一个种还是多个种? 简化基因组及其形态学证据揭示中国白桫椤植物的物种多样性分化

doi:10.17520/biods.2019146

生物多样性 ›› 2019, Vol. 27 ›› Issue (11): 1196-1204. DOI: 10.17520/biods.2019146

所属专题：物种形成与系统进化

一个种还是多个种? 简化基因组及其形态学证据揭示中国白桫椤植物的物种多样性分化

莫日根高娃^1,²,商辉¹,刘保东²,康明³,严岳鸿^1,^*()

1 上海辰山植物园, 中国科学院上海辰山植物科学研究中心, 上海 201602
2 哈尔滨师范大学黑龙江省普通高等学校植物生物学重点实验室, 哈尔滨 150025
3 中国科学院华南植物园植物资源保护与可持续利用重点实验室, 广州 510650

收稿日期:2019-04-29 接受日期:2019-06-29 出版日期:2019-11-20 发布日期:2020-01-17
通讯作者: 严岳鸿
基金资助:
国家自然科学基金(31770350);上海市绿化和市容管理局科技攻关项目(G182411);湖南省教育厅科学研究项目(10C0720)

One or more species? GBS sequencing and morphological traits evidence reveal species diversification of Sphaeropteris brunoniana in China

Morigengaowa ^1,²,Hui Shang¹,Baodong Liu²,Ming Kang³,Yuehong Yan^1,^*()

1 Shanghai Chenshan Botanical Garden; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602
2 Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin 150025
3 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650

Received:2019-04-29 Accepted:2019-06-29 Online:2019-11-20 Published:2020-01-17
Contact: Yan Yuehong

摘要/Abstract

摘要：

物种是生物多样性的基本单元, 生殖隔离被认为是物种形成的关键; 然而物种并不是静止的而是处于不断的分化演变之中, 已经稳定成型但尚未到达分化后期的物种可能存在不完全的生殖隔离。对于物种的认识不能单从某一侧面或局部特征来界定, 而应通过“整合物种概念”来确定物种地位。Flora of China记载了中国产白桫椤属(Sphaeropteris) 2种, 即白桫椤(S. brunoniana)和笔筒树(S. lepifera), 并认为原产中国海南的海南白桫椤(S. hainanensis)和白桫椤为同一物种而将其并入白桫椤; 但海南白桫椤在形态上已出现了分化。为探讨白桫椤及其近缘物种的亲缘关系和物种多样性分化的情况, 本文采集到9个居群共21个样本, 通过GBS简化基因组测序技术获得单核苷酸变异位点(SNP), 进行系统发育树的构建和主成分及遗传结构的分析, 并结合叶片数量性状的统计分析和孢子形态的观察测量。结果表明, 海南白桫椤不仅与云南产白桫椤的基因型不同, 且在叶片特征和孢子纹饰上有明显差异; 但两个居群的生殖隔离较弱, 在广西沿海地区形成杂交产物, 其叶片特征为亲本的中间类型。因此, 我们认为海南白桫椤是由于地理隔离而形成的一个处在分化路上的物种, 建议恢复其物种地位; 广西产白桫椤为自然杂交群体, 应另处理为独立的自然杂交分类群——广西白桫椤(S. brunoniana × hainanensis)。

关键词: 白桫椤属, 海南白桫椤, 物种分化, 自然杂交, 基于测序的基因分型, 单核苷酸多态性

Abstract

Species are not static, but in the process of continuous differentiation and evolution. In this context, reproductive isolation is considered the key to most speciation events. However, species that may be only partially reproductively isolated may disturb our understanding of a species, as stated by ‘The integrative species concept’. In the Flora of China, Chinese Sphaeropteris contains two species, S. brunoniana and S. lepifera. S. brunoniana is thought to be the same species as a Hainan native, S. hainanensis, however, S. hainanensis seems to have differentiated morphologically. This study further explores the genetic relationship between S. brunoniana and its related species by collecting 21 samples from 9 populations for GBS reduced-representation genome sequencing for phylogenetic analysis. Using both genetic and morphological data, our results indicate that S. hainanensis differs genetically from S. brunoniana, but is also morphologically distinct based on leaf characteristics and spore ornamentation. Although the reproductive isolation of the two populations is weak, hybrids are formed in the coastal areas of Guangxi and leaves mimic intermediate morphology between parents. Therefore, our results suggest that S. hainanensis is in the process of speciation due to geographic isolation and suggests to restore its species status. S. brunoniana × hainanensis which the sample from Guangxi should be considered an independent natural hybrid taxon.

Key words: Sphaeropteris, S. hainanensis, speciation, natural hybridization, GBS, SNP

莫日根高娃, 商辉, 刘保东, 康明, 严岳鸿 (2019) 一个种还是多个种? 简化基因组及其形态学证据揭示中国白桫椤植物的物种多样性分化. 生物多样性, 27, 1196-1204. DOI: 10.17520/biods.2019146.

Morigengaowa , Hui Shang, Baodong Liu, Ming Kang, Yuehong Yan (2019) One or more species? GBS sequencing and morphological traits evidence reveal species diversification of Sphaeropteris brunoniana in China. Biodiversity Science, 27, 1196-1204. DOI: 10.17520/biods.2019146.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019146

https://www.biodiversity-science.net/CN/Y2019/V27/I11/1196

图/表 9

表1 白桫椤属的样品采集信息

Table 1 Sample details of Sphaeropteris

类群 Taxon	采样地点 Location	样本数量及采集号 Sample size and voucher no.
白桫椤 S. brunoniana	广西东兴 Dongxing, Guangxi	3: CFH09001403, CFH09001405, CFH09001406
白桫椤 S. brunoniana	海南琼中 Qiongzhong, Hainan	2: SG2100, SG2103
白桫椤 S. brunoniana	海南五指山 Wuzhishan, Hainan	6: SG2005, SG2014, SG2021, SG2030, SG2050, SG2054
白桫椤 S. brunoniana	云南河口 Hekou, Yunnan	3: CFH09000322, CFH09000324, CFH09000325
白桫椤 S. brunoniana	云南麻栗坡 Malipo, Yunnan	1: YN384
白桫椤 S. brunoniana	云南屏边 Pingbian, Yunnan	2: CFH09000301, ZXL05870
笔筒树 S. lepifera	福建福州 Fuzhou, Fujian	1: GBJ02954
笔筒树 S. lepifera	福建平潭 Pingtan, Fujian	1: GBJ04090
笔筒树 S. lepifera	台湾兰屿 Lanyu, Taiwan	2: ZXL06026, ZXL09919

图1 运用贝叶斯法和最大似然法, 基于核基因和叶绿体基因构建的白桫椤属系统发育树。横线上方的数字表示贝叶斯后验概率(PP ≥ 0.95), 横线下方的数字表示ML自展支持率(BS ≥ 50%)。样品信息见表1。

Fig. 1 The nuclear genes (A) and chloroplast genes (B) phylogenetic tree of Sphaeropteris based on Bayes and Maximum likelihood method. Numbers above the branches are posterior probability (PP ≥ 0.95) from the BI analysis, and numbers under the branches are bootstrap percentages (BS ≥ 50%) of maximum likelihood analysis. The sample information is shown in Table 1.

图2 基于核基因的SNP位点构建的白桫椤属邻接网络图

Fig. 2 Neighbor-Net network of Sphaeropteris based on nuclear SNPs

图3 白桫椤属基于SNP位点的主成分分析。图中每个点代表1个样品。

Fig. 3 Principal component analysis of Sphaeropteris based on SNPs. Each sample is represented by a point.

图4 通过ΔK的统计方法获得最优K

Fig. 4 The optimal K is obtained by the statistical method of ΔK

图5 白桫椤属Structure分析结果。每一个柱形代表1个样本, 每种颜色代表1个遗传簇。

Fig. 5 Structure of Sphaeropteris. Each sample is represented by a histogram, which is partitioned into different colors. Each color represents a genetic cluster.

图6 白桫椤属种间叶性状差异显著分析

Fig. 6 The significant difference analysis in leaf traits of Sphaeropteris

图7 白桫椤属孢子形态。A: 笔筒树; B-D: 白桫椤。B样品采自云南; C样品采自广西; D样品采自海南, 引自王全喜和戴锡玲(2010)

Fig. 7 The spore morphology of Sphaeropteris. A, Sphaeropteris lepifera; B-D, Sphaeropteris brunoniana. B, Sample from Yunnan; C, Sample from Guangxi; D, Sample from Hainan, adopted from Wang & Dai (2010).

表2 白桫椤属各种的孢子形态特征

Table 2 Spore morphological characteristics of Sphaeropteris

	笔筒树 S. lepifera	白桫椤 S. brunoniana
	笔筒树 S. lepifera	云南 Yunnan	广西 Guangxi	海南 Hainan
孢子大小 Spore size	34 μm × 46 μm	31 μm × 47 μm	35 μm × 45 μm	37 μm × 45 μm
极面观 Polar view	三角形, 三边内凹 Triangle, inset edge	三角形, 三边内凹 Triangle, inset edge	三角形, 三边直 Triangle, straight edge	三角形, 三边直 Triangle, straight edge
赤道面观 Equatorial view	扇形或近半圆形 Sector or approximate semicircle	扇形或近半圆形 Sector or approximate semicircle	扇形 Sector	扇形 Sector
表面纹 Ornamentation	短刺状 Short-echinulate	颗粒状, 细小 Granulate, small	颗粒状, 粗大 Granulate, thick	颗粒状, 细小 Granulate, small

参考文献 37

1	Arnold ML ( 1997) Natural Hybridization and Evolution. Oxford University Press, Oxford.
2	Bunawan H, Yen CC, Yaakop S, Noor NM ( 2017) Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences. BMC Research Notes, 10, 67.
3	Coyne JA, Orr HA ( 2004) Speciation. Sinauer Associates, Sunderland, MA.
4	Darriba D, Taboada GL, Doallo R, Posada D ( 2012) jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772.
5	Dong SY, Zuo ZY ( 2018) On the recognition of Gymnosphaera as a distinct genus in Cyatheaceae. Annals of the Missouri Botanical Garden, 103, 1-23.
6	Evanno G, Regnaut S, Goudet J ( 2005) Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14, 2611-2620.
7	Falush D, Stephens M, Pritchard JK ( 2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
8	Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences(2013) Flora of Guangxi,Vol. 6. Guangxi Science and Technology Publishing House,Xining. (in Chinese)
	[ 广西壮族自治区中国科学院广西植物研究所( 2013) 广西植物志,第6卷. 广西科学技术出版社, 西宁.]
9	Hong DY ( 2016) Biodiversity pursuits need a scientific and operative species concept. Biodiversity Science, 24, 979-999. (in Chinese with English abstract)
	[ 洪德元 ( 2016) 生物多样性事业需要科学、可操作的物种概念. 生物多样性, 24, 979-999.]
10	Johri BM ( 1984) Embryology of Angiosperms. Springer-Verlag, Berlin.
11	Klekowski EJ ( 1969) Reproductive biology of the Pteridophyta. II. Theoretical considerations. Botanical Journal of the Linnean Society, 62, 347-359.
12	Klekowski EJ, Lloyd RM ( 1968) Reproductive biology of the Pteridophyta. I. General considerations and a study of Onoclea sensibilis L. Botanical Journal of the Linnean Society, 60, 315-324.
13	Kong HZ ( 2016) Biodiversity undertakings call for extensive discussion on species concept and the criteria for species delimitation. Biodiversity Science, 24, 977-978. (in Chinese)
	[ 孔宏智 ( 2016) 生物多样性事业呼唤对物种概念和物种划分标准的深度讨论. 生物多样性, 24, 977-978.]
14	Li H, Durbin R ( 2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
15	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R ( 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
16	Li XX, Zhou ZY, Guo SX ( 1981) The Development and Evolution of the Plant Kingdom. Science Press,Beijing. (in Chinese)
	[ 李星学, 周志炎, 郭双兴 ( 1981) 植物界的发展和演化.科学出版社, 北京.]
17	Lischer HEL, Excoffier L ( 2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28, 298-299.
18	Liu JQ ( 2016) “The integrative species concept” and “species on the speciation way”. Biodiversity Science, 24, 1004-1008. (in Chinese with English abstract)
	[ 刘建全 ( 2016) “整合物种概念”和“分化路上的物种”. 生物多样性, 24, 1004-1008.]
19	Miller MA, Pfeiffer W, Schwartz T ( 2010) Creating the CIPRES science gateway for inference of large phylogenetic trees.In: Proceedings of the Gateway Computing Environments Workshop (GCE),New Orleans.
20	Morrison DA ( 2009) Using data-display networks for exploratory data analysis in phylogenetic studies. Molecular Biology Evolution, 27, 1044-1057.
21	Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang ZH, Schneider H, Donoghue PCJ ( 2018) The timescale of early land plant evolution. Proceedings of the National Academy of Sciences, USA, 115, 2274-2283.
22	Pritchard JK, Stephens M, Donnelly P ( 2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
23	Ranker TA, Tyron AF, Lugardon B ( 1993) Spores of the Pteridophyta: Surface, wall structure, and diversity based on electron microscope studies. Systematic Botany, 18, 377-378.
24	Rieseberg LH, Wood TE, Baack EJ ( 2006) The nature of plant species. Nature, 440, 524-527.
25	Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP ( 2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Software for Systematics and Evolution, 61, 539-542.
26	Rothfels CJ, Johnson AK, Hovenkamp PH, Swofford DL, Roskam HC, Fraser-Jenkins CR, Windham MD, Pryer KM ( 2015) Natural hybridization between genera that diverged from each other approximately 60 million years ago. The American Naturalist, 185, 433-442.
27	Soltis DE, Soltis PS ( 1987) Polyploidy and breeding systems in homosporous pteridophyta: A reevaluation. The American Naturalist, 130, 219-232.
28	Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M, Belzile F ( 2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE, 8, e54603.
29	Stamatakis A ( 2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312-1313.
30	Tryon RM, Tryon AF, Rudolph ED ( 1982) Ferns and allied plants with special reference to tropical America. American Fern Journal, 73(3), 94-95.
31	Wang QX, Dai XL ( 2010) Spores of Polypodiales (Filicales) from China. Science Press, Beijing. (in Chinese)
	[ 王全喜, 戴锡玲 ( 2010) 中国水龙骨目(真蕨目)植物孢子形态的研究. 科学出版社, 北京.]
32	Wang QX, Yu J ( 2003) Classification of spore ornamentation in filicales under SEM. Acta Botanica Yunnanica, 25, 313-320. (in Chinese with English abstract)
	[ 王全喜, 于晶 ( 2003) 扫描电镜下真蕨目孢子表面纹饰的分类. 云南植物研究, 25, 313-320.]
33	Wang WS, Mauleon R, Hu ZQ, Chebotarov D, Tai SS, Wu ZC, Li M, Zheng TQ, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu JL, Sun C, Fu BY, Zhang HL, Gao YM, Zhao XQ, Shen F, Cui X, Yu H, Li ZC, Chen ML, Detras J, Zhou YL, Zhang XY, Zhao Y, Kudrna D, Wang CC, Li R, Jia B, Lu JY, He XC, Dong ZT, Xu JB, Li YH, Wang M, Shi JX, Li J, Zhang DB, Lee SH, Hu WS, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu YC, Yue Z, Naredo MEB, Talag J, Wang XQ, Li JJ, Fang XD, Yin Y, Glaszmann JC, Zhang JW, Li JY, Hamilton RS, Wing RA, Ruan J, Zhang GY, Wei CC, Alexandrov N, McNally KL, Li ZK, Leung H ( 2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557, 43-49.
34	Wang ZJ, Guan KY ( 2011) Genetic structure and phylogeography of a relict tree fern, Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations: Implications for conservation. Journal of Systematics and Evolution, 49, 72-79.
35	Xie P ( 2016) A brief review on the historical changes in the concept of species. Biodiversity Science, 24, 1014-1019. (in Chinese with English abstract)
	[ 谢平 ( 2016) 浅析物种概念的演变历史. 生物多样性, 24, 1014-1019.]
36	Yang J, Lee SH, Goddard ME, Visscher PM ( 2011) GCTA: A tool for genome-wide complex trait analysis. American Journal of Human Genetics, 88, 76-82.
37	Zhang XC, Nishida H ( 2013) Cyatheaceae. In: Flora of China,vol. 2-3(Pteridophytes) (eds Wu ZY, Raven PH, Hong DY), pp.134-138. Science Press, Beijing & Missouri Botanical Garden, St. Louis.

[1]	蒋际宝, 邱江平. 中国巨蚓科蚯蚓的起源与演化[J]. 生物多样性, 2018, 26(10): 1074-1082.
[2]	魏宇昆, 黄艳波, 李桂彬. 同域分布共享传粉者的鼠尾草属植物的生殖隔离[J]. 生物多样性, 2017, 25(6): 608-614.
[3]	郑硕理, 田晓玲, 黄承玲, 王灵军, 冯元, 张敬丽. 结合分子手段和形态分析验证大白杜鹃与马缨杜鹃的自然杂交[J]. 生物多样性, 2017, 25(6): 627-637.
[4]	田代科, 李春, 肖艳, 付乃峰, 童毅, 吴瑞娟. 中国秋海棠属植物的自然杂交发生及其特点[J]. 生物多样性, 2017, 25(6): 654-674.
[5]	商辉, 严岳鸿. 自然杂交与生物多样性保护[J]. 生物多样性, 2017, 25(6): 683-688.
[6]	周秋杰, 蔡亚城, 黄伟伦, 吴伟, 代色平, 王峰, 周仁超. 野牡丹属两个海南特有种与同属广布种自然杂交的分子证据[J]. 生物多样性, 2017, 25(6): 638-646.
[7]	王玉国. 自然杂交与物种形成[J]. 生物多样性, 2017, 25(6): 565-576.
[8]	刘建全. “整合物种概念”和“分化路上的物种”[J]. 生物多样性, 2016, 24(9): 1004-1008.
[9]	邹喻苹, 葛颂. 新一代分子标记——SNPs及其应用[J]. 生物多样性, 2003, 11(5): 370-382.
[10]	张大勇, 姜新华. 群落内物种多样性发生与维持的一个假说^*[J]. 生物多样性, 1997, 05(3): 161-167.

一个种还是多个种? 简化基因组及其形态学证据揭示中国白桫椤植物的物种多样性分化

One or more species? GBS sequencing and morphological traits evidence reveal species diversification of Sphaeropteris brunoniana in China

RichHTML

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

图/表 9

参考文献 37

相关文章 10

编辑推荐

Metrics

本文评价