龙脑香科青梅小尺度空间遗传结构研究

Fine-scale spatial genetic structure of Vatica mangachapoi (Dipterocarpaceae)

摘要

青梅 （Vatica mangachapoi ） 隶属龙脑香科 （Dipterocarpaceae） 青梅属 （Vatica），是海南岛热带低地雨林的优势种。研究其遗传动态与小尺度基因扩散格局，对理解热带森林更新机制和优势种的生态适应具有重要意义。本研究以海南热带雨林国家公园内的青梅为对象，采集霸王岭与吊罗山高低海拔 4 个种群共 372 个样本，利用 7 对微卫星分子标记 （simple sequence repeats, SSR） 系统评估其遗传多样性、种群结构及小尺度空间遗传结构 （fine-scale spatial genetic structure, FSGS）。结果表明，青梅总体遗传多样性水平较高 （N_a = 7.107, H_e = 0.726），明显高于海南岛龙脑香科的坡垒 （Hopea hainanensis, N_a = 2.458，H_e = 0.432） 和铁凌 （H. reticulata, N_a = 3.636，H_e = 0.599）。Structure 显示部分个体的遗传组分混杂，其中，霸王岭高海拔群体 （BW-H）的遗传组分表现出一定分化。PCoA 和 NJ 树显示不同种群来源的个体混杂，未形成清晰分组。FSGS 分析结果表明，两个高海拔种群的基因型存在更强的空间聚集 （Sp = 0.036 0～0.044 0），显著高于低海拔种群 （Sp = 0.009 6～0.016 8）。本研究揭示青梅种群的遗传动态受海拔等环境因子影响，为龙脑香科树种保护与种质资源管理提供了科学依据。

Abstract

Vatica mangachapoi Blanco, a member of the genus Vatica (Dipterocarpaceae), is a dominant species in the tropical lowland rainforests of Hainan Island. Understanding its genetic dynamics and fine-scale gene dispersal patterns is essential for elucidating the ecological adaptation of dominant tree species in tropical ecosystems. In this context 372 individuals across different elevational gradients were sampled from Bawangling and Diaoluoshan within Hainan Tropical Rainforest National Park to evaluate genetic diversity, population structure, and fine-scale spatial genetic structure (FSGS) using seven microsatellite loci. The results revealed a relatively high overall genetic diversity inV. mangachapoi (N_a = 7.107, H_e = 0.726), markedly higher than that of other two dipterocarps on Hainan Island, Hopea hainanensis (N_a = 2.458, H_e = 0.432) and H. reticulata (N_a = 3.636, H_e = 0.599). Structure analysis found that the high altitude population at Bawangling (BW-H) differentiated to some extent with the other three populations, while PCoA and NJ tree analyses could not detect clear genetic differentiation among the four populations. FSGS analyses indicated stronger spatial clustering of genotypes in high-elevation populations (Sp = 0.036 0-0.044 0) than that in low-elevation populations (Sp = 0.009 6−0.016 8). Overall, all the findings indicate that the genetic dynamics of V. mangachapoi populations are influenced by elevational environmental gradients and provide scientific insights for the conservation and management of tropical dipterocarps.

关键词

青梅 / 海南热带雨林国家公园 / SSR 标记 / 遗传多样性 / 小尺度空间遗传结构

Key words

Vatica mangachapoi Blanco / SSR markers / Hainan Tropical Rainforest National Park / genetic diversity / fine-scale spatial genetic structure (FSGS)

参考文献

[1] 李周园, 叶小洲, 王少鹏. 生态系统稳定性及其与生物多样性的关系 [J]. 植物生态学报 , 2021, 45(10): 1127-1139. https://doi.org/10.17521/cjpe.2020.0116

[2] Salgotra R K, Chauhan B S. Genetic diversity, conservation, and utilization of plant genetic resources[J]. Genes, 2023, 14(1): 174. https://doi.org/10.3390/genes14010174

[3] Fremout T, Thomas E, Taedoumg H, et al. Diversity for Restoration (D4R): guiding the selection of tree species and seed sources for climate-resilient restoration of tropical forest landscapes[J]. Journal of Applied Ecology, 2022, 59(3): 664-679. https://doi.org/10.1111/1365-2664.14079

[4] 韦伊, 刘慧, 贺鹏程, 等. 南亚热带不同演替阶段森林优势树种叶片构建成本与机械抗性的协同关系[J]. 热带亚热带植物学报, 2022, 30(4): 483-491. https://doi.org/10.11926/jtsb.4502

[5] Hofhansl F, Chacón‐ Madrigal E, Brännström å, et al. Mechanisms driving plant functional trait variation in a tropical forest[J]. Ecology and Evolution, 2021, 11(9): 3856-3870. https://doi.org/10.1002/ece3.7256

[6] Zhang C F, Guo L L. The theoretical and methodological innovations in geomorphology: Current status, application frontiers, and future prospects[J]. Geographical Research Bulletin, 2025, 4: 538-569. https://doi.org/10.50908/grb.4.0_538

[7] Vekemans X, Hardy O J. New insights from fine-scale spatial genetic structure analyses in plant populations[J]. Molecular Ecology, 2004, 13(9): 921-935. https://doi.org/10.1046/j.1365-294X.2004.02076.x

[8] Escobar S, Vigouroux Y, Karubian J, et al. Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm[J]. Biotropica, 2023, 55(1): 160-172. https://doi.org/10.1111/btp.13172

[9] 彭国清. 淡黄金花茶精细空间遗传结构[D]. 桂林: 广西师范大学, 2016. https://doi.org/10.7666/d.Y3080921

[10] Nakanishi A, Goto S, Sumiyoshi C, et al. Directional seed and pollen dispersal and their separate effects on anisotropy of fine‐scale spatial genetic structure among seedlings in a dioecious, wind‐ pollinated, and wind-dispersed tree species, Cercidiphyllum japonicum [J]. Ecology and Evolution, 2021, 11(12): 7754-7767. https://doi.org/10.1002/ece3.7609

[11] Miguel-Peñaloza A, Cultid-Medina C A, Pérez-Alquicira J, et al. Do habitat fragmentation and degradation influence the strength of fine-scale spatial genetic structure in plants? A global meta-analysis[J]. AoB Plants, 2023, 15(3): plad019. https://doi.org/10.1093/aobpla/plad019

[12] Ashton P S, Morley R J, Heckenhauer J, et al. The magnificent Dipterocarps: précis for an Epitaph?[J]. Kew Bulletin, 2021, 76(2): 87-125. https://doi.org/10.1007/s12225-021-09934-7

[13] 李婧涵, 张顺卫, 杨小波, 等. 海南省分布的国家重点保护野生植物组成及区系特征[J]. 广西植物, 2024, 44(11): 2021-2032. https://doi.org/10.11931/guihaia.gxzw202401028

[14] 谭珂, 董书鹏, 卢涛, 等. 被子植物翅果的多样性及演化[J]. 植物生态学报, 2018, 42(8): 806-817. https://doi.org/10.17521/cjpe.2018.0053

[15] 兰国玉, 陈伟, 周小飞. 海南霸王岭青梅林群落特征研究[J]. 西北植物学报, 2007, 27(9): 1861-1868. https://doi.org/10.3321/j.issn:1000-4025.2007.09.025

[16] 陈伟文, 戚华沙, 符瑞侃, 等. 海南岛青梅种质资源调查与种群动态分析[J]. 分子植物育种, 2021, 19(14): 4846-4854. https://doi.org/10.13271/j.mpb.019.004846

[17] Tang L, Liao X Z, Tembrock L R, et al. A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae) [J]. DNA Research, 2022, 29(2): dsac005. https://doi.org/10.1093/dnares/dsac005

[18] Wang R, Liu C N, Segar S T, et al. Dipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests[J]. Nature Communications, 2024, 15(1): 1683. https://doi.org/10.1038/s41467-024-45836-5

[19] Duan J Y, Wang H Y, Tang L. Effects of habitat fragmentation on the coastal Vatica mangachapoi forest (Dipterocarpaceae) in Shimei Bay, Hainan Island, China [J]. Tropical Plants, 2023, 2(1): 8. https://doi.org/10.48130/TP-2023-0008

[20] 肖书文, 詹晨, 王梦桥, 等. 国家公园资源利用体系优化策略——以海南热带雨林国家公园霸王岭片区为例[J]. 北京林业大学学报 (社会科学版), 2021, 20(2): 35-43. https://doi.org/10.13931/j.cnki.bjfuss.2021083

[21] 李晨笛, 梁宜文, 杨小波, 等. 吊罗山热带天然林物种多样性的海拔分布格局[J]. 广西植物, 2023, 43(5): 991-922. https://doi.org/10.11931/guihaia.gxzw202201056

[22] Yang H, Liu S R, Cao K F, et al. Characteristics of typhoon disturbed gaps in an old-growth tropical montane rainforest in Hainan Island, China[J]. Journal of Forestry Research, 2017, 28(6): 1231-1239. https://doi.org/10.1007/s11676-017-0402-y

[23] Arellano G, Cala V, Fuentes A, et al. A standard protocol for woody plant inventories and soil characterisation using temporary 0.1-ha plots in tropical forests[J]. Journal of Tropical Forest Science, 2016, 28(4): 508-516.

[24] Gemeinholzer B, Rey I, Weising K, et al. Organizing specimen and tissue preservation in the field for subsequent molecular analyses[J]. Manual of Field Recording Techniques and Protocols for All Taxa Biodiversity Inventories, 2010(8): 129-157.

[25] Rachmat H H, Yulita K S, Dwiyanti F G, et al. Optimizing DNA extraction and selecting suitable regions for biodiversity assessment: a study on Shorea leprosula [J]. Jurnal Manajemen Hutan Tropika, 2024, 30(1): 144-154. https://doi.org/10.7226/144

[26] Guo J J, Shang S B, Wang C S, et al. Twenty microsatellite markers for the endangered Vatica mangachapoi (Dipterocarpaceae) [J]. Applications in Plant Sciences, 2017, 5(2): 1600134. https://doi.org/10.3732/apps.1600134

[27] Hulce D, Li X, Snyder-Leiby T, et al. GeneMarker® genotyping software: tools to increase the statistical power of DNA fragment analysis[J]. Journal of Biomolecular Techniques, 2011, 22(Suppl): S35-S36.

[28] Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data[J]. Genetics, 1992, 131(2): 479-491. https://doi.org/10.1093/genetics/131.2.479

[29] Earl D A, vonHoldt B M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method[J]. Conservation Genetics Resources, 2012, 4(2): 359-361. https://doi.org/10.1007/s12686-011-9548-7

[30] Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 2021, 38(7): 3022-3027. https://doi.org/10.1093/molbev/msab120

[31] Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees[J]. Molecular Biology and Evolution, 1987, 4(4): 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

[32] Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study[J]. Molecular Ecology, 2005, 14(8): 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

[33] Hardy O J, Vekemans X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels[J]. Molecular Ecology Notes, 2002, 2(4): 618-620. https://doi.org/10.1046/j.1471-8286.2002.00305.x

[34] Botstein D, White R L, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. The American Journal of Human Genetics, 1980, 32(3): 314-331.

[35] Wang C, Ma X, Ren M X, et al. Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China [J]. PLoS One, 2020, 15(11): e0241452. https://doi.org/10.1371/journal.pone.0241452

[36] 蔡颖, 段继煜, 朱思奇, 等. 基于 SSR 标记的无翼坡垒遗传多样性研究[J]. 热带生物学报, 2022, 13(2): 127-135. https://doi.org/10.15886/j.cnki.rdswxb.2022.02.004

[37] Ng K K S, Lee S L, Koh C L. Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels[J]. Molecular Ecology, 2004, 13(3): 657-669. https://doi.org/10.1046/j.1365-294X.2004.02094.x

[38] Tang L, Duan J Y, Cai Y, et al. Low genetic diversity and small effective population size in the endangered Hopea reticulata (Dipterocarpaceae) on Hainan Island, China [J]. Global Ecology and Conservation, 2024, 50: e02846. https://doi.org/10.1016/j.gecco.2024.e02846

[39] Dai Z C, Si C C, Zhai D L, et al. Genetic effects of historical anthropogenic disturbance on a long-lived endangered tropical tree Vatica mangachapoi [J]. Journal of Forestry Research, 2018, 29(2): 291-299. https://doi.org/10.1007/s11676-017-0470-z

[40] Smith J R, Bagchi R, Ellens J, et al. Predicting dispersal of auto‐gyrating fruit in tropical trees: a case study from the Dipterocarpaceae[J]. Ecology and Evolution, 2015, 5(9): 1794-1801. https://doi.org/10.1002/ece3.1469

[41] Hamrick J L, Godt M J W, Sherman-Broyles S L. Factors influencing levels of genetic diversity in woody plant species[J]. New Forests, 1992, 6(1/4): 95-124. https://doi.org/10.1007/BF00120641

[42] Ony M A, Nowicki M, Boggess S L, et al. Habitat fragmentation influences genetic diversity and differentiation: fine-scale population structure of Cercis canadensis (eastern redbud) [J]. Ecology and Evolution, 2020, 10(8): 3655-3670. https://doi.org/10.1002/ece3.6142

[43] Ghazoul J. Dipterocarp biology, ecology, and conservation [M]. Oxford: Oxford University Press, 2016: 89-125. https://doi.org/10.1093/acprof:oso/9780199639656.001.0001

[44] Bacles C F E, Burczyk J, Lowe A J, et al. Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L. [J]. Evolution, 2005, 59(5): 979-990. https://doi.org/10.1111/j.0014-3820.2005.tb01037.x

[45] Kikuchi S, Shibata M, Tanaka H. Effects of forest fragmentation on the mating system of a cool-temperate heterodichogamous tree Acer mono [J]. Global Ecology and Conservation, 2015, 3: 789-801. https://doi.org/10.1016/j.gecco.2015.04.005

[46] Schlötterer C. The evolution of molecular markers-just a matter of fashion?[J]. Nature Reviews Genetics, 2004, 5(1): 63-69. https://doi.org/10.1038/nrg1249

[47] Mishra G, Bhandari M S, Meena R K, et al. Contemporary spatial association of genetic diversity determinants in Asian Dipterocarps: a systematic review[J]. Annals of Silvicultural Research, 2023, 48(2): 73-86. https://doi.org/10.12899/asr-2444

[48] Lee S L, Ng K K S, Ng C H, et al. Spatial studies of Shorea parvifolia spp. parvifolia (Dipterocarpaceae) in a lowland and hill dipterocarp forest [J]. Journal of Tropical Forest Science, 2016, 28(5): 309-317.

[49] Konuma A, Tsumura Y, Lee C T, et al. Estimation of gene flow in the tropical-rainforest tree Neobalanocarpus heimii (Dipterocarpaceae), inferred from paternity analysis [J]. Molecular Ecology, 2000, 9(11): 1843-1852. https://doi.org/10.1046/j.1365-294x.2000.01081.x

[50] Kenta T, Isagi Y, Nakagawa M, et al. Variation in pollen dispersal between years with different pollination conditions in a tropical emergent tree[J]. Molecular Ecology, 2004, 13(11): 3575-3584. https://doi.org/10.1111/j.1365-294X.2004.02345.x

[51] Kettle C J, Hollingsworth P M, Burslem D F R P, et al. Determinants of fine-scale spatial genetic structure in three co-occurring rain forest canopy trees in Borneo[J]. Perspectives in Plant Ecology, Evolution and Systematics, 2011, 13(1): 47-56. https://doi.org/10.1016/j.ppees.2010.11.002

[52] Harata T, Nanami S, Yamakura T, et al. Fine-scale spatial genetic structure of ten dipterocarp tree species in a Bornean rain forest[J]. Biotropica, 2012, 44(5): 586-594. https://doi.org/10.1111/j.1744-7429.2011.00836.x

[53] Tito de Morais C, Ghazoul J, Maycock C R, et al. Understanding local patterns of genetic diversity in dipterocarps using a multi-site, multi-species approach: implications for forest management and restoration[J]. Forest Ecology and Management, 2015, 356: 153-165. https://doi.org/10.1016/j.foreco.2015.07.023

[54] 段继煜, 蔡颖, 饶朝康, 等. 海南岛特有濒危龙脑香科树种铁凌小尺度空间遗传结构[J]. 生态学杂志, 2025, 44(8): 2582-2590. https://doi.org/10.13292/j.1000-4890.202508.024

[55] Finger A, Kettle C J, Kaiser-Bunbury C N, et al. Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae) [J]. Molecular Ecology, 2012, 21(10): 2369-2382. https://doi.org/10.1111/j.1365-294X.2012.05543.x

[56] Ismail S A, Ghazoul J, Ravikanth G, et al. Fragmentation Genetics of Vateria indica: implications for management of forest genetic resources of an endemic dipterocarp [J]. Conservation Genetics, 2014, 15(3): 533-545. https://doi.org/10.1007/s10592-013-0559-6

基金资助

海南省科技专项基金项目(ZDYF2023RDYL01)

海南国家公园研究院基金项目(KY-24ZK02)