Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan

Abstract

Background: Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geographic area in Japan and additionally identified putative environmental drivers and their effect on co-existing multiple stonefly species. Double-digest restriction-associated DNA (ddRAD) libraries were independently sequenced for 219 individuals from 23 sites across four geographical regions along a nationwide latitudinal gradient in Japan.

Results: A total of 4251 candidate single nucleotide polymorphisms (SNPs) strongly associated with local adaptation were discovered using Latent mixed models; of these, 294 SNPs showed strong correlation with environmental variables, specifically precipitation and altitude, using distance-based redundancy analysis. Genome-genome comparison among the seven species revealed a high sequence similarity of candidate SNPs within a geographical region, suggesting the occurrence of a parallel evolution process.

Conclusions: Our results revealed genomic signatures of local adaptation and their influence on multiple, co-occurring species. These results can be potentially applied for future studies on river management and climatic stressor impacts.

Keywords: Adaptation; Environmental associations; Landscape genetics; ddRAD.

Fig. 1

Map depicting areas of Japan used for sampling stonefly nymphs for this study. Filled circles indicate the four geographical regions (left) included in the study, and open circles indicate the sampling sites within each region (right). The map was prepared using QGIS v 2.18 under the GNU free documentation License with area boundaries from the Global Database of Administrative Areas (https://gadm.org/)

Fig. 2

Genome-wide multivariate genome-environmental associations. Panels show the multidimensional scaling analysis (MDS1 and MDS2) of 4251 candidate SNPs of seven stoneflies species across four regions of Japan. Colored circles represent different regions: red, Matsuyama; black, Gifu; green, Sendai; and blue, Sapporo