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 while 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 non-neutral processes are occurring. Here, we generated a draft genome and a restriction-site associated DNA sequencing dataset 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 amongst 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.

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

“…In the summer‐winter spatial series, the majority of the variation in the data was explained by collection site where PC 1 differentiated the PAG from the GO. This microbial differentiation was congruent with previous analyses on the genetic structure of the host species, which showed two populations, one in the PAG and one in the GO (Ketchum et al, 2020). The Musandam collection site is located within the Strait of Hormuz and is geographically situated at the connection between the two seas.…”

Revealing the coexistence of differentiation and communication in an endemic hare, Lepus yarkandensis (Mammalia, Leporidae) using specific-length amplified fragment sequencing

“…Genetic drift may also account for the higher degree of genetic differentiation found between TX and the other southwest populations compared with that found between TX and the north populations. Given that the TX population is geographically located in the southwest of the Tarim Basin, the identified population structure might also reflect the different environmental conditions across the Tarim Basin (i.e., temperature and altitude), which may impose different types of selective pressure on Yarkand hares, as observed for other species such as Diptychus maculates [ 24 ] and urchins [ 72 ] according to genome-wide SNP-based analysis. Future studies should include historical demographic events such as range expansions and population bottlenecks in such analyses, which may shape allele frequency patterns between populations, to explore these hypotheses based on genome-wide SNP markers.…”

Physical-biological interactions underlying the phylogeographic patterns of coral-dependent fishes around the Arabian Peninsula

“…Weak genetic discontinuity between the Gulf and the adjacent Sea of Oman has been shown for a coral species Platygyra daedalea (Howells et al, 2016), which spawn mainly from February to May (Bauman et al, 2011), and a sea urchin Echinometra sp. (Ketchum et al, 2020), whose PLD within the genus vary from 18 to 30 days (McClanahan & Muthiga, 2007). On the other hand, population genetics studies showed that for reef fish species, such as C. hemistiktos (Priest et al, 2016) and P. maculosus (Torquato et al, 2019), the Gulf and the Sea of Oman represent a single phylogeographic province.…”