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

• 研究报告 • 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. 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
  • 通讯作者: 文亚峰 E-mail:wenyafeng7107@163.com
  • 作者简介:

    # 共同第一作者

  • 基金项目:
    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 Wen1, *()   

  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
  • Contact: Wen Yafeng E-mail:wenyafeng7107@163.com
  • About author:

    # Co-first authors

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(FST = 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

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 (FST = 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

表1

丹霞梧桐9个群体的地理位置及样本数量"

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

表2

18个位点在丹霞梧桐样本中的遗传多样性参数"

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
(FST)
标准遗传分
化系数
Gene
differentiation
factor (GST)
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

表3

丹霞梧桐9个群体的遗传多样性参数"

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 (FIS)
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

表4

丹霞梧桐两组群间的遗传多样性参数"

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 (GST)
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

表5

丹霞梧桐群体间分子方差分析(AMOVA)(P < 0.01)"

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 -

图1

基于EST-SSR标记的丹霞梧桐群体遗传分析。(a)基于Evanno等(2005)所得的相应的ΔK; (b) STRUCTURE分析的直方图(K = 2时, ΔK值最大)。每个竖条代表1个群体。DXS代表丹霞山组群; NX代表南雄组群。"

图2

基于CLUMPP和DISTRUCT分析的丹霞梧桐群体遗传结构(K = 2, 3, 4)。缩写含义同表1。"

图3

基于Nei’s无偏距离的NJ法(Neighbor-joining, NJ)构建的丹霞梧桐9个群体的聚类图。缩写含义同表1。"

图4

丹霞梧桐9个群体中两种SSR表型的主成分分析(PCoA)。缩写含义同表1。"

图5

丹霞梧桐9个群体的地理距离与遗传距离的相关性 检验"

表6

丹霞梧桐群体瓶颈效应检测"

群体
Population
编号
Codes
Wilcoxon检验 Wilcoxon test
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

图6

基于近似贝叶斯算法的丹霞梧桐4个进化事件模型(K = 2)。缩写含义同表1。DXS代表丹霞山组群, NX代表南雄组群。PP代表后验概率, N1, N2, N1b, NA分别代表有效群体大小, t1, ta, tb分别代表进化代数。"

表7

基于近似贝叶斯算法的各进化事件的后验分布的中值估计"

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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