Sexual system reconstruction of aquatic families.

<p>Bars at nodes represent the ancestrial states. Blue lines represent anemophilous pollination modes. Red lines represent intermediate and true hydrophilous pollination modes. <i>Potamogeton</i> and <i>Callitriche</i> have both colors of lines.</p

The correlations of life form, sexual system, pollination mode and marine angiosperms.

<p>Red words represent the four requisites of marine angiosperms.</p

Pollination mode reconstruction of aquatic families.

<p>Bars at nodes represent the ancestrial states. Deep blue words and lines represent marine genera.</p

Chloroplast DNA Phylogeography Reveals Repeated Range Expansion in a Widespread Aquatic Herb <i>Hippuris vulgaris</i> in the Qinghai-Tibetan Plateau and Adjacent Areas

<div><p>Background</p><p>The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown.</p> <p>Methodology and Principal Findings</p><p>We studied the phylogeography and demographic history of the widespread aquatic herb <i>Hippuris vulgaris</i> from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of <i>H</i>. <i>vulgaris</i>. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in <i>H</i>. <i>vulgaris</i>, we found a very high level of population differentiation (<i>G</i>_ST = 0.819) but the phylogeographical structure remained obscure (<i>N</i>_ST = 0.853><i>G</i>_ST = 0.819, <i>P</i>>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM).</p> <p>Conclusions/Significance</p><p>This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.</p> </div

Phylogeny of the eight chloroplast haplotypes (A–H) detected in <i>H</i>. <i>vulgaris</i>.

<p>(<b>A</b>) Neighbor-joining clustering of the eight chloroplast haplotypes. Numbers above branches indicate the bootstrap values (>50% are shown) for NJ (Left, 1,000 replicates) and Bayesian analyses (Right). HPG: Haplogroup; (<b>B</b>) 95% plausible network of the eight chloroplast haplotypes. Each solid line represents one mutational step that interconnects two haplotypes for which parsimony is supported at the 95% level. The distribution of a certain haplotype is marked in the circles. The small open circle indicates an inferred intermediate haplotype not deteched in this investigation. The size of each circle is proportional to the haplotype frequency.</p

Bayesian analyses of the divergent time (Myr) between chloroplast DNA haplotypes.

<p>Bayesian analyses of the divergent time (Myr) between chloroplast DNA haplotypes.</p

Collection localities (population codes as in Table 1) and the geographical distributions of eight chloroplast haplotypes (A–H) found in 47 populations of <i>H</i>. <i>vulgaris</i> in the Qinghai-Tibetan Plateau and neighboring areas.

<p>Collection localities (population codes as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060948#pone-0060948-t001" target="_blank">Table 1</a>) and the geographical distributions of eight chloroplast haplotypes (A–H) found in 47 populations of <i>H</i>. <i>vulgaris</i> in the Qinghai-Tibetan Plateau and neighboring areas.</p

Zhao et al. Ranunculus Dataset.zip

Data for the paper Zhao et al., 'RNA-seq of Ranunculus sceleratus and identifying orthologous genes of four Ranunculus species'. Submitted to Frontiers in Plant Sciences.<br><br>File 'Unigenes of Ranunculus sceleratus.fa' includes all the unigenes assembled using program Trinity and TGICL.<br><br>Folder '1. Phylogenetic analyses' lists the ITS sequences and cpDNA sequences of four Ranunculus species, which was used for phylogenetic analyses.<br><br>Folder '2. All the orthologous clusters' lists sequences of the 3455 putative orthologous clusters identified using program OrthoMCL.<br><br>Folder '3. Orthologous clusters after filters' lists sequences of the 884 orthologous clusters after filtering the possible paralogous clusters.<br><br><br>Species name abbreviation:<br>Rbu = Ranunculus bungei<br>Rch = R. cantoniensis<br>Rsc = R. sceleratus <br>Rta = R. brotherusii <br><br>If you have any question, please contact Ling-Yun Chen ([email protected])

Mismatch distribution analyses and estimation of expansion time.

<p>Mismatch distribution analyses and estimation of expansion time.</p

Details of sample locations, samples size (<i>N</i>), haplotypes and haplotype diversity (<i>h</i>) of 47 populations of <i>Hippuris vulgaris</i> surveyed for DNA sequence variation at four combined chloroplast regions.

<p>Details of sample locations, samples size (<i>N</i>), haplotypes and haplotype diversity (<i>h</i>) of 47 populations of <i>Hippuris vulgaris</i> surveyed for DNA sequence variation at four combined chloroplast regions.</p