Ketchum RN et al. (2020), Population Genomic Analyses of the Sea Urchin E...

ECB-ART-49723

Genome Biol Evol 2020 Oct 01;1210:1819-1829. doi: 10.1093/gbe/evaa150.

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Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient.

Ketchum RN , Smith EG , DeBiasse MB , Vaughan GO , McParland D , Leach WB , Al-Mansoori N , Ryan JF , Burt JA , Reitzel AM .

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Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E sp. EZ's life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was among the highest recorded for an echinoderm at 4.5%. We recovered 918 high-quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

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References [+] :

Bauman, Multiple environmental factors influence the spatial distribution and structure of reef communities in the northeastern Arabian Peninsula. 2013, Pubmed

	Fig. 1. Map of the seven E. sp. EZ sampling locations.
	Fig. 2. (A) Plot of the individual ancestry inference for K = 2 based on 918 loci. The population abbreviations are as follows: DH, Dhabiya; SA, Saadiyat; RG, Ras Ghanada; MS, Musandam; DB, Dibba Rock; AF, Al Fiquet; AA, Al Aqah. (B) Box plot of eigenvalues for 85 individuals explained by principal component one, generated in the smartpca package.
	Fig. 3. Phylogenetic network of the inferred relationships between seven populations of E. sp. EZ. The population abbreviations are: DH, Dhabiya; SA, Saadiyat; RG, Ras Ghanada; MS, Musandam; DB, Dibba Rock; AF, Al Fiquet; AA, Al Aqah. Population abbreviations were colored based on their Gulf of origin (PAG, red; GO, blue). Migration edges are colored according to percent ancestry received from the donor population and SE represents the standard error of migration rates. (A) M0 represents a phylogram with no migration edges. (B) M6 contains six migration edges. Next to each phylogenetic network are the corresponding residual plots.