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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae). Mol Phylogenet Evol 2023; 184:107808. [PMID: 37156329 DOI: 10.1016/j.ympev.2023.107808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.
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Affiliation(s)
- Qing-Hui Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA; Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Zhai Mingguo Academician Work Station, Sanya University, Sanya 572022, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA; BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Hua-Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou 570228, China.
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Rana SK, Rana HK, Stöcklin J, Ranjitkar S, Sun H, Song B. Global warming pushes the distribution range of the two alpine 'glasshouse' Rheum species north- and upwards in the Eastern Himalayas and the Hengduan Mountains. FRONTIERS IN PLANT SCIENCE 2022; 13:925296. [PMID: 36275548 PMCID: PMC9585287 DOI: 10.3389/fpls.2022.925296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Alpine plants' distribution is being pushed higher towards mountaintops due to global warming, finally diminishing their range and thereby increasing the risk of extinction. Plants with specialized 'glasshouse' structures have adapted well to harsh alpine environments, notably to the extremely low temperatures, which makes them vulnerable to global warming. However, their response to global warming is quite unexplored. Therefore, by compiling occurrences and several environmental strata, we utilized multiple ensemble species distribution modeling (eSDM) to estimate the historical, present-day, and future distribution of two alpine 'glasshouse' species Rheum nobile Hook. f. & Thomson and R. alexandrae Batalin. Rheum nobile was predicted to extend its distribution from the Eastern Himalaya (EH) to the Hengduan Mountains (HM), whereas R. alexandrae was restricted exclusively in the HM. Both species witnessed a northward expansion of suitable habitats followed by a southerly retreat in the HM region. Our findings reveal that both species have a considerable range shift under different climate change scenarios, mainly triggered by precipitation rather than temperature. The model predicted northward and upward migration for both species since the last glacial period which is mainly due to expected future climate change scenarios. Further, the observed niche overlap between the two species presented that they are more divergent depending on their habitat, except for certain regions in the HM. However, relocating appropriate habitats to the north and high elevation may not ensure the species' survival, as it needs to adapt to the extreme climatic circumstances in alpine habitats. Therefore, we advocate for more conservation efforts in these biodiversity hotspots.
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Affiliation(s)
- Santosh Kumar Rana
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, United States
| | - Hum Kala Rana
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jürg Stöcklin
- Institute of Botany, University of Basel, Basel, Switzerland
| | - Sailesh Ranjitkar
- N. Gene Solution of Natural Innovation, Kathmandu, Nepal
- School of Development Studies, Lumbini Buddhist University, Devdaha, Nepal
- MICD, Faculty of Humanities and Social Science, Mid-West University, Lalitpur, Nepal
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Bo Song
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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You J, Lougheed SC, Zhao Y, Zhang G, Liu W, Lu F, Wang Y, Zhang W, Yang J, Qiong L, Song Z. Comparative phylogeography study reveals introgression and incomplete lineage sorting during rapid diversification of Rhodiola. ANNALS OF BOTANY 2022; 129:185-200. [PMID: 34718397 PMCID: PMC8796671 DOI: 10.1093/aob/mcab133] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Many plant taxa in the Qinghai-Tibetan Plateau (QTP) and the Hengduan Mountains (HM) radiated rapidly during the Quaternary but with frequent secondary contact between diverging populations. Incomplete lineage sorting and introgressive hybridization might be involved during the rapid radiation, but their effects on phylogeography have not been fully determined. METHODS We investigated the chloroplast DNA (cpDNA)/internal transcribed spacer (ITS) sequence variations of 611 samples of Rhodiola bupleuroides, R. discolor, R. fastigiata and R. chrysanthemifolia from the QTP and HM to compare the phylogeographic patterns between the four species with different evolutionary histories, geographic ranges and reproductive modes. KEY RESULTS The divergence times of these species were consistent with the last peak of in situ speciation in the HM. While closely related species exhibited different phylogeographic patterns, they shared several ribotypes and haplotypes in sympatric populations, suggesting introgressive hybridization. A significant phylogenetic discordance between ribotypes and haplotypes was detected in three species, implying incomplete lineage sorting. Rhodiola discolor houses an extraordinary richness of cpDNA haplotypes, and this finding may be attributed to adaptive radiation. CONCLUSION In addition to geographic isolation and climate oscillations during the Quaternary, both introgressive hybridization and incomplete lineage sorting play important roles in species that experienced rapid diversification in the QTP and HM.
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Affiliation(s)
- Jianling You
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
- BGI-Yunnan, BGI-Shenzhen, Kunming, China
| | | | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Wensheng Liu
- College of Life Science and Technology, Central South University of Forestry and Techonology, Changsha, China
| | - Fan Lu
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Yuguo Wang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Wenju Zhang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - Ji Yang
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
| | - La Qiong
- Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Tibet University, Thasa, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Institute of Botany, Tibet University–Fudan University Joint Laboratory for Biodiversity and Global Change, Fudan University, Shanghai, China
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Li Y, Song F, Zhang XN, Lv GH. Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1612966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Li
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Feng Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Xue-Ni Zhang
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Guang-Hui Lv
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
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