Spreadsheet: 44562333-0f13-4ce8-b3fe-7a3be06e62e4
Sheet: Sheet1

Supplementary Table 2.  Genbank accession numbers used in this study. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24 | Unnamed: 25 | Unnamed: 26 | Unnamed: 27 | Unnamed: 28 | Unnamed: 29 | Unnamed: 30 | Unnamed: 31 | Unnamed: 32 | Unnamed: 33 | Unnamed: 34 | Unnamed: 35 | Unnamed: 36 | Unnamed: 37 | Unnamed: 38
 | examplars used for hybrid sequences in 24 taxa matrix | exemplar used in Dunn et al. | 18S | 28S | 5.8S | ACT | BRA | BTU | CDC42 | DCR | EF1A | HSP70-8 | ATP1a | PAX | RAN | [NAME] | RPOIII | EIF2 | mt genome | bp143 | bp156 | bp169 | [NAME] | bp179 | bp184 | bp186 | bp193 | bp199 | bp200 | [NAME] | bp213 | bp225 | bp232 | bp233 | bp235 | [NAME] | bp243
Trichoplax adhaerens |  |  | AY652578 | AY652583 | AY652535 | XP_002112714 | CAD70269 | FJ387017 | FJ387001 | XP_002108012 | CAD70273 | FJ387002 | FJ387004 | AAY68376 | FJ387005 | FJ387006 | FJ387007 | FJ387008 | NC_008151 | XP_002117025 | XP_002110205 | XP_002109942 | XP_002118301 | XP_002109185 | XP_002108089 | XP_002117056 | XP_002108712 | XP_002111084 | XP_002108894 | XP_002109240 | XP_002108622 | XP_002114050 | XP_002108947 | XP_002108420 | XP_002109491 | XP_002107880 | XP_002118295
Demospongiae | Suberites, Axinella, Ephydatia, Geodia | Suberites domuncula | AJ627184 | AJ620113 |  | ABB29650 | CAD66614 | CAD79598 | ABD65425 |  | CAE45763 | ABB29640 | [NAME] | BAA36346 |  | ABB29648 | ABB29656 | ABB29637 | NC_006990 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Calcarea | Leucosolenia, Sycon, [NAME] |  | AJ622898 | AY026372 | AJ622898 | ABB29677 |  | AAP49558 | ABB29665 |  | AAZ30661 | ABB29670 | ABB29688 |  | [NAME] | ABB29676 | ABB29684 | ABB29667 | AF362006
Hexactinellida | Aphrocallistes, Rhabdocalyptus, Oopsacas |  | AM886406 | AY026379 | AJ633901 | ABB29700 | AAU95753 | AAP49560 | ABB29689 |  | AAP49569 | ABB29693 | ABB29713 |  | ABB29690 | ABB29699 | ABB29707 | ABB29691 | NC_009627 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Hydrozoa | Hydra, Hydractinia, Obelia | [NAME] magnipapillata | DQ683368 | AY026371 |  | AAA29205 | [NAME] | AAX47550 | CAA55332 |  | CAA92323 | DQ286045 | AAU93957 | CAA75669 | DN604252 |  | DT620045 | DN814082 | AAF27982, AAF27981, AAF27980, AAT00199, EF059927, EF059941, AY530429, [NAME], ABK58278
Cubozoa | Carybdea, [NAME],Chironex |  | AF358108 | AY920787 | CFU65477 |  |  |  |  |  |  |  | FJ386998 | AAQ17211 |  | FJ386999 |  | FJ387000 | AF360118
Scyphozoa | Aurelia, Chrysaora |  | EU272604 | EU272547 | EU332745 | AAN85104 |  | AAP49562 |  |  | AAP49571 | AY836653 |  | AAB58294 | AAX09921 |  |  |  | NC_008446
Anthozoa | Nematostella, Aiptasia, Metridium, Zoopilus, Pocillopora | [NAME] vectensis | AF254382 | AY345871 | EU149858 | AAG61116 | AAO27886 | AAP49561 | AAQ23388 |  | [NAME] | AB201749 | AAU93961 | AAP88434 | DY581467 |  | DV081393 | [NAME] | NC_008164 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Ctenophora | Pleurobrachia, Mnemiopsis, [NAME] | Mnemiopsis leydii | AF293678 | AY026373 | AB377608 | AAN85103 | ABL68078 | [NAME] |  |  | BAA08662 | AAC05357 | AAP51224 | AAO45633 |  |  |  |  | AF362019, AF362008,AAK27370, [NAME] | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Mammalia | Homo, Mus | Homo sapiens | X03205 | NR_003287 | NR_003285 | NP_033736 | NP_033335 | NP_666228 | NP_033991 |  | NP_034236 | NP_112442 | NP_659170 | [NAME] | NP_033417 | XP_620794 | NP_081699 | XP_001481179 | NC_005089 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Drosophila melanogaster |  | Drosophila melanogaster | M21017 | M21017 | U20145 | NP_523625 | NP_524031 | NP_523795 | NP_476950 |  | NP_477375 | NP_524356 | NP_996248 | NP_524638 | NP_651969 | NP_476874 | NP_523706 | NP_731994 | NC_001709 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Echinodermata | Strongylocentrotus | Strongylocentrotus purpuratus | D14365 | AF212171 |  | NP_999634 | XP_782140 | XP_791790 | XP_780276 |  | XP_001176381 | XP_802129 | XP_795226 | NP_999759 | XP_786730 | XP_781777 | XP_001184185 | XP_001178408 | NC_001453 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Choanoflagellata | Monosiga | Monosiga ovata | AF174375 | AY026374 |  | XP_001747496 |  | XP_001743437 | ABB29714 |  | AAK27413 | AAG45150 | XP_001742517 |  | XP_001749950 | XP_001745849 | [NAME] | XP_001747009 | NC_004309
Cryptococcus neoformans |  | Cryptococcus neoformans | BR000310 | BR000310 | BR000310 | XP_566845 |  | XP_569650 | XP_571459 |  | XP_568462 | XP_569545 | XP_566813 |  | XP_571000 | XP_571691 | XP_572718 | XP_570286 | NC_004336 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Saccharomyces cerevisae |  | Saccharomyces | Z73326 | AY048154 | FM177899 | NP_116614 |  | NP_116616 | NP_013330 |  | NP_009676 | NP_009396 | NP_011348 |  | NP_013396 | NP_011392 | NP_014850 | NP_010942 | NC_001224 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Tetrahymena thermophila |  |  | X56165 | X54512 | EF608219 | XP_001016672 |  | XP_001023006 |  |  | XP_001032213 | XP_001030820 |  |  | XP_001019989 | XP_001014441 | XP_001022929 |  | NC_003029
Trypanosoma brucei |  |  | AF416562 | AC008031 | Tb927.3.3448 | XP_828467 |  | XP_001218933 |  |  | XP_828111 | XP_845695 |  |  | XP_828678 | XP_827949 | XP_822531
Dictyostelium discoideum |  | Dictyostelium | NW_001852778 | NW_001852778 | NW_001852778 | XP_643865 |  | XP_646162 | XP_642196 |  | XP_645839 | XP_646617 | XP_647420 |  | XP_635125 | XP_628967 | XP_636731 | XP_641922 | NC_000895 | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D | D
Acanthoscurria gomesiana
[NAME] |  |  | AF038032 |  | AF228239
Amoebidium parasiticum |  |  | Y19155 | DQ273802 |  |  |  |  | DQ273802 | DQ273802
Anoplodactylus eroticus
Aplysia californica |  |  | AY039804 | AY026366 |  |  |  | AAP13560 | AY026366 | AY026366 | ABK80814 |  |  |  | ABS87394 |  |  |  | NC_005827
Argopecten irradians |  |  |  |  |  |  |  |  | AY145391 | AY145391 |  |  |  |  |  |  |  |  | NC_009687
Asterina pectinifera |  |  | AB084551 |  |  |  |  |  |  |  | AAT06175
Biomphalaria glabrata |  |  | U65224 | AF435694 | AY030377 |  |  |  | AF435694 | AF435694 | AF435694
Boophilus microplus |  |  | AF018656 | AF200189 | U97715 |  |  |  | AF200189 | AF200189 | AF200189
Branchiostoma floridae |  |  | M97571 | AF061796 |  |  |  |  | AF061796 | AF061796 | BAB63216 |  |  |  | ABU49827 |  |  |  | NC_000834
[NAME] sp |  |  | U67323 | AY364863 |  |  |  |  | AY364863 | AY364863 | BAA25735
Capsaspora owczarzaki |  |  | AY363957 |  | AY363957
Carcinoscorpius rotundicauda |  |  | U91491 |  |  |  |  |  |  |  | [NAME]
Carcinus maenas |  |  | DQ079757 | DQ079782 |  |  |  |  | DQ079782 | DQ079782 | DQ079782 |  |  |  |  |  |  |  | DQ079782
[NAME] mutabilis |  |  |  | AJ436887 |  |  |  |  | AJ436887 | AJ436887 | AJ436887
Cerebratulus lacteus |  |  | AY145368 | AY145396 |  |  |  |  | AY145396 | AY145396 | ABI13285
Chaetoderma nitidulum |  |  | AY340425
Chaetopleura apiculata |  |  | AY145370 | AY145398 |  |  |  |  | [NAME] | [NAME] | AAC03161
[NAME] sp |  |  |  |  |  |  |  |  |  |  | AAT06176
Ciona intestinalis |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | NC_004447
Crassostrea virginica |  |  | L78851 | AY145400 | EU072460 |  |  |  | AY145400 | AY145400 | AY145400 |  |  |  |  |  |  |  | NC_007175
Cyanea capillata |  |  |  |  | U65481
Daphnia magna |  |  | AM490278 | AF532883 |  |  |  |  | AF532883 | AF532883 | AF532883 |  |  |  |  |  |  |  | NC_000844
Dugesia japonica |  |  | AF013153 | DQ665966 |  |  |  |  |  | DQ665966
Echinococcus granulosus |  |  | U27015 |  | AY185194 |  |  | ACF49481 |  |  | BAF63675 |  |  |  | ACB70418 |  |  |  | NC_008075
Echinoderes horni
Euperipatoides kanangrensis
Euprymna scolopes
Fenneropenaeus chinensis |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | NC_009679
Gallus gallus
Haementeria depressa
Hydractinia echinata |  |  | AY920763
Hypsibius dujardini
Lumbricus rubellus |  |  | Z83753
Macrostomum lignano |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | NC_001673
Mertensiid sp |  |  | AF293680
Mytilus galloprovincialis |  |  | [NAME] | AB103129 |  |  |  |  | AB103129 | AB103129 | [NAME] |  |  |  |  |  |  |  | NC_006886
Paraplanocera sp
Phoronis vancouverensis |  |  | [NAME] | AF342797 | AF342797 |  |  |  | AF342797 |  | AF342797
Platynereis dumerilii |  |  | EF117897 |  |  |  |  | ABB29610 |  | AF342797 |  |  |  |  |  |  |  |  | NC_000931
Priapulus caudatus |  |  | Z38009 | AY210840 | AY210840 |  |  | ABB29632 | AY210840 | AY210840 | AAT06193 |  |  |  |  |  |  |  | NC_008557
Ptychodera flava |  |  | AF278681 |  |  |  |  |  |  |  | AAT06192
Richtersius coronifer |  |  | DQ839604 |  |  |  |  |  |  |  | AAQ88244
Saccoglossus kowalevskii |  |  | L28054 | AF212175 | AF212175 |  |  |  | AF212175 | AF212175 | AAT06190
Schmidtea mediterranea |  |  |  | DQ665992 | AF047854 |  |  |  | DQ665992 | DQ665992 | DQ665992 |  |  |  |  |  |  |  | NC_007438
Scutigera coleoptrata |  |  | AF173238 | DQ222141 | AY859601 |  |  |  | DQ222141 | DQ222141 | [NAME]
Sphaeroforma arctica |  |  | Y16260 |  |  |  |  |  |  |  | ABD67498 |  |  |  |  |  |  |  | NC_005870
Spinochordodes tellinii |  |  | AF421773
Terebratalia transversa |  |  | AF025945 | AF342802 | AF342802 |  |  |  |  | AF342802
Themiste lageniformis |  |  | AF519249 |  |  |  |  |  | AF342802 |  | ABI13290 |  |  |  |  |  |  |  | NC_003086
Trichinella spiralis |  |  | U60231 | AF342803 | AF342803 |  |  |  | AF342803 | AF342803 | AF342803 |  |  |  |  |  |  |  | NC_002681
Turbanella ambronensis
Urechis caupo |  |  | AF119076 | AF342804 | AF342804 |  |  |  | AF342804 | AF342804 | ABI13284 |  |  |  |  |  |  |  | NC_006379
Xenoturbella bocki |  |  | AY291292 |  |  |  |  |  |  |  | ABI99487 |  |  |  |  |  |  |  | NC_008556
Xiphinema index |  |  | AY687997
 | 24 taxa analysis
 | fill in from Dunn et al 2008
gene abbreviations:
18S | 18S ribosomal RNA
28S | 28S ribosomal RNA
5.8S | 5.8S ribosomal RNA
ACT | actin
BRA | brachyury
BTU | beta tubulin
CDC42 | cell division cycle 42
DCR | Dicer
EF1A | eukaryotic translation elongation factor 1 alpha
HSP70 | Heat shock protein
ATP1a | Na+/K+ -ATPase alpha
PAX | paired box gene
RAN | RAN, member RAS oncogene family
[NAME] | ribosomal protein S2
RPOIII | DNA directed RNA polymerase III
EIF2 | translation initiation factor (eIF-2) gamma