This data paper reports tree census data collected in a network of 34 forest sites in Japan. This is the largest forest data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Forty-two permanent plots, usually 1 ha in size, were established in old-growth or secondary natural forests. Censuses of woody species ‡15 cm girth at breast height were conducted every year or once during 2004 to 2009. The data provide species abundance, survivorship and stem girth growth of 52,534 individuals of 334 tree and liana species. The censuses adopted common census protocol, which provide good opportunities for meta-analyses and comparative studies among forests. The data have been used for ecological studies as well as for the biodiversity reports published by the Ministry of the Environment.

Seedling and tree‐establishment microhabitats of Tsuga diversifolia and Abies mariesii were examined on the herb‐ and dwarf bamboo‐dominated forest floor on Mount Hayachine, a mountain under intermediate snow conditions in northern Honshu, Japan. The four microsite types were fallen logs, buttresses, rocks and ground. The ground substratum was further divided into four subtypes by dominant undergrowth species: Lycopodium, Pteridophyllum, Carex and dwarf bamboo. The establishment of T. diversifolia seedlings on the ground was scarce, and depended mostly on non‐ground microsites (i.e. fallen logs, buttresses and rocks). The seedling establishment of A. mariesii was not dependent on specific substrata, although on the ground, establishment sites were limited to the Lycopodium subtype situated on convex sites. Among the microhabitats for seedling establishment, larger trees of A. mariesii rarely occurred on higher portions of the non‐ground microsites. In contrast, T. diversifolia could grow up to the height of canopy‐layer trees in such microsites. Thus, non‐ground microsites seem to be unsuitable for tree establishment in A. mariesii, and are probably useful microhabitats for regenerating T. diversifolia to avoid competition with A. mariesii. We also compared seedling‐establishment microhabitats for the two conifers between Mount Hayachine and two other mountain regions under different undergrowth conditions (moss‐dominated and dense dwarf bamboo‐dominated). Our findings suggested that seedling recruitment in non‐ground microsites was primarily determined by undergrowth conditions; T. diversifolia preferred such microsites where the moss‐covered area was low, and A. mariesii preferred where dwarf bamboo‐covered area was high.

We examined microsites for the seedling establishment of Tsuga diversifolia, Abies veitchii and Abies mariesii in a subalpine coniferous forest with moss-type undergrowth dominated by Hylocomium splendens and Pleurozium schreberi on Mt. Fuji, a lesssnowy mountain located on the Pacific Ocean side of the central part of Honshu Island, Japan, and compared these microsites with cases in other regions of Japan with different undergrowth vegetation (herb type, dwarfbamboo type) under snowier conditions. L-shaped size structures with abundant seedlings and small trees were identified for all three species. Established seedlings of T. diversifolia showed remarkable preference for elevated microsites such as fallen logs and convex ground (i.e. ground raised around trunk bases), while A. veitchii and A. mariesii indicated no significant bias toward such elevated microsites in the large seedling stage. However, the relative frequency of T. diversifolia seedlings established on flat ground reached high values of 54-77%, since the relative occupation area of the flat ground was large (85-89%). Such a large share suggests that flat ground should be regarded as the most important microsite for the seedling establishment of T. diversifolia in forests with moss-type undergrowth. This preference trait for T. diversifolia observed with moss-type undergrowth has not been reported in previous studies examining forests with herb-and dwarf bamboo-type undergrowth, where T. diversifolia seedlings are scarce on the ground and restricted to elevated microsites. We conclude that the major microsite for T. diversifolia seedling establishment changes according to the undergrowth vegetation type: a large ground share for moss-type undergrowth and a small ground share for herb-and dwarf bamboo-type undergrowth.

In this paper we first mathematically formulate spatial genetic models that rely on dispersal kernels, using the genetic inhomogeneous Poisson process. On the basis of mapped and genotyped data pertaining to adult and juvenile trees we are able to estimate three fundamental variables of population dynamics: individual female reproductive success, seed dispersal, and pollen flow. The model was applied to a secondary Fagus crenata stand in northern Japan, regenerated after shelterwood harvesting. Highly polymorphic microsatellite data revealed that most of the juveniles around one adult tree were not that tree's progeny and that some minor alleles were clustered there. These data suggested that another mother tree had formerly been present in the vicinity, produced offspring there and died. Inferring its genotype and location, we applied the genetic inhomogeneous Poisson process. Results confirmed that we would have wrongly assessed the regeneration if we had been unaware of the existence of the dead mother. The average distances for seed dispersal and pollen flow were 18 and 193 m, respectively. The contribution of outside mothers, simultaneously assessed using the dispersal variables in the models, ranged from 10 to 50% depending on their positions relative to preserved adults. Individual female reproductive success varied as much as fiftyfold among the eight preserved adults. Our comprehensive approach, utilizing currently available genetic information, mathematical models, and previous forestry records, helped elucidation of the past forest‐regeneration processes.

The genetic structure of Sakhalin spruce (Picea glehnii) was studied across the natural range of the species, including two small isolated populations in south Sakhalin and Hayachine, by using six microsatellite loci and maternally inherited mitochondrial gene sequences. We also analyzed P. jezoensis, a sympatric spruce in the range. Genetic diversity of P. glehnii was higher in central Hokkaido and the lowest in the Hayachine. Bayesian clustering and principal coordinate analysis by using the microsatellites indicated that the Hayachine was clearly distinct from other populations, implying that it had undergone strong genetic drift since the last glacial period. P. glehnii harbored four mitochondrial haplotypes, two of which were shared with P. jezoensis. One of the two was observed without geographical concentration, suggesting its derivation from ancestral polymorphism. Another was observed in south Sakhalin and in P. jezoensis across Sakhalin. The Bayesian clustering--by using four microsatellite loci, including P. jezoensis populations--indicated unambiguous species delimitation, but with possible admixture of P. jezoensis genes into P. glehnii in south Sakhalin, where P. glehnii is abundantly overwhelmed by P. jezoensis; this might explain the occurrence of introgression of the haplotype of P. jezoensis into P. glehnii.