Biology subjects

Destombe, C.

Publications and source records attributed to Destombe, C..

6 recordsLinked to original sources

bioRxiv2026

Haplotype tagging sheds light on speciation between two divergent cryptic species of the brown algae Ectocarpus

Understanding how genome-wide divergence translates to barriers to gene flow is a central question in speciation research, particularly in marine environments where interconnected habitats frequently accommodate cryptic diversity. Using linked-read whole-genome data from the brown alga Ectocarpus, we investigated genome-wide reproductive isolation between two cryptic brown algal species E. siliculosus and E. crouaniorum across replicated hybrid zones in Europe and Chile. We first uncover deep genetic structure within E. crouaniorum, revealing a more intricate species complex than previously recognized. Despite this complexity, we found parallel patterns of asymmetric introgression that emerged independently in Europe and Chile, where we detected both, F1 and low-level introgressed individuals. However, the specific lineage pairs involved in hybridization depended on local demographic history. Demographic modeling further indicated that reproductive isolation strengthens gradually with divergence time and differs markedly between geographic regions, with ongoing asymmetric gene flow even between lineage pairs where hybrids were not detected in the field. In all cases, the genomic landscape of hybridization is consistent with a polygenic, genome-wide barrier to gene flow rather than a few large-effect regions. Our results show that cryptic speciation in brown algae is driven by repeatable, regionally parallel architectures of genome-wide reproductive isolation which is shaped by ecological and demographic context.

evolutionary biology↗

bioRxiv2025

Wild and farmed Saccharina latissima in Europe: genetic insights for sustainable cultivation, traceability and environmental challenges

Kelp cultivation is expanding rapidly worldwide, although the aquaculture of Saccharina latissima (sugar kelp) in Europe remains in its early stages. However, major concerns have emerged about the potential impact of selected cultivars of the species on native populations of S. latissima which are already vulnerable to stressors including climate change. To address these concerns and support sustainable cultivation, it is essential to characterise genetic diversity and structure of wild kelp populations to monitor potential farm-to-wild gene flow. In this study we used 21 microsatellite loci to characterise the genetic structure of 24 natural and 3 farmed populations of S. latissima along European coasts. Results confirmed strong genetic differentiation between the northern and southern coasts, refining the boundaries between these two clusters compared to previous studies. Within each cluster, a clear genetic substructure was detected, with population differentiation being far more pronounced in the southern cluster. Cultivated sporophytes exhibited pedigrees that were all traced back to the local parent populations. Bayesian model-based structure analysis, discriminant analysis of principal components and assignment tests revealed no significant genetic differentiation between the farms and their wild populations. This indicates that farmed populations and neighbouring populations share the same gene pool, reflecting current cultivation practices. These findings contribute to understanding risks of gene flow between wild and farmed populations and demonstrate that strain traceability is feasible. Additionally, the study highlights the challenge European seaweed farmers face in securing reliable seedling stock, especially in the context of global change.

genetics↗

bioRxiv2024

Structural and evolutionary features of red algal UV sex chromosomes

BackgroundSex chromosomes in red algae have remained relatively understudied, despite their fundamental role in understanding the evolution of sex determination across eukaryotes. In this study, we investigate the structure, gene composition, and evolutionary history of the U and V sex chromosomes in four Gracilaria species, which diverged approximately 100 million years ago (MYA). ResultsOur findings reveal that UV sex chromosomes, previously identified in green and brown algae as well as bryophytes, have also evolved in red algae, contributing to the diversity of sex determination systems across eukaryotes. The shared orthology of conserved sex-determining region (SDR) genes between Gracilaria and distantly related red algae suggests that this system may have originated approximately 390 MYA, making it one of the oldest known sex chromosome systems. The SDR in Gracilaria is relatively small but contains conserved gametologs and V-specific genes involved in transcriptional regulation and signaling, suggesting their essential role in sexual differentiation. Unlike the conserved V-specific genes, U-specific genes appear absent, pointing to a dominant role of the V chromosome in sex determination. The evolution of Gracilaria sex chromosomes involved recombination suppression, gene relocations, duplications, and potential gene loss. Despite their ancient origin, the sex chromosomes show low levels of degeneration, likely due to haploid purifying selection during the gametophytic phase of the life cycle. ConclusionThis study provides the first detailed characterization of the U and V sex chromosomes in red algae, preparing the ground for future studies on reproductive life cycles and speciation in this understudied group of eukaryotes.

evolutionary biology↗

bioRxiv2023

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

The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species demographic history should be considered. Furthermore, we provided compelling evidence of positive selection through the examination of allele frequency changes over time, offering additional insights into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low levels of genetic diversity, that further decreased over time. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.

evolutionary biology↗

bioRxiv2023

THE RHODOEXPLORER PLATFORM FOR RED ALGAL GENOMICS AND WHOLE GENOME ASSEMBLIES FOR SEVERAL GRACILARIA SPECIES

Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales are highly diverse and widely distributed order whose species can serve as ecosystem engineers in intertidal habitats, including several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

genomics↗

bioRxiv2019

Evolution of life cycles and reproductive traits: insights from 1 the brown algae

Brown algae are characterized by a remarkable diversity of life cycles, sexual systems, and reproductive modes, and these traits seem to be very labile across the whole group. This diversity makes them ideal models to test existing theories on the evolution of alternation between generations, and to examine correlations between life cycle and reproductive life history traits. In this study, we investigate the dynamics of trait evolution for four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assign states to up to 70 species in a multi-gene phylogeny of brown algae, and use maximum likelihood and Bayesian analyses of correlated evolution, taking phylogeny into account, to test for correlations between life history traits and sexual systems, and to investigate the sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth may evolve because it allows the complementation of deleterious mutations, and that haploid sex determination is ancestral in relation to diploid sex determination. However, the idea that increased zygotic and diploid growth is associated with increased sexual dimorphism is not supported by our analysis. Finally, it appears that in the brown algae isogamous species evolved from anisogamous ancestors.

evolutionary biology↗