Many evolutionary analyses require accurate phylogenies of the species being studied. The following are trees that I have built for Drosophila species using different methods and sequences. The species are D. melanogaster (dmel), D. simulans (dsim), D. yakuba (dyak), D. erecta (dere), D. ananassae (dana), D. pseudoobscura (dpse), D. mojavenis (dmoj), D. virilis (dvir) and D. grimshawi (dgri). Please contact me if you plan to publish anything using these trees so that you can properly cite this work.

Using a set of 5067 orthologous genes identified using a tBlastn->Genewise->BlastP approach (please see http://rana.lbl.gov/~venky/annotation/ for more information) I built multiple alignments with TCoffee, ran Paml's codeml program (with a fixed dN:dS ratio across the tree) and got Time (substitutions per codon), dS and dN values for each branch in the topology. Here I am reporting the median values for each branch because mean values are biased due to the high value outliers occasionally produced by Paml. Please note that the following trees differ in topology from the trees that were previously posted here with regard to the placement of dere and dyak relative to dmel and dsim. This topology has the best support of the three possible trees relating these species, however, a high level of incongruence is present and thus, this species tree may not represent the history of all regions of the genome.

Median Time Tree (subsitutions per codon):

(((((dmel:0.06185, dsim:0.048265):0.057735, (dyak:0.09789, dere:0.088775):0.03448):0.425435, dana:0.590605):0.290085, dpse:0.535315):0.31104, ((dmoj:0.476425, dvir:0.28919):0.13216, dgri:0.45018):0.30115);

Median dS Tree:

(((((dmel:0.0699, dsim:0.0544):0.06555, (dyak:0.1106, dere:0.102):0.0389):0.47865, dana:0.6622):0.3237, dpse:0.59585):0.35745, ((dmoj:0.5375, dvir:0.3259):0.14865, dgri:0.51015):0.3434);

Median dN Tree:

(((((dmel:0.0055, dsim:0.0042):0.0049, (dyak:0.0085, dere:0.0079):0.0029):0.03835, dana:0.0525):0.0261, dpse:0.0483):0.0251, ((dmoj:0.0425, dvir:0.026):0.0115, dgri:0.0405):0.02485);