TCS haplotype network.

TCS haplotype network of 129 haplotypes found in R. crataegifolius (81 haplotypes in open circles) and R. takesimensis (48 haplotypes in closed circles). Dots indicate hypothetical missing intermediate haplotypes. The size of each circle is proportional to the relative haplotype frequency. Two major haplotype groups (A and B) of R. crataegifolius are shown.</p

Map of haplotypes found in <i>R</i>. <i>crataegifolius</i>.

Distribution of 81 haplotypes found in R. crataegifolius. The size of each circle is proportional to the population size. Different colored and patterned portions in each pie chart represent haplotype frequencies.</p

List of populations and number of individuals of <i>R</i>. <i>crataegifolius</i> and <i>R</i>. <i>takesimensis</i> sampled in this study.

For each population, haplotype and number of individuals in each haplotype are shown in parentheses.</p

Map of haplotypes found in <i>R</i>. <i>takesimensis</i>.

Distribution of each haplotype and its frequency found in R. takesimensis from Ulleung Island. The size of each circle is proportional to the population size. Different colored and patterned portions in each pie chart represent haplotype frequencies.</p

Neutrality and population expansion tests for <i>Rubus crataegifolius</i> and <i>R</i>. <i>takesimensis</i>.

Neutrality and population expansion tests for Rubus crataegifolius and R. takesimensis.</p

Summary of genetic diversity statistics of the continental progenitor <i>R</i>. <i>crataegifolius</i> and the insular derivative <i>R</i>. <i>takesimensis</i> based on chloroplast DNA noncoding sequences.

Summary of genetic diversity statistics of the continental progenitor R. crataegifolius and the insular derivative R. takesimensis based on chloroplast DNA noncoding sequences.</p

Summary of analyses of molecular variance (AMOVA) in <i>R</i>. <i>crataegifolius</i> and <i>R</i>. <i>takesimensis</i>, showing degree of freedom (<i>df</i>), sum of squares (SS), variance components, and the total variance contributed by each component (%) and its associated significance (<i>n</i> = 1,023 permutations).

Summary of analyses of molecular variance (AMOVA) in R. crataegifolius and R. takesimensis, showing degree of freedom (df), sum of squares (SS), variance components, and the total variance contributed by each component (%) and its associated significance (n = 1,023 permutations).</p

Mismatch analysis.

Mismatch distribution analysis inferring the demographic history of R. crataegifolius (a) and R. takesimensis (b). The x-axis represents the number of pairwise differences, while the y-axis represents the relative frequencies of pairwise comparisons.</p

Phylogenetic tree.

Strict consensus tree of 605 equally most parsimonious trees (TL = 296, CI = 0.67, and RI = 0.96), showing the relationship between the continental progenitor R. crataegifolius (in black) and the insular derivative R. takesimensis (in blue).</p

Data_Sheet_1_Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation.docx

Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.</p