东亚孑遗植物柳杉属的遗传分化及其种群进化历史

doi:10.11707/j.1001-7488.20220607

Abstract

Abstract:

Objective: The aim of this study is to explore the genetic variation, population genetic differentiation, and demographic history of Cryptomeria populations in East Asia, so as to provide a scientific basis for the flora evolution study of East Asia and the conservation of this species genetic resources. Method: Fourteen nuclear microsatellite markers (nSSR) were used to detect the genetic variation of 18 natural (or ancient) populations of Cryptomeria from China and Japan. The level and pattern of genetic differentiation were analyzed, and the demographic history of the populations was simulated by DIY ABC. Result: The results showed that Cryptomeria in East Asia had moderate genetic diversity (H_o = 0.472, H_e = 0.488), and high genetic differentiation existed among populations (F_ST = 0.136). Molecular analysis of variance (AMOVA) showed that the genetic variation of Cryptomeria in East Asia was mainly from individuals within the populations (86.37%, P < 0.001). Consistent with the geographic origin, Cryptomeria in East Asia was able to be divided into two geographical populations of C. japonica var. sinensis and C. japonica var. japonica, as well as four lineages including southeast (CHS) and Lushan populations in China (LS), and the sea coast (Ura-sugi) and Pacific coast populations (Omote-sugi) in Japan by STRUCTURE and DAPC analyses. The genetic diversity of C. japonica var. sinensis (N_a = 4.571, H_o = 0.442) was lower than that of C. japonica var. japonica (N_a = 4.634, H_o = 0.510), but there was high genetic differentiation among populations. The results of the DIY ABC simulation showed that the divergence event of populations and lineages of Cryptomeria in East Asia occurred between 110 000 ~ 340 000 years ago. Conclusion: Affected by the third glacial period of Quaternary (Lushan glacial substage), the effective populations of Cryptomeria in East Asia were decreased rapidly, retreated to the refuges in Southeast China and Southwest Japan, and diverged into two populations (C. japonica var. sinensis and C. japonica var. japonica) with independent evolutionary routes. Our findings suggest that climate change in Quaternary, geographical isolation and human disturbance since Holocene play an important role in the formation of genetic variation pattern of Cryptomeria in East Asia. Compared with C. japonica var. japonica, C. japonica var. sinensis has abundant resources in China, but its genetic diversity is low, natural forest populations are seriously damaged, and scientific and effective conservation is urgently needed.

Key words: Cryptomeria, genetic differentiation, genetic structure, demographic history, microsatellite markers

CLC Number:

S718.46

Xinyu Li,Minqiu Wang,Meiling Yuan,Ueno Saneyoshi,Xingtong Wu,Mengying Cai,Tsumura Yoshihiko,Yafeng Wen. Genetic Differentiation and Demographic History of Cryptomeria, A Relict Plant, in East Asia[J]. Scientia Silvae Sinicae, 2022, 58(6): 66-78.

Figures/Tables 12

Table 1

Locality information and sample size of Cryptomeria populations"

编号 NO.	组群 Group	种群 Population	谱系 Lineage	样本数量 Sample size	样本来源 Location	纬度 Latitude(N)	经度 Longitude(E)	海拔 Elevation/m
1	柳杉 Cryptomeria japonica var. sinensis (CHN)	黄山 Huangshan (WT)	CHS	17	安徽黄山 Anhui Huangshan	29.462 1°	118.266 9°	436
2		天目山 Tianmushan (XTM)	CHS	23	浙江临安 Zhejiang Lin’an	30.338 1°	119.435 8°	1 089
3		天台山 Tiantaishan (TT)	CHS	24	浙江天台 Zhejiang Tiantai	29.2 495°	121.0 948°	897
4		屏南 Pingnan (PNSL)	CHS	23	福建屏南 Fujian Pingnan	27.003 9°	118.871 8°	1 254
5		福州 Fuzhou (FZ)	CHS	21	福建福州 Fujian Fuzhou	26.090 3°	119.396 9°	731
6		天宝岩高海拔 Tianbaoyan high altitude (TB)	CHS	10	福建永安 Fujian Yong’an	25.918 3°	117.557 5°	1 500
7		天宝岩 Tianbaoyan (TBY)	CHS	20	福建永安 Fujian Yong’an	25.965 6°	117.512 3°	1 132
8		南平 Nanping (YTG)	CHS	8	福建南平 Fujian Nanping	26.738 4°	118.146 8°	846
9		武夷山 Wuyishan (WYS)	CHS	20	福建武夷山 Fujian Wuyishan	27.759 8°	117.693 6°	892
10		庐山 Lushan (LS)	LS	23	江西庐山 Jiangxi Lushan	29.549 7°	115.966 8°	895
1	日本柳杉 Cryptomeria japonica var. japonica (JAN)	青森 Ajigasawa (AJG)	Ura-sugi	17	日本青森县 Japan Aomori	40.675 6°	140.205 3°	319
2		秋田 Nibetsu (NBT)	Ura-sugi	16	日本秋田县 Japan Akita	39.806 1°	140.260 0°	315
3		新泻 Donden (DND)	Ura-sugi	16	日本新泻县 Japan Niigata	38.139 7°	138.383 3°	725
4		富山 Bijodaira (BJD)	Ura-sugi	16	日本富山县 Japan Toyama	36.576 1°	137.458 9°	628
5		京都 Ashu (ASH)	Ura-sugi	18	日本京都府 Japan Tokyo	35.307 8°	135.773 9°	802
6		宫崎 Oninome (ONN)	Ura-sugi	6	日本宫崎县 Japan Miyazaki	32.698 4°	131.518 2°	1 170
7		鹿儿岛 Yakushima (YKU)	Omote-sugi	7	日本鹿儿岛县 Japan Kagoshima	30.303 5°	130.573 1°	1 071
8		宫城 Ishinomaki (ISN)	Omote-sugi	13	日本宫城县 Japan Miyagi-ken	38.328 6°	141.491 9°	195

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序号 NO.	位点 Locus	等位基因数 Number of allele (N_a)	总的遗传变异 Total genetic diversity for the species (H_t)	种群内遗传多样性 Genetic diversity within populations (H_s)	种群间遗传分化系数 Genetic differentiation 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)	位点来源 Locus source
1	CS1895M	29	0.715	0.664	0.093	0.072	0.594	Tani N. et al., (2003)
2	BY900902	7	0.636	0.592	0.063	0.069	0.516	Moriguchi Y. et al., (2014)
3	Cjgssr31	33	0.919	0.857	0.071	0.067	0.798	Moriguchi Y. et al., (2003)
4	BY894091	3	0.038	0.038	0.010	0.003	0.034	Moriguchi Y. et al., (2014)
5	CS1737M	2	0.499	0.449	0.096	0.100	0.337	Tani N. et al., (2003)
6	Cjgssr175	20	0.644	0.493	0.231	0.235	0.417	Moriguchi Y. et al., (2005)
7	Cjgssr7	22	0.774	0.672	0.150	0.132	0.588	Moriguchi Y. et al., (2003)
8	BY896143	3	0.315	0.290	0.068	0.079	0.234	Moriguchi Y. et al., (2014)
9	BY898881	11	0.693	0.624	0.095	0.099	0.547	Moriguchi Y. et al., (2014)
10	Cjgssr120	26	0.604	0.482	0.201	0.202	0.441	Moriguchi Y. et al., (2003)
11	Cjgssr181	31	0.635	0.560	0.103	0.118	0.481	Moriguchi Y. et al., (2003)
12	BJ939490	5	0.313	0.281	0.123	0.102	0.236	Moriguchi Y. et al., (2014)
13	CS1522M	18	0.597	0.541	0.098	0.094	0.490	Tani N. et al., (2003)
14	BY909057	9	0.597	0.562	0.060	0.058	0.458	Moriguchi Y. et al., (2014)
均值	Mean	15.643	0.570	0.508	0.112	0.109	0.441

种群 Population	等位基因数 Number of alleles(N_a)	观测杂合度 Observed heterozygosity (H_o)	期望杂合度 Expected heterozygosity (H_e)	近交系数 Inbreeding coefficient (F_IS)	等位基因丰富度 Allelic richness (Ar)	私有等位基因丰富度 Private alleles richness (PAr)
黄山Huangshan (WT)	3.357	0.303	0.412	0.294	2.636	0.148
天目山Tianmushan (XTM)	4.000	0.508	0.491	-0.012	2.826	0.125
天台山Tiantaishan (TT)	4.643	0.464	0.511	0.113	3.083	0.209
屏南Pingnan (PNSL)	4.143	0.493	0.502	0.041	3.111	0.125
福州Fuzhou (FZ)	4.643	0.439	0.486	0.121	3.158	0.143
天宝岩高海拔Tianbaoyan high altitude (TB)	2.714	0.293	0.360	0.236	2.453	0.144
天宝岩Tianbaoyan (TBY)	5.143	0.461	0.512	0.125	3.360	0.233
南平Nanping (YTG)	2.857	0.439	0.431	0.050	2.752	0.065
武夷山Wuyishan (WYS)	4.929	0.446	0.499	0.131	3.409	0.202
庐山Lushan (LS)	9.286	0.575	0.695	0.194	5.271	0.976
中国平均值CHN Mean	4.571	0.442	0.490	0.123	3.206	0.240
青森Ajigasawa (AJG)	4.500	0.471	0.454	-0.006	3.216	0.089
秋田Nibetsu (NBT)	4.643	0.477	0.493	0.064	3.364	0.072
新泻Donden (DND)	4.929	0.463	0.448	-0.002	3.239	0.200
富山Bijodaira (BJD)	4.786	0.536	0.493	-0.055	3.316	0.217
京都Ashu (ASH)	5.714	0.477	0.492	0.060	3.535	0.293
宫崎Oninome (ONN)	3.071	0.536	0.450	-0.100	3.071	0.107
鹿儿岛Yakushima (YKU)	4.357	0.611	0.528	-0.080	4.073	0.684
宫城Ishinomaki (ISN)	5.071	0.511	0.529	0.073	3.672	0.284
日本平均值JAN Mean	4.634	0.510	0.486	0.009	3.436	0.243
总平均值Total Mean	4.599	0.472	0.488	0.060	3.308	0.240

变异来源 Source of variation	自由度 df	方差总和 Sum of squares	变异组分 Variance components	变异百分比 Percentage of variation (%)	P
组间 Among groups	1	70.972	0.199	4.85	< 0.001
种群间 Among populations	16	246.363	0.361	8.78	< 0.001
种群内 Within populations	578	2 052.437	3.551	86.37	< 0.001
总计 Total	595	2 369.772	4.092	100.00	-
	F_ST=0.136 N_m=1.588

	事件1 Scenario 1	事件2 Scenario 2	事件3 Scenario 3	事件4 Scenario 4
后验概率Posterior probability (PP)	0.000 8	0.000 0	0.991 9	0.007 3
种群大小Effective population size (N₁)	4 490	6 930	3 820	4 690
种群大小Effective population size (N₂)	8 870	9 700	7 840	8 800
种群大小Effective population size (N₃)	2 600	5 550	4 850	4 740
种群大小Effective population size (N₄)	2 950	6 870	7 350	7 190
种群大小Effective population size (N_A)	-	22.5	44.6	42.3
代数Generation (t₁)	720	2 540	1 140	1 450
代数Generation (t₂)	559	1 840	-	1 360
代数Generation (t₃)	205	1 790	-	-

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Genetic Differentiation and Demographic History of Cryptomeria, A Relict Plant, in East Asia

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