Figure_1b_tree

Newick file for figure 1b. Neighbor-joining tree of 502 sorghum accessions for 265,487 SNP

Figure_S4b_tree

Newick file for figure S4b. Neighbor-joining tree of 502 sorghum accessions for 194,852 SNPs with MAF>=0.02 and missing rate<=50

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

BAPS6 geographical clustering using Voronoi tesellations and bar representations of genotypes at three K values based on population averages (K = 2, 5, 15).

<p>State boundaries overlaid for K = 15 for visual guidance. Clustering based on individual genotypes (lower bars) is included for K = 15. The two parental species <i>Sorghum bicolor</i> and <i>Sorghum propinquum</i> are labeled as PAR.</p

Saturation plot of <i>Sorghum halepense</i> genotypes after STRUCTURE runs based on Evanno Method (top).

<p>K values reach an asymptote between 15 and 26. DISTRUCT bar graph visualization of results after permuted by CLUMPP at four different K cluster assumptions (K = 2, 5, 15, 26). Clustering based on population averages (lower bars) and individual genotypes (upper bars). The two parental species <i>Sorghum bicolor</i> and <i>Sorghum propinquum</i> are labeled as PAR.</p

Map of sampling sites and N-J tree with an optimized leaf ordering along east–west geographical axis for <i>Sorghum halepense</i> genotypes.

<p>One of the progenitor species, <i>S</i>. <i>propinquum</i>, is used as outgroup. Colonization is outlined in 5 phases (P1-P5). Major gene flow pathways are shown using arrows in four colors (red, green, blue, gray). Initial colonization from southeastern US starting from SC (red arrows) are followed by the second introduction from AZ (S2, S4 green arrows). Gene flow from TX into NM, GA and VA (P3, blue arrows) happens concurrent with local gene flow among GA-AL-SC (P3 arrows not shown for clarity). From CA, there is a massive eastward radiation into NE, KY, FL and VA (P5a, gray arrows). While there is no detectable gene flow among KS, NE and TX (P5c) there is southbound gene flow from NE to FL (S5c, gray arrow) and KS into AL and GA (P5c, arrows not shown for clarity).</p