distribution points used in MAXENT

This file covers Atraphaxis frutescens’distribution coordinates which we obtained by a GPS in the field. The file can be used for MAXENT directly

Haplotype sequences for Atraphaxis frutescens

This file covers all the sequences (psbK-psbI, psbB-psbH) used in the publication for analyses.H1-H10 are the names for 10 haplotypes used in the publication.They were sequenced using an ABI 3730 automated sequencer by Shanghai SBS, Biotech Ltd., China.And we aligned using CLUSTAL_W program. H1-H10 sequences have been deposited in GenBank databases (KM452785-KM452796). Fagopyrum esculentum is an outgroup and the sequence is from GenBank databases (EU254477)

Direct Particle Tracking Observation and Brownian Dynamics Simulations of a Single Nanoparticle Optically Trapped by a Plasmonic Nanoaperture

Optical trapping using plasmonic nanoapertures has proven to be an effective means for the contactless manipulation of nanometer-sized particles under low optical intensities. These particles have included polystyrene and silica nanospheres, proteins, coated quantum dots and magnetic nanoparticles. Here we employ fluorescence microscopy to directly observe the optical trapping process, tracking the position of a polystyrene nanosphere (20 nm diameter) trapped in water by a double nanohole (DNH) aperture in a gold film. We show that position distribution in the plane of the film has an elliptical shape. Comprehensive simulations are performed to gain insight into the trapping process, including of the distributions of the electric field, temperature, fluid velocity, optical force, and potential energy. These simulations are combined with stochastic Brownian diffusion to directly model the dynamics of the trapping process, that is, particle trajectories. We anticipate that the combination of direct particle tracking experiments with Brownian motion simulations will be valuable tool for the better understanding of fundamental mechanisms underlying nanostructure-based trapping. It could thus be helpful in the development of the future novel optical trapping devices

Phylogeographic History of <i>Atraphaxis</i> Plants in Arid Northern China and the Origin of <i>A</i>. <i>bracteata</i> in the Loess Plateau

<div><p>In China, species of <i>Atraphaxis</i> (Polygonaceae) primarily inhabit arid zones across temperate steppe and desert regions. The complex geologic history (e.g., expansion of deserts) and extreme climate shifts of the region appear to have played an important role in shaping the phylogeography of <i>Atraphaxis</i>. The present study focuses on species-level phylogeographic patterns of <i>Atraphaxis</i> in China, with the goal of determining the impact of past environmental changes, in northern China, on the evolutionary history of the genus. Five hundred and sixty-four individuals distributed among 71 populations of 11 species of <i>Atraphaxis</i> from across the geographic range of the genus were studied using sequence data from two plastid spacers, <i>psb</i>K-<i>psb</i>I and <i>psb</i>B-<i>psb</i>H. The results demonstrate that most chloroplast haplotypes are species-specific, except for some present among widespread species. The phylogeny of <i>Atraphaxis</i> was well structured, and molecular dating analyses suggest that the main divergence events occurred during the late Pliocene and Pleistocene (5.73–0.03 million years ago). The statistical dispersal-vicariance analysis (S-DIVA) results provide evidence that phylogeographic patterns for the genus were characterized by both vicariance events and regional dispersal. The presented data suggest that the rapid expansion of deserts and climatic changes in northern China during the late Pliocene and Pleistocene have driven the diversification and spread of <i>Atraphaxis</i> in the region. The expansion of the Tengger Desert provided appropriate conditions for the origin of <i>A</i>. <i>bracteata</i>. Additionally, a contact zone in the north of the Hexi Corridor was identified as having played a significant role as a migratory route for species in adjacent areas.</p></div

Bayesian phylogenetic tree for <i>Atraphaxis</i> based on combined cpDNA matrix.

<p>Numbers above branches indicate range of divergence time in millions of years (Ma), and posterior probabilities larger than 0.95 are shown. Clades 1–5 denote five main clades based on identified haplotypes. Haplotype numbers refer to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163243#pone.0163243.t001" target="_blank">Table 1</a>. Colors of each species are consistent with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163243#pone.0163243.g002" target="_blank">Fig 2</a>.</p

Details of <i>Atraphaxis</i> populations in study, sample sizes and cpDNA haplotypes observed.

<p>Details of <i>Atraphaxis</i> populations in study, sample sizes and cpDNA haplotypes observed.</p

Results of Tajima’s <i>D</i> and Fu’s <i>Fs</i> tests and mismatch analyses for 11 species of <i>Atraphaxis</i>.

<p>Results of Tajima’s <i>D</i> and Fu’s <i>Fs</i> tests and mismatch analyses for 11 species of <i>Atraphaxis</i>.</p

Historical demography for each species and total samples inferred from cpDNA sequences.

<p>(A) Mismatch distribution analysis for each species and total samples. (B) Extended Bayesian skyline plot (EBSP) analyses for each species and total samples, showing effective population size as a function of time.</p

Median-joining network of 32 haplotypes of <i>Atraphaxis</i> sampled in northern China.

<p>Each circle (H1-H32) represents a unique haplotype, with circle size reflecting haplotype frequencies. Black circles indicate potentially unsampled or extinct haplotypes. The colors within each species are consistent in all Figures.</p

Sampling locations and distributions of populations in 11 species of <i>Atraphaxis</i> in arid northern China.

<p>Population codes are consistent with population names in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163243#pone.0163243.t001" target="_blank">Table 1</a>.</p