Table 1. List of species of Pristigasteridae (21), specimens (45) and molecular markers (with GenBank accession numbers) examined in this study (abbreviations: GB, GenBank; COI, cytochrome oxidase I; cytb, cytochrome b; rag1, recombination activating gene 1; rag2 recombination activating gene 2). GenBank accession numbers of newly determined sequences in this study are in bold. “/” indicates that the respective sequence is not determined. Generic classification of Pristigasteridae follows Whitehead (1985).

Taxa	Specimen code	COI	12S	16S	cytb	rag1	rag2
Raconda
Raconda russeliana	KU02b	MH325626	MH325563	MH325533	MH325593	MH325506	MH325475
	KU03b	MH325627	MH325564	MH325534	MH325594	/	MH325476
Ilisha
Ilisha elongata	WJC2067	MH325628	MH325565	MH325535	MH325595	MH325507	MH325477
	ILEL (GB)	AP009141	AP009141	AP009141	AP009141	JX255541	DQ912160
	KU23b	MH325629	MH325566	MH325536	MH325596	MH325508	MH325478
Ilisha melastoma	HH51	MH325630	MH325568	MH325537	MH325597	MH325509	MH325479
	HH70	MH325631	MH325569	MH325538	MH325598	MH325510	MH325480
	MAY22	MH325632	MH325570	MH325539	MH325599	MH325511	MH325481
	MAY29	MH325633	MH325571	MH325540	MH325600	MH325512	MH325482
	MAY219	MH325634	MH325572	MH325541	MH325601	MH325513	MH325483
	SRI79	/	MH325573	MH325542	MH325602	MH325514	MH325484
	SRI80	/	MH325574	MH325543	MH325603	MH325515	MH325485
Ilisha cf. megaloptera	DDB3240 (GB)	/	/	KJ158118	KJ158079	/	KJ158099
Ilisha filigera	KU15	MH325635	MH325575	MH325544	MH325604	MH325516	MH325486
	KU17	MH325636	MH325576	MH325545	MH325605	/	MH325487
	KU30b	MH325637	MH325567	MH325546	MH325606	MH325517	MH325488
	MAY362	/	MH325577	MH325547	MH325607	MH325518	MH325489
Ilisha pristigastroides	MAY543	MH325638	MH325578	MH325548	MH325608	MH325519	MH325490
	MAY544	MH325639	MH325579	MH325549	MH325609	MH325520	MH325491
	KU15b	MH325640	MH325580	MH325550	MH325610	MH325521	MH325492
	KU16b	MH325641	MH325581	MH325551	MH325611	MH325522	MH325493
Ilisha macrogaster	KU14	/	MH325582	MH325552	MH325612	MH325523	MH325494
	SI05	MH325642	MH325583	MH325553	MH325613	MH325524	MH325495
Ilisha striatula	SRI03	/	MH325584	MH325554	MH325614	MH325525	MH325496
	SRI04	/	MH325585	MH325555	MH325615	/	/
	Ra37	MH325643	/	/	MH325616	MH325526	MH325497
Ilishakampeni	CL04 (GB)	AP011609	AP011609	AP011609	AP011609	/	/
	Bk03	MH325644	/	/	MH325617	MH325527	MH325498
	Ra42	MH325645	/	/	MH325618	MH325528	MH325499
Ilisha sirishae	SRI77	MH325646	MH325586	MH325556	MH325619	/	/
	SRI78	MH325647	MH325587	MH325557	MH325620	/	MH325500
Ilisha africana	ILAF (GB)	AP009140	AP009140	AP009140	AP009140	/	/
Ilisha amazonica	DDB717 (GB)	/	/	KJ158134	KJ158097	KJ158151	KJ158115
Opisthopterus
Opisthopterus tardoore	MAY20	MH325648	MH325588	MH325558	MH325621	/	MH325501
	MAY118	MH325649	MH325589	MH325559	MH325622	MH325529	MH325502
	SRI01	/	MH325590	MH325560	MH325623	MH325530	MH325503
	SRI02	/	MH325591	MH325561	MH325624	MH325531	MH325504
Opisthopterus valenciennesi	KU21b	/	MH325592	MH325562	MH325625	MH325532	MH325505
Pellona
Pellona ditchela	/ (GB)	JF494121	/	/	/	/	/
Pellona flavipinnis	/ (GB)	AP009619	AP009619	AP009619	AP009619	AY430206	DQ912134
Pellona harroweri	DDB4309 (GB)	JX124858	KJ158143	KJ158126	KJ158088	KJ158143	KJ158107
Pristigaster
Pristigaster cayana	DDB657 (GB)	/	/	KJ158133	KJ158096	/	KJ158114
Pristigaster whiteheadi	DDB4397 (GB)	/	/	KJ158127	KJ158089	KJ158144	/
Odontognathus
Odontognathus mucronatus	DDB3595 (GB)	JX124826	/	KJ158122	KJ158082	/	/
Chirocentrodon
Chirocentrodon bleekerianus	DDB3452 (GB)	/	/	KJ158121	/	/	/
Ougroup (family Engraulidae):
Coilia nasus	/ (GB)	AP009135	AP009135	AP009135	AP009135	DQ912123	DQ912157