Central Ryukyus Research Articles

An extraordinary case in human history: Prehistoric hunter-gatherer adaptation to the islands of the Central Ryukyus (Amami and Okinawa archipelagos), Japan

The islands of the Central Ryukyus (Amami and Okinawa archipelagos), Japan, were continuously occupied by hunter-gatherers for several thousand years during the Holocene. This occupation would seem to represent a unique example of island settlement by hunter-gatherers. Homo sapiens had expanded into all continents except Antarctica by 10,000 BP, demonstrating high adaptability to various environments, but few islands had been settled by that time. Most islands appear to have been too small to support hunter-gatherer subsistence. Many islands were indeed first colonized by agriculturalists. Some islands located close to large landmasses, having a large surface area, or with reliable sea mammal populations or translocated plants and animals were successfully colonized by hunter-gatherers, but none of these features characterize the prehistoric Central Ryukyu Islands, which were successfully colonized by hunter-gatherers by at least the early–middle Holocene. Furthermore, this colonization was likely accomplished with smaller populations and foraging territories than previously documented for hunter-gatherers. Coral reef resources with nuts (and possibly yams) appear to have played a crucial role in this island colonization. The only similar case to prehistoric Okinawa comes from the Andaman Islands, where hunter-gatherers have occupied small tropical islands for thousands of years. The final part of this paper provides a brief comparison of the Andaman data in light of the results from the Central Ryukyus described here.

Phylogeographic Study of Whip Scorpions (Chelicerata: Arachnida: Thelyphonida) in Japan and Taiwan.

Whip scorpions (Thelyphonida), comprising an order in the class Arachnida, are distributed from tropical to temperate zones. Two species occur exclusively in Japan and Taiwan, but the border of their distributional ranges is ambiguous in the Central Ryukyus (Japan). We collected new specimens from the Central Ryukyus and revealed that the border of distribution of the two species lies between the Central and Southern Ryukyus, i.e., the Kerama Gap. Moreover, the estimated divergence time (15.8 Mya) of the two species, based on the mitochondrial COI gene, was older than the recently estimated time (1.55 Mya) of formation of the Kerama Gap. These results highlight the risks of a priori assumption solely on the basis of geological data for applying it as a calibration point to some terrestrial animals in this region. Typopeltis stimpsonii was genetically divided into four lineages, two of which turned out to be endemic to the Okinawa Islands. All specimens from the main island of Japan and Shikoku were in one lineage, which was also found in the Amami Islands and Hachijojima Island. This suggests that these specimens may have been dispersed by human activity. Typopeltis crucifer included five genetic lineages. Species collected from Ishigakijima and Iriomotejima Islands were genetically diversified not between the borders of these islands but within Ishigakijima Island. This study also suggests that phylogenetic diversity of the species in the Southern Ryukyus have increased through two times of invasions from Taiwan.

Middle Pleistocene to Holocene mammal faunas of the Ryukyu Islands and Taiwan: An updated review incorporating results of recent research

This paper presents an updated review on Middle Pleistocene to Holocene land mammal fossil localities and their faunas in the main part of the Ryukyu Islands (Central and Southern Ryukyus) and in Taiwan. We reconstruct the successions of land mammal faunas from the Middle Pleistocene to Holocene mainly on Okinawa Island in the Central Ryukyus, and on Miyako and Ishigaki Islands in the Southern Ryukyus, as well as in Taiwan. We also discuss the faunal relationships among the three islands and Taiwan, and paleogeographic inferences based on the results. The fauna on Okinawa Island has been of an insular type, and has shown a high degree of endemism since the Middle Pleistocene. With the exception of the wild boar (Sus scrofa), no mammals have immigrated onto the island since the Middle Pleistocene, indicating that the island has been isolated from other regions by the sea since at least the Middle Pleistocene. The appearance of the wild boar in the later part of the Late Pleistocene is suggestive of human introduction. On Miyako Island, the presence of the steppe mammoth (Mammuthus trogontherii) in the Middle Pleistocene indicates that this species immigrated from Taiwan across a temporary land bridge formed between the island and Taiwan (probably via Ishigaki Island) during a cold stage of the late Middle Pleistocene. It is probable that this land bridge did not reach Okinawa Island. The Late Pleistocene faunas of Miyako and Ishigaki Islands are also of an insular type, and non-flying forms of the two faunas are markedly different from one another, and are also different from their counterparts on Okinawa Island. These observations indicate that Miyako and Ishigaki Islands were separated from one another and from Okinawa Island in the Late Pleistocene. The Holocene faunas of Miyako and Ishigaki Islands also indicate isolated conditions. As on Okinawa Island, it is suggested that humans introduced the wild boar, probably in the later part of the Late Pleistocene. The Middle Pleistocene to Holocene mammal faunas of Taiwan are of a continental type, and differ greatly from those of the Ryukyu Islands. Thus, Taiwan has been separated from the islands since the Middle Pleistocene, with the exception of the land bridge stage.

History of commensal rodents on Ishigaki Island (southern Ryukyus) reconstructed from Holocene fossils, including the first reliable fossil record of the house mouse Mus musculus in Japan

The history of commensal rodents in mainland Japan and the Ryukyu Islands (Ryukyus) has been poorly understood owing to the paucity of reliable fossil records. Recent excavation of the Shiraho-Saonetabaru cave site on Ishigaki Island of the southern Ryukyus yielded a large number of rodent fossils from well-dated sediments ranging from the Late Pleistocene to the Holocene. Some of the fossils were preliminarily assigned to Mus musculus and Rattus sp. They are described here to confirm their taxonomic positions. These forms are considered to be commensal rodents.A history of commensal rodents on Ishigaki Island is reconstructed based on the stratigraphic position and relative abundance of the commensal forms as well as the non-commensal native rodent, Niviventer sp., which is very abundant in most of the horizons of the sediments. Before the end of the Pleistocene, no commensal forms inhabited the island, and the rodent fauna consisted only of the non-commensal form. In the early Holocene, one of the commensal forms, M. musculus, invaded the island, but the continued abundance of the non-commensal form afterward indicates that the invasion did not affect the fauna. In the late Holocene, a second invasion, by Rattus sp., probably caused the rapid decline and extinction of the non-commensal form. Since the extinction, the rodent fauna of the island has comprised only the commensal forms.In Japan, there are no known reliable fossil occurrences of M. musculus, in contrast to several occurrences of Rattus at Middle Pleistocene to Holocene fossil localities. Thus, the fossil of M. musculus described here records the first reliable occurrence of the species in Japan, and is very important for documenting the first appearance of M. musculus in the southern Ryukyus in the early Holocene. The species is considered to have appeared much later in mainland Japan and the central Ryukyus.

Late Pleistocene-Holocene amphibians from Okinawajima Island in the Ryukyu Archipelago, Japan: Reconfirmed faunal endemicity and the Holocene range collapse of forest-dwelling species

Amphibian fossils excavated from two Late Pleistocene-Holocene fissures in the southern part of Okinawajima Island in the Ryukyu Archipelago were identified through detailed comparisons with skeletal specimens of extant taxa. The identified species (eight frogs and two newts) were confined to extant elements on the island and were mostly endemic to either the island or the central part of the archipelago including it. Previous Late Pleistocene records of extralimital frogs (two mainland Japanese species [Glandirana rugosa and Rana tagoi] and one Southeast Asian frog currently naturalized in the Ryukyus [Polypedates leucomystax]) from one of the study sites (the Minatogawa Fissure) are therefore considered misidentifications. This may also be the case with Fejervarya kawamurai, a synanthropic frog currently widely distributed in East Asia, including the Central Ryukyus. Of the species obtained from the Late Pleistocene deposits at these sites, five frogs (Limnonectes namiyei, Babina holsti, Odorrana ishikawae, O. narina, and Rana ulma) are forest-dwellers currently confined to the northern forested area of Okinawajima. Additionally, none of these species were detected in the middle Holocene deposits from one of the sites, the Sashiki Fissure. Our findings indicate that the southern limestone area of Okinawajima in the Late Pleistocene harbored a dense and humid forest with diverse lotic habitats, similar to the northern forested area of the island at present, and that these environmental conditions were lost by the midpoint of the Holocene Period.

Pleistocene Coral Assemblages on Irabu-Jima, South Ryukyu Islands, Japan

Abstract. We identified 40 genera and 83 species of scleractinian corals from middle Pleistocene reef limestones on Irabu-jima, located in the South Ryukyu Islands (South Ryukyus); these data were then combined with previously published data sets on Pleistocene coral assemblages on Okinawa-jima (southern Central Ryukyus), and Kikai-jima (northern Central Ryukyus) to perform statistical analyses, including cluster analysis and multidimensional scaling (MDS) ordination of Bray—Curtis (BC) similarity coefficients applied to coral taxa (R-type analysis) and coral assemblages (Q-type analysis). Results of the analyses, combined with field descriptions of the coral assemblages, allowed interpretations of reef paleoenvironments. Outcrops of Quaternary reef deposits in the Ryukyus comprise both shallow- and deep-water coral assemblages. Generally, coral diversity increases southward along the island chain. The statistical analyses highlight differences in the taxonomic compositions of fossil coral assemblages in ...

Notes on the Chelonian Bones Included in an Old Collection of Vertebrate Remains from the Ogido Shell Mound on Okinawajima Island, Japan, with Special Reference to the Soft-Shell TurtlePelodiscus sinensisReported for that Collection

Abstract: Chelonian skeletal remains from the Ogido Shell Mound were examined. Detailed comparisons of the remains with skeletal materials of extant and extinct turtles known from Okinawajima Island and adjacent waters revealed that the Ogido remains do not contain representatives of Pelodiscus sinensis or any other trionychids at all, although recent literature referred to the original excavation report of this shell mound as the only prehistoric record of the soft-shell turtles from the Central Ryukyus. Instead, two of the three bone pieces identified to particular taxa with certainty, were identified to Geoemyda japonica, and the other to a cheloniid species. Discovery of G. japonica from this site further supports the idea that this species, currently confined to the northern part on Okinawajima, had a much broader distribution on this island until recently.

Phylogenetic relationships, genetic divergence, historical biogeography and conservation of an endangered gecko, Goniurosaurus kuroiwae (Squamata: Eublepharidae), from the Central Ryukyus, Japan.

The Kuroiwa's eyelid gecko Goniurosaurus kuroiwae is an endangered species in a state of relict endemism in the Central Ryukyus, Japan, and is divided into five subspecies. We analyzed variations in sequence data for approximately 1900 base positions of mitochondrial 12S and 16S rRNA, and cytochrome b genes from samples representing all recognized subspecies of G. kuroiwae together with those from congeneric species in order to test the relevant previous phylogenetic hypotheses and discuss biogeographical implications in the degree and pattern of genetic divergence within G. kuroiwae. Our results, while confirming a previous molecular phylogenetic hypothesis proposed on the basis of much smaller data set, negate the relationships hypothesized on morphological grounds by explicitly supporting: 1) the primary dichotomy, with substantial genetic divergence, between G. k. splendens from the Amami Island Group and the remaining subspecies all from the Okinawa Island Group; and 2) the presence of at least six independent lineages within the latter, indicating non-monophyly for two of the subspecies, G. k. kuroiwae and G. k. orientalis, in the current taxonomic definitions. The marked genetic divergence between populations of the two island groups seems to have initiated in the middle Miocene, i.e., prior to formation of straits that have consistently been separating these two island groups since the early Pleistocene. All populations of G. kuroiwae are regarded as endangered from the viewpoint of conservation genetics.

Divergence and Long-Distance Overseas Dispersals of Island Populations of the Ryukyu Five-Lined Skink, Plestiodon Marginatus (Scincidae: Squamata), in the Ryukyu Archipelago, Japan, as Revealed by Mitochondrial DNA Phylogeography

We assessed the historical biogeography of the Ryukyu five-lined skink, Plestiodon marginatus, and related species (P. stimpsonii and P. elegans). Our specific aims were to reveal the origin, tim- ing, and route of the colonization to three volcanic islands in the northern Tokara Group of the northern Ryukyus: Kuchinoshima, Nakanoshima, and Suwanosejima. We conducted phylogenetic analyses and divergence time estimation using a partial sequence of the mitochondrial cytochrome b gene for P. marginatus collected from across its whole range (the northern and central Ryukyus), and for P. stimpsonii (from the Yaeyama Group of the southern Ryukyus) and P. elegans (from Taiwan). Our results suggest three major clades (A, B, and C). Clades A and B consist of P. marginatus, excluding the Kuchinoshima population, and Clade C consisted of the Kuchinoshima population, P. stimpsonii, and P. elegans. These clades are estimated to have diverged during the Late Miocene to the Late Pliocene. Among the three examined northern Tokara populations, the Kuchinoshima population was shown to be a sister group of P. stimpsonii. The two other populations from Nakanoshima and Suwanosejima Islands were closely related to P. marginatus from the northern part of the Okinawa Group and that from Kodakarajima Island in the southern Tokara Group, respectively. These populations are estimated to have diverged from their respective related spe cies in various ages of the Early to Late Pleistocene, suggesting that they colonized the islands by independent overseas dispersals of approximately 50-850 km via the Kuroshio Current. Taxonomic implications for P. marginatus are also discussed.

琉球弧の地質と岩石：沖縄島を例として

琉球弧の地質と岩石：沖縄島を例として

Origins ofLaticauda laticaudataandLaticauda semifasciata(Elapidae: Laticaudinae) Individuals Collected from the Main Islands of Japan as Inferred from Molecular Data

The two laticaudine sea kraits, Laticauda laticaudata and L. semifasciata, are distributed in the tropical waters of the western Pacific and the northernmost limit of their breeding populations is considered to be the Northern Ryukyus, Japan. These two species, however, have been occasionally reported from the main islands of Japan, which are located further north. To determine the origins of such individuals, we examined partial sequences of the mitochondrial cytochrome b gene of one specimen of L. laticaudata from Yamaguchi and two specimens of L. semifasciata from Oita and Mie. Comparisons of the sequences with published data for apparently stable populations in the Ryukyu-Taiwan region revealed that sequence of the Yamaguchi specimen was identical with a haplotype previously detected from a broad range of the Ryukyu-Taiwan region and we could not specify its origin. Sequences of the Mie and Oita specimens were identical with, or very close to, haplotypes detected only from the Central Ryukyus and the Southern Ryukyus-Taiwan region, respectively. These results indicate that they were drifters from the Central Ryukyus and further south, corroborating the unconfirmed belief that sea kraits found on the main islands were accidentally transported by the Kuroshio Current from the south. Considering that both species exhibit certain degree of genetic differentiation among island groups in the Ryukyu-Taiwan region, the putative transportations by the Kuroshio seldom contribute to effective gene flow among local populations. The Kuroshio probably poses threats to their survival as the current may carry individuals out of their habitats and distributional range.

Invasion of Yakushima Island, Japan, by the Subtropical LizardJapalura polygonatapolygonata (Squamata: Agamidae)

Abstract: Japalura polygonata is an arboreal agamid lizard native to the subtropical East Asian islands. Recent studies reported that this species had been introduced to southern and southeastern Kyushu, Japan. Here, we report that this species has also been introduced to Yakushima Island, a Natural World Heritage site located between Kyushu and Amamioshima Island (the northernmost extremity of its native range). Morphological examination of the Yakushima specimens revealed that this lizard population belongs to the nominotypical subspecies (J. p. polygonata), which is endemic to the Amami and Okinawa Groups of the Central Ryukyus, Japan. Observations of the gonadal condition revealed that females collected in April and June possessed shelled eggs in their oviducts. A few juveniles collected in late April and early August were considered hatchlings based on their body size. These lines of evidence strongly suggest that J. p. polygonata has already established a breeding colony on Yakushima Island. Based o...

An Attempt at Captive Breeding of the Endangered Newt Echinotriton andersoni, from the Central Ryukyus in Japan.

Simple SummaryWe naturally bred the endangered Anderson’s crocodile newt (Echinotriton andersoni) and tested a laboratory farming technique using near-biotopic breeding cages with several male and female pairs collected from Okinawa, Amami, and Tokunoshima Islands. This is the first published report of successfully propagating an endangered species by using breeding cages in a laboratory setting for captive breeding. Our findings on the natural breeding and raising of larvae and adults are useful in breeding this endangered species, and can be applied to the preservation of other similarly wild and endangered species.Anderson’s crocodile newt (Echinotriton andersoni) is distributed in the Central Ryukyu Islands of southern Japan, but environmental degradation and illegal collection over the last several decades have devastated the local populations. It has therefore been listed as a class B1 endangered species in the IUCN Red List, indicating that it is at high risk of extinction in the wild. The species is also protected by law in both Okinawa and Kagoshima prefectures. An artificial insemination technique using hormonal injections could not be applied to the breeding of this species in the laboratory. In this study we naturally bred the species, and tested a laboratory farming technique using several male and female E. andersoni pairs collected from Okinawa, Amami, and Tokunoshima Islands and subsequently maintained in near-biotopic breeding cages. Among 378 eggs derived from 17 females, 319 (84.4%) became normal tailbud embryos, 274 (72.5%) hatched normally, 213 (56.3%) metamorphosed normally, and 141 (37.3%) became normal two-month-old newts; in addition, 77 one- to three-year-old Tokunoshima newts and 32 Amami larvae are currently still growing normally. Over the last five breeding seasons, eggs were laid in-cage on slopes near the waterfront. Larvae were raised in nets maintained in a temperature-controlled water bath at 20 °C and fed live Tubifex. Metamorphosed newts were transferred to plastic containers containing wet sponges kept in a temperature-controlled incubator at 22.5 °C and fed a cricket diet to promote healthy growth. This is the first published report of successfully propagating an endangered species by using breeding cages in a laboratory setting for captive breeding. Our findings on the natural breeding and raising of larvae and adults are useful in breeding this endangered species and can be applied to the preservation of other similarly wild and endangered species such as E. chinhaiensis.

Austronesian’ and ‘Jōmon’ identities in the Neolithic of the Ryukyu Islands

This paper examines Neolithic cultural identities in the Ryukyu Islands of southwest Japan. It is argued that there were two different identities in this archipelago: a ‘Jōmon’ identity in the northern and central Ryukyus and an ‘Austronesian’ identity in the southern Ryukyus. These identities were constructed despite broad similarities in subsistence adaptation in both cultural zones.

Development of Microsatellite Markers forCynops ensicauda(Amphibia: Caudata) by Using Next-Generation Sequencing Technology

We isolated and characterized seven microsatellite markers including di-, tri-, and tetra-nucleotide repeats for Cynops ensicauda, which is a near-threatened species and endemic to the Central Ryukyus, Japan, using next-generation sequencing. Six out of the seven loci that showed polymorphism in Cynops ensicauda popei on Okinawajima Island were also amplified in C. e. ensicauda on Amamioshima Island. Expected heterozygosities of these markers were 0.00–0.738 (mean, 0.429) and 0.00–0.791 (mean, 0.459) in C. e. popei and C. e. ensicauda, respectively. These markers will be useful for genetic studies, such as evaluating the genetic diversity within and between populations of this species.

Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): Taxonomic relationships and distributional changes associated with climatic oscillations

We investigated the phylogenetic relationships and estimated the historical demography of the Japanese fire-bellied newt, Cynops pyrrhogaster, from Japanese mainlands using 1407-bp sequences of the mitochondrial DNA (NADH6, tRNAglu, cyt b) and 1208-bp sequences of nuclear DNA (Rag-1) genes. Phylogenetic trees based on mitochondrial DNA revealed four major haplotype clades (NORTHERN, CENTRAL, WESTERN, and SOUTHERN clades) within this species. Degree of genetic differentiation among major haplotype clades was very large for intraspecific variation, suggesting this species to be composed of four species lineages that replace each other geographically. Nuclear genetic variation presented no obvious patterns of geographic structure except for the distinctness of populations diagnosed by NORTHERN clade of mitochondrial haplotypes, suggesting results of incomplete lineage sorting. Current distribution and estimated divergence times for the genus Cynops suggest that the common ancestor of two Japanese species (C. pyrrhogaster and C. ensicauda from the Ryukyu Islands) had diverged at the edge of the continent corresponding to the present East China Sea and Central Ryukyus. Subsequent range expansion to Japanese mainland seems to have occurred in the middle Miocene. Population-genetic analyses indicated that all species lineages, except for the SOUTHERN one, experienced geographic population reductions and expansions associated with glacial and postglacial climatic oscillations.

Taxonomic Study of theBurmoniscus ocellatusComplex (Crustacea, Isopoda, Oniscidea) in Japan Shows Genetic Diversification in the Southern Ryukyus, Southwestern Japan

To clarify the taxonomic status of the Burmoniscus ocellatus complex in Japan, we carried out morphological observations and phylogenetic analyses of specimens collected from Yonagunijima, Iriomotejima, Ishigakijima, and Miyakojima Islands of the southern Ryukyus and from Okinawajima Island of the central Ryukyus in southwestern Japan. Observations of the holotypes of Aphiloscia iriomotensis ( Nunomura, 1986 ), Ap. ishigakiensis ( Nunomura, 1986 ), and Ap. yonakuniensis ( Nunomura, 1986 ), in addition to the specimens newly collected from the five islands, indicated that these specimens belong to the genus Burmoniscus. Analyses of five morphological characters of 268 specimens collected from the five islands showed that the body size of Okinawajima specimens is distinctly smaller than those of the specimens from the southern Ryukyus. The ranges of the five morphological characters tended to overlap among the specimens from Yonagunijima, Iriomotejima, Ishigakijima and Miyakojima Islands; these morphological characters were congruent with those of 6. ocellatus (Verhoeff, 1928). The phylogenetic analyses were based on three regions of mitochondrial DNA-COI, 12S rRNA, and 16S rRNA-and indicated that the specimens collected from the southern Ryukyus constitute a monophyletic group, which is clearly distinct from the clade composed of the Okinawajima specimens. These results strongly suggest that Ap. iriomotensis, Ap. ishigakiensis, and Ap. yonakuniensis are synonymous with B. ocellatus, a species widely distributed in the southern Ryukyus. On the other hand, the species from Okinawajima Island in the central Ryukyus is considered to be an undescribed Burmoniscus species, which is closely related to but clearly distinct from S. ocellatus.

Phylogeny and biogeography of the Anderson’s crocodile newt, Echinotriton andersoni (Amphibia: Caudata), as revealed by mitochondrial DNA sequences

The Anderson’s crocodile newt, Echinotriton andersoni, is considered a relic and endangered species distributed in the Central Ryukyus. To elucidate phylogenetic relationships and detailed genetic structures among populations, we analyzed variation in the mitochondrial cytochrome b gene. Results strongly support a primary dichotomy between populations from the Amami and Okinawa Island Groups with substantial genetic divergence, favoring a primary divergence between the two island groups. Within the latter, populations from the southern part of Okinawajima Island are shown to be more closely related to those from Tokashikijima Island than to those from the northern and central parts of Okinawajima. The prominent genetic divergence between the two island groups of the Central Ryukyus seems to have initiated in the Miocene, i.e., prior to formation of the strait that has consistently separated these island groups since the Pleistocene. The ancestor of the southern Okinawajima—Tokashikijima is estimated to have migrated from the northern and central parts of Okinawajima into southern Okinawajima at the Pleistocene, and dispersed into Tokashikijima subsequently.

Lasioglossum (Evylaeus) tadauchii sp. nov. (Hymenoptera, Halictidae) from Amami-Ôshima, southwestern Japan

Lasioglossum (Evylaeus) tadauchii sp. nov. is described and illustrated based on female speci- mens collected from Amami-Oshima, the central Ryukyus, southwestern Japan. This new species to the sexstrigatum species group in the carinaless Evylaeus. A modified key to the carinaless Evylaeus species occurring in the central and southern Ryukyus is provided, as well as data on some bionomical notes of this new species.

Late Pleistocene lineage divergence among populations ofNeolitsea sericea(Lauraceae) across a deep sea‐barrier in the Ryukyu Islands

AbstractAim Our goals were: (1) to assess the population genetic structure and demographic divergence history of a bird‐dispersed tree,Neolitsea sericea, endemic to East Asian land‐bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc.Location Japan–Ryukyu–Taiwan Island Arc and Chinese/Korean offshore islands.Methods We applied 10 nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker (psbA–trnH intergenic spacer) to 31 populations (397 and 326 individuals, respectively) from throughout the species’ range to infer current patterns of genetic diversity and structure, and pollen‐to‐seed migration ratios (r). A coalescent‐based isolation‐with‐migration (IM) model was applied to the combined nSSR/cpDNA data set to estimate lineage divergence times and population demographic parameters.Results The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the ‘Tokara Gap’, a narrow (c. 37 km wide) but deep (> 1000 m) sea‐strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages toc. 0.07 Ma (90% highest posterior density interval: 0.02–0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post‐divergence gene flow between them.Main conclusions The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an ‘ancient sea‐barrier hypothesis’ for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence ofN. sericea, including not only land‐bridge submergence, but also island configuration, and/or constraints on adaptation along a latitudinal temperature gradient.