Biology subjects

Derome, N.

Publications and source records attributed to Derome, N..

7 recordsLinked to original sources

bioRxiv2026

Delayed bleaching-induced coral mortality limits reef recovery after a marine heatwave

The increased frequency and intensity of coral bleaching events expose reefs to disturbance-recovery cycles that threaten their long-term dynamics. Understanding the impact of thermal stress requires evaluating coral mortality and recovery rates after disturbances. By integrating two long-term monitoring datasets, we examined coral mortality and recovery patterns at 13 sites in Mo'orea, French Polynesia, following the 2019 bleaching event, the most severe heat stress on record for the island. The maximum accumulated heat stress (AHSmax) varied from 5.76 to 6.26 {degrees} C weeks and enabled a direct analysis of heat-stress-related mortality. One year after bleaching, Pocillopora mortality increased with AHSmax, reducing mean coral cover from 35% to 17%. Regardless of AHSmax, Acropora mortality was high at all sites (median: 84%), reducing mean cover from 5% to 1% and indicating greater heat tolerance of Pocillopora than Acropora. Within four years after the bleaching event, no recovery occurred, and coral cover further declined relative to pre-bleaching levels. This decline was stronger for sites exposed to more intense heat stress. The impact of colony size was assessed by tracking 3090 individual Pocillopora colonies over six years and estimating size-dependent mortality and growth with a Bayesian mixed model. Immediately after the bleaching event, large Pocillopora corals exhibited a higher probability of complete and partial mortality than smaller colonies, highlighting size-specific consequences of bleaching. Even three years after the heat stress ended, large Pocillopora corals remained stressed, as evidenced by the continuously high probability of partial mortality. The lack of recovery observed here may be related to increased spatial competition with macroalgae. The disappearance of large fecund colonies and high mortality of coral recruits could have catastrophic consequences for the resilience of Mo'orea's reefs.

ecology↗

bioRxiv2025

The Genomic Architecture of Local Adaptation in Two Connected Populations of Three-Spined Stickleback.

Populations often adapt to their local environments despite the homogenizing effects of gene flow, but the genomic mechanisms enabling this process remain unclear. Theory predicts that adaptive divergence under high connectivity is favored when beneficial alleles cluster in regions of reduced recombination, a pattern that can be reinforced by structural variants (SVs). We investigated this in three-spined sticklebacks (Gasterosteus aculeatus) from the St. Lawrence Estuary, where distinct freshwater and marine ecotypes meet and interbreed along a short ecological gradient. Using long- and short-read whole-genome sequencing, we mapped fine-scale recombination landscapes, catalogued SVs, and examined their relationship with adaptive genomic regions. Recombination landscapes differed between populations, with population-specific shifts in recombination rate estimated by an LD-based method. Putatively adaptive regions were not confined to low-recombination regions, yet SVs (inversions, insertions, and deletions) frequently coincided with local recombination suppression and elevated differentiation, suggesting they may contribute to local adaptation. Differentiated regions also overlapped disproportionately with previously-identified regions involved in repeated local adaptation across the species range, which tended to be strongly enriched on chromosomes IV, VII and XXI. These repeated regions were associated with lower recombination rates, suggesting that recombination suppression may contribute to their reuse across populations. As found in stickleback populations from other regions, the St. Lawrence populations exhibit elements suggestive of concentrated architectures clustered in a few genomic regions, along with relatively diffuse patterns of highly differentiated regions distributed genome-wide, across a wide range of recombination rates. These results highlight the intertwined roles of recombination variation and structural variation in shaping evolutionary trajectories in connected populations. Article SummaryThis study investigates how recombination and structural variants shape local adaptation in the three-spined stickleback (Gasterosteus aculeatus). Using long- and short-read genome sequencing, the authors compared recombination landscapes and structural variants between marine and freshwater populations from the St. Lawrence Estuary. They found population-specific changes in recombination rate and frequent overlap between structural variants, reduced recombination, and genomic regions showing high differentiation. These findings suggest that variation in recombination and structural variants jointly influence how adaptation proceeds in connected populations, providing new insights into the genomic mechanisms that maintain diversity despite ongoing gene flow.

evolutionary biology↗

bioRxiv2025

Decoding cryptic diversity of moss populations in a forest-tundra ecotone

Cryptic speciation is widespread among bryophytes, and it appears common in arctic and subarctic mosses where cryptic lineages may occur sympatrically in the environment. However, cryptic lineages are rarely considered in genetic diversity assessments. This situation poses a challenge, as the complex population structure resulting from cryptic speciation, along with factors like the predominance of clonality, can lead to inaccurate estimates of biodiversity. In this sense, we studied two populations of the subarctic moss Racomitrium lanuginosum in the forest-tundra ecotone to test the impact of accounting for differentiated genetic groups on moss genetic diversity estimates, clonal structure and microbial covariation. We performed genotyping-by-sequencing to infer genetic diversity and structure in the forest tundra and the shrub tundra. Genetic groups were identified using haplotype-based coancestry matrices and phylogenetic analyses. The clonal structure was explored by determining multilocus genotypes at the population and a finer scale (225 cm2). The covariation between genetic groups and microbial communities (bacterial and diazotrophic) was explored. The recognition of cryptic lineages in genetic diversity estimations revealed differences between habitats that remained undetected when treating R. lanuginosum as a single species. Clonal growth seemed to predominate and affect the genetic structure at the local scale. Finally, genetic groups did not host specific microbiomes, suggesting that moss microbial associations in the forest-tundra ecotone did strongly respond to a genetic component. This study highlights the importance of accounting for cryptic lineages in genetic diversity estimations for a precise biodiversity assessment in subarctic and arctic ecosystems.

ecology↗

bioRxiv2023

Differentially abundant bacteria drive the N2-fixation of a widespread moss in the forest-tundra transition zone

Bryophytes maintain symbiosis with epiphytic bacteria influencing the local nutrient budget. Moss bacterial communities are composed of a core microbiome and bacteria recruited from environmental sources. Notably, symbiotic N2-fixing bacteria contribute to the N budget in northern ecosystems through biological nitrogen fixation. This process may be affected by the abundance of diazotrophs and moss nutrient content. We used the abundant moss Racomitrium lanuginosum in a forest tundra and shrub tundra in Northern Quebec, Canada, to investigate the bacterial and diazotrophic communities associated with habitat type using amplicon sequencing of the bacterial 16S rRNA and nifH genes and test whether the moss core microbiome has recruitment from the soil bacteria community. The nifH amplicons and element analysis were used to test the effect of diazotrophic abundance and moss nutrient content on N2-fixation activity estimated by acetylene reduction assays. Moss microbial communities between tundra types hosted similar bacterial diversity but differentially abundant groups. The core microbiome of R. lanuginosum is composed of bacteria strongly associated with northern mosses with no significant recruitment from the soil. The relative abundances of dominant diazotrophs are significantly correlated with acetylene reduction rates. In contrast, the moss nutrient content did not significantly drive N2-fixation. The proteobacterial genera Azorhizobium and Rhodomicrobium represent newly reported bacteria associated with N2-fixation rates in the tundra. We identified critical bacterial groups related to moss-bacterial symbiosis and N2-fixation in the forest-tundra transition zone, a changing environment susceptible to climate warming.

microbiology↗

bioRxiv2022

Genomic and environmental factors shape gill microbiome activity in an Amazonian teleost holobiont

Fish microbiomes provide functions critical for their hosts survival in contrasting environments. These communities are sensitive to a range of environmental-specific factors (i.e. physicochemical parameters, free-living bacterioplankton) and host-specific factors (i.e. host genetic background). The relative contribution of these genomic and environmental factors shaping Amazonian fish microbiomes is still unknown. Here, we investigated this topic by analyzing the gill microbiomes of 240 wild flag cichlids (Mesonauta festivus) from four different populations (genetic clusters) distributed in 12 sites of two contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). The transcriptionally active gill microbiomes were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed in light of comprehensive datasets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplanktonic pool of bacteria (16S rRNA) and a set of 34 environmental parameters. Results show that the transcriptional activity of gill microbiome samples was significantly different between the genetic clusters and between water types. However, they suggest that the contribution of the hosts genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different gill microbiome transcripts. This result was also confirmed by a mixed-effects modeling analysis, which suggested that the dissimilarity between the transcriptional activity of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill microbiomes transcripts, while pairwise fixation indexes (FST) from the hosts genetic data only had a weak explicative power. We discuss these results in terms of microbiome assembly processes and flag cichlid fish ecology. ImportanceHost-associated microbial communities respond to a range of factors specific to the host physiology, genetic backgrounds and life history. However, these communities also show different degrees of sensitivity to environment-dependant factors such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host-versus environment-associated factors in shaping teleost microbiomes is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost microbiomes using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the hosts genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill microbiomes, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.

ecology↗

bioRxiv2020

Evenness-richness scatter plots: a graphical, intuitive approach to alpha diversity analysis

Shannons diversity index is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent of both those parameters, there is theoretically an infinite number of richness / evenness value combinations translating into the same index score. By decoupling both components measured by Shannons index, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as PERMANOVA can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise.

bioinformatics↗

bioRxiv2018

Intestinal microbiota of whitefish (Coregonus sp.) species pairs and their hybrids in natural and controlled environment.

It is becoming increasingly clear that wild animals have never existed without symbiotic interactions with microbiota. Therefore, investigating relationships between microbiota and their host is essential towards a full understanding of how animal evolve and adapt to their environment. The Lake Whitefish (Coregonus clupeaformis) is a well-documented model for the study of ecological speciation, where the dwarf species (limnetic niche specialist) evolved independently and repeatedly from the normal species (benthic niche specialist). In this study, we compared the transient intestinal microbiota among five wild sympatric species pairs of whitefish as well as captive representatives of dwarf and normal species and their reciprocal hybrids reared in identical controlled conditions. We sequenced the 16s rRNA gene V3-V4 regions of the transient intestinal microbiota present in a total of 185 whitefish to (i) test for parallelism in the transient intestinal microbiota among sympatric pairs of whitefish, (ii) test for transient intestinal microbiota differences among dwarf, normal and both hybrids reared under identical conditions and (iii) compare intestinal microbiota between wild and captive whitefish. A significant effect of host species on microbiota taxonomic composition was observed in the wild when all lakes where analyzed together, and species effect was observed in three of the five species pairs. In captive whitefish, an influence of host (normal, dwarf and hybrids) was also detected on microbiota taxonomic composition and tens of genera specific to dwarf, normal or hybrids were highlighted. Hybrid microbiota was not intermediate; instead its composition fell outside of that observed in the parental forms and this was observed in both reciprocal hybrid crosses. Interestingly, six genera formed a bacterial core which was present in captive and wild whitefish, suggesting a horizontal microbiota transmission. Although diet appeared to be a major driving force for microbiota evolution, our results suggested a more complex interaction among the host, the microbiota and the environment leading to three distinct evolutionary paths of the intestinal microbiota.

evolutionary biology↗