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The overabundance of sika deer has become a significant threat to plant communities across Japan. As a result of the deer overgrazing, rare plants are undergoing a demographic bottleneck, leading to a loss of genetic diversity. Genetic diversity is crucial for the reproductive success of self‐incompatible plants, and it also provides evolutionary potential, which increases their long‐term population viability. Therefore, it is essential to appropriately manage the remaining genotypes to conserve local genetic resources. In this study, we exemplify this, via a conservation genetic analysis of Parasenecio peltifolius populations impacted by deer. Genetic data revealed that the small populations confined to isolated refugial sites consisted of effectively single genets. Recent reproductive failures in these populations may be attributed to the loss of genotypic diversity. Despite the bottlenecks, the remaining genets exhibited high individual heterozygosity, which is a good indicator that they have not been affected by severe inbreeding. Hybrid simulations suggested that interpopulation outbreeding between the unique genotypes can be a viable option to promote sexual reproduction and re‐establish genetic diversity within the local populations. Establishing artificial progenies in botanical gardens can serve as a vital genetic resource for the long‐term viability of threatened P. peltifolius populations. [ABSTRACT FROM AUTHOR]

Premise: Light is essential for plants, and local populations exhibit adaptive photosynthetic traits depending on their habitats. Although plastic responses in morphological and/or physiological characteristics to different light intensities are well known, adaptive divergence with genetic variation remains to be explored. This study focused on Saxifraga fortunei (Saxifragaceae) growing in sun‐exposed and shaded habitats. Methods: We measured the leaf anatomical structure and photosynthetic rate of plants grown in their natural habitats and in a common greenhouse (high‐ and low‐intensity light experimental sites). To assess differences in ecophysiological tolerance to high‐intensity light between the sun and shade types, we evaluated the level of photoinhibition of photosystem II and the leaf mortality rate under high‐intensity light conditions. In addition, population genetic analysis was conducted to investigate phylogenetic origins. Results: Clear phenotypic differences were found between the sun and shade types despite their recent phylogenetic origin. The leaf anatomical structure and photosynthetic rate showed plastic changes in response to growing conditions. Moreover, the sun type had a well‐developed palisade parenchyma and a higher photosynthetic rate, which were genetically fixed, and a lower level of photoinhibition under high‐intensity light. Conclusions: Our findings demonstrate that light intensity is a selective pressure that can rapidly promote phenotypic divergence between the sun and shade types. While phenotypic changes in multiple photosynthetic traits were plastic, genetic divergence in specific traits related to adaptation to high‐intensity light would be fundamental for ecotypic divergence to different light regimes. [ABSTRACT FROM AUTHOR]

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 rear‐edge populations. [ABSTRACT FROM AUTHOR]