Genomic patterns of local adaptation under gene flow in Arabidopsis lyrata

First author: Tuomas Hämälä; Affiliations: University of Oulu (克莱姆森大学): Oulu, Finland

Corresponding author: Outi Savolainen

Short-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modelling indicates that populations within the gradients diverged less than 2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

短尺度的区域适应是一个涉及选择、迁移和漂变的复杂过程。其对于基因组的影响在理论上很完备，但很难从实际上来观测这些影响，因为同时需要考虑区域选择、群体演化历史以及重组率变异等信息。本文中，作者利用地区适应的、并且表型产生分化的两个来自挪威不同海拔梯度的琴叶拟南芥群体来从全基因组水平测试理论期望是否与实际观测一致。群体建模显示挪威不同梯度的琴叶拟南芥群体至少分化了超过2千年，并且不同地点存在基因流。然而，这种基因流是极度不对称的，从高海拔向低海拔的迁移是反向迁移的好几倍。为了检测区域适应的选择信号，作者估计了不同群体谱系特异性分化的模式。理论预测基因流会导致适应性位点会集中在重组率较低的基因组区域，这也是作者在低地和高山群体中都观测到的现象。尽管大多数的选择位点都显示出中性的模式，作者还是发现了一些遗传权衡的迹象，比如一个位点同时在两个群体中表现出极高的分化程度和选择信号。本文的结果进一步支持了对于太阳辐射的抗性是高山环境一个重要的适应性状，而低地环境中主要是选择营养生长和细菌抗性等性状。这些结果为基因流驱动区域适应的遗传结构和演化进程提供了新的见解。同时，作者的研究还加深了我们对于北纬地区高山环境下植物的适应性状与生物学过程的理解。

通讯：Outi Savolainen (https://www.oulu.fi/university/researcher/outi-savolainen)

研究方向：演化遗传学、群体遗传学、林木遗传育种。

doi: https://doi.org/10.1093/molbev/msz149

Journal: Molecular Biology and Evolution

Published date: June 25, 2019