Phylogeographic study of natural populations of Amorphophallus yunnanensis (Araceae) in China

doi:10.17521/cjpe.2023.0220

Abstract

Abstract:

Aims The mountainous region of Southwestern China has been recognized as one of the biodiversity hotspots in the world. The extremely complicated and fragmented geography promotes the process of population divergence, and increases species diversity in this area. Some species in the Amorphophallus genus are important cash crops that native to Southern China and Indo-China Peninsula. Wild resources of this genus are distributed as isolated populations. The demographic history and differentiation mechanisms of natural Amorphophallus populations need to be investigated.

Methods Five chloroplast DNA fragments were used to characterize the phylogeographic pattern among 16 populations of A. yunnanensis, a species that mainly resided in mountainous region of Southwestern China. The factors that contribute to the genetic differentiation pattern of A. yunnanensis were also investigated.

Important findings Genetic diversity analyses found a low level of genetic variation (nucleotide diversity ranged from 0.000 07 to 0.001 82) within populations of A. yunnanensis, and a high level of genetic differentiation with an average fixation index value of 0.363. Phylogenetic analysis revealed a clear east-west genetic differentiation, with two distinct genetic lineages inhabiting Guizhou Plateau and Yunnan Plateau, respectively. We discovered demographic expansion of the Guizhou Plateau lineage and recent hybridization in populations at the contact region. Based on the population demographic history as well as the significant level of isolation by distance, mountain systems, historical river capture events and Pleistocene climatic changes might contribute to differentiation of A. yunnanensis.

Key words: phylogeograhpy, Yungui Plateau, genetic structure, Amorphophallus yunnanensis, chloroplast DNA

YIN Si, YANG Yi-Ting, LU Rui-Ling, NIAN Rui, HAO Zhuan, GAO Yong. Phylogeographic study of natural populations of Amorphophallus yunnanensis (Araceae) in China[J]. Chin J Plant Ecol, 2025, 49(2): 308-319.

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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2023.0220

https://www.plant-ecology.com/EN/Y2025/V49/I2/308

Figures/Tables 11

References 47

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编号 No.	种群编号 Population ID	纬度 Latitude (N)	经度 Longitude (E)	海拔 Altitude (m)	采样点 Sample Site
1	YSXS	28.78°	110.22°	317	湖南永顺 Yongshun, Hunan
2	LDNR	25.40°	106.61°	436	贵州罗甸 Luodian, Guizhou
3	WMNS	25.16°	106.25°	726	贵州望谟 Wangmo, Guizhou
4	WMXY	25.22°	106.12°	1 075	贵州望谟 Wangmo, Guizhou
5	WMZX	24.98°	106.12°	432	贵州望谟 Wangmo, Guizhou
6	LYLZ	24.28°	106.67°	396	广西凌云 Lingyun, Guangxi
7	FHG	24.61°	104.25°	1 249	云南师宗 Shizong, Yunnan
8	SQG	24.96°	102.63°	2 216	云南昆明 Kunming, Yunnan
9	FYND	24.25°	102.19°	1 527	云南玉溪 Yuxi, Yunnan
10	BMGD	22.66°	101.16°	1 680	云南普洱 Pu’er, Yunnan
11	LCYD	24.24°	99.58°	1 329	云南临沧 Lincang, Yunnan
12	HHLC	23.02°	102.38°	1 715	云南红河 Honghe, Yunnan
13	HDR	21.95°	100.41°	1 177	云南西双版纳 Xishuangbanna, Yunnan
14	DSQ	24.73°	100.51°	2 340	云南大理 Dali, Yunnan
15	JDXC	24.26°	101.05°	1 754	云南景东 Jingdong, Yunnan
16	ZYHC	23.96°	100.96°	1 897	云南镇沅 Zhenyuan, Yunnan

编号 No.	种群编号 Population ID	纬度 Latitude (N)	经度 Longitude (E)	海拔 Altitude (m)	采样点 Sample Site
1	YSXS	28.78°	110.22°	317	湖南永顺 Yongshun, Hunan
2	LDNR	25.40°	106.61°	436	贵州罗甸 Luodian, Guizhou
3	WMNS	25.16°	106.25°	726	贵州望谟 Wangmo, Guizhou
4	WMXY	25.22°	106.12°	1 075	贵州望谟 Wangmo, Guizhou
5	WMZX	24.98°	106.12°	432	贵州望谟 Wangmo, Guizhou
6	LYLZ	24.28°	106.67°	396	广西凌云 Lingyun, Guangxi
7	FHG	24.61°	104.25°	1 249	云南师宗 Shizong, Yunnan
8	SQG	24.96°	102.63°	2 216	云南昆明 Kunming, Yunnan
9	FYND	24.25°	102.19°	1 527	云南玉溪 Yuxi, Yunnan
10	BMGD	22.66°	101.16°	1 680	云南普洱 Pu’er, Yunnan
11	LCYD	24.24°	99.58°	1 329	云南临沧 Lincang, Yunnan
12	HHLC	23.02°	102.38°	1 715	云南红河 Honghe, Yunnan
13	HDR	21.95°	100.41°	1 177	云南西双版纳 Xishuangbanna, Yunnan
14	DSQ	24.73°	100.51°	2 340	云南大理 Dali, Yunnan
15	JDXC	24.26°	101.05°	1 754	云南景东 Jingdong, Yunnan
16	ZYHC	23.96°	100.96°	1 897	云南镇沅 Zhenyuan, Yunnan

标记名称 Marker ID	正向引物 Forward Primer (5′-3′)	反向引物 Reverse Primer (5′-3′)	退火温度 Annealing temperature (℃)
trnK-matK	CTTGCAGTTTTCATTGCACA	TTCACTTTTGGTCTCAACCC	56
rbcL	ATGTCACAACAAACAGAAAC	TCCTTTTAGTAAAAGATTGGGCCGAG	56
trnL	CGAAATCGGTAGACGCTACG	GGGGATAGAGGGACTTGAAC	56
psaB	AAATATCACAAGTACCACCTCG	ACAATCGGATTACGCACCA	56
rps2	CTGGAATCGAAATATCTGC	GTATCAACGGTCAATCCTC	56

标记名称 Marker ID	正向引物 Forward Primer (5′-3′)	反向引物 Reverse Primer (5′-3′)	退火温度 Annealing temperature (℃)
trnK-matK	CTTGCAGTTTTCATTGCACA	TTCACTTTTGGTCTCAACCC	56
rbcL	ATGTCACAACAAACAGAAAC	TCCTTTTAGTAAAAGATTGGGCCGAG	56
trnL	CGAAATCGGTAGACGCTACG	GGGGATAGAGGGACTTGAAC	56
psaB	AAATATCACAAGTACCACCTCG	ACAATCGGATTACGCACCA	56
rps2	CTGGAATCGAAATATCTGC	GTATCAACGGTCAATCCTC	56

单倍型群组 Haplogroup	种群编号 Population ID	样本数 n	单倍型 Haplotype	单倍型多样性 H_d	突变位点 S	核苷酸多样性 π	Tajima’s D	Fu’s Fs
东部支系 East clade		104		0.826	87	0.000 94	-31.168^*	-2.567^*
	YSXS	19	H_17, 64, 65, 66, 67, 68, 69	0.538	9	0.000 29	-1.999^*	-2.533^*
	LDNR	12	H_17, 20, 21, 22, 23, 50	0.818	40	0.001 82	1.968^*	-2.153^*
	WMNS	8	H_17, 18, 19, 20	0.643	6	0.000 39	-0.422	-1.640
	WMXY	14	H_16, 17, 24, 25, 26, 27, 28, 29, 30	0.835	15	0.000 72	-3.436^*	-1.836^*
	WMZX	9	H_17, 58, 59, 60	0.643	16	0.001 55	2.661	-0.172
	LYLZ	7	H_17, 51, 52	0.524	1	0.000 07	-0.095	-1.006
	FHG	7	H_12, 53, 54, 55, 56, 57	0.857	5	0.000 54	-1.447	0.132
	SQG	5	H_12, 61, 62, 63	0.900	3	0.000 31	-1.938	-1.048
	FYND	5	H_12, 13, 14, 15	0.900	5	0.000 62	-0.701	0.000
	BMGD	8	H_1, 2	0.250	4	0.000 26	-1.535	1.946
	LCYD	10	H_45, 46, 47, 48, 49	0.756	10	0.000 59	-0.318	-1.590
西部支系 West clade		36		0.887	27	0.000 96	-12.337^*	-1.503
	HHLC	8	H_31, 32, 33, 34, 35, 36	0.929	12	0.000 78	-1.609	-0.665
	HDR	6	H_3, 4, 5, 6, 37, 38	1.000	11	0.001 07	-2.552	-0.859
	DSQ	8	H_7, 8, 9, 10, 11	0.786	5	0.000 32	-2.238	-1.595
	JDXC	7	H_9, 39, 40, 41, 42, 43, 44	1.000	4	0.000 42	-0.538	-0.040
	ZYHC	7	H_9, 11, 70, 71	0.714	2	0.000 20	-0.438	-0.275