Publications by Oliver Michele Selmoni

The Reef Environment Centralized InFormation System (RECIFS) : An integrated geo‐environmental database for coral reef research and conservation

Motivation: Host to intricate networks of marine species, coral reefs are among the most biologically diverse ecosystems on Earth. Over the past few decades, major degradations of coral reefs have been observed worldwide, which is largely attributed to the effects of climate change and local stressors related to human activities. Now more than ever, characterizing how the environment shapes the dynamics of the reef ecosystem (e.g., shifts in species abundance, community changes, emergence of locally adapted populations) is key to uncovering the environmental drivers of reef degradation, and developing efficient conservation strategies in response. To achieve these objectives, it is pivotal that environmental data describing the processes driving such ecosystem dynamics, which occur across specific spatial and temporal scales, are easily accessible to coral reef researchers and conservation stakeholders alike. Main types of variable contained Multiple environmental variables characterizing various facets of the reef environment, including water chemistry and physics (e.g., temperature, pH, chlorophyll concentration), local anthropogenic pressures (e.g., boat traffic, distance from agricultural or urban areas) and sea currents patterns. Spatial location and grain Worldwide reef cells of 5 by 5 km. Time period and grain Last 3–4 decades, monthly and yearly resolution. Major taxa and level of measurement Environmental data important for coral reefs and associated biodiversity. Software format Interactive web application available at https://recifs.epfl.ch.

2023

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

Véronique Berteaux-Lecellier, Stéphane Joost, Oliver Michele Selmoni

Coral reefs around the world are under threat from anomalous heat waves that are causing the widespread decline of hard corals. Different coral taxa are known to have different sensitivities to heat, although variation in susceptibilities have also been observed within the same species living in different environments. Characterizing such taxa-specific variations is key to enforcing efficient reef conservation strategies. Here, we combine worldwide-reef-survey data with remote sensed environmental variables to evaluate how local differences in taxa-specific coral cover are associated with past trends of thermal anomalies, as well as of non-heat related conditions. While the association with non-heat related environmental variation was seldom significant, we found that heat stress trends matched local differences in coral cover. Coral taxa were sorted based on the different patterns of associations with recent heat stress (measured the year before the survey) and past heat stress (measured since 1985). For branching, tabular and corymbose Acroporidae, reefs exposed to recent heat stress had lower coral cover than locally expected. Among such reefs, those previously exposed to frequent past heat stress displayed relatively higher coral cover, compared to those less frequently exposed. For massive and encrusting Poritidae, and for meandroid Favidae and Mussidae, we observed a negative association of coral cover with recent heat stress. However, unlike with Acroporidae, these associations were weaker and did not vary with past heat exposure. For Pocilloporidae, we found a positive association between coral cover and recent heat stress for reefs frequently exposed to past heat, while we found a negative association at reefs less frequently exposed to past heat. A similar pattern was observed for the branching Poritidae, although the associations were weaker and not statistically significant. Overall, these results show taxa-specific heat association patterns that might correspond to taxa-specific responses to past heat exposure, such as shifts in the assembly of coral communities, evolutionary adaptation or physiological acclimation.

FRONTIERS MEDIA SA2022

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Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that have been exposed to recurrent thermal stress over the years and whose corals appear to have been tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover the molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs), frequencies of which were associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress-associated SNPs located in proximity of genes involved in pathways well known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways, and DNA damage-repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underline the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.

WILEY2021

Spatial areas of genotype probability: Predicting the spatial distribution of adaptive genetic variants under future climatic conditions

Stéphane Joost, Estelle Rochat, Oliver Michele Selmoni

In a context of rapid global change, one of the key components for the survival of species is their genetic evolutionary potential for adaptation. Many methods have been developed to identify genetic variants underpinning adaptation to climate, but few tools were made available to integrate this knowledge into conservation management. We present here the SPatial Areas of Genotype probability (SPAG), a method to transpose the results of genotype-environment association studies into an evolutionary potential spatial prediction framework. We define a univariate model predicting the spatial distribution of a single-locus adaptive genotype and three multivariate models allowing the integration of several adaptive loci in a composite genotype. Unlike existing methods, SPAGs provide (a) a flexible approach to combine loci under different types of intergenic relationships and (b) a cross-validation framework to assess the pertinence of evolutionary potential predictions. SPAGs can be integrated with climate change projections to forecast the future spatial distribution of genotypes. The analysis of the mismatch between current and future SPAGs ("genomic offset") makes it possible to identify vulnerable populations potentially lacking the adaptive genotypes necessary for future survival. We tested the SPAG approach on a simulated population and applied it to characterize the evolutionary potential of 161 Moroccan goats to bioclimatic conditions. We identified seven regions of the Moroccan goat genome strongly associated with the precipitation seasonality and used the SPAG approach to predict the evolutionary potential. We then forecasted the shift in SPAGs under a strong climate change scenario and uncovered the goat populations likely to be threatened in future conditions. The SPAG methodology is an efficient and flexible tool to characterize the evolutionary potential across a landscape and to transpose evolutionary information into conservation frameworks.

WILEY2021

Coral cover surveys corroborate predictions on reef adaptive potential to thermal stress

Véronique Berteaux-Lecellier, Stéphane Joost, Oliver Michele Selmoni

As anomalous heat waves are causing the widespread decline of coral reefs worldwide, there is an urgent need to identify coral populations tolerant to thermal stress. Heat stress adaptive potential is the degree of tolerance expected from evolutionary processes and, for a given reef, depends on the arrival of propagules from reefs exposed to recurrent thermal stress. For this reason, assessing spatial patterns of thermal adaptation and reef connectivity is of paramount importance to inform conservation strategies. In this work, we applied a seascape genomics framework to characterize the spatial patterns of thermal adaptation and connectivity for coral reefs of New Caledonia (Southern Pacific). In this approach, remote sensing of seascape conditions was combined with genomic data from three coral species. For every reef of the region, we computed a probability of heat stress adaptation, and two indices forecasting inbound and outbound connectivity. We then compared our indicators to field survey data, and observed that decrease of coral cover after heat stress was lower at reefs predicted with high probability of adaptation and inbound connectivity. Last, we discussed how these indicators can be used to inform local conservation strategies and preserve the adaptive potential of New Caledonian reefs.

2020

Correction to: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae) (vol 20, 583, 2019)

Oliver Michele Selmoni

2020

Sampling strategy optimization to increase statistical power in landscape genomics: a simulation-based approach

Annie Sandrine Guillaume, Stéphane Joost, Estelle Rochat, Oliver Michele Selmoni, Elia Vajana

An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. The implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistic constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic datasets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographic representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites(20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.

2020

Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north‐western Pacific Acropora digitifera

Stéphane Joost, Estelle Rochat, Oliver Michele Selmoni

Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heatwaves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set‐up to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between genotype frequencies and environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against heat stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination of these results portrayed the adaptive potential of this population: we were able to identify reefs carrying potential heat stress adapted genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reefs in warming oceans.

2020

Seascape genomics to empower coral reef conservation strategies

Oliver Michele Selmoni

The future of coral reefs is under threat since anomalous heat waves are causing the death of reef building corals around the world. This phenomenon, known as "coral bleaching", has already resulted in widespread loss of coral over the past 30 years. Without corals, the entire reef ecosystem is expected to collapse, threatening the survival of up to one third of marine wildlife. Despite the catastrophic perspectives, a glimmer of hope is brought by corals that persist at reefs exposed to recurrent heat waves. Evolutionary adaptation might underpin these observations. Characterizing the adaptive potential of corals is therefore essential, as conservation efforts could be oriented towards coral breeds resistant to future thermal conditions. To date, however, the characterization of heat adaptation in corals shows substantial gaps at different scales. At the molecular level, more needs to be discovered about the cellular pathways implicated. At a population level, there are no well-established frameworks to detect heat-tolerant corals for use in defining conservation priorities. In this research, we employed a seascape genomics approach to contribute to filling these gaps. This approach combines the environmental characterization of the seascape with a genomic analysis of populations, with the goal to identify genetic variants underpinning an adaptive role. Seascape genomics therefore constitutes an exploratory approach that portrays the adaptive potential across a population, and this facilitates the transposition of results to a conservation perspective. Furthermore, the use of genomic analyses also provides the bases to formulate hypotheses from the molecular side of adaptation. The first two articles of this thesis prepare the ground for the application of seascape genomics to corals. The first focuses on the optimization of sampling strategies. By using computer simulations, we defined the practical guidelines to organize a sampling strategy securing sufficient statistical power. The second is the proof-of-concept for the application of seascape genomics to corals. We retrieved a pre-existing genomic dataset on corals from Japan, and used it to characterize adaptive potential against heat stress and to compute conservation priorities accordingly. The third and the fourth articles of this thesis are based on new data collected in the frame of a project dedicated to the study of adaptation in three coral species from New Caledonia (Southwestern Pacific). We organized the sampling strategy using the guidelines of the first article, and processed data using the framework described in the second. The result is a dataset tailored to the needs of seascape genomics, and this enabled to refine our methods. In the third article we focus on the molecular side of adaptation and disclose cellular pathways potentially involved in heat stress adaptation. The fourth article emphasizes the role of adaptive potential under a conservation perspective. We employed pre-existing field survey data to show that reefs predicted with higher adaptive potential suffered reduced coral loss after heat stress. Together, this thesis highlights the value of the seascape genomics approach for characterizing the adaptive potential of corals and for supporting reef conservation strategies. More broadly, this work shows that building bridges from academic research to tangible conservation actions is not only possible but also essential to face this crisis.

EPFL2020

Using Modern Conservation Tools for Innovative Management of Coral Reefs: The MANACO Consortium

Véronique Berteaux-Lecellier, Stéphane Joost, Anders Meibom, Oliver Michele Selmoni

Coral reefs are under threat and innovative management strategies are urgently required. However, discoveries from innovative fields of coral reef research are rarely transposed in practical conservation actions. This is mainly due to the difficulties in knowledge exchange between scientists and conservation stakeholders. The ManaCo consortium (http://manaco.ird.nc/) is an international network federating conservation stakeholders and researchers in a common effort to preserve the coral reefs. The focus is on using modern tools to build a bridge between indigenous knowledge and scientific innovation. ManaCo aims to orientate research toward relevant conservation needs and to facilitate the transposition of research into concrete management strategies. This will allow to coordinate a collaborative response against coral reef decline. We invite anyone sharing the same interests in joining us.

2020