Abstract
Following a global coral bleaching event in 1998, Acropora corals surrounding most of Okinawa island (OI) were devastated, although they are now gradually recovering. In contrast, the Kerama Islands (KIs) only 30 km west of OI, have continuously hosted a great variety of healthy corals. Taking advantage of the decoded Acropora digitifera genome and using genome-wide SNP analyses, we clarified Acropora population structure in the southern Ryukyu Archipelago (sRA). Despite small genetic distances, we identified distinct clusters corresponding to specific island groups, suggesting infrequent long-distance dispersal within the sRA. Although the KIs were believed to supply coral larvae to OI, admixture analyses showed that such dispersal is much more limited than previously realized, indicating independent recovery of OI coral populations and the necessity of local conservation efforts for each region. We detected strong historical migration from the Yaeyama Islands (YIs) to OI, and suggest that the YIs are the original source of OI corals. In addition, migration edges to the KIs suggest that they are a historical sink population in the sRA, resulting in high diversity. This population genomics study provides the highest resolution data to date regarding coral population structure and history.
Highlights
For studying population structure and historical migration patterns of various organisms[17,18] including fishes[19,20] and a seahorse[21]
We collected a total of 155 individual colonies from OI, the KIs and the Yaeyama Islands (YIs) (Fig. 1b–e)
Subsequent removal of SNPs that showed extensive deviation (p < 0.001) from Hardy-Weinberg equilibrium (HWE), with a call rate less than 99% and with a very low minor allele frequency, yielded 905,561 SNPs
Summary
For studying population structure and historical migration patterns of various organisms[17,18] including fishes[19,20] and a seahorse[21]. Using the decoded genome of A. digitifera, we performed the first genome-wide SNP analysis of corals and succeeded in mapping detailed population structure and migration patterns of A. digitifera in the sRA. We tried to estimate individual ancestries of A. digitifera populations in the sRA using model-based clustering methods, ADMIXTURE26 and fastSTRUCTURE27 (for an example, see Supplementary Fig. 3), but we failed to detect clear population structure.
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