<p>Online Resource 2 Programs and Parameters</p><p>Below are the programs used for each analysis. Any parameter not listed in the “Parameters” column used the default value. Specific commands are separated by “;” within each analysis. For the gene trees, the model and partial deletion values are indicated in the </p><p>“Parameters” column. “ML” stands for Maximum Likelihood, and “NJ” stands for Neighbor-joining. Not all of the parameters available for the Maximum Likelihood model were available for the Neighbor-joining analysis, so only those that were available were used to create the NJ tree. </p><p>Analysis Program Version Parameters Removal of rRNA reads DeconSeq 0.4.2 -i 95; -c 90 Assembly of reads into transcripts Trinity r2013-02-25 --seqType fq; --JM 50G; --CPU 48; --bflyHeapSpaceMax 8G; --bflyCPU 12 Annotation of transcript ORFs Trinotate r2013-02-25 -max_target_seqs 1 Mapping the reads to the transcripts RSEM/Bowtie 1.2.0/1.0.0 -p 8; --calc-ci; --time;--bowtie-chunkmbs 512 Viewing and editing sequence alignments Jalview 2.8.0b1 N/A Initial and group Alignments MUSCLE 3.8.31 all defaults Tree building and viewing MEGA 5.2.2 see each tree Selection of phylogenetic model parameters PROTTEST 3.2 Base tree for likelihood calculations: BIONJ JTT Combining group alignments Lobster/COACH 11/21/2002 Linux msa2hmm; align; all defaults Creating some of the group alignments HMMER 3.1b all defaults KoRV Tree MEGA 5.2.2 ML: Model = JTT+G, partial deletion = 65; NJ: Model = JTT+G, partial deletion = 65 MHC-I-A Tree MEGA 5.2.2 ML: Model = JTT+I+G, partial deletion = 95; NJ: Model = JTT+G, partial deletion = 95 MHC-II-A Tree MEGA 5.2.2 ML: Model = JTT+I+G, partial deletion = 95; NJ: Model = JTT+G, partial deletion = 95 MHC-II-B Tree MEGA 5.2.2 ML: Model = JTT+I+G+F, partial deletion = 95; NJ: Model = JTT+G, partial deletion = 95 RLR Tree MEGA 5.2.2 ML: Model = JTT+I+G+F, partial deletion = 95; NJ: Model = JTT+G, partial deletion = 95 TLR Tree MEGA 5.2.2 ML: Model = JTT+I+G, partial deletion = 95; NJ: Model = JTT+G, partial deletion = 95 SNP Discovery-Samtools SAMtools 0.1.18 rmdup; mpileup: -ugD -d 351208 -C 50; varFilter: -d 10 Calling variants in RNAseq workflow (Van der Auwera 2014), excluding the STAR SNP Discovery-GATK GATK/Picard tools 3.1.1/1.113 mapping steps</p><p>SNP Visualization IGV 2.3.34 N/A Extraction of child GO terms MATLAB r2013a getdescendants(ID) = 2376 </p>