Fig. 3

Interchromosomal gene shuffling increases with evolutionary distance, further supporting integrity of B. coprophila chromosome-scale scaffolds. A Known taxonomic and phylogenetic information regarding B. coprophila and four other Dipteran species. With respect to B. coprophila, the species are presented here from left to right in order of the most closely related to most distantly related. The color scheme from left to right (dark purple to light yellow-green) reflects the entropy scores between B. coprophila and these species as in C-E. The species are presented in this order in each sub-figure below as well. B Species tree produced by OrthoFinder [84, 85] using the proteomes of these five species reproduces the expected relationships amongst these Dipteran flies. C Scatter plots of SCO locations along the chromosomes of each of the five species (x-axis) plotted against B. coprophila (y-axis). Inter-chromosomal SCO scattering increases with evolutionary distance as expected. Blue dots represent SCO locations. Colored boxes along x- and y- axes represent chromosomes. The chromosome box color scheme reflects the entropy score color scheme in D-E. D The pairwise min–max normalized entropy scores for B. coprophila computed against all five species. The entropy scores increase with evolutionary distance as expected. Although the entropy scores approach a fully random state with evolutionary distance from B. coprophila, pairwise relationships of chromosomal SCO groupings still display a bit of non-randomness even in the most distantly related fly species tested (D. melanogaster). E Matrix of all pairwise min–max normalized entropy (MMNE) scores among the five species presented as a hierarchically-clustered heatmap. The dendrogram from pairwise entropy scores reproduces the expected relationships among these Dipteran flies. Altogether, as the SCO dispersion and entropy of chromosomal gene sets follows evolutionary expectations, the location of genes in the chromosome-scale scaffolds we report here for B. coprophila are non-random and suggest the contigs were grouped correctly by chromosome