Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications
Abstract Background Rheum pumilum, an endemic species on the Qinghai-Tibetan Plateau (QTP), serves as an ideal material for investigating the phylogeography of alpine plants. This study employs chloroplast DNA fragments (trnL-F, trnS-G, and matK) to delve into how Rh. pumilum adapted to the extreme...
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2025-02-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06164-y |
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| author | Shuliang Liu Jianxin Gao Bo Xiao Wenjie Guo Qiushi Yu Ailan Wang Weiwei Li |
| author_facet | Shuliang Liu Jianxin Gao Bo Xiao Wenjie Guo Qiushi Yu Ailan Wang Weiwei Li |
| author_sort | Shuliang Liu |
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| description | Abstract Background Rheum pumilum, an endemic species on the Qinghai-Tibetan Plateau (QTP), serves as an ideal material for investigating the phylogeography of alpine plants. This study employs chloroplast DNA fragments (trnL-F, trnS-G, and matK) to delve into how Rh. pumilum adapted to the extreme environmental changes on the QTP, during its evolutionary process through phylogenetic geographical analysis, revealing its population differentiation and historical dynamics. Results The examination of 39 haplotypes across 26 populations of Rh. pumilum reveals distinct regional distribution, reflecting a phylogeographic pattern resembling “alpine-island”. The total genetic diversity of Rh. pumilum is remarkably high (Ht = 0.910), with the majority of genetic variation primarily occurred among populations (84.5%) with limited gene flow, indicating geographic isolation influenced by diverse habitats of plateau. The geographic isolation model is further supported by various analytical methods, including AMOVA analysis, UPGMA dendrogram, PCoA, Structure analysis, and Mantel test. Micro-refugia for Rh. pumilum during the Quaternary ice ages are supported by haplotype network and genetic diversity analysis. The absence of a typical “star-shape” pattern in the overall haplotype network suggests that Rh. pumilum likely maintains a stable state without experiencing rapid expansion, which has been supported by mismatch distribution analysis. Ecological Niche Modeling (ENM) indicates sensitivity of Rh. pumilum to humidity, temperature and altitude, aligning with a historical distribution resembling a “displacement refugia” model during the Quaternary ice ages. The involvement of Rh. kialense and Rh. sublanceolatum in the origin and gene introgression of Rh. pumilum is suggested, possibly as maternal ancestors of closely related haplotypes. Haplotype divergence of Rh. pumilum approximately 11 million years ago, with notable divergence peaks observed during the late Miocene, as well as the Pliocene, Pleistocene and Holocene. Conclusion These findings suggest a correlation between genetic diversity, haplotype lineage divergence and key geological and climatic events, notably the uplift of the QTP, monsoon climate changes, and the climatic oscillations during the Quaternary ice ages. This study might provide valuable insights into the formation mechanisms of plant diversity on the QTP, crucial for biodiversity conservation and sustainable species development in extreme environments. |
| format | Article |
| id | doaj-art-332060c61b934d3582fc7e1e7cc9d545 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-332060c61b934d3582fc7e1e7cc9d5452025-02-09T12:27:52ZengBMCBMC Plant Biology1471-22292025-02-0125111710.1186/s12870-025-06164-yGenetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implicationsShuliang Liu0Jianxin Gao1Bo Xiao2Wenjie Guo3Qiushi Yu4Ailan Wang5Weiwei Li6School of Life Sciences, Ludong UniversitySchool of Life Sciences, Ludong UniversitySchool of Life Sciences, Ludong UniversitySchool of Life Sciences, Ludong UniversityGansu Academy of ForestrySchool of Life Sciences, Ludong UniversitySchool of Life Sciences, Ludong UniversityAbstract Background Rheum pumilum, an endemic species on the Qinghai-Tibetan Plateau (QTP), serves as an ideal material for investigating the phylogeography of alpine plants. This study employs chloroplast DNA fragments (trnL-F, trnS-G, and matK) to delve into how Rh. pumilum adapted to the extreme environmental changes on the QTP, during its evolutionary process through phylogenetic geographical analysis, revealing its population differentiation and historical dynamics. Results The examination of 39 haplotypes across 26 populations of Rh. pumilum reveals distinct regional distribution, reflecting a phylogeographic pattern resembling “alpine-island”. The total genetic diversity of Rh. pumilum is remarkably high (Ht = 0.910), with the majority of genetic variation primarily occurred among populations (84.5%) with limited gene flow, indicating geographic isolation influenced by diverse habitats of plateau. The geographic isolation model is further supported by various analytical methods, including AMOVA analysis, UPGMA dendrogram, PCoA, Structure analysis, and Mantel test. Micro-refugia for Rh. pumilum during the Quaternary ice ages are supported by haplotype network and genetic diversity analysis. The absence of a typical “star-shape” pattern in the overall haplotype network suggests that Rh. pumilum likely maintains a stable state without experiencing rapid expansion, which has been supported by mismatch distribution analysis. Ecological Niche Modeling (ENM) indicates sensitivity of Rh. pumilum to humidity, temperature and altitude, aligning with a historical distribution resembling a “displacement refugia” model during the Quaternary ice ages. The involvement of Rh. kialense and Rh. sublanceolatum in the origin and gene introgression of Rh. pumilum is suggested, possibly as maternal ancestors of closely related haplotypes. Haplotype divergence of Rh. pumilum approximately 11 million years ago, with notable divergence peaks observed during the late Miocene, as well as the Pliocene, Pleistocene and Holocene. Conclusion These findings suggest a correlation between genetic diversity, haplotype lineage divergence and key geological and climatic events, notably the uplift of the QTP, monsoon climate changes, and the climatic oscillations during the Quaternary ice ages. This study might provide valuable insights into the formation mechanisms of plant diversity on the QTP, crucial for biodiversity conservation and sustainable species development in extreme environments.https://doi.org/10.1186/s12870-025-06164-yRheum pumilumPhylogeographycpDNAThe Qinghai-Tibetan PlateauEcological niche |
| spellingShingle | Shuliang Liu Jianxin Gao Bo Xiao Wenjie Guo Qiushi Yu Ailan Wang Weiwei Li Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications BMC Plant Biology Rheum pumilum Phylogeography cpDNA The Qinghai-Tibetan Plateau Ecological niche |
| title | Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications |
| title_full | Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications |
| title_fullStr | Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications |
| title_full_unstemmed | Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications |
| title_short | Genetic differentiation and historical dynamics of the endemic species Rheum pumilum on the Qinghai-Tibetan Plateau inferred from phylogeography implications |
| title_sort | genetic differentiation and historical dynamics of the endemic species rheum pumilum on the qinghai tibetan plateau inferred from phylogeography implications |
| topic | Rheum pumilum Phylogeography cpDNA The Qinghai-Tibetan Plateau Ecological niche |
| url | https://doi.org/10.1186/s12870-025-06164-y |
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