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.2015 Dec 10:5:18211.
doi: 10.1038/srep18211.

Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

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Genome-wide SNP analysis explains coral diversity and recovery in the Ryukyu Archipelago

Chuya Shinzato et al. Sci Rep..

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.

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Figures

Figure 1
Figure 1. A scleractinian coral,Acropora digitifera, and sampling locations in the southern Ryukyu Archipelago.
(a) Typical habitat ofA. digitifera colonies used in this study. Some colonies are exposed to air at low tide. Photo taken at Uehara, Iriomote Island. (b) Overview of Okinawa prefecture. Blue arrows indicate the Kuroshio Current in May 2014, based on the Japan Meteorological Agency website (http://www.jma.go.jp/jma/indexe.html). (c) Sampling sites at Okinawa Island, (d) the Kerama islands, (e) the Yaeyama islands (Ishigaki and Iriomote islands are identified). A shape file for Okinawa prefecture was downloaded from National Land Numerical Information, Japan (http://nlftp.mlit.go.jp/ksj/gmlold/index.html) and was visualized as maps using maptools in R (version 3.1.1). All maps are oriented with North at the top.
Figure 2
Figure 2. Principal components analysis and genetic distances and suggest the existence of four clusters in the sRA, located in Okinawa, the KIs, Yaeyama North, and Yaeyama South.
(a) Principal components analysis (PCA) of the filtered dataset of 122 individuals and 905,561 SNPs after trimming of related samples with smartrel and outliers with smartpca. Tracy-Widom statistical significance of PC1 and PC2 was <1e−35. Individuals from Okinawa Island, the KIs, and the YIs are shown with squares, circles, and triangles, respectively. Four subpopulations, Okinawa, Kerama, Yaeyama-North, and Yaeyama-South are circled in green, pink, blue, and purple dotted lines, respectively. (b) Heatmap showing pairwiseFst values based on Weir and Cockerham weighted estimates between sampling sites. All points were clustered by pairwiseFst values, based on the Complete Linkage Clustering method. Site combinations without boxed bold lines indicate significant differences (p-value < 0.001, ANOVA statistics across 10 eigenvectors in PCA).
Figure 3
Figure 3. Migration patterns ofA. digitifera in the sRA, showing that the YI populations function as source populations for OI, while the KIs constitute a historical sink.
Inferred tree ofA. digitifera populations in the sRA with thirteen migration events. Migration arrows are colored according to their weight. The migration weight represents the fraction of ancestry derived from the migration edge. Migration edges with p-value estimated by jackknife to be below 0.01 are shown. Migration edges with bootstrap support less than 50% are shown with dotted lines. Horizontal branch lengths are proportional to the amount of genetic drift that has occurred in each branch.
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