The voyage(s) to and the early settlement of the Ryukyu islands

Shiraho-Saonetsbaru, Ishigaki Island remains

We review here a recent paper throwing light on the early peopling of the Ryukyu Islands.

The first of which is the work of Shinoda and Adachi, who assign to the Shiraho-Saonetobaru remains, haplogroup  B4e, R and M7a (Mitochondrial DNA) – while these are not the earliest remains found on the Japanese archipelago, they are the earliest DNA to be extracted, and from the archipelago’s southernmost position, on Ishigaki Island (adjacent to Taiwan).

Excerpts from the paper follow below:

Ancient DNA analysis of Palaeolithic Ryukyu Islanders

The genesis of the modern Japanese population is an area of intense study in anthropology, archaeology, and genetics in East Asia. In this context, because of its geographical location, Ishigaki Island is thought to have played a significant role in the migration route from Taiwan and Southeast Asia to the Ryukyu and Japanese archipelagos. According to archaeological evidence, the Sakishima area (Figure 3.1), consisting of the Miyako and Yaeyama island groups, including Isigaki Island, formed a different cultural area from the main island of Okinawa until the twelfth century AD. There was no influence from the mainland of Japan (Jomon and Yayoi cultures), and from archaeological remains, the Sakishima area seems to have a lot in common with the southeastern regions of Asia. Perhaps the sea lying between the main islands of Okinawa and Sakishima was the boundary of the expansion of Japanese culture to the south (Takamiya 2005) and possibly Austronesian expansion from Taiwan towards the north (see Hudson, Chapter 10, this volume).
Due to its complex history, it is not surprising that the Ryukyu Islands have often attracted the interest of population geneticists (e.g. Jinam et al. 2012). Nevertheless, very little is known about the genetic history of their human population. To learn more about the genetic characteristics of the first inhabitants of this westernmost island of Japan, we analysed mtDNA from human remains that were excavated from an archaeological site belonging to the Late Paleolithic period. …. five of the 10 samples were successfully typed to the smallest named haplogroup they belonged to (Figures 3.2 and 3.3). Thus, three samples were assigned to haplogroup M7a and the other samples to haplogroups B4 and R. In the case where D-loop sequence was revealed, we classified them further based on the mutations observed in these regions. Therefore, we assigned the B4 samples to haplogroup B4e. More detailed data has been previously described by Shinoda and Adachi (2014). Owing to the small sample size, it was difficult to verify genetic characteristics by statistical methods, although the existence of these haplogroups is noteworthy.

Though small in number, the distribution of mtDNA haplogroups in this period provides insights into regional population history. Haplogroups B4 and R are the most prevalent in Southeast Asia, especially in the coastal region (Trejaut et al. 2005), indicating that this haplogroup may have been introduced to Japan from Southeast Asia. Interestingly, haplogroup B was also found in ancient Chinese samples (Fu et al. 2012). It seems that the ancestral population of coastal East Asia and Island Southeast Asia was enriched by the founder lineages of haplogroup B4, and the Ryukyu Islands may be one of the northernmost regions where this population arrived in the Palaeolithic period. ***This finding indicates that the southeast influx into the ancient Ryukyu population affected their genetic makeup and that the ancestors of the Aboriginal Taiwanese or Asian coastal region populations might be the main source of this haplogroup in the Ryukyu Islands.

***[It would be perhaps premature to conclude that the B4 arrived from the south, so far all other B4e finds are modern DNA extractions  – eight of the Shiraho-Saonetabaru remains were dated to between 27,000~7,000ybp in the light of the Tianyuan Man discovery. The journey it seems is extremely perilous in the face of strong currents — two attempts to recreate the first migrational journey from Taiwan to Okinawa failed, despite the short distance…the currents have swept the reed-boats onto the Korean coast. While the third attempt carried out last month alone succeeded(scroll down to see the Japan Times report),

Nevertheless, a neutral survey of B’s origins might be better, given the more northerly and early dates of Tianyuan(B4’5) Man….or until haplotyping of both B4e populations can be carried out to ascertain the direction of ancestry. Taiwanese aboriginals are said to have only inhabited the island from about 6ybp, see Ko et al., Early Austronesians: Into and Out of Taiwan]

The geographic specificity of haplogroup M7a is the most intriguing result of this study. Its ancestral haplogroup M7, although a characteristic of East Asian populations, was not found in the northeast region of the continent (Torroni et al. 1993; Derenko et al. 2007). Haplogroup M7a is absent or scarce in the East and Southeast Asian populations outside Japan. Moreover, M7a is one of the prevailing haplogroups not only among modern Japanese, including Honshu, Okinawa islanders, and Ainu populations (Tanaka et al. 2004), but also in the Jomon population (Adachi et al. 2011). The frequency of haplogroup M7a among modern Japanese is highest in the Okinawa islanders (23.3 per cent; Umetsu et al. 2005) – gradually decreasing towards the northern part of Honshu (Shinoda 2007). This finding indicates that this haplogroup may have a southern origin. Moreover, the age of haplogroup M7a was calculated to be ca. 23,000 BP, and the age likely falls within the onset of the Last Glacial Maximum (LGM; Adachi et al. 2011).
Our results confirm that the haplogroup M7a entered Japan, with the earliest settlers more than 20,000 years ago from Southeast Asia or the southern region of the Asian continent. The fact that positive proof of human occupation by haplogroup M7a on Ishigaki Island appears about 30,000–20,000 BP fits this scenario.
The peopling in Japan can be seen as a complex process, as the earliest settlements and recent migrations affected the resident populations differently. Although we can draw limited conclusions from this study, our results of ancient mtDNA analysis help to shed light on late Palaeolithic human migrations to, and within, the Japanese archipelagos from Southeast Asia.

Since hot and humid conditions are unfavourable for DNA preservation, there is a low possibility of finding well-preserved DNA in regions with a tropical climate, like the Ryukyu Islands. However, the present study shows that sufficient amounts of DNA were available in the human skeletal samples from the late Palaeolithic period obtained from the Ryukyu Islands because the remains were protected within caves. It seems that caves are favourable burial sites from the viewpoint of DNA preservation (Fehren-Schmitz et al. 2011). However, further studies are necessary to obtain more details on the human skeletal remains excavated from this region.

The significance of Shirono-Saonetobaru should not escape us. M7a(30-20kya and M7a1 (54kya) are of special interest because the haplotypes are found in 23.3pct of modern Okinawans, as well as across the Japanese archipelago, and is well-established as a founding or ancestral haplogroup. The status B4e is less certain, was it an isolate? Did the early lineage die out? Other rare B4f are sporadically found in various parts of Japan, and from the early Shomyouji (middle Jomon to Heian) site in Kanagawa…but B4 proliferated and diversified since  over 40kya and it is likely other B4 haplotypes arrived with later immigrants into the archipelago. But B4e is not B4f nor close to any other B4 alphabets as each of the lineages are thousands of years old and separated sons ago. Lineage sorting can only take place as more samples from all over Asia are obtained and added to the Mitochondrial phylogenetic tree, and until a finer resolution of the emerging picture of a tree with more twigs of mutations as well as ancestral branches are obtained, we can only make educated guesses, through more holistic and interdisciplinary approaches that involve painstaking archaeology, craniotomy-morphological comparisons and other novel methods such as virus or disease markers.

Summerhayes in his An Austronesian presence in the Sakishima Islands, observing the absence of Austronesian traits that are usually documented archaeologically in Out-of-Taiwan migrations to other islands, and cautions against premature conclusions of ancestry in his review of the finds of Shirato-Saonetobaru cave remains:

“… the colonisation of Yaeyama was of a completely different nature to the movement of peoples south into the Philippines. Once Yaeyama was occupied it was culturally isolated with the nature of subsequent interaction for the next millennia unknown and uncertain (see Yamagiwa 2015, 2016). This explains the absence of spindle whorls, jade and other items which were exported out of Taiwan at a later period of time. Whatever the nature of interaction that occurred between Taiwan and Yaeyama, it is of a different nature to that which occurred between Taiwan and the Philippines. We must recognise that not all colonising groups were successful, and this would affect the trajectory of that group.“

Mark Hudson in Ryukyu Islands and the Northern Frontier of the Prehistoric Austronesian Settlement discusses in detail the lack of an Austronesian cultural package and dissimilarities between the Taiwanese and the “Ryukyu pre-Austronesian” settlements. More about the Austronesian hypotheses here.

Jinam et al. write in their 2016 paper Human genetic diversity in the Japanese archipelago: Dual structure and beyond

The Ainu and Ryukyuan populations are indigenous groups who now mostly reside in Hokkaido and the Ryukyu Islands, respectively. Because of similarities in their cranial and skeletal morphologies with those of the Jomon people (Yamaguchi and Dodo, 1980; Hanihara, 1991), they are thought to be the more direct descendants of the Jomon people than the Mainland Japanese. In fact, early anthropologists already noticed that the similarities between the Ainu and Ryukyuans might be due to shared ancestry (von Baelz, 1911). The Ainu in particular exhibit physical features that are distinct from the Hondo Japanese, leading to various hypotheses regarding their origins, including genetic links to West Eurasians. The Ainu have traditionally been associated with a hunting-gathering lifestyle that is common to other populations surrounding the Sea of Okhotsk, such as the Nivkhi in Sakhalin. Rather than being an isolated group, the Ainu most likely experienced cultural and genetic exchange with their neighboring populations. A study of dental measurements showed similarities between the Ainu and the Okhotsk culture people from the 5th to 12th century A.D. (Hanihara, 2010), while mtDNA analysis showed phylogenetic clustering of the Ainu, Nivkhi and Okhotsk people (Adachi et al., 2011). A study of the ABCC11 gene that is responsible for ear wax type further suggests gene flow from Northeast Asia (possibly by Okhotsk people) into the Ainu in Hokkaido (Sato et al., 2009).

Early mtDNA analysis of the Ainu using a limited number of restriction enzymes showed similarities with Hondo Japanese (Harihara et al., 1986), but later studies showed high affinities between the Ainu and Nivkhi from Sakhalin (Tajima et al., 2004), supporting previous suggestions of genetic influence from North Eurasian populations. Analysis using another uniparental marker, the Y-chromosome, showed the presence of haplogroup D-M125 in the Ainu. This Y-haplogroup is endemic to the Japanese Archipelago and is found in high frequencies in the Ainu and Ryukyuans (Tajima et al., 2004; Hammer et al., 2006), further adding support for the idea of shared ancestry between these two groups. This was further supported by a genome-wide single nucleotide polymorphism (SNP) study that showed the Ainu and Ryukyuans cluster with 100% bootstrap probability on the phylogenetic tree (Jinam et al., 2012). Furthermore, autosomal SNP data also revealed signs of recent admixture between the Ainu and Hondo Japanese (Jinam et al., 2015).

The Ryukyu Islands can be geographically classified into four main clusters, but the most populated island is Okinawa Island. Archeological findings suggest that there were different cultures that developed in the northern part of the Ryukyu Islands (closer to Kyushu and Honshu) and the southern part (closer to Taiwan) (Asato, 2003). Previous genetic studies mostly focused on individuals from Okinawa Island and found that they have high genetic similarities with the Ainu in Hokkaido, even though these two groups are geographically very distant (Omoto, 1995; Omoto and Saitou, 1997). Genome-wide SNP studies show that the Okinawans form a distinct cluster from the Hondo Japanese (Yamaguchi-Kabata et al., 2008), while a more detailed genetic survey of individuals from three main islands in the Ryukyu cluster found differentiation between the island groups that was attributed to genetic drift (Sato et al., 2014).

Previous studies employed genetic markers such as mitochondrial, Y-chromosomal and autosomal DNA to tackle the issues surrounding the origins of the Japanese. Support for the dual-structure hypothesis included studies based on mtDNA sequences (Horai et al., 1996; Tanaka et al., 2004), Y-chromosomal SNPs and short tandem repeat polymorphisms (Hammer et al., 2006). Analyses involving classical protein markers led to partial support for the dual-structure model, supporting the shared ancestry of the Ainu and Ryukyuans dating back to the Jomon people, but found no close relationship between them and Southeast Asians (Omoto and Saitou, 1997).

A genome-wide SNP study of three Japanese groups (Hondo Japanese mostly from Tokyo, Ainu and Ryukyuan) (Jinam et al., 2012) adds support to the dual-structure model. Phylogenetic tree analysis shows that the Hondo Japanese are located between an Ainu-Ryukyuan cluster and continental Asians, suggesting that they are admixed between these two population clusters. A follow-up to that study used a formal test for admixture (Patterson et al., 2012) to show that the Hondo Japanese are indeed the result of admixture between the ancestors of the Ainu and Han Chinese or Korean: the Jomon and Yayoi people, respectively. Furthermore, they estimated the proportion of Jomon component in the Hondo Japanese to be approximately 18% and that the admixture event occurred at least 1.4 KYA (Jinam et al., 2015). Other studies have tried to estimate the proportion of Jomon ancestry in the Japanese population. Using Y-chromosomal markers in the Ainu, Ryukyuan and Hondo Japanese from several locations, Rasteiro and Chikhi (2009) estimated the Jomon component in the Hondo Japanese using likelihood-based methods and reported a range of 20% to 50%.

We could not do wrong to heed Jinam’s urging to understand population substructure and to further search for the origins of the lesser obvious signals of demic variations in the genes of the Japanese people. More holistic and interdisciplinary research approaches could yield more insights in future. 

A study by He et al. (2012) used approximately 50,000 autosomal SNPs to estimate a value of 23% to 40% Jomon component in the Hondo Japanese. These studies generally agree with the dual-structure model and add further details such as admixture proportions, but the dual-structure model alone may not be sufficient to explain the genetic substructure observed in Hondo Japanese. … It is clear from these studies that the Japanese people are not homogeneous, but to establish whether the observed differentiation can be explained purely by genetic drift or other migration waves will require further study.


Watch the YouTube video of the replicated ancient migratory voyage from Taiwan to Okinawa

Team successfully replicates imagined ancient sea migration from Taiwan to Okinawa 

Kyodo news, via Japan Times July 9, 2019

A team of Japanese and Taiwanese paddlers in a dugout canoe on Tuesday successfully replicated a hypothetical human migration between Taiwan and Okinawa about 30,000 years ago.

During the two-day, 200-kilometer voyage from Taitung County, southeastern Taiwan, to Yonaguni Island, Okinawa Prefecture, the team of five paddlers — one Taiwanese, three Japanese men and one Japanese woman — relied solely on the stars, sun and wind for their bearings.

They departed Taiwan on Sunday afternoon in their 7.6-meter-long, 70-centimeter-wide wooden canoe, crossing the Black Stream, which begins off the Philippines and flows northeastward past Japan.

The voyage was one of multiple research projects signed in 2017 between Japan’s National Museum of Nature and Science and Taiwan’s National Museum of Prehistory. The team achieved success after two failed attempts in 2017 and 2018.

According to Yosuke Kaifu, 50, leader of the team who accompanied the canoe aboard an escort ship, Japanese archaeologists have found that early humans migrated to Japan via three routes, and one of them is along the course of the Black Stream. However, it is unknown how they actually traveled to the Japanese islands.

The project involving the two museums was intended to shed light on how difficult the journey would have been, Kaifu said.

“I was worried when (they) temporarily went off course, but am glad to see them arrive,” Kaifu said after the paddlers reached Yonaguni.

“It was a perfect voyage,” said Koji Hara, a 47-year-old lead paddler. “The Black Stream carried the canoe and all we did was steer it a little.” The five were tired, but did not have any health issues.

As the boat reached the island, it was welcomed by several hundred cheering local residents.

“They have all returned safely. I want to say ‘thank you’ to them,” said Mitsuko Maeso, a 71-old housewife living on Yonaguni.

“I can’t imagine how people traveled 30,000 years ago, but for this journey I think they risked their lives,” she said.

The discovery of relics dating back more than 30,000 years on several islands of the Ryukyu Archipelago made archaeologists speculate that a group of ancient settlers migrated to Japan from what is now Taiwan in the Paleolithic era, which extends from some 2.6 million years ago to around 15,000 years ago.

Kaifu has said that even if the project is successful, he would not jump to the conclusion that some ancestors of the Japanese people came from Taiwan, but at least it would show the possibility is quite high.

The other two routes for early human migration to Japan are from the Korean Peninsula across the Tsushima Strait about 38,000 years ago and from Eurasia across the Tsugaru Strait that separates the main islands of Honshu and Hokkaido.

Before Kaifu persuaded the two museums to fund the project, he initiated a similar project in 2016 when two primitive canoes made from local straw departed from Yonaguni Island bound for Taiwan. They only managed to reach the neighboring island of Iriomote, about 75 km away.

The 2017 voyage, on a boat made of bamboo and rattan grown in Taiwan, made it from Dawu Township, Taitung County, to Green Island, which is about 66 km away.

The 2018 boat was also made of bamboo and rattan, but it was smaller and carried fewer people. It did not last long on the open sea.