Visualization 1: Low-coherence wavelength shifting interferometry for high-speed quantitative phase imaging

Boar sperm motions. Originally published in Optics Letters on 01 August 2016 (ol-41-15-3431

Media 1: Spectral modulation interferometry for quantitative phase imaging

Originally published in Biomedical Optics Express on 01 February 2015 (boe-6-2-473

Divergence time estimates for Asparagales, based on four cpDNA genes (atpB, matK, ndhF and rbcL).

<p>The maximum clade credibility tree from the divergence times estimated with BEAST. The 95% highest posterior density (HPD) estimates for each well-supported clade are represented by bars. Numbers at nodes are fossil calibration points: 93 Ma, age for the most recent common ancestor (MRCA) of extant Asparagales; 83.5 Ma, age for the MRCA of Zingiberales; 106.5±5.5 (93–120) Ma, age for the root of the tree (The upper age constraint of 120 Ma corresponds to the oldest known Monocot fossil). Detailed descriptions see the section of material and methods in text.</p

Sampling and age estimates for families and subfamilies of Asparagales.

<p>Sampling and age estimates for families and subfamilies of Asparagales.</p

Vouchers with GenBank accession number for taxa included in this study.

<p>Vouchers with GenBank accession number for taxa included in this study.</p

Consensus tree from Bayesian analysis of the four combined cpDNA datasets.

<p>The 50% majority rule consensus phylogram from partitioned Bayesian analysis of a combined matrix of 284 accessions and 6699 bp from four plastid genes: <i>atpB</i>, <i>matK</i>, <i>ndhF</i> and <i>rbcL</i>. The 400,000 generations before the point when the SDSF permanently fell below 0.01 (0.0016 at termination) were discarded as burn-in. Three types of support (bootstrap percentages for parsimony analyses with equal weights [EW]/successive approximations weighting [SW]/posterior probabilities for Bayesian analysis [PP]) are indicated on each branch. Major clades are named following the subfamily classification of three expanded asparagalean families proposed by Chase et al. (2009) and APG III (2009). The tree is subdivided as follows: <b>part A</b>, Asparagaceae and subfamilies; <b>part B</b>, Amaryllidaceae and Xanthorrhoeaceae and their subfamilies plus Xeronemataceae; <b>part C</b>, the basal nodes of Asparagales and outgroups (non-Asparagales taxa).</p

Statistics for the four genes analysed in this study.

<p>Statistics for the four genes analysed in this study.</p

Neighbour net for Asparagales and outgroups.

<p>Neighbour net for Asparagales and outgroups with uncorrected p-distances, based on 284 species using four plastid genes: <i>atpB</i>, <i>matK</i>, <i>ndhF</i>, and <i>rbcL</i>. Families and subfamilies circumscriptions follow APG III (2009) and Chase et al. (2009) are colour-coded. Scale bar, 0.01.</p

Scaffolds

The Scaffolds.zip file is a compressed zip file containing a directory with the scaffolds corresponding to the microsatellite loci. The Scaffolds directory contains the sequence of the scaffolds that had microsatellites identified on them. The files are bz2 compressed zip files. The unzipped file is a fasta file with all of the scaffolds corresponding to the loci in the LocusInfo directory

GCF_000004515.3_V1.1_genomic

The script "BLAST_to_Coding_SSR.R” (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS"). This file is the gff file needed for the script