Mitogenome phylogeographic analysis of a planktonic crustacean.

Graphical abstract Highlights • The average nucleotide identity within D. magna ranged between 98.9% and 95.9%. • π showed a decreasing cline in moving from the Middle East to Northern Europe. • The HPDI of divergence between West and East populations had a median of ∼290 kBP. • The value of ω ranged between 0.04 and 0.17. • ω of genomes sampled from non-rock pools was 0.0798 and rock pools was 0.1603. Abstract Phylogeography places population genetics in an explicitly spatial context, and in doing so attempts to reconstruct the historical and contemporary evolutionary processes acting across a species range through space and time. Here we present the phylogeographical structure of Daphnia magna as determined for full mitochondrial genomes from samples of 60 populations throughout much of the species known range, including Europe, the Middle East, and Asia. Contrary to previous analyses, the present analysis of the mitochondrial genome reveals coarse-grained (continental scale) evidence for spatial structure, and in particular a deep split between Western Eurasia and East Asian D. magna lineages. In contrast to previous analyses with nuclear genetic markers, our mitogenomic analysis reveals much less structure within lineages. We quantify divergence between species using the full mitochondrial genome sequence of a closely related species, D. similis. The distribution of European and Middle Eastern genetic diversity is consistent with a rapid demographic expansion following the end of the most recent ice age about 10,000 years before present. By estimating species wide distributions of d N /d S in mtDNA, we provide evidence that the effectiveness of purifying selection on protein coding genes in the mitochondrial genome of coastal rock pool populations, which have pronounced extinction-colonization dynamics, is reduced compared to larger and more stable non-rock pool populations. The present study adds important insights into the evolutionary history of a widely used model organism in ecology, evolution and ecotoxicology, and highlights the utility of phylogeographic analysis of organellar genomes to understand evolutionary processes. [ABSTRACT FROM AUTHOR]