I ran HISAT2 to get alignments for the E5 Porites data using P. lobata and P. evermanni references from here. Looks like the P. evermanni reference wins out with higher overall alignments.

Porites lobata

Run Paired Reads Aligned Concordantly 0 Times Aligned Concordantly Exactly 1 Time Aligned Concordantly >1 Times Aligned Discordantly 1 Time Overall Alignment Rate
1 50,831,351 16,973,703 8,204,327 25,653,321 510,835 73.58%
2 51,385,213 12,840,566 5,019,290 33,525,357 327,247 79.12%
3 49,828,147 15,597,984 7,821,811 26,408,352 440,009 74.77%
4 49,976,568 10,802,392 5,426,523 33,747,653 349,808 82.63%
5 48,908,730 20,325,695 9,895,038 18,687,997 609,205 67.15%

Porites evermanni

Run Paired Reads Aligned Concordantly 0 Times Aligned Concordantly Exactly 1 Time Aligned Concordantly >1 Times Aligned Discordantly 1 Time Overall Alignment Rate
1 50,831,351 11,712,763 30,209,320 8,909,268 2,145,413 86.40%
2 51,385,213 11,914,068 28,680,866 10,790,279 2,306,668 87.10%
3 49,828,147 11,096,891 29,566,240 9,165,016 1,929,423 85.96%
4 49,976,568 10,514,435 27,932,980 11,529,153 2,532,283 89.07%
5 48,908,730 12,403,366 28,498,490 8,006,874 2,215,956 84.18%