Biology subjects

Linares, C.

Publications and source records attributed to Linares, C..

5 recordsLinked to original sources

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2024

Recurrent extreme climatic events are driving gorgonian populations to local extinction: low adaptive potential to marine heatwaves.

Extreme climatic events (ECEs), such as marine heatwaves (MHWs), are a major threat to biodiversity. Understanding the variability in ecological responses to recurrent ECEs within species and underlying drivers arise as a key issue owing to their implications for conservation and restoration. Yet, our knowledge on such ecological responses is limited since it has been mostly gathered following "single-event approaches" focused on one particular event. These approaches provide snapshots of ecological responses but fall short of capturing heterogeneity patterns that may occur among recurrent ECEs, questioning current predictions regarding biodiversity trends. Here, we adopt a "multi-event" perspective to characterize the effects of recurrent ECEs and the ecological responses in Paramuricea clavata, a Mediterranean temperate coral threatened by MHWs. Through a common-garden experiment repeated three consecutive years with the same individuals from three populations, we assessed the respective roles of environmental (year effect), genetic (population effect) and phenotypic (population-by-environment interactions effect) components in the ecological response to recurrent heat stress. The environmental component (year) was the main driver underlying the responses of P. clavata colonies across experiments. To build on this result, we showed that: i) the ecological responses were not related to population (genetic isolation) and individual (multilocus heterozygosity) genetic make-up, ii) while all the individuals were characterized by a high environmental sensitivity (genotype-by-environment interactions) likely driven by in-situ summer thermal regime. We confront our experimental results to in situ monitoring of the same individuals conducted in 2022 following two MHWs (2018, 2022). This confirms that the targeted populations harbor limited adaptive and plastic capacities to on-going recurrent ECEs and that P. clavata might face unavoidable population collapses in shallow Mediterranean waters. Overall, we suggest that biodiversity forecasts based on "single event" experiments may be overly optimistic and underscore the need to consider the recurrence of ECEs in assessing threats to biodiversity.

ecology↗

bioRxiv2023

Marine heatwaves favour resistant Mediterranean octocoral populations at the expense of their speed of recovery

1. The effects of climate change are now more pervasive than ever. Marine ecosystems have been particularly impacted by climate change, with Marine Heat Waves (MHWs) being a strong driver of mass mortality events. Even in the most optimistic greenhouse gas emission scenarios, MHWs will continue to increase in frequency, intensity, and duration. For this reason, understanding the resilience of marine species to the increase of MHWs is crucial to predicting their viability under future climatic conditions. 2. In this study, we explored the consequences of Marine Heatwaves (MHWs) on the resilience of a Mediterranean key octocoral species, Paramuricea clavata, to further disturbances to their population structure. To quantify P. clavatas capacity to resist and recover from future disturbances, we used demographic information collected from 1999 to 2022, from two different sites in the NW Mediterranean Sea. 3. Our results showed that the differences in the dynamics of populations exposed and those not exposed to MHWs were driven mostly by differences in mean survivorship and growth. We also showed that after MHWs P. clavata populations had slower rates of recovery but did not experience changes in resistance. Populations exposed to MHWs had lower resistance elasticity to progression but higher stasis compared to unexposed populations. In contrast, the only demographic process showing some differences when comparing the speed of recovery elasticity values between populations exposed and unexposed to MHWs was stasis. Finally, under scenarios of increasing frequency of MHWs, the extinction of P. clavata populations will accelerate and their capacity to recover after further disturbances will be hampered. 4. Overall, these findings confirm that future climatic conditions will make octocoral populations even more vulnerable to further disturbances. These results highlight the importance of limiting local impacts on marine ecosystems to dampen the consequences of climate change.

ecology↗

bioRxiv2019

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 and 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 hybrid assembly accounting for 712.4 Mb and 107,682 scaffolds. The contig and scaffold N50 are 15.85 Kb and 17.01 Kb, respectively. Despite of the low contiguity of the assembly, the gene completeness was relatively high, including 86% of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 76,508 protein-coding genes and 85,763 transcripts 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, the genome of P. clavata will help to understand various aspects of its evolutionary ecology and to elaborate effective conservation plans such as active restoration actions to overcome the threats of global change.

genomics↗

bioRxiv2019

Aquatic and terrestrial organisms display contrasting life history strategies as a result of environmental adaptations

AimsAquatic and terrestrial realms display stark differences in key environmental factors and phylogenetic composition. Despite such differences, their consequences for the evolution of species life history strategies remain poorly understood. Here, we examine whether and how life history strategies vary between terrestrial and aquatic species.\n\nLocationGlobal.\n\nTime periodVariable, the earliest year being in 1906 and the most recent in 2015.\n\nMajor taxa studiesMacroscopic animals and plants species.\n\nMethodsWe use demographic information for 638 terrestrial and 117 aquatic animal and plant species, to derive key life history traits capturing their population turnover, and investments in survival, development, and reproduction. We use phylogenetically corrected least squares regression to explore the differences in the trade-offs between life history traits in both realms. We then quantify the life history strategies of aquatic and terrestrial species using a phylogenetically corrected principal component analysis.\n\nResultsWe find that the same trade-offs structure terrestrial and aquatic life histories, resulting in two dominant axes of variation describing species pace- of-life and reproductive spread through time. Life history strategies differ between aquatic and terrestrial environments, with phylogenetic relationships playing a minor role. We show that adaptations of plants and animals to terrestrial environments have resulted in different life history strategies, particularly with their reproductive mode and longevity. Terrestrial plants display a great diversity of life history strategies, including the species with the longest lifespans. Aquatic animals, on the contrary, exhibit higher reproductive frequency than terrestrial animals, likely due to reproductive adaptations (i.e. internal fecundation) of the later to land.\n\nMain conclusionsOur findings show that aquatic and terrestrial species are ruled by the same life history principles, but have evolved different strategies due to distinct selection pressures. Such contrasting life history strategies have important consequences for the conservation and management of aquatic and terrestrial species.

ecology↗