Reconstructing the survival history of relict herbs endemic to the heavy snowfall regions of Japan during the Pleistocene.

The effects of past environmental changes on the demography and genetic diversity of relict species remain poorly understood. Such studies have rarely been conducted across multiple phylogenetically distant species, largely because of their rarity. Here, we investigated impacts of long-term climatic changes on the evolution and survival of three herbaceous Tertiary relict species endemic to heavy snowfall regions of Japan. Using population genomic analyses based on plastome sequences, we reconstructed phylogeographic patterns, including demographic histories, and explored potential drivers of similarities and differences among the species. Divergence times from close relatives were estimated at ca. 64 Ma for Glaucidium palmatum, 23 Ma for Ranzania japonica, and 12 Ma for Paris japonica, all of which predate the Pleistocene. The time to the most recent common ancestor (tMRCA) for each species ranged from approximately 0.03 to 3 Ma. Effective population sizes of species and regional groups expanded rapidly between approximately 100,000 and 10,000 years before present. Patterns of genetic diversity and geographic structure among the three relict species appear to reflect differences in dispersal ability and the locations of climatic refugia. Despite variation in tMRCAs among the three species, demographic expansions consistently occurred during the late Pleistocene and were likely associated with the development of heavy snowfall climate.