A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main‐island Japanese

The Sakishima islands are members of the Ryukyu island chain, stretching from the southwestern tip of the Japanese archipelago to Taiwan in the East China Sea. Archaeological data indicate cultural similarities between inhabitants of prehistoric Sakishima and Neolithic Taiwan. Recent studies based on tooth crown traits show remarkably high inter‐island diversity among Ryukyu islanders, suggesting that the Sakishima islanders might have genetic backgrounds distinct from main‐island Okinawa people. To investigate the genetic diversity of the Ryukyu islanders, we analyzed mtDNA, Y chromosome, and autosomal short tandem repeat loci in a sample of main‐island Okinawa people and Sakishima (Miyako and Ishigaki) islanders whose participated in a previous study of tooth crown morphology. Our phylogenetic analysis of maternal (mtDNA) and paternal (Y chromosome) lineages shows that the Sakishima islanders are more closely related to people from the Japanese archipelago than to Taiwan aborigines. Miyako islanders and the Hokkaido Ainu have the first and second highest frequencies (respectively) of the Y‐chromosomal Alu‐insertion polymorphism, which is a presumable Jomon marker. Genetic diversity statistics show no evidence of demographic reduction or of extreme isolation in each island's population. Thus, we conclude that 1) Neolithic expansion from Taiwan did not contribute to the gene pool of modern Sakishima islanders, 2) male‐lineage of the Ryukyu islanders likely shares a common ancestor with the Hokkaido Ainu who are presumably direct descendants of the Jomon people, and 3) frequent reciprocal gene flow among islands has masked the trace of common ancestry in the Ryukyu island chain. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Vicariance of Pyrocoelia fireflies (Coleoptera: Lampyridae) in the Ryukyu islands,Japan

We performed molecular phylogenetic analyses based on the mitochondrial COI gene (687 bp) and the nuclear 28S rRNA gene (715 bp) and reconstructed phylogenetic trees of the Pyrocoelia fireflies in the Ryukyu Islands and eastern Asia. Age calibration was done using a robust geological constraint: the Okinawa trough and associated straits began to rift at 1.55 Ma, isolating the Ryukyu Islands from the Chinese continent, Japanese islands, Taiwan island and some of the islands from each other. We suggest that the physical isolation of these islands began to generate the allopatric speciation within these islands, so the timing of this isolation was assigned to an appropriate node. The topology is completely concordant among phylogenetic trees reconstructed using MEGA (maximum‐likelihood), raxmlGUI (maximum‐likelihood) and BEAST (Bayesian inference; including combined analysis of COI and 28S rRNA genes). Two lineages are recognized, related to their emergence time; spring to summer, and autumn. In each lineage, vicariance is inferred to have begun at 1.55 Ma from our phylogenetic and geological analyses. In lineage 1, P. oshimana (Amami), P. matsumurai (Okinawa), P. discicollis (W. Japan), P. fumosa (E. Japan) and P. abdominalis (Yaeyama) were differentiated. In lineage 2, P. rufa (Tsushima and Korea), P. miyako (Miyako‐jima), P. atripennis (Ishigaki‐jima) and P. praetexta (Taiwan and HongKong) were differentiated. Pyrocoelia analis (Taiwan and China) emerges throughout the year except for winter, and constitutes another lineage. We suggest that Pyrocoelia fireflies differentiated at 2 Ma to generate these three lineages. The base substitution rate for the COI gene is estimated as 4.48% Myr^–1 and that for the 28S rRNA gene is 0.394%  Myr^–1, and these rates were used in a combined BEAty analysis in BEAST.     

Relict distribution of Microhyla (Amphibia: Microhylidae) in the Ryukyu Archipelago: High diversity in East Asia maintained by insularization

The Ryukyu Archipelago, located at the southwestern part of Japan, is known as a group of continental islands and harbours many endemic taxa, supposedly reflecting its fairly long isolation from the Eurasian continent, Taiwan and the Japanese main islands. Microhyla okinavensis has been known as an endemic member of the terrestrial fauna of this archipelago. Molecular phylogenetic analyses using samples from nearly all island populations of the species and representative samples of other east Asian congeneric species revealed that M. okinavensis consists of four distinct subclades, of which the Amami, Okinawa and Miyako subclades, though exhibiting distinct genetic differentiations from each other, formed a monophyletic group (clade A). The remaining Yaeyama subclade was exclusively sister to M. mixtura from inland China, forming another monophyletic group (clade B), rendering M. okinavensis in the current definition paraphyletic. These results, as well as estimated dates of divergence from related taxa, indicate that M. okinavensis actually includes more than one distinct species. The results indicate that M. okinavensis and M. mixtura are relict species with disjunct distributions which had been most probably caused by invasion of M. fissipes in intervening areas.     

Vicariant speciation due to 1.55 Ma isolation of the Ryukyu islands,Japan, based on geological and GenBank data

The Ryukyu island arc, originally a continental margin arc, separated from the Chinese continent by the rifting of the Okinawa trough, a process which began at 1.55 million years ago (Ma) and continues to the present. In addition, the Ryukyu arc was simultaneously divided into the northern Amami–Okinawa and southern Yaeyama islands by the Kerama rift valley, and consequently formed two isolated island units. The Kuroshio warm current began to flow into the Okinawa trough from the Yonaguni Strait, and flow out through the Tsushima and Tokara straits also at 1.55 Ma, and these seaways effectively acted as barriers between the Ryukyu islands and Taiwan, China and Japan. Through this geological process, vicariant speciation generated Ryukyu endemic animal species. We support this hypothesis by drawing linearized maximum likelihood (ML) phylogenetic trees of the species in four endemic insect groups (peacock butterfly, Chinese windmill butterfly, golden‐ringed dragonfly, window firefly) using GenBank sequence data. We determined the precise branching ages for these phylogenetic trees, and show simultaneous speciation at 1.55 Ma for Amami–Okinawa and Yaeyama units. The Taiwan and Tsushima straits, barriers between Taiwan and China, and Japan and Korea, respectively, did not form sufficient barriers to migration during glacial low stands, and species were intermingled. A marine embayment may have posed as a migration barrier between northern and southern China in the Quaternary or a little earlier. From our study we also estimate the precise molecular evolution rate and justify the molecular clock.     

Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago

The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis on genome-wide single-nucleotide polymorphisms, genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 single-nucleotide polymorphisms to infer population history within the Miyako Islands, including Miyakojima, Irabu, and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 − 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about seven generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.     

Biogeography of the subspecies of Parides (Byasa) alcinous (Lepidoptera: Papilionidae) based on a phylogenetic analysis of mitochondrial ND5 sequences

Abstract. The phylogeny of the butterflies Parides (Byasa) alcinous caught at various localities in Japan and the Ryukyu Islands and in the eastern part of the Eurasian Continent was analysed using mitochondrial DNA sequences coding for NADH dehydrogenase subunit 5 (778 bp). The same phylogenetic relationship among P. (B.) alcinous subspecies was obtained with all analytical methods used, and was supported by high bootstrap values. The female butterfly wing pattern that characterizes each subspecies was unrelated to the phylogenetic relationship among the subspecies. The phylogenetic trees show that one group composed of ssp. alcinous and yakushimanus, which are distributed in the main area of the Japan Archipelago, the Korean Peninsula and southern Primorski of Russia, and the other group comprised of ssp. loochooanus, bradanus and miyakoensis, all of which are distributed in the Ryukyu Islands, diverged from a common ancestor. The ssp. loochooanus distributed in Amami and Okinawa Islands then diverged, and ssp. bradanus and miyakoensis distributed in Yaeyama and the Miyako Islands, respectively, finally diverged. This divergence order nearly agrees with the palaeogeography of the Ryukyu Islands that has been established in Pliocene and Pleistocene (0.2–2 MYA), suggesting that P. (B.) alcinous has been isolated in the Ryukyu Islands since the establishment of the islands.     

Characterization of six microsatellite loci in the mangrove cricket Apteronemobius asahinai

The mangrove cricket Apteronemobius asahinai is endemic to mangrove forest floors in China, Southeast Asia and the Ryukyu archipelago (Amamiohsima, Okinawa, Miyako, Ishigaki and Iriomote Islands) of Japan. We developed six polymorphic microsatellite markers for the mangrove cricket from genomic DNA libraries enriched for CA, GA, AAG and ATG motifs. The M13‐tailed primer method was used in the process of screening of amplification and polymorphism of primers. A total of 64 specimens from two populations (one from Okinawa and the other from Iriomote) were genotyped for allelic diversity. The average number of alleles per locus was 4.67 and 6.67 for Okinawa and Iriomote populations, respectively. A significant genetic differentiation was detected between the two populations (pairwise F_ST 0.2404). These polymorphic microsatellite loci will be useful in ongoing studies of the population genetic structure of the mangrove cricket including several populations in the Ryukyu archipelago.     

Complex inter‐island colonization and peripatric founder speciation promote diversification of flightless Pachyrhynchus weevils in the Taiwan–Luzon volcanic belt

Aim

We investigated the spatial and temporal patterns of diversification among colourful and flightless weevils, the Pachyrhynchus orbifer complex, to test the stepping‐stone hypothesis of colonization across the Taiwan–Luzon volcanic belt.

Location

Southeast Asia.

Methods

The phylogeny of the P. orbifer complex was reconstructed from a multi‐locus data set of mitochondrial and nuclear genes using maximum likelihood in RAxML and Bayesian inference in MRBAYES. Likelihood‐based tests in CONSEL were used to evaluate alternative tree topologies. Divergence times were estimated in beast based on a range of mutation rates. Ancestral range and biogeographical history were reconstructed using Bayesian binary MCMC (BBM) methods in RASP and in BioGeoBEARS. Demographic histories were inferred using the extended Bayesian skyline plot (EBSP). Species boundaries were tested using BPP.

Results

The phylogeny of the P. orbifer complex indicated strong support for seven reciprocally monophyletic lineages grouped by current island boundaries (Camiguin, Fuga, Dalupiri, Calayan, Babuyan, Orchid and Yaeyama Islands), except for a sister Green + Itbayat lineage. Complex and stochastic colonization of P. orbifer was inferred to have involved both northward and southward directions with short‐ and long‐distance dispersal events, which are strongly inconsistent with the strict stepping‐stone hypothesis. Divergence time estimates for all extant island lineages (<1 Myr of Middle Pleistocene) are much more recent than the geological ages (22.4–1.7 Myr) and subaerial existence (c. 3 Myr) of the islands. The statistically delimited seven cryptic species imply that the diversity of Pachyrhynchus from small peripheral islands continues to be largely under‐estimated.

Main conclusions

The non‐linear, more complex spatial and temporal settings of the archipelago and stochastic dispersal were probable key factors shaping the colonization history of the P. orbifer complex. Speciation of the P. orbifer complex may have occurred only between islands, indicating that peripatric speciation through the founders of stochastic dispersals was the major evolutionary driver.     

Unexpectedly complex gradation of coral population structure in the Nansei Islands,Japan

To establish effective locations and sizes of potential protected areas for reef ecosystems, detailed information about source and sink relationships between populations is critical, especially in archipelagic regions. Therefore, we assessed population structure and genetic diversity of Acropora tenuis, one of the dominant stony coral species in the Pacific, using 13 microsatellite markers to investigate 298 colonies from 15 locations across the Nansei Islands in southwestern Japan. Genetic diversity was not significant among sampling locations, even in possibly peripheral locations. In addition, our results showed that there are at least two populations of A. tenuis in the study area. The level of genetic differentiation between these populations was relatively low, but significant between many pairs of sampling locations. Directions of gene flow, which were estimated using a coalescence‐based approach, suggest that gene flow not only occurs from south to north, but also from north to south in various locations. Consequently, the Yaeyama Islands and the Amami Islands are potential northern and southern sources of corals. On the other hand, the Miyako Islands and west central Okinawa Island are potential sink populations. The Kerama Islands and the vicinity of Taketomi Island are potential contact points of genetic subdivision of coral populations in the Nansei Islands. We found that genetic population structure of A. tenuis in the Nansei Islands is more complex than previously thought. These cryptic populations are very important for preserving genetic diversity and should be maintained.     

Phylogenetic relationships between the tideland snails Batillaria flectosiphonata in the Ryukyu Islands and B. multiformis in the Japanese Islands

Phylogenetic relationships between two sibling species of Japanese tideland snails, namely, Batillaria multiformis from the Japanese Islands and B. flectosiphonata from the Ryukyu Islands, were analyzed on the basis of the nucleotide sequences of the mitochondrial gene for cytochrome oxidase I. Populations of B. multiformis were genetically distinct from those of B. flectosiphonata with the exception of a population from Amami-Oshima Island, which corresponded to the boundary between the distributions of these two species. Individuals with the mitochondrial gene of B. multiformis and those with the mitochondrial gene of B. flectosiphonata were collected from the same tidal flat on Amami-Oshima Island. All the snails with the mitochondrial gene of B. multiformis could be divided into two genetically distinct groups but there was no geographical structure to the distribution of these two groups. Individual populations of B. flectosiphonata in the Amami, Okinawa, Miyako and Yaeyama insular groups each consisted exclusively of a unique set of haplotypes, with the exception of a population at a northern site on Okinawajima Island, which included a few individuals with sequences related to those of individuals in the Amami insular group. All individuals from South Ryukyu formed a well-supported monophyletic group, while the monophyly of individuals from Central Ryukyu was not supported. The monophyly of B. multiformis was clearly demonstrated but there was no evidence to support that of B. flectosiphonata. Batillaria multiformis might have been derived from immigrants from the Ryukyu Islands, which became isolated and diverged genetically on the Japanese Islands.     

Morphometric variation in the pusillus group of the genus Rhinolophus (Mammalia: Chiroptera: Rhinolophidae) in East Asia

Based on 203 specimens belonging to the Rhinolophus "pusillus group" (Mammalia: Chiroptera: Rhinolophidae), univariate and multivariate morphometric analyses using 19 characters were performed to assess the confused species taxonomy. The results indicated that R. pusillus (including calidus, parcus, and szechuanus) in the continental region and Hainan Island of China and "R. cornutus" in Japan are morphologically divergent species. Rhinolophus cornutus should be further split into R. cornutus (including orii, pumilus, and miyakonis) in the main islands of Japan, the Amami and Okinawa Group of the central Ryukyu Archipelago, and Miyako Group of the southern Ryukyus; and R. perditus and R. imaizumii from the Yaeyama Group in the southern Ryukyus. Rhinolophus monoceros from Taiwan is morphologically more similar to species in Japan than to R. pusillus. In addition to R. pusillus, another form that is morphologically similar to species in Japan was recognized from Langzhong in Sichuan Province; this may represent an undescribed species, and further examination is necessary to determine its taxonomic status. Specimens from Guang'an in Sichuan Province, China, are also different from the others, and are characterized by the smallest skull size. Although further studies are required, these specimens were tentatively identified as R. subbadius.     

Evolutionary origin of a periodical mass‐flowering plant

The evolutionary origin of periodical mass‐flowering plants (shortly periodical plants), exhibiting periodical mass flowering and death immediately after flowering, has not been demonstrated. Within the genus Strobilanthes (Acanthaceae), which includes more than 50 periodical species, Strobilanthes flexicaulis on Okinawa Island, Japan, flowers gregariously every 6 years. We investigated the life history of S. flexicaulis in other regions and that of closely related species together with their molecular phylogeny to reveal the evolutionary origin of periodical mass flowering. S. flexicaulis on Taiwan Island was found to be a polycarpic perennial with no mass flowering and, in the Yaeyama Islands, Japan, a monocarpic perennial with no mass flowering. Molecular phylogenetic analyses indicated that a polycarpic perennial was the ancestral state in this whole group including S. flexicaulis and the closely related species. No distinctive genetic differentiation was found in S. flexicaulis among all three life histories (polycarpic perennial, monocarpic perennial, and periodical plant). These results suggest that among S. flexicaulis, the periodical mass flowering on Okinawa Island had evolved from the polycarpic perennial on Taiwan Island via the monocarpic perennial in the Yaeyama Islands. Thus, the evolution of life histories could have taken at the level of local populations within a species.     

Prehistoric Introduction of Domestic Pigs onto the Okinawa Islands: Ancient Mitochondrial DNA Evidence

Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes; 574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites) are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa islands in the early Yayoi-Heian period (1700–2000 BP), or earlier.     

A taxonomic study of the Rana narina complex, with description of three new species (Amphibia: Ranidae)

A morphometric and electrophoretic survey was conducted to examine taxonomic relationships among eight population samples of the Rana narina complex from the Ryukyu Archipelago of Japan and Taiwan. Five discrete morphotypes are differentiated, and these showed considerable genetic differentiation from each other. From the available information, each of the five morphotypes is judged to represent a species, and three are described as new. Rana utsunomiyaorum sp. nov. and R. supranarina sp. nov. are sympatric in Ishigakijima and Iriomotejima islands of the Yaeyama Group, and differ from the other members by having a shorter hindlimb. Rana utsunomiyaorum is the smallest in the complex, while R. supranarina is the largest. Rana amamiensis sp. nov . occurs on Amamioshima and Tokunoshima islands of the Amami Group and, like R. narina from Okinawajima of the Okinawa Group, has a long hindlimb; it differs from the latter species by having a larger body and relatively small tympanum. These two species differ from R. swinhoana from Taiwan by having a narrower disk on the third finger. A key to known species of the complex is given. Further, syslematics of the R. narina complex within Rana , body size in the two sympatric species, and sexual dimorphism found in this complex are discussed.     

Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands,the Ryukyu Archipelago,Japan

Aim Phylogeographical patterns in the Ryukyu Archipelago have been explained primarily by landbridge formation and the opening of two straits in the Pliocene, namely the Tokara and Kerama gaps. These old straits have been considered to be the barriers most likely to determine genetic boundaries. To test this, we conducted a molecular analysis of the herb Ophiorrhiza japonica. We discuss the causes of and processes involved in its phylogeographical structure and explore aspects of island separation other than the duration of the straits to explain genetic boundaries at the gaps. Location Ryukyu Archipelago, Japan. Methods Plants were collected from 40 localities in the archipelago and vicinity. Non‐coding regions of chloroplast DNA were sequenced. The genealogical relationships among haplotypes were estimated using a statistical parsimony network. To examine the phylogeographical structure, we compared two parameters of population differentiation, namely G_ST and N_ST, and conducted correlation analysis of genetic and geographical distances. Genetic boundaries were identified using Monmonier’s maximum difference algorithm. To test vicariance–dispersal hypotheses, that is, vicariance after migration via the Pliocene landbridge or over‐sea dispersal in the Pleistocene, molecular dating analysis was conducted. Results A statistical parsimony network revealed that the haplotypes from the Ryukyu Archipelago and northwards coalesce to one ancestral haplotype in Taiwan. A clear phylogeographical structure was observed: plants within the same population and populations in geographical proximity were phylogenetically close. A genetic boundary was recognized across the Kerama Gap, but not across the Tokara Gap. Dating analysis suggested that population divergence across the Kerama Gap occurred in the early to late Pleistocene. Main conclusions The statistical parsimony network suggests migration from Taiwan and northward range expansion in the archipelago. Based on the divergence time, over‐sea dispersal in the Pleistocene is likely, although migration via a Pliocene landbridge is not totally rejected. Negligible genetic differentiation across the Tokara Gap suggests recent over‐sea dispersal, possibly facilitated by the small geographical width of the gap. Conversely, the large genetic differentiation across the Kerama Gap is probably explained by the large geographical distance across it. The past splitting of a landbridge would have had a significant influence on population differentiation after a certain geographical distance was reached.     

Climate,host phylogeny and the connectivity of host communities govern regional parasite assembly

Aim

Identifying barriers that govern parasite community assembly and parasite invasion risk is critical to understand how shifting host ranges impact disease emergence. We studied regional variation in the phylogenetic compositions of bird species and their blood parasites (Plasmodium and Haemoproteus spp.) to identify barriers that shape parasite community assembly.

Location

Australasia and Oceania.

Methods

We used a data set of parasite infections from >10,000 host individuals sampled across 29 bioregions. Hierarchical models and matrix regressions were used to assess the relative influences of interspecies (host community connectivity and local phylogenetic distinctiveness), climate and geographic barriers on parasite local distinctiveness and composition.

Results

Parasites were more locally distinct (co‐occurred with distantly related parasites) when infecting locally distinct hosts, but less distinct (co‐occurred with closely related parasites) in areas with increased host diversity and community connectivity (a proxy for parasite dispersal potential). Turnover and the phylogenetic symmetry of parasite communities were jointly driven by host turnover, climate similarity and geographic distance.

Main conclusions

Interspecies barriers linked to host phylogeny and dispersal shape parasite assembly, perhaps by limiting parasite establishment or local diversification. Infecting hosts that co‐occur with few related species decreases a parasite's likelihood of encountering related competitors, perhaps increasing invasion potential but decreasing diversification opportunity. While climate partially constrains parasite distributions, future host range expansions that spread distinct parasites and diminish barriers to host shifting will likely be key drivers of parasite invasions.     

Repeated landmass reformation limits diversification in the widespread littoral zone mosquito Anopheles sundaicus sensu lato in the Indo‐Oriental Region

Southeast Asia harbours abundant biodiversity, hypothesized to have been generated by Pliocene and Pleistocene climatic and environmental change. Vicariance between the island of Borneo, the remaining Indonesian archipelago and mainland Southeast Asia caused by elevated sea levels during interglacial periods has been proposed to lead to diversification in the littoral zone mosquito Anopheles (Cellia) sundaicus (Rodenwaldt) sensu lato. To test this biogeographical hypothesis, we inferred the population history and assessed gene flow of A. sundaicus s.l. sampled from 18 populations across its pan‐Asian species range, using sequences from mitochondrial cytochrome c oxidase subunit 1 (CO1), the internal transcribed spacer 2 (ITS2) and the mannose phosphate isomerase (Mpi) gene. A hypothesis of ecological speciation for A. sundaicus involving divergent adaptation to brackish and freshwater larval habitats was also previously proposed, based on a deficiency of heterozygotes for Mpi allozyme alleles in sympatry. This hypothesis was not supported by Mpi sequence data, which exhibited no fixed differences between brackish and freshwater larval habitats. Mpi and CO1 supported the presence of up to eight genetically distinct population groupings. Counter to the hypothesis of three allopatric species, divergence was often no greater between Borneo, Sumatra/Java and the Southeast Asian mainland than it was between genetic groupings within these landmasses. An isolation‐with‐migration (IM) model indicates recurrent gene flow between the current major landmasses. Such gene flow would have been possible during glacial periods when the current landmasses merged, presenting opportunities for dispersal along expanding and contracting coastlines. Consequently, Pleistocene climatic variation has proved a homogenizing, rather than diversifying, force for A. sundaicus diversity.     

Conservation of biodiversity: a critical time for the hermatypic corals of Japan

Results of a long-term study of the taxonomy, distribution and abundance of the hermatypic corals of the Ryukyu Is. and mainland Japan indicate that the present high diversity is threatened by a quantitative and qualitative decrease in available habitat caused by Acanthaster planci predation and human-induced environmental deterioration. Ninety-eight sites were studied, allowing detailed comparison between the three main groups of the Ryukyu Is. (Yaeyama, Okinawa and Amami Groups) and seven principal coral regions of mainland Japan (Tanegashima, Amakusa Is., the Tosashimizu and Kushimoto regions, and the Shirahama, Izu and Tateyama Peninsulas). Within this area, 400 species have been recorded and 9 additional species are recorded from the literature, from additional localities, or with doubt, from the Ryukyu Is. In non-mutually exclusive distribution and abundance categories for the Ryukyu Is. and mainland Japan: 129 species are common in at least some Japanese localities; 24 are widely dispersed within the Indo-Pacific, but occur in small, perhaps disjunct populations in Japan; 149 are uncommon throughout their Indo-west Pacific distribution ranges including Japan; 38 are restricted to the Yaeyama Group where all but three are uncommon or rare; 69 purely reefal (Ryukyu Is.) species are rare; 17 are rare in the Ryukyu Is. but are relatively common in mainaland locations; and 8 species appear to be endemic to mainland Japan and adjacent Asian countries. Some 37% of all Japanese hermatypic corals are uncommon throughout their range in Japan and are at some risk of regional extinction, 29% of others are rare and at substantial risk as they occur only in very limited areas of high diversity or in species-specific refuges. These sites are dientified. Of the 8 endemic species, 5 are primarily restricted to species-specific refuges. These data indicate an unstable situation. At least one third of all Japanese hermatypic species will eventually be at risk if the present causes of diversity decrease are not remedied.     

Quaternary vicariance of tiger beetle,Cicindela chinensis,in Ryukyu,Japan, Taiwan and Korea–China

We show vicariance of Cicindela chinensis in Okinawa, Japan (differentiated within Japan) and Korea–China through construction of Bayesian inference trees by BEAST2. Calibration was done using an assumption of the MRCA expansion of C. chinensis at 1.55 Ma (=geologically obtained formative time of the Ryukyu islands) following the protocol of BEAUti. We derived substitution rates for mitochondrial COI (1.66%/m.y.) and nuclear 28SrRNA (0.109%/m.y.) of analyzed Cicindela. Cicindela ferriei is a sister of C. chinensis, and these two species differentiated from each other at ca. 3 Ma before the expansion of C. chinensis. However, they are not strongly differentiated between Amami‐Oshima and Tokuno‐shima, although they display different color. Vicariance at 1.55 Ma is also recognized between Cicindela batesi in Taiwan and Cicindela aurulenta and virgula in continental China. From the sequence data we obtained, it is also evident that C. c. okinawana recently colonized Ishigaki‐jima from Okinawa‐jima, as did C. batesi in Iriomote‐jima from Taiwan.