Figure S2. Strict consensus of four maximum parsimony trees for 21AA data set plus bootstrap values (above branches) from 20AA (left) and 21AA (right) analyses.

MP topology based on 250 search replicates. 100 100 Antheraea Bootstrap results based on 1000 bootstrap Lepidoptera 100 100 Cydia Neoptera [23] 44 Dermaptera Prodoxus replicates (5 search reps / bootstrap rep). 68 66 Forficula Blattodea Pterygota 92 96 Periplaneta Orthoptera 96 97 Acheta # : bootstrap percentage (20AA 21AA) Ephemeroptera Dicondylia 100 100 Hexagenia Paleoptera [37] 52 Ephemerella 98 98 Odonata 100 100 Ischnura [ ] : node not present in 20AA Insecta Libellula MP strict consensus 100 100 Zygentoma 100 100 Ctenolepisma Nicoletia Archaeognatha : Identifies 6 taxa with Hexapoda 100 100 Pedetontus 89 86 Machiloides Entomobryomorpha Tomoceridae large differences in BP Collembola 70 76 Tomocerus between degen1 and 100 100 Entomobryidae Orchesella Entognatha 82 82 Poduridae Podura 20AA analyses. Diplura 100 100 Campodeidae Japygidae Eumesocampa Remipedia Metajapyx Xenocarida [31] 51 Speleonectes Cephalocarida Hutchinsoniella Altocrustacea Thoracica Sessilia 88 83 Semibalanus [14] 31 100 100 Chthamalus Thecostraca 100 100 Pedunculata Lepas Communostraca Rhizocephala Loxothylacus 96 89 Eumalacostraca 84 85 Eucarida Libinia Malacostraca 100 100 Peracarida Armadillidium Multicrustacea 100 100 Hoplocarida 69 84 Neogonodactylus Phyllocarida Nebalia Cyclopoida 100 100 Mesocyclops Copepoda 100 100 Acanthocyclops Pancrustacea 65 82 Calanoida Eurytemora 96 100 Diplostraca 100 100 Cladocera Daphnia Phyllopoda 93 94 Spinicaudata Limnadia 100 100 Laevicaudata Vericrustacea Branchiopoda Lynceus 100 100 Notostraca Triops Anostraca 100 100 Streptocephalus Artemia Podocopa 57 64 Cypridopsis 35 48 Mystacocarida Mandibulata Derocheilocaris 88 83 Oligostraca 58 74 Myodocopa 100 100 Harbansus Ichthyostraca Branchiura Skogsbergia 100 100 Argulus Pentastomida Armillifer Chilognatha Callipodida Abacion 100 100 Polyzoniida Polyzonium Diplopoda 77 79 Spirobolida Narceus Polyxenida Polyxenus Symphyla 100 100 Hanseniella Edafopoda 59 76 Myriapoda 99 99 Scutigerella Pauropoda Eurypauropus 83 80 Scolopendromorpha Lithobiomorpha Scolopendra Chilopoda 100 100 Lithobius Craterostigmomorpha Craterostigmus Arthropoda Scutigeromorpha Scutigera 95 99 Pedipalpi Uropygi 97 98 Schizomida Stenochrus Tetrapulmonata 89 88 Thelyphonida Mastigoproctus Pulmonata 85 94 Amblypygi Phrynus 82 84 Araneae Aphonopelma Scorpiones 100 100 Heterometrus Ricinulei Hadrurus 28 22 86 85 Cryptocellus Solifugae Eremocosta 19 17 Xiphosura 100 100 Limulus Pseudoscorpiones Carcinoscorpius Euchelicerata [26] 34 Idiogaryops 100 100 24 31 Acari: Parasitiformes Amblyomma Opiliones Leiobunum 59 55 Palpigrada Prokoenenia Acari: Acariformes Dinothrombium 81 85 Tanystylum Ammotheidae 57 64 Achelia 93 92 Ammothea Pycnogonida 100 100 Endeididae Nymphonidae Endeis Nymphon Peripatopsidae 100 100 Peripatoides Onychophora 100 100 Peripatidae Euperipatoides Peripatus Tardigrada 100 100 Parachela Thulinius Apochela Milnesium Commentary on Figure S2: Miracrustacea (BP, 24%), Progoneata (BP, 33%), and Chelicerata (BP, 57%) are all present in subsets of the four MP trees for the 21AA analysis. Miracrustacea (BP, 12%) and Xenocarida (BP, 31%) are both present in subsets of the five MP trees for the 20AA analysis, but not Altocrustacea (BP, 14%) and Chelicerata (40%). Progoneata (BP, 35%) is present in the strict consensus of the 20AA analysis.