Data from: Contribution of range-wide and short-scale chemical soil variation to local adaptation in a tropical montane forest tree

Local adaptation is a fundamental process that allows populations to
thrive in their native environment, often increasing genetic
differentiation from neighboring stands. However, detecting the molecular
basis and selective factors responsible for local adaptation remains a
challenge, particularly in sessile, non-model species with long life
cycles, such as forest trees. Local adaptation in trees is not only
modeled by climatic factors, but also by soil variation. Such variation
depends on dynamic geological and ecological processes that generate a
highly heterogeneous selective mosaic that may differentially condition
tree adaptation both at the range-wide and local scales. This could be
particularly manifest in species inhabiting mountain ranges that were
formed by diverse geological events, like sacred fir (Abies religiosa), a
conifer endemic to the mountains of central Mexico. Here, we used
landscape genomics approaches to investigate how chemical edaphic
variation influences the genetic structure of this species at the
range-wide and local scales. After controlling for neutral genetic
structure, we performed genotype-environment associations and identified
49 and 23 candidate SNPs at the range-wide and local scales, respectively,
with little overlap between scales. We then developed polygenic models
with such candidates, which accounted for ~20% of the range-wide variation
in soil Ca2+ concentration, electric conductivity (EC), and pH, and for
the local variation in soil EC and organic carbon content (OC). Spatial
Principal Component Analyses further highlighted the role of geography and
population isolation in explaining this genetic-soil co-variation. Our
findings reveal that local adaptation in trees is the result of an
intricate interaction between soil chemical properties and the local
population’s genetic makeup, and that the selective factors driving such
adaptation greatly vary and are not necessarily predictable across spatial
scales. These results highlight the need to consider edaphic variation in
forest genetic studies (including common garden experiments), and in
conservation, management, and assisted migration programs.

本地适应（local adaptation）是使种群得以在原生境中繁茂生长的核心过程，通常会加剧种群与邻近林分间的遗传分化。然而，解析本地适应的分子基础与介导其发生的选择因子仍是一项挑战，尤其对于固着生长、生命周期漫长的非模式物种而言，林木便是典型代表。林木的本地适应不仅受气候因子调控，同时也与土壤异质性息息相关。这类土壤异质性由动态的地质与生态过程塑造，形成高度异质性的选择镶嵌体，可在分布区尺度与局域尺度上差异化调控林木的适应过程。这一现象在由多样地质活动塑造的山地物种中尤为显著，比如神圣冷杉（Abies religiosa）——一种特生于墨西哥中部山地的针叶树种。本研究采用景观基因组学（landscape genomics）方法，探究了土壤化学异质性如何在分布区与局域尺度上影响该物种的遗传结构。在控制中性遗传结构的干扰后，我们开展了基因型-环境关联分析，分别在分布区尺度与局域尺度上鉴定出49个与23个候选单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点，且两个尺度的位点重合度极低。随后我们利用这些候选位点构建了多基因模型，该模型可解释分布区尺度下土壤钙离子（Ca²+）浓度、电导率（electric conductivity，EC）与pH值约20%的变异，同时也能解释局域尺度下土壤EC与有机碳含量（organic carbon content，OC）的变异。空间主成分分析进一步证实了地理因素与种群隔离对该遗传-土壤协同变异的调控作用。本研究结果表明，林木的本地适应是土壤化学性质与局域种群遗传构成复杂互作的产物，且驱动本地适应的选择因子存在显著异质性，在不同空间尺度上未必具有可预测性。上述研究结果凸显了在林木遗传研究（包括同质园实验）、物种保护、资源管理与辅助迁移计划中纳入土壤异质性考量的必要性。