Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan

Abstract

Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of the coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.

Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict‐containing dioecious forest tree

“…This is because many sexually reproducing forest tree species in Japan underwent similar range contractions/expansions over the last glacial–interglacial cycle(s) (e.g. Castanopsis sieboldii : Aoki et al., 2019). Nonetheless, apomixis could have provided a benefit to Japanese L. glauca by increasing its inter‐/postglacial colonization ability (Bierzychudek, 1985; Hojsgaard et al., 2014; Law & Crespi, 2002).…”

A strong east–west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

“…Summary statistics used for ABC are given in Appendix S2. Model selection and parameter estimation was done according to Aoki et al (). Confusion matrix, misclassification rate and model selection were performed in R with the Random forest approach implemented in the abcrf package (Pudlo et al, ).…”

A Disjunctive Marginal Edge of Evergreen Broad-Leaved Oak (Quercus gilva) in East Asia: The High Genetic Distinctiveness and Unusual Diversity of Jeju Island Populations and Insight into a Massive, Independent Postglacial Colonization

“…Regardless of the latitude, the distribution of warm temperate evergreen broad-leaved forests in East Asia, such as in Korea, China, and Japan, is clearly related to the flow of the Kuroshio warm current (KC), showing a unique distribution structure [ 34 , 72 , 73 ]. Therefore, despite being located at relatively high latitudes, the southwestern portions of the Japanese main islands (i.e., southern areas of Kyushu, Shikoku, and Honshu) have long been regarded as crucial refugia with high genetic variation for evergreen broad-leaved trees that resulted from southward range shifts that paralleled glacial cycles [ 74 , 75 , 76 ].…”

“…Fossils and pollen grains could be utilized for unraveling evolutionary clues that contribute to present genetic diversity, but the situation is complicated by historically complex distribution changes [ 33 , 34 ]. However, such past data are largely absent in East Asia, because the area in which the evergreen forests appear to have been historically distributed is now in the sea.…”