The peopling of Ryukyu Islands: when and how did the first humans arrive?

The Ryukyu Islands located to the southwest of the Japanese archipelago are distributed over an area of 610 km from the north to the south, and 840 km from the east to the west.

The point where the first cluster of the Japanese Yaeyama Islands lie, is where the rising sun rises over the horizon as viewed from the Hasendo coast of Taiwan.  It has been long thought that the first humans arrived during the Late Paleolithic by island-hopping from Taiwan.

Ken-ichi Shinoda and Noboru Adachi,  Ancient DNA Analysis of Palaeolithic Ryukyu Islanders
pp. 51-60 (10 pages) Chap 3 DOI: 10.2307/j.ctt1pwtd26.10 https://www.jstor.org/stable/j.ctt1pwtd26.10
The mtDNA of the Ishigaki skeletal remains excavated from Shiraho-Saonetabaro was determined to be B4e and M7a which hinted at the linkage with SEA and late Pleistocene Ryukyu Islands.

But how did they get there?

FIG. 1.

Despite the widely accepted view of experts that the Ryukyu Islanders share a common origin with the Ainu, the origin and migration routes employed by the the first arrivals to Japan are still mysterious and controversial. The results of DNA studies showed the native people of the Ryukyu islands and those of Taiwan are in different genetic groups. According to the research results, the people of the Yaeyama islands are genetically not related to those living in Taiwan despite their geographical proximity.

This past week (July 2018),  NHK TV featured in this segment of its documentary about Homo Erectus’ journey out of Africa to Japan, focused on a group of the work of a team of 68 researchers who are trying to prove that early humans could have arrived in Japan by sailing from Taiwan’s Hasendo to Japan’s Ishigaki Island.  The researchers built a kusabune reedboat out of himegama reeds which were naturally available resources from the coast of Taiwa’s Hasendo(first attempt) and bamboo boat (second attempt) and tried to sail the boats from Taiwan to Japan’s Ishigakijima island over a distance of 110 km.

Both those attempts to sail the boats failed. On the first attempt, the reedboat never made it far from the coast of Taiwan, it was found that the Kuroshio Current flows along, and close to the entire length of  and to the north of Taiwan’s coast, making it impossible for the reedboat to even sail in the direction of Japan. On the second attempt, both the current and the large opposing waves again worked against the bamboo boat. Buoys had also been released from the coast of Taiwan, they never reached the coast of Japan.

As examination of the early bone remains of the Shirahojin man showed the characteristics of surfer’s ear, the individual is widely believed to have hailed from one of SEA’s islands, Japanese scientists are trying to prove the theory that the earliest Japanese had made the journey from Taiwan to Japan by island-hopping in boats or rafts. (They will be making a third attempt next year by hollowing out a wooden dugout)

Nevertheless, the genetic evidence from the research paper led by Takehiro Sato (excerpted below) on the origins and peopling of the Ryukyu Islands appears to accord with the dismal results by the scientists’ attempts.

Takehiro Sato et al., Genome-Wide SNP analysis reveals population structure and demographic history of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago  … Show more

Molecular Biology and Evolution, Volume 31, Issue 11, 1 November 2014, Pages 2929–2940, https://doi.org/10.1093/molbev/msu230

ABSTRACT

Archaeological findings show that two different cultures developed in the northern and southern Ryukyus during prehistoric times (Asato 2003). The distributions of these cultures reflected the geography of the region, with the Amami Islands and the OK belonging to the northern Ryukyu cultural group, and the MY(Miyako Island) and the YE(Yaeyama Island) belonging to the southern Ryukyu cultural group (fig. 1). In northern Ryukyu, Shellmound Period has extended from 6,700 to 1,000 before present (BP) (Asato 2003). Based on pottery characteristics, the culture of this period is considered to have been similar to that of the Jomon period on the mainland of Japan (i.e., the islands of Hokkaido, Honshu, Shikoku, Kyushu: fig. 1). These apparent similarities prompted some archaeologists to propose that northern Ryukyu was settled by immigrants from mainland Japan (MJ) (Asato 2003). Two prehistoric periods have been characterized in southern Ryukyu: The Shimotabaru Period, which spanned from 4,500 to 3,000 BP and was characterized by a specific style of pottery, and the Aceramic Period from 2,500 to 800 BP, during which no pottery was produced in this region. As no affinity has been observed between the northern and the southern Ryukyu cultures in these prehistoric periods, some archaeologists have hypothesized that there was no human migration between the northern and southern Ryukyu during these periods (Asato 2003). However, in the subsequent Gusuku Period (800–600 BP), the cultures of both the northern and southern Ryukyus were unified after rice cultivation was introduced to the Ryukyu Islands.

Introduction

The peopling of the Ryukyu Islands is considered central to understanding the origin of the Japanese people. The dual structure model of Japanese origin, which is based on cranial and dental morphology, hypothesizes that 1) the first inhabitants of the Japanese archipelago originated from somewhere in Southeast Asia, and that initial colonization occurred during the Upper Paleolithic age (probably through the Ryukyu Islands). These colonialists are considered to have given rise to the native hunter-gatherers in the Japanese Archipelago, or Jomon people. 2) This initial wave of migration was then followed by a second wave of migration from northeast Asia, which occurred during in and after the Aeneolithic Yayoi age. Finally, 3) the populations of both lineages (Jomon and Yayoi people) gradually mixed with each other on MJ, except for in Hokkaido. According to this hypothesis, the marked similarities between the Ainu and the Ryukyu Islanders are due to their common origin from the Jomon people (Hanihara 1991). Of the numerous anthropological studies that have been conducted to date to verify the dual structure model, most concur with the idea that the Japanese have a dual structure and that the Ryukyu Islanders share a common origin with the Ainu (Hanihara 1993; Matsumura 1994; Hammer and Horai 1995; Horai et al. 1996; Omoto and Saitou 1997; Tajima et al. 2002; Tajima et al. 2004; Matsumura and Hudson 2005; Fukumine et al. 2006; Ishida et al. 2009; Matsukusa et al. 2010; Jinam et al. 2012; Koganebuchi et al. 2012). Nonetheless, the origin and migration routes employed by the Jomon people are still open to debate. In these previous studies, individuals from Okinawa-jima have been considered to be representative of the Ryukyu Islanders, but no consideration has been given to the geographical and cultural boundary that exists between the northern and southern Ryukyus.

Indeed, relatively few studies have examined the population structure of the inhabitants of the Ryukyu Islands to date. Of the studies that have been undertaken, some have reported the existence of local variations in morphological and genetic characteristics (Naito 1976; Omoto et al. 1976; Haneji et al. 2007; Toma et al. 2007; Matsukusa et al. 2010). However, the population structure within the Ryukyu Islands remains unclear due to a lack of comprehensive data and due to incompatibilities between the findings of previous studies. In this study, we performed a comprehensive genetic analysis based on genome-wide single nucleotide polymorphism (SNP) data of the Ryukyu Islanders. Specifically, we included individuals from the OK, the MY, and the YE. We also discuss the demographic history of the Ryukyu Islanders and provide evidence for genetic differentiation between the inhabitants of the Okinawa and Miyako island groups.

The Ryukyu Islands located to the southwest of the Japanese archipelago are distributed over an area of 610 km from the north to the south, and 840 km from the east to the west. The archipelago consists primarily of the Amami Islands, Okinawa Islands (OK), Miyako Islands (MY), and the Yaeyama Islands (YE) (fig. 1). Of the numerous straits in the Ryukyu Archipelago, the Kerama Gap between Okinawa-jima (the largest of the OK) and Miyako-jima (the largest of the MY) is the largest at 260 km wide (here, “-jima” is used for “Island” to distinguish it from “Islands”) (Kishimoto 2003). This strait divides the Ryukyu Islands into the northern Ryukyu and southern Ryukyu islands.

FIG. 1.

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Map of the Japanese archipelago and neighboring regions. The Japanese archipelago consists of four main islands (Hokkaido, Honshu, Shikoku, and Kyushu), the Ryukyu Islands, and numerous other islands. The Ryukyu Islands consist of the Amami Islands, the OK, the MY, and the YE.

RESULTS AND DISCUSSION

POPULATION STRUCTURE IN THE RYUKYU ISLANDERS

…population genetics-based analyses were performed. Figure 2 shows the results of principal component analysis (PCA) using 540,451 SNPs shared among data sets including individuals from the OK, MY, YE, MJ, Korea (KR), and two HapMap populations (Chinese Han in Beijing, CHB; Japanese in Tokyo, JPT). Four main clusters (Ryukyu Islanders, mainland Japanese, Koreans, and Han Chinese) were observed in PC1. The observation that almost all Japanese individuals were grouped into two main clusters (Ryukyu and MJ clusters) was consistent with a previous study (Yamaguchi-Kabata et al. 2008). Under the dual structure model of Japanese origin (Hanihara 1991), PC1 can be interpreted as being associated with the Jomon and Yayoi components of individual ancestry. Meanwhile, a biplot of PC1 versus PC2 produced a “U” shape (fig. 2a), implying that PC2 is unlikely to directly reflect any demographic events; this pattern is remarkably similar to a pattern of mathematical artifacts that has previously been observed in a simulation of one-dimensional stepping stone-like habitats (Novembre and Stephens 2008). The OK and MY individuals were separated into two clusters (Okinawa and Miyako clusters) in PC3, and YE individuals were plotted between the Okinawa and Miyako clusters (fig. 2b).

THE GENETIC RELATIONSHIP BETWEEN THE RYUKYU ISLANDERS AND THE ABORIGINAL TAIWANESE

data demonstrated the genetic differentiation between the island groups in the Ryukyu. Alternative possible explanation instead of genetic drift is gene flow from a neighboring population, such as the aboriginal Taiwanese. To examine this possibility, we added data for aboriginal Taiwanese, Ami (AM) and Atyal (AT), from the HUGO Pan-Asian SNP (PASNP) Consortium (2009) database, and performed PCA and ADMIXTURE analysis using 12,488 SNPs overlapping between the data sets. The results of PCA (fig. 2c) and ADMIXTURE analysis (supplementary fig. S3, Supplementary Material online) demonstrated no genetic affinities between the aboriginal Taiwanese and any of the Ryukyu individuals. In addition, we calculated D statistics to assess the admixture. D (CEU, AM; MY, OK) and D (CEU, AT; MY, OK) did not significantly depart from zero (table 2). These results suggest that genetic differentiation between the people of the MY and of the OK are unlikely to have resulted from gene flow from Taiwan, but rather due to genetic drift after the Miyako ancestors migrated from the northern Ryukyu to the southern Ryukyu. A previous study based on mtDNA, Y chromosomal STRs, and autosomal STRs also showed that there was no evidence of any contribution from the aboriginal Taiwanese populations to the gene pool of the Ryukyu Islanders (Matsukusa et al. 2010). Similarly, using a large number of SNP markers, this study verified that there is a clear genetic gap between Taiwan and the Ryukyu Islands.

DEMOGRAPHIC RECONSTRUCTION AMONG THE RYUKYU

Fig. 6

We tested 12 alternative models that vary in migration rate (m) and prior distribution of divergence time (T) (table 4, fig. 6, and supplementary table S3, Supplementary Material online). Then, the best fitting model was chosen from these models using approximated Bayes factor (aBF)…reject[ing] models with higher migration rates (m = 0.01 and 0.1). The divergence time between the Okinawa and Miyako Islanders under the likely models with m = 0 and LN(50, 50²) and with m = 0.001 and LN(100, 100²) was estimated to be 1,800 ± 150 and 2,600 ± 250 BP, respectively (table 4 and supplementary table S3, Supplementary Material online). These results suggested that the divergence event between the Okinawa and the Miyako Islanders dates from the Holocene, even when the effect of migration is considered.

REMARKS ON THE PEOPLING OF THE RYUKYU ISLANDS

Human remains dating from the Pleistocene have been discovered on the Ryukyu Islands. One of the most famous Pleistocene sites is the Minatogawa Fissure on Okinawa-jima (northern Ryukyu) that was discovered by an amateur archaeologist, Seiho Oyama (Suzuki 1975). A total of four skeletons have been excavated at this site, and two charcoal fragments found in the vicinity of human remains were dated to 16,600 ± 300 and 18,250 ± 650 BP by ¹⁴C dating (Matsu’ura 1999; Hashimoto et al. 2002). On Miyako-jima (southern Ryukyu), 26,000-year-old human remains were excavated from the Pinza-Abu Cave site (Sakura 1985). More recently, a 20,000-year-old human bone fragment was excavated from the Shiraho-Saonetabaru Cave site on Ishigaki-jima, the main island of the YE (Nakagawa et al. 2010). Our estimates for the parameters T_RK–CH and T_OK–MY were more recent than the ages of these Pleistocene humans. If these ancient people had made marked contributions to the gene pools of the modern inhabitants of the islands where they were excavated, then the estimates of T_RK–CH and T_OK–MY should have been dated within the Pleistocene. Therefore, our findings suggest that the first inhabitants of the Ryukyu Islands during the Pleistocene were unlikely to have contributed substantially, or at all, to the modern inhabitants of the island. Indeed, our analysis suggested that more recent divergence would sufficiently explain the population structure of the modern inhabitants of the Ryukyu Islands. A previous study proposed that the first sustained colonization of the Ryukyu Islands occurred during the Holocene (Takamiya 2006), and our results strongly support this hypothesis.

This study proposed that large migrations of the modern Ryukyu Islanders occurred during the Holocene, even though the T_OK–MY estimated in our analyses varied depending on which model was employed, and that these migrations could not be assigned to a particular period, such as Simotabaru (4,500–3,000 BP), Aceramic (2,500–800 BP), or Gusuku (800–600 BP) periods. This uncertainty in the estimation is due to limitations in demographic reconstruction using SNP genotyping data. Whole-genome sequencing data will enable us to more accurately estimate demographic parameters. Therefore, accumulation of whole-genome sequencing data is considered necessary to derive a more detailed demographic history of the Ryukyu Islanders.

…

See also Ryukyu Shimpo’s report on Sato’s research study

Genetic DNA of Okinawan people similar to people in the main islands of Japan

 

September 17, 2014 Ryukyu Shimpo

Modern people living in the Ryukyu Islands are genetically more closely related to those in the main islands of Japan than people in Taiwan or mainland China, a research team has found. The researchers announced their findings on September 16 after analyzing nuclear genomic DNA. The team consists of Takehiro Sato Ph.D, a research scholar of the University of the Ryukyus, who specializes in medical research, an associate professor of the university Ryosuke Kimura and researchers of the Institute of Statistical Mathematics of Kitasato University. According to the researchers, people started moving from the Ryukyu islands to Miyako and Yaeyama islands 10,000 years ago. The team concluded the Pinza-Abu Cave Man, which was found in Miyako Island and dated to 26,000 years ago, and the Shiraho saonetabaru Cave Man, dated to 20,000 years ago, of Ishigaki island, are not the main ancestors of the people living in Miyako and Yaeyama today.

Previous research results have also shown the people of the Ryukyu Islands are more similar to those in the main islands of Japan than mainland China or Taiwan from bones and DNA analysis of remains. However, this new analysis of nuclear genomic DNA got the same results.

The research results could help further study of the origin of the people of the Ryukyu Islands.

The team collected DNA from a few hundred of people from the main islands of Okinawa, Miyako and Yaeyama islands. The researchers analyzed 600,000 Single Nucleotide Polymorphisms in the human genome. The results showed the native people of the Ryukyu islands and those of Taiwan are in different genetic groups. According to the research results, the people of the Yaeyama islands are genetically not related to those living in Taiwan despite their geographical proximity.

A representative of the team said, “We analyzed the migrations of people of the Ryukyu Islands and Han in China after the Jomon Period. We found that it is highly possible that Minatogawa Man is not the main ancestor of the people in the Okinawa islands.” The researchers said further investigation was needed.

…

A study on human longevity has contributed to our understanding of the genetic affinities of Okinawan Islanders.

Nasrine Bendjilal, Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population
J Gerontol A Biol Sci Med Sci. 2014 Dec; 69(12): 1474–1484. 2014 Jan 20. doi: 10.1093/gerona/glt203

Abstract

…. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome—more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λ_s) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans.

We used the SNP data from the five populations and their projection onto the primary PCA axes. Figure 2A shows the projection of the Okinawan samples along with the four HapMap samples on the top three principal components. The top PC divided the populations into three main clusters (Asian = [Okinawan, JPT, CHB], CEU, YRI). PCA revealed a good separation between the Okinawan samples and the YRI as well as the CEU. In addition, the Okinawans were close to both the JPT and the CHB HapMap samples as indicated by the plot, they are all clustered together. However, performing PCA using only the Okinawan and the Asian HapMap samples suggested that the Okinawan population is a homogeneous group and was distinct from the Japanese and the Chinese (Figure 2B). We also observed that the Okinawan centenarians were somewhat grouped together forming one cluster when compared with the middle-aged Okinawans. This may suggest that the Okinawan centenarians have a similar genetic background that contributes to their longevity.

Using STRUCTURE to discern global ancestry and admixture proportions, we found that the Okinawans clustered consistently with East Asians, with individual ancestry estimates (ie, the estimated membership coefficients for each individual in each of the seven predefined world regions) ranging from 0.928 to 0.997. No other world population present in the reference dataset had a significant contribution to the Okinawan participants (Figure 4A). The maximum ancestry estimate of any Okinawan individual in non-East Asian clusters was 1.6% African, 0.8% European, 1.2% Middle Eastern, 1.6% Central/South Asian, 1.0% Americas, and 6.5% Oceanian.

Figure 4.

Summary plot of individual admixture proportions. (A) Summary plot of individual admixture proportions. These data demonstrate Okinawan ancestry proportions on a global scale from comparisons with 944 Human Genome Diversity Cell Line Panel (HGDP) participants, grouped into seven main global regions/continents (Africa, Europe, Middle East, Central/South Asia, Americas, and Oceania). From the admixture proportions plot, the Okinawans cluster primarily with East Asians and very little contribution (<1% individual ancestry estimates) from the remaining global region

Based on these results, we next determined Okinawan admixture estimates within East Asian Chinese and Japanese populations only. For this analysis, our reference populations included the Han North and South Chinese, Japanese participants from HGDP, and the HapMap CHB in Beijing, and Japanese participants. On average, the Okinawans were found to share 80.8% (±11.2 SD) admixture with Japanese and 19.2% (±11.2 SD) admixture with Chinese. Individual admixture estimates were quite variable and ranged from 5.84% to 57.82% Chinese admixture (Figure 4B).

….

See also:

(2012) The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. Read more from Asian Scientist Magazine at: https://www.asianscientist.com/2012/12/in-the-lab/ryukyuan-ainu-people-genetically-similar-2012/

Ken-ichi Shinoda et al., Ancient DNA Analyses of Human Skeletal Remains from
the Gusuku Period in the Ryukyu Islands, Japan Bull. Natl. Mus. Nat. Sci., Ser. D, 39, pp. 1–8, November 22, 2013

Haplogroups M7a, M7b, D4, A, and B were observed in these individuals, with M7a and D4 predominant in both archaeological sites, indicating characteristics of the contemporary Okinawan population.
The geographic distribution of haplogroups M7a and D4 at both sites seems to support the claim inferred from the archaeological evidence for a relationship between the Okinawa and Sakishima Islands during the Gusuku period. The fact that all these haplogroups were observed with relatively high frequencies in the late Kaizuka, Gusuku, and contemporary Ryukyu populations implies that formation of the extinct population from the Ryukyu Islands might result from a population expansion after the late Kaizuka period.

Figure 2 shows the haplogroup frequencies of the Gusuku period (present study), modern Ryukyu, and Taiwanese aboriginal populations.
Regardless of their geographical location, the Ryukyu and Taiwanese aboriginal populations differed when compared according to their share of haplogroups. Taiwanese aborigines do not have haplogroup M7a and D4 that dominate the extant Ryukyu and Gusuku populations. Therefore, we assume there was no genetic connection between the Taiwanese and Gusuku populations, who had different origins and population histories overall.

The biased distribution pattern of haplogroup M7a in Japan may have diversified from the ancestral M7 haplogroup, which was introduced to Japan around the Last Glacial Maximum within the Japanese archipelago (Adachi et al., 2011). The Ryukyu Islands are candidates for the origin of this haplogroup (Shinoda, 2007). On the other hand, haplogroup D4 is observed in northeastern China and Korea as well as mainland Japan (Tanaka et al., 2004) and there is no biased distribution among the mainland Japan.
Moreover, this haplogroup apparently occurred at a low frequency in the Jomon population (Shinoda and Kanai, 1999; Adachi et al., 2011). A reasonable theory is that the Yayoi immigrants were predominantly from haplogroup D4.
Archaeological findings indicate that travel and trade between mainland Japan and the Ryukyu archipelago began around the twelfth century. There are also some indications that waves of immigrants moved to Okinawa from mainland Japan and reached the Sakishima area (Asato, 1996). The geographic distribution of haplogroups M7a and D4 in both sites seems to support the claim inferred from the archaeological evidence that a relationship existed between
the Okinawa, Sakishima, and Hateruma Islands in the Gusuku period.

This study identified four distinct haplogroups (M7a, M7b, D4, A, B) in the archaeological specimens sampled from the Okinawa and Hateruma Islands, which agree well with the genetic variation of extant Okinawan and mainland Japanese populations (Figure 2). It follows that the these mtDNA haplogroups except M7b have been present in the late Kaizuka population (Shinoda et al., 2012) and that haplogroup D4 most probably reached the Okinawa Islands from mainland Japan at least by the end of the late Kaizuka period.

High frequencies of haplogroups M7a and D4 are characteristic of the contemporary Okinawan population (Tanaka et al. 2004). The distribution of these haplogroups among the late Kaizuka, Gusuku, and modern Ryukyu populations suggests that the formation of the extinct Ryukyu Islands population was the result of population expansion within the Japanese archipelago (Adachi et al., 2011).

The Ryukyu Islands are candidates for the origin of this haplogroup (Shinoda, 2007). On the other hand, haplogroup D4 is observed in northeastern China and Korea as well as mainland Japan (Tanaka et al., 2004) and there is no biased distribution among the  mainland Japan.
Moreover, this haplogroup apparently occurred at a low frequency in the Jomon population (Shinoda and Kanai, 1999; Adachi et al., 2011). A reasonable theory is that the Yayoi immigrants were predominantly from haplogroup D4.
Archaeological findings indicate that travel and trade between mainland Japan and the Ryukyu archipelago began around the twelfth century. There are also some indications that waves of immigrants moved to Okinawa from mainland Japan and reached the Sakishima area (Asato, 1996). The geographic distribution of haplogroups M7a and D4 in both sites seems to support the claim inferred from the archaeological evidence that a relationship existed between the Okinawa, Sakishima, and Hateruma Islands in the Gusuku period.
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