Fig 1.
Plotting the multiple sequence alignments with a phylogenetic tree.
The phylogenetic tree belonging to the mitochondrial cty b gene of 120 Bombus terrestris dalmatinus and nucleotide differences have been schematized. Colors both on the phylogenetic tree and on the branch scale represent genetic distance. mtDNA cyt b sequences have been colored by four different colors shown in the ‘seq’ column for each nucleotide. Color changes on the aligned sequences represent nucleotide differences.
Table 1.
Sequences and frequencies of haplotypes.
Table 2.
Number of haplotypes per population.
Table 3.
Haplotype distance matrix using Hamming distance method.
Fig 2.
Heat map based on the number of nucleotide differences between the haplotypes.
Each branch of the phylogenetic tree represents the corresponding haplotype in the matrix. We defined the close relationships with "darkred" color and far relationships with "white" color.
Fig 3.
Haplotype network represented by individuals.
Each slice in the circles represents an individual. Branch lengths between the circles have been represented by genetic distance between haplotypes. Every dash on the lines is a representation of one nucleotide. The rainbow() command was used for coloring the individuals. Haplotype network was demonstrated using the plot() command and names of individuals were added with the legend() command.
Fig 4.
Haplotype networks for populations (a) and groups (b).
(a) Populations have been colored in blue, red, and green representing the groups (greenhouse, firm and nature) they belong to. (b) Groups have been colored compatibly with the population haplotype network. Circle sizes were calculated based on the number of individuals they had. Each slice in the circles represents an individual. Every dash on the lines is a representation of one nucleotide. To visualize the two plots at the same time, the plot(new, TRUE) command was used after the first plot command and was continued with the second plot command.
Fig 5.
Colorized phylogenetic tree representing populations.
The distance scale has shown 0.6% genetic variation per nucleotide substitution.
Fig 6.
Colorized phylogenetic tree representing DNA distance.
The distance scale has shown 0.6% genetic variation per nucleotide substitution.
Fig 7.
Neighbor-joining (NJ) tree for cyt b haplotypes of B. terrestris dalmatinus.
Colored internal nodes represent the bootstrap confidence level.