Appendix 1—table 2. Details of molecular datasets and supermatrix.
Statistics for raw reads and assemblies are shown for datasets incorporated in this study relative to the sampling of Mongiardino Koch et al., 2018 and Mongiardino Koch and Thompson, 2021d, where similar statistics can be found for the other datasets. Taxa are shown in alphabetical order; those identified with ‘OG’ are outgroup taxa (i.e., non-echinoids). Novel datasets correspond to Illumina pair-end transcriptomes, except for two draft genomes (Bathysalenia phoinissa and Micropyga tuberculata). Mean insert size is expressed in number of base pairs. For transcriptomes, read pairs (initial) shows numbers input into Agalma (Dunn et al., 2013), that is, after processing with Trimmomatic (Bolger et al., 2014) or UrQt (Modolo and Lerat, 2015), while read pairs (retained) show those that passed the Agalma curation checks (including ribosomal, adapter, quality, and compositional filters), and represent the final number of read pairs used for assembly. For genomes, see information in the bioinformatic details above. Assemblies were further sanitized with either alien_index (Ryan, 2014) alone or in combination with CroCo (Simion et al., 2018), and the number of assembled transcripts/contigs shows the size of datasets after these curation steps. The number of loci shows the occupancy of terminals in the supermatrix output by Agalma (1346 loci at 70% occupancy), after which loci were further removed by TreeShrink (Mai and Mirarab, 2018), resulting in the final occupancy scores.
| Species | Mean insert size | Read pairs (initial) | Read pairs (retained) | Assembled transcripts/contigs | Number of loci | Removed by TreeShrink | Final occupancy |
|---|---|---|---|---|---|---|---|
| Abatus agassizii | – | – | – | – | 522 | 5 | 38.4 |
| Abatus cordatus | – | – | – | – | 497 | 2 | 36.8 |
| Acanthaster planci (OG) | – | – | – | – | 864 | 8 | 63.6 |
| Amphiura filiformis (OG) | 180.1 | 61,558,173 | 52,206,727 | 416,946 | 761 | 8 | 55.9 |
| Apatopygus recens | 415.3 | 74,315,687 | 56,898,850 | 274,380 | 1152 | 5 | 85.2 |
| Apostichopus japonicus (OG) | – | – | – | – | 849 | 9 | 62.4 |
| Araeosoma leptaleum | – | – | – | – | 1184 | 2 | 87.8 |
| Arbacia lixula | – | – | – | – | 1234 | 1 | 91.6 |
| Aspidodiadema hawaiiense | 228.7 | 109,716,219 | 104,518,714 | 311,032 | 1060 | 11 | 77.9 |
| Asterias rubens (OG) | 230.4 | 31,890,613 | 25,495,009 | 103,090 | 805 | 9 | 59.1 |
| Asthenosoma varium | – | – | – | – | 1254 | 7 | 92.6 |
| Astrophyton muricatum (OG) | 195.9 | 25,191,954 | 22,281,829 | 149,146 | 478 | 5 | 35.1 |
| Bathysalenia phoinissa | – | – | – | 154,120 | 605 | 6 | 44.5 |
| Brissus obesus | – | – | – | – | 773 | 0 | 57.4 |
| Caenopedina hawaiiensis | – | – | – | – | 1094 | 2 | 81.1 |
| Clypeaster japonicus | 198.6 | 10,505,520 | 9,298,316 | 74,743 | 829 | 1 | 61.5 |
| Clypeaster rosaceus | – | – | – | – | 1242 | 2 | 92.1 |
| Clypeaster subdepressus | – | – | – | – | 1233 | 3 | 91.4 |
| Colobocentrotus atratus | – | – | – | – | 1158 | 0 | 86.0 |
| Conolampas sigsbei | – | – | – | – | 1001 | 5 | 74.0 |
| Cystechinus c.f. giganteus | – | – | – | – | 661 | 0 | 49.1 |
| Dendraster excentricus | – | – | – | – | 337 | 1 | 25.0 |
| Diadema setosum | – | – | – | – | 305 | 1 | 22.6 |
| Echinarachnius parma | – | – | – | – | 1187 | 3 | 88.0 |
| Echinocardium cordatum | – | – | – | – | 1012 | 2 | 75.0 |
| Echinocardium mediterraneum | – | – | – | – | 1185 | 1 | 88.0 |
| Echinocyamus crispus | – | – | – | – | 709 | 6 | 52.2 |
| Echinometra mathaei | – | – | – | – | 1055 | 0 | 78.4 |
| Echinothrix calamaris | 203.9 | 68,871,087 | 60,443,904 | 251,788 | 1252 | 4 | 92.7 |
| Encope emarginata | 206.2 | 12,015,888 | 10,461,870 | 66,241 | 1076 | 1 | 79.9 |
| Eucidaris metularia | 321.6 | 38,802,159 | 29,047,401 | 83,318 | 412 | 2 | 30.5 |
| Eucidaris tribuloides | – | – | – | – | 414 | 0 | 30.8 |
| Evechinus chloroticus | – | – | – | – | 1196 | 1 | 88.8 |
| Fellaster zelandiae | 313.9 | 62,619,791 | 51,742,748 | 168,598 | 1269 | 1 | 94.2 |
| Heliocidaris erythrogramma | – | – | – | – | 931 | 0 | 69.2 |
| Histocidaris variabilis | 329.2 | 84,103,672 | 73,884,180 | 144,044 | 1189 | 5 | 88.0 |
| Holothuria forskali (OG) | – | – | – | – | 743 | 8 | 54.6 |
| Lamberticrinus messingi (OG) | 195.0 | 22,989,820 | 20,234,597 | 59,049 | 351 | 3 | 25.9 |
| Leodia sexiesperforata | 203.8 | 16,211,182 | 14,174,475 | 68,964 | 1064 | 1 | 79.0 |
| Leptosynapta clarki (OG) | – | – | – | – | 403 | 4 | 29.6 |
| Lissodiadema lorioli | – | – | – | – | 770 | 0 | 57.2 |
| Loxechinus albus | – | – | – | – | 1265 | 1 | 93.9 |
| Lytechinus variegatus | – | – | – | – | 1257 | 2 | 93.2 |
| Mellita tenuis | – | – | – | – | 1002 | 1 | 74.4 |
| Meoma ventricosa | – | – | – | – | 1053 | 0 | 78.2 |
| Mesocentrotus nudus | – | – | – | – | 1247 | 0 | 92.6 |
| Metacrinus rotundus (OG) | 198.5 | 23,791,832 | 20,900,345 | 83,718 | 642 | 7 | 47.2 |
| Micropyga tuberculata | – | – | – | 170,514 | 415 | 4 | 30.5 |
| Ophiocoma echinata (OG) | 278.5 | 28,427,026 | 24,836,025 | 130,153 | 712 | 7 | 52.4 |
| Paracentrotus lividus | – | – | – | – | 1266 | 0 | 94.1 |
| Patiria miniata (OG) | – | – | – | – | 740 | 8 | 54.4 |
| Peronella japonica | 208.3 | 17,696,287 | 15,707,931 | 106,110 | 1043 | 6 | 77.0 |
| Prionocidaris baculosa | – | – | – | – | 794 | 3 | 58.8 |
| Psammechinus miliaris | – | – | – | – | 1173 | 1 | 87.1 |
| Rhyncholampas pacificus | 346.8 | 63,116,413 | 52,160,741 | 234,910 | 1070 | 2 | 79.3 |
| Saccoglossus kowalevskii (OG) | – | – | – | – | 668 | 6 | 49.2 |
| Scaphechinus mirabilis | 401.7 | 10,169,195 | 8,796,067 | 127,664 | 974 | 4 | 72.1 |
| Sinaechinocyamus mai | 297.2 | 60,208,172 | 52,265,201 | 164,646 | 1233 | 1 | 91.5 |
| Sphaerechinus granularis | – | – | – | – | 1214 | 1 | 90.1 |
| Sterechinus neumayeri | 207.3 | 26,376,279 | 21,308,840 | 122,001 | 1097 | 1 | 81.4 |
| Stereocidaris nascaensis | 327.0 | 69,962,495 | 60,316,050 | 121,508 | 1200 | 6 | 88.7 |
| Stomopneustes variolaris | – | – | – | – | 908 | 0 | 67.5 |
| Strongylocentrotus purpuratus | – | – | – | – | 1266 | 5 | 93.7 |
| Tetrapygus niger | 202.5 | 63,040,541 | 52,761,671 | 163,084 | 1287 | 2 | 95.5 |
| Tripneustes gratilla | 154.6 | 62,962,239 | 57,015,692 | 130,376 | 1309 | 1 | 97.2 |
| Tromikosoma hispidum | 300.4 | 57,208,357 | 47,909,038 | 234,502 | 1238 | 7 | 91.5 |