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

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 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.

SUBMITTER: Ketchum RN

PROVIDER: S-EPMC7594579 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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

Ketchum Remi N RN Smith Edward G EG DeBiasse Melissa B MB Vaughan Grace O GO McParland Dain D Leach Whitney B WB Al-Mansoori Noura N Ryan Joseph F JF Burt John A JA Reitzel Adam M AM

Genome biology and evolution 20201001 10

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 ...[more]

PMID: 32697837

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Project description:BackgroundIn temperate macroalgal forests, sea urchins are considered as a keystone species due to their grazing ability. Given their potential to shape benthic communities, we monitored the habitat use by three sympatric sea urchin species and compared their behaviors in a vegetated habitat (VH) and an adjacent isoyake habitat (IH).MethodsWe monitored the environmental conditions and sea urchin density along deep and shallow transects of the VH and IH for over a year. The benthic rugosity at both sites were also surveyed. A mark-recapture experiment was conducted on the two most abundant sea urchins, Diadema setosum and Heliocidaris crassispina, to elucidate sea urchin movement patterns and group dynamics.ResultsWe found that exposure to waves was highest at the VH while the IH was sheltered. The deep IH experienced the least amount of light due to high turbidity. Water temperature patterns were similar across sites. The VH benthic topography was more rugose compared to the smoother and silt-covered IH substate. Peak macroalgal bloom occurred three months earlier in IH, but macroalgae persisted longer at the shallow VH. Among the sympatric sea urchins, H. crassispina was most abundant at the shallow VH and was observed in pits and crevices. The most abundant across IH and in the deep VH was D. setosum, preferring either crevices or free-living, depending on hydrodynamic conditions. The least abundant species was D. savignyi, and most often observed in crevices. Small and medium sea urchins were most often observed at the IH site, whereas larger sea urchins were more likely observed at the VH. The mark-recapture study showed that D. setosum was found to displace further at the IH, and H. crassispina was more sedentary. Additionally, D. setosum was always observed in groups, whereas H. crassispina was always solitary.DiscussionThe behaviors of sympatric urchins, Diadema savignyi, D. setosum and H. crassispina, differed in response to changes in the benthic environment and physical conditions. Sea urchin displacement increased when rugosity and wave action were low. Habitat preference shifted to crevices in seasons with high wave action. In general, the mark-recapture experiment showed that sea urchins displaced further at night.

Project description:The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains before gastrulation indicating that they may operate near the top of a conserved neural gene regulatory network. A family of genes encoding voltage-gated ion channels is present but, surprisingly, genes encoding gap junction proteins (connexins and pannexins) appear to be absent. Genes required for synapse formation and function have been identified and genes for synthesis and transport of neurotransmitters are present. There is a large family of G-protein-coupled receptors, including 874 rhodopsin-type receptors, 28 metabotropic glutamate-like receptors and a remarkably expanded group of 161 secretin receptor-like proteins. Absence of cannabinoid, lysophospholipid and melanocortin receptors indicates that this group may be unique to chordates. There are at least 37 putative G-protein-coupled peptide receptors and precursors for several neuropeptides and peptide hormones have been identified, including SALMFamides, NGFFFamide, a vasotocin-like peptide, glycoprotein hormones and insulin/insulin-like growth factors. Identification of a neurotrophin-like gene and Trk receptor in sea urchin indicates that this neural signaling system is not unique to chordates. Several hundred chemoreceptor genes have been predicted using several approaches, a number similar to that for other animals. Intriguingly, genes encoding homologues of rhodopsin, Pax6 and several other key mammalian retinal transcription factors are expressed in tube feet, suggesting tube feet function as photosensory organs. Analysis of the sea urchin genome presents a unique perspective on the evolutionary history of deuterostome nervous systems and reveals new approaches to investigate the development and neurobiology of sea urchins.

Dataset Information

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

Publications

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

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