plosone-phylo
pone.0056200.g004
Consensus tree and population substructure estimated from SPP markers.At the top, a Fitch & Margoliash tree of 40 C. annuum lines, rooted with C. frutescens and C. Chinense. The majority-rule consensus cladogram (overall equal branch lengths) was generated from 13,621 SPP markers. Numbers associated with branches indicate percent support based on 7,500 bootstrap replicates. Branches with less than 50% support have been collapsed. At the bottom is shown C. annuum population substructure determined using Structure with 2,712 mapped SPP markers for K = 2 to K = 6. Each genotype is represented by a vertical column and genotypes are ordered according to the cladogram. Each color bar represents a different subpopulation and the proportion of a given variety's color bar represents the proportion that variety belongs to the corresponding subpopulation. The branches of the cladogram are colored according to the highest proportion subpopulation assignment when K = 6 with grey branches indicating highly admixed individuals, having no more than a 0.60 fraction assigned to any subpopulation. Grouping by common structure subpopulation constitution is indicated by colored border with assigned names shown below. Long Yellow Marconi and Lange Westlandse Rode are abbreviated L. Yellow Marconi and L. W. Rode, respectively.
pone.0056200.g004
Consensus tree and population substructure estimated from SPP markers.At the top, a Fitch & Margoliash tree of 40 C. annuum lines, rooted with C. frutescens and C. Chinense. The majority-rule consensus cladogram (overall equal branch lengths) was generated from 13,621 SPP markers. Numbers associated with branches indicate percent support based on 7,500 bootstrap replicates. Branches with less than 50% support have been collapsed. At the bottom is shown C. annuum population substructure determined using Structure with 2,712 mapped SPP markers for K = 2 to K = 6. Each genotype is represented by a vertical column and genotypes are ordered according to the cladogram. Each color bar represents a different subpopulation and the proportion of a given variety's color bar represents the proportion that variety belongs to the corresponding subpopulation. The branches of the cladogram are colored according to the highest proportion subpopulation assignment when K = 6 with grey branches indicating highly admixed individuals, having no more than a 0.60 fraction assigned to any subpopulation. Grouping by common structure subpopulation constitution is indicated by colored border with assigned names shown below. Long Yellow Marconi and Lange Westlandse Rode are abbreviated L. Yellow Marconi and L. W. Rode, respectively.