High-throughput gene expression enables powerful studies of evolutionary transcriptomics in the lab and in the wild

The power and promise of next generation sequencing systems remains largely untapped by studies of evolutionary transcriptomics in natural populations. Although costs are falling, this technology still remains out of reach for many who require large sample sizes to capture subtle patterns. To resolve this, I updated and validated an alternative RNAseq library construction method, TagSeq. TagSeq produces data that is at least as high quality, if not better, than the current industry standard. Next, I applied this method to two large scale experiments in Threespine Stickleback (Gasterosteus aculeatus). First, I tested for change in stickleback gene expression in response to infection by a macroparasite, Schistocephalus solidus. Expression depended on genotype, infection status, and their interaction. Coexpression network analysis suggested clusters of genes which are correlated with immune phenotypes, and thus both candidate genes and pathways for further study. Candidates identified here are involved in immune responses known to contribute to stickleback resistance to S. solidus. Additionally, stickleback genotypes have vastly different expression networks; a resistant population showed a diverse and dynamic expression profile while a susceptible populations remained static. But parasites are not the only challenge that stickleback face. Stickleback are a classic example of colonizing new environments and this challenge involves multiple biotic and abiotic factors. Second, I measured stickleback gene expression in samples from a prior lake-stream reciprocal transplant with TagSeq. I tested whether migrants showed a plastic response to new environments that enabled them to converge on the expression profile of natives. The majority of gene expression differences between lake and stream are static, but some genes respond plastically to the environment. The expression profile of immigrants converged on that of natives, suggesting plasticity, and the degree of plasticity is genotype dependent. Gene expression plasticity appears to soften the impact of selection on migrants in new habitats, but plasticity is not strong enough to homogenize performance of immigrants and natives. In summary, the updated and validated TagSeq protocol offers users the chance to increase sample sizes in order to ask bigger questions in ecological transcriptomics, from candidate gene discovery to whole transcriptome level analysis.