Y-chromosome phylogeny using Complete Genomics data

Since taking a trip to Innsbruck on a day's notice is out of the question, and since I don't want to wait for the eventual journal publication, I figured I'd try my hand at using the Complete Genomics data for myself to build a Y-chromosome phylogeny.

With the aid of PhyML (default parameters and 100 bootstrap replicates), here is what I get:

Note that the above was done by isolating the Y-SNPs on 28 unrelated males in the data. I also threw out all SNPs that had no-calls. I tried to infer terminal classifications for the different individuals based on current ISOGG nomenclature, although it's possible that there are downstream mutations that I missed. NA18940 that is cut off in the figure is D2a-M11 and, NA19649 is R1b1a2a1a1b2a1a-L20. I couldn't quite figure out NA19670.

Here is the tree code for anyone who wants to play with it:

  (NA21732_MKK_E1b1b1a1c-V22:0.00295296,NA21737_MKK_E1b1b1a1c-V22:0.00270971,(NA20510_TSI_E1b1b1a1b-V13:0.02092798,((NA19239_YRI_E1a2-P110:0.08297556,(NA18940_JPT_D2a-M11
6.1:0.12168757,((NA12891_Utah_I1a4-Z63:0.01039303,(NA06994_CEU_I1a3a1b-Z73:0.00945249,NA20511_TSI_I1a3a1a-Z140:0.01697537)54:0.00049670)100:0.07005125,(NA19670_MXL_?:0.
08181470,(NA18558_CHB_NO-M214:0.10352315,(NA19735_MXL_Q1a3a1-M3:0.05725892,(NA20845_GIH_R2a1a-L294:0.05384443,((NA20846_GIH_R1a1a1b2-Z93:0.01116683,NA20850_GIH_R1a1a1b2
-Z93:0.00810758)100:0.02945897,(((NA12889_Utah_R1b1a2a1a1b5-DF19:0.01118764,HG00731_PUR_R1b1a2a1a1b1-DF27:0.00955759)24:0.00020607,NA07357_CEU_R1b1a2a1a1b2-U152:0.00963
759)21:0.00012284,(NA19649_MXL_R1b1a2a1a1b2a1a-L20:0.05342631,(NA20509_TSI_R1b1a2a1a1b2c3-Z146:0.00943290,NA10851_CEU_R1b1a2a1a1b3-L21:0.01307073)15:0.00019824)5:0.0000
0002)100:0.03211886)100:0.00848072)100:0.00921281)100:0.02274049)100:0.00299324)54:0.00000005)100:0.03274296)100:0.01917298)100:0.00999561,((NA18504_YRI_E1b1a1a1f1a1-U1
74:0.01490192,(NA19026_LWK_E1b1a1a1f1a1-U174:0.01033155,NA19834_ASW_E1b1a1a1f1a1-U174:0.00961706)75:0.00031406)100:0.00787632,(NA18501_YRI_E1b1a-V38:0.00966164,((NA1902
0_LWK_E1b1a-V38:0.01193590,NA19025_LWK_E1b1a-V38:0.00793484)100:0.00317626,(NA19700_ASW_E1b1a-V38:0.01130782,NA19703_ASW_E1b1a-V38:0.01054823)77:0.00022885)100:0.001228
37)100:0.00457000)100:0.04581828)100:0.04898306)100:0.01922685);