Genetic analysis and identification of genetic lineages

Tissue was collected from a subset of colonies present in the photoquadrats used to estimate mortality. Tissue was collected in February from a total of 68 colonies from Sites 1 (n = 7), 2 (n = 30), 3 (n = 19), and 5 (n = 12). Of these 68 colonies, 51 colonies were tracked between February 2019 (before the bleaching) and August 2019 (after the bleaching). Tissue was collected in August from a total of 394 colonies from Sites 1 (n = 65), 2 (n = 69), 3 (n = 42), 4 (n = 83), 5 (n = 68), and 6 (n = 67; Table 1).

Mitochondrial Open Reading Frame (mtORF) haplotypes (type 1–8 after Pinzón and LaJeunesse [2011], Pinzón et al. [2013] and type 10 and 11 after Forsman et al. [2013]), nominal species (after Gélin et al. [2017] and Johnston et al. [2017]), and sample sizes from February and August 2019 used in this study.

Genus is Pocillopora. PSH, Primary Species Hypothesis, after Gélin et al. (2017).

Following extensive previous genetic studies of Pocillopora throughout the Indo‐Pacific (Flot and Tillier 2007, Souter 2010, Pinzón and LaJeunesse 2011, Pinzón et al. 2013, Forsman et al. 2013, Marti‐Puig et al. 2014, Schmidt‐Roach et al. 2014, Gélin et al. 2017, Johnston et al. 2017, 2018), we used the mitochondrial Open Reading Frame (mtORF) marker, using the FATP6.1 and RORF primers found in Flot et al. (2008), to haplotype individuals (see Appendix S1 for details on the genetic methods). This marker is the most widely used and informative marker currently available for Pocillopora (Johnston et al. 2017). We differentiated P. meandrina and P. eydouxi using a restriction fragment length polymorphism (RFLP) gel‐based assay following Johnston et al. (2018). Samples were identified to haplotype based on previously published sequences of mtORF haplotypes, using the naming conventions in Pinzón and LaJeunesse (2011), Pinzón et al. (2013), Forsman et al. (2013), Edmunds et al. (2016), and Johnston et al. (2017).