RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish

Abstract Background Messenger RNA sequencing is becoming more common in studies of non-model species and most often used for gene expression-based investigations. However, the method holds potential numerous other applications as well—including analyses alternative splicing, population structure, signatures selection. To maximize utility mRNA data sets, distinct may be combined such by exploring dynamics between expression with selection context structure. Here, we compare two published sets describing populations a minnow endemic to San Francisco Estuary (Sacramento splittail, Pogonichthys macrolepidotus ): microsatellite set showing an whole transcriptome obtained after were exposed salinity challenge. We compared measures structure genetic variation using single nucleotide polymorphisms (SNPs) called from study those patterns determined microsatellites. For investigating plasticity evolution, intra- inter-population was investigated differential expression, exon usage, variation. Outlier SNP analysis also performed on phenotypic individual-gene basis. Results found that revealed consistent microsatellites, but lower magnitudes differentiation widespread purifying expected when mRNA. In addition, within individual genes, or almost mutual exclusion (except heatr6 , nfu1 slc22a6 sya mmp13 ). Conclusions These results show have multiple uses, including mechanistic interplay evolution adaptation. MRNA thus complements traditional methods genetics, addition its plasticity.