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Summary Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine‐scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing.We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally.These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

Plants sense light and temperature changes to regulate flowering time. Here, we show that expression of the Arabidopsis florigen gene, FLOWERING LOCUS T (FT), peaks in the morning during spring, a different pattern than we observe in the laboratory. Providing our laboratory growth conditions with a red/far-red light ratio similar to open-field conditions and daily temperature oscillation is sufficient to mimic the FT expression and flowering time in natural long days. Under the adjusted growth conditions, key light signalling components, such as phytochrome A and EARLY FLOWERING 3, play important roles in morning FT expression. These conditions stabilize CONSTANS protein, a major FT activator, in the morning, which is probably a critical mechanism for photoperiodic flowering in nature. Refining the parameters of our standard growth conditions to more precisely mimic plant responses in nature can provide a powerful method for improving our understanding of seasonal response.

Little empirical evidence is available whether allopolyploid species combine or merge adaptations of parental species. The allopolyploid species Arabidopsis kamchatica is a natural hybrid of the diploid parents A. halleri, a heavy metal hyperaccumulator, and A. lyrata, a non-hyperaccumulating species. Zinc and cadmium were measured in native soils and leaf tissues in natural populations, and in hydroponic cultures of A. kamchatica and A. halleri. Pyrosequencing was used to estimate homeolog expression ratios. Soils from human modified sites showed significantly higher Zn concentrations than non-modified sites. Leaf samples of A. kamchatica collected from 40 field localities had > 1,000 µg g-1 Zn in over half of the populations, with significantly higher amounts of Zn concentrations in plants from human modified sites. In addition, serpentine soils were found in two populations. Most genotypes accumulated >3000 µg g-1 of Zn in hydroponic culture with high variability among them. Genes involved in hyperaccumulation showed a bias in the halleri-derived homeolog. A. kamchatica has retained constitutive hyperaccumulation ability inherited from A. halleri. Our field and experimental data provides a compelling example in which the inheritance of genetic toolkits for soil adaptations likely contributed to the habitat expansion of an allopolyploid species.

Herbivore damage can induce the host plant to alter the chemical and physical qualities of its leaves, which is thought to be a plant strategy—termed “induced response”—for avoiding further herbivory. In woody plants, many studies have considered variation in induced response with resource availability, but few studies have examined this variation in relation to growth patterns of woody plants. We studied the phenotypic variability of induced response within successively flushing Quercus serrata seedlings. Q. serrata seedlings were grown under controlled conditions. The controlled factors were herbivore damage (herbivore-damaged and -undamaged) and soil fertility (low and high). At each flush stage, the concentrations of condensed tannin (CT), total phenolics (TP), and nitrogen (N) in leaves were analyzed, and the leaf mass per area (LMA) was measured. CT and TP concentrations in leaves and LMA were higher in herbivore-damaged seedlings. Leaves of the first flushes showed greater sensitivity to herbivore damage and had a higher CT concentration than leaves of the later flushes. Furthermore, seedlings growing in low-fertility soil showed a greater induced response. The results suggest that the induced response of Q. serrata seedlings was related to the contributions of the tissue to current productivity. Leaves of the first flush showed a greater induced response, possibly because they play an important role in subsequent growth. The potential of Q. serrata seedlings to adjust the properties of leaves depending on herbivory and soil fertility in relation to growth patterns may be advantageous on the forest floor, where seedlings grow in soil of heterogeneous fertility and are constantly exposed to herbivory.