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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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Wang L, Li Y, Noshiro S, Suzuki M, Arai T, Kobayashi K, Xie L, Zhang M, He N, Fang Y, Zhang F. Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species ( Toxicodendron vernicifluum, Anacardiaceae) in East Asia. FRONTIERS IN PLANT SCIENCE 2022; 13:920054. [PMID: 35720535 PMCID: PMC9201781 DOI: 10.3389/fpls.2022.920054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Species' phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the "middle step", which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the "low step", which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).
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Affiliation(s)
- Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shuichi Noshiro
- Center for Obsidian and Lithic Studies, Meiji University, Tokyo, Japan
| | | | | | | | - Lei Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mingyue Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Na He
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Feilong Zhang
- Xi’an Research Institute of Chinese Lacquer, All China Federation of Supply and Marketing Cooperatives, Xi’an, China
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Shen Y, Xia H, Tu Z, Zong Y, Yang L, Li H. Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments. Mol Ecol 2021; 31:916-933. [PMID: 34773328 DOI: 10.1111/mec.16271] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022]
Abstract
Ecological adaptive differentiation alters both the species diversity and intraspecific genetic diversity in forests, thus affecting the stability of forest ecosystems. Therefore, knowledge of the genetic underpinnings of the ecological adaptive differentiation of forest species is critical for effective species conservation. In this study, single-nucleotide polymorphisms (SNPs) from population transcriptomes were used to investigate the spatial distribution of genetic variation in Liriodendron to assess whether environmental variables can explain genetic divergence. We examined the contributions of environmental variables to population divergence and explored the genetic underpinnings of local adaptation using a landscape genomic approach. Niche models and statistical analyses showed significant niche divergence between L. chinense and L. tulipifera, suggesting that ecological adaptation may play a crucial role in driving interspecific divergence. We detected a new fine-scale genetic structure in L. chinense, and divergence of the six groups occurred during the late Pliocene to early Pleistocene. Redundancy analysis (RDA) revealed significant associations between genetic variation and multiple environmental variables. Environmental association analyses identified 67 environmental association loci (EALs; nonsynonymous SNPs) that underwent interspecific or intraspecific differentiation, 28 of which were associated with adaptive genes. These 28 candidate adaptive loci provide substantial evidence for local adaptation in Liriodendron. Our findings reveal ecological adaptive divergence pattern between Liriodendron species and provide novel insight into the role of heterogeneous environments in shaping genetic structure and driving local adaptation among populations, informing future L. chinense conservation efforts.
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Affiliation(s)
- Yufang Shen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Hui Xia
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhonghua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaxian Zong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Wang JY, Yan SY, Hui WK, Gong W. SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1797531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Jing-Yan Wang
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Security on the Upper Reaches of Yangtze River, Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Si-Yu Yan
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Security on the Upper Reaches of Yangtze River, Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Wen-Kai Hui
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Security on the Upper Reaches of Yangtze River, Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Wei Gong
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Security on the Upper Reaches of Yangtze River, Sichuan Province Key Laboratory of Ecological Forestry Engineering on the Upper Reaches of Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan, PR China
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Ríos N, Casanova A, Hermida M, Pardo BG, Martínez P, Bouza C, García G. Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region. Genes (Basel) 2020; 11:genes11010109. [PMID: 31963477 PMCID: PMC7017130 DOI: 10.3390/genes11010109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/16/2022] Open
Abstract
Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isolated. Here, we investigated the genetic diversity pattern of this taxon in the Southern Neotropical Basin system that includes the La Plata Basin, Patos-Merin lagoon basin and the coastal lagoons draining to the SW Atlantic Ocean, through a population genomics approach using 2b-RAD-sequencing-derived single nucleotide polymorphisms (SNPs). The genomic scan identified selection footprints associated with divergence and suggested local adaptation environmental drivers. Two major genomic clusters latitudinally distributed in the Northern and Southern basins were identified, along with consistent signatures of divergent selection between them. Population structure based on the whole set of loci and on the presumptive neutral vs. adaptive loci showed deep genomic divergence between the two major clusters. Annotation of the most consistent SNPs under divergent selection revealed some interesting candidate genes for further functional studies. Moreover, signals of adaptation to a coastal lagoon environment mediated by purifying selection were found. These new insights provide a better understanding of the complex evolutionary history of R. quelen in the southernmost basin of the Neotropical region.
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Affiliation(s)
- Néstor Ríos
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
- Correspondence: ; Tel.: +598-25258618 (ext. 140)
| | - Adrián Casanova
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
| | - Belén G. Pardo
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela, Avenida Carballo Calero s/n, E-27002 Lugo, Spain; (A.C.); (M.H.); (B.G.P.); (P.M.); (C.B.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, Campus Vida s/n, E-15782 Santiago de Compostela, Spain
| | - Graciela García
- Sección Genética Evolutiva, Facultad de Ciencias, UdelaR, Iguá 4225, Montevideo 11400, Uruguay;
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Integrating Phylogeographic Analysis and Geospatial Methods to Infer Historical Dispersal Routes and Glacial Refugia of Liriodendron chinense. FORESTS 2019. [DOI: 10.3390/f10070565] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liriodendron chinense (Hemsl.), a Tertiary relic tree, is mainly distributed in subtropical China. The causes of the geographical distribution pattern of this species are poorly understood. In this study, we inferred historical dispersal routes and glacial refugia of this species by combining genetic data (chloroplast DNA (cpDNA), nuclear ribosomal DNA (nrDNA), and nuclear DNA (nDNA)) and geospatial data (climate and geology) with the methods of landscape genetics. Additionally, based on sequence variation at multiple loci, we employed GenGIS and Barrier software to analyze L. chinense population genetic structure. Dispersal corridors and historical gene flow between the eastern and western populations were detected, and they were located in mountainous regions. Based on species distribution model (SDMs), the distribution patterns in paleoclimatic periods were consistent with the current pattern, suggesting the presence of multiple refuges in multiple mountainous regions in China. The genetic structure analysis clustered most eastern populations into a clade separated from the western populations. Additionally, a genetic barrier was detected between the eastern and western populations. The dispersal corridors and historical gene flow detected here suggested that the mountains acted as a bridge, facilitating gene flow between the eastern and western populations. Due to Quaternary climatic fluctuations, the habitats and dispersal corridors were frequently inhabited by warm-temperate evergreen forests, which may have fragmented L. chinense habitats and exacerbated the differentiation of eastern and western populations. Ultimately, populations retreated to multiple isolated mountainous refugia, shaping the current geographical distribution pattern. These dispersal corridors and montane refugia suggested that the mountains in subtropical China play a crucial role in the conservation of genetic resources and migration of subspecies or related species in this region.
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Yang A, Zhong Y, Liu S, Liu L, Liu T, Li Y, Yu F. New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east-west lineage split and genetic mixture within western subtropical China. PeerJ 2019; 7:e6355. [PMID: 30723627 PMCID: PMC6361005 DOI: 10.7717/peerj.6355] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/26/2018] [Indexed: 11/20/2022] Open
Abstract
Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots of haplotype diversity in the Dalou Mountains and Wuling Mountains likely benefited from gene flow from the Wu Mountains and Yungui Plateau. Collectively, these results indicate that mountain regions should be the main units for conserving and collecting genetic resources of L. chinense and other similar species in subtropical China.
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Affiliation(s)
- Aihong Yang
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yongda Zhong
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Shujuan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Lipan Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Tengyun Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Yanqiang Li
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Faxin Yu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
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