Table 1 Information on the species and sequences used in the analysis. Sampling locality is shown for newly sequenced taxa, citations for data obtained from the literature. For deep-sea specimens, sampling depth is also reported
From: A phylogenomic resolution of the sea urchin tree of life
Clade | Species | Data typea | Sampling locality (depth)/Source | Voucher number | SRA/Genome numbers |
|---|---|---|---|---|---|
Arbacioida Gregory, 1900 | Arbacia punctulata (Lamarck, 1816) | T | [43] | SIO-BIC E6740 | SRR2843235 |
Camarodonta Jackson, 1912 | Colobocentrotus atratus (Linnaeus, 1758) | T | Kailua Kona, Hawaii Island | SIO-BIC E7012 | SRR7513588 |
| Â | Echinometra mathaei (Blainville, 1825) | T | Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia | SIO-BIC E6896 | SRR7513581 |
|  | Evechinus chloroticus (Valenciennes, 1846) | T | [131] | – | SRR1014619 |
|  | Heliocidaris erythrogramma (Valenciennes, 1846) | T | [132] | – | SRR1211283 |
|  | Lytechinus variegatus (Lamarck, 1816) | T | [5] | – | SRR1139214 |
|  | Mesocentrotus nudus (A. Agassiz, 1864) | T | [133] | – | SRR5017175 |
|  | Paracentrotus lividus (Lamarck, 1816) | T | [134] | – | SRR1735501 |
|  | Sphaerechinus granularis (Lamarck, 1816) | T | [5] | – | SRR1139199 |
|  | Strongylocentrotus purpuratus (Stimpson, 1857) | G | [45]; Spur_4.2 | – | GCF 000002235.4 |
Cidaroida Claus, 1880 | Eucidaris tribuloides (Lamarck, 1816) | T | [43] | SIO-BIC E6742 | SRR2844625 |
| Â | Prionocidaris baculosa (Lamarck, 1816) | T | Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia | SIO-BIC E6897 | SRR7513584 |
Clypeasteroida sensu A. Agassiz, 1872-1874 | Clypeaster rosaceus (Linnaeus, 1758) | T | Bocas del Toro, Panama | – | SRR7513591 |
|  | Clypeaster subdepressus (Gray, 1825) | T | Bocas del Toro, Panama | – | SRR7513586 |
| Â | Dendraster excentricus (Eschscholtz, 1831) | T | [43] | SIO-BIC E5640 | SRR2844623 |
|  | Echinarachnius parma (Lamarck, 1816) | T | [5] | – | SRR1139193 |
| Â | Echinocyamus crispus Mazetti, 1893 | T | Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia | SIO-BIC E6903 | SRR7513576 |
| Â | Mellita tenuis H.L. Clark, 1940 | T | Apalachee Bay, Wakulla County, Florida | SIO-BIC E7015 | SRR7513583 |
Diadematoida Duncan, 1889 | Diadema setosum (Leske, 1778) | T | Al-Fahal Reef, Red Sea, Makkah, Saudi Arabia | SIO-BIC E6905 | SRR7513577 |
| Â | Lissodiadema lorioli Mortensen, 1903 | T | Kaneohe Bay, Honolulu, Hawaii Island | UF Echino 18893 | SRR7513580 |
Echinolampadoida Kroh & Smith, 2010 | Conolampas sigsbei (A. Agassiz, 1878) | T | Willemstad, Curaçao (233–300 m) | – | SRR7513579 |
Echinothurioida Claus, 1880 | Araeosoma leptaleum A. Agassiz & H.L. Clark, 1909 | T | Mount Quepos, Pacific Ocean, Costa Rica (1097 m) | SIO-BIC E7021 | SRR7513578 |
|  | Asthenosoma varium Grube, 1868 | T | Momi Bay, Viti Levu, Fiji | – | SRR7513575 |
Holasteroida Durham & Melville, 1957 | Pilematechinus sp. | T | Axial Seamount, Juan de Fuca Ridge (1550 m) | SIO-BIC E6947 | SRR7513585 |
Pedinoida Mortensen, 1939 | Caenopedina hawaiiensis H.L. Clark, 1912 | T | Mount Quepos, Pacific Ocean, Costa Rica (1908 m) | SIO-BIC E7020 | SRR7513589 |
Spatangoida L. Agassiz, 1840 | Brissus obesus Verrill, 1867 | T | San Clemente Island, California | SIO-BIC E7018 | SRR7513590 |
|  | Meoma ventricosa (Lamarck, 1816) | T | Bocas del Toro, Panama | – | SRR7513582 |
Stomopneustoida Kroh & Smith, 2010 | Stomopneustes variolaris (Lamarck, 1816) | T | Sohoa, Mayotte | SIO-BIC E7014 | SRR7513587 |
Holothuroidea de Blainville, 1834 | Holothuria forskali Delle Chiaje, 1823 | T | [135] | – | SRR5109955 |
Asteroidea de Blainville, 1830 | Acanthaster planci (Linnaeus, 1758) | G | [136]; OKI-Apl_1.0 | – | GCA 001949145.1 |
|  | Patiria miniata (Brandt, 1835) | G | [44]; Pmin_1.0 | – | GCA 000285935.1 |
Hemichordata Bateson, 1885 | Saccoglossus kowalevskii A. Agassiz 1873 | G | [137]; Skow_1.1 | – | GCA 000003605.1 |