丹霞梧桐群体遗传结构及其遗传分化

doi:10.17520/biods.2018223

生物多样性 ›› 2018, Vol. 26 ›› Issue (11): 1168-1179. DOI: 10.17520/biods.2018223

• 研究报告: 植物多样性 • 上一篇下一篇

丹霞梧桐群体遗传结构及其遗传分化

武星彤¹, 陈璐¹, 王敏求¹, 张原¹, 林雪莹¹, 李鑫玉¹, 周宏², 文亚峰^1,^*()

1 中南林业科技大学风景园林学院, 长沙 410004
2 广东省韶关市野生动植物保护办公室, 广东韶关 512000

收稿日期:2018-08-13 接受日期:2018-11-28 出版日期:2018-11-20 发布日期:2019-01-08
通讯作者: 文亚峰
作者简介:# 共同第一作者
基金资助:
国家林业局野生植物保护项目和韶关市野生动植物保护办公室项目(2016ZWZY06)

Population structure and genetic divergence in Firmiana danxiaensis

Xingtong Wu¹, Lu Chen¹, Minqiu Wang¹, Yuan Zhang¹, Xueying Lin¹, Xinyu Li¹, Hong Zhou², Yafeng Wen^1,^*()

1 Central South University of Forestry and Technology, Changsha 410004
2 Wildlife Conservation Office of Shaoguan, Guangdong, Shaoguan, Guangdong 512000

Received:2018-08-13 Accepted:2018-11-28 Online:2018-11-20 Published:2019-01-08
Contact: Wen Yafeng
About author:# Co-first authors

摘要/Abstract

摘要：

丹霞梧桐(Firmiana danxiaensis)是分布于我国韶关地区北部丹霞地貌的特有物种, 其分布范围狭窄, 种群数量小。本文利用EST-SSR分子标记位点, 分析丹霞梧桐群体(丹霞山组群和南雄组群)的遗传多样性和遗传结构, 研究群体的分化历史, 探讨该物种的可能分布和科学保护策略。结果表明: 丹霞梧桐总的遗传多样性中等(Ht = 0.631), 群体内遗传多样性较高(Hs = 0.546), 遗传变异主要存在于群体内(79.66%), 但不同地理组群间存在显著的遗传分化(F_ST= 0.150)。长期地理隔离和现代人为干扰是形成丹霞梧桐当前遗传变异模式的主要原因。STRUCTURE分析可将研究群体划分为清晰的两个基因库(gene pool), 其遗传结构与系统发育地理格局之间有密切关系。丹霞梧桐不同地理群体经历了独立的进化路线, 但丹霞山群体的杂合性高, 遗传背景更为复杂。近似贝叶斯运算法(Approximate Bayesian Computation, ABC)分析表明, 丹霞山和南雄地理群体在10万年前由同一个祖先群体分化而来, 分化时有效群体大小分别为7,290和5,550。结合丹霞梧桐的遗传变异和生态位信息, 可推测丹霞梧桐曾广泛分布于南岭地区, 受第四纪第三次亚冰期的影响, 南岭北部的丹霞梧桐群体因气候剧烈变化而灭绝, 仅在南岭南部适宜的环境中得以保存并繁衍至今, 丹霞山和南雄是丹霞梧桐最主要的两个冰期避难所。在全面掌握丹霞梧桐的自然分布, 开展就地保护的基础上, 通过建立种质资源圃、人工种苗扩繁、自然回归试验等措施, 对于该物种的异地保护、种群恢复和开发利用具有重要意义。

关键词: 群体遗传结构, 遗传分化, 遗传多样性, 近似贝叶斯算法, 微卫星标记, 丹霞梧桐

Abstract

Firmiana danxiaensis is an endemic plant species which is narrowly distributed in the northern parts of Shaoguan, Guangdong, China. To devise appropriate conservation strategies for this rare species, we examined the population structure and estimated the demographic history of nine natural populations using 18 EST-SSR markers. The results revealed a moderate degree of total genetic diversity (Ht = 0.631) at the species level but high genetic diversity within populations (Hs = 0.546). Strong genetic differentiation existed between two groups of Danxiashan and Nanxiong (F_ST= 0.150). This current pattern might have arisen from prolonged geographical isolation and human disturbances. STRUCTURE analysis demonstrated that whole population can be divided into two distinct gene pools, closely related by their geographic location and having experienced independent evolutionary routes. The genetic background of Danxiashan was more complicated than that of Nanxiong. Approximate Bayesian Computation (ABC) analysis indicated that divergence time between the two groups could be 100,000 years BP, and their effective population size were 7,290 and 5,550 individuals, respectively. Combining the information of genetic variation with niche modelling, we inferred that F. danxiaensis might have been widely distributed around the Nanling Mountain in the Quaternary period. Populations located in the northern of Nanling Mountain likely became extinct due to climate change. Danxiashan and Nanxiong provided the main refuges for the species during the last ice age. Being a rare species with small population sizes, better ecological investigation of natural populations and in situ conservation and implementation of restoration strategy are important measures to conserve this species.

Key words: population genetic structure, genetic divergence, genetic diversity, Approximate Bayesian Computation, EST-SSR marker, Firmiana danxiaensis

武星彤, 陈璐, 王敏求, 张原, 林雪莹, 李鑫玉, 周宏, 文亚峰 (2018) 丹霞梧桐群体遗传结构及其遗传分化. 生物多样性, 26, 1168-1179. DOI: 10.17520/biods.2018223.

Xingtong Wu, Lu Chen, Minqiu Wang, Yuan Zhang, Xueying Lin, Xinyu Li, Hong Zhou, Yafeng Wen (2018) Population structure and genetic divergence in Firmiana danxiaensis. Biodiversity Science, 26, 1168-1179. DOI: 10.17520/biods.2018223.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2018223

https://www.biodiversity-science.net/CN/Y2018/V26/I11/1168

图/表 13

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组群 Group	群体 Population	编号 Codes	纬度 Latitude (N)	经度 Longitude (E)	数量 Number
丹霞山 Danxiashan (DXS)	锦湖 Jinhu	JH	25°2°20.24?	113°44°52.80?	23
	老苗圃 Laomiaopu	LMP	25°2°22.24?	113°44°59.51?	21
	韶石山 Shaoshishan	SS	24°56°43.33?	113°45°17.60?	15
	阳元山 Yangyuanshan	YYS	25°2°46.08?	113°44°7.32?	30
	长老峰 Zhanglaofeng	ZLF	25°1°34.70?	113°44°19.87?	29
南雄 Nanxiong (NX)	鸳鸯湖 Yuanyanghu	QWT	25°6°58.53?	114°11°30.70?	27
	水库1 Shuiku1	SK1	25°6°58.63?	114°12°25.62?	23
	水库2 Shuiku2	SK2	25°7°12.58?	114°12°30.57?	21
	柴岭 Chailing	WT	25°7°17.53?	114°12°16.21?	24

组群 Group	群体 Population	编号 Codes	纬度 Latitude (N)	经度 Longitude (E)	数量 Number
丹霞山 Danxiashan (DXS)	锦湖 Jinhu	JH	25°2°20.24?	113°44°52.80?	23
	老苗圃 Laomiaopu	LMP	25°2°22.24?	113°44°59.51?	21
	韶石山 Shaoshishan	SS	24°56°43.33?	113°45°17.60?	15
	阳元山 Yangyuanshan	YYS	25°2°46.08?	113°44°7.32?	30
	长老峰 Zhanglaofeng	ZLF	25°1°34.70?	113°44°19.87?	29
南雄 Nanxiong (NX)	鸳鸯湖 Yuanyanghu	QWT	25°6°58.53?	114°11°30.70?	27
	水库1 Shuiku1	SK1	25°6°58.63?	114°12°25.62?	23
	水库2 Shuiku2	SK2	25°7°12.58?	114°12°30.57?	21
	柴岭 Chailing	WT	25°7°17.53?	114°12°16.21?	24

位点 Locus	等位基因数 Number of allele (Na)	总遗传多样性 Total genetic diversity for the species (Ht)	群体内遗传多样性 Genetic diversity within populations (Hs)	遗传分化系数 Interpersonal inbreeding coefficient (F_ST)	标准遗传分化系数 Gene differentiation factor (G_ST)	多态性信息含量 Polymorphism information content (PIC)	登录号 Accession number
unigene_21904	9	0.651	0.590	0.102	0.094	0.577	MH053446
unigene_9882	9	0.670	0.546	0.217	0.185	0.608	MH053447
unigene_33644	7	0.726	0.618	0.171	0.148	0.680	MH053448
unigene_15157	8	0.800	0.722	0.094	0.098	0.765	MH053449
unigene_23055	9	0.562	0.500	0.136	0.111	0.486	MH053450
unigene_60653	5	0.692	0.598	0.153	0.137	0.639	MH053451
unigene_30066	6	0.588	0.554	0.064	0.057	0.498	MH053452
unigene_37667	3	0.402	0.320	0.223	0.205	0.331	MH053453
unigene_25213	4	0.578	0.510	0.135	0.118	0.515	MH053454
unigene_36790	13	0.745	0.582	0.240	0.219	0.717	MH053455
unigene_5197	9	0.638	0.514	0.219	0.194	0.611	MH053456
unigene_48018	5	0.525	0.506	0.038	0.035	0.419	MH053457
unigene_31908	15	0.700	0.640	0.080	0.085	0.659	MH053458
unigene_25861	4	0.526	0.523	0.007	0.006	0.418	MH053459
unigene_42278	7	0.745	0.632	0.165	0.152	0.704	MH053460
unigene_35652	10	0.733	0.597	0.205	0.186	0.711	MH053461
Fir_SSR25d-F	5	0.549	0.478	0.126	0.130	0.475	KF048045
Fir_SSR81d-F	3	0.527	0.398	0.285	0.244	0.422	KF048051
均值 Mean	7.278	0.631	0.546	0.150	0.135	0.569

位点 Locus	等位基因数 Number of allele (Na)	总遗传多样性 Total genetic diversity for the species (Ht)	群体内遗传多样性 Genetic diversity within populations (Hs)	遗传分化系数 Interpersonal inbreeding coefficient (F_ST)	标准遗传分化系数 Gene differentiation factor (G_ST)	多态性信息含量 Polymorphism information content (PIC)	登录号 Accession number
unigene_21904	9	0.651	0.590	0.102	0.094	0.577	MH053446
unigene_9882	9	0.670	0.546	0.217	0.185	0.608	MH053447
unigene_33644	7	0.726	0.618	0.171	0.148	0.680	MH053448
unigene_15157	8	0.800	0.722	0.094	0.098	0.765	MH053449
unigene_23055	9	0.562	0.500	0.136	0.111	0.486	MH053450
unigene_60653	5	0.692	0.598	0.153	0.137	0.639	MH053451
unigene_30066	6	0.588	0.554	0.064	0.057	0.498	MH053452
unigene_37667	3	0.402	0.320	0.223	0.205	0.331	MH053453
unigene_25213	4	0.578	0.510	0.135	0.118	0.515	MH053454
unigene_36790	13	0.745	0.582	0.240	0.219	0.717	MH053455
unigene_5197	9	0.638	0.514	0.219	0.194	0.611	MH053456
unigene_48018	5	0.525	0.506	0.038	0.035	0.419	MH053457
unigene_31908	15	0.700	0.640	0.080	0.085	0.659	MH053458
unigene_25861	4	0.526	0.523	0.007	0.006	0.418	MH053459
unigene_42278	7	0.745	0.632	0.165	0.152	0.704	MH053460
unigene_35652	10	0.733	0.597	0.205	0.186	0.711	MH053461
Fir_SSR25d-F	5	0.549	0.478	0.126	0.130	0.475	KF048045
Fir_SSR81d-F	3	0.527	0.398	0.285	0.244	0.422	KF048051
均值 Mean	7.278	0.631	0.546	0.150	0.135	0.569

群体 Population	编号 Codes	等位基因数 Number of allele (Na)	期望杂合度 Expected heterozygosity (He)	观测杂合度 Observed heterozygosity (Ho)	等位基因丰富度 Allelic richness (Ar)	私有等位基因丰富度 Private allelic richness (pAr)	近交系数 Inbreeding coefficient (F_IS)
锦湖 Jinhu	JH	3.778	0.539	0.719	3.520	0.320	-0.345***
老苗圃 Laomiaopu	LMP	3.778	0.543	0.638	3.540	0.190	-0.189***
韶石山 Shaoshishan	SS	3.389	0.544	0.765	3.370	0.150	-0.409***
阳元山 Yangyuanshan	YYS	4.444	0.548	0.673	3.820	0.220	-0.203***
长老峰 Zhanglaofeng	ZLF	4.389	0.584	0.665	3.850	0.380	-0.178***
鸳鸯湖 Yuanyanghu	QWT	4.056	0.533	0.648	3.580	0.230	-0.198***
水库1 Shuiku1	SK1	3.167	0.447	0.495	2.990	0.140	-0.056***
水库2 Shuiku2	SK2	3.778	0.544	0.712	3.470	0.130	-0.310***
柴岭 Chailing	WT	4.222	0.545	0.623	3.770	0.150	-0.175***
平均值 Mean		3.889	0.536	0.660	3.546	0.212	-0.229

丹霞梧桐群体遗传结构及其遗传分化

Population structure and genetic divergence in Firmiana danxiaensis

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组群 Group	期望杂合度 Expected heterozygosity (He)	群体内遗传多样性 Genetic diversity within populations (Hs)	等位基因丰富度 Allelic richness (Ar)	私有等位基因丰富度 Private allelic richness (pAr)	标准遗传分化系数 Gene differentiation factor (G_ST)	基因流 Gene flow (Nm)
丹霞山 Danxiashan (DXS)	0.552	0.564	5.371	1.602	0.075	6.941
南雄 Nanxiong (NX)	0.517	0.527	4.836	1.065	0.053	9.326

变异来源 Source of variation	自由度 d.f.	方差和 Sum of squares	变异组分 Variance components	占总变异比例 Percentage of variation (%)
组群间 Among groups	1	171.218	0.7352	15.06
群体间 Among populations	7	111.824	0.2576	5.28
群体内 Within populations	417	1,621.42	3.8883	79.66
总计 Total	425	1,904.462	4.8811	-

群体 Population	编号 Codes	Wilcoxon检验 Wilcoxon test
群体 Population	编号 Codes	双相突变模型 Two-phased mutation model (TPM)	逐步突变模型 Stepwise mutation model (SMM)
锦湖 Jinhu	JH	0.00200	0.22115
老苗圃 Laomiaopu	LMP	0.16236	0.95929
韶石山 Shaoshishan	SS	0.00005	0.20856
阳元山 Yangyuanshan	YYS	0.12310	0.95063
长老峰 Zhanglaofeng	ZLF	0.13226	0.98288
鸳鸯湖 Yuanyanghu	QWT	0.16236	0.94518
水库1 Shuiku1	SK1	0.00237	0.22115
水库2 Shuiku2	SK2	0.00694	0.63314
柴岭 Chailing	WT	0.05935	0.64906

	进化事件1 Scenario 1	进化事件2 Scenario 2	进化事件3 Scenario 3	进化事件4 Scenario 4
后验概率 Posterior probability (PP)	0.4303	0.2740	0.1724	0.1233
代数 Generation (t1)	2,870	3,210	2,500	4,910
代数 Generation (ta)	-	1,510	1,880	-
代数 Generation (tb)	-	-	-	1,880
群体大小 Effective population size (N1b)	-	4,830	6,070	646
群体大小 Effective population size (N1)	7,290	7,800	8,260	7,220
群体大小 Effective population size (N2)	5,550	5,700	5,430	5,630
群体大小 Effective population size (N3)	-	-	-	-
群体大小 Effective population size (NA)	4,450	4,130	-	-

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