Biology subjects

Selmoni, O.

Publications and source records attributed to Selmoni, O..

12 recordsLinked to original sources

bioRxiv2026

Spatiotemporal patterns of genetic diversity in the world's coral reefs

Coral reefs face widespread declines under global change, yet the status of their genetic diversity remains largely unknown. Here, we compiled genome-wide DNA sequencing data for 2,520 individuals from 18 reef taxa--including corals, fish, sharks, oysters, shrimp, sea anemones, and manta rays. These data were used to assess spatiotemporal patterns of genetic distances across 173 reefs worldwide between 1998-2018. While we did not observe an overall temporal decline in genetic distances, within-reef distances showed negative temporal trends, potentially reflecting population-level diversity loss. These effects varied across species but did not show clear distinctions between taxa. We then used satellite-derived seascape variables to predict local effects on genetic distances across reefs globally. Negative effects were predicted for the Red Sea, Northern Caribbean, and Coral Triangle, while positive effects were found across the South Pacific. Key predictors included declining oxygen levels, increasing nitrate concentrations, and rising water temperatures--variables that can be tracked in real time via Earth observation, enabling early warning for coral reef genetic diversity loss.

evolutionary biology↗

bioRxiv2025

marApp: An R package and web portal to calculate mutations- and genetic diversity-area relationship for conservation

International conservation policies including the Kunming-Montreal Global Biodiversity Framework now consider genetic diversity of wild species in their targets. However, scalable, theory-driven tools to assess and predict genetic diversity loss are still emerging, limiting their use in conservation planning. Analogous to the species-area relationship, recent work has shown that genetic diversity scales with area, described by the mutations-area relationship (MAR) or genetic-diversity-area relationship (GDAR), can approximate the genetic diversity loss in a species from habitat reduction. To enable application of these insights for conservation practitioners and policy makers, we present the mar R package and marApp web portal, a fast and user-friendly tool for MAR/GDAR analysis. The mar package connects genetic diversity patterns in space to ecological theory, and automates steps from reading genetic and geographic data to simulating various habitat extinction scenarios using MAR/GDAR. The mar package estimates only short-term genetic diversity, providing a lower-limit for the far greater long-term genetic losses, underscoring the need to maximize present-day habitat conservation before it becomes irreversible. As a case example, we showcase predictions of coral (Acropora sp.) genetic diversity loss from reef coverage impacts. We demonstrate the usage of marApp without requirements for prior genetics or coding experiences, and provide downloadable reports for conservation.

ecology↗

bioRxiv2025

Coral genetic structure in the Western Indian Ocean mirrors ocean circulation and thermal stress

Global warming and rising sea temperatures are pushing many reef-building coral species towards extinction. As thermal tolerance in corals is partially heritable, identifying genes under thermal selection is critical for targeted biodiversity management. However, it remains unclear how large breaks in connectivity (>100 km of open sea) affect the spread of adaptive alleles for different coral species in discontinuous reef networks such as the West Indian Ocean (WIO). To address this, we applied a seascape genomics approach to model (i) population connectivity and (ii) thermal adaptive potentials for two keystone coral species, Acropora muricata and Pocillopora damicornis, across the WIO. For both species, corals from the Seychelles were predominantly genetically isolated from corals in Rodrigues and Mauritius, putatively an effect of regional oceanographic barriers. Furthermore, sea currents during reproductive periods better predicted genetic connectivity than did Euclidean distances for both species, highlighting that connectivity models can serve as proxies to understand dispersal potential depending on reproductive strategies. Spatial patterns of neutral genetic variation were best explained by sea surface temperature variability and mean degree heating weeks. When used in genotype- environment association (GEA) analyses, we identified hundreds of loci under putative thermal selection from linked to known heat stress responses. In A. muricata, five Sacsin genes--co- chaperones of the Hsp70 heat-shock protein involved in thermal stress response--were identified, alongside genes related to immune defence, antioxidant response, signalling, and protein folding. In contrast, only the centromere protein V, involved in mitosis, was enriched in P. damicornis. By integrating patterns of gene flow with molecular adaptations to estimate species-specific adaptive potentials, we found that large sea distances and strong oceanographic barriers inhibit the genetic exchange of adapted genotypes across the WIO, providing valuable insights to guide local and regional biodiversity management in this region.

evolutionary biology↗

bioRxiv2024

Genetic diversity loss in the Anthropocene will continue long after habitat destruction ends

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations Global Biodiversity Framework (GBF). However, we lack large-scale mathematical frameworks to quantify how much genetic diversity has already been lost, let alone to predict future losses under 21st century conservation scenarios. To fill this gap, we developed an area-based spatio-temporal predictive framework of genetic diversity calibrated with population-scale genomic data of 29 plant and animal species. To estimate present genetic diversity loss with our framework, we used species habitat area and population sizes losses reported in the Living Planet Index, the Red List, and new GBF indicators across 13,808 species for the last 5 decades. Applying our evolutionary framework across these species, we estimate genetic diversity loss lags behind population and habitat area declines, with an estimated current 13-22% {pi} genetic diversity loss. However, we forecast future genetic diversity losses will reach 41-76% even if populations are not further contracted. These results highlight that safeguarding existing habitats is insufficient to maintain the genetic health of species and relying solely on continuous genetic monitoring underestimates lagging long term impacts. Significance statementGenetic diversity is crucial for both species adaptation and survival. Recently, it has been included as a target for protection in the United Nations Global Biodiversity Framework. However, we lack large-scale predictive methods to quantify current and future losses of genetic diversity across species. Here, we develop an area-based spatio-temporal predictive framework trained with high-quality genome-wide data from 29 plant and animal species to enable quantitative predictions of genetic biodiversity at global scales. We infer global genetic diversity losses are beyond the preliminary UN targets to protect 90% of genetic diversity of species, evolutionary models dramatic genetic losses will occur in the future even with habitat protection if populations across species are not recovered.

genomics↗

bioRxiv2024

Global coral genomic vulnerability explains recent reef losses

The dramatic decline of reef-building corals calls for a better understanding of coral adaptation to ocean warming. Here, we characterized genetic diversity of the widespread genus Acropora by building a genomic database of 595 coral samples from different oceanic regions--from the Great Barrier Reef to the Persian Gulf. Through genome-environment associations, we found that different Acropora species showed parallel evolutionary signals of heat-adaptation in the same genomic regions, pointing to genes associated with molecular heat shock responses and symbiosis. We then projected the present and the predicted future distribution of heat-adapted genotypes across reefs worldwide. Reefs projected with low frequency of heat-adapted genotypes display higher rates of Acropora decline, indicating a potential genomic vulnerability to heat exposure. Our projections also suggest a transition where heat-adapted genotypes will spread at least until 2040. However, this transition will likely involve mass mortality of entire non-adapted populations and a consequent erosion of Acropora genetic diversity. This genetic diversity loss could hinder the capacity of Acropora to adapt to the more extreme heatwaves projected beyond 2040. Genomic vulnerability and genetic diversity loss estimates can be used to reassess which coral reefs are at risk and their conservation.

evolutionary biology↗

bioRxiv2022

RECIFS: a centralized geo-environmental database for coral reef research and conservation

Host to intricated networks of marine species, coral reefs are among the most biologically diverse ecosystems on Earth. Over the past 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 is key to (1) uncovering the environmental drivers of reef degradation, and (2) enforcing efficient conservation strategies in response. To achieve these objectives, it is pivotal that environmental data characterizing such ecosystem dynamics, which occur across specific spatial and temporal scales, are easily accessible to coral reef researchers and conservation stakeholders alike. Here we present the Reef Environment Centralized Information System (RECIFS), an online repository of datasets describing reef environments worldwide over the past few decades. The data served through RECIFS originate from remote sensed datasets available in the public domain, and characterize various facets of the reef environment, including water chemistry and physics (e.g. temperature, pH, chlorophyll concentration), as well as anthropogenic local pressures (e.g. boat detection, distance from agricultural or urban areas). The datasets from RECIFS can be accessed at different spatial and temporal resolutions and are delivered through an intuitive web-application featuring an interactive map requiring no prior knowledge working with remote sensing or geographic information systems. The RECIFS web-application is available in complete open access at https://recifs.epfl.ch. We describe two case studies showing possible implementations of RECIFS to 1) characterize coral diversity in the Caribbean and 2) investigate local adaptation of a reef fish population in Northwest Australia.

ecology↗

bioRxiv2021

Worldwide reef surveys highlight different adaptive responses to heat between coral taxa

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 heat stress. For branching, tabular and corymbose Acroporidae, reefs exposed to recent heat stress (measured the year before the survey) had lower coral cover than locally expected; and among these reefs, those previously exposed to frequent past heat stress (measured since 1985) 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.

ecology↗

bioRxiv2020

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

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.

evolutionary biology↗

bioRxiv2020

Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species

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 had been exposed to recurrent thermal stress over the years and whose corals appeared 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 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) of which frequencies 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 neighborhood. In each of the studied species, we found heat stress associated SNPs notably located in proximity of genes coding for well-established actors of the cellular responses against heat. Among these, we can mention proteins involved in DNA damage-repair, protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways. In some cases, the same putative molecular targets of heat stress adaptation recurred among species. Together, these results underscore 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.

evolutionary biology↗

bioRxiv2019

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

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.\n\nIn 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.\n\nOur 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.

evolutionary biology↗

bioRxiv2019

Characterizing the adaptive potential of north-western Pacific reef corals to empower conservation strategies: a role for seascape genomics

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 of anomalous heat waves, 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 the set-up of preservation frameworks 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 frequencies of genetic markers with that of 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 thermal 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 between the results of these analyses portrayed the adaptive potential of this population: we were able to identify reefs carrying potential adaptive 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 reef in warming oceans.

evolutionary biology↗

bioRxiv2018

Indication of spatially random infection of chlamydia-like organisms in Bufo bufo tadpoles from ponds located in the Geneva metropolitan area

Occurrence of bacteria belonging to the order Chlamydiales was investigated for the first time in common toad (Bufo bufo) tadpole populations collected from 41 ponds in the Geneva metropolitan area, Switzerland. A Chlamydiales-specific Real-Time PCR was used to detect and amplify the Chlamydiales 16S rRNA-encoding gene from the tails of 375 tadpoles. We found the studied amphibian populations to be infected by \"Chlamydia-like organisms\" (CLOs) attributable to the genera Similichlamydia, Neochlamydia, Protochlamydia and Parachlamydia (belonging to the family Parachlamydiaceae), Simkania (family Simkaniaceae) and Estrella (family Criblamydiaceae); additionally, DNA from the genus Thermoanaerobacter (family Thermoanaerobacteriaceae) was detected. A global autocorrelation analysis did not reveal a spatial structure in the observed CLOs infection rates, and association tests involving land cover characteristics did not evidence any clear effect on CLOs infection rates in B. bufo. Despite preliminary, these results suggest a random and ubiquitous distribution of CLOs in the environment, which would support the biogeographical expectation \"everything is everywhere\" for the concerned microorganisms and their amoeba vectors.

epidemiology↗