Geographical distributions of the 34 sampled populations used in this study.

<p>Detailed information on the populations is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091836#pone.0091836.s004" target="_blank">Table S1</a>. Pie charts suggest the STRUCTURE-derived ancestry of each population based on the coloring used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091836#pone-0091836-g003" target="_blank">Figure 3</a>.</p

STRUCTURE analysis of <i>Ipomoea pes-caprae</i> populations based on 7 nuclear markers.

<p>Vertical bars represent the membership coefficients (Q) of individual plants when K = 3. The horizontal axes correspond to the regional grouping of populations. Left to right: subsp. <i>pes-caprae</i>, Indian Ocean, West Pacific, East Pacific, West Atlantic and East Atlantic regions. Numbers on the upper side designate the population numbers as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091836#pone-0091836-g001" target="_blank">Figure 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091836#pone.0091836.s004" target="_blank">Table S1</a>.</p

Number of migrants per generation (Nm) between different regional populations.

<p>Nm were calculated by a Bayesian method implementation in MIGRATE-N. Regional populations used are East Pacific (EP), West Atlantic (WA), East Atlantic (EA), Indian Ocean (IO), and West Pacific (WP).</p

Long-Distance Dispersal by Sea-Drifted Seeds Has Maintained the Global Distribution of <i>Ipomoea pes-caprae</i> subsp. <i>brasiliensis</i> (Convolvulaceae)

<div><p><i>Ipomoea pes-caprae</i> (Convolvulaceae), a pantropical plant with sea-drifted seeds, is found globally in the littoral areas of tropical and subtropical regions. Unusual long-distance seed dispersal has been believed to be responsible for its extraordinarily wide distribution; however, the actual level of inter-population migration has never been studied. To clarify the level of migration among populations of <i>I. pes-caprae</i> across its range, we investigated nucleotide sequence variations by using seven low-copy nuclear markers and 272 samples collected from 34 populations that cover the range of the species. We applied coalescent-based approaches using Bayesian and maximum likelihood methods to assess migration rates, direction of migration, and genetic diversity among five regional populations. Our results showed a high number of migrants among the regional populations of <i>I. pes-caprae</i> subsp. <i>brasiliensis</i>, which suggests that migration among distant populations was maintained by long-distance seed dispersal across its global range. These results also provide strong evidence for recent trans-oceanic seed dispersal by ocean currents in all three oceanic regions. We also found migration crossing the American continents. Although this is an apparent land barrier for sea-dispersal, migration between populations of the East Pacific and West Atlantic regions was high, perhaps because of trans-isthmus migration via pollen dispersal. Therefore, the migration and gene flow among populations across the vast range of <i>I. pes-caprae</i> is maintained not only by seed dispersal by sea-drifted seeds, but also by pollen flow over the American continents. On the other hand, populations of subsp. <i>pes-caprae</i> that are restricted to only the northern part of the Indian Ocean region were highly differentiated from subsp. <i>brasiliensis</i>. Cryptic barriers that prevented migration by sea dispersal between the ranges of the two subspecies and/or historical differentiation that caused local adaptation to different environmental factors in each region could explain the genetic differentiation between the subspecies.</p></div

Parsimony networks of haplotypes of <i>Ipomoea pes-caprae</i> from 7 nuclear loci.

<p>Each circle shows different haplotypes and each color represents haplotypes from different geographical regions. Red represents haplotypes of subsp. <i>pes-caprae</i>. Brown, orange, yellow, green, and blue represent subsp. <i>brasiliensis</i> from the Indian Ocean, West Pacific, East Pacific, West Atlantic, and East Atlantic, respectively.</p

Summary of polymorphisms for the studied loci.

<p>Number of polymorphism (K), Number of haplotypes (H), Haplotype diversity (Hd), Nucleotide diversity of all sites (πtotal), that of noncoding regions (πnc), synonymous (πs) and nonsynonymous sites (πa) calculated by DnaSP.</p><p>* Suggest the data was obtained from a previous study (Miryeganeh et al. (in press)).</p

Bayesian estimates of genetic diversity (θ), Migration rates (M) and number of migrants per generation (Nm) obtained by MIGRATE-N.

<p>WA: West Atlantic, EA: East Atlantic, IO: Indian Ocean, WP: West Pacific, EP: East Pacific. θ = 4 Neµ, where Ne is the effective population size and µ is the mutation rate per site per generation. M = m/µ, where m is the rate of migration for each locus. Nm is number of migrants per generation (Nm = Mθ/4).</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

Mitotic metaphase chromosome plates of <i>Meehania urticifolia</i> and <i>Glechoma</i> species stained with DAPI.

<p><b>(A)</b><i>Meehania urticifolia</i> (Gapyeong, Korea). <b>(B)</b> <i>Glechoma grandis</i> (Tottori, Japan). <b>(C)</b> <i>G</i>. <i>hederacea</i> (Perchtoldsdorf, Austria). <b>(D)</b> <i>G</i>. <i>hederacea</i> (Katowice, Poland). <b>(E)</b> <i>G</i>. <i>hederacea</i> (Vienna, Austria). <b>(F)</b> <i>G</i>. <i>hederacea</i> (Lilaste, Latvia). <b>(G)</b> <i>G</i>. <i>hirsuta</i> (Leopoldsberg, Austria). <b>(H)</b> <i>G</i>. <i>hirsuta</i> (Perchtoldsdorf, Austria). <b>(I)</b> <i>G</i>. <i>longituba</i> (Hubei, China). <b>(J)</b> <i>G</i>. <i>longituba</i> (Munsan, Korea). Scale bars = 5 um.</p

Phylogenetic trees derived from maximum likelihood analysis of ITS (A) and 5S rDNA NTS (B) sequences.

Shown are cladograms (above) with bootstrap support values > 50% and, below, phylograms (topology only) with scale bars (substitutions per site). Numbers after species names refer to different accessions (Table 1) and to clone numbers (after dash). Arrows in (B) indicate two monomer types.</p