Evolutionary significance of relocated γ duplicates.

<p>(A) Comparison of Ks among γ, relocated γ and transposed duplicates. (B) Comparison of Ka/Ks among γ, relocated γ and transposed duplicates. (C) Comparison of expression divergence among γ, relocated γ and transposed duplicates. (D) Comparison of gene regulation divergence among γ, relocated γ and transposed duplicates.</p

Functional comparison of different origins of duplicates.

<p>(A) Clustering of functional profiles. (B) Comparison of fold enrichment for essential genes. (C) Comparison of fold enrichment for the genes involved in protein-protein interactions (PPIs).</p

Different retention rates of dispersed duplicates during the evolution of core eudicots.

<p>(A) Phylogenetic relationships between <i>Arabidopsis thaliana</i> and its outgroups used for estimating the epochs (ages) of dispersed duplicates according to colinearity conservation. (B) Retention rates of <i>Arabidopsis thaliana</i> dispersed duplicates in different epochs. Abbreviations: At: <i>Arabidopsis thaliana</i>; Al: <i>Arabidopsis lyrata</i>; Br: <i>Brassica rapa</i>; Cp: <i>Carica papaya</i>; Tc: <i>Theobroma cacao</i>; Pt: <i>Populus trichocarpa</i>; Vv: <i>Vitis vinifera</i>; St: <i>Solanum tuberosum</i>; Os: <i>Oryza sativa</i>. Dispersed duplicates created after At-Br divergence were named transposed duplicates, while those created between At-Pt and At-St divergence were named relocated γ duplicates. (C) Phylogenetic relationships between <i>Lotus japonicus</i> and its outgroups used for estimating the epochs (ages) of dispersed duplicates according to colinearity conservation. (D) Retention rates of <i>Lotus japonicus</i> dispersed duplicates in different epochs. Abbreviations: Lj: <i>Lotus japonicas</i>; Mt: <i>Medicago truncatula</i>; Gm: <i>Glycine max</i>; Md: <i>Malus x domestica</i>; Pt: <i>Populus trichocarpa</i>; At: <i>Arabidopsis thaliana</i>; Vv: <i>Vitis vinifera</i>; St: <i>Solanum tuberosum</i>; Os: <i>Oryza sativa</i>.</p

Comparison of Ks distributions among WGD, local and dispersed duplicates in the investigated core eudicot genomes.

<p>For <i>Glycine max</i>, <i>Solanum tuberosum</i> and <i>Malus x domestica</i> whose genomes are large and recent duplicates are rampant, a second plot is provided to show the right tails of Ks distributions.</p

Supplemental Figures

This file includes three supplemental figures which are related to the paper. The figure legends are given below each figure

Supplemental Tables

This file includes four supplemental tables which are relevant to the paper. The supplemental table 1 lists the locus name, GenBank accession number, primer sequence and annealing temperature for all loci studied in this research. Supplemental table 2 is about the diversities revealed in the pair wise comparison including extended and single deletion, insertion, SNP, polymorphic sites, and polymorphic base pairs. Supplemental table 3 is about SNPs, polymorphic sites, and polymorphic base pairs between A and D ancestral genomes. Supplemental table 4 is about diversities revealed in the three way comparison including extended and single deletion, insertion, SNP, polymorphic sites, and polymorphic base pairs

Supplemental Material for Kong et al., 2018

File S1 contains genotypes for the bin map. File S2 contains genotypes for the original map. File S3 contains the genomic positional information for bin markers. File S4 and S5 contain phenotypes from 2011 and 2012 respectively. Supplemental tables are included in the docx

Multi-Phase US Spread and Habitat Switching of a Post-Columbian Invasive, <i>Sorghum halepense</i>

<div><p>Johnsongrass (<i>Sorghum halepense</i>) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimized Neighbor-Joining tree, pairwise FST, mismatch analysis, principle coordinate analysis, Tajima’s D, Fu’s F and Bayesian clusterings of population structure. Evidence indicates two geographically distant introductions of divergent genotypes, which spread across much of the US in <200 years. Based on geophylogeny, gene flow patterns can be inferred to have involved five phases. Centers of genetic diversity have shifted from two introduction sites separated by ~2000 miles toward the middle of the range, consistent with admixture between genotypes from the respective introductions. Genotyping provides evidence for a ‘habitat switch’ from agricultural to non-agricultural systems and may contribute to both Johnsongrass ubiquity and aggressiveness. Despite lower and more structured diversity at the invasion front, Johnsongrass continues to advance northward into cooler and drier habitats. Association genetic approaches may permit identification of alleles contributing to the habitat switch or other traits important to weed/invasive management and/or crop improvement.</p></div

Multi-Phase US Spread and Habitat Switching of a Post-Columbian Invasive, <i>Sorghum halepense</i> - Fig 2

<p><b>(a)</b> Pairwise comparisons of Nei’s distances (net and raw distances) among (lower/upper diagonal) and within (along diagonal) <i>Sorghum halepense</i> populations. <b>(b)</b> Pairwise comparisons of Fst among populations. Populations diverge as they get farther away from GA and TX. The two progenitor genotypes <i>S</i>. <i>propinquum</i>, <i>S</i>. <i>bicolor</i> and the laboratory standard <i>S</i>. <i>halepense</i> are grouped as PBH.</p

Contingency table showing observed frequency of <i>Sorghum halepense</i> accessions belonging to each genetic cluster, found in each habitat type (Χ² = 121.79; df = 12; P < 0.0001).

<p>Contingency table showing observed frequency of <i>Sorghum halepense</i> accessions belonging to each genetic cluster, found in each habitat type (Χ² = 121.79; df = 12; P < 0.0001).</p