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290 §3.5.2. The Ryukyu Islands
291 Several Palaeolithic sites are known in the Ryukyu islands, some with human skeletal
292 remains35. Debate continues over whether this Palaeolithic settlement was from the north or
293 south36,37. At most Ryukyu sites there is no evidence of settlement continuity between the
294 Palaeolithic and Neolithic. In the northern (Amami) and central (Okinawa) islands, there
295 seems to have been re-settlement from Kyushu in the middle Holocene38. In the southern
296 (Sakishima) islands, the Shiraho-Saonetabaru site on Ishigaki has a longer sequence of
297 human skeletal remains39, but it is unclear if the same population continued to inhabit the
298 island. Elsewhere in the southern Ryukyus, no Holocene sites are known until the third
299 millennium BC. Archaeological research began in the southern Ryukyus in 1889 and over 50
300 prehistoric sites are currently known dating to between ca. 2300 BC and AD 1000. None of
301 these sites have any clear archaeological evidence of contact with Okinawa or Japan to the
302 north. Two cultural phases are usually recognised: an Early Neolithic or Shimotabaru phase
303 dated ca. 2300 – 1200 BC and a Late Neolithic or a-ceramic phase dated ca. 800 BC to AD
304 100040. A hiatus of perhaps 400 years between these two phases is usually understood as
305 reflecting a transition between two different populations. Given that no archaeological
306 evidence exists of contact with the Jōmon world, most scholars have assumed that the
307 Neolithic populations of the southern Ryukyus arrived from the Austronesian world to the
308 south. Early Neolithic Shimotabaru pottery has similarities with Taiwan and an origin on that
309 island has been seen as most probable41,42. The appearance of the first Early Neolithic sites in
310 the southern Ryukyus at around the same time as the onset of Austronesian voyaging from
311 Taiwan may suggest a link between the two processes43. In the Late Neolithic, pottery was no
312 longer used or made and Tridacna shell adzes became the most diagnostic artefacts (see SI 12
313 Fig. 13). For some archaeologists this has suggested the possibility that the Late Neolithic
314 people re-colonised the southern Ryukyus from the Philippines44.
315 Our results suggest the need for a major re-evaluation of existing interpretations of the
316 prehistory of the southern Ryukyus. Instead of an origin in Taiwan or the Philippines, the
317 DNA of the prehistoric inhabitants of the Nagabaka site shows that they were probably
318 originated in the Jōmon world to the north. The Okinawa islands 250 km to the north are the
319 most likely source, but a longer voyage from Japan cannot be ruled out. As explained in SI
320 12, the stratigraphy of the Nagabaka site provides no evidence for a hiatus in occupation
321 between the Early and Late Neolithic phases. We have samples from both the Early
322 (‘Nagabaka_early’) and Late (‘Nagabaka_late’) Neolithic phases on Miyako island. Our
323 DNA data likely supports continuity between the Early and Late Nagabaka samples (SI 13
324 Figs. 3 and 7); although the former was low in coverage and might be subject to some degree
325 of West Eurasian contamination (See qpAdm admixture modelling in SI 16), the latter can be
326 safely identified as harbouring a characteristic Jōmon genetic profile (SI 13 Figs. 3 and 8). By
327 historic times, new ancestry ultimately related to West Liao River Basin millet farmers was
328 added to the preceding populations, changing their genetic profile from majority Jōmon
329 ancestry to majority millet farmer ancestry (SI 13 Fig. 9). We find no evidence of genetic
330 contribution from Taiwan to the Nagabaka individuals (See qpAdm admixture modelling in
331 SI 16), although we cannot rule out the possibility that other Neolithic sites in the southern
332 Ryukyus were settled from Taiwan. The southern Ryukyu islands are extremely important as
333 the prehistoric boundary between the Jōmon and Austronesian worlds and further research is
334 needed to explore the population history of this region.
SI 13 Fig. 7. The genetic difference between Early and Late Nagabaka individuals from Miyako island.