Table 1 Detailed taxonomic placement and GenBank accession numbers of taxa included in the current study

Cidaroida, Cidaridae

Cidaroid

sp.

–

–

MG198151^b,d

MNHN IE-2007-3745

Cidaroida, Cidaridae

Eucidaris

metularia

–

–

MG198152^b,d

SMNH Ec 25,624

Cidaroida, Cidaridae

Prionocidaris

sp.

–

–

MG198153^b,d

MNHN IE-2007-3764

Cidaroida, Cidaridae

Prionocidaris

sp.

–

–

MG198154^b,d

MNHN IE-2013-8705

Echinothurioida, Echinothuriidae

Araeosoma

splendens

–

–

MG198163^b,d

MNHN IE-2007-1143

Echinothurioida, Echinothuriidae

Asthenosoma

varium

–

–

MG198164^b,d

SMNH Ec 25,628

Diadematoida, Diadematidae

Diadema

setosum

KX385835^c,b

KX385835^c,b

KX385835^c,b

Diadematoida, Diadematidae

Diadema

setosum

–

–

MG198159^b,d

SMNH Ec 25,437

Diadematoida, Diadematidae

Diadema

setosum

–

–

MG198160^b,d

SMNH Ec 25,625

Diadematoida, Diadematidae

Diadema

setosum

–

–

MG198161^b,d

SMNH Ec 25,626

Diadematoida, Diadematidae

Diadema

setosum

–

–

MG198162^b,d

SMNH Ec 25,627

Diadematoida, Diadematidae

Echinothrix

diadema

KX385836^c

KX385836^c

KX385836^c

Micropygoida, Micropygidae

Micropyga

tuberculata

–

–

MG198165^b,d

MNHN IE-2007-1152

Salenioida, Saleniidae

Salenia

phoinissa

–

–

MG198166^b,d

MNHN IE-2007-3765

Stomopneustoida, Glyptocidaridae

Glyptocidaris

crenularis

KX638403^c,a

KX638403^c,a

KX638403^c,a

Arbacioida, Arbaciidae

Arbacia

lixula

X80396^c,b

X80396^c,b

X80396^c,b

Camarodonta, Echinidae

Sterechinus

neumayeri

KJ680295^c

KJ680295^c

KJ680295^c

Camarodonta, Echinidae

Sterechinus

neumayeri

KF214257^c,a

KF214257^c,a

KF214257^c,a

Camarodonta, Echinometridae

Echinometra

mathaei

KJ680291^c

KJ680291^c

KJ680291^c

Camarodonta, Echinometridae

Echinometra

sp.

–

–

MG198122^b,d

SMNH OB ZNZ16

Camarodonta, Echinometridae

Echinometra

sp.

–

–

MG198123^b,d

SMNH OB ZNZ37

Camarodonta, Echinometridae

Echinometra

sp.

–

–

MG198124^b,d

SMNH OB ZNZ54

Camarodonta, Echinometridae

Heliocidaris

crassispina

KC479025^c

KC479025^c

KC479025^c

Camarodonta, Echinometridae

Heterocentrotus

mammillatus

KJ680292^c

KJ680292^c

KJ680292^c

Camarodonta, Echinometridae

Zenocentrotus

kellersi

–

–

MG198150^b,d

USNM E40502

Camarodonta, Parechinidae

Loxechinus

albus

JX888466^c,b

JX888466^c,b

JX888466^c,b

Camarodonta, Parechinidae

Loxechinus

albus

KC490910^c,b

KC490910^c,b

KC490910^c,b

Camarodonta, Parechinidae

Paracentrotus

lividus

J04815^c,b

J04815^c,b

J04815^c,b

Camarodonta, Parechinidae

Paracentrotus

lividus

–

–

MG198127^b,d

SMNH Ec 25,622

Camarodonta, Strongylocentrotidae

Hemicentrotus

pulcherrimus

KC898202^c,a

KC898202^c,a

KC898202^c,a

Camarodonta, Strongylocentrotidae

Hemicentrotus

pulcherrimus

KC490911^c,b

KC490911^c,b

KC490911^c,b

Camarodonta, Strongylocentrotidae

Mesocentrotus

franciscanus

KJ526170^c,a

KJ526170^c,a

KJ526170^c,a

Camarodonta, Strongylocentrotidae

Mesocentrotus

nudus

JX263663^c,b

JX263663^c,b

JX263663^c,b

Camarodonta, Strongylocentrotidae

Mesocentrotus

nudus

KC898201^c,a

KC898201^c,a

KC898201^c,a

Camarodonta, Strongylocentrotidae

Pseudocentrotus

depressus

KC490913^c

KC490913^c

KC490913^c

Camarodonta, Strongylocentrotidae

Strongylocentrotus

droebachiensis

EU054306^c,a

EU054306^c,a

EU054306^c,a

Camarodonta, Strongylocentrotidae

Strongylocentrotus

droebachiensis

AM900391^c,b

AM900391^c,b

AM900391^c,b

Camarodonta, Strongylocentrotidae

Strongylocentrotus

fragilis

KC898198^c,a

KC898198^c,a

KC898198^c,a

Camarodonta, Strongylocentrotidae

Strongylocentrotus

intermedius

KC490912^c

KC490912^c

KC490912^c

Camarodonta, Strongylocentrotidae

Strongylocentrotus

intermedius

KC898200^c,a

KC898200^c,a

KC898200^c,a

Camarodonta, Strongylocentrotidae

Strongylocentrotus

pallidus

AM900392^c

AM900392^c

AM900392^c

Camarodonta, Strongylocentrotidae

Strongylocentrotus

purpuratus

X12631^c,b

X12631^c,b

X12631^c,b

Camarodonta, Temnopleuridae

Mespilia

globulus

KJ680293^c

KJ680293^c

KJ680293^c

Camarodonta, Temnopleuridae

Microcyphus

rousseaui

–

–

MG198126^b,d

SMNH Ec 25,621

Camarodonta, Temnopleuridae

Salmacis

bicolor bicolor

–

–

MG198130^b,d

SMNH Ec 25,623

Camarodonta, Temnopleuridae

Salmacis

bicolor rarispina

KU302104^c

KU302104^c

KU302104^c

Camarodonta, Temnopleuridae

Salmacis

sphaeroides

KU302103^c

KU302103^c

KU302103^c

Camarodonta, Temnopleuridae

Temnopleurus

hardwickii

KP070768^c,b

KP070768^c,b

KP070768^c,b

Camarodonta, Temnopleuridae

Temnopleurus

reevesii

KU302106^c

KU302106^c

KU302106^c

Camarodonta, Temnopleuridae

Temnopleurus

toreumaticus

KU302105^c

KU302105^c

KU302105^c

Camarodonta, Toxopneustidae

Lytechinus

variegatus

–

–

MG198125^b,d

SMNH Ec 25,620

Camarodonta, Toxopneustidae

Pseudoboletia

indiana

–

–

MG198128^b,d

AIM MA 121531.1

Camarodonta, Toxopneustidae

Pseudoboletia

indiana

–

–

MG198129^b,d

AIM MA 121531.2

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198131^b,d

NHMW-DNAtis_26362

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198132^b,d

NHMW-DNAtis_26363

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198133^b,d

NHMW-DNAtis_26364

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198134^b,d

NHMW-DNAtis_26365

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198135^b,d

NHMW-DNAtis_26366

Camarodonta, Toxopneustidae

Tripneustes

depressus

–

–

MG198136^b,d

NHMW-DNAtis_26367

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

KY268294^c,a

KY268294^c,a

KY268294^c,a

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

KJ680294^c

KJ680294^c

KJ680294^c

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

KY515261^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

KY515262^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

KY515263^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

KY515264^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198149^b,d

CAS 187197

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198137^b,d

NHMW 2017/0125/0001

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198138^b,d

NHMW 2017/0125/0003

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198139^b,d

NHMW 2017/0125/0004

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198140^b,d

NHMW Ev 20,497

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198141^b,d

NHMW Ev 20,498

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198142^b,d

NHMW Ev 20,499

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198143^b,d

NHMW 2016/0329/0001

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198144^b,d

NHMW 2016/0329/0002

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198145^b,d

NHMW 2016/0329/0003

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198146^b,d

NHMW 2016/0329/0004

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198147^b,d

NHMW Ev 20,500

Camarodonta, Toxopneustidae

Tripneustes

gratilla gratilla

–

–

MG198148^b,d

NHMW Ev 20,501

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515254^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515255^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515256^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515257^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515258^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515259^b

Camarodonta, Toxopneustidae

Tripneustes

gratilla elatensis

–

–

KY515260^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515241^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515242^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515243^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515244^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515245^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515246^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515247^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515248^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515249^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515250^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515251^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515240^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515252^b

Camarodonta, Toxopneustidae

Tripneustes

kermadecensis

–

–

KY515253^b

Clypeasteroida, Clypeasteroidae

Arachnoides

sp.

–

–

MG198155^b,d

QM NO1_F4

Clypeasteroida, Clypeasteroidae

Arachnoides

sp.

–

–

MG198156^b,d

QM NO1_F4B

Clypeasteroida, Clypeasteroidae

Clypeaster

rarispinus

–

–

MG198157^b,d

MNHN IE-2013-8702

Clypeasteroida, Clypeasteroidae

Clypeaster

rarispinus

–

–

MG198158^b,d

MNHN IE-2013-8704

Spatangoida, Loveniidae

Echinocardium

cordatum

FN562581^c,b

FN562581^c,b

FN562581^c,b

Spatangoida, Maretiidae

Nacospatangus

alta

KC990834^c,b

KC990834^c,b

KC990834^c,b

Spatangoida, Pericosmidae

Pericosmus

bidens

–

–

MG198167^b,d

MNHN IE-2007-1138

Spatangoida, Pericosmidae

Pericosmus

bidens

–

–

MG198168^b,d

MNHN IE-2013-8706

Spatangoida, Pericosmidae

Pericosmus

bidens

–

–

MG198169^b,d

MNHN IE-2013-8707

Spatangoida, Pericosmidae

Pericosmus

bidens

–

–

MG198170^b,d

MNHN IE-2013-8708