LAUSR

Abstract With 104 endemic species family Candonidae is one of the most diverse crustacean groups in Lake Baikal, yet their phylogenetic relationships and position in the family have not been addressed so far. Here, we study the phylogenetic position of Baikal candonids within the family and their evolutionary history using molecular markers for the first time since their original description. We choose 10 Baikal and 28 species from around the world, and three ribosomal RNA‐s (18S, 28S, and 16S), and analyze individual and concatenated datasets using Bayesian Inference in MrBayes and BEAST. For molecular divergence time estimates, four fossil records are used to calibrate the root and three internal nodes. The 28S dataset is tested under the strict molecular clock, while for other data we use relaxed clocks. Resulting trees show incongruence between molecular and fossil divergence time estimates, with the former suggesting older ages. Strict molecular clock analysis results in narrower node age confidence intervals and younger time estimates than other analysis. All trees support at least two candonid lineages in Baikal, with two independent colonization events, and 28S suggests a major radiation between 12 and 5 Mya. This divergence time estimate mostly agrees with another, unrelated, ostracod group in the lake and other lake animals as well. Baikal candonid clades show a close phylogenetic relationship with Palearctic lineages, but their deep divergence is indicative of separate genera. Results also suggest a monophyly of tribes that today live exclusively in subterranean waters, and we offer several hypotheses of their evolutionary history.