基于叶绿体和核基因片段序列的甘蒙柽柳谱系地理研究

doi:10.11707/j.1001-7488.20200106

Abstract

Abstract:

Objective: Tamarix austromongolica is an endemic species distributed along the Yellow River Basin in China. The purpose of this study was to explore the genetic structure and diversity of the T. austromongolica populations. Method: Using the chloroplast DNA fragment (trnQ-rps16) and the nuclear gene fragment,the Internal Transcribed Spacer (ITS) to study the genetic diversity,the genetic structure and the historical dynamics of 266 individuals in seventeen populations of T. austromongolica distributed in the Yellow River basin of China by PCR amplification and sequencing. Result: Four chloroplast haplotypes in 207 individuals and 32 nuclear haplotypes in 232 individuals were detected. The genetic diversity of T. austromongolica based on chloroplast gene analysis was low (H_T=0.13),however,the genetic diversity of nuclear genes was high (H_T=0.82). The AMOVA analysis of chloroplast gene(cpDNA) and nuclear gene(nDNA) fragments showed that the genetic variation of T. austromongolica populations mainly occurred within populations. The genetic differentiation coefficients N_ST (cpDNA:0.15; nDNA:0.22) and G_ST (cpDNA:0.19; nDNA:0.24) were not significant (P>0.05),indicating no significant phylogeographic structure between populations. The Tajima's D and Fu's Fs of neutrality tests both showed negative results and the mismatch analysis showed that the distribution curve of the expected population expansion is consistent with the actual observed distribution curve,indicating that the T. austromongolica has undergone a rapid population expansion. According to the results revealed by the chloroplast genes,the haplotypes,polymorphisms and nucleotide diversity of T. austromongolica distributed in Yongjing county and Jishishan county,Gansu province,were significantly higher than those in other regions,and had unique haplotypes (H2,H4),indicating that T. austromongolica near these areas was the oldest. The population of T. austromongolica migrated to the upstream (Qinghai province) and the middle and lower reaches respectively from Gansu province. The founder effect caused the genetic diversity of newly-built populations to be lower. Conclusion: This study revealed the genetic structure and diversity of T. austromongolica. The genetic variation of populations of T. austromongolica mainly occurred in the population,and there is no significant phylogeographic structure between populations. The species has experienced a rapid expansion. It is speculated that its origin center was near Jishishan county and Yongjing county in Gansu province. And the population of T. austromongolica migrated from Gansu province to the upstream and the middle and lower reaches respectively with the formation of the Yellow River. Our results suggest that the formation of Yellow River is an important factor leading to the migration and expansion of the populations of T. austromongolica.

Key words: Tamarix austromongolica, phylogeography, genetic variation, population, Yellow River basin

CLC Number:

S718.46

Yuexian Wen, Honghao Gan, Shengqing Shi, Zeping Jiang, Lilu Wu, Jianmin Chu. Phylogeography of Tamarix austromongolica Based on the Sequences of Chloroplast and Nuclear Gene Fragments[J]. Scientia Silvae Sinicae, 2020, 56(1): 55-64.

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居群代码 Population code	采样地 Sampling location	样品数量 Number of samples	经度 Longitude(E)	纬度 Latitude(N)	海拔 Altitude/m
TD	青海同德县Tongde county, Qinghai	20	100°15′	35°19′	2 710
JS	甘肃积石山县Jishishan county, Gansu	20	102°54′	35°51′	1 875
TJ	甘肃永靖县太极镇Taiji town, Yongjing county, Gansu	20	103°14′	35°57′	1 614
LY	甘肃永靖县兰永公路 Lanyong highway, Yongjing county, Gansu	20	103°14′	36°17′	1 612
LZ	甘肃兰州市Lanzhou city, Gansu	10	103°46′	36°05′	1 525
YN	宁夏永宁县Yongning county, Ningxia	13	106°20′	38°18′	1 100
YCS	宁夏银川市Yinchuan city, Ningxia	8	106°23′	38°23′	1 101
YCX	宁夏盐池县Yanchi county, Ningxia	25	107°19′	37°09′	1 345
DK	内蒙古磴口县Dengkou county, Inner Mongolia	10	106°57′	40°19′	1 050
DB	陕西定边县Dingbian county, Shaanxi	25	108°05′	37°34′	1 367
JB	陕西靖边县Jinbian county, Shaanxi	15	108°44′	37°36′	1 325
DT	山西大同市Datong city, Shanxi	10	113°10′	39°56′	1 030
YJ	山西永济市Yongji city, Shanxi	10	110°28′	34°55′	350
JY	河南济源市Jiyuan city, Henan	15	112°29′	34°56′	146
BZ	山东滨州市Binzhou city, Shandong	10	117°58′	37°22′	9
DY	山东东营市Dongying city, Shandong	25	118°40′	37°25′	3
CY	山东昌邑市Changyi city, Shandong	10	119°22′	37°04′	11

引物名称 Fragments	碱基序列 Base sequences(5′—3′)	退火温度 Annealing temperature/℃	文献 Reference
trnQ-rps16	F GCGTGGCCAAGYGGTAAGGC R GTTGCTTTYTACCACATCGTTT	58	Oxelman et al., 1997
trnK	F GGGTGCCCGGGACTCGAAC R CAACGGTAGAGTACTCGGCTTTT	55	Johnson et al., 1994
trnH-trnK	F ACGGGAATTGAACCCGCGCA R CCGACTAGTTCCGGGTTCGA	60	Demesure et al., 1995
ITS	F AGAAGTCGTAACAAGGTTTCCGTA R TCCTCCGCTTATTGATATGC	58	White et al., 1990

居群代码 Population code	cpDNA					nDNA
居群代码 Population code	n	单倍型(样本数量) Haplotype (number)	H	H_d	π (×10^-3)	n	单倍型(样本数量) Haplotype (number)	H	H_d	π (×10^-3)
TD	20	H1(20)	1	0	0	19	R1(17), R5(4), R10(3), R11(4), R12(10)	5	0.721	1.53
JS	14	H1(9), H2 (5)	2	0.495	0.84	18	R1(34), R5(2)	2	0.108	0.18
TJ	11	H1(7), H4(4)	2	0.509	0.86	16	R1(22), R3(2), R5(2), R20(1), R21(3), R30(2)	6	0.522	1.41
LY	16	H1(14), H2(1), H4(1)	3	0.242	0.64	17	R1(22), R3(2), R5(2), R19(3), R31(4), R32(1)	6	0.569	4.45
LZ	9	H1(9)	1	0	0	9	R1(8), R2(6), R13(2), R14(2)	4	0.706	2.22
YN	13	H1(13)	1	0	0	13	R1(18), R5(3), R19(1), R26(1), R27(1), R28(1), R29(1)	7	0.520	1.64
YCS	7	H1(7)	1	0	0	6	R1(5), R19(1), R20(1), R21(4), R25(1)	5	0.758	2.60
YCX	22	H1(22)	1	0	0	25	R1(17), R3(28), R5(3), R14(2)	4	0.577	2.33
DK	10	H1(10)	1	0	0	10	R1(10), R15(2), R16(2), R17(2), R18(2), R19(2)	6	0.736	3.54
DB	21	H1(21)	1	0	0	25	R1(37), R3(3), R4(1), R5(5), R18(1), R22(2), R24(1)	7	0.445	1.21
JB	14	H1(14)	1	0	0	15	R1(7), R3(7), R5(2), R9(1), R22(12), R23(1)	6	0.749	3.09
DT	9	H1(9)	1	0	0	9	R1(4), R3(8), R4(4), R20(1), R21(1)	5	0.739	2.15
YJ	9	H1(9)	1	0	0	8	R1(2), R4(14)	2	0.233	0.38
JY	11	H1(11)	1	0	0	6	R2(6), R3(2), R4(4)	3	0.667	2.28
BZ	3	H1(3)	1	0	0	3	R2(2), R5(2), R8(1), R9(1)	4	0.867	3.16
DY	13	H1(13)	1	0	0	23	R1(6), R2(8), R3(6), R4(8), R5(12), R6(2), R7(2), R8(2)	5	0.850	2.59
CY	6	H1(5), H3(1)	2	0.333	1.13	10	R1(2), R2(2), R4(8), R5(7), R7(1)	5	0.732	2.07
总计Total	207		4	0.120	0.21	232		32	0.760	2.59

变异来源	自由度	方差总和	方差分量	方差分量百分比
Source of variation	df	Sum of squares	Variance components	Percentage of variance (%)
cpDNA
群体间Among populations	15	2.845	0.011 53	16.53
群体内Within populations	190	10.135	0.053 34	76.42
总体Total	205	12.980	0.064 87
nDNA
群体间Among populations	15	66.529	0.142 28	16.92
群体内Within populations	447	284.469	0.636 40	75.68
总体Total	462	350.998	0.778 68

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Phylogeography of Tamarix austromongolica Based on the Sequences of Chloroplast and Nuclear Gene Fragments

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