We were involved in the sequencing and assembly of the first D. mojavensis genome (from Catalina Island) (D12GC 2007). Currently we have set out to sequence, assemble and annotate the genomes of the other three host populations (Baja California, Mojave Desert and mainland Sonora Desert). We have generated both short and long insert (180 bp and 3 kb, respectively) libraries and have sequenced them in a HiSeq 2500 at HudsonAlpha. For each genome we have obtain approximately 16 billion base pairs of sequence. Using the previously assembled Catalina Island genome we have been able to construct the great majority of the genome scaffold (93-97%, see table). We are currently generating de novo assemblies using the mate pair sequences. From our initial draft assemblies we have been able to obtain the sequences of 14,238 genes from each of the three host populations, which is the majority (~98%) of the genes annotated in the published genome (14,581). We have performed a series of analyses on the pattern of molecular evolution across the four host population’s genomes (Allan and Matzkin, in prep). The figure on the left illustrates the distribution of log2 of dN/dS values calculated using PAML (ω). Values for 10,788 loci out of the 13,821 loci assembled are shown. Loci with five or fewer substitutions (2,974 loci), sequence alignment uncertainties (417) and with undeterminable dN/dS or ka/ks values (59 loci) were filtered from the primary dataset (Allan and Matzkin, in prep). PAML analysis have shown 422 loci (after FDR correction, there were 1,151 loci prior to correction) that show evidence of positive selection. Further investigations on these genes have illustrated the changes associated with local ecological adaptation across the host populations.