### Supplemental data for Graves et al, Genomics of Parallel Experimental Evolution in Drosophila ### Transposable elements (TEs) Contact Kate Hertweck (k8hertweck@gmail.com) with questions Files compiled during analysis of TE insertion frequency using T-lex2 (http://petrov.stanford.edu/cgi-bin/Tlex.html). Further details about TE analysis can be found at https://github.com/k8hertweck/flyPopGenomics # Each file includes the following columns: ID: unique identifier for TE, references Drosophila r5.53 chr: chromosome on which TE insertion is located start: chromosome location start, base 1 end: chromosome location end, base 1 TE_family: taxonomic identification from T-lex reannotated TEs (http://petrov.stanford.edu/cgi-bin/Tlex.html) TE_type: classification for TE from http://flybase.org # TE.reads.all.csv Read counts for all TEs analyzed, extracted from T-lex2 output Columns indicate reads supporting presence (p) and absence (a) for a given population (treatment replicate). Reads supporting presence on each flanking region to TE insertion were averaged. # TE.freq.all.csv Population frequencies for all TEs analyzed were extracted directly from the Tfreq file in Tlex2 output. # TE.cmh.csv Cochran-Mantel-Haenszel p-values for 177 variable TE insertions analyzed, with Bonferroni correction. NA indicates one or more population comparison was missing data/invariable (these were not included in Bonferroni correction). Fbti0060253 and Fbti0062820 were removed from summaries of this analysis because of the relatively high number of read counts mapping to these insertions (see TE.reads.all.csv) column names: pvals_X_X (Bonferroni corrected p-value for comparisons as follows:) pvals_ACO_BO ACO1-BO1-ACO2-BO2-ACO3-BO2-ACO4-BO4-ACO5-BO5 pvals_ACO_AO ACO1-AO1-ACO2-AO2-ACO3-AO3-ACO4-AO4-ACO5-AO5 pvals_ACO_B ACO1-B5-ACO2-B4-ACO3-B1-ACO4-B3-ACO5-B2 pvals_ACO_CO ACO1-CO1-ACO2-CO2-ACO3-CO3-ACO4-CO4-ACO5-CO5 pvals_ACO_NCO ACO1-NCO1-ACO2-NCO2-ACO3-NCO3-ACO4-NCO4-ACO5-NCO5 pvals_AO_B AO1-B5-AO2-B4-AO3-B1-AO4-B3-AO5-B2 pvals_AO_BO AO1-BO1-AO2-BO2-AO3-BO3-AO4-BO4-AO5-BO5 pvals_AO_NCO AO1-NCO1-AO2-NCO2-AO3-NCO3-AO4-NCO4-AO5-NCO5 pvals_AO_CO AO1-CO1-AO2-CO2-AO3-CO3-AO4-CO4-AO5-CO5 pvals_B_BOord B1-BO1-B2-BO2-B3-BO3-B4-BO4-B5-BO5 pvals_B_BOunord B1-BO5-B2-BO4-B3-BO1-B4-BO3-B5-BO2 pvals_CO_B CO1-B5-CO2-B4-CO3-B1-CO4-B3-CO5-B2 pvals_CO_NCO CO1-BO1-CO2-BO2-CO3-BO3-CO4-BO4-CO5-BO5 pvals_CO_BO CO1-NCO1-CO2-NCO2-CO3-NCO3-CO4-NCO4-CO5-NCO5 pvals_NCO_B NCO1-B5-NCO2-B4-NCO3-B1-NCO4-B3-NCO5-B2 pvals_NCO_BO NCO1-BO1-NCO2-BO2-NCO3-BO3-NCO4-BO4-NCO5-BO5 pvals_C_A ACO1-CO1-ACO2-CO2-ACO3-CO3-ACO4-CO4-ACO5-CO5-AO1-NCO1-AO2-NCO2-AO3-NCO3-AO4-NCO4-AO5-NCO5