Supplementary Table 1: Primers Used to Screen for Insertional Polymorphism of Putative Mites

Supplementary Table 4a: Identification of grouped MITE elements

Number Group Identity Number Identity Number Identity Group 1 CACTA Caspar Group 24 Retroelement Barbara/Inga Group 47 CACTA Caspar Group 2 unclassified Group 25 unclassified Group 48 unclassified Stowaway MITE Group 3 Group 26 CACTA Caspar Group 49 Stowaway MITE Group 4 StowawayMITEDamocles MITE Group 27 unclassified Group 50 Stowaway MITE Group 5 Stowaway MITE Group 28 unclassified Group 51 unclassified Group 6 Stowaway MITE Group 29 unclassified Group 52 unclassified Group 7 unclassified Group 30 Stowaway MITE Group 53 unclassified Stowaway MITE Group 8 Stowaway MITE Hades Group 31 Group 54 unclassified Group 9 Stowaway MITE Group 32 RetroelementMITEAthos Sabrina Group55 unclassified Retroelement Group10 Barfly Group 33 Group 56 unclassified Group 11 Stowaway MITE Group 34 RetroelementSabrina/Bagy2/Wilma Wilma/Bagy2 Group 57 Retroelement Sabrina/Bagy2 Group 12 Stowaway MITE Group 35 CACTA Caspar Group 58 unclassified Group 13 Stowaway MITE Group 36 unclassified Group 59 unclassified Group 14 Stowaway MITE Group 37 unclassified Group 60 Retroelement Wham Stowaway MITE Group 15 Group 38 Stowaway MITE Group 61 Stowaway MITE Group 16 StowawayMITEIcarus MITE Group 39 CACTA Caspar Group 62 Stowaway MITE Athos Stowaway MITE Group 17 Stowaway MITE Group 40 CACTA Caspar Group 63 Stowaway MITE Group 18 Group 41 CACTA Caspar Group 64 StowawayMITEDamocles/Thalos MITE Hades Group 19 unclassifiedMITEIcarus Group 42 CACTA Caspar Group 65 Stowaway MITE Icarus Stowaway MITE Group 20 Group 43 CACTA TAT Group 66 Stowaway MITE Oleus Stowaway MITE Group 21 unclassifiedMITEAthos Group 44 Retroelement BARE1 Group 67 Group 22 unclassified Group 45 unclassified Group 68 POLYMITEPan/HorMITE1 A/T Group 23 unclassified Group 46 Retroelement Sabrina/Wilma Group 69 Stowaway MITE

Supplementary Table 4b: Identification of singleton MITEs

Putative MITE Identification Putative MITE Identification AF427791_24 CACTA Caspar AY013246_6 Retroelement LTR-Copia BARE1 HO10M16S_1 #246 Stowaway MITE MITEHv AY013246_10 #258 Stowaway MITE MITEHv AF474072_9 DNA Transposon George X80068_1 #253 Stowaway MITE MITEHv AF474072_16 LITE Apollo AY133225_1 Pangrangja AF474982_3 Retroelement LTR-Copia Inga AY133240_1 Pangrangja Segment3_4 Retroelement LTR-Copia Inga Segment5_6 Retroelement TREP46 – unnamed Copia AF254799_5 Retroelement LTR-Gypsy Sukkula Segment5_7 Retroelement LTR-Gypsy Latidu AF427791_7 HorMITE2 GBne01_SQ2_E01_1 Retroelement LTR-Athila Sabrina AF474373_3 #275 MITE1 Gbne01_SQ2_J13_1 Retroelement LTR-CopiaWIS/Bare1 AF474373_16 DNA Transposon Mutator Hormu Gbne01_SQ9_B22_1 Retroelement LTR-Gypsy BAGY2 AY013246_4 Retroelement LTR Gypsy Ikeros