The data of individual 454 runs (and the compilation of normal and normalized MD OCT-pool data) was compared against the NCBI non-redundant protein database (BLASTX-nr) with an evalue of 1e -4 to identify transcript RNA-derived tags. To filter repetitive elements, RepeatMasker (http://www.repeatmasker. org) was used to scan the mule deer sequences, with the latest version of Repbase 13.04 [61] . The output files were analyzed with the program MEGAN [32] version 3.7.2.