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During spawning, the eggs and sperm were separated and then mixed, resulting in larvae from 30 distinct familial crosses. These crosses include three produced from two parents sourced from the warm far northern reef (WW1, WW2, WW3), one cross with a warm dam and cool sire (WC) and one with a cool dam and warm sire (CW).\nThis study focused on the five familial crosses sequenced at both the larval stage (27.5&deg;C) and the juvenile stage (27.5&deg;C and 31&deg;C). Aposymbiotic juveniles were infected with Symbiodinium tridacnidorum, Cladocopium goreaui, and Durusdinium trenchii with cultured material obtained from the AIMS Symbiont Culture Facility. Full details of the collection, environmental parameters of each location, permits, spawning, larval and juvenile rearing, and symbiosis establishment can be found in Quigley et al. (2020)\nIndividual larvae were genotyped (total n = 68) across five families representing three population crosses (n = WW: 34, WC: 15, CW: 19).\nStatistical analysis of SNP metrics were conducted in R, along with modelling SNP frequency distributions. 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