Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides

doi:10.17520/biods.2021508

Abstract

Abstract:

Aims: Understanding the mechanism that leads species to endangerment is crucial to the conservation of biodiversity. Adiantum nelumboides is a key wild plant that is protected at the national level, and its genetic diversity and endangerment mechanism are controversial.
Methods: A total of 28 A. nelumboides samples, from six populations, were used to obtain single-nucleotide variation sites (SNP) by the genotyping by sequencing (GBS) method. The genetic diversity and structure of the population were analyzed and combined with the change in the potential distribution area of species under different climate scenarios. Then the possible causes of endangerment and scientific protection strategies of A. nelumboides were discussed.
Results: The results showed that 29.6 Gb of data was obtained based on the GBS sequencing, and 9,423 high-quality SNP loci were screened. Adiantum nelumboides had low genetic diversity (H_o = 0.138, H_e = 0.232, P_i = 0.373), low genetic differentiation (F_st = 0.0202) and gene flow (N_m = 1.9613). The A. nelumboides samples are from two ancestral haplotypes, their genome size was 5.01‒5.83 Gb, they were tetraploid, and the GC content was about 39%‒41%. Under future climate change, the potential distribution area of A. nelumboides will increase slightly, in which the area of high fitness is lost. The primary areas that are suitable for the plant are distributed in Wanzhou, Chongqing and further north. The dominant factors affecting its distribution are monthly mean differences in diurnal temperatures and precipitation during the coldest season.
Conclusions: Due to the low genetic diversity, lack of gene exchange between different populations, and changes in climatic conditions, suitable growth areas for A. nelumboides become narrow, resulting in a sharp decline in species diversity and population size. Therefore, their low regeneration ability and excessive disturbance from human activities might be the main reasons for the endangered status of A. nelumboides. It was recommended to strengthen in situ conservation of A. nelumboides. Measures such as habitat restoration and natural regression must be discussed to increase gene exchange across populations. At the same time, a core germplasm of this species must be constructed to prevent the aggravation of genetic resource loss.

Key words: genetic structure, species distribution models, dominant climate factor, genetic diversity, genotyping- by-sequencing

Weiyue Sun, Jiangping Shu, Yufeng Gu, Morigengaowa, Xiajin Du, Baodong Liu, Yuehong Yan. Conservation genomics analysis revealed the endangered mechanism of Adiantum nelumboides[J]. Biodiv Sci, 2022, 30(7): 21508.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2021508

https://www.biodiversity-science.net/EN/Y2022/V30/I7/21508

Figures/Tables 8

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

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

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 H_o	期望杂合度 H_e	核苷酸多样性 P_i	近交系数 F_is
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

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

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.

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.

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.

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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