Species diversity.

Fig. 1

Maximum likelihood (ML) phylogeny of Lilium inferred from complete plastome DNA sequences. Numbers at nodes represent maximum likelihood bootstrap (BS) percentages. An asterisk indicates that BP is 100. The sectional treatments of Comber (1949) and the section Nomocharis defined by Gao et al. (2012) are indicated on the right. Species with newly sequenced plastomes are highlighted in red.

Fig. 2

Molecular dating in Lilium based on complete plastome DNA sequences. Numbers above/under the tree branches represent mean divergent ages and 95% confidence interval of divergence times. Red arrows indicate the calibration points for the molecular dating (see text). Divergence time and the timeline are indicated in mega-annum (Ma).

Fig. 3

Lineage through time (LTT) plot analysis.

Fig. 4

Bayesian Analysis of Macro-evolutionary Mixtures (BAMM) based on the time-calibrated maximum clade credibility tree from BEAST. Colors on the branch represent the mean of the posterior density of net diversification rate (speciation rate minus extinction rate).

Fig. 5

Reconstruction of ancestral area of Lilium using S-DIVA analysis inferred from plastid tree. Lilium species assigned to five areas based on their current distributions: A. Southwest China and QTP, B. East, Central, South China and northern Indochina, C. North China and Northeast Asia, D. Central Asia and Europe, E. North America.

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