Effects of the last glacial period on genetic diversity and genetic differentiation in Cryptomeria japonica in East Asia

To understand how historical and environmental factors have shaped genetic diversity and spatial genetic patterns of tree species, we characterized the genetic diversity and the genetic structure of a coniferous species, Cryptomeria japonica, which is distributed in Japan (two taxonomic groups) and some parts of southeastern China (C. japonica var. sinensis). We investigated population samples for three groups using high-throughput SNP genotyping, sequencing of multiple genes, and then estimated level of genetic diversity, the genetic differentiation, and the divergence time between the three groups. We also investigated the natural distribution during LGM using species distribution modeling. The genetic variation in the Chinese population, var. sinensis, was lower compared to Japanese populations but it harbored some unique genotypes. The species distribution modeling showed that the Chinese population has decreased since Last Glacial Maximum (LGM) because of lower precipitation than present time, but in Japan the favored environment have remained available for this species even in the LGM. Estimated divergence times of the three groups mostly correspond with the time since the Last Glacial. Our data supports the hypothesis that the glacial period, particularly limitations associated with precipitation, strongly influenced the distribution of C. japonica populations. Our findings suggest that climate change plays an important role in speciation processes of C. japonica.