Biology subjects

Le Moan, A.

Publications and source records attributed to Le Moan, A..

13 recordsLinked to original sources

bioRxiv2026

Comparison of the performance of sporophytes derived from narrow and wide genetic crosses between strains of the cultivated kelp Saccharina latissima

Seaweed mariculture allows sustainable production of large quantities of biomass for multiple downstream applications but the genotypes cultivated by this industry need to be improved to increase efficiency and cost-effectiveness. It is important that the genetic improvement of cultivated strains does not lead to the introduction of foreign genetic material into wild seaweed populations, which are already under threat from global heating. To circumvent this problem, efforts are being made to develop breeding approaches based on the use of locally-resourced genetic material. The aim of this study was to evaluate the potential effectiveness of this 'local' breeding strategy compared to a classical breeding approach based on wide genetic crosses. Analyses of growth rates and cell wall composition of F1 hybrids derived from either intra- or inter-population crosses between Saccharina latissima strains from two localities, southern Brittany, France and the Faroe Islands, did not identify any clear advantage of inter- compared to intra-population crosses. Breeding based on locally-resourced strains would therefore appear to be a valid approach for current strain selection programs. The study also established a large collection of gametophyte strains from multiple sites for future breeding programs and showed that these strains retained the capacity to become fertile after more than ten years in culture.

genetics↗

bioRxiv2026

Inversions support both parallel and location-specific adaptations in snail ecotypes

Replicated hybrid zones between ecotypes established over within shore environmental gradients provide an opportunity to study the genomic architecture of barriers to gene flow. The marine snail Littorina fabalis segregates locally into dwarf and large ecotypes over wave-exposure gradients on northwestern European shores. Previous work focusing on a hybrid zone in Sweden revealed strong genetic differentiation between the ecotypes, concentrated in 12 putative chromosomal inversions. Here we compare the Swedish hybrid zone with samples from France distributed across a similar wave-exposed gradient. Our aims were to test if similar exposure gradients promote parallel ecotype distributions and hybrid zones, and if similar genomic architectures contribute to divergence and adaptation across the gradients. Unpredictably, we found that the shell size cline was reversed in France compared to Sweden, with small individuals occupying the more-sheltered end of the environmental gradient in Sweden but the more-exposed end in France. We also observed a cline in shell colour in France, whereas nearly all Swedish snails were yellow. Using whole-genome sequencing, we found similar levels of genetic differentiation between ecotypes in both places. Most of the differences were accounted for by the same 15 inversions, and the arrangement clines showed similar associations to the wave-exposure gradient in both hybrid zones. These inversions were enriched in SNPs differentiating the ecotypes that were either specific to one hybrid zone or showed reversed cline patterns between zones. Genome-wide association studies (GWAS) detected significant associations between genomic regions within inversions and shell size in Sweden, while one inversion was associated with colour in France. Our results show that the same inversions play a dual role: they support ecotype differences across similar environmental gradients in distant locations, while also contribute site-specific variation contributing to local adaptation.

evolutionary biology↗

bioRxiv2025

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

Predicting the genetic consequences of population decline is a major problem in conservation genomics. Time lags following demographic bottlenecks can delay genomic erosion and make it difficult to determine a populations current and future risk, especially when pre-bottleneck genomic baselines are unavailable. Black abalone (Haliotis cracherodii) suffered a severe disease bottleneck in the 1980s, resulting in an estimated 99% population decline. However, recent work found surprisingly high genetic diversity and little population structure in current black abalone populations, raising questions of whether genomic erosion has been delayed. To investigate this, we applied ancient DNA methods to pre-bottleneck abalone shells, generating 59 whole genomes including one 34-fold coverage genome from a 1,500-year-old specimen. These data show that heterozygosity, runs of homozygosity, genetic load and population structure remained stable up to and following the bottleneck. Simulations reveal that this stability is consistent with even severe bottleneck scenarios because too few generations have lapsed since the decline. Projections suggest that future genomic erosion may be avoided even in limited recovery scenarios. Following the bottleneck we observe widespread balancing selection at genes with immune function, along with parallel increases of two inversions on separate chromosomes that are in linkage disequilibrium, where the disease bottleneck was most severe. Altogether, these findings explain why genomic change has thus far been limited, outline recovery scenarios that minimize genomic erosion, and identify loci likely that may harbor adaptive variation key to the success of future black abalone populations.

evolutionary biology↗

bioRxiv2024

Ecotype formation in the European anchovy fuelled by structural variants of different origins and genetic interactions with a southern lineage

The formation of ecotypes is shaped by mechanisms that reduce gene flow through complex interactions between ecological, historical, and genomic factors. In the European anchovy (Engraulis encrasicolus), marine and coastal ecotypes have been identified in the North-East Atlantic and Mediterranean Sea, yet the genomic basis of their divergence remains unclear. Here, we present the first genome-scale analysis of this species complex, integrating whole-genome sequencing (WGS) and RAD-seq data from populations across its distribution range. In addition to the marine and coastal ecotypes, we identify a previously undetected lineage which is present in southern Morocco, the Canary Islands and even in South Africa. This southern Atlantic lineage exhibits a gradient of admixture with northern populations near the Atlantic-Mediterranean transition zone. Genomic differentiation landscapes reveal large regions of high linkage disequilibrium, likely corresponding to thirteen structural variants (SVs) segregating within or between the lineages. Notably, three of the six SVs contributing to the gene flow barrier between northern ecotypes originated in the southern lineage, supporting a partially shared evolutionary history between the coastal ecotype and the southern lineage. Our findings suggest that anchovy ecotype divergence has been shaped by a combination of ancient structural variation, admixture, and local adaptation. This study highlights how SVs that arose between geographically isolated lineages can act as key genetic elements in ecotype formation, reinforcing reproductive isolation through distinct evolutionary pathways.

evolutionary biology↗

bioRxiv2024

Population divergence manifested by genomic rearrangements in a keystone Arctic species with high gene flow

Genomic rearrangements have in recent years gained attention due to their evolutionary role in processes related to adaptation to local environmental conditions as well as diversification and speciation. In this study, we report on genomic rearrangements in the cold-water adapted polar cod (Boreogadus saida), a keystone Arctic fish species. By taking advantage of a new chromosome-level genome assembly in combination with whole-genome population sequencing data from specimens across the northern Barents Sea and adjacent regions, we identified a substantial number of larger chromosomal inversions (n=20) and characterized the previously identified chromosomal fusions (n=5). These genomic features -- encompassing over 20% of the genome -- exhibited genetic divergence, strong internal linkage disequilibrium, and signals of selection. Two of the identified inversions were associated with the two previously described hemoglobin clusters, while a third chromosomal region was found to differentiate between males and females. Moreover, clustering analyses on genotype frequencies of inversions revealed sub- structuring according to five geographic sub-groups suggesting sub-populations and/or the existence of cryptic ecotypes. These results provide novel insights into the impact of genomic rearrangements in population divergence and thus, potentially local adaptation, especially in species with high gene flow.

genomics↗

bioRxiv2024

Chromosome-scale genome assembly and gene annotation of the hydrothermal vent annelid Alvinella pompejana yield insight into animal evolution in extreme environments

The types of genomic change needed for environmental adaptation are of great interest. Annelid worms are a large phylum found in a rich diversity of habitats, giving opportunities to explore this issue. We report the chromosome level genome sequence of the Pompeii worm, the annelid Alvinella pompejana, an inhabitant of an extreme deep-sea hydrothermal vent environment. We find strong but heterogeneously distributed genetic divergence between populations taken from either side of the equator. Using transcript data, we produced a set of gene models and analysed the predicted protein set in the light of past hypotheses about the thermotolerance of Alvinella, and compared it to other recently sequenced annelid vent worms. We do not find evidence of a more extreme genome wide amino acid composition than other species, neither do we find evidence for rapid genome evolution in the form of disrupted synteny. We discount the hypothesis of loss of amino acid biosynthesis genes associated with obligate symbioses reported in siboglinid annelids. We do find evidence of a parallel increase in the number of globin encoding genes and loss of light sensitive opsins and cryptochromes. Alvinella encodes several respiratory enzymes unusual for bilaterian animals, suggesting an ability to better tolerate hypoxic environments.

genomics↗

bioRxiv2023

Coupling of 12 chromosomal inversions maintains a strong barrier to gene flow between ecotypes

Chromosomal rearrangements lead to the coupling of reproductive barriers, but whether and how they contribute to completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between taxa segregating for inversion arrangements, providing opportunities to study this question. Here, we analysed two adjacent transects across hybrid zones between large and dwarf ecotypes of Littorina fabalis covering wave exposure gradients in a Swedish island. Applying whole-genome sequences we found 12 putative inversions reaching near differential fixation between the opposite ends of each transect, and being in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent SNPs. Bimodal hybrid zones in both transects indicate that the two ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact due to strong coupling between inversion clines that strengthened the reproductive barrier. The bimodality resulting from the linked inversions extends into collinear parts of the genome, suggesting a genome-wide coupling. Demographic inference suggests that the coupling built up during a period of allopatry, and has been maintained for more than 1K generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Importantly, two of the inversions overlap with inverted genomic regions associated with ecotype differences in a closely-related species (L. saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.

evolutionary biology↗

bioRxiv2023

Selection on many loci drove the origin and spread of a key innovation

Key innovations are fundamental to biological diversification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. Samples do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.

evolutionary biology↗

bioRxiv2022

Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?

AO_SCPLOWBSTRACTC_SCPLOWHuman-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.

evolutionary biology↗

bioRxiv2021

An introgression breakthrough left by an anthropogenic contact between two ascidians

Human-driven translocations of species have diverse evolutionary consequences such as promoting hybridization between previously geographically isolated taxa. This is well-illustrated by the solitary tunicate, Ciona robusta, native to the North East Pacific and introduced in the North East Atlantic. It is now co-occurring with its congener C. intestinalis in the English Channel, and C. roulei in the Mediterranean Sea. Despite their long allopatric divergence, first and second generation crosses showed a high hybridization success between the introduced and native taxa in the laboratory. However, previous genetic studies failed to provide evidence of recent hybridization between C. robusta and C. intestinalis in the wild. Using SNPs obtained from ddRAD-sequencing of 397 individuals from 26 populations, we further explored the genome-wide population structure of the native Ciona taxa. We first confirmed results documented in previous studies, notably i) a chaotic genetic structure at regional scale, and ii) a high genetic similarity between C. roulei and C. intestinalis, which is calling for further taxonomic investigation. More importantly, and unexpectedly, we also observed a genomic hotspot of long introgressed C. robusta tracts into C. intestinalis genomes at several locations of their contact zone. Both the genomic architecture of introgression, restricted to a 1.5 Mb region of chromosome 5, and its absence in allopatric populations suggest introgression is recent and occurred after the introduction of the non-indigenous species. Overall, our study shows that anthropogenic hybridization can be effective in promoting introgression breakthroughs between species at a late stage of the speciation continuum.

evolutionary biology↗

bioRxiv2019

Beyond parallel evolution: when several species colonize the same environmental gradient

Genomic signatures associated with population divergence, speciation and the evolutionary mechanisms responsible for these are key research topics in evolutionary biology. Evolutionary radiations and parallel evolution have offered opportunities to study the role of the environment by providing replicates of ecologically driven speciation. Here, we apply an extension of the parallel evolution framework to study replicates of ecological speciation where multiple species went through a process of population divergence during the colonization of a common environmental gradient. We used the conditions offered by the North Sea - Baltic Sea environmental transition zone and found clear evidence of population structure linked to the Baltic Sea salinity gradient in four flatfish species. We found highly heterogeneous signatures of population divergence within and between species, and no evidence of parallel genomic architecture across species associated with the divergence. Analyses of demographic history suggest that Baltic Sea lineages are older than the age of the Baltic Sea itself. In most cases, divergence appears to involve reticulated demography through secondary contact, and our analyses revealed that genomic patterns of divergence were likely the result of a combination of effects from past isolation and subsequent adaptation to a new environment. In one case, we identified two large structural variants associated with the environmental gradient, where populations were inferred to have diverged in the presence of gene flow. Our results highlight the heterogeneous genomic effects associated with complex interplays of evolutionary forces, and stress the importance of genomic background for studies of parallel evolution.

evolutionary biology↗

bioRxiv2019

Evolution at two-time frames shape structural variants and population structure of European plaice (Pleuronectes platessa)

Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ancient alleles that in time become associated with novel environmental gradients. The European plaice (Pleuronectes platessa) is a marine flatfish showing large allele frequency differences at two putative SVs associated with environmental variation. In this study, we explored the contribution of these SVs to population structure across the North East Atlantic. We compared genome wide population structure using sets of RAD sequencing SNPs with the spatial structure of the SVs. We found that in contrast to the rest of the genome, the SVs were only weakly associated with an isolation-by-distance pattern. Indeed, both SVs showed important allele frequency differences associated with two different environmental gradients, with the same allele increasing both along the salinity gradient of the Baltic Sea, and the latitudinal gradient along the Norwegian coast. Nevertheless, both SVs were found to be polymorphic across most sampling sites, even in the Icelandic population inferred to originate from a different glacial refuge than the remaining populations from the European continental shelf. Phylogenetic analyses suggested that the SV alleles are much older than the age of the Baltic Sea itself. These results suggest that the SVs are older than the age of the environmental gradients with which they currently co-vary. Interestingly, both SVs shared similar phylogenetic and genetic diversity, suggesting that they have a common origin. Altogether, our results suggest that the plaice SVs were shaped by evolutionary processes occurring at two time-frames, firstly following their common origin and secondly related to their current association with more recent environmental gradients such as those found in the North Sea - Baltic Sea transition zone.

evolutionary biology↗

bioRxiv2019

Fine scale population structure linked to neutral divergence in the common sole (Solea solea), a marine fish with high dispersal capacity

The Baltic Sea provides a classical example of how an environmental gradient is associated with the distribution of marine species. Here, numerous genetic studies have revealed clear patterns of population structuring linked to the physical features of the gradient itself. Nevertheless, it remains difficult to distinguish clearly between the different micro-evolutionary processes that shape these structured populations in situ. The common sole (Solea solea) is a benthic flatfish that rarely occurs within the Baltic Sea, but that exhibits a clear genetic break between populations from the North Sea - Baltic Sea transition zone and the remainder of the Atlantic Ocean. Here, we aim to evaluate the extent to which natural selection is involved in the observed patterns of divergence of sole populations occurring in the transition zone by comparing them with population structures of other flatfish species that have successfully colonized the Baltic Sea. By using several thousand of ddRAD-derived SNPs, we identified a fine-scale pattern of isolation-by-distance (IBD) of sole populations in the region. However, despite strong biological similarities among the flatfishes compared here, the sole IBD was, by far, the lowest detected across the transition zone. While selection was inferred to strongly influence all other flatfishes evolutionary histories, the analytical inference on the sole demographic history suggests that this fine-scale IBD is mainly maintained by neutral processes due to low effective population size of sole in the transition zone and asymmetrical gene flow. Our work contributes to a growing body of evidence suggesting that the strength of the different micro-evolutionary processes is species-specific, even when species occur in the same environment.

evolutionary biology↗