Fig 1.
Map of sampling locations in the Fiji Islands adapted from Lal et al. [17], where wild and farmed P. margaritifera were collected.
Reef outlines are presented in dark grey, and site colours correspond to population colour codes used for Figs 2 and 3. Solid circles represent wild oyster collection sites, while circles superimposed with a cross indicate farm locations. Site codes represent the following locations: YW, Naviti Island in the Yasawa group; RA, farm site at Namarai, Ra; SW, farm site at Wailevu, Savusavu; SH, farm site at Wailevu, Savusavu for hatchery produced oysters; SV, farm site at Vatubukulaca, Savusavu; RV, farm site at Raviravi; UD, Vunikodi, Udu Point; TV, farm site at Wailoa, Taveuni; LN, Nayau Island in the Lau group; KG, Galoa Island off Kadavu Island and KR, Ravitaki on Kadavu Island.
Table 1.
Genetic diversity indices for the wild and farmed P. margaritifera populations examined.
Fig 2.
Discriminant Analysis of Principal Components (DAPC) scatter plot (A) and individual density plot on the first discriminant function (B), drawn across 427 P. margaritifera individuals in the R package adegenet. Dots represent individuals, with colours denoting sampling origin and inclusion of 95% inertia ellipses. Site colours correspond with Fig 1, and site numbers are as follows: (1) farm site at Namarai, Ra; (2) farm site at Raviravi; (3) Lau group; (4) Yasawa group; (5) Udu Point; (6) Taveuni; (7) Kadavu (Galoa Island); (8) Kadavu (Ravitaki); (9) farm site at Savusavu (Vatubukulaca); (10) farm site at Savusavu (Wailevu) and (11) farm site at Savusavu (Wailevu, hatchery produced oysters).
Fig 3.
Population network of P. margaritifera individuals created using the Netview P v.0.4.2.5 pipeline after Steinig et al. [64].
The network has been visualised at a maximum number of nearest neighbour (k-NN) threshold of 40, using 4,123 SNPs and 427 individuals. Each dot represents a single individual, and population colours correspond with Figs 1 and 2.
Table 2.
Numbers of putative directional and balancing Fst outlier loci discovered.
Tests were carried out at three False Discovery Rate (FDR) thresholds using BayeScan 2.1 [70] and LOSITAN [72]. Jointly-identified loci were identified using both outlier detection platforms.
Fig 4.
Results of 2009 particle dispersal simulation.
Particle seed locations are shown in the day 1 position output, with the sampling regions colour coded as follows: Kadavu group (red), Yasawa group (pink), Ra (green), Raviravi (purple), Savusavu (orange), Udu Point (brown), Taveuni (light blue) and the central Lau group (dark blue). Simulated particle positions are shown at 15, 30 and 60 day outputs. An animation of dispersal simulation is provided as S4 Fig.