Biodiversity Science ›› 2018, Vol. 26 ›› Issue (11): 1168-1179.doi: 10.17520/biods.2018223

• Original Papers • Previous Article     Next Article

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:2019-01-08
  • Wen Yafeng E-mail:wenyafeng7107@163.com
  • About author:

    # Co-first authors

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

Table 1

Locality information and sample size of the nine Firmiana danxiaensis populations"

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

Table 2

Genetic diversity of 18 loci for Firmiana danxiaensis"

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

Table 3

Genetic diversity parameters of the nine Firmiana danxiaensis populations"

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

Table 4

Genetic diversity parameters of the two Firmiana danxiaensis groups"

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

Table 5

Results of analysis of molecular variance (AMOVA) from populations of Firmiana danxiaensis (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 -

Fig. 1

Genetic structure for Firmiana danxiaensis based on EST-SSR markers. (a) The corresponding ΔK statistics calculated according to Evanno et al (2005). (b) Histogram of the structure analysis for the model with K = 2 (showing the highest ΔK). Each vertical bar represents one population. DXS represent Danxiashan group; NX represent Nanxiong group."

Fig. 2

Genetic structure for Firmiana danxiaensis based on CLUMPP and DISTRUCT (K = 2, 3, 4). Meanings of abbreviations are shown in Table 1."

Fig. 3

Neighbor-joining network illustrating the genetic relationships among the nine Firmiana danxiaensis populations, based on Nei’s (1987) unbiased genetic distance. Meanings of abbreviations are shown in Table 1."

Fig. 4

Principal coordinates analysis (PCoA) of two SSR phenotypes from all nine populations of Firmiana danxiaensis. Meanings of abbreviations are shown in Table 1."

Fig. 5

Geographical distance against genetic distance for the nine Firmiana danxiaensis populations"

Table 6

Bottleneck detection for Firmiana danxiaensis"

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

Fig. 6

Four scenarios for Firmiana danxiaensis based on Approximate Bayesian Computation (K = 2). Meanings of abbreviations are shown in Table 1. DXS represents Danxiashan group. NX represents Nanxiong group. PP represents posterior probability. N1, N2, N1b, NA represent effective population size, respectively. t1, ta, tb represent generation."

Table 7

Median estimation of posterior distributions for each scenario based on Approximate Bayesian Computation (ABC)"

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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