Abstract
BackgroundEnvironmental 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.ResultsA 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.ConclusionsOur 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.
Highlights
Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology
We found no significant correlations between geographical and genetic distance for all species (Mantel test, H. japonica r = 0.2, P = 0.98; N. ovocercia r = 0.04, P = 0.75; R. japonica r = 0.068, P = 0.67; O. femoralis r = 0.075, P = 0.68; I. nipponica r = 0.2, P = 0.98; A. longispina r = 0.3, P = 0.98; and S. japonicus r = 0.15, P = 0.99), which indicated that the genome variation of the candidate single nucleotide polymorphisms (SNPs) was not affected by geographical distance
Genome-wide restriction site associated DNA sequencing (RAD-Seq) analysis of seven stream stonefly species conducted in this study successfully identified candidate SNPs associated with environmental conditions along a nationwide latitudinal gradient in Japan
Summary
Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Environmental information, as a combination of landscape effects [10] and environmental clines [11], provides stronger evidence for examining adaptive divergence This type of analysis considers the effect of population structure and geographical scale and expects that genome signatures of Gamboa and Watanabe BMC Genomics (2019) 20:84 selection become more pronounced with increasing geographical scale (isolation by distance) owing to larger environmental gradient differences [12]. Overall, reported studies have highlighted that the selective pressure resulting from environmental changes can be explained by the evolutionary response of population along these gradients These studies investigating this association have been based on a single species [14, 15, 18, 19], neglecting the potential effect of this association on multiple species that co-occur in the same habitat
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