Table 1.

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

Order, Family	Genus	Species	COI	16S	CRA	Voucher No.
Cidaroida, Cidaridae	Cidaroid	sp.	–	–	MG198151b,d	MNHN IE-2007-3745
Cidaroida, Cidaridae	Eucidaris	metularia	–	–	MG198152b,d	SMNH Ec 25,624
Cidaroida, Cidaridae	Prionocidaris	sp.	–	–	MG198153b,d	MNHN IE-2007-3764
Cidaroida, Cidaridae	Prionocidaris	sp.	–	–	MG198154b,d	MNHN IE-2013-8705
Echinothurioida, Echinothuriidae	Araeosoma	splendens	–	–	MG198163b,d	MNHN IE-2007-1143
Echinothurioida, Echinothuriidae	Asthenosoma	varium	–	–	MG198164b,d	SMNH Ec 25,628
Diadematoida, Diadematidae	Diadema	setosum	KX385835c,b	KX385835c,b	KX385835c,b
Diadematoida, Diadematidae	Diadema	setosum	–	–	MG198159b,d	SMNH Ec 25,437
Diadematoida, Diadematidae	Diadema	setosum	–	–	MG198160b,d	SMNH Ec 25,625
Diadematoida, Diadematidae	Diadema	setosum	–	–	MG198161b,d	SMNH Ec 25,626
Diadematoida, Diadematidae	Diadema	setosum	–	–	MG198162b,d	SMNH Ec 25,627
Diadematoida, Diadematidae	Echinothrix	diadema	KX385836c	KX385836c	KX385836c
Micropygoida, Micropygidae	Micropyga	tuberculata	–	–	MG198165b,d	MNHN IE-2007-1152
Salenioida, Saleniidae	Salenia	phoinissa	–	–	MG198166b,d	MNHN IE-2007-3765
Stomopneustoida, Glyptocidaridae	Glyptocidaris	crenularis	KX638403c,a	KX638403c,a	KX638403c,a
Arbacioida, Arbaciidae	Arbacia	lixula	X80396c,b	X80396c,b	X80396c,b
Camarodonta, Echinidae	Sterechinus	neumayeri	KJ680295c	KJ680295c	KJ680295c
Camarodonta, Echinidae	Sterechinus	neumayeri	KF214257c,a	KF214257c,a	KF214257c,a
Camarodonta, Echinometridae	Echinometra	mathaei	KJ680291c	KJ680291c	KJ680291c
Camarodonta, Echinometridae	Echinometra	sp.	–	–	MG198122b,d	SMNH OB ZNZ16
Camarodonta, Echinometridae	Echinometra	sp.	–	–	MG198123b,d	SMNH OB ZNZ37
Camarodonta, Echinometridae	Echinometra	sp.	–	–	MG198124b,d	SMNH OB ZNZ54
Camarodonta, Echinometridae	Heliocidaris	crassispina	KC479025c	KC479025c	KC479025c
Camarodonta, Echinometridae	Heterocentrotus	mammillatus	KJ680292c	KJ680292c	KJ680292c
Camarodonta, Echinometridae	Zenocentrotus	kellersi	–	–	MG198150b,d	USNM E40502
Camarodonta, Parechinidae	Loxechinus	albus	JX888466c,b	JX888466c,b	JX888466c,b
Camarodonta, Parechinidae	Loxechinus	albus	KC490910c,b	KC490910c,b	KC490910c,b
Camarodonta, Parechinidae	Paracentrotus	lividus	J04815c,b	J04815c,b	J04815c,b
Camarodonta, Parechinidae	Paracentrotus	lividus	–	–	MG198127b,d	SMNH Ec 25,622
Camarodonta, Strongylocentrotidae	Hemicentrotus	pulcherrimus	KC898202c,a	KC898202c,a	KC898202c,a
Camarodonta, Strongylocentrotidae	Hemicentrotus	pulcherrimus	KC490911c,b	KC490911c,b	KC490911c,b
Camarodonta, Strongylocentrotidae	Mesocentrotus	franciscanus	KJ526170c,a	KJ526170c,a	KJ526170c,a
Camarodonta, Strongylocentrotidae	Mesocentrotus	nudus	JX263663c,b	JX263663c,b	JX263663c,b
Camarodonta, Strongylocentrotidae	Mesocentrotus	nudus	KC898201c,a	KC898201c,a	KC898201c,a
Camarodonta, Strongylocentrotidae	Pseudocentrotus	depressus	KC490913c	KC490913c	KC490913c
Camarodonta, Strongylocentrotidae	Strongylocentrotus	droebachiensis	EU054306c,a	EU054306c,a	EU054306c,a
Camarodonta, Strongylocentrotidae	Strongylocentrotus	droebachiensis	AM900391c,b	AM900391c,b	AM900391c,b
Camarodonta, Strongylocentrotidae	Strongylocentrotus	fragilis	KC898198c,a	KC898198c,a	KC898198c,a
Camarodonta, Strongylocentrotidae	Strongylocentrotus	intermedius	KC490912c	KC490912c	KC490912c
Camarodonta, Strongylocentrotidae	Strongylocentrotus	intermedius	KC898200c,a	KC898200c,a	KC898200c,a
Camarodonta, Strongylocentrotidae	Strongylocentrotus	pallidus	AM900392c	AM900392c	AM900392c
Camarodonta, Strongylocentrotidae	Strongylocentrotus	purpuratus	X12631c,b	X12631c,b	X12631c,b
Camarodonta, Temnopleuridae	Mespilia	globulus	KJ680293c	KJ680293c	KJ680293c
Camarodonta, Temnopleuridae	Microcyphus	rousseaui	–	–	MG198126b,d	SMNH Ec 25,621
Camarodonta, Temnopleuridae	Salmacis	bicolor bicolor	–	–	MG198130b,d	SMNH Ec 25,623
Camarodonta, Temnopleuridae	Salmacis	bicolor rarispina	KU302104c	KU302104c	KU302104c
Camarodonta, Temnopleuridae	Salmacis	sphaeroides	KU302103c	KU302103c	KU302103c
Camarodonta, Temnopleuridae	Temnopleurus	hardwickii	KP070768c,b	KP070768c,b	KP070768c,b
Camarodonta, Temnopleuridae	Temnopleurus	reevesii	KU302106c	KU302106c	KU302106c
Camarodonta, Temnopleuridae	Temnopleurus	toreumaticus	KU302105c	KU302105c	KU302105c
Camarodonta, Toxopneustidae	Lytechinus	variegatus	–	–	MG198125b,d	SMNH Ec 25,620
Camarodonta, Toxopneustidae	Pseudoboletia	indiana	–	–	MG198128b,d	AIM MA 121531.1
Camarodonta, Toxopneustidae	Pseudoboletia	indiana	–	–	MG198129b,d	AIM MA 121531.2
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198131b,d	NHMW-DNAtis_26362
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198132b,d	NHMW-DNAtis_26363
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198133b,d	NHMW-DNAtis_26364
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198134b,d	NHMW-DNAtis_26365
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198135b,d	NHMW-DNAtis_26366
Camarodonta, Toxopneustidae	Tripneustes	depressus	–	–	MG198136b,d	NHMW-DNAtis_26367
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	KY268294c,a	KY268294c,a	KY268294c,a
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	KJ680294c	KJ680294c	KJ680294c
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	KY515261b
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	KY515262b
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	KY515263b
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	KY515264b
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198149b,d	CAS 187197
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198137b,d	NHMW 2017/0125/0001
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198138b,d	NHMW 2017/0125/0003
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198139b,d	NHMW 2017/0125/0004
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198140b,d	NHMW Ev 20,497
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198141b,d	NHMW Ev 20,498
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198142b,d	NHMW Ev 20,499
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198143b,d	NHMW 2016/0329/0001
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198144b,d	NHMW 2016/0329/0002
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198145b,d	NHMW 2016/0329/0003
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198146b,d	NHMW 2016/0329/0004
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198147b,d	NHMW Ev 20,500
Camarodonta, Toxopneustidae	Tripneustes	gratilla gratilla	–	–	MG198148b,d	NHMW Ev 20,501
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515254b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515255b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515256b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515257b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515258b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515259b
Camarodonta, Toxopneustidae	Tripneustes	gratilla elatensis	–	–	KY515260b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515241b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515242b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515243b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515244b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515245b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515246b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515247b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515248b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515249b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515250b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515251b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515240b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515252b
Camarodonta, Toxopneustidae	Tripneustes	kermadecensis	–	–	KY515253b
Clypeasteroida, Clypeasteroidae	Arachnoides	sp.	–	–	MG198155b,d	QM NO1_F4
Clypeasteroida, Clypeasteroidae	Arachnoides	sp.	–	–	MG198156b,d	QM NO1_F4B
Clypeasteroida, Clypeasteroidae	Clypeaster	rarispinus	–	–	MG198157b,d	MNHN IE-2013-8702
Clypeasteroida, Clypeasteroidae	Clypeaster	rarispinus	–	–	MG198158b,d	MNHN IE-2013-8704
Spatangoida, Loveniidae	Echinocardium	cordatum	FN562581c,b	FN562581c,b	FN562581c,b
Spatangoida, Maretiidae	Nacospatangus	alta	KC990834c,b	KC990834c,b	KC990834c,b
Spatangoida, Pericosmidae	Pericosmus	bidens	–	–	MG198167b,d	MNHN IE-2007-1138
Spatangoida, Pericosmidae	Pericosmus	bidens	–	–	MG198168b,d	MNHN IE-2013-8706
Spatangoida, Pericosmidae	Pericosmus	bidens	–	–	MG198169b,d	MNHN IE-2013-8707
Spatangoida, Pericosmidae	Pericosmus	bidens	–	–	MG198170b,d	MNHN IE-2013-8708

COI - cytochrome c oxidase subunit I, 16S rRNA – ribosomal RNA, CRA -control region area (including the control, adjacent tRNAs and a part of the 12S rRNA genes). Sequence type indicates whether the source sequence was generated by Sanger or next generation sequencing

^asequence data generated by NGS

^bsequence data generated by Sanger sequencing

^cdata retrieved from complete mitochondrial genome sequence

^dsequences generated in the current study

AIM Auckland War Memorial Museum, CAS California Academy of Sciences, MNHN Muséum national d'Histoire naturelle, NHMW Natural History Museum Vienna, QM Queensland Museum, SMNH Steinhardt Museum of Natural History, USNM Smithsonian Institution National Museum of Natural History