Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex

doi:10.1016/j.pld.2025.12.004

Plant Diversity ›› 2026, Vol. 48 ›› Issue (03): 474-486.DOI: 10.1016/j.pld.2025.12.004

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Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex

Hum Kala Rana^a,b, Santosh Kumar Rana^c, Jacob B. Landis^d, Hang Sun^a, Dong Luo^a,e

a Yunnan Key Laboratory for Plant Diversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b University of Chinese Academy of Sciences, Beijing 100049, China;
c Department of Chemical and Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA;
d School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA;
e State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China

Received:2025-07-30 Revised:2025-12-04 Online:2026-06-10 Published:2026-05-25
Contact: Hang Sun,E-mail:sunhang@mail.kib.ac.cn;Dong Luo,E-mail:luodong@mail.kib.ac.cn
Supported by:
This work was supported by the Guangdong S&T Program (2022B1111230001) and National Key R&D Program of China (2024YFF1307400).

Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex

Hum Kala Rana^a,b, Santosh Kumar Rana^c, Jacob B. Landis^d, Hang Sun^a, Dong Luo^a,e

a Yunnan Key Laboratory for Plant Diversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b University of Chinese Academy of Sciences, Beijing 100049, China;
c Department of Chemical and Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA;
d School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA;
e State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China

通讯作者: Hang Sun,E-mail:sunhang@mail.kib.ac.cn;Dong Luo,E-mail:luodong@mail.kib.ac.cn
基金资助:
This work was supported by the Guangdong S&T Program (2022B1111230001) and National Key R&D Program of China (2024YFF1307400).

Abstract

Abstract: Decoding how adaptation and vulnerability are distributed across rugged landscape is essential for anticipating biodiversity responses to climatic change. We investigated the Saussurea obvallata complex, a group of closely related lineages distributed across the Himalayan-Hengduan Mountains (HHM), to ask how climatic heterogeneity and historical isolation shape genomic variation, ecological divergence, and the speciation continuum. To address these questions, we integrated plastome and RAD-seq based nuclear SNPs with genotype-environment association (GEA) analyses, gradient forest (GF), generalized dissimilarity modeling (GDM), and ensemble species distribution models (SDMs). Projected genomic offset under future climate scenarios (2070) and ensemble SDMs were used to map genomic vulnerability and forecast habitat shifts. Nuclear SNPs resolve shallow divergence and cytonuclear discordance consistent with incomplete lineages sorting and episodic introgression. After formally accounting for background population structure and spatial effects, the pure environmental fraction remains modest but significant, with within-population label-permutation nulls falling well below observed values. Concordant signals across partial redundancy analysis, latent factor mixed model (notably June cloud metrics), and GF/GDM (temperature seasonality, slope/elevation, cloud regime) indicate a genuine environment-linked component of allele-frequency turnover, while acknowledging that reduced-representation data may under detect polygenic architecture. Genomic offset maps highlight vulnerability hotspots along the southern Western and Eastern Himalayas and parts of the Hengduan Mountains, whereas the central HHM shows lower offset and potential refugial stability. Together, results support a speciation continuum shaped by both isolation and environmental selection and motivate a dual conservation strategy: safeguard diversity-rich, low-offset refugia while mitigating risk in high-offset peripheral regions through enhanced connectivity, microrefugia, and genomic monitoring.

Key words: Genomic offset, Genotype-environment association, Himalaya-Hengduan mountains, Local adaptation, Conservation genomics

摘要： Decoding how adaptation and vulnerability are distributed across rugged landscape is essential for anticipating biodiversity responses to climatic change. We investigated the Saussurea obvallata complex, a group of closely related lineages distributed across the Himalayan-Hengduan Mountains (HHM), to ask how climatic heterogeneity and historical isolation shape genomic variation, ecological divergence, and the speciation continuum. To address these questions, we integrated plastome and RAD-seq based nuclear SNPs with genotype-environment association (GEA) analyses, gradient forest (GF), generalized dissimilarity modeling (GDM), and ensemble species distribution models (SDMs). Projected genomic offset under future climate scenarios (2070) and ensemble SDMs were used to map genomic vulnerability and forecast habitat shifts. Nuclear SNPs resolve shallow divergence and cytonuclear discordance consistent with incomplete lineages sorting and episodic introgression. After formally accounting for background population structure and spatial effects, the pure environmental fraction remains modest but significant, with within-population label-permutation nulls falling well below observed values. Concordant signals across partial redundancy analysis, latent factor mixed model (notably June cloud metrics), and GF/GDM (temperature seasonality, slope/elevation, cloud regime) indicate a genuine environment-linked component of allele-frequency turnover, while acknowledging that reduced-representation data may under detect polygenic architecture. Genomic offset maps highlight vulnerability hotspots along the southern Western and Eastern Himalayas and parts of the Hengduan Mountains, whereas the central HHM shows lower offset and potential refugial stability. Together, results support a speciation continuum shaped by both isolation and environmental selection and motivate a dual conservation strategy: safeguard diversity-rich, low-offset refugia while mitigating risk in high-offset peripheral regions through enhanced connectivity, microrefugia, and genomic monitoring.

关键词: Genomic offset, Genotype-environment association, Himalaya-Hengduan mountains, Local adaptation, Conservation genomics

Hum Kala Rana, Santosh Kumar Rana, Jacob B. Landis, Hang Sun, Dong Luo. Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex[J]. Plant Diversity, 2026, 48(03): 474-486.

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Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex

Decoding the genomic basis of adaptive capacity and vulnerability in the high-altitude Saussurea obvallata complex

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[2]	You Wu, Rong Liu, Wei-Jia Wang, De-Zhu Li, Kevin S. Burgess, Wen-Bin Yu, Hong Wang. High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites [J]. Plant Diversity, 2025, 47(06): 920-930.
[3]	Zhao-Yang Jing (景昭阳), Ren-Gang Zhang (张仁纲), Yang Liu (刘阳), Ke-Guang Cheng (程可光), De-Tuan Liu (刘德团), Heng Shu (舒恒), Jiali Kong (孔佳莉), Zhong-Hua Liu (刘忠华), Yong-Peng Ma (马永鹏), Ping-Li Liu (刘平丽). Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense [J]. Plant Diversity, 2025, 47(05): 759-771.
[4]	Nana Peng (彭娜娜), Lihua Yang (杨丽华), Xizuo Shi (史习佐), Hanghui Kong (孔航辉), Ming Kang (康明). Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species [J]. Plant Diversity, 2025, 47(05): 746-758.
[5]	Quan Jiang, Yufang Shen, Lianhai Wu, Zhengwang Jiang, Xiaohong Yao. Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit [J]. Plant Diversity, 2025, 47(05): 733-745.
[6]	Yiqing Chen, Lina Dong, Huiqin Yi, Catherine Kidner, Ming Kang. Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts [J]. Plant Diversity, 2024, 46(05): 575-584.
[7]	Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang. Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis [J]. Plant Diversity, 2024, 46(03): 294-308.
[8]	Ya-Ping Chen, Cun-Zhong Huang, Yue Zhao, Chun-Lei Xiang. Molecular and morphological evidence for a new species of Isodon (Lamiaceae) from southern China [J]. Plant Diversity, 2021, 43(01): 54-62.
[9]	Xie He, Kevin S. Burgess, Lian-Ming Gao, De-Zhu Li. Distributional responses to climate change for alpine species of Cyananthus and Primula endemic to the Himalaya-Hengduan Mountains [J]. Plant Diversity, 2019, 41(01): 26-32.
[10]	Jian-Ling Guo, Wen-Juan Cao, Zhi-Min Li, Yong-Hong Zhang, Sergei Volis. Conservation implications of population genetic structure in a threatened orchid Cypripedium tibeticum [J]. Plant Diversity, 2019, 41(01): 13-18.