Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)

doi:10.1016/j.pld.2025.09.006

Plant Diversity ›› 2026, Vol. 48 ›› Issue (02): 231-245.DOI: 10.1016/j.pld.2025.09.006

Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)

Deng-Feng Xie^a, Yi-Yang Zhang^a,b, Jing Cai^a,c, Rui-Yu Cheng^a, Yuan Wang^a, Jin-Bo Tan^a, Yan Yu^a, Xing-Jin He^a, Song-Dong Zhou^a

a. Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China;
b. Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China;
c. College of Ecology, Lanzhou University, Lanzhou 730000, Gansu, China

收稿日期:2025-05-01 修回日期:2025-09-08 出版日期:2026-03-25 发布日期:2026-05-19
通讯作者: Song-Dong Zhou,E-mail:zsd@scu.edu.cn
基金资助:
We thank Dr. Minjie Li (College of Ecology, Lanzhou university) for her valuable suggestions in preparing this manuscript. This work was supported by the National Natural Science Foundation of China (Grant Nos. 32100180, 32470216, 32170209), the China Postdoctoral Science Foundation (2020M683303), the Sichuan Science and Technology Program (Grant Number 2025ZNSFSC1129), the Key project at central government level: the ability establishment of sustainable use for valuable Chinese medicine resources (2060302).

Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)

Deng-Feng Xie^a, Yi-Yang Zhang^a,b, Jing Cai^a,c, Rui-Yu Cheng^a, Yuan Wang^a, Jin-Bo Tan^a, Yan Yu^a, Xing-Jin He^a, Song-Dong Zhou^a

a. Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, China;
b. Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China;
c. College of Ecology, Lanzhou University, Lanzhou 730000, Gansu, China

Received:2025-05-01 Revised:2025-09-08 Online:2026-03-25 Published:2026-05-19
Contact: Song-Dong Zhou,E-mail:zsd@scu.edu.cn
Supported by:
We thank Dr. Minjie Li (College of Ecology, Lanzhou university) for her valuable suggestions in preparing this manuscript. This work was supported by the National Natural Science Foundation of China (Grant Nos. 32100180, 32470216, 32170209), the China Postdoctoral Science Foundation (2020M683303), the Sichuan Science and Technology Program (Grant Number 2025ZNSFSC1129), the Key project at central government level: the ability establishment of sustainable use for valuable Chinese medicine resources (2060302).

摘要/Abstract

摘要： Urophysa (Ranunculaceae) are plants endemic to the limestone regions of southern China, representing an attractive model for studying species differentiation, endangerment, and adaptive evolution in karst environments. Here, we assembled a chromosome-level genome of U. rockii, and re-sequenced 97 individuals of two Urophysa species. The final genome size was 303.21 Mb with a heterozygosity level of approximately 0.26%. Demographic analyses revealed that U. rockii diverged from U. henryi around 5.95 million years ago, dramatic orogenies and climatic shifts in the Hengduan Mountain (HDM) during the Late Miocene to Pleistocene enhanced population divergence and accelerated allopatric speciation. Extremely low genetic diversity was detected in U. rockii, particularly in the populations CXS and PZ (8.7 × 10^-5 and 9.6 × 10^-5). Long-term bottleneck effects, limited gene flow, habitat specialization and severe inbreeding collectively contributed to its endangerment status. Genomic scan (top 5% F_ST and π ratio) of Urophysa species identified 257 selected genes linked to karst adaptation. Complementary physiological experiments and transcriptome analyses further detected multiple candidate genes under positive selection and expansion (e.g., TPC1, PTR/POT, and CAX3). Maintaining cell wall integrity, regulating ion absorption and excretion, and sequestering excess ions into organelles (e.g., vacuole and mitochondrion) are key survival strategies for Urophysa species in harsh limestone rocky environments. Our findings elucidate the evolutionary patterns and mechanisms underlying species adaptation to karst ecosystems, and identify key drivers of endangerment within such ecologically specialized habitats.

关键词: Urophysa, Demographic history, Species divergence, Endangerment, Karst adaptation

Abstract: Urophysa (Ranunculaceae) are plants endemic to the limestone regions of southern China, representing an attractive model for studying species differentiation, endangerment, and adaptive evolution in karst environments. Here, we assembled a chromosome-level genome of U. rockii, and re-sequenced 97 individuals of two Urophysa species. The final genome size was 303.21 Mb with a heterozygosity level of approximately 0.26%. Demographic analyses revealed that U. rockii diverged from U. henryi around 5.95 million years ago, dramatic orogenies and climatic shifts in the Hengduan Mountain (HDM) during the Late Miocene to Pleistocene enhanced population divergence and accelerated allopatric speciation. Extremely low genetic diversity was detected in U. rockii, particularly in the populations CXS and PZ (8.7 × 10^-5 and 9.6 × 10^-5). Long-term bottleneck effects, limited gene flow, habitat specialization and severe inbreeding collectively contributed to its endangerment status. Genomic scan (top 5% F_ST and π ratio) of Urophysa species identified 257 selected genes linked to karst adaptation. Complementary physiological experiments and transcriptome analyses further detected multiple candidate genes under positive selection and expansion (e.g., TPC1, PTR/POT, and CAX3). Maintaining cell wall integrity, regulating ion absorption and excretion, and sequestering excess ions into organelles (e.g., vacuole and mitochondrion) are key survival strategies for Urophysa species in harsh limestone rocky environments. Our findings elucidate the evolutionary patterns and mechanisms underlying species adaptation to karst ecosystems, and identify key drivers of endangerment within such ecologically specialized habitats.

Key words: Urophysa, Demographic history, Species divergence, Endangerment, Karst adaptation

Deng-Feng Xie, Yi-Yang Zhang, Jing Cai, Rui-Yu Cheng, Yuan Wang, Jin-Bo Tan, Yan Yu, Xing-Jin He, Song-Dong Zhou. Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)[J]. Plant Diversity, 2026, 48(02): 231-245.

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Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)

Speciation, endangerment and adaptation in limestone rocky environment of Urophysa (Ranunculaceae)

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