Scientists face obstacles in giving an accurate account of the earliest arrivals in the Japanese archipelago — where, when and how

On the Pleistocene Population History in the Japanese Archipelago | Current Anthropology: Vol 58, No S17, Nakagawa
This paper provides a current understanding of human population history in the Pleistocene Japanese Archipelago, particularly with respect to the routes and timing of hunter-gatherer migrations, by incorporating multiple lines of evidence from the records of archaeology, human paleontology, and genetic studies. The human fossil remains are concentrated on the Ryukyu Islands in southwestern Japan, suggesting that there may have been a northward migration via the Ryukyu Islands. In contrast, studies of ancient mitochondrial DNA demonstrate genetic continuity among Holocene hunter-gatherer populations in the Paleo-Sakhalin-Hokkaido-Kurile Peninsula, whereas the Pleistocene genetic history is little explored. Although it is largely supported, the assumed population continuity from the Pleistocene to the Holocene inside the Japanese Archipelago is also challenged by an examination of the Paleolithic record and a comparison of the short- and long-term chronologies of the Japanese Paleolithic, implying that the Japanese Paleolithic record was created by hunter-gatherer population migrations from the north and south with substantial time lag and endemic technological invention and transformation during the Late Pleistocene.

How Do the DNA Studies Tell Us about the Routes of Human Entry into Japan?

The Holocene human fossil record supports an admixture model in which the Paleolithic population originated from both southeastern and northeastern Asia (e.g., Hanihara 1991). The mitochondrial DNA (mtDNA) analyses of modern Japanese revealed that non-African superhaplogroups M and N originally derived from modern H. sapiens dispersing out of Africa (Forster 2004) that eventually came to be the Japanese indigenous populations of Ainu and Ryukuan (e.g., Tanaka et al. 2004; cf. Maca-Meyer et al. 2001). Because Ainu and Ryukuan are descendants of the original Jomon populations (Hanihara 1991; Horai et al. 1996; Omoto and Saitou 1997) and M and N superhaplogroups represent southern and northern routes of human migrations, respectively (Tanaka et al. 2004), the Holocene Jomon population was founded by both northward and southward gene flows.

Studies of ancient mtDNA from the Jomon skeletal remains of Hokkaido show genetic relations between Jomon and Ainu, because both populations retain high frequencies of the haplogroup N9b (Adachi et al. 2011), whereas N9b is scarce among East Asian populations other than Japanese (Tanaka et al. 2004:1842) and is likely skewed to northern regions in Japan (Shinoda 2007). Because the coalescent time of N9b is estimated to be approximately 22,000 year ago (Adachi et al. 2011:355), populations that have this haplogroup emerged around the LGM. In Hokkaido, Epi-Jomon human remains in Hokkaido also have N9b (Adachi et al. 2011), which suggests some degree of gene flow during the LGM to the late Holocene in Hokkaido (22,000–2000 years ago).

As discussed above, both genetic studies based on ancient Jomon mtDNA and those based on modern mtDNA more or less support the “dual-structure model” (Hanihara 1991). This also suggests a complex population history even during the Holocene. Nevertheless, what do these genetic implications tell us about Pleistocene population migrations into Japan? In other words, what does the genetic affinity of the Jomon peoples tell us about Paleolithic population dynamics? In general, because the descendants of Jomon and Yayoi both contributed to the formation of the current Japanese population, Paleolithic foragers should be regarded as the founding population of the Jomon (Hanihara 1991). However, the extent to which Pleistocene Paleolithic populations contributed to modern Japanese is largely unidentified, mainly because there are few genetic and human fossil records, with the exception of some good fossil specimens, notably Minatogawa Man (Baba, Narasaki, and Ohyama 1998; Suzuki 1982). The remaining question is how we understand the complexity in Japanese Paleolithic population history. A question that will not be addressed here is whether there is clear evidence that the Jomon were the direct descendents of the Japanese Paleolithic foragers and whether both hunter-gatherer populations were genetically continuous for the past 30,000 years in Japan.


What Does Archaeology Tell Us about Human Entry into Japan?

The Paleolithic archaeological record provides a basic picture of Pleistocene human population history in Japan. Although the number of Paleolithic sites during the 1960s was only slightly more than 300 (Ohyi 1968:52), the number of registered sites is now greater than 15,000 (Japan Palaeolithic Research Association 2010). Some clarification is necessary, however, regarding this latter number. The “sites” in the recent database include assemblages and collections of artifacts recorded in various contexts, ranging from extensively excavated sites to a few specimens collected on the surface. Because a single cultural level in a deeply excavated multilayered Paleolithic open-air site is counted as a single site, a single location was sometimes counted multiple times, and site size and artifact density from a single site are not standardized among the recorded sites. Although some bias is present in the record, the database is still useful to explore to understand general macro- and microregional patterns of human occupation across the entire Japanese Archipelago.

Considering the regional geographic features and Paleolithic culture history, I divided the 47 prefectures into 7 broader regions (fig. 2). From north to south, they are labeled as north (N), northeast (NE), southeast (SE), central (C), southwest (SW), south (S), and far south (FS). N, S, and FS are isolated islands corresponding to Hokkaido, Kyushu, and Ryukyu islands. NE, SE, C, and SW are the divisions of Honshu Island, the main island in the archipelago along with adjacent Shikoku. Divisions of NE, SE, C, and SW are based on the presence of mountain chains, plains, and the Pleistocene paleogeography. For example, C is the region characterized by high-altitude mountains and plains mostly above 600–1,000 m asl. SW is the region in the middle of the Pleistocene Paleo-Honshu Island. Using the site location data recorded in the database, the number of archaeological sites is counted according to the microregions (table 2). The microregions are then sorted by site density using the areal extent data announced by the Geospatial Information Authority of Japan (2015). SE is the microregion with the highest density, followed by S, C, SW, NE, N, and FS. The highest density in SE is probably explained by sampling bias, due to the high population density in the Tokyo area. It is also because the deeply excavated sites yielded multiple levels of human occupation on the Musashino and Sagamino Uplands in the southern part of SE (e.g., Yajima and Suzuki 1976; Yamaoka 2010). Except for the microregions with the highest density (SE) and lowest density (FS), the site density shows a south to north inclination. High site density in SE, followed by a gradual increase from C to SW, NE, and N, is observed. The sites are all attributed to the Pleistocene, whereas the chronological affiliations of these sites vary depending on the region, especially between N (the southern part of Paleo-SHK) and the rest of the microregions (i.e., Paleo-Honshu and Ryukyuan islands). The Paleolithic in the Paleo-Honshu record started at the beginning of the Upper Paleolithic, around 40,000–37,000 years ago, and ended around 11,500 years ago (Yamaoka 2010; Yoshikawa 2014), whereas the beginning of the Paleolithic record in Hokkaido is not earlier than 30,000 years ago (Izuho et al. 2012; Naoe and Kudo 2014). Thus, the time depth of the Paleo-Honshu Paleolithic record is approximately 27,000 years, as opposed to 18,500 years for Paleo-SHK, because the reliable dates obtained from the hearths in the Agonki-5 site in Sakhalin are 23,500 years ago (Kuzmin et al. 2004; Vasilevski 2003). Because of the difference in time depths, the south to north inclination of site density implies that the earlier Paleolithic sites are more abundant in southern Japan than in northern Japan. High site density in the S microregion (Kyushu) next to the SE of the southern Kanto region in Honshu suggests that waves of the earlier hunter-gatherers would have migrated into Kyushu and spread to the north along Paleo-Honshu Island. Conversely, the likelihood of earlier human population migrations in the early Upper Paleolithic (EUP) from eastern Siberia via Paleo-SHK is not supported. On the one hand, site density patterns alone do not answer the question of timing and size of northerly migratory populations from Paleo-Honshu to Paleo-SHK. The lowest density of the FS microregion of the Ryukyu Islands suggests that human arrivals into the Ryukyu Islands were relatively low and that occupations were not necessarily continuous, unlike the situation in the microregions in Paleo-Honshu. Relatively high site density in C (the central region in Paleo-Honshu) suggests that humans occupied high-elevation regions during the Upper Paleolithic. Good examples are represented by the open-air sites located on the Nobeyama Plateau, where Paleolithic hunter-gatherers could have followed seasonal movements between the central highlands and southern Kanto regions in SE (e.g., Tsutsumi 2011), similar to pastoral transhumance (e.g., Chang and Tourtellotte 1993), and where groups of hunter-gatherers seasonally aggregating to kill large herbivores around lakes would have sometimes succeeded (e.g., Norton et al. 2010b). Given the population entry routes (fig. 1), the observed south to north inclination of site density in the Paleo-Honshu suggests that the majority of Paleolithic migratory groups were from the Korean Peninsula and southern China. If so, routes 1 and 5 are the best-supported routes for early hunter-gatherers’ dispersals into the Japanese Archipelago.


Figure 2. Microregions in the Japanese Archipelago. Bold lines represent the boundaries of microregions. Dotted lines within the islands define the current 47 administrative prefectures. Locations with numbers show the human paleontological and/or pre–Upper Paleolithic archaeological sites mentioned in the text. The sites are Minatogawa (1), Yamashita-cho (2), Pinza-abu (3), Shiraho-Saonetabaru (4), Shimojibaru (5), Kanedori (6), Takesa-Nakahara (7), Hamakita (8), Sunabara (9), Iriguchi (10), Sozudai (11), and Ōno (12). C = central; FS = far south; N = north; NE = northeast; S = south; SE = southeast; SW = southwest.


Table 2. Counts, areal extent, and density of Late Pleistocene sites in Japan