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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 conclusionsThe 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.

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Background and Aims The genus Asarum sect. Heterotropa (Aristolochiaceae) probably experienced rapid diversification into 62 species centred on the Japanese Archipelago and Taiwan, providing an ideal model for studying island adaptive radiation. However, resolving the phylogeny of this plant group using Sanger sequencing-based approaches has been challenging. To uncover the radiation history of Heterotropa, we employed a phylogenomic approach using double-digested RAD-seq (ddRAD-seq) to yield a sufficient number of phylogenetic signals and compared its utility with that of the Sanger sequencing-based approach. Methods We first compared the performance of phylogenetic analysis based on the plastid matK and trnL–F regions and nuclear ribosomal internal transcribed spacer (nrITS), and phylogenomic analysis based on ddRAD-seq using a reduced set of the plant materials (83 plant accessions consisting of 50 species, one subspecies and six varieties). We also conducted more thorough phylogenomic analyses including the reconstruction of biogeographic history using comprehensive samples of 135 plant accessions consisting of 54 species, one subspecies, nine varieties of Heterotropa and six outgroup species. Key Results Phylogenomic analyses of Heterotropa based on ddRAD-seq were superior to Sanger sequencing-based approaches and resulted in a fully resolved phylogenetic tree with strong support for 72.0–84.8 % (depending on the tree reconstruction methods) of the branches. We clarified the history of Heterotropa radiation and found that A. forbesii, the only deciduous Heterotropa species native to mainland China, is sister to the evergreen species (core Heterotropa) mostly distributed across the Japanese Archipelago and Taiwan. Conclusions The core Heterotropa group was divided into nine subclades, each of which had a narrow geographic distribution. Moreover, most estimated dispersal events (22 out of 24) were between adjacent areas, indicating that the range expansion has been geographically restricted throughout the radiation history. The findings enhance our understanding of the remarkable diversification of plant lineages in the Japanese Archipelago and Taiwan.

An antitropical distribution represents an intriguing disjunction, in which a given species or sister lineages occupy regions north and south of the tropics but are absent from the intervening areas. Solenogyne mikadoi endemic to the Ryukyu Archipelago is regarded as an Australian element. Testing the phylogenetic relationship with Australian congeners and discussing the onset timing and causes of the disjunction would potentially enhance the understanding of antitropical distribution. A nuclear ribosomal DNA phylogeny was reconstructed using Bayesian and most parsimonious criteria with allied genera. Solenogyne was monophyletic and clustered with Lagenophora huegelii endemic to Australia, indicating the antitropical distribution and Australian origin of Solenogyne. Multispecies coalescent analysis based on nuclear ribosomal DNA and chloroplast DNA indicated the divergence of S. mikadoi and Australian congeners in the Plio-Pleistocene. Phylogenetic network analyses suggested that the ancestral lineage of S. mikadoi first colonized the southernmost island in the archipelago and then dispersed northward. The migration to the archipelago likely followed the flourishing of Solenogyne in open vegetation communities that radiated in south-eastern Australia during the late Pliocene. This disjunction might arise through long-distance dispersal across the tropics or, alternatively, through extinction in the tropics as a result of unsuitably high temperatures during climate oscillation and/or competitions from diverse tropical flora surviving since the early Tertiary.

Equatorward contraction and re‐expansion during and after the last glacial maximum has been reported for temperate plants, but little is known about latitudinal shifts of tropical plants in insular Asia. We used molecular methods to test the post‐glacial migration hypothesis for Begonia fenicis at the northern limit of tropical insular Asia, namely, the northern Philippines, southern Taiwan and the southern Ryukyus of Japan. Based on internal transcribed spacer sequences, analyses of phylogeographical structure suggested long‐term survival of island populations and negated recent northward migration; demographic analyses indicated spatial expansion in the early Pleistocene and subsequent stable demography. Based on nuclear microsatellites, Bayesian clustering and other spatial analyses indicated inter‐island differentiation, and coalescent analysis of migration indicated the lack of inter‐island migration during and after the last glacial maximum. Our results refuted the postglacial migration hypothesis for B. fenicis and suggest in situ survival through the last glacial maximum. The stable historical distribution and demography are probably attributable to the Kuroshio Current bringing warm and humid air, which washed these islands even during the glacial periods. Additionally, because these are low islands, absence of competition with montane plants descending to the lowlands during cooler periods may have mitigated the influence of temperature lowering and facilitated their survival. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 305–325.

Foliar flavonoids of Crossostephium chinense in Japan and Taiwan were isolated and further characterized. Eighteen flavonoid aglycones, luteolin, apigenin, hispidulin, chrysoeriol, 5,7,4′-trihydroxy-6,3′,5′-trimethoxyflavone, jaceosidin, cilsimaritin, quercetin 3-methyl ether, axillarin, chrysosplenol-D, cirsiliol, apometzgerin, 5,7,3′-trihydroxy-6,4′,5′-trimethoxyflavone, luteolin 3′,4′-dimethyl ether, cirsilineol, eupatilin, nepetin and 5,7,3′,4′-tetrahydroxy-6,5′-dimethoxyflavone, were identified by UV, 1H and 13C NMR spectroscopic, LC-MS and HPLC comparisons with authentic samples. The compounds existed on the leaf surface. Four flavonoid glycosides, quercetin 3,7-di- O-glucoside, quercetin 3- O-rutinoside, luteolin 7- O-glucoside and apigenin 7- O-rutinoside, were also isolated as the intracellular flavonoids. It was shown by HPLC survey that variation of the species’ flavonoids occurs among the collection sites.

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