Compressed archive of social amoeba population genetic data

Data showing molecular evolutionary differences between (1) genes with chimera-biased expression vs. genomic background, and (2) genes expressed in pre-spore cells vs. altruistic pre-stalk cells in wild-isolated strains of Dictyostelium discoideum social amoebas

Genomic sequence variation in wild social amoebas

Archive of the variant call format files used to generate the population genetic data

Triplet repeat density in <i>D. discoideum</i> exons.

<p>The inset shows the frequency distribution of triplet-repeat loci in exons of <i>D. discoideum</i>, grouped by the number of uninterrupted repeat units. The main figure histogram compares density of such exon repeats with other taxa, which were scored for triplet repeat of length 4 or higher in exons <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046150#pone.0046150-Toth1" target="_blank">[39]</a>. The <i>D. discoideum</i> data include all loci with 5 or more repeats and is therefore slightly conservative.</p

Average Gene diversity (expected heterozygosity) of the 8 triplet microsatellite loci in the multiple-repeat sample, divided by subpopulation.

<p>The error bars mark the bootstrap 95% confidence intervals, estimated using 1000 bootstrap samples of individuals with replacement.</p

Gene diversity (expected heterozygosity) of microsatellites in the multiple-repeat and clone-rich samples.

<p>White bars show 8 microsatellites genotyped in the multiple-repeat sample, from the known genes <i>dimA</i>, <i>yakA</i> and <i>atg1</i>. Grey bars show the 8 microsatellite loci from the clone-rich sample of 316 clones. Error bars are 95% confidence intervals, estimated using 1000 bootstrap samples of individuals with replacement.</p

Amino acid diversity of the genes <i>yakA</i>, <i>arg1</i> and <i>dimA</i>.

<p>The average amino acid diversity (or the average heterozygosity per amino acid position) was calculated for <i>D. discoideum</i> for <i>yakA</i>, <i>arg1</i> and <i>dimA</i> loci using only variation in numbers of amino acids in the assayed repeats. The value of Drosophila <i>Adh</i> locus is from Kreitman <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046150#pone.0046150-Kreitman1" target="_blank">[40]</a> and Hartl <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046150#pone.0046150-Hartl1" target="_blank">[41]</a>, and values of Human <i>HLA-A</i> and <i>HLA-B</i> loci are from Hedrick <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046150#pone.0046150-Hedrick1" target="_blank">[27]</a>, both based on substitutions.</p

The frequency distribution of genotypes of eight coding triplet repeats from the gene <i>dimA, yakA,</i> and <i>atg1</i>.

<p>These were genotyped from a sample of 115 clones isolated from various North American locations.</p

A Sample Bioverse-Predicted Interaction Network for Defense Proteins and Their Direct Neighbors

<p>The symbols are colored to indicate some of the major GO categories under “molecular function.” We draw a cross over the symbol for an NH gene. Rectangles indicate proteins that are manually classified as being R-genes. They appear on genes that are not colored as defense, because some genes have multiple functions, not because of an annotation error. The white circles with green outline are unannotated genes that might also belong to this network, at a lower confidence.</p

Distribution of Substitutions per Silent Site (Ks) for Homolog Pairs in Segmental, Tandem, and Background Duplications

<p>In (A), contributions from the recent segmental duplication on Chromosomes 11 and 12 are colored in red. The tandem duplication data are shown on two different scales, one to emphasize the magnitude of the zero peak (B) and another to highlight the exponential decay (C). Background duplications are shown in (D).</p

Functional Classifications from GO, Focused on Plant-Specific Categories Outlined by Gramene

<p>(A) compares predicted genes from <i>Arabidopsis</i> and Beijing <i>indica</i>. (B) compares predicted genes from Beijing <i>indica</i> with nr-KOME cDNAs. We ignore categories with less than 0.1% of the genes.</p