Differential expression and genetic differentiation in Lake Baikal's endemic copepod Epischura baikalensis
Predicting organisms’ adaptability in response to climate change is especially critical for endemic and threatened species. Epischura baikalensis, an endemic, threatened calanoid copepod, makes up the vast majority of Lake Baikal’s primary consumer trophic level (100% of zooplankton assemblage in some samples). We were interested in examining how E. baikalensis from different regions of Lake Baikal differ in gene expression and genetic differentiation, given the lake’s large expanse over temperature, latitudinal, and depth gradients. Because of E. baikalensis’s pivotal role in Baikal’s otherwise species-depauperate pelagic food web, it is important to predict whether E. baikalensis possesses sufficient phenotypic plasticity to react to increases in water temperature. Additionally, conservation and monitoring programs could benefit from understanding the degree of genetic variation among local populations. Here we report the first step toward answering these questions: a Next-Generation Sequencing-based comparison of expression levels across a partial transcriptome and differentiation at SNPs comparing local populations from various lake regions. Samples were taken from across a latitudinal and temperature gradient from each of the lake’s three main basins and a shallower and warmer inlet, Maloe More. Understanding how E. baikalensismay respond to climate change will give insights to the future of biodiversity in the world’s oldest, deepest, and largest lake.
We found that not only were transcripts differentially expressed in different local environments but that these same transcripts were also the most highly differentiated, implying that E. baikalensis may be able to adapt to a changing climate. We used a de novo assembly to produce a partial transcriptome, representing the pool of RNAs highly expressed in adult E. baikalensis. The four stations sampled differed significantly in gene expression profile, with the greatest differences occurring across latitudinal and temperature gradients. Four clusters of co-regulated transcripts were detected. Additionally, latitude and warmer/shallower (Maloe More) vs. the rest of Baikal signals were apparent among geographically distinct samples. Gene ontology enrichment analysis indicated that two GO categories were overrepresented (FDR<0.005): protein binding and response to stimulus, suggesting the importance of these two protein groups in climate change mitigation. Moreover, samples exhibited higher differentiation for non-synonymous than synonymous SNPs, implying that maintaining genetic differentiation may be by selective pressure rather than drift, furthering the hypothesis for the local adaptation of geographically distinct populations. The observed plastic and genetic effects may allow E. baikalensis to adapt rapidly to a changing climatic landscape.