Data from: Genetic tradeoffs and conditional neutrality contribute to local adaptation

Divergent natural selection promotes local adaptation and can lead to reproductive isolation of populations in contrasting environments; however, the genetic basis of local adaptation remains largely unresolved in natural populations. Local adaptation might result from antagonistic pleiotropy, where alternate alleles are favored in distinct habitats, and polymorphism is maintained by selection. Alternatively, under conditional neutrality some alleles may be favored in one environment but neutral at other locations. Antagonistic pleiotropy maintains genetic variation across the landscape; however, there is a systematic bias against discovery of antagonistic pleiotropy since the fitness benefits of local alleles need to be significant in at least two environments. Here, we develop a generally applicable method to investigate polygenic local adaptation and identify loci that are the targets of selection. This approach evaluates allele frequency changes after selection at loci across the genome to distinguish antagonistic pleiotropy from conditional neutrality and deleterious variation. We investigate local adaptation at the QTL-level in field experiments, in which we expose 177 F6 recombinant inbred lines (RILs) and parental lines of Boechera stricta (Brassicaceae) to their parental environments over two seasons. We demonstrate polygenic selection for native alleles in both environments, with 2.8% of the genome exhibiting antagonistic pleiotropy, and 8% displaying conditional neutrality. Our study strongly supports antagonistic pleiotropy at one large-effect flowering phenology QTL (nFT): native homozygotes had significantly greater probabilities of flowering than foreign homozygotes in both parental environments. Such large-scale field studies are essential to elucidate the genetic basis of adaptation in natural populations.趋异自然选择（divergent natural selection）可促进局部适应，还能使处于异质环境中的种群形成生殖隔离；然而，自然种群局部适应的遗传基础在很大程度上仍未得到阐明。局部适应可能源于拮抗多效性（antagonistic pleiotropy）：不同生境中会被不同等位基因所青睐，且种群多态性由选择作用维持。或者，在条件中性（conditional neutrality）模型下，部分等位基因可在某一环境中受青睐，但在其他环境中呈现中性效应。拮抗多效性可维持整个分布区域的遗传变异；然而，由于本地等位基因的适合度收益至少需要在两种环境中均表现显著，当前对拮抗多效性的检出存在系统性偏倚。 本研究开发了一种通用方法，用于探究多基因局部适应，并鉴定作为选择靶标的基因座（loci）。该方法通过评估全基因组各基因座在选择后的等位基因频率变化，实现拮抗多效性、条件中性效应与有害变异的区分。我们在田间试验中开展了数量性状基因座（Quantitative Trait Locus, QTL）水平的局部适应研究：将177个F6代重组自交系（RILs）以及十字花科（Brassicaceae）硬叶南芥（Boechera stricta）的亲本株系，在两季时间内置于其原生生长环境中开展试验。我们证实，两种环境中均存在针对本地等位基因的多基因选择：全基因组中有2.8%的区域表现出拮抗多效性，另有8%的区域呈现条件中性效应。本研究在一个效应显著的开花物候QTL（nFT）上，为拮抗多效性提供了强有力的证据：在两种原生环境中，本地纯合子的开花概率均显著高于外来纯合子。此类大规模田间研究，对于阐明自然种群适应的遗传基础至关重要。