LAUSR

Abstract We have reconstructed major demographic and phylogenetic events for two closely related copepod species: Epischura baikalensis Sars, 1900 (Copepoda, Calanoida), a key endemic species of the plankton community from Lake Baikal, and E. chankensis Rylov, 1928, a key zooplankton species from Lake Khanka. The reconstructions were based on the nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (CO1) using the BEAST software package and recently identified calibrations for the Baikal amphipods Gmelinoides fasciatus. The time span to a common ancestor for E. baikalensis and E. chankensis is 13.7 million years (95% confidence interval is 8.3–21.4 million years. Both species studied have experienced abrupt changes in the effective population size in the past. These changes are likely associated with climate and geological shifts in their habitat areas. For E. baikalensis, these changes can be associated with alternating glacier and interglacial periods as well as an increase in depth of Lake Baikal; for E. chankensis with formation and increase in the area of Lake Khanka, which was also due to climate and geological shifts in the Khanka basin.