Arnica mallotopus Makino is a perennial herb of Asteraceae endemic to Honshu and its adjacent islands in Japan (Ohashi et al., 2016). The species occurs preferentially on rock outcrops along mountain streams that are well watered by snowmelt and are often maintained by natu-

Aims: Quaternary climate changes dramatically affected species' distributions and thus impacted genetic diversity patterns, particularly for rear-edge populations.Empirical studies have shown the southernmost (rear-edge), fragmented populations of Japanese woody plants can harbour high genetic diversity owing to their origin in southern glacial refugia. The effect of Holocene climate warming on rear-edge populations has, however, rarely been demonstrated. We assessed whether the genetic structure of populations of temperate plants in Japan can be interpreted to show legacies of both icy (Last Glacial Maximum, LGM) and warm (Holocene) climates.Location: Japanese Archipelago. Taxon: Hemerocallis middendorffii (Asphodelaceae).Methods: Population genetic profiles of 737 individuals from 41 populations were analysed to examine population structure and past population demography, using 12 EST-SSR markers. Present and past suitable habitat areas during the LGM and the Holocene climatic optimum were estimated by ecological niche modelling (ENM).Reconstructed palaeodistribution was combined with population genetics to statistically predict population demographics in relation to past climate changes.Results: Genetic analysis of the 41 populations revealed 6 regional population groups.Four groups widely dominating the northern-central ranges harboured high genetic diversity, whereas genetic divergence within the groups was low. In contrast, the two groups at the southwestern edge were geographically and genetically isolated, and they showed the lowest genetic diversity. The estimated palaeodistributions showed a decrease in the suitable range during the Holocene in comparison with that at the LGM, and only habitat suitability in the Holocene was able to predict the genetic diversity across the range. Main conclusions:Populations at the centre of the current distribution harbour high genetic diversity because they remained stable during both cold and warm periods.However, habitat fragmentation and population decline in relation to climate warming during the Holocene resulted in genetic isolation and impoverishment of the rearedge populations.

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Background Quaternary climate changes significantly impacted population demography of temperate organisms by shifting their distribution. Notably, the rear-edge populations are considered to be more prone to these changes, but empirical studies showed the southernmost fragmented populations of Japanese woody plants to harbor high genetic diversities due to their southern glacial refugia origin. Therefore, the impacts of Holocene climate warming on rear-edge populations have been rarely demonstrated. For the better interpretation of genetic backgrounds of temperate plants, the association of paleodistributions under both icy and warm climates with species-specific demographic changes is required. A perennial daylily Hemerocallis middendorffii (Asphodelaceae) is widely distributed in temperate and cool-temperate zones of East Asia. In Japan, larger populations are found in central ranges, while few small populations survive on harsh rock walls in southernmost regions. We focused on these variable populations and aimed to predict the population demography in relation to past climate changes by statistically combining population genetics with paleodistribution modeling.Results EST-SSR analysis of 737 individuals from 41 populations revealed 6 regional population groups. Four groups widely dominating the northern–central ranges harbored high genetic diversity, whereas genetic divergence within the groups was low. However, two groups at the southwest edge were geographically and genetically isolated and showed the lowest genetic diversity. Estimated paleodistributions showed a decrease of suitable range during Holocene climate optimum in comparison with LGM, and a sole variable of habitat suitability in the Holocene optimum was able to predict genetic diversity across its range. Conclusions We concluded that habitat fragmentation and population decline in relation to the climate warming during the Holocene optimum and interspecific competition with woody plants resulted in genetic isolation and impoverishment of the rear-edge populations.