Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics of Taxus cuspidata

IF 3.5 2区 生物学 Q1 EVOLUTIONARY BIOLOGY
Yanjun Luo, Wei Qin, Yu Yan, Kangquan Yin, Runguo Zang, Fang K. Du
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Abstract

The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, Taxus cuspidata Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in T. cuspidata. Outlier detection by FST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of T. cuspidata under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.

Abstract Image

第三纪孑遗树种的气候变化脆弱性和保护策略:Taxus cuspidata景观基因组学的启示。
前所未有的栖息地破碎化或丧失已经威胁到许多物种的生存。因此,了解这些物种能否以及如何适应环境变化至关重要。景观基因组学的最新优势使我们能够识别适应的分子特征,并预测种群将如何应对不断变化的环境,从而为物种保护提供新的见解。本文研究了分布于中国东北及其邻近地区的第三纪孑遗树种 Taxus cuspidata Sieb.我们利用限制性位点相关DNA测序(RAD-seq)和七个核微卫星(nSSRs)数据集研究了遗传多样性和分化模式。我们进一步探索了该物种的濒危机制,预测了其未来的脆弱性,并为该物种的保护和管理提供了指导。RAD-seq 在自然种群中发现了 16,087 个单核苷酸多态性(SNPs)。SNPs 和 nSSRs 数据集都显示出 T. cuspidata 具有较高的遗传多样性和较低的遗传分化。通过 F ST 离群点分析和基因型-环境关联(GEAs)检测离群点,发现了 598 个离群点 SNPs 为推定的适应性 SNPs。线性冗余分析(RDA)和非线性梯度森林(GF)表明,气候对遗传变异的贡献大于地理,降水在推定适应性遗传变异中起着重要作用。此外,遗传偏移和不适应风险(RONA)表明,东北边缘的物种在未来可能更加脆弱。这些结果表明,虽然该物种在近期栖息地丧失和破碎化的情况下保持了较高的遗传多样性,但未来的气候变化可能会威胁到该物种的生存。温度(Bio03)和降水(Prec05)变量有可能被用来预测 T. cuspidata 在未来气候条件下的反应。本研究为未来气候变化背景下野生动物物种的保护和管理策略提供了一个理论框架。
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来源期刊
Evolutionary Applications
Evolutionary Applications 生物-进化生物学
CiteScore
8.50
自引率
7.30%
发文量
175
审稿时长
6 months
期刊介绍: Evolutionary Applications is a fully peer reviewed open access journal. It publishes papers that utilize concepts from evolutionary biology to address biological questions of health, social and economic relevance. Papers are expected to employ evolutionary concepts or methods to make contributions to areas such as (but not limited to): medicine, agriculture, forestry, exploitation and management (fisheries and wildlife), aquaculture, conservation biology, environmental sciences (including climate change and invasion biology), microbiology, and toxicology. All taxonomic groups are covered from microbes, fungi, plants and animals. In order to better serve the community, we also now strongly encourage submissions of papers making use of modern molecular and genetic methods (population and functional genomics, transcriptomics, proteomics, epigenetics, quantitative genetics, association and linkage mapping) to address important questions in any of these disciplines and in an applied evolutionary framework. Theoretical, empirical, synthesis or perspective papers are welcome.
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