基于简化基因组测序揭示水角的濒危机制

RAD-seq revealed the endangered mechanism of Hydrocera triflora(Balsaminaceae)

关键词:  生境片段化, 简化基因组测序, 遗传多样性, 遗传结构, 物种分布模型, 种群历史动态

Key words:  habitat fragmentation, Restriction-site Associated DNA sequencing(RAD-seq), genetic diversity, genetic structure, species distribution models, demographic history

摘要:

物种的遗传多样性是决定物种适应性和生存能力的关键因素。生境片段化是造成生物多样性丧失的重要因素之一,对植物种群的遗传多样性有着重要影响。水角(Hydrocera triflora)作为一种濒危植物,其遗传多样性状况和濒危机制尚未有报道。该文收集了水角7个种群共计34个样本,利用简化基因组测序技术(RAD-seq)获得了单核苷酸变异位点(SNP)。通过种群遗传多样性和遗传结构的分析,并结合种群历史动态分析和不同气候情景下物种潜在分布区预测,探讨了水角的濒危机制。结果表明:(1)水角遗传多样性较低(H_o=0.156 9、H_e=0.165 4、π=0.186 5),遗传分化系数较高; AMOVA分析表明,遗传变异主要发生在种群内。(2)Mantel检测表明环境距离与遗传距离、地理距离均呈显著正相关,分别为P=0.041 2和P=0.008 2。(3)水角的有效种群大小从全新世中期开始持续下降,与琼北火山群的喷发时间一致。(4)与当代气候相比,虽然在未来气候变化下水角的潜在分布区总面积变动不大,但在高CO₂排放的情景下,大量的高适生区将会丧失并转化为低适生区,特别是位于马来群岛的适生区几乎完全消失。该研究结果表明,生境片段化导致了水角较低的遗传多样性和有效种群大小的持续下降。因此,自身更新能力低以及人为活动干扰、城市化等不利的环境条件是导致其濒危的主要原因。建议加强对水角的就地保护,采用人工授粉等方法提高其基因流以增加其种群的遗传多样性,同时,要着重保护湿地免遭破坏。

Abstract:

The genetic diversity of species is a key factor in their adaptability and survival capability. Habitat fragmentation is recognized as one of the key factors causing biodiversity loss, and it has significant impacts on the genetic diversity of plant populations. Hydrocera triflora is an endangered species. Its genetic diversity is unclear and endangered mechanism has not been reported. In this study, 34 samples of H. triflora from seven populations were used to obtain single-nucleotide polymorphisms(SNP)by Restriction-site Associated DNA sequencing(RAD-seq). We discussed the endangered mechanisms of H. triflora by analyzing population genetic diversity and structure. Additionally, we combined these results with historical population dynamics analysis and predictions of potential species distribution in different climate scenarios. The results were as follows:(1)H. triflora had low genetic diversity(H_o=0.156 9, H_e=0.165 4, π=0.186 5)and high genetic differentiation coefficient; AMOVA analysis showed that genetic variation mainly occurred within populations.(2)The Mantel test indicated that there was a significant positive correlation between environmental distance and genetic distance, as well as geographical distance, with respective P-values of 0.041 2 and 0.008 2.(3)The effective population size of H. triflora had been continuously declining since the mid-Holocene.(4)The total potential distribution area of H. triflora change slightly in the future compared to that in the modern climate. However, in scenarios of high CO₂ emissions, the high suitable area decreased significantly and changed into low suitable area, especially in the Malay Islands where the suitable habitat was almost to extinction. The results indicate that habitat fragmentation caused a sustained decrease in the genetic diversity and effective population size of H. triflora. Therefore, the low self-renewal capacity, as well as detrimental environmental conditions such as human disturbance and urbanization, are the primary factors contributing to its endangered state. It is recommended to strengthen the in-situ protection of H. triflora, employing techniques such as artificial pollination to enhance gene flow among populations and thereby increase genetic diversity, and at the same time, we should focus on protecting wetlands from destruction.