A transcriptome-wide assessment of differentially expressed genes among two highly divergent, yet sympatric, lineages of the freshwater Atyid shrimp, Paratya australiensis

In this study, we used a comparative transcriptomic approach using 35nt paired-end reads from three individuals each from two highly divergent lineages of the Australian freshwater shrimp, Paratya australiensis. The two lineages are widespread and largely sympatric in many regions; however, they occupy slightly differing habitats within respective river systems. From BLAST searches, we were able to identify 50 genes, based on gene ontology, involved in temperature tolerance, egg size control and more broadly osmoregulation, as well as genes associated with reproduction and life history characteristics predicted to be associated with adaptation to local aquatic environments. Differential gene expression analysis revealed 660 highly differentially expressed transcripts between the populations. Divergence in SNPs detected in the two lineages was consistent with the level of neutral divergence found in previous studies, but they appear not to correlate with differentially expressed candidate genes. However, we hypothesise that the 2554 filtered SNPs identified in this study will continue to further our understanding of how these lineages have evolved and adapted to their respective habitats and will contribute to further our interpretation of the enigmatic biogeographical history of the species.