Peralta-Serrano M et al. (2024), Population genomic structure of the sea urchin ...

ECB-ART-53281

Sci Rep 2024 Sep 28;141:22494. doi: 10.1038/s41598-024-73354-3.

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Population genomic structure of the sea urchin Diadema africanum, a relevant species in the rocky reef systems across the Macaronesian archipelagos.

Peralta-Serrano M , Hernández JC , Guet R , González-Delgado S , Pérez-Sorribes L , Lopes EP , Pérez-Portela R .

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The sea urchin Diadema africanum is a macro-herbivore found in the rocky reef systems of the West African region and Macaronesian archipelagos. Over several decades, high densities of this species have generated marine barrens in certain areas at the Canary Islands. In contrast, more recently, during the last few years, the species has suffered mass mortality events that continue to the present day. In this study, we used 9,109 Single Nucleotide Polymorphisms (SNPs) and a fragment of a mitochondrial gene to evaluate the species' population structure, effects of mass mortalities on its diversity, and potential local adaptation across the Canary Islands and Cabo Verde. Our research provides compelling evidence of low genomic diversity and homogeneity across the studied area for neutral markers, along with recent demographic fluctuations. The high connectivity among distant areas likely allows a rapid recovering of the populations from local mortality events. Interestingly, we also observed genomic sub-structure from 405 SNPs identified as candidate loci under selection for seawater temperature. The lack of divergence among distant sites and the low diversity found can be attributed to the species' divergence from a small ancestral genomic pool, followed by a contemporary demographic expansion, and ongoinggene flow.

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	Fig. 1. Sampling sites of Diadema africanum for the COI analyses (black dots) and the SNPs analyses (red dots). The pie charts represent the frequency of COI haplotypes in which each colour partitions correspond to a different haplotype, except for the white colour that represents private haplotypes. (a) General map of the area, (b) the Canary Islands, (c) Cabo Verde, and (d) image of individuals of D. africanum from Tenerife (Canary Islands). (HAP = haplotypes from COI). The maps were created using QGIS v.3.16.16 and edited in Adobe Illustrator. The D. africanum picture belongs to J.C. Hernández.
	Fig. 2. Haplotype network from the COI dataset. Each haplotype is depicted by a circle, and colour partitions indicate the sampling sites where it was sampled. The size of each circle is proportional to the haplotype frequency. Connecting lines among haplotypes represents a mutational step, and asterisks illustrate the non-synonymous substitution. Only the most common haplotypes are presented by their numbers (H1, H3, H4, H6, H8, H12, H14, H25, H29, and H33). This image was created using Popart v.1.7 and edited in Adobe Illustrator.
	Fig. 3. Heatmaps obtained from the FST values using SNPs. (a) Results from the FST obtained from the neutral SNPs dataset, and the candidate SNPs dataset (b). Values and significance of the FST statistics are included as Supplementary material (Tables S3 and S4). Codes are described in Table 1.
	Fig. 4. Structure results. Sampling sites map (a), STRUCTURE barplots from the neutral SNPs (b), and candidate SNPs (c). The barplots are represented with the most probable number of genetic clusters (K = 3 and 2 for (b) and (c), respectively). *The asterisk indicates the sites affected by the 2018 mass mortality event. This map was created in QGIS v.3.16.16 and edited with Adobe Illustrator.
	Fig. 5. Demographic history of Diadema africanum inferred by Stairway Plot 2. The red line represents the effective population size (Ne) estimated over time, and the grey lines the 75% and 95% intervals of confidence. Axes represent time (x) and effective population size (y), and both are logarithmically scaled.