The study of phenotypic and genotypic variation within species represents one of the main aspects of functional biogeography. This preface presents the geographic and historical background of genetic differentiation, its role as a foundation species, and the effects of variation in functional traits on ecosystem function based on the evolutionary ecology of Japanese cedar. Functional biogeography is an outgrowth of trait ecology, and aims at understanding the mechanisms of community assemblages and ecosystem function at broad spatial scales by using functional traits of organisms as common currency. On the other hand, the study of phenotypic and genotypic variation within species represents one of the main aspects of the functional biogeography (Violle et al., 2014). It is Earth's dynamic nature over thousand- to million-year timescales and at regional spatial scales that fundamentally shape the incipient speciation and distribution of species (Dolby et al., 2022). Then, efforts to quantify both the phenotypic and genetic variation within species will provide useful insights into the evolutionary ecological drivers of species distributions, and help bridge functional ecology and evolutionary biology. In this context, this special issue represents the functional biogeography in the Japanese cedar (Cryptomeria japonica), the most dominant tree in Japan. It presents the geographic and historical background of genetic differentiation, its role as a foundation species, and the effects of variation in functional traits on ecosystem function. Tree species that are dominant in forest ecosystems play an important role as foundation species due to their high biomass (Ellison et al., 2005). Tree species with wide distributions and large geographic variation in their functions provide unique forest structure and biotic interactions at each local ecosystem, as it has been shown, for example, in beech (Fagus crenata) (Hiura, 1995, 1998; Hiura & Nakamura, 2013; Nakamura et al., 2014), which is the most dominant angiosperm in the cool temperate zone of the Japanese archipelago (Forestry Agency, 2011). The most dominant gymnosperm in Japan (Forestry Agency, 2011), the Japanese cedar, is also widely distributed in the warm and cool-temperate zones of the Japanese archipelago, from Yaku island (30°015′N, 130°30′E) to Ajigasawa (40°42′N, 140°12′E) (Hayashi, 1960). It is one of the most investigated tree species in Japan due to its large biomass accumulation and usefulness in forestry (e.g., Osone et al., 2020; Sakaguchi, 1983). Its amount of academic information is comparable to that of the European beech (Fagus sylvatica), the Scots pine (Pinus sylvestris), and the Norway spruce (Picea abies) in Europe (e.g., Benavides et al., 2021; Schulze, 2000; Vila-Cabrera et al., 2015). In the case of the Japanese cedar, the genetic diversity remained after the presence of several refugia even in the Last Glacial Maximum (LGM; Takahara et al., 2023; Tsumura, 2022), and therefore, it is expected that the geographic, genetic, and functional variations are also large. Based on these characteristics, the Japanese cedar will provide a good material for investigating the response of each local forest ecosystem under climate change, based on the geographic functional differentiation and its cascading effects. For this study purpose, it is first necessary to clarify the historical background of the species. To approach this, it is essential to complement both methods to estimate the distribution transition based on plant remains and pollen fossils, and the methods based on neutral genes. In this special issue, Takahara et al. review the distributional transition of the Japanese cedar since the LGM based on the results of pollen analyses. They showed that the Japanese cedar is now only locally distributed in restricted natural forests, but since at least 7000 years ago until modern times, it has been widely distributed in the Japanese archipelago except in Hokkaido, and was the dominant species in the temperate zone of Japan due to its large biomass. Tsumura (Tsumura, 2023) outlines the distributional transitions and local adaptations inferred from the genetic variation of the Japanese cedar in the Japanese archipelago and China, and proposes methods to prevent genetic disturbance of geographically differentiated populations. Genetic differentiation occurred as a result of restricted gene flow and local adaptation due to distributional area fragmentation or fluctuation with warming from the coldest glacial period and recolonization from the Hypsithermal period to the modern era. Genetic analysis suggests that the LGM refugia existed at least near the Izu Peninsula, southern Kii Peninsula, southern Shikoku, Wakasa Bay, and Yaku Island (Tsumura, 2023). Since pollen fossils during the LGM have been found at four of these sites from regions other than the southern Kii Peninsula, as well as from Sado Island, Oki Island, and western Chugoku (Takahara et al., 2023), it is considered that the LGM expanded its distribution from at least these eight regions to form its present distribution area with global warming (Figure 1). Therefore, it is presumed that the variation in functional traits of the Japanese cedar also reflects the characteristics of these refugial populations to some extent. The Japanese cedar is one of the largest tree species in Japan in terms of both diameter and height (maximum diameter of about 5 m and maximum height of about 60 m (Tsumura, 2011). It is thought to have played an important role in the ecosystem as a foundation species due to its high biomass (Ellison et al., 2005). It is not only makes a significant contribution to carbon sequestration by raising forest biomass (Aiba et al., 2007), but it also prevents soil acidification under certain conditions (Baba et al., 2004; Tanikawa et al., 2014), thereby contributing to the rich soil fauna (Ohta et al., 2019; Ohta & Hiura, 2023). In particular, among the functional traits that the cedar possesses, the calcium abundance in trunk and leaves may be related to these ecosystem functions. High calcium concentration contributes to supporting large individual biomass, such as making cell walls robust (Schaberg et al., 2001) and calcium bridge is important for water storage in tall canopy leaves (Azuma et al., 2017). In addition, the abundance of calcium ions in the soil prevents acidification by acting as a counter ion to nitrate and other ions (Baba et al., 2004; Berg et al., 2017; Tanikawa et al., 2014). The family Cupressaceae, including Cryptomeria, has a higher calcium concentration in leaf litter than trees of other families, of which Japanese cedar is one of the species with the highest calcium concentration (Figure 2). Then, how is calcium acquired, which is present in high concentrations in the tree body? The Japanese cedar in the southern Kii Peninsula (Yoshino-sugi) has up to 3–4 times higher root exudation rate than other dominant tree species growing in Japan (Chamaecyparis obtusa, F. crenata, Quercus myrsinifolia, Quercus crispula, and Quercus serrata) and has higher calcium driving capacity (Ohta & Hiura, 2016). This results in 3–4 times higher calcium concentrations in soil and freshwater in cedar-dominated watersheds than in watersheds dominated by broad-leaved forests, higher densities of crustaceans and other small invertebrates, and dozens of times higher densities of Gammarus species in freshwater (Ohta et al., 2013, 2014). Analyses of strontium isotopes, used as a proxy for calcium isotopes, revealed that isotopic ratios in cedar and cedar forest stream water were relatively close to the values in the parent rock, whereas isotopic ratios in hardwood and hardwood forest stream water were close to the values in rainfall. This means that cedars in this region are leaching calcium from the parent rock through the release of abundant organic acids from their roots, providing biologically available calcium in the ecosystem (Ohta et al., 2018). Although the cedar has the functional characteristics described above, it is possible that the geographical differentiation in morphology and function has occurred due to interactions with weather and soil conditions, coexisting organisms, or genetic drift during the distribution transition process associated with climate change. However, reports on the cedar variation have so far compared samples obtained from various regions, such as needle leaf morphology, chlorophyll content (Takahara & Kawana, 1955), clonal reproduction (Kimura et al., 2013), and growth of tree height relative to diameter (Nishizono et al., 2014). Most of them might be plastic traits, and verification of whether they are plastic or genetic traits is very limited (Kimura et al., 2013). Because the functional differentiation of individuals cascades over into interactions with other organisms, determining whether the functional differentiation is genetically determined is essential for assessing its impact on local community structure and the ecosystem function as a foundation species under rapid climate change that may involve changes in distribution range. Common garden experiments are useful to clarify whether such geographic functional differentiation is a genetic trait. We are revealing geographic differentiation of some functional traits from common garden experiments in the Japanese cedar (Azuma et al., 2023; Hiura et al., 2021; Ohta et al., 2019; Ohta & Hiura, 2023; Saito et al., 2023). Biogenic volatile organic compounds (BVOCs) emitted by plants are an important component of atmospheric chemistry, and play a major role in plant resistance to various environmental stresses. However, little is known about how the geographic biotic environment relates to the diversity of BVOC. We used genetically differentiated regional populations of Japanese cedar to determine the variation in terpenes emitted in a common garden (Figure 3; Hiura et al., 2021). Terpenoids were highly diversified among the 12 populations and their geographic structure was also revealed. The total amount of terpenes accumulated in leaves was negatively affected by warmer and less snowy climates. On the other hand, inter-population variation of some emitted terpenoid species was correlated with pathogen species inhabiting the cedar, suggesting that diversification in composition and abundance of stored and emitted terpenoids in the cedar is structured not only by climate but also by pathogen groups through biological interactions. Among terpenes, diterpenes with large molecular weight have been recently been shown to be released as gases (Matsunaga et al., 2012; Otsuka et al., 2004). However, the mechanism of their volatilization is not yet fully understood, and the estimated emission profiles did not fit a thermodynamic algorithm (Saito et al., 2023). Genetic differences among individual trees might be suggested to be responsible for the high tree-to-tree variation in terpene emissions. The great intraspecific variations in terpene emissions with a linkage with their leaf contents call for further studies on the relationships between emissions and leaf contents. Such volatile organic compounds with large molecular weight have a large impact on atmospheric chemical processes due to their high reactivity, and may even affect local meteorology when the biomass and the emitted amount are large on a regional scale (Mentel et al., 2013; Simpraga et al., 2019), as in the case of the cedar (Matsunaga et al., 2012). It is not only the BVOC that interact with climate and weather in the Japanese cedar. Climate and weather influences can lead to geographic differentiation of various morphologies and functions from the organ level to the individual level. Canopy-level traits related to photosynthesis and hydraulic structure at the leaf level not only reflect modes of carbon acquisition and water use, but also influence individual competition and forest productivity. Growth rates of mature trees growing in a common garden differed among populations, with Yoshino-sugi and Yanase-sugi having faster growth rates and Yaku-sugi having significantly slower growth rates. Overall, this intraspecific variation in growth characteristics was found to be controlled by whole-individual rather than leaf-level characteristics (Azuma et al., 2023). Comparisons using the same common garden also revealed that, as mentioned above, fast-growing Yoshino-sugi utilizes calcium from the parent rock through abundant root exudation (low molecular mass organic acids [LMMOAs]), whereas slow-growing Yaku-sugi has only about one fifth the amount of root exudation of Yoshino-sugi, and utilizes calcium mainly from rainfall (Ohta et al., 2019). The calcium concentration in the Yaku-sugi soil was therefore low, and the density of crustaceans and other small invertebrates was found to be only one fifth of that of Yoshino-sugi (Ohta et al., 2019). It is possible that the steepness of the slope of the southern Kii Peninsula, southern Shikoku, and Yaku Island, where these populations grow, and the nearly 4000 mm annual rainfall, which prevents the accumulation of an organic layer in the soil, acted as a selection pressure on root function. In addition, the calcium-rich or calcium-poor parent rock may or may not have been a factor in the strategy to increase the amount of exudation from the roots. However, the interaction of mycorrhizal fungi and other factors remains to be elucidated, and further research is needed. The study of intraspecific variation in physiological growth characteristics of trees in such a wide range of native habitats is expected to be an effective indicator for predicting changes in growth potential and forest dynamics in response to climate change in each habitat. The natural cedar biomass, which had been distributed in various regions due to human logging since the modern era, declined sharply along with the Japanese cypress (C. obtusa; Totman, 1989). In the modern era, the Japanese cedar has been planted in large numbers along with the Japanese cypress as a result of a postwar afforestation expansion, and the single species now accounts for 18% of the forest area in Japan (Forestry Agency, 2011). In other words, the cedar has replaced the natural forests of the past as the main component of planted forests. In the process of afforestation, attention has been focused on high growth rates and good wood quality (Sakaguchi, 1983), and little attention has been paid to the various other functional differentiation unique to each region. The effects of the cedar species on the nutrient cycling and soil faunal community differ among artificial cultivars (Ohta & Hiura, 2023). The effects of artificially created cultivars on ecosystem functions and services should also be noted in the future, as their cascading effects differ from those of naturally selected natural geographic variations. Furthermore, although BVOC and LMMOA emissions are a small proportion of the carbon cycling used by the entire population, they play an important role in interactions and communication (Hagiwara et al., 2021) with other organisms above and below ground, but the accumulation of information is very limited. Future analyses of the relationships among traits (e.g., Osone et al., 2021) using trait databases (e.g., Osone et al., 2020) are desirable, and studies on functional traits such as BVOC and LMMOA that have cascading effects on other trophic levels and other ecosystem functions in various regions are also warranted. In the field of functional biogeography, there are several specific areas in which intraspecific variation should be accounted for, especially when characterizing phenotypic variation within the functional space of a given species and its distribution range (Violle et al., 2014). A more adequate assessment of intraspecific variation within a species' distributional range, complemented by the quantification of genetic variation, should provide new insights into the eco-evolutionary factors of species biogeography and functional niche under the global climate change. The author appreciates the comments on the manuscript from Drs. Y Tsumura and T Saito. This study was partly supported by JSPS KAKENHI (JP21H02227) and Transformative Research Areas (21H05316). The author declares no conflict of interest.