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

林业科学 ›› 2020, Vol. 56 ›› Issue (1): 55-64.doi: 10.11707/j.1001-7488.20200106

基于叶绿体和核基因片段序列的甘蒙柽柳谱系地理研究

温月仙¹,甘红豪¹,史胜青¹,江泽平²,吴利禄¹,褚建民^1,*

1. 中国林业科学研究院林业研究所国家林业和草原局林木培育重点实验室北京 100091
2. 中国林业科学研究院森林生态环境与保护研究所北京 100091

收稿日期:2019-02-14 出版日期:2020-01-25 发布日期:2020-02-24
通讯作者: 褚建民
基金资助:
中央级公益性科研院所基本科研业务费专项资金项目(CAFYBB2016ZD001);中央级公益性科研院所基本科研业务费专项资金项目(CAFYBB2016SY005);中国林业科学研究院林业研究所林木培育重点实验室专项资金(ZDRIF201710)

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

Yuexian Wen¹,Honghao Gan¹,Shengqing Shi¹,Zeping Jiang²,Lilu Wu¹,Jianmin Chu^1,*

1. Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration Research Institute of Forestry, Chinese Academy of Forestry Beijing 100091
2. Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry Beijing 100091

Received:2019-02-14 Online:2020-01-25 Published:2020-02-24
Contact: Jianmin Chu
Supported by:
中央级公益性科研院所基本科研业务费专项资金项目(CAFYBB2016ZD001);中央级公益性科研院所基本科研业务费专项资金项目(CAFYBB2016SY005);中国林业科学研究院林业研究所林木培育重点实验室专项资金(ZDRIF201710)

摘要/Abstract

摘要：

目的: 甘蒙柽柳为我国黄河流域特有种，本研究旨在探讨该物种各居群间的谱系地理结构以及黄河形成对甘蒙柽柳居群分布、遗传结构的影响。方法: 利用叶绿体基因trnQ-rps16片段和核基因片段ITS序列信息，通过PCR扩增、测序，对分布于我国黄河流域的甘蒙柽柳17个居群共266个个体的序列进行分析，研究其遗传多样性、遗传结构及种群历史动态。结果: 在甘蒙柽柳居群中，共检测得到4个叶绿体单倍型（207个个体）和32个核基因单倍型（232个个体）。该物种的叶绿体基因遗传多样性较低（H_T=0.13），但其核基因的遗传多样性较高（H_T=0.82）。甘蒙柽柳居群的遗传变异主要发生在居群内，叶绿体基因（cpDNA）和核基因（nDNA）的遗传分化系数N_ST（cpDNA：0.15；nDNA：0.22）和G_ST（cpDNA：0.19；nDNA：0.24）均不显著（P>0.05），且N_ST小于G_ST，表明该物种无明显的谱系地理结构。中性检验结果Tajima's D和Fu's Fs均为负值，且失配分析表明期望扩张群体的分布曲线与实际观测到的分布曲线基本吻合，期望分布曲线呈单峰，表明甘蒙柽柳居群经历过快速扩张，这可能与黄河的贯通形成有关。单倍型分布及网络结构分析结果表明，叶绿体单倍型H1、核基因单倍型R1频率最高，位于网络结构图中心位置，且分布最为广泛，可能为古老单倍型。叶绿体基因的结果: 显示，甘肃省永靖县、积石山县的甘蒙柽柳单倍型种类、多态性及核苷酸多样性显著高于其他地区，且具有特有单倍型（H2、H4），推测其在永靖县、积石山县附近最为古老，以此为起源中心，分别向上游（青海省）和中下游迁移，奠基者效应造成新建居群的遗传多样较低。结论: 本研究揭示了我国黄河流域主要甘蒙柽柳居群的遗传结构及其历史迁移动态。甘蒙柽柳的叶绿体基因遗传多样性水平较低，核基因的遗传多样性较高，遗传变异主要发生在居群内，无明显的谱系地理结构。该物种经历过快速扩张，其起源中心可能为甘肃省积石山县、永靖县附近，随着黄河的形成分别向黄河上游和中下游迁移，推测黄河的形成贯通是导致甘蒙柽柳居群迁移扩散的重要因素。

关键词: 甘蒙柽柳, 谱系地理, 遗传变异, 居群, 黄河流域

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

中图分类号:

S718.46

温月仙, 甘红豪, 史胜青, 江泽平, 吴利禄, 褚建民. 基于叶绿体和核基因片段序列的甘蒙柽柳谱系地理研究[J]. 林业科学, 2020, 56(1): 55-64.

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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基于叶绿体和核基因片段序列的甘蒙柽柳谱系地理研究

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

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