Genetic structure and its causes of an important woody oil plant in Southwest China, Prinsepia utilis (Rosaceae)

doi:10.17520/biods.2021341

Abstract

Abstract:

Aims: Prinsepia utilis is an important woody oil species in temperate forests in Southwest China, however, almost nothing is known about its population genetic structure and the causes. So, we aim to study its evolutionary history through multiple nuclear microsatellite loci (nSSRs).
Methods: We sampled 377 individuals from 32 natural populations across all distribution range of P. utilis. All individuals were amplified and scored using seven self-developed nSSRs markers. Genetic structure was inferred using STRUCTURE software and principal component analysis. The most possible demographic scenario and corresponding parameters were modeled and estimated in DIYABC. Genetic diversity and genetic differentiation of each population, locus and genetic cluster were calculated. Contributions of geographic distance and environmental differences to genetic differentiation were calculate through Mantel test and partial Mantel test. At last, environmental differences among different genetic clusters was evaluated through principal component analysis using 19 climatic variables.
Results: All population can be divided into four genetic groups that are Himalayas, Hengduan Mountains, west and east Yunnan-Guizhou Plateau genetic groups from west to east. The greatest genetic differentiation occurs between populations in the Himalayas and other regions. In comparison with the Himalayan and east Yunnan-Guizhou Plateau groups, the Hengduan Mountains and west Yunnan-Guizhou Plateau groups have higher proportion of genetic mixture from other groups. Population demographic history analysis indicate two central groups are formed after Himalayas and east Yunnan-Guizhou Plateau groups, all divergences are occurred in late Pleistocene. The analyses of isolation by distance and isolation by environment show that the genetic differentiation of P. utilis is mainly caused by environmental difference. Environmental difference analysis using 19 climatic variables shows various difference among groups with significant difference exist between Himalayas and east Yunnan-Guizhou Plateau groups.
Conclusion: The distinct genetic structure of P. utilis is formed through the combination of Pleistocene climatic changes, complicated environment and its own biological characters. Combined with ecological niche modeling analysis in different periods, we suggest protection of genetic resources in Himalayas and Yunnan-Guizhou Plateau should be first priority.

Key words: nuclear microsatellites, genetic diversity, principal component analysis, Himalayas

Junwei Ye, Bin Tian. Genetic structure and its causes of an important woody oil plant in Southwest China, Prinsepia utilis (Rosaceae)[J]. Biodiv Sci, 2021, 29(12): 1629-1637.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2021341

https://www.biodiversity-science.net/EN/Y2021/V29/I12/1629

Figures/Tables 6

References 32

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代号 Code	地点 Site	经纬度 Location	海拔 Altitude (m)	n	A_O	H_E	H_O	R_S	P_AR	F_IS
BAZY	云南昆明 Kunming, Yunnan	102.72˚ E, 25.40˚ N	2,370	9	20	0.45	0.63	2.45	0.01	-0.35
BBM	西藏波密 Bomi, Xizang	95.34˚ E, 29.99˚ N	2,750	14	22	0.54	0.76	2.61	0	-0.37
BDC	四川稻城 Daocheng, Sichuan	100.30˚ E, 28.58˚ N	3,310	12	21	0.46	0.62	2.55	0.12	-0.31
BDCQ	云南会泽 Huize, Yunnan	103.10˚ E, 25.94˚ N	2,220	10	22	0.48	0.67	2.74	0.07	-0.35
BES	云南峨山 E’shan, Yunnan	102.11˚ E, 24.28˚ N	2,060	6	15	0.38	0.62	-	-	-0.58
BHD	四川会东 Huidong, Sichuan	102.78˚ E, 26.55˚ N	2,370	14	22	0.47	0.65	2.61	0	-0.36
BHQ	云南鹤庆 Heqing, Yunnan	100.18˚ E, 26.56˚ N	2,200	15	27	0.64	0.86	3.28	0	-0.31
BJL	西藏吉隆 Jilong, Xizang	85.36˚ E, 28.39˚ N	3,140	12	19	0.46	0.65	2.40	0.03	-0.38
BJP	云南澄江 Chengjiang, Yunnan	102.86˚ E, 24.73˚ N	2,180	15	25	0.58	0.81	2.93	0	-0.38
BLD	云南玉龙 Yulong, Yunnan	99.46˚ E, 27.18˚ N	2,630	16	21	0.56	0.88	2.59	0	-0.54
BLJ	云南丽江 Lijiang, Yunnan	100.23˚ E, 27.18˚ N	3,650	5	19	0.52	0.78	-	-	-0.47
BLJS	云南老君山 Laojun Mountains, Yunnan	103.93˚ E, 23.30˚ N	1,640	15	25	0.55	0.84	2.83	0	-0.51
BLJW	贵州安顺 Anshun, Guizhou	105.94˚ E, 26.25˚ N	1,400	15	23	0.49	0.69	2.63	0.10	-0.36
BLLX	贵州龙里 Longli, Guizhou	106.90˚ E, 26.43˚ N	1,150	10	18	0.45	0.61	2.30	0	-0.37
BLP	云南兰坪 Lanping, Yunnan	99.42˚ E, 26.46˚ N	2,540	12	24	0.61	0.98	2.93	0	-0.57
BMG	云南马关 Maguan, Yunnan	104.39˚ E, 23.02˚ N	1,340	12	24	0.53	0.79	2.80	0.02	-0.45
BML	四川木里 Muli, Sichuan	101.25˚ E, 27.97˚ N	2,500	12	26	0.61	0.96	3.05	0.19	-0.55
BNH	云南南华 Nanhua, Yunnan	101.01˚ E, 25.33˚ N	2,320	9	21	0.52	0.75	2.73	0	-0.39
BQJ	云南曲靖 Qujing, Yunnan	103.91˚ E, 25.36˚ N	1,900	8	20	0.49	0.74	-	-	-0.44
BQL	贵州贵阳 Guiyang, Guizhou	106.69˚ E, 26.60˚ N	1,160	6	17	0.45	0.60	-	-	-0.24
BSZ	云南师宗 Shizong, Yunnan	103.98˚ E, 24.82˚ N	1,870	12	25	0.52	0.71	2.91	0.03	-0.34
BTM	西藏林芝 Linzhi, Xizang	96.58˚ E, 30.50˚ N	4,720	15	25	0.59	0.85	2.83	0.09	-0.41
BWM	云南禄劝 Luquan, Yunnan	102.83˚ E, 26.02˚ N	2,760	14	22	0.47	0.69	2.49	0	-0.46
BWN	贵州威宁 Weining, Guizhou	104.11˚ E, 26.74˚ N	2,450	13	24	0.48	0.68	2.61	0	-0.38
BWX	云南维西 Weixi, Yunnan	99.02˚ E, 27.80˚ N	2,290	9	24	0.59	0.87	2.97	0.05	-0.43
BXC	四川西昌 Xichang, Sichuan	102.35˚ E, 27.70˚ N	2,680	11	20	0.39	0.57	2.38	0.03	-0.41
BXCX	云南西畴 Xichou, Yunnan	104.79˚ E, 23.38˚ N	1,450	9	25	0.53	0.75	2.86	0	-0.37
BXJ	云南文山新街 Xinjie, Wenshan, Yunnan	104.00˚ E, 23.20˚ N	1,880	15	23	0.53	0.81	2.76	0	-0.49
BXZC	云南开远 Kaiyuan, Yunnan	103.62˚ E, 23.79˚ N	1,480	10	21	0.54	0.80	2.77	0	-0.43
BYG	西藏波密 Bomi, Xizang	95.57˚ E, 30.50˚ N	5,230	15	22	0.58	0.88	2.79	0.01	-0.48
BYXB	四川越西 Yuexi, Sichuan	102.45˚ E, 28.76˚ N	2,970	12	16	0.39	0.60	2.12	0	-0.49
BZNX	云南文山 Wenshan, Yunnan	104.42˚ E, 23.69˚ N	1,570	15	25	0.55	0.81	2.97	0	-0.45

代号 Code	地点 Site	经纬度 Location	海拔 Altitude (m)	n	A_O	H_E	H_O	R_S	P_AR	F_IS
BAZY	云南昆明 Kunming, Yunnan	102.72˚ E, 25.40˚ N	2,370	9	20	0.45	0.63	2.45	0.01	-0.35
BBM	西藏波密 Bomi, Xizang	95.34˚ E, 29.99˚ N	2,750	14	22	0.54	0.76	2.61	0	-0.37
BDC	四川稻城 Daocheng, Sichuan	100.30˚ E, 28.58˚ N	3,310	12	21	0.46	0.62	2.55	0.12	-0.31
BDCQ	云南会泽 Huize, Yunnan	103.10˚ E, 25.94˚ N	2,220	10	22	0.48	0.67	2.74	0.07	-0.35
BES	云南峨山 E’shan, Yunnan	102.11˚ E, 24.28˚ N	2,060	6	15	0.38	0.62	-	-	-0.58
BHD	四川会东 Huidong, Sichuan	102.78˚ E, 26.55˚ N	2,370	14	22	0.47	0.65	2.61	0	-0.36
BHQ	云南鹤庆 Heqing, Yunnan	100.18˚ E, 26.56˚ N	2,200	15	27	0.64	0.86	3.28	0	-0.31
BJL	西藏吉隆 Jilong, Xizang	85.36˚ E, 28.39˚ N	3,140	12	19	0.46	0.65	2.40	0.03	-0.38
BJP	云南澄江 Chengjiang, Yunnan	102.86˚ E, 24.73˚ N	2,180	15	25	0.58	0.81	2.93	0	-0.38
BLD	云南玉龙 Yulong, Yunnan	99.46˚ E, 27.18˚ N	2,630	16	21	0.56	0.88	2.59	0	-0.54
BLJ	云南丽江 Lijiang, Yunnan	100.23˚ E, 27.18˚ N	3,650	5	19	0.52	0.78	-	-	-0.47
BLJS	云南老君山 Laojun Mountains, Yunnan	103.93˚ E, 23.30˚ N	1,640	15	25	0.55	0.84	2.83	0	-0.51
BLJW	贵州安顺 Anshun, Guizhou	105.94˚ E, 26.25˚ N	1,400	15	23	0.49	0.69	2.63	0.10	-0.36
BLLX	贵州龙里 Longli, Guizhou	106.90˚ E, 26.43˚ N	1,150	10	18	0.45	0.61	2.30	0	-0.37
BLP	云南兰坪 Lanping, Yunnan	99.42˚ E, 26.46˚ N	2,540	12	24	0.61	0.98	2.93	0	-0.57
BMG	云南马关 Maguan, Yunnan	104.39˚ E, 23.02˚ N	1,340	12	24	0.53	0.79	2.80	0.02	-0.45
BML	四川木里 Muli, Sichuan	101.25˚ E, 27.97˚ N	2,500	12	26	0.61	0.96	3.05	0.19	-0.55
BNH	云南南华 Nanhua, Yunnan	101.01˚ E, 25.33˚ N	2,320	9	21	0.52	0.75	2.73	0	-0.39
BQJ	云南曲靖 Qujing, Yunnan	103.91˚ E, 25.36˚ N	1,900	8	20	0.49	0.74	-	-	-0.44
BQL	贵州贵阳 Guiyang, Guizhou	106.69˚ E, 26.60˚ N	1,160	6	17	0.45	0.60	-	-	-0.24
BSZ	云南师宗 Shizong, Yunnan	103.98˚ E, 24.82˚ N	1,870	12	25	0.52	0.71	2.91	0.03	-0.34
BTM	西藏林芝 Linzhi, Xizang	96.58˚ E, 30.50˚ N	4,720	15	25	0.59	0.85	2.83	0.09	-0.41
BWM	云南禄劝 Luquan, Yunnan	102.83˚ E, 26.02˚ N	2,760	14	22	0.47	0.69	2.49	0	-0.46
BWN	贵州威宁 Weining, Guizhou	104.11˚ E, 26.74˚ N	2,450	13	24	0.48	0.68	2.61	0	-0.38
BWX	云南维西 Weixi, Yunnan	99.02˚ E, 27.80˚ N	2,290	9	24	0.59	0.87	2.97	0.05	-0.43
BXC	四川西昌 Xichang, Sichuan	102.35˚ E, 27.70˚ N	2,680	11	20	0.39	0.57	2.38	0.03	-0.41
BXCX	云南西畴 Xichou, Yunnan	104.79˚ E, 23.38˚ N	1,450	9	25	0.53	0.75	2.86	0	-0.37
BXJ	云南文山新街 Xinjie, Wenshan, Yunnan	104.00˚ E, 23.20˚ N	1,880	15	23	0.53	0.81	2.76	0	-0.49
BXZC	云南开远 Kaiyuan, Yunnan	103.62˚ E, 23.79˚ N	1,480	10	21	0.54	0.80	2.77	0	-0.43
BYG	西藏波密 Bomi, Xizang	95.57˚ E, 30.50˚ N	5,230	15	22	0.58	0.88	2.79	0.01	-0.48
BYXB	四川越西 Yuexi, Sichuan	102.45˚ E, 28.76˚ N	2,970	12	16	0.39	0.60	2.12	0	-0.49
BZNX	云南文山 Wenshan, Yunnan	104.42˚ E, 23.69˚ N	1,570	15	25	0.55	0.81	2.97	0	-0.45

遗传群组 Genetic cluster	等位基因数量 A_O	观测杂合度 H_O	期望杂合度 H_E	等位基因丰富度 R_S	私有等位基因丰富度 P_AR
喜马拉雅 Himalayas	30	0.79	0.62	3.18	0.70
横断山 Hengduan Mountains	35	0.86	0.65	3.39	0.53
云贵高原西部 West Yunnan-Guizhou Plateau	36	0.73	0.56	3.04	0.19
云贵高原东部 East Yunnan-Guizhou Plateau	26	0.65	0.50	2.69	0.24

遗传群组 Genetic cluster	等位基因数量 A_O	观测杂合度 H_O	期望杂合度 H_E	等位基因丰富度 R_S	私有等位基因丰富度 P_AR
喜马拉雅 Himalayas	30	0.79	0.62	3.18	0.70
横断山 Hengduan Mountains	35	0.86	0.65	3.39	0.53
云贵高原西部 West Yunnan-Guizhou Plateau	36	0.73	0.56	3.04	0.19
云贵高原东部 East Yunnan-Guizhou Plateau	26	0.65	0.50	2.69	0.24

	n1	n2	n3	n4	T1	T2	T3	μ	P
中位值 Median	6.84×10⁴	6.30×10⁴	5.84×10⁴	3.90×10⁴	8.53×10⁴	1.25×10⁵	5.11×10⁵	4.30×10^-6	0.21
95%置信区间下限 95% HPD lower	3.30×10⁴	2.68×10⁴	2.39×10⁴	1.21×10⁴	1.80×10⁴	2.73×10⁴	1.92×10⁵	2.19×10^-6	0.11
95%置信区间上限 95% HPD upper	9.53×10⁴	9.44×10⁴	9.15×10⁴	8.50×10⁴	3.49×10⁵	4.49×10⁵	8.82×10⁵	1.01×10^-5	0.70