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R Soc Open Sci
2016 Aug 31;38:160253. doi: 10.1098/rsos.160253.
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Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore''s populations of the broadcast spawning sea star Protoreaster nodosus.
Tay YC
,
Chng MW
,
Sew WW
,
Rheindt FE
,
Tun KP
,
Meier R
.
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The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore''s populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.
Figure 1. Locations of Protoreaster nodosus populations from Singapore and Crandall et al. [10] analysed in this study (numbered black circles). Corresponding specific site names are in the electronic supplementary material, table S1. Sampling locations in Singapore are presented in the inset map. Boundaries of the Coral Triangle are highlighted with a dotted line.
Figure 2. Average genetic diversities of three sampling localities in Singapore and nine from within the Coral Triangle based on COI data. Different sample sizes were accounted for by 30 sets of random subsamples of 15 individuals per sampling locality. Number of haplotypes per site are represented on the x-axis, haplotype diversities on the y-axis. Standard error bars are indicated. Specific site diversity and standard error values are in the electronic supplementary material, table S1.
Figure 3. Minimum spanning network for Protoreaster nodosus populations in Singapore and the Coral Triangle based on COI sequence data. All samples from within the Coral Triangle are grouped together as the lightest shade of grey. Each haplotype is represented by one circle and separated by one mutational step, unless indicated by additional hatch marks. Diameters of circles are proportionate to the frequency of each haplotype occurrence, ranging from 1 to 29, except for the most common haplotype (178) which was scaled down.
Figure 4. Frequency distribution of the number of pairwise sequence differences among individuals from each sampling locality in Singapore ((a)(i–iii)), and across the Coral Triangle ((b–d)(i–iii)). *p-value of SSD test for goodness-of-fit with the model of sudden population expansion was significant at the 0.05 level.
Figure 5. STRUCTURE barplots at K = 2 and K = 4 calculated over 10 iterations (dataset of 6140 SNPs; M = 4, m = 5,10, MAF > 0.06). Each bar depicts the genotype assignment for each individual. Barplots at other SNP-calling parameter sets showed similar profiles (data not shown).
Figure 6. DAPC plots when one (a) and two (b) discriminant functions were retained (dataset of 6140 SNPs; M = 4, m = 5,10, MAF > 0.06). Similar cluster profiles were observed for other SNP-calling parameter sets (electronic supplementary material, figures S7–S9).
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