生物多样性 ›› 2022, Vol. 30 ›› Issue (7): 21508. DOI: 10.17520/biods.2021508
孙维悦1,2, 舒江平2,3, 顾钰峰1,4, 莫日根高娃4, 杜夏瑾2, 刘保东1,*(), 严岳鸿2,*()
收稿日期:
2021-12-09
接受日期:
2022-04-09
出版日期:
2022-07-20
发布日期:
2022-06-21
通讯作者:
刘保东,严岳鸿
作者简介:
99bd@163.com基金资助:
Weiyue Sun1,2, Jiangping Shu2,3, Yufeng Gu1,4, Morigengaowa4, Xiajin Du2, Baodong Liu1,*(), Yuehong Yan2,*()
Received:
2021-12-09
Accepted:
2022-04-09
Online:
2022-07-20
Published:
2022-06-21
Contact:
Baodong Liu,Yuehong Yan
摘要:
理解物种的濒危机制对生物多样性的科学保护至关重要。荷叶铁线蕨(Adiantum nelumboides)作为国家一级重点保护野生植物, 其遗传多样性状况和濒危机制一直存在较大争议。本文利用简化基因组测序技术(genotyping by sequencing, GBS)对来自6个居群的28个荷叶铁线蕨样本测序, 共获得29.6 Gb的数据, 并筛选得到9,423个高质量单核苷酸变异位点(SNP), 通过遗传多样性和居群遗传结构分析, 并结合不同气候情景下物种潜在分布区差异, 探讨了荷叶铁线蕨的濒危原因和科学保护策略。结果表明: (1)荷叶铁线蕨具有较低的遗传多样性(Ho = 0.138、He = 0.232、Pi = 0.373), 同时种群间具有较低的遗传分化(Fst = 0.0202)和基因流(Nm = 1.9613); (2)所有样本均来自2个遗传分组, 基因组大小为 5.01‒5.83 Gb, 且均为四倍体, GC含量约为 39%‒41%; (3)生态位模拟表明, 与现代气候相比, 在未来气候变化下荷叶铁线蕨的潜在分布区面积略有增加, 但高适生区面积减小。其主要适生区向北迁移, 影响其分布的主导因子为昼夜温差月均值和最冷季降水量。正是由于荷叶铁线蕨遗传多样性低, 不同种群间遗传分化较低, 再加上气候条件的变化, 其适生区狭窄, 导致其遗传多样性和种群数量急剧下降。因此, 自身更新能力低以及过度的人为活动干扰可能是导致其濒危的主要原因。建议加强对荷叶铁线蕨的就地保护; 通过生境恢复及自然回归等措施, 增加居群间的基因交流, 防止遗传资源丢失加剧。
孙维悦, 舒江平, 顾钰峰, 莫日根高娃, 杜夏瑾, 刘保东, 严岳鸿 (2022) 基于保护基因组学揭示荷叶铁线蕨的濒危机制. 生物多样性, 30, 21508. DOI: 10.17520/biods.2021508.
Weiyue Sun, Jiangping Shu, Yufeng Gu, Morigengaowa, Xiajin Du, Baodong Liu, Yuehong Yan (2022) Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides. Biodiversity Science, 30, 21508. DOI: 10.17520/biods.2021508.
居群 Population | 采样地点 Sampling localities | 样本数量 Sample size | 样本采集号 Voucher no. |
---|---|---|---|
石柱 SZ | 重庆市石柱县西沱镇 Xituo Town, Shizhu County, Chongqing | 10 | YYH15105, YYH15106, YYH15107, YYH15108, YYH15109, YYH15110, YYH15111, YYH15112, YYH15113, YYH15116 |
南川 NC | 重庆市南川区 Nanchuan District, Chongqing | 3 | YSR0101, YSR0201, YSR0204 |
新乡 XX | 重庆市万州区新乡镇 Xinxiang Town, Wanzhou District, Chongqing | 8 | YYH15091, YYH15071, YYH15072, YYH15088, YYH15087, YYH15092, YYH15090, YYH15086 |
燕山 YS | 重庆市万州区燕山乡 Yanshan Town, Wanzhou District, Chongqing | 1 | YYH15070 |
武陵 WL | 重庆市万州区武陵镇 Wuling Town, Wanzhou District, Chongqing | 5 | YYH15117, YYH15118, YYH15119, YYH15120, YYH15121 |
忠县 ZX | 重庆市忠县石宝镇 Shibao Town, Zhong County, Chongqing | 1 | YYH15114 |
表1 荷叶铁线蕨样品采集信息
Table 1 Sample details of Adiantum nelumboides
居群 Population | 采样地点 Sampling localities | 样本数量 Sample size | 样本采集号 Voucher no. |
---|---|---|---|
石柱 SZ | 重庆市石柱县西沱镇 Xituo Town, Shizhu County, Chongqing | 10 | YYH15105, YYH15106, YYH15107, YYH15108, YYH15109, YYH15110, YYH15111, YYH15112, YYH15113, YYH15116 |
南川 NC | 重庆市南川区 Nanchuan District, Chongqing | 3 | YSR0101, YSR0201, YSR0204 |
新乡 XX | 重庆市万州区新乡镇 Xinxiang Town, Wanzhou District, Chongqing | 8 | YYH15091, YYH15071, YYH15072, YYH15088, YYH15087, YYH15092, YYH15090, YYH15086 |
燕山 YS | 重庆市万州区燕山乡 Yanshan Town, Wanzhou District, Chongqing | 1 | YYH15070 |
武陵 WL | 重庆市万州区武陵镇 Wuling Town, Wanzhou District, Chongqing | 5 | YYH15117, YYH15118, YYH15119, YYH15120, YYH15121 |
忠县 ZX | 重庆市忠县石宝镇 Shibao Town, Zhong County, Chongqing | 1 | YYH15114 |
样品 Sample | 倍性 Ploidy level | 内参荧光强度 Relative fluorescence intensity | 待测荧光 强度 Mean | 基因组大小 Genome size |
---|---|---|---|---|
YYH15105 | 4X | 62.96 | 151.86 | 5.55 |
YYH15111 | 4X | 60.30 | 140.32 | 5.35 |
YYH15112 | 4X | 60.06 | 130.77 | 5.01 |
YYH15116 | 4X | 67.82 | 171.92 | 5.83 |
表2 荷叶铁线蕨相对荧光强度
Table 2 Relative fluorescence intensity of Adiantum nelumboides
样品 Sample | 倍性 Ploidy level | 内参荧光强度 Relative fluorescence intensity | 待测荧光 强度 Mean | 基因组大小 Genome size |
---|---|---|---|---|
YYH15105 | 4X | 62.96 | 151.86 | 5.55 |
YYH15111 | 4X | 60.30 | 140.32 | 5.35 |
YYH15112 | 4X | 60.06 | 130.77 | 5.01 |
YYH15116 | 4X | 67.82 | 171.92 | 5.83 |
居群名称 Population | 观察杂合度 Ho | 期望杂合度 He | 核苷酸多样性 Pi | 近交系数 Fis |
---|---|---|---|---|
石柱 SZ | 0.206 | 0.214 | 0.316 | 0.172 |
南川 NC | 0.211 | 0.287 | 0.683 | 0.27 |
新乡 XX | 0.104 | 0.285 | 0.1166 | 0 |
燕山 YS | 0.106 | 0.135 | 0.105 | 0 |
武陵 WL | 0.198 | 0.187 | 0.54 | 0.117 |
忠县 ZX | 0.218 | 0.286 | 0.48 | 0.303 |
平均值 Average | 0.173 | 0.232 | 0.373 | 0.143 |
表3 不同居群荷叶铁线蕨遗传多样性。样品信息同表1。
Table 3 Genetic diversity indices of different groups of Adiantum nelumboides. The sample information see Table 1.
居群名称 Population | 观察杂合度 Ho | 期望杂合度 He | 核苷酸多样性 Pi | 近交系数 Fis |
---|---|---|---|---|
石柱 SZ | 0.206 | 0.214 | 0.316 | 0.172 |
南川 NC | 0.211 | 0.287 | 0.683 | 0.27 |
新乡 XX | 0.104 | 0.285 | 0.1166 | 0 |
燕山 YS | 0.106 | 0.135 | 0.105 | 0 |
武陵 WL | 0.198 | 0.187 | 0.54 | 0.117 |
忠县 ZX | 0.218 | 0.286 | 0.48 | 0.303 |
平均值 Average | 0.173 | 0.232 | 0.373 | 0.143 |
居群 Population | 石柱 SZ | 南川 NC | 燕山 YS | 忠县 ZX | 武陵 WL | 新乡 XX |
---|---|---|---|---|---|---|
石柱 SZ | 1.108 | 1.957 | 2.023 | 2.486 | 2.157 | |
南川 NC | 0.0216 | 1.795 | 2.417 | 2.186 | 1.957 | |
燕山 YS | 0.0194 | 0.0312 | 1.864 | 2.167 | 2.035 | |
忠县 ZX | 0.0165 | 0.0216 | 0.0183 | 2.341 | 1.628 | |
武陵 WL | 0.0186 | 0.0298 | 0.0161 | 0.0176 | 1.439 | |
新乡 XX | 0.0154 | 0.0251 | 0.0148 | 0.0193 | 0.0169 |
表4 荷叶铁线蕨居群间的遗传分化系数(Fst: 对角线下)与基因流(Nm: 对角线上), 样品信息同表1。
Table 4 Genetic differentiation coefficient (Fst: below the diagonal) and gene flow (Nm: above the diagonal). The sample information is shown in Table 1.
居群 Population | 石柱 SZ | 南川 NC | 燕山 YS | 忠县 ZX | 武陵 WL | 新乡 XX |
---|---|---|---|---|---|---|
石柱 SZ | 1.108 | 1.957 | 2.023 | 2.486 | 2.157 | |
南川 NC | 0.0216 | 1.795 | 2.417 | 2.186 | 1.957 | |
燕山 YS | 0.0194 | 0.0312 | 1.864 | 2.167 | 2.035 | |
忠县 ZX | 0.0165 | 0.0216 | 0.0183 | 2.341 | 1.628 | |
武陵 WL | 0.0186 | 0.0298 | 0.0161 | 0.0176 | 1.439 | |
新乡 XX | 0.0154 | 0.0251 | 0.0148 | 0.0193 | 0.0169 |
图1 基于SNP的荷叶铁线蕨遗传结构分析。A: 当K = 2时每个个体的遗传成分分析结果和基于9,423个SNP的最大似然法建树结果示。每一个柱形代表1个样本, 每种颜色代表1个遗传簇; B: 最佳聚类结果的地理分布, 其中的饼状图代表每个居群的遗传簇; C: 主成分分析结果, 图中每个点代表1个样品。样品信息同表1。
Fig. 1 Analysis of population structure based on identified SNP. A, Results of the admixture proportions for each individual with K = 2 and maximum likelihood tree based on 9,423 SNPs. Each sample is represented by a histogram, which is partitioned into different colors. Each color represents a genetic cluster. Numbers in the nodes are the bootstrap values from 100 replicates; B, The distribution of best results in clusters by Structure. The pie chart represents the genetic cluster of each population; C, Results of the principal component analysis. Each sample is represented by a point. The sample information is shown in Table 1.
图2 荷叶铁线蕨有效群体大小变化分析。A: 位点频谱; B: Stairway Plot基于SFS的群体大小变化。粗线为中位数, 阴影部分为95%置信区间。LGM: 末次盛冰期; LGP: 末次冰期。
Fig. 2 Changes in population size of Adiantum nelumboides. A, Folded site frequency spectrum (SFS); B, Changes in population size inferred by Stairway plot using folded site frequency spectrum (SFS). Thick lines represent the median, and shaded areas represent the 95% confidence intervals. LGM, Last glacial maximum; LGP, Last glacial period.
图3 不同时期荷叶铁线蕨适宜性生境分布。A: 末次盛冰期气候情景; B: 末次间冰期气候情景; C: 现代(1970?2000)气候情景; D: 未来(2081?2100) RCP2.6气候情景。
Fig. 3 Distribution of suitable habitats for Adiantum nelumboides in different periods. A, Last glacial maximum climate scenarios; B, Last interglacial climate scenarios; C, Contemporary (1970?2000) climate scenarios; D, Future (2081?2100) RCP2.6 climate scenarios.
图4 植物遗传多样性与濒危程度分析。CR: 极危; EN: 濒危; VU: 易危; LC: 无危; NE: 未予评估。图中数据来源于附录4参考文献。
Fig. 4 Genetic diversity and endangered degree. CR, Critically Endangered; EN, Endangered; VU, Vulnerable; LC, Least Concern; NE, Not Evaluated. Data in the figure were from the references listed in Appendix 4.
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