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

doi:10.1016/j.pld.2023.07.009

. 2023 Aug 3;46(2):219-228.

doi: 10.1016/j.pld.2023.07.009. eCollection 2024 Mar.

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

Nian Zhou^{1

2}, Ke Miao^{1

2}, Changkun Liu³, Linbo Jia¹, Jinjin Hu¹, Yongjiang Huang¹, Yunheng Ji^{1

4}

Affiliations

¹ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
² University of Chinese Academy of Sciences, Beijing 100049, China.
³ Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China.
⁴ Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

PMID: 38807906
PMCID: PMC11128834
DOI: 10.1016/j.pld.2023.07.009

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

Nian Zhou et al. Plant Divers. 2023.

. 2023 Aug 3;46(2):219-228.

doi: 10.1016/j.pld.2023.07.009. eCollection 2024 Mar.

Authors

Nian Zhou^{1

2}, Ke Miao^{1

2}, Changkun Liu³, Linbo Jia¹, Jinjin Hu¹, Yongjiang Huang¹, Yunheng Ji^{1

4}

Affiliations

¹ CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
² University of Chinese Academy of Sciences, Beijing 100049, China.
³ Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China.
⁴ Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

PMID: 38807906
PMCID: PMC11128834
DOI: 10.1016/j.pld.2023.07.009

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.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

**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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References

1. Adams J.S. Springer Berlin; Heidelberg: 2009. Species Richness: Patterns in the Diversity of Life.
1. Allen A.P., Gillooly J.F., Savage V.M., et al. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U.S.A. 2006;103:9130–9135. - PMC - PubMed
1. An Z.S., Kutzbach J.E., Prell W.L., et al. Evolution of Asian monsoons and phased uplift of the Himalaya–Tibetan plateau since Late Miocene times. Nature. 2001;411:62–66. - PubMed
1. Baranova M. A synopsis of the system of the genus Lilium (Liliaceae) Bot. Zh. 1988;73:1319–1329.
1. Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. - PMC - PubMed

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[1] Adams J.S. Springer Berlin; Heidelberg: 2009. Species Richness: Patterns in the Diversity of Life.

[2] Adams J.S. Springer Berlin; Heidelberg: 2009. Species Richness: Patterns in the Diversity of Life.

[3] Allen A.P., Gillooly J.F., Savage V.M., et al. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U.S.A. 2006;103:9130–9135. - PMC - PubMed

[4] Allen A.P., Gillooly J.F., Savage V.M., et al. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U.S.A. 2006;103:9130–9135. - PMC - PubMed

[5] An Z.S., Kutzbach J.E., Prell W.L., et al. Evolution of Asian monsoons and phased uplift of the Himalaya–Tibetan plateau since Late Miocene times. Nature. 2001;411:62–66. - PubMed

[6] An Z.S., Kutzbach J.E., Prell W.L., et al. Evolution of Asian monsoons and phased uplift of the Himalaya–Tibetan plateau since Late Miocene times. Nature. 2001;411:62–66. - PubMed

[7] Baranova M. A synopsis of the system of the genus Lilium (Liliaceae) Bot. Zh. 1988;73:1319–1329.

[8] Baranova M. A synopsis of the system of the genus Lilium (Liliaceae) Bot. Zh. 1988;73:1319–1329.

[9] Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. - PMC - PubMed

[10] Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

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