Navigating the Currents of Seascape Genomics: How Spatial Analyses can Augment Population Genomic Studies

Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis onmarine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations

Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats

Background: Divergent natural selection across environmental gradients has been acknowledged as a major driver of population and species divergence, however its role in the diversification of scleractinian corals remains poorly understood. Recently, it was demonstrated that the brooding coral Seriatopora hystrix and its algal endosymbionts (Symbiodinium) are genetically partitioned across reef environments (0-30 m) on the far northern Great Barrier Reef. Here, we explore the potential mechanisms underlying this differentiation and assess the stability of host-symbiont associations through a reciprocal transplantation experiment across habitats ('Back Reef', 'Upper Slope' and 'Deep Slope'), in combination with molecular (mtDNA and ITS2-DGGE) and photo-physiological analyses (respirometry and HPLC)

Mesophotic coral ecosystems of the Great Barrier Reef are understudied and underexplored

Mesophotic coral ecosystems (MCEs) are characterized by the presence of photosynthetically active organisms such as corals and algae, and associated communities at depths ranging from 30 to 150 m in tropical and subtropical regions. Due to the increased awareness of the potential importance of these reefs as an integral part of coral reef ecosystems (i.e., deep reef refuge, specialized biodiversity, transition zone between shallow and deep-sea environments, and recreational and intrinsic values), interest from the scientific community has grown around the world over the last two decades. Several nations have already made management declarations and started to extend marine protected areas and fishery management to MCEs. The estimated area of Australian MCEs is likely equivalent to that of shallow reef ecosystems down to 30 m; however, Australian MCEs attract limited research effort compared to other major coral reef regions around the world. In this perspective, we briefly explore the reasons for this scarcity of research on mesophotic ecosystems of the Great Barrier Reef (GBR) of Australia (e.g., strict diving regulations, new researchers’ involvement, and logistics and cost). At present, research efforts on the mesophotic ecosystems of the GBR are in decline and if this trajectory is maintained, the global disparity in knowledge between MCEs near Australia and those from the other main coral reef regions worldwide will sharpen deeply. We call for action from the research community, grant agencies, and decision-makers toward a wider understanding of these important ecosystems in Australia

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

Background: Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.\ud \ud Methodology/Principal Findings: Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a ~30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.\ud \ud Conclusions/Significance: This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix

In vivo assessment of three dimensional coronary anatomy using electron beam computed tomography after intravenous contrast administration

Intravenous coronary angiography with electron beam computed tomography (EBCT) allows for the non-invasive visualisation of coronary arteries. With dedicated computer hardware and software, three dimensional renderings of the coronary arteries can be constructed, starting from the individual transaxial tomograms. This article describes image acquisition, postprocessing techniques, and the results of clinical studies. EBCT coronary angiography is a promising coronary artery imaging technique. Currently it is a reasonably robust technique for the visualisation and assessment of the left main and left anterior descending coronary artery. The right and circumflex coronary arteries can be visualised less consistently. Improvements in image acquisition and postprocessing techniques are expected to improve visualisation and diagnostic accuracy of the technique

Intravenous coronary angiography by electron beam computed tomography: a clinical evaluation

BACKGROUND:-Noninvasive detection of coronary stenoses with electron beam CT (EBCT) after intravenous injection of contrast medium has recently emerged. We sought to determine the diagnostic accuracy of EBCT angiography in the clinical setting using conventional coronary angiography as the "gold standard." METHODS AND RESULTS: Thirty-seven patients (30 men) were investigated. After intravenous injection of 150 mL of contrast medium, 40 to 60 consecutive transaxial tomograms, covering the proximal and middle parts of the coronary arteries, were obtained with ECG triggering at end diastole during breath-holding. Three-dimensional reconstructions of the proximal and middle parts of the arteries were compared with the conventional angiograms. Of the 259 proximal and middle coronary segments, 211 (81%) were analyzable by EBCT. Of the left anterior descending coronary artery (LAD) segments, 95% were assessable. Right coronary artery (RCA) and left circumflex artery (LCx) segments were assessable in 66% and 76%, respectively. Overall sensitivity and specificity to detect a >50% diameter stenosis were 77% and 94%, respectively. This was 82% and 92% for the LAD, 60% and 97% for the RCA, and 83% and 89% for the LCx (all figures based on assessable lesions). CONCLUSIONS: Intravenous EBCT coronary angiography is a promising coronary imaging technique. The technique is not yet robust enough to be an alternative to conventional coronary angiography. It can detect and rule out significant coronary artery disease of the left main proximal and mid portions of the LAD with good accuracy

Mesophotic coral ecosystems of French Polynesia are hotspots of alpha and beta generic diversity for scleractinian assemblages

Aim: Revealing how diversity varies across the depth gradient is key for understanding the role of mesophotic coral ecosystems in the functioning of coral reefs. We quantitatively examined how alpha and beta generic diversity of scleractinian coral assemblages vary across a wide depth gradient for coral reefs. Location: Sixteen sites in eight islands of three archipelagos in French Polynesia. Methods: We studied generic diversity patterns of scleractinian corals, as derived from the analysis of photo-quadrats, across the seafloor from shallow to lower mesophotic depths (6–120 m) and on a wide geographic scale. Our sampling considered quantitative coral cover to explore the patterns of alpha and beta components of diversity across depth and horizontal space. Results: We show that in French Polynesia, mesophotic coral ecosystems host higher alpha and beta generic diversity than shallow reefs despite decreasing coral cover with depth. The variation of coral genus richness across the depth gradient is mainly driven by a mid-domain effect with a peak at 40 m depth. At the same time, we found that the differences in coral genera across islands (spatial beta-diversity) increased steadily along the depth gradient. Main conclusions: Our findings report the first quantitative results of coral cover and diversity from mesophotic coral ecosystems in French Polynesia and also present one of the few existing studies to examine the broad breadth of the mesophotic depth gradient. We demonstrate that mesophotic depths can host unexpectedly high generic richness of scleractinian coral assemblages. At the same time, we showed that increasing depth increases the differences in generic diversity composition across islands, whereas shallow reefs are similar in between. While a single island could conserve shallow regional biodiversity, mesophotic depths containing the richest diversity require site-specific measures, suggesting that considering these mesophotic depths in conservation is necessary to maintain regional diversity

Microbiome variation in corals with distinct depth distribution ranges across a shallow-mesophotic gradient (15-85 m)

Mesophotic coral ecosystems (MCEs) are generally poorly studied, and our knowledge of lower MCEs (below 60 m depth) is largely limited to visual surveys. Here, we provide a first detailed assessment of the prokaryotic community associated with scleractinian corals over a depth gradient to the lower mesophotic realm (15-85 m). Specimens of three Caribbean coral species exhibiting differences in their depth distribution ranges (Agaricia grahamae, Madracis pharensis and Stephanocoenia intersepta) were collected with a manned submersible on the island of Cura double dagger ao, and their prokaryotic communities assessed using 16S rRNA gene sequencing analysis. Corals with narrower depth distribution ranges (depth-specialists) were associated with a stable prokaryotic community, whereas corals with a broader niche range (depth-generalists) revealed a higher variability in their prokaryotic community. The observed depth effects match previously described patterns in Symbiodinium depth zonation. This highlights the contribution of structured microbial communities over depth to the coral's ability to colonize a broader depth range.Austrian Science Fund (FWF); Catlin Group Limited; Global Change Institute; Eddie Bauer Grant for Expeditions by The Explorers Club; Marie Curie Fellowship [FP7-299320]; Lise Meitner Program of the Austrian Science Fund (FWF) [M1363-B20]info:eu-repo/semantics/publishedVersio