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

Genome Biology and Evolution
Remi N KetchumAdam M Reitzel

Abstract

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...Continue Reading

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Datasets Mentioned

BETA
NC034767.1
AC165428.1

Methods Mentioned

BETA
restriction
PCA

Software Mentioned

Trimmomatic
FastqSifter
CLUMPP
Arlequin
dDocent
Platanus
R package pcadapt
custom Perl script
EIGENSOFT
CEGMA

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