Drosophila species gene-match phylogenetic trees

These phylogenetic trees are based on genome matches to the D. melanogaster proteome (13,400 genes). Gene similarity (tBLASTn match strength) and gene order (pairs of nearest genes) statistics are both used. Three outgroup genomes ( C. elegans:cele, crustacean Daphnia: dpulex, and insect Anopholes:agam) are included with Drosophila (Dmel to Dgri). Distance matrices were computed from blast scores and adjacent gene pairs found in each genome using R, phylogenies were computed with PHYLIP:Fitch from distances, and drawn with Phylodendron.

These gene trees for the most part match the accepted phylogenies. One notable phylogenetic outlier is D.simulans. Since this Dsim assembly is a mosaic from several populations, the population-level differences are likely affecting a species view of this genome. The D. willistoni placement by gene similarity also differs somewhat from accepted phylogeny, and from the gene order placement.

Gene similarity (phenogram) PDF	Gene similarity (tree) PDF	Gene similarity (newick/nh data)
		#title "D_melanogaster-gene similarity tree; v5; Fitch/global" (( ((( (((dmel:4.71283,dsec:3.65378):1.07592, dsim:7.28995):1.03928, (dere:4.31795,dyak:4.84720):0.67972):8.69153, dana:7.31418):3.70898, (dpse:5.45575,dper:6.20616):3.22088):1.40775, (dwil:8.30782, ((dvir:6.18222,dmoj:6.54571):0.57520, dgri:8.21919):2.90892):1.12245):22.87624, agam:15.81995):13.25293, dpulex:17.77181,celegans:33.34570);
Gene order (phenogram) PDF	Gene order (tree) PDF	Gene order (newick/nh data)
		#title "D_melanogaster-gene order tree; v3; Fitch" (( (((( (((dmel:0.01827,dsec:0.02429):0.00603, (dyak:0.03563,dere:0.02713):0.00236):0.01063, dsim:0.05923):0.04342, dana:0.07688):0.01803, (dper:0.03366,dpse:0.03456):0.05543):0.01591, dwil:0.11533):0.00376, ((dmoj:0.05285,dvir:0.05136):0.01047, dgri:0.06706):0.04471):0.07426, agam:0.14761):0.00716, dpulex:0.09651,celegans:0.09016);

Don Gilbert, April 2006