Walden Nora, Lucek Kay, Willi Yvonne
Department of Environmental Sciences, University of Basel, Basel, Switzerland.
Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany.
Mol Ecol. 2020 Apr;29(8):1436-1451. doi: 10.1111/mec.15338. Epub 2020 Jan 13.
Adaptation to local climatic conditions is commonly found within species, but whether it involves the same intraspecific genomic variants is unknown. We studied this question in North American Arabidopsis lyrata, whose current distribution is shaped by post-glacial range expansion from two refugia, resulting in two distinct genetic clusters covering comparable climatic gradients. Using pooled whole-genome sequence data of 41 outcrossing populations, we identified loci associated with three niche-determining climatic variables in the two clusters and compared these outliers. Little evidence was found for parallelism in climate adaptation for single nucleotide polymorphisms (SNPs) and for genes with an accumulation of outlier SNPs. Significantly increased selection coefficients supported them as candidates of climate adaptation. However, the fraction of gene ontology (GO) terms shared between clusters was higher compared to outlier SNPs and outlier genes, suggesting that selection acts on similar pathways but not necessarily the same genes. Enriched GO terms involved responses to abiotic and biotic stress, circadian rhythm and development, with flower development and reproduction being among the most frequently detected. In line with GO enrichment, regulators of flowering time were detected as outlier genes. Our results suggest that while adaptation to environmental gradients on the genomic level are lineage-specific in A. lyrata, similar biological processes seem to be involved. Differential loss of standing genetic variation, probably driven by genetic drift, can in part account for the lack of parallel evolution on the genomic level.
物种内常见对当地气候条件的适应性，但这是否涉及相同的种内基因组变异尚不清楚。我们在北美琴叶拟南芥中研究了这个问题，其当前分布是由两个避难所的冰期后范围扩张形成的，导致两个不同的遗传簇覆盖了相当的气候梯度。利用41个异交种群的全基因组序列池数据，我们在这两个簇中鉴定了与三个决定生态位的气候变量相关的位点，并比较了这些异常值。在单核苷酸多态性（SNP）和具有异常SNP积累的基因的气候适应中，几乎没有发现平行性的证据。显著增加的选择系数支持它们作为气候适应的候选者。然而，与异常SNP和异常基因相比，簇间共享的基因本体（GO）术语比例更高，这表明选择作用于相似的途径，但不一定是相同的基因。富集的GO术语涉及对非生物和生物胁迫的反应、昼夜节律和发育，其中花发育和繁殖是最常检测到的。与GO富集一致，开花时间调节因子被检测为异常基因。我们的结果表明，虽然在基因组水平上对环境梯度的适应在琴叶拟南芥中是谱系特异性的，但似乎涉及相似的生物学过程。可能由遗传漂变驱动的现有遗传变异的差异丧失，在一定程度上可以解释基因组水平上缺乏平行进化的原因。
