Table 6 Details about the sampling and methods used for SNP discovery for each species.

Species	Source	Method	Samples	Origin
Tambaqui	Hatchery 1—broodstock	ddRADseq^a	11	South Brazil
	Hatchery 2—broodstock	ddRADseq^a	17	South Brazil
	Hatchery 3—broodstock	ddRADseq^a	17	South Brazil
	Hatchery 4—broodstock	ddRADseq^a	15	North Brazil
	Hatchery 5—broodstock	ddRADseq^a	18	North Brazil
	Hatchery 6—broodstock	ddRADseq^a	21	North Brazil
	Hatchery 7—broodstock	ddRADseq^a	15	Colombia
	Hatchery 8—broodstock	ddRADseq^a	16	Colombia
	Hatchery 9—broodstock	ddRADseq^a	31	Peru
	Hatchery 10—broodstock	ddRADseq^a	8	Peru
	Breeding nucleus (Caunesp)—broodstock	ddRADseq^a	29	South Brazil
	Breeding nucleus (Caunesp)—20 full-sib families	ddRADseq^b	600	South Brazil
	Nunes et al.¹⁶—1 full-sib family	GBS	124	North Brazil
	Ariede et al.¹⁴—pool of 10 random individuals	RNA-Seq	10	South Brazil
	Gomes et al.⁴⁷—pool of 8 random individuals	RNA-Seq	8	North Brazil
Pacu	Mastrochirico-Filho et al.¹⁷—14 full-sib families	RADseq	400	South Brazil
	Breeding nucleus (Caunesp)—3 full-sib families	ddRADseq^a	100	South Brazil
	Mastrochirico-Filho et al.⁴⁶—3 full-sib families	RNA-Seq	36	South Brazil

^aEnzyme combination I (SphI and MluCI).
^b3 families used the enzyme combination I (SphI and MluCI) and 17 families used the combination II (NlaIII and MluCI).

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