Volume 8, Issue 3, Pages 427-438 (March 2015) Frequent Introgressions from Diploid Species Contribute to the Adaptation of the Tetraploid Shepherd’s Purse (Capsella bursa-pastoris)  Ting-Shen Han, Qiong Wu, Xing-Hui Hou, Zi-Wen Li, Yu-Pan Zou, Song Ge, Ya-Long Guo  Molecular Plant  Volume 8, Issue 3, Pages 427-438 (March 2015) DOI: 10.1016/j.molp.2014.11.016 Copyright © 2015 The Author Terms and Conditions

Figure 1 Identification of Diploid and Tetraploid Samples. (A) Histogram obtained by flow cytometric analysis. (B) Genome size variation. (C) Cytological analyses of C. orientalis and C. bursa-pastoris. (D) Sequencing to confirm the polyploids and diploids. Samples showing a few heterozygous sites are polyploids, and samples with homozygous sites at the same position are diploids. Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions

Figure 2 Population Structure Analysis for All Four Species with the Cluster Number K from 2 to 4. Samples are arranged according to species and geographic regions of C. bursa-pastoris (indicated by the gray bars above: WE, western Eurasia; NWC, northwestern China; EC, eastern China). Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions

Figure 3 Haplotype Networks for All Four Species. Colors in the pie chart represent the origin of each haplotype: red, C. rubella; green, C. grandiflora; orange, C. orientalis; blue, C. bursa-pastoris. The size of each pie is proportional to the haplotype frequency found in these four species. Branch lengths longer than one mutation step are marked by short lines on each branch or illustrated by dotted lines with the number of mutation steps. Unsampled or predicated haplotypes are represented by gray pies. Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions

Figure 4 ABC Simulation of the Origin History of C. bursa-pastoris. Each ABC scenario is presented by a graphic figure, graph with frame indicating the best model. Effective population sizes (N1–N7) are colored differently (black, crown ancestry; red, C. rubella; green, C. grandiflora; orange, C. orientalis; yellow, C. bursa-pastoris A subgenome; blue, C. bursa-pastoris B subgenome; purple, ancestor of C. bursa-pastoris A subgenome and B subgenome). Times of events (t0–t3 and 0) are marked by small bars along a gray line (not to scale). Scenario AP2 and Allo3 are presented together with the graph of AP1 and Allo2, respectively, by changing the position of C. bursa-pastoris A subgenome (dotted lines) to a new time node (t1) in gray. Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions

Figure 5 Predicted Distributions of Capsella Species at the Present Time, the LGM (Last Glacial Maximum), and the LIG (Last Interglacial), Respectively, Based on Ecological Niche Modeling Using MaxEnt. Warmer colors show areas with higher probability for the species’ inhabitation, while colder colors represent areas with lower probability for its inhabitation. The predictive power is shown in the image at the present time for each species, using the area under the curve (AUC) of receiver-operating characteristic for testing data. The value of AUC represents the real test of the models’ fitness. MYA, million years ago. Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions

Figure 6 Ecological Niche Modeling of the Niche Differentiation between the Introgressed and Non-Introgressed C. bursa-pastoris. (A) Predicted distributions of introgressed (intro) or non-introgressed (non-intro) C. bursa-pastoris from northwestern China at the present time, the LGM time, and the LIG time, respectively. MYA, million years ago. The annotation of color and value is the same as for Figure 5. (B) The niche identity tests between C. orientalis and introgressed C. bursa-pastoris in northwestern China based on present environmental data. (C) The niche identity tests between C. orientalis and non-introgressed C. bursa-pastoris in northwestern China based on present environmental data. In (B) and (C), arrows indicate the observed identity values, and histograms of gray bars indicate the simulated identity values generated from 100 randomizations. (D) The niche identity (I and D) between introgressed and non-introgressed C. bursa-pastoris at different probability of suitable conditions. Molecular Plant 2015 8, 427-438DOI: (10.1016/j.molp.2014.11.016) Copyright © 2015 The Author Terms and Conditions