Four heterochronous spore and pollen complexes (SPC) have been identified in the deposits of the submarine Yamato Rise: SPC-1 (Early Miocene), SPC-2 (the end of Early and the beginning of the Middle Miocene), SPC-3 (Middle–Late Miocene), and SPC-4 (Late Miocene). Pollen of various woody plants dominates in SPC-1; the families of gymnosperms (Pinaceae) also prevail in this complex. The climate was moderate and humid because of the proximity to the water area. The complex SPC-2 differs from SPC-1 in the highly increased role of thermophile angiosperms due to the impact of the climatic optimum between the Early and Middle Miocene. The complex SPC-3 is distinguished by the diversity and predominance of broad-leaved woody plants. Gymnosperms are mainly represented by pine families. The composition of palynoflora points to a dissected relief and the burial of pollen not far from the places of its growth. Gymnosperms with a predominance of the Taxodiaceae family are characteristic of SPC-4. The SPC-4 composition is indicative of humid habitat conditions, marshy shoreland, and pollen burial in places of plants growth. The climate was moderate and humid. Palynological investigation suggests the existence of a dry land in the area of the current Yamato Rise throughout the Miocene. The relief was highly dissected and mountainous in the Early and early Middle Miocene; then, the relief roughness and firm-land area reduced dramatically.

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