Appendix S3. Species composition of actual and predicted communities. We examined 50 species, and species in actual community but not examined in this study are not shown. Because the predictions generated by the statistical models represented the probability of occurrence of each species, we used a threshold probability to obtain the species list of the predicted community. As the threshold probability, we used the average probability of occurrence of all species in the focal community. If a predicted probability exceeded this threshold, the species was listed as a member of the community. A: actual community, L: community predicted by logistic regression, D: community predicted by decision tree analysis. 1: present, 0: absent.

Evergreen broad-leaved forest / Abandoned coppice forest / Managed coppice forest / Meadow community / Weed community in winter and spring / Weed community in summer and autumn
Species / Family / A / L / D / A / L / D / A / L / D / A / L / D / A / L / D / A / L / D
Carpinus tschonoskii / Betulaceae / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Adenophora triphylla var. japonica / Campanulaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Myosoton aquaticum / Caryophyllaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 1 / 0 / 0 / 1 / 1
Euonymus sieboldianus / Celastraceae / 0 / 0 / 1 / 0 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Chenopodium pumilio / Chenopodiaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 1 / 1
Chloranthus serratus / Chloranthaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Commelina communis / Commelinaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 1 / 1
Erigeron philadelphicus / Compositae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 1 / 1 / 1 / 0 / 1 / 1 / 1
Eupatorium chinense / Compositae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 1 / 1 / 0 / 1 / 0 / 0 / 1 / 1
Gnaphalium affine / Compositae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1
Ixeris dentata / Compositae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 1 / 0 / 0 / 0 / 1 / 0 / 1
Solidago virgaurea ssp. asiatica / Compositae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 0 / 0 / 1 / 0 / 0 / 1 / 0
Calystegia japonica / Convolvulaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Cardamine flexuosa / Cruciferae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 0 / 1 / 1
Dryopteris erythrosora / Dryopteridaceae / 1 / 1 / 1 / 0 / 0 / 0 / 1 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Equisetum arvense / Equisetaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 1 / 1 / 1 / 1 / 1 / 0 / 1 / 1 / 1
Castanopsis sieboldii / Fagaceae / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Quercus serrata / Fagaceae / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Geranium carolinianum / Geraniaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 0 / 1 / 1
Geranium nepalense ssp. thunbergii / Geraniaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Ajuga nipponensis / Labiatae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Lamium amplexicaule / Labiatae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1
Lilium auratum / Liliaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Scilla scilloides / Liliaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Smilax nipponica / Liliaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Mollugo pentaphylla / Molluginaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 0 / 1
Ligustrum obtusifolium / Oleaceae / 0 / 1 / 0 / 0 / 1 / 0 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Oenothera parviflora / Onagraceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Oxalis bowieana / Oxalidaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Oxalis corniculata / Oxalidaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1
Trachycarpus fortunei / Palmae / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Macleaya cordata / Papaveraceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Echinochloa crus-galli var. caudata / Poaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 1 / 1
Eragrostis ferruginea / Poaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Festuca parvigluma / Poaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Paspalum dilatatum / Poaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1
Trisetum bifidum / Poaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 1 / 0 / 1 / 0 / 0 / 1 / 1
Chaenomeles japonica / Rosaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 1 / 0
Rubus palmatus var. coptophyllus / Rosaceae / 0 / 1 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1 / 0
Sanguisorba officinalis / Rosaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 0
Paederia scandens / Rubiaceae / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 1 / 1 / 1
Lygodium japonicum / Schizaeaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 1 / 1 / 1 / 0 / 1 / 0 / 0 / 1 / 1
Mazus pumilus / Scrophulariaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 1 / 1 / 1
Veronica persica / Scrophulariaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1
Styrax japonicus / Styracaceae / 0 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Eurya japonica / Theaceae / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Callicarpa mollis / Vervenaceae / 0 / 0 / 0 / 1 / 0 / 0 / 1 / 1 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0
Viola grypoceras / Violaceae / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 1 / 1 / 0 / 0 / 1 / 0 / 1
Viola hondoensis / Violaceae / 0 / 1 / 0 / 0 / 0 / 0 / 1 / 1 / 0 / 0 / 1 / 1 / 0 / 1 / 1 / 0 / 1 / 1
Viola mandshurica / Violaceae / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / 0 / 0 / 0 / 1