Local adaptation and phenotypic plasticity are main mechanisms of organisms’ resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal’s zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal’s zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures.

Lake Baikal (Siberia, Russia) is the oldest, the deepest and the most voluminous lake on Earth. During the last century, Baikal has experienced gradual increases in temperature but remains highly oligotrophic with increases in primary productivity limited to the warmest parts of the lake. Using whole body RNA:DNA ratio as an indicator of metabolic rate, we demonstrate that the key primary consumer in Baikal's plankton, Epischura baikalensis (Copepoda: Calanoida), is a capital breeder that relies on lipid storage to maintain productivity. In individuals from nature, the RNA:DNA ratio correlated with lipid content in samples from cold, low phytoplankton density locations from Baikal's North and Central basins, but not in samples from warmer South basin and Maloe More strait. Lipid reserves, both visually assessed and measured by Nile Red fluorescence, correlated positively with phytoplankton density. In laboratory experiments the RNA:DNA ratio responded to starvation and temperature in non-reproducing, low lipid storage females, but not in individuals with developed ovaries or high lipid storage. This indicates that, unlike many other zooplankton crustaceans, E. baikalensis uses resource storage to support current reproduction, which buffers the dependency of metabolic rate on current feeding conditions. We discuss possible effects of such buffering on E. baikalensis competition with non-endemic, largely income-feeding zooplankton species whose frequency is currently increasing in Baikal pelagia.

The future of Lake Baikal’s biodiversity is uncertain in response to climate change. Unlike its diverse benthos, Lake Baikal’s zooplankton is species poor, with up to 96% of its biomass being composed of a single Calanoid copepod species, Epischura baikalensis. This study characterizes the genetic differentiation and differential gene expression of E. baikalensis. Using partial-transcriptome sequences obtained by 454 Rosche and Illumina sequencing technologies, the genetic differentiation at inferred single nucleotide polymorphism (SNP) sites and differential gene expression in populations sampled from various parts of the lake were analyzed. The functional genomics of genes showed significant differential expression among the lake’s regions with some genes being highly up-or down-regulated. High genetic differentiation among regions suggests isolated subpopulations. Moreover, significantly differentially expressed transcripts were significantly more genetically differentiated than transcripts exhibiting no differential expression. These results suggest high potential phenotypic plasticity and adaptability in response to climate change, e.g., temperature.