Population genetic diversity of Rhodiola dumulosa in Northern China inferred from AFLP makers

doi:10.3773/j.issn.1005-264x.2010.09.009

Abstract

Abstract:

Aims Rhodiola dumulosa (Crassulaceae) is a perennial herbaceous plant. It grows among rocks on mountains at 1 600-3 900 m, and its populations are spatially scattered in their areas of distribution. Our objectives were to study the population genetic diversity and genetic structure of R. dumulosa in northern China and determine relationships between genetic diversity and environmental factors.

Methods We analyzed 776 individuals from 25 natural populations using amplified fragment length polymorphism (AFLP) markers.

Important findings We obtained 398 unambiguous bands from the four pairs of selective primers, 312 bands (78.46%) of which were polymorphic across all individuals. The Nei’s gene diversity was 0.364 9, and the Shannon’s information index was 0.542 2 at the species level. Therefore, there was a high level of genetic diversity within R. dumulosa populations in northern China. The population genetic differentiation index G_st was 0.150 7, and the indirect estimate of gene flow Nm was 2.82, which indicated that genetic differentiation among northern populations was low and gene exchange was frequent. Analysis of molecular variance (AMOVA) revealed that the majority of AFLP variations resided within populations (67.9%). The STRUCTURE and UPGMA cluster analyses showed that the closely related populations are geographically restricted and occur in proximity to each other. This result was confirmed by the Mantel test, which revealed a significant positive correlation (r = 0.512 9, p < 0.001) between geographical distance and genetic distance. In addition, the correlation analysis of population genetic diversity and altitude showed a significant negative relationship (p < 0.05), i.e., population genetic diversity decreased with increasing altitude. However, there was no significant correlation between genetic diversity and slope direction. The software Dfdist was used to detect outliers caused by altitude, but the results were non-significant. All research results showed that geographical distance affected genetic distance significantly.

Key words: amplified fragment length polymorphism (AFLP), environmental factor, genetic diversity, natural island distribution, Rhodiola dumulosa

ZHANG Yun-Hong, HOU Yan, LOU An-Ru. Population genetic diversity of Rhodiola dumulosa in Northern China inferred from AFLP makers[J]. Chin J Plant Ecol, 2010, 34(9): 1084-1094.

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Figures/Tables 6

References 43

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样地 Sampling site		海拔 Altitude (m)	纬度 Latitude (N)	经度 Longitude (E)	坡向 Slope aspect
山西 Shanxi	荷叶坪1 Heyeping1 (HYP-1)	2 709	38.722°	111.837°	北偏西40° North by west 40°
	荷叶坪2 Heyeping2 (HYP-2)	2 596	38.729°	111.862°	南偏西10° South by west 10°
	荷叶坪3 Heyeping3 (HYP-3)	2 504	38.729°	111.874°	南偏西10° South by west 10°
	荷叶坪4 Heyeping4 (HYP-4)	2 435	38.730°	111.885°	南偏西10° South by west 10°
	芦芽山1 Luyashan1 (LYS-1)	2 701	38.750°	111.926°	西偏南30° West by south 30°
	芦芽山2 Luyashan2 (LYS-2)	2 580	38.744°	111.926°	南偏西10° South by west 10°
	关帝山 Guandishan (GDS)	2 557	37.895°	111.518°	北坡 North slope
	五台山中台顶 Wutaishanzhongtaiding (WTZ)	2 895	39.047°	113.531°	南坡 South slope
	五台山西台顶 Wutaishanxitaiding (WTX)	2 783	39.037°	113.492°	北偏东2.5° North by east 2.5°
	五台山北台顶1 Wutaishanbeitaiding1 (WTB-1)	3 066	39.080°	113.568°	东偏北3° East by north 3°
	五台山北台顶2 Wutaishanbeitaiding2 (WTB-2)	3 066	39.080°	113.568°	南偏北 South by north
河北 Hebei	白石山 Baishishan (BSS)	1 940	39.208°	114.698°	南偏西25° South by west 25°
	雾灵山 Wulingshan (WLS)	1 939	40.577°	117.461°	东坡 East slope
	小五台山B Xiaowutaishan B (XWTB)	2 500	39.945°	115.061°	东偏北5.7° East by north 5.7°
	小五台山C Xiaowutaishan C (XWTC)	2 706	39.943°	115.047°	东偏北5.7° East by north 5.7°
	小五台山A Xiaowutaishan A (XWTA)	2 480	39.912°	114.968°	西偏南8.9° West by south 8.9°
北京 Beijing	百花山 Baihuashan (BHS)	2 033	39.813°	115.582°	西坡 West slope
	东灵山1 Donglingshan1 (DLS-1)	2 303	40.031°	115.454°	西偏南30° West by south 30°
	东灵山2 Donglingshan2 (DLS-2)	2 202	40.031°	115.462°	东偏南30° East by south 30°
	东灵山3 Donglingshan3 (DLS-3)	2 160	40.029°	115.451°	西坡 West slope
	东灵山4 Donglingshan4 (DLS-4)	2 106	40.034°	115.471°	西偏南15° East by south 15°
	东灵山5 Donglingshan5 (DLS-5)	2 018	40.033°	115.475°	东偏北40° East by north 40°
内蒙古 Inner Mongolia	大青山 Daqingshan (DQS)	2 068	40.838°	111.259°	北偏西30° North by west 30°
宁夏 Ningxia	贺兰山1 Helanshan 1 (HLS-1)	3 428	38.838°	105.944°	西坡 West slope
	贺兰山2 Helanshan 2 (HLS-2)	2 900	38.846°	105.944°	北坡 North slope

样地 Sampling site		海拔 Altitude (m)	纬度 Latitude (N)	经度 Longitude (E)	坡向 Slope aspect
山西 Shanxi	荷叶坪1 Heyeping1 (HYP-1)	2 709	38.722°	111.837°	北偏西40° North by west 40°
	荷叶坪2 Heyeping2 (HYP-2)	2 596	38.729°	111.862°	南偏西10° South by west 10°
	荷叶坪3 Heyeping3 (HYP-3)	2 504	38.729°	111.874°	南偏西10° South by west 10°
	荷叶坪4 Heyeping4 (HYP-4)	2 435	38.730°	111.885°	南偏西10° South by west 10°
	芦芽山1 Luyashan1 (LYS-1)	2 701	38.750°	111.926°	西偏南30° West by south 30°
	芦芽山2 Luyashan2 (LYS-2)	2 580	38.744°	111.926°	南偏西10° South by west 10°
	关帝山 Guandishan (GDS)	2 557	37.895°	111.518°	北坡 North slope
	五台山中台顶 Wutaishanzhongtaiding (WTZ)	2 895	39.047°	113.531°	南坡 South slope
	五台山西台顶 Wutaishanxitaiding (WTX)	2 783	39.037°	113.492°	北偏东2.5° North by east 2.5°
	五台山北台顶1 Wutaishanbeitaiding1 (WTB-1)	3 066	39.080°	113.568°	东偏北3° East by north 3°
	五台山北台顶2 Wutaishanbeitaiding2 (WTB-2)	3 066	39.080°	113.568°	南偏北 South by north
河北 Hebei	白石山 Baishishan (BSS)	1 940	39.208°	114.698°	南偏西25° South by west 25°
	雾灵山 Wulingshan (WLS)	1 939	40.577°	117.461°	东坡 East slope
	小五台山B Xiaowutaishan B (XWTB)	2 500	39.945°	115.061°	东偏北5.7° East by north 5.7°
	小五台山C Xiaowutaishan C (XWTC)	2 706	39.943°	115.047°	东偏北5.7° East by north 5.7°
	小五台山A Xiaowutaishan A (XWTA)	2 480	39.912°	114.968°	西偏南8.9° West by south 8.9°
北京 Beijing	百花山 Baihuashan (BHS)	2 033	39.813°	115.582°	西坡 West slope
	东灵山1 Donglingshan1 (DLS-1)	2 303	40.031°	115.454°	西偏南30° West by south 30°
	东灵山2 Donglingshan2 (DLS-2)	2 202	40.031°	115.462°	东偏南30° East by south 30°
	东灵山3 Donglingshan3 (DLS-3)	2 160	40.029°	115.451°	西坡 West slope
	东灵山4 Donglingshan4 (DLS-4)	2 106	40.034°	115.471°	西偏南15° East by south 15°
	东灵山5 Donglingshan5 (DLS-5)	2 018	40.033°	115.475°	东偏北40° East by north 40°
内蒙古 Inner Mongolia	大青山 Daqingshan (DQS)	2 068	40.838°	111.259°	北偏西30° North by west 30°
宁夏 Ningxia	贺兰山1 Helanshan 1 (HLS-1)	3 428	38.838°	105.944°	西坡 West slope
	贺兰山2 Helanshan 2 (HLS-2)	2 900	38.846°	105.944°	北坡 North slope

种群 Population	样本数 Sample size	多态位点数 No. of polymorphic bands	多态位点百分率 PPL (%)	Nei’s基因多样性 H	Shannon多态性信息指数 I
荷叶坪1 Heyeping1 (HYP-1)	32	331	83.17	0.241 8 (0.186 7)	0.369 3 (0.256 4)
荷叶坪2 Heyeping2 (HYP-2)	32	338	84.92	0.266 6 (0.177 1)	0.405 6 (0.242 3)
荷叶坪3 Heyeping3 (HYP-3)	32	335	84.17	0.272 2 (0.179 4)	0.411 5 (0.246 5)
荷叶坪4 Heyeping4 (HYP-4)	32	333	83.67	0.278 2 (0.179 9)	0.419 0 (0.246 4)
芦芽山1 Luyashan1 (LYS-1)	31	328	82.41	0.264 0 (0.180 0)	0.400 3 (0.2485)
芦芽山2 Luyashan2 (LYS-2)	32	309	77.64	0.240 2 (0.188 1)	0.365 5 (0.260 7)
关帝山 Guandishan (GDS)	32	367	92.21	0.303 6 (0.174 4)	0.455 1 (0.231 1)
五台山中台顶 Wutaishanzhongtaiding (WTZ)	30	293	73.62	0.249 5 (0.190 8)	0.374 7 (0.268 7)
五台山中台顶 Wutaishanxitaiding (WTX)	29	309	77.64	0.258 2 (0.193 1)	0.386 9 (0.268 1)
五台山北台顶1 Wutaishanbeitaiding1 (WTB-1)	31	290	72.86	0.233 7 (0.191 3)	0.353 6 (0.269 1)
五台山北台顶2 Wutaishanbeitaiding2 (WTB-2)	28	309	77.64	0.268 1 (0.190 7)	0.400 7 (0.264 7)
百花山 Baihuashan (BHS)	32	274	68.84	0.220 8 (0.193 3)	0.333 9 (0.273 8)
白石山 Baishishan (BSS)	32	352	88.44	0.297 9 (0.167 3)	0.448 7 (0.226 5)
雾灵山 Wulingshan (WLS)	29	291	73.12	0.249 0 (0.193 0)	0.373 1 (0.272 0)
小五台山A Xiaowutaishan A (XWTA)	30	281	70.60	0.222 2 (0.189 9)	0.337 7 (0.268 7)
小五台山B Xiaowutaishan B (XWTB)	30	246	61.81	0.202 0 (0.198 7)	0.304 0 (0.282 3)
小五台山C Xiaowutaishan C (XWTC)	30	305	76.63	0.246 0 (0.181 4)	0.374 1 (0.256 0)
东灵山1 Donglingshan1 (DLS-1)	32	273	68.59	0.224 2 (0.194 4)	0.338 3 (0.274 9)
东灵山2 Donglingshan2 (DLS-2)	32	298	74.87	0.245 9 (0.189 3)	0.370 6 (0.266 7)
东灵山3 Donglingshan3 (DLS-3)	32	310	77.89	0.254 7 (0.182 7)	0.385 8 (0.255 7)
东灵山4 Donglingshan4 (DLS-4)	32	352	88.44	0.284 8 (0.170 3)	0.431 9 (0.229 6)
东灵山5 Donglingshan5 (DLS-5)	32	319	80.15	0.250 4 (0.182 7)	0.380 6 (0.254 7)
大青山 Daqingshan (DQS)	32	325	81.66	0.277 4 (0.185 1)	0.415 6 (0.255 0)
贺兰山1 Helanshan1 (HLS-1)	30	321	80.65	0.283 1 (0.186 2)	0.422 1 (0.257 0)
贺兰山2 Helanshan2 ( HLS-2)	30	318	79.90	0.266 5 (0.186 4)	0.400 5 (0.258 3)
种群水平 Population level				0.256 0 (0.185 3)	0.384 6 (0.257 3)
物种水平 Species level	776	312	78.46	0.364 9 (0.122 9)	0.542 2 (0.146 8)

种群 Population	样本数 Sample size	多态位点数 No. of polymorphic bands	多态位点百分率 PPL (%)	Nei’s基因多样性 H	Shannon多态性信息指数 I
荷叶坪1 Heyeping1 (HYP-1)	32	331	83.17	0.241 8 (0.186 7)	0.369 3 (0.256 4)
荷叶坪2 Heyeping2 (HYP-2)	32	338	84.92	0.266 6 (0.177 1)	0.405 6 (0.242 3)
荷叶坪3 Heyeping3 (HYP-3)	32	335	84.17	0.272 2 (0.179 4)	0.411 5 (0.246 5)
荷叶坪4 Heyeping4 (HYP-4)	32	333	83.67	0.278 2 (0.179 9)	0.419 0 (0.246 4)
芦芽山1 Luyashan1 (LYS-1)	31	328	82.41	0.264 0 (0.180 0)	0.400 3 (0.2485)
芦芽山2 Luyashan2 (LYS-2)	32	309	77.64	0.240 2 (0.188 1)	0.365 5 (0.260 7)
关帝山 Guandishan (GDS)	32	367	92.21	0.303 6 (0.174 4)	0.455 1 (0.231 1)
五台山中台顶 Wutaishanzhongtaiding (WTZ)	30	293	73.62	0.249 5 (0.190 8)	0.374 7 (0.268 7)
五台山中台顶 Wutaishanxitaiding (WTX)	29	309	77.64	0.258 2 (0.193 1)	0.386 9 (0.268 1)
五台山北台顶1 Wutaishanbeitaiding1 (WTB-1)	31	290	72.86	0.233 7 (0.191 3)	0.353 6 (0.269 1)
五台山北台顶2 Wutaishanbeitaiding2 (WTB-2)	28	309	77.64	0.268 1 (0.190 7)	0.400 7 (0.264 7)
百花山 Baihuashan (BHS)	32	274	68.84	0.220 8 (0.193 3)	0.333 9 (0.273 8)
白石山 Baishishan (BSS)	32	352	88.44	0.297 9 (0.167 3)	0.448 7 (0.226 5)
雾灵山 Wulingshan (WLS)	29	291	73.12	0.249 0 (0.193 0)	0.373 1 (0.272 0)
小五台山A Xiaowutaishan A (XWTA)	30	281	70.60	0.222 2 (0.189 9)	0.337 7 (0.268 7)
小五台山B Xiaowutaishan B (XWTB)	30	246	61.81	0.202 0 (0.198 7)	0.304 0 (0.282 3)
小五台山C Xiaowutaishan C (XWTC)	30	305	76.63	0.246 0 (0.181 4)	0.374 1 (0.256 0)
东灵山1 Donglingshan1 (DLS-1)	32	273	68.59	0.224 2 (0.194 4)	0.338 3 (0.274 9)
东灵山2 Donglingshan2 (DLS-2)	32	298	74.87	0.245 9 (0.189 3)	0.370 6 (0.266 7)
东灵山3 Donglingshan3 (DLS-3)	32	310	77.89	0.254 7 (0.182 7)	0.385 8 (0.255 7)
东灵山4 Donglingshan4 (DLS-4)	32	352	88.44	0.284 8 (0.170 3)	0.431 9 (0.229 6)
东灵山5 Donglingshan5 (DLS-5)	32	319	80.15	0.250 4 (0.182 7)	0.380 6 (0.254 7)
大青山 Daqingshan (DQS)	32	325	81.66	0.277 4 (0.185 1)	0.415 6 (0.255 0)
贺兰山1 Helanshan1 (HLS-1)	30	321	80.65	0.283 1 (0.186 2)	0.422 1 (0.257 0)
贺兰山2 Helanshan2 ( HLS-2)	30	318	79.90	0.266 5 (0.186 4)	0.400 5 (0.258 3)
种群水平 Population level				0.256 0 (0.185 3)	0.384 6 (0.257 3)
物种水平 Species level	776	312	78.46	0.364 9 (0.122 9)	0.542 2 (0.146 8)

分组 Group	变异来源 Source of variation	自由度 df	平方和 Sum of squares	方差分量 Variance components	方差分量百分率 Percentage of variation (%)	F 统计值 F statistics
所有种群为一组 All populations were divided into one group	种群间	24	18 857.993	23.700 46	32.10	0.321 00*
	Among populations	24	18 857.993	23.700 46	32.10
	种群内	751	37 649.060	50.131 90	67.90
	Within populations	751	37 649.060	50.131 90	67.90
基于UPGMA分两组Two groups based on UPGMA	地理单元间	1	6 111.456	17.509 04	20.87	0.208 71*
	Among geographic units	1	6 111.456	17.509 04	20.87	0.208 71*
	地理单元内	23	12 746.537	16.249 94	19.37	0.244 79*
	Among populations within geographic unit	23	12 746.537	16.249 94	19.37	0.244 79*
	种群内	751	37 649.060	50.131 9	59.76	0.402 42*
	Within populations	751	37 649.060	50.131 9	59.76	0.402 42*
基于山脉分五组 Five groups based on the mountains	地理单元间	4	9 597.026	16.750 0	20.90	0.208 98*
	Among geographic units	4	9 597.026	16.750 0	20.90	0.208 98*
	地理单元内	20	9260.967	13.270 7	16.56	0.209 31*
	Among populations within geographic unit	20	9260.967	13.270 7	16.56	0.209 31*
	种群内	751	37 649.060	50.131 9	62.55	0.374 54*
	Within populations	751	37 649.060	50.131 9	62.55	0.374 54*