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Luo L, Ye P, Lin Q, Liu M, Hao G, Wei T, Sahu SK. From sequences to sustainability: Exploring dipterocarp genomes for oleoresin production, timber quality, and conservation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112139. [PMID: 38838990 DOI: 10.1016/j.plantsci.2024.112139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/23/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
Dipterocarp species dominate tropical forest ecosystems and provide key ecological and economic value through their use of aromatic resins, medicinal chemicals, and high-quality timber. However, habitat loss and unsustainable logging have endangered many Dipterocarpaceae species. Genomic strategies provide new opportunities for both elucidating the molecular pathways underlying these desirable traits and informing conservation efforts for at-risk taxa. This review summarizes the progress in dipterocarp genomics analysis and applications. We describe 16 recently published Dipterocarpaceae genome sequences, representing crucial genetic blueprints. Phylogenetic comparisons delineate evolutionary relationships among species and provide frameworks for pinpointing functional changes underlying specialized metabolism and wood development patterns. We also discuss connections revealed thus far between specific gene families and both oleoresin biosynthesis and wood quality traits-including the identification of key terpenoid synthases and cellulose synthases likely governing pathway flux. Moreover, the characterization of adaptive genomic markers offers vital resources for supporting conservation practices prioritizing resilient genotypes displaying valuable oleoresin and timber traits. Overall, progress in dipterocarp functional and comparative genomics provides key tools for addressing the intertwined challenges of preserving biodiversity in endangered tropical forest ecosystems while sustainably deriving aromatic chemicals and quality lumber that support diverse human activities.
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Affiliation(s)
- Liuming Luo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Peng Ye
- College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Gang Hao
- College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China.
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2
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Raman G, Choi KS, Park S. Population Structure and Genetic Diversity Analyses Provide New Insight into the Endemic Species Aster spathulifolius Maxim. and Its Evolutionary History. PLANTS (BASEL, SWITZERLAND) 2023; 13:88. [PMID: 38202396 PMCID: PMC10780962 DOI: 10.3390/plants13010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
Aster spathulifolius, an ecologically significant plant species native to the coastal regions of Korea and Japan, remains understudied in terms of its genetic structure and evolutionary history. In this study, we employed four chloroplast markers and the nuclear ITS region from 15 populations of A. spathulifolius from both Korea and Japan, including their islands, to unravel the spatial genetic structure, differentiation, gene flow, phylogenetic, and biogeographical relationships. Analysis based on multiple methods identified a low level of genetic diversity, genetic differentiation and gene flow among A. spathulifolius populations. Network analysis and principal coordinates analysis showed that 15 populations could be divided into two groups: mainland and island. Furthermore, UPGMA, neighbor-net, maximum-likelihood and Bayesian inference-based phylogenetic tree confirmed that these populations formed two distinct clades. Therefore, the island populations might be treated as A. spathulifolius populations rather than A. oharai populations. Divergence time analysis estimated the divergence of A. spathulifolius lineages approximately 23.09 million years ago, while ancestral area reconstruction analysis suggested Korea as the potential origin, conflicting with alternative scenarios. These findings contribute to a comprehensive understanding of the evolutionary history, genetic structure, and adaptive strategies of A. spathulifolius in coastal environments. Our study challenges previous assumptions and underscores the necessity for further population studies to elucidate the intricate dynamics of this distinctive plant species.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
| | - Kyoung Su Choi
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea;
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongsanbuk-do, Republic of Korea;
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3
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Wu Q, Dong S, Zhao Y, Yang L, Qi X, Ren Z, Dong S, Cheng J. Genetic diversity, population genetic structure and gene flow in the rare and endangered wild plant Cypripedium macranthos revealed by genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:254. [PMID: 37189068 DOI: 10.1186/s12870-023-04212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Genetic diversity, genetic structure, and gene flow in plant populations and their influencing factors are important in conservation biology. Cypripedium macranthos is one of the few wild orchids with high ornamental value in northern China. However, over the past decade, excessive collection, trading, tourism development, habitat fragmentation, deceptive pollination, and seed germination difficulties have all caused a sharp decline in the number of C. macranthos individuals and its population. In order to propose a scientific and effective conservation strategy, the genetic diversity, genetic structure and gene flow of the current CM population are urgent scientific issues to be clarified. RESULTS Here, 99 individuals of C. macranthos from north and northeast China were analyzed to evaluate the genetic diversity, gene flow among populations, and genetic structure by genotyping-by-sequencing. More than 68.44 Gb high-quality clean reads and 41,154 SNPs were obtained. Our data based on bioinformatics methods revealed that C. macranthos has lower genetic diversity, high levels of historical gene flow, and moderate-to-high genetic differentiation between populations. The gene migration model revealed that the direction of gene flow was mainly from northeast populations to north populations in China. The results of genetic structure analysis showed that 11 C. macranthos populations can be considered as two groups, and further divided into four subgroups. Moreover, the Mantel test detected no significant "Isolation by Distance" between populations. CONCLUSIONS Our study demonstrates that the present genetic diversity and genetic structure of C. macranthos populations were mainly caused by biological characteristics, human interference, habitat fragmentation, and restricted gene flow. Finally, constructive measures, which can provide a basis for the proposal of conservation strategies, have been suggested.
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Affiliation(s)
- Qi Wu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shang Dong
- Department of Yichun, Heilongjiang Academy of Forestry, Yichun, Heilongjiang, China
| | - Yuxin Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Yang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiujin Qi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhihe Ren
- Management Office of Hebei Dahaituo National Nature Reserve, Chicheng, Hebei, China
| | - Shubin Dong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
| | - Jin Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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4
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Mishra G, Meena RK, Kant R, Pandey S, Ginwal HS, Bhandari MS. Genome-wide characterization leading to simple sequence repeat (SSR) markers development in Shorea robusta. Funct Integr Genomics 2023; 23:51. [PMID: 36707443 PMCID: PMC9883139 DOI: 10.1007/s10142-023-00975-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Abstract
Tropical rainforests in Southeast Asia are enriched by multifarious biota dominated by Dipterocarpaceae. In this family, Shorea robusta is an ecologically sensitive and economically important timber species whose genomic diversity and phylogeny remain understudied due to lack of datasets on genetic resources. Smattering availability of molecular markers impedes population genetic studies indicating a necessity to develop genomic databases and species-specific markers in S. robusta. Accordingly, the present study focused on fostering de novo low-depth genome sequencing, identification of reliable microsatellites markers, and their validation in various populations of S. robusta in Uttarakhand Himalayas. With 69.88 million raw reads assembled into 1,97,489 contigs (read mapped to 93.2%) and a genome size of 357.11 Mb (29 × coverage), Illumina paired-end sequencing technology arranged a library of sequence data of ~ 10 gigabases (Gb). From 57,702 microsatellite repeats, a total of 35,049 simple sequence repeat (SSR) primer pairs were developed. Afterward, among randomly selected 60 primer pairs, 50 showed successful amplification and 24 were found as polymorphic. Out of which, nine polymorphic loci were further used for genetic analysis in 16 genotypes each from three different geographical locations of Uttarakhand (India). Prominently, the average number of alleles per locus (Na), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were recorded as 2.44, 0.324, 0.277 and 0.252, respectively. The accessibility of sequence information and novel SSR markers potentially enriches the current knowledge of the genomic background for S. robusta and to be utilized in various genetic studies in species under tribe Shoreae.
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Affiliation(s)
- Garima Mishra
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Rajendra K Meena
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Rama Kant
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun - 248 006, Uttarakhand, Dehradun, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun - 248 195, Uttarakhand, Dehradun, India.
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5
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Ku JE, Choi SG. Population Structure of Finless Porpoise (Neophocaena phocaenoides) Discovered off Coastal Waters, Republic of Korea. Genes (Basel) 2022; 13:genes13101701. [PMID: 36292586 PMCID: PMC9602366 DOI: 10.3390/genes13101701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The finless porpoise (Neophocaena phocaenoides Cuvier, 1829) is distributed in the coastal waters of Asia, throughout Indonesia to the east, and as far north as the Taiwan Strait. The finless porpoise has been declared critically endangered by the WWF (World Wide Fund for Nature), and in 2017 was rated vulnerable on the IUCN Red Threatened Species List. Since this species is distributed near the coast and has many interactions with humans, effective conservation of the species requires further studies into their genetic diversity and population. In this study, 45 samples were obtained from bycatch or stranded individuals in the East, South, and West Seas, where Korean porpoises were mainly distributed from 2017–2021. We compared 473 bp mtDNA sequences from the control region. Pairwise fixation indices (FST) revealed that the two populations differed significantly (FST = 0.4557, p = 0.000). In contrast to high levels of genetic differentiation, gene flow was identified as medium levels (Nm of 0.04–0.71). Our data suggest that finless porpoises may have undergone a historic differentiation event, and that finless porpoises in the three regions could be divided into two populations: West and East/South.
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6
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Minh Nguyen D, Lan Phan Nguyen H, Minh Nguyen T. Genetic structure of the endemic Dipterocarpus condorensis revealed by microsatellite markers. AOB PLANTS 2022; 14:plac007. [PMID: 35440974 PMCID: PMC9011383 DOI: 10.1093/aobpla/plac007] [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: 08/05/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Anthropogenic disturbances in tropical forests often affect the genetic diversity of a species. Dipterocarpus condorensis is an endangered species in the tropical forests of south-eastern Vietnam, both from its over-exploitation and habitat loss. Therefore, knowledge of population genetic diversity and population structure is essential for identifying the species conservation measures. In the present study, we evaluated genetic diversity and population structure using nine microsatellites for 183 individual trees from eight populations, representing the distribution range of D. condorensis in Vietnam. Two clustering approaches (Bayesian analysis and discriminant analysis of principal components) revealed that all studied individuals clustered into three genetic groups, which were related to gene flow across the range of D. condorensis in the lowland tropical forests of south-eastern Vietnam. Limited gene flow was implicated in anthropogenic disturbance. Genetic differentiation among populations was relatively low (the Weir and Cockerham index of 0.122 and the Hedrick index of 0.149) and showed significant differentiation. The genetic variability of the populations was low (H O = 0.298 and H E = 0.324), which suggested the negative effects of habitat degradation and over-exploitation. Our studies also determined that D. condorensis populations can have undergone recent bottlenecks. We recommend conservation activities for this species based on these results.
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Affiliation(s)
- Duc Minh Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Hong Lan Phan Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Tam Minh Nguyen
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
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7
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Karunarathne P, Hojsgaard D. Single Independent Autopolyploidization Events From Distinct Diploid Gene Pools and Residual Sexuality Support Range Expansion of Locally Adapted Tetraploid Genotypes in a South American Grass. Front Genet 2021; 12:736088. [PMID: 34671384 PMCID: PMC8520906 DOI: 10.3389/fgene.2021.736088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/07/2021] [Indexed: 12/02/2022] Open
Abstract
Polyploidy plays a major role in plant evolution. The establishment of new polyploids is often a consequence of a single or few successful polyploidization events occurring within a species’ evolutionary trajectory. New polyploid lineages can play different roles in plant diversification and go through several evolutionary stages influenced by biotic and abiotic constraints and characterized by extensive genetic changes. The study of such changes has been crucial for understanding polyploid evolution. Here, we use the multiploid-species Paspalum intermedium to study population-level genetic and morphological variation and ecological differentiation in polyploids. Using flow cytometry, amplified fragment length polymorphism (AFLP) genetic markers, environmental variables, and morphological data, we assessed variations in ploidy, reproductive modes, and the genetic composition in 35 natural populations of P. intermedium along a latitudinal gradient in South America. Our analyses show that apomictic auto-tetraploids are of multiple independent origin. While overall genetic variation was higher in diploids, both diploids and tetraploids showed significant variation within and among populations. The spatial distribution of genetic variation provides evidence for a primary origin of the contact zone between diploids and tetraploids and further supports the hypothesis of geographic displacement between cytotypes. In addition, a strong link between the ecological differentiation of cytotypes and spatial distribution of genetic variation was observed. Overall, the results indicate that polyploidization in P. intermedium is a recurrent phenomenon associated to a shift in reproductive mode and that multiple polyploid lineages from genetically divergent diploids contributed to the successful establishment of local polyploid populations and dispersal into new environments.
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Affiliation(s)
- Piyal Karunarathne
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Georg-August University School of Science, University of Goettingen, Goettingen, Germany.,Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Diego Hojsgaard
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Taxonomy & Evolutionary Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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8
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Ng KKS, Kobayashi MJ, Fawcett JA, Hatakeyama M, Paape T, Ng CH, Ang CC, Tnah LH, Lee CT, Nishiyama T, Sese J, O'Brien MJ, Copetti D, Isa MNM, Ong RC, Putra M, Siregar IZ, Indrioko S, Kosugi Y, Izuno A, Isagi Y, Lee SL, Shimizu KK. The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests. Commun Biol 2021; 4:1166. [PMID: 34620991 PMCID: PMC8497594 DOI: 10.1038/s42003-021-02682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.
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Affiliation(s)
- Kevin Kit Siong Ng
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Masaki J Kobayashi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Forestry Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jeffrey A Fawcett
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
- RIKEN iTHEMS, Wako, Saitama, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Timothy Paape
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Choon Cheng Ang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia
| | - Tomoaki Nishiyama
- Division of Integrated Omics research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- AIST-Tokyo Tech RWBC-OIL, Meguro-ku, Tokyo, Japan
- Humanome Lab Inc., Chuo-ku, Tokyo, Japan
| | - Michael J O'Brien
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n., E-28933, Móstoles, Spain
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | | | - Mahardika Putra
- Faculty of Forestry, Bogor Agricultural University, Bogor, Indonesia
| | | | - Sapto Indrioko
- Faculty of Forestry, Gadjah Mada University, Yogyakarta, Indonesia
| | - Yoshiko Kosugi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ayako Izuno
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia (FRIM), Kepong, Selangor, Malaysia.
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- URPP Global Change and Biodiversity, University of Zurich, Zurich, Switzerland.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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9
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Major EI, Höhn M, Avanzi C, Fady B, Heer K, Opgenoorth L, Piotti A, Popescu F, Postolache D, Vendramin GG, Csilléry K. Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.). Mol Ecol 2021; 30:5247-5265. [PMID: 34365696 PMCID: PMC9291806 DOI: 10.1111/mec.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 12/03/2022]
Abstract
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
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Affiliation(s)
- Enikő I Major
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Mária Höhn
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Bruno Fady
- Ecology of Mediterranean Forests (URFM), INRAE, UR629, Avignon, France
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Dragos Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Katalin Csilléry
- Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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10
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Nguyen TM, Vu DD, Dang HP, Bui XTT, Nguyen HPL, Nguyen DM. Population genetic structure and demographic history of the dipterocarp species Anisoptera costata Korth revealed by microsatellite analysis. PLANTA 2021; 253:66. [PMID: 33582857 DOI: 10.1007/s00425-021-03584-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Moderate levels of genetic diversity and differentiation of Anisoptera costata were determined. A population divergence occurred during Younger Dryas. The anthropogenic disturbance had significantly affected the genetic diversity of the species in low tropical forests. Anisoptera costata Korth, an endangered species, is mainly distributed in the lowland tropical forests of the Southeast region in Vietnam, which has not been explored for genetic diversity and demographic history. In this study, eight polymorphic microsatellite markers were used to analyze 232 wild trees of A. costata at nine different populations, representing the natural distribution range of the species in Vietnam. Genetic diversity within the populations was determined with mean values of 0.284 and 0.327 observed and expected heterozygosity, respectively, while genetic differentiation among populations was found with Weir and Cockerham index of 0.12 and Hedrick index of 1.38. These results indicated that habitat fragmentation by the anthropogenic disturbance may be the major factor for the low heterozygosity values and affected the number of alleles in all the targeted populations of A. costata in lowland tropical forests. Populations in the Central Southeast area had a higher level of genetic diversity than the populations in the Coastal and Western Southeast areas. The analysis of molecular variance showed that high genetic variation existed within populations (86.15%) compared to the variation among populations. A reduction in the population size of A. costata was determined by BOTTLENECK. Different clustering methods (Bayesian analysis, the neighbor-joining tree, and principal coordinate analysis) suggested optimal genetic clusters related to gene flow among different areas. Approximate Bayesian computation suggested that population divergence occurred during Younger Dryas. We also discussed the measures for species conservation based on these results.
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Affiliation(s)
- Tam Minh Nguyen
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.
| | - Duy Dinh Vu
- Vietnam-Russia Tropical Centre, Nguyen Van Huyen, Cau Giay, Hanoi, 100000, Vietnam
| | - Hien Phan Dang
- Department of Experimental Taxonomy and Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Xuan Thi Tuyet Bui
- Department of Plant Ecology, Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
| | - Hong Phan Lan Nguyen
- Faculty of Biotechnology, Hanoi Open University, Nguyen Trai, Thanh Xuan, Hanoi, 100000, Vietnam
| | - Duc Minh Nguyen
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam
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Cheng J, Kao H, Dong S. Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC PLANT BIOLOGY 2020; 20:391. [PMID: 32842966 PMCID: PMC7448513 DOI: 10.1186/s12870-020-02594-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. RESULTS In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. CONCLUSIONS This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.
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Affiliation(s)
- Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huixia Kao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shubin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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12
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Comparative studies on population genetic structure of two closely related selfing and outcrossing Zingiber species in Hainan Island. Sci Rep 2019; 9:17997. [PMID: 31784623 PMCID: PMC6884562 DOI: 10.1038/s41598-019-54526-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/15/2019] [Indexed: 02/04/2023] Open
Abstract
How mating system impacts the genetic diversity of plants has long fascinated and puzzled evolutionary biologists. Numerous studies have shown that self-fertilising plants have less genetic diversity at both the population and species levels than outcrossers. However, the phylogenetic relationships between species and correlated ecological traits have not been accounted for in these previous studies. Here, we conduct a comparative population genetic study of two closely related selfing and outcrossing Zingiber species, with sympatric distribution in Hainan Island, and obtain a result contrary to previous studies. The results indicate that selfing Z. corallinum can maintain high genetic diversity through differentiation intensified by local adaptation in populations across the species’ range. In contrast, outcrossing Z. nudicarpum preserves high genetic diversity through gene exchange by frequent export of pollen within or among populations. Contrary to expectations, the major portion of genetic variation of outcrossing Z. nudicarpum may exist among populations, depending on the dispersal ability of pollen and seed. Our results also reveal that the main factor affecting population structure of selfing Z. corallinum is mountain ranges, followed by a moist climate, while that of outcrossing Z. nudicarpum is likely moisture, but not mountain ranges, due to gene flow via pollen.
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Schroeder JW, Tran HT, Dick CW. Fine scale spatial genetic structure in Pouteria reticulata (Engl.) Eyma (Sapotaceae), a dioecious, vertebrate dispersed tropical rain forest tree species. Glob Ecol Conserv 2014. [DOI: 10.1016/j.gecco.2014.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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14
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Fine scale spatial genetic structure of the endangered Heptacodium miconioides endemic to China. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Polyploid origin, genetic diversity and population structure in the tetraploid sea lavender Limonium narbonense Miller (Plumbaginaceae) from eastern Spain. Genetica 2012; 139:1309-22. [DOI: 10.1007/s10709-012-9632-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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16
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Harata T, Nanami S, Yamakura T, Matsuyama S, Chong L, Diway BM, Tan S, Itoh A. Fine-scale Spatial Genetic Structure of Ten Dipterocarp Tree Species in a Bornean Rain Forest. Biotropica 2011. [DOI: 10.1111/j.1744-7429.2011.00836.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Tsuyoshi Harata
- Graduate School of Science; Osaka City University; Sugimoto 3-3-138, Sumiyoshi-ku; Osaka; 558-8585; Japan
| | - Satoshi Nanami
- Graduate School of Science; Osaka City University; Sugimoto 3-3-138, Sumiyoshi-ku; Osaka; 558-8585; Japan
| | - Takuo Yamakura
- Graduate School of Science; Osaka City University; Sugimoto 3-3-138, Sumiyoshi-ku; Osaka; 558-8585; Japan
| | - Shuhei Matsuyama
- Graduate School of Science; Osaka City University; Sugimoto 3-3-138, Sumiyoshi-ku; Osaka; 558-8585; Japan
| | - Lucy Chong
- Botanical Research Centre, Forestry, Sarawak Forestry Corporation; Sarawak; Malaysia
| | - Bibian M. Diway
- Botanical Research Centre, Forestry, Sarawak Forestry Corporation; Sarawak; Malaysia
| | - Sylvester Tan
- Botanical Research Centre, Forestry, Sarawak Forestry Corporation; Sarawak; Malaysia
| | - Akira Itoh
- Graduate School of Science; Osaka City University; Sugimoto 3-3-138, Sumiyoshi-ku; Osaka; 558-8585; Japan
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Kettle CJ, Maycock CR, Ghazoul J, Hollingsworth PM, Khoo E, Sukri RSH, Burslem DFRP. Ecological implications of a flower size/number trade-off in tropical forest trees. PLoS One 2011; 6:e16111. [PMID: 21408110 PMCID: PMC3052255 DOI: 10.1371/journal.pone.0016111] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/12/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND In angiosperms, flower size commonly scales negatively with number. The ecological consequences of this trade-off for tropical trees remain poorly resolved, despite their potential importance for tropical forest conservation. We investigated the flower size number trade-off and its implications for fecundity in a sample of tree species from the Dipterocarpaceae on Borneo. METHODOLOGY/PRINCIPAL FINDINGS We combined experimental exclusion of pollinators in 11 species, with direct and indirect estimates of contemporary pollen dispersal in two study species and published estimates of pollen dispersal in a further three species to explore the relationship between flower size, pollinator size and mean pollen dispersal distance. Maximum flower production was two orders of magnitude greater in small-flowered than large-flowered species of Dipterocarpaceae. In contrast, fruit production was unrelated to flower size and did not differ significantly among species. Small-flowered species had both smaller-sized pollinators and lower mean pollination success than large-flowered species. Average pollen dispersal distances were lower and frequency of mating between related individuals was higher in a smaller-flowered species than a larger-flowered confamilial. Our synthesis of pollen dispersal estimates across five species of dipterocarp suggests that pollen dispersal scales positively with flower size. CONCLUSIONS AND THEIR SIGNIFICANCE Trade-offs embedded in the relationship between flower size and pollination success contribute to a reduction in the variance of fecundity among species. It is therefore plausible that these processes could delay competitive exclusion and contribute to maintenance of species coexistence in this ecologically and economically important family of tropical trees. These results have practical implications for tree species conservation and restoration. Seed collection from small-flowered species may be especially vulnerable to cryptic genetic erosion. Our findings also highlight the potential for differential vulnerability of tropical tree species to the deleterious consequences of forest fragmentation.
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Affiliation(s)
- Chris J Kettle
- Ecosystem Management, Institute of Terrestrial Ecosystems, ETH Zurich, Zurich, Switzerland.
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Pandey M, Geburek T. Genetic differences between continuous and disjunct populations: some insights from sal (Shorea robusta Roxb.) in Nepal. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9940-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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When sex is not enough: ecological correlates of resprouting capacity in congeneric tropical forest shrubs. Oecologia 2009; 161:43-56. [DOI: 10.1007/s00442-009-1353-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 04/08/2009] [Indexed: 11/26/2022]
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PARDINI EA, HAMRICK JL. Inferring recruitment history from spatial genetic structure within populations of the colonizing tree Albizia julibrissin (Fabaceae). Mol Ecol 2008; 17:2865-79. [DOI: 10.1111/j.1365-294x.2008.03807.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Pickup M, Young AG. Population size, self-incompatibility and genetic rescue in diploid and tetraploid races of Rutidosis leptorrhynchoides (Asteraceae). Heredity (Edinb) 2007; 100:268-74. [DOI: 10.1038/sj.hdy.6801070] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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22
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Fukue Y, Kado T, Lee SL, Ng KKS, Muhammad N, Tsumura Y. Effects of flowering tree density on the mating system and gene flow in Shorea leprosula (Dipterocarpaceae) in Peninsular Malaysia. JOURNAL OF PLANT RESEARCH 2007; 120:413-20. [PMID: 17387430 DOI: 10.1007/s10265-007-0078-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2006] [Accepted: 01/30/2007] [Indexed: 05/14/2023]
Abstract
Pristine tropical rainforests in Southeast Asia have rich species diversity and are important habitats for many plant species. However, the extent of these forests has declined in recent decades and they have become fragmented due to human activities. These developments may reduce the genetic diversity of species within them and, consequently, the species' ability to adapt to environmental changes. Our objective in the study presented here was to clarify the effect of tree density on the genetic diversity and gene flow patterns of Shorea leprosula Miq. populations in Peninsular Malaysia. For this purpose, we related genetic diversity and pollen flow parameters of seedling populations in study plots to the density of mature trees in their vicinity. The results show that gene diversity and allelic richness were not significantly correlated to the mature tree density. However, the number of rare alleles among the seedlings and the selfing rates of the mother trees were negatively correlated with the density of the adult trees. Furthermore, in a population with high mature tree density pollination distances were frequently <200 m, but in populations with low adult tree density the distances were longer. These findings suggest that the density of flowering trees affects selfing rates, gene flow and, thus, the genetic diversity of S. leprosula populations. We also found an individual S. leprosula tree with a unique reproductive system, probably apomictic, mating system.
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Affiliation(s)
- Yoko Fukue
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Jones FA, Hubbell SP. Demographic spatial genetic structure of the Neotropical tree, Jacaranda copaia. Mol Ecol 2006; 15:3205-17. [PMID: 16968265 DOI: 10.1111/j.1365-294x.2006.03023.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We used genotypes from six microsatellite loci and demographic data from a large mapped forest plot to study changes in spatial genetic structure across demographic stages, from seed rain to seedlings, juveniles, and adult diameter classes in the Neotropical tree, Jacaranda copaia. In pairwise comparisons of genetic differentiation among demographic classes, only seedlings were significantly differentiated from the other diameter classes; F(ST) values ranged from 0.006 to 0.009. Furthermore, only seedlings showed homozygote excess suggesting biparental inbreeding in the large diameter reproductive adults. We found very low levels of relatedness in the first distance class of trees, 1-26 cm diameter (F(ij) = 0.011). However, there was a 5- to 10-fold rise in relatedness in the smallest distance class, from the smallest to the largest tree diameter classes (F(ij) = 0.110 for individuals > 56 cm diameter). A variety of non-mutually exclusive mechanisms have been invoked perviously to explain such a pattern, including natural selection, history, or nonequilibrium population dynamics. The long-term demographic data available for this species allow us to evaluate these mechanisms. Jacaranda is a fast-growing, light-demanding species with low recruitment rates and high mortality rates in the smaller diameter classes. It successfully regenerates only in large light gaps, which occur infrequently and stochastically in space and time. These factors contribute to the nonequilibrium population dynamics and observed low genetic structure in the small size classes. We conclude that the pattern of spatial genetic transitions in Jacaranda is consistent with overlapping related generations and strong but infrequent periods of high recruitment, followed by long periods of population decline.
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Affiliation(s)
- F A Jones
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Ancon, Balboa, Republic of Panama.
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CHUNG JAEMIN, LEE BYEUNGCHEUN, KIM JINSEOK, PARK CHONGWOOK, YOON CHUNG MI, GI CHUNG MYONG. Fine-scale genetic structure among genetic individuals of the clone-forming monotypic genus Echinosophora koreensis (Fabaceae). ANNALS OF BOTANY 2006; 98:165-73. [PMID: 16675603 PMCID: PMC2803556 DOI: 10.1093/aob/mcl083] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Revised: 12/22/2005] [Accepted: 02/13/2006] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. METHODS Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, F(ij)) for total samples and samples excluding clones. KEY RESULTS A high degree of differentiation between populations was observed (phi(ST(g)) = 0.184, P < 0.001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at < or = 6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0.072-0.154), but these patterns were not significantly different from each other. At small interplant distances (< or = 2 m), however, jackknifed 95% CIs revealed that the total samples exhibited significantly higher F(ij) values than the same samples excluding clones. CONCLUSION The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high F(ij) values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10-12 m should be collected across entire populations of E. koreensis.
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Affiliation(s)
- JAE MIN CHUNG
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - BYEUNG CHEUN LEE
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - JIN SEOK KIM
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - CHONG-WOOK PARK
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - MI YOON CHUNG
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - MYONG GI CHUNG
- Division of Specimen and Genetic Resources, National Arboretum, Korea Forest Service, Gyeonggi Province, 487-821, Republic of Korea, School of Biological Sciences, Seoul National University, Seoul 151-742, Republic of Korea and Department of Biology and Institute of Basic Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
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Jones FA, Hamrick JL, Peterson CJ, Squiers ER. Inferring colonization history from analyses of spatial genetic structure within populations of Pinus strobus and Quercus rubra. Mol Ecol 2006; 15:851-61. [PMID: 16499707 DOI: 10.1111/j.1365-294x.2005.02830.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many factors interact to determine genetic structure within populations including adult density, the mating system, colonization history, natural selection, and the mechanism and spatial patterns of gene dispersal. We examined spatial genetic structure within colonizing populations of Quercus rubra seedlings and Pinus strobus juveniles and adults in an aspen-white pine forest in northern Michigan, USA. A 20-year spatially explicit demographic study of the forest enables us to interpret the results in light of recent colonization of the site for both species. We assayed 217 Q. rubra seedlings and 171 P. strobus individuals at 11 polymorphic loci using nine allozyme systems. Plant genotypes and locations were used in an analysis of spatial genetic structure. Q. rubra and P. strobus showed similar observed levels of heterozygosity, but Q. rubra seedlings have less heterozygosity than expected. Q. rubra seedlings show spatial genetic clumping of individuals on a scale to 25 m and levels of genetic relatedness expected from the clumped dispersion of half-siblings. In contrast, P. strobus has low levels of genetic relatedness at the smallest distance class and positive spatial genetic structure at scales < 10 m within the plot. The low density of adult Q. rubra outside the study plot and limited, spatially clumped rodent dispersal of acorns is likely responsible for the observed pattern of spatial genetic structure and the observed heterozygote deficit (i.e. a Wahlund effect). We attribute weaker patterns observed in P. strobus to the longer dispersal distance of seeds and the historical overlap of seed shadows from adults outside of the plot coupled with the overlap of seed shadows from younger, more recently established reproductive adults. The study demonstrates the utility of long-term demographic data in interpreting mechanisms responsible for generating contemporary patterns of genetic structure within populations.
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Affiliation(s)
- F A Jones
- Department of Plant Biology, University of Georgia, Athens, 30602, USA.
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