Myriam Valero

Many organisms alternate between distinct life stages and can reproduce either sexually or asexually, yet the mechanisms coordinating these developmental and reproductive transitions remain poorly understood. Here, we investigate the molecular basis of life stage identity and reproductive mode in the kelp Laminaria pallida , a multicellular organism with a complex life cycle. By combining gene expression analyses with developmental experiments and natural population-level approaches, we characterize the transcriptional signatures associated with developmental state transitions in both sexual and asexual contexts. We show that asexual reproduction is associated with endoreduplication and reduced fitness, while it is retained but rarely expressed in two natural populations. Moreover, we find that the presence of potential mating partners reduces asexual development, revealing that reproductive mode is adjusted in response to reproductive opportunities. Together, these findings suggest that asexual reproduction functions as a conditional alternative to sex, promoting persistence when sexual reproduction is constrained while preserving the long-term benefits of sexual reproduction when mates are available. More broadly, our results reveal how organisms integrate developmental, environmental, and reproductive cues to balance alternative reproductive strategies across complex life cycles.

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 (RI) between two cryptic brown algal species E. siliculosus and E. crouaniorum across replicated hybrid zones in Europe and Chile. We first uncovered 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 RI 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 barriers to gene flow, with lineage-specific demographic history playing an important role in shaping the extent of RI.

The sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and Northeast Pacific, but genetic improvement has been hindered by a limited understanding of the genetic basis of economically important traits. We conducted a genome‐wide association study (GWAS) for this species using 202 self‐fertilized pseudo‐F1 individuals derived from 12 of 13 sampled populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD‐seq‐derived single nucleotide polymorphism markers and phenotyped in a common‐garden experiment for four morphological traits (blade length, blade width, blade area, and stipe length) and six metabolic traits related to nitrogen metabolism. We identified 18 significant marker–trait associations, with individual loci explaining 1.37% to 10.93% of phenotypic variance (PVE). Rather than major‐effect quantitative trait locus (QTL), the associated loci each accounted for a small‐to‐moderate proportion of trait variance, the largest being for nitrogen‐metabolism traits (up to 10.93% PVE), and a single locus on chromosome 17 influenced both blade length and blade area. Marker‐based heritability was high for morphological traits (0.75–0.99) but ranged widely for metabolic traits (0–0.99), with large standard errors throughout. Cross‐validated genomic selection models yielded predictive abilities of 0.21–0.59 across traits, the only exception being for protein content, for which both heritability and predictive ability were effectively null. Overall, these results indicate a mixed genetic architecture, comprising moderate‐effect loci amenable to marker‐assisted selection and polygenic traits better suited to genomic selection, and they provide a foundation for genomics‐assisted breeding in kelp aquaculture.

Domestication genomics is well established in terrestrial domesticates, yet remains broadly unexplored in marine macroalgae, where life-history traits and marine connectivity differ fundamentally from terrestrial systems. In Gracilaria chilensis (Rhodophyta), domestication is driven by sustained vegetative propagation and differentiated farming habitats, potentially reshaping genetic diversity and imposing selective pressures. We investigated genomic signatures of incipient domestication using 6,058 ddRADseq markers across six wild and nine farmed Chilean populations. Our results reveal genomic consequences of clonality on farms, with high clonal rates (0.52 vs. 0.02 in wild populations), excess of heterozygotes (mean FIS = -0.183 vs. -0.027), and broad intraclonal variation. These patterns suggest accumulation of somatic mutations in clonal lineages, which may underlie declines in farm yield due to thallus aging. Although clonal drift may limit the detection of selective sweeps, an FST outlier analysis between wild and farmed populations identified 69 divergent loci (q-value ≤ 0.001) linked to 49 candidate genes. Functional enrichment analysis grouped these genes into five biological clusters associated with stress tolerance, growth-reproduction trade-offs, and holobiont restructuring. Population structure analysis showed geographic differentiation among wild populations, contrasting with a genetically homogenised farm network sustained by widespread exchange of clonal strains. Gene flow analysis revealed complex wild-farm connectivity, with high risk of crop-to-wild introgression posing a conservation risk to wild gene pools. Our findings demonstrate that recent seaweed domestication can generate detectable adaptive divergence, highlighting the challenges of managing genetic resources in asexual crops while mitigating risks to wild population integrity through metapopulation-scale conservation strategies.

Unlike other red algae, the perennial species Palmaria palmata exhibits pronounced sexual dimorphism with a microscopic female gametophytic phase that does not produce cystocarps. To investigate how these unique features of its life cycle influence its reproductive mode, we analyzed the relative proportion of macroscopic individuals (tetrasporophytes vs. male gametophytes) across multiple geographic scales and between intertidal and subtidal habitats along the western coast of France (892 individuals collected from 17 locations). Because female gametophytes are microscopic and cannot be directly sampled in the field, their frequencies were inferred under two alternative hypotheses: (H1) assuming an equal sex ratio (i.e., the proportion of females equal to males) and (H2) assuming the proportion of females equals tetrasporophytes, given that tetrasporophytes develop directly on a female gametophyte. Under H1, our results predict a demographic advantage of tetrasporophytes over gametophytes. Moreover, tetrasporophytes were significantly more abundant in intertidal than in subtidal zones, likely reflecting their greater resilience to environmental fluctuations. Conversely, under H2, the sex ratio was significantly biased toward female gametophytes and the estimated proportion of tetrasporophytes was lower than that of gametophytes. In addition, the relative contribution of self‐fertilization and clonal reproduction were assessed using 11 microsatellite markers. These findings confirm that this species reproduces mainly sexually and suggest that sexual dimorphism may limit selfing and enhance the survival of the tetrasporophyte, which develops directly on the female, thereby compensating for the absence of cystocarps. Overall, our results provide valuable insights into the reproductive strategies and adaptive potential of this commercially important alga.

Germplasm banks are important for preserving genetic diversity, yet the availability and long-term maintenance of macroalgal strains in germplasm banks is currently limited in European collections. To support future food security, restoration efforts, and biotechnological innovation, a strategy was recently developed for the long-term preservation of macroalgal genetic diversity. A foundational step in this effort is to assess the existing biodiversity, biogeographical distribution, and commercial relevance of seaweed cultures maintained in European collections. Using a universal data-collection template distributed widely across European seaweed networks, we compiled and analysed information on these seaweed cultures. As of November 2025, the resulting SeaStrains Database of European Seaweed Collections contains 2541 cultures representing 426 species, accounting for only 4% of global and 15% of European macroalgal diversity. The dataset reveals strong taxonomic bias: 74% are brown seaweeds (Ochrophyta), dominated by Laminaria , Saccharina , and Ectocarpus . Saccharina latissima is the most preserved species due to its scientific and commercial importance. Red and green algae are markedly underrepresented (11% and 14%, respectively), likely reflecting cultivation challenges and life-cycle knowledge gaps. Biogeographically, most cultures originate from cold- to warm-temperate zones, with limited representation of the South Atlantic, Indian Ocean, polar and remote regions. Over 60% of cultures are maintained at two institutions: the Culture Collection of Algae and Protozoa (Scotland) and the Alfred Wegener Institute (Germany). This work provides transparent, accessible information on Europe’s macroalgal germplasm resources and represents a crucial step toward a more robust and sustainable European seaweed sector aligned with UN SDG Target 2.5.

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.

The sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and North-East Pacific but genetic improvement has been hindered by limited understanding of the genetic basis of economically important traits. We conducted the first genome-wide association study (GWAS) for this species using 202 self-fertilised pseudo-F1 individuals derived from 12 populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD-seq-derived SNP markers and phenotyped in a common garden experiment for four morphological traits (blade length, blade width, blade area, stipe length) and six metabolic traits related to nitrogen metabolism. We identified 26 significant marker-trait associations, with phenotypic variance explained (PVE) ranging from 0.65% to 52.44%. Major-effect loci were detected for blade width (52.44% PVE) and blade area (45.22% PVE) and a locus on chromosome 17 influenced both blade length and blade area. Marker-based heritability estimates ranged from 0.75 to 0.99 for morphological traits and from 0.00 to 0.99 for metabolic traits, though with large standard errors. Cross-validation of genomic selection models yielded predictive abilities of 0.21-0.59 across traits. Our findings reveal a mixed genetic architecture with major-effect loci suitable for marker-assisted selection and polygenic traits amenable to genomic selection, providing a foundation for genomics-assisted breeding programs in kelp aquaculture.

Background: Sex 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. Results: Our 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 genes between Gracilaria and distantly related red algae suggests that this system may have originated approximately 390 million years ago, making it one of the oldest known sex chromosome systems. The sex-determining region 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. 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. Conclusions: This study provides the first large-scale comparative genomic and transcriptomic analysis of the U and V sex chromosomes across multiple red algal species, preparing the ground for future studies on reproductive life cycles and speciation in this understudied group of eukaryotes.