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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. [ABSTRACT FROM AUTHOR]

Highlights • We constructed a high-density genetic linkage map of bronze loquat by using SNP markers generated by RAD-Seq. • The map of bronze loquat consisted of 960 loci including 793 SNPs, 166 SSRs (98 apple, 8 loquat and 60 pear SSRs), and the loquat canker resistance gene Pse-a. • This map covered 17 linkage groups over a total length of 1707.4 cM with an average distance of 1.78 cM between markers. • The High-density genetic linkage map using SNP markers can be applicable for studies of the identification of QTLs of an agricultural trait. Abstract We constructed a high-density genetic linkage map of bronze loquat (Eriobotrya deflexa) for a three-way cross of loquat (Eriobotrya japonica) × (loquat × bronze loquat) by using single nucleotide polymorphism (SNP) markers generated by RAD-Seq, with the combination of simple sequence repeat (SSR) markers, which have been used in the previous study. The map of bronze loquat ('Taiwan loquat No. 1') consisted of 960 loci including 793 SNPs, 166 SSRs (98 apple, 8 loquat and 60 pear SSRs), and the loquat canker resistance gene Pse-a. This map covered 17 linkage groups over a total length of 1707.4 cM with an average distance of 1.78 cM between markers. The number of linkage groups corresponded to the basic chromosome number (n = 17). The analysis of the markers that can be anchored to apple draft genome showed that almost all loquat linkage groups were aligned to the apple draft genome. The constructed map will enable us to determine the location of quantitative trait loci and genes of interest, and to analyze genome synteny in the tribe Pyreae, subfamily Spiraeoideae of the family Rosaceae. [ABSTRACT FROM AUTHOR]