Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly
affected by climatic change and geographical isolation. In the present
study, we applied restriction-site-associated DNA sequencing (RAD-seq) to
analyze the genetic structure and to simulate the demographic history of
two extant Cryptomeria species in
Japan (C. japonica) and Southeastern China
(C. japonica var. sinensis). Thirteen natural
populations representing the entire species distributed in East
Asia were collected from Japan and China.
At the species level, the genetic diversity of
Cryptomeria was moderate (Ho = 0.217, He =
0.203) with a significant genetic differentiation among
populations (85.30%, P < 0.001), especially between Japan and China
lineages (FST = 0.147). Except for the Lushan
(LS) population in China, all populations were clustered
into two lineages (Japanese and Chinese), which was consistent with their
geographical distribution. Approximate Bayesian
computations (ABC) model indicated that the current two
geographical lineages diverged from a common ancestral lineage
and that their divergence time was about
0.417 ~ 0.139 million years ago
(Mya). Geographical isolation, climate change
in the Quaternary, and human disturbance
played important roles in genetic variation and
distribution patterns of Cryptomeria in East Asia. Our results
shed light on the speciation processes of
Cryptomeria and provide a reference for the conservation
of this species.