Hinoki cypress in Japan and Taiwan genetically diverged 1 million years ago

Japanese and Taiwanese hinoki cypress diverged genetically approximately 1 million years ago due to the fragmentation of the Ryukyu Archipelago. Researcher Takaki Aihara and Professor Emeritus Yoshihiko Tsumura, both of the Institute of Life and Environmental Sciences at the University of Tsukuba, and their colleagues conducted population genetic analyses covering the entire genome across the distribution range of natural Japanese hinoki and Taiwanese hinoki forests that should be conserved as genetic resources, revealing genetic diversity, the genetic regionality of each population, and the history of divergence. They also found that hinoki in Japan can be classified into three groups, which differ from the current boundaries for seedling transfer, indicating the need to revise management divisions. Their findings were published in Ecology and Evolution.

Hinoki, with its straight grain, beautiful wood pattern, and excellent workability, is treated as premium construction timber, ranking second in plantation area and timber production in Japan after Japanese cedar. However, its natural forests remain only in scattered pockets on mid-mountain slopes and ridges in steep mountainous areas from Fukushima Prefecture in the north to Kagoshima Prefecture and Yakushima Island in the south, with almost no giant trees exceeding 1,000 years of age.

Meanwhile, the Taiwanese hinoki (a variety of Taiwan cypress) is widely distributed in the mountainous regions of Taiwan, where large trees exceeding 1,000 years of age still remain. Japan once imported these logs as construction material for shrines and temples. Natural forests of useful timber species are valuable genetic resources, and appropriate conservation of these is crucial for ensuring sustainable use of useful timber.

The research team conducted a comprehensive genomic evaluation using SNPs across the entire distribution range of natural hinoki and Taiwanese hinoki forests. They examined the genetic characteristics and genetic diversity of each regional population, as well as how populations diverged regionally, on a geological time scale.

The results showed that Japanese and Taiwanese hinoki are genetically distant, and the phylogenetic tree estimated that they diverged approximately 1 million years ago (early Quaternary Pleistocene). The arc-shaped chain of islands extending from the southern tip of Kyushu to Taiwan is called the Ryukyu Arc. Once connected to Taiwan by land, the Ryukyu Arc is believed to have fragmented into islands approximately 1 million years ago. This fragmentation is inferred to have led to the genetic divergence of Japanese hinoki and Taiwanese hinoki. Additionally, the climatic conditions of potential distribution areas, statistically estimated from locations where the organisms were confirmed (presence data) and environmental data (topography, vegetation, climate, etc.), also differed between the two. It is suggested that Taiwanese hinoki prefers colder environments with more winter precipitation while Japanese hinoki prefers warmer environments with more summer precipitation, indicating different environmental adaptations.

Looking at hinoki populations within Japan, three major regions could be genetically distinguished: Yakushima, western central Honshu and beyond, and northern central Honshu and beyond. This is estimated to reflect differences in distribution during the Last Glacial Maximum approximately 22,000 years ago, when Japan's average temperature was about 5-7℃ lower than present. In particular, the population at the northern limit in Fukushima Prefecture and the population at the southern limit on Yakushima Island are genetically distinctive and have high conservation priority. Meanwhile, populations within Taiwan showed no clear geographical trend in genetic differentiation, suggesting that populations are fragmenting and declining.

Currently, seedling transfer of hinoki in Japan is managed in three divisions based mainly on differences in climatic conditions under the Forestry Seeds and Seedlings Act. In contrast, this study showed that populations can be genetically distinguished into the broad categories of Yakushima, western central Honshu and beyond, and northern central Honshu and beyond. Distribution based on differences in weather conditions may cause outbreeding depression in each region, and seedling transfer needs to be regulated based on the three divisions shown in this study. Furthermore, populations at the northern and southern limits are estimated to possess distinctive genes and require particularly prioritized conservation.

Journal Information
Publication: Ecology and Evolution
Title: The Historical Biogeography of Divergence in the Relict Cypress Chamaecyparis obtusa, and the Implications for Conservation and Management in East Asia
DOI: 10.1002/ece3.72240