Evolution of the CLOCK and BMAL1 genes in a subterranean rodent species (Lasiopodomys mandarinus)

Lasiopodomys mandarinus, a subterranean rodent, spends its entire life underground. To test whether the CLOCK and BMAL1 genes of L. mandarinus have undergone adaptive evolution to underground darkness, we cloned and analyzed their complete cDNA sequences, using Lasiopodomys brandtii as a control. The phylogenetic trees of the CLOCK and BMAL1 genes were similar to the trees of the conserved Cyt b gene，further, L. mandarinus clustered with L. brandtii and Microtus ochrogaster in the phylogenetic tree. The Q-rich region of the CLOCK gene in L. mandarinus was different from that of other subterranean rodents. Using phylogenetic analysis maximum likelihood (PAML), the ω value (ω<1) in different lineages showed that both genes have undergone purifying selection. The M8 model identified some positive selection sites in the CLOCK gene, most of which were located in the trans-transcription activation domain (TAD). In conclusion, CLOCK and BMAL1 genes did not exhibit convergent molecular evolution in subterranean rodents. Moreover, our study highlights the important functionality of the TAD, which is putatively of functional relevance to CLOCK protein activity. The present findings provide novel insights into adaptation to underground darkness, at the gene level, in subterranean rodents.