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Song Y, Xu GB, Long KX, Wang CC, Chen R, Li H, Jiang XL, Deng M. Ensemble species distribution modeling and multilocus phylogeography provide insight into the spatial genetic patterns and distribution dynamics of a keystone forest species, Quercus glauca. BMC PLANT BIOLOGY 2024; 24:168. [PMID: 38438905 PMCID: PMC10910841 DOI: 10.1186/s12870-024-04830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Forests are essential for maintaining species diversity, stabilizing local and global climate, and providing ecosystem services. Exploring the impact of paleogeographic events and climate change on the genetic structure and distribution dynamics of forest keystone species could help predict responses to future climate change. In this study, we combined an ensemble species distribution model (eSDM) and multilocus phylogeography to investigate the spatial genetic patterns and distribution change of Quercus glauca Thunb, a keystone of East Asian subtropical evergreen broad-leaved forest. RESULTS A total of 781 samples were collected from 77 populations, largely covering the natural distribution of Q. glauca. The eSDM showed that the suitable habitat experienced a significant expansion after the last glacial maximum (LGM) but will recede in the future under a general climate warming scenario. The distribution centroid will migrate toward the northeast as the climate warms. Using nuclear SSR data, two distinct lineages split between east and west were detected. Within-group genetic differentiation was higher in the West than in the East. Based on the identified 58 haplotypes, no clear phylogeographic structure was found. Populations in the Nanling Mountains, Wuyi Mountains, and the southwest region were found to have high genetic diversity. CONCLUSIONS A significant negative correlation between habitat stability and heterozygosity might be explained by the mixing of different lineages in the expansion region after LGM and/or hybridization between Q. glauca and closely related species. The Nanling Mountains may be important for organisms as a dispersal corridor in the west-east direction and as a refugium during the glacial period. This study provided new insights into spatial genetic patterns and distribution dynamics of Q. glauca.
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Affiliation(s)
- Ying Song
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Gang-Biao Xu
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ke-Xin Long
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Chun-Cheng Wang
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Ran Chen
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - He Li
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China
| | - Xiao-Long Jiang
- College of Forestry, The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, Changsha, 410004, Hunan, China.
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan, 650500, China.
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Tian X, Guo J, Song Y, Yu Q, Liu C, Fu Z, Shi Y, Shao Y, Yuan Z. Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses. Ecol Evol 2024; 14:e11119. [PMID: 38469045 PMCID: PMC10927362 DOI: 10.1002/ece3.11119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 01/08/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.
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Affiliation(s)
- Xiangyu Tian
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Jia Guo
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education)Guangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinGuangxiChina
| | - Qunfei Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnanChina
| | - Chao Liu
- College of Biological Resource and Food EngineeringQujing Normal UniversityQujingYunnanChina
| | - Zhixi Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Yuhua Shi
- School of Life SciencesZhengzhou UniversityZhengzhouHenanChina
| | - Yizhen Shao
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhiliang Yuan
- College of Life SciencesHenan Agricultural UniversityZhengzhouHenanChina
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Yang R, Deng YW, Liu Y, Zhao J, Bao L, Ge JP, Wang HF. Genetic structure and trait variation within a maple hybrid zone underscore North China as an overlooked diversity hotspot. Sci Rep 2022; 12:13949. [PMID: 35977961 PMCID: PMC9385851 DOI: 10.1038/s41598-022-17538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022] Open
Abstract
Tertiary relict flora in East Asia can be divided into northern and southern regions. North China is a diversity hotspot because it can be the secondary contact zone of ancient lineages from the two regions. To test the extent of ancient lineages hybridization and distinguish between the putative species pair Acer pictum subsp. mono and Acer truncatum, we conducted genetic and ecological studies within a maple hybrid zone in North China. Our results suggest that the two lineages of Acer coexist in the hybrid zone and that adult and offspring populations show typical bimodal genetic patterns. Hybrid individuals are established at intermediate altitudes between the two parental lineages. Flowering phenology is divergent between lineages, whereas the complex sexual system of Acer may ensure pollination among lineages. Leaf and fruit morphologies are different between the northern and southern origin lineages, corresponding to A. pictum subsp. mono and A. truncatum, respectively. Reduced gene flow between lineages suggests that they should be considered as two species. However, large morphological variations within each species and the existence of hybrids offer low reliability of species identification based solely on morphological traits. Our study underscores North China as an overlooked diversity hotspot that requires further study in the future.
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Affiliation(s)
- Rui Yang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ya-Wen Deng
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yan Liu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jing Zhao
- Daheishan Administrative District, Beipiao City, 122000, Liaoning Province, China
| | - Lei Bao
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jian-Ping Ge
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hong-Fang Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China. .,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China. .,College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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