Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species

Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations

The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species' demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.

When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral

Climate change is impacting ecosystems worldwide, and the Mediterranean Sea is no exception. Extreme climatic events, such as marine heat waves (MHWs), are increasing in frequency, extent and intensity during the last decades, which has been associated with an increase in mass mortality events for multiple species. Coralligenous assemblages, where the octocoral Paramuricea clavata lives, are strongly affected by MHWs. The Medes Islands Marine Reserve (NW Mediterranean) was considered a climate refugia for P. clavata, as their populations were showing some resilience to these changing conditions. In this study, we assessed the impacts of the MHWs that occurred between 2016 and 2022 in seven shallow populations of the octocoral P. clavata from a Mediterranean Marine Protected Area. The years that the mortality rates increased significantly were associated with the ones with strong MHWs, 2022 being the one with higher mortalities. In 2022, with 50 MHW days, the proportion of total affected colonies was almost 70%, with a proportion of the injured surface of almost 40%, reaching levels never attained in our study site since the monitoring was started. We also found spatial variability between the monitored populations. Whereas few of them showed low levels of mortality, others lost around 75% of their biomass. The significant impacts documented here raise concerns about the future of shallow P. clavata populations across the Mediterranean, suggesting that the resilience of this species may not be maintained to sustain these populations face the ongoing warming trends.

Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.

Exploring the response of a key Mediterranean gorgonian to heat stress across biological and spatial scales

Understanding the factors and processes that shape intra-specific sensitivity to heat stress is fundamental to better predicting the vulnerability of benthic species to climate change. Here, we investigate the response of a habitat-forming Mediterranean octocoral, the red gorgonian Paramuricea clavata (Risso, 1826) to thermal stress at multiple biological and geographical scales. Samples from eleven P. clavata populations inhabiting four localities separated by hundreds to more than 1500 km of coast and with contrasting thermal histories were exposed to a critical temperature threshold (25 °C) in a common garden experiment in aquaria. Ten of the 11 populations lacked thermotolerance to the experimental conditions provided (25 days at 25 °C), with 100% or almost 100% colony mortality by the end of the experiment. Furthermore, we found no significant association between local average thermal regimes nor recent thermal history (i.e., local water temperatures in the 3 months prior to the experiment) and population thermotolerance. Overall, our results suggest that local adaptation and/or acclimation to warmer conditions have a limited role in the response of P. clavata to thermal stress. The study also confirms the sensitivity of this species to warm temperatures across its distributional range and questions its adaptive capacity under ocean warming conditions. However, important inter-individual variation in thermotolerance was found within populations, particularly those exposed to the most severe prior marine heatwaves. These observations suggest that P. clavata could harbor adaptive potential to future warming acting on standing genetic variation (i.e., divergent selection) and/or environmentally-induced phenotypic variation (i.e., intra- and/or intergenerational plasticity).

Lethal and sublethal effects of thermal stress on octocorals early life-history stages

The frequency and severity of marine heatwaves causing mass mortality events in tropical and temperate coral species increases every year, with serious consequences on the stability and resilience of coral populations. Although recovery and persistence of coral populations after stress events is closely related to adult fitness, as well as larval survival and settlement, much remains unknown about the effects of thermal stress on early life-history stages of temperate coral species. In the present study, the reproductive phenology and the effect of increased water temperature (+4°C and +6°C above ambient, 20°C) on larval survival and settlement was evaluated for two of the most representative Mediterranean octocoral species (Eunicella singularis and Corallium rubrum). Our study shows that reproductive behavior is more variable than previously reported and breeding period occurs over a longer period in both species. Thermal stress did not affect the survival of symbiotic E. singularis larvae but drastically reduced the survival of the non-symbiotic C. rubrum larvae. Results on larval biomass and caloric consumption suggest that higher mortality rates of C. rubrum exposed to increased temperature were not related to depletion of endogenous energy in larvae. The results also show that settlement rates of E. singularis did not change in response to elevated temperature after 20 days of exposure, but larvae may settle fast and close to their native population at 26°C (+6°C). Although previous experimental studies found that adult colonies of both octocoral species are mostly resistant to thermal stress, our results on early life-history stages suggest that the persistence and inter-connectivity of local populations may be severely compromised under continued trends in ocean warming.

Population collapse of habitat-forming species in the Mediterranean: a long-term study of gorgonian populations affected by recurrent marine heatwaves

Understanding the resilience of temperate reefs to climate change requires exploring the recovery capacity of their habitat-forming species from recurrent marine heatwaves (MHWs). Here, we show that, in a Mediterranean highly enforced marine protected area established more than 40 years ago, habitat-forming octocoral populations that were first affected by a severe MHW in 2003 have not recovered after 15 years. Contrarily, they have followed collapse trajectories that have brought them to the brink of local ecological extinction. Since 2003, impacted populations of the red gorgonian Paramuricea clavata (Risso, 1826) and the red coral Corallium rubrum (Linnaeus, 1758) have followed different trends in terms of size structure, but a similar progressive reduction in density and biomass. Concurrently, recurrent MHWs were observed in the area during the 2003-2018 study period, which may have hindered populations recovery. The studied octocorals play a unique habitat-forming role in the coralligenous assemblages (i.e. reefs endemic to the Mediterranean Sea home to approximately 10% of its species). Therefore, our results underpin the great risk that recurrent MHWs pose for the long-term integrity and functioning of these emblematic temperate reefs.

The Genome Sequence of the Octocoral Paramuricea clavata - A Key Resource To Study the Impact of Climate Change in the Mediterranean

The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change.

From depth to regional spatial genetic differentiation of Eunicella cavolini in the NW Mediterranean

Connectivity studies in the marine realm are of great importance to understand the evolutionary potential of populations in a context of growing pressures on the marine environment. Here, we investigated the effect of the local, regional, and depth spatial scale on the population genetic structure of the yellow gorgonian Eunicella cavolini, one of the most common octocoral species of the Mediterranean hard-bottom communities. This species, along with other sessile metazoans typical of coralligenous ecosystems, plays an important role in supporting biodiversity, but is also impacted by direct and indirect consequences of human activities, such as physical destruction or mortality events due to thermal anomalies. Samples were taken from 15 sites located in the Ligurian Sea (NW Mediterranean) in two adjacent regions 100 kilometres apart, i.e. from the areas of Marseille (France) and Portofino (Genoa, Italy), and were analysed using six microsatellite loci. A pattern of isolation by distance was observed at the regional as well as the local scales. Although E. cavolini showed less genetic structure than other Mediterranean octocorallian species, we observed a significant genetic differentiation between populations a few kilometres apart. A low genetic differentiation was also observed between shallow and deep populations. The occurrence of genetically differentiated populations of E. cavolini at the scale of kilometres has important consequences for the management of this species and of the associated communities.

Chasing genetic structure in coralligenous reef invertebrates: patterns, criticalities and conservation issues

Conservation of coastal habitats is a global issue, yet biogenic reefs in temperate regions have received very little attention. They have a broad geographic distribution and are a key habitat in marine ecosystems impacted by human activities. In the Mediterranean Sea coralligenous reefs are biodiversity hot spots and are classified as sensitive habitats deserving conservation. Genetic diversity and structure influence demographic, ecological and evolutionary processes in populations and play a crucial role in conservation strategies. Nevertheless, a comprehensive view of population genetic structure of coralligenous species is lacking. Here, we reviewed the literature on the genetic structure of sessile and sedentary invertebrates of the Mediterranean coralligenous reefs. Linear regression models and meta-analytic approaches are used to assess the contributions of genetic markers, phylum, pelagic larval duration (PLD) and geographical distance to the population genetic structure. Our quantitative approach highlight that 1) most species show a significant genetic structure, 2) structuring differs between phyla, and 3) PLD does not appear to be a major driver of the structuring. We discuss the implication of these finding for the management and conservation, suggesting research areas that deserve attention, and providing recommendations for broad assessment and monitoring of genetic diversity in biogenic reefs species.

Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species

The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitat-forming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 °C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change.

Beyond the beaten path: improving natural products bioprospecting using an eco-evolutionary framework - the case of the octocorals

Marine natural products (NPs) represent an impressive source of novel bioactive molecules with major biotechnological applications. Nevertheless, the usual chemical and applied perspective leading most of bioprospecting projects come along with various limitations blurring our understanding of the extensive marine chemical diversity. Here, we propose several guidelines: (i) to optimize bioprospecting and (ii) to refine our knowledge on marine chemical ecology focusing on octocorals, one of the most promising sources of marine NPs. We identified a significant phylogenetic bias in the octocoral bioprospecting, which calls for the development of a concerted discovery strategy. Given the gap existing between the number of isolated NPs and the knowledge regarding their functions, we provide an ecologically centered workflow prioritizing biological function ahead of chemical identification. Furthermore, we illustrate how -omic technologies should rapidly increase our knowledge on solving different aspects of the ecology and evolution of marine NPs.

Impact of life history traits on gene flow: A multispecies systematic review across oceanographic barriers in the Mediterranean Sea

BACKGROUND

Marine species can demonstrate strong genetic differentiation and population structure despite the hypothesis of open seas and high connectivity. Some suggested drivers causing the genetic breaks are oceanographic barriers and the species' biology. We assessed the relevance of seven major oceanographic fronts on species connectivity while considering their dispersal capacity and life strategy.

METHODS

We systematically reviewed the scientific articles reporting population genetic differentiation along the Mediterranean Sea and across the Atlantic-Mediterranean transition. We retained those considering at least one sampling locality at each side of an oceanographic front, and at least two localities with no-front between them to correctly assess the effect of the front. To estimate the impact of life history characteristics affecting connectivity we considered the planktonic larval duration (PLD) and adult life strategy.

RESULTS

Oceanographic barriers in the Mediterranean Sea seem to reduce gene flow globally; however, this effect is not homogeneous considering the life history traits of the species. The effect of the oceanographic fronts reduces gene flow in highly mobile species with PLD larger than 2-4 weeks. Benthic sessile species and/or with short PLD (< 2 weeks) have more significant genetic breaks between localities than species with higher motility; however, genetic differentiation occurs independently of the presence of a front.

CONCLUSION

Genetic connectivity is important for populations to recover from anthropogenic or natural impacts. We show that species with low mobility, mostly habitat-formers, have high genetic differentiation but low gene flow reduction mediated by the front, therefore, considering the importance of these species, we emphasize the vulnerability of the Mediterranean ecosystems and the necessity of protection strategies based on the whole ecosystem.

Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals

Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.

Lack of recognition of genetic biodiversity: International policy and its implementation in Baltic Sea marine protected areas

Genetic diversity is needed for species' adaptation to changing selective pressures and is particularly important in regions with rapid environmental change such as the Baltic Sea. Conservation measures should consider maintaining large gene pools to maximize species' adaptive potential for long-term survival. In this study, we explored concerns regarding genetic variation in international and national policies that governs biodiversity and evaluated if and how such policy is put into practice in management plans governing Baltic Sea Marine Protected Areas (MPAs) in Sweden, Finland, Estonia, and Germany. We performed qualitative and quantitative textual analysis of 240 documents and found that agreed international and national policies on genetic biodiversity are not reflected in management plans for Baltic Sea MPAs. Management plans in all countries are largely void of goals and strategies for genetic biodiversity, which can partly be explained by a general lack of conservation genetics in policies directed toward aquatic environments.

Genetic Diversity and Local Connectivity in the Mediterranean Red Gorgonian Coral after Mass Mortality Events

Estimating the patterns of connectivity in marine taxa with planktonic dispersive stages is a challenging but crucial task because of its conservation implications. The red gorgonian Paramuricea clavata is a habitat forming species, characterized by short larval dispersal and high reproductive output, but low recruitment. In the recent past, the species was impacted by mass mortality events caused by increased water temperatures in summer. In the present study, we used 9 microsatellites to investigate the genetic structure and connectivity in the highly threatened populations from the Ligurian Sea (NW Mediterranean). No evidence for a recent bottleneck neither decreased genetic diversity in sites impacted by mass mortality events were found. Significant IBD pattern and high global F_ST confirmed low larval dispersal capability in the red gorgonian. The maximum dispersal distance was estimated at 20–60 km. Larval exchange between sites separated by hundreds of meters and between different depths was detected at each site, supporting the hypothesis that deeper subpopulations unaffected by surface warming peaks may provide larvae for shallower ones, enabling recovery after climatically induced mortality events.