Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

Abstract

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

Prehistoric Migration of Homo sapiens in the Ryukyu Islands

“…Moreover, Minatogawa I in Okinawa and Shiraho 4 in Ishigaki have similarities in short facial height and short cranium length, but they have different characteristics, such as the width of the frontal region and protrusion of the temporal region [43]. They also differ in genetics; Minatogawa I was haplogroup M [45], whereas Shiraho specimens were determined as haplogroups B4e and R [44]. If these studies indicate different origins of the Paleolithic people, we need to consider multiple migrations from different areas of Southeast Asia to the Ryukyus.…”

“…However, recent morphological analyses have identified many differences between Minatogawa and modern Japanese and/ or Jomon in the glabellar region [61], cranium shape [62], tooth root size [63], and mandibular shape [42]. From a genetic perspective, the mitochondrial DNA (mtDNA) of Minatogawa I has been identified as haplogroup M [45]. It is one of the ancestral haplogroups of M7a and N9, which are popular among the mainland Jomon people, although haplogroup M is not a direct ancestor of them [45,64].…”

“…From a genetic perspective, the mitochondrial DNA (mtDNA) of Minatogawa I has been identified as haplogroup M [45]. It is one of the ancestral haplogroups of M7a and N9, which are popular among the mainland Jomon people, although haplogroup M is not a direct ancestor of them [45,64]. In contrast, morphological analysis of the skull of Shiraho 4 shows similarities to prehistoric Southeast Asia and the Jomon people [43].…”

Starch granules from human teeth: New clues on the Epi-Jomon diet

“…For instance, starch granules derived from dental calculus may be poorly preserved, and taxonomic identification of plant food at the species level is often difficult. Furthermore, as the Japanese Archipelago is covered extensively with acidic soil made of volcanic ash (e.g., Shibutani, 2014;Mizuno et al, 2021), the acidic conditions make bone material analysis challenging (Nafte, 2000). Thus, the reliability of starch granule analysis of dental calculus has not been adequately validated.…”

Endemic demographics of the Jomon people estimated based on complete mitogenomes reveal their regional diversity

“…More recently, the Bayesian Skyline plot (BSP) (Drummond et al ., 2005) analysis has been applied to multiple whole-mitogenome nucleotide sequences from present-day individuals in the Japanese archipelago with the aim of estimating the prehistoric demography (Jinam et al ., 2021; Mizuno et al ., 2021). These previous BSPs show a rapid growth in effective populations size after the end of the Jomon period and with the beginning of the Yayoi period, coinciding with the advent of wet rice cultivation.…”