Nathanaëlle Saclier

GC-biased gene conversion (gBGC) is a widespread recombination-associated process that favours the fixation of GC alleles independently of their fitness. In coding regions, it can oppose purifying selection and favour the accumulation of deleterious AT to GC mutations.In mammals where recombination hotspots are predominantly determined by PRDM9, the deleterious effect of gBGC is expected to be episodic due to the rapid turnover of hotspots. The deleterious impact of gBGC episodes on proteins has been well documented, particularly in rodents and primates. However, the evolutionary response of the affected proteins after the episodes end has been scarcely investigated. Theory predicts that a decline in gBGC intensity should trigger a compensatory response that enables previous damage to be repaired. Recently, we reported evidence for pervasive compensatory evolution following gBGC episodes in Hydromyini rodents. Here, we aimed to investigate whether this post-gBGC compensation is widespread among mammals in which gBGC is episodic. Using a phylogenetic approach, we analysed substitution patterns in coding exons from five mammalian taxa spanning a range of effective population size (Ne): Murini , Rattini , Cetacea , Cercopithecidae and Hominoidae . We detected thousands of gBGC episodes, characterised by an increased rate of non-synonymous AT to GC substitutions.We found evidence for compensatory evolution in non-primate taxa, and a lack of signal in Primates. Although the influence of Ne remains unclear, our study highlights both the evolutionary significance of post-gBGC compensation and the methodological challenges in detecting it.

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction—for example, parthenogens with rare sex or species where the paternal genome is set aside—have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly “genetically useless,” males.

Background: Skeletal mineralisation, achieved through the controlled precipitation of calcium phosphate, represents a major evolutionary innovation in early vertebrates. While this process has been extensively studied in bony species, it remains poorly understood in cartilaginous fishes, which lack endochondral bone. In this study, the small-spotted catshark ( Scyliorhinus canicula ) was used as a model to investigate the genetic basis of cartilage differentiation and subsequent mineralisation. Results: Two stages in late embryogenesis were examined: one preceding and one following the onset of vertebral mineralisation. Using a bulk RNA sequencing approach, we identified a set of genes characterising the early differentiation of chondrocytes and cartilage synthesis, shared among jawed vertebrates. Strikingly, only a very limited number of genes previously identified in mammalian skeletogenesis showed upregulated expression in the catshark mineralising chondrocytes. Among these, particular attention was given to the spp2 (secreted phosphoprotein 2) gene family. Unlike in bony vertebrates, where spp2 exists as a single and rather little-studied gene, cartilaginous fishes possess multiple gene duplicates with contrasted sites of expression. Through phylogenetic analyses and gene expression studies in the catshark, we showed how, despite the presence of shared molecular components likely inherited from their last jawed vertebrate ancestor, cartilaginous and bony fishes have independently evolved distinct cartilage mineralisation strategies. Conclusions: This work highlights the diversity of skeletal development mechanisms and underscores the importance of cartilaginous fishes in broadening our understanding of how vertebrate mineralisation evolved. By contrasting conserved and lineage-specific features, the study provides new insights into the independent trajectories that shaped the skeletal structures of modern vertebrates.

La vitesse à laquelle les séquences d’ADN évoluent varie selon les espèces. Ces différences peuvent venir de caractéristiques intrinsèques de l’espèce (taux métabolique, traits d’histoire de vie) ou de son environnement (rayonnements ionisants). L’objectif de cette thèse est de tester les principales hypothèses expliquant les variations de taux d’évolution moléculaire entre les espèces. Pour cela, les particularités des Asellidae souterrains ont été couplées avec des données de séquençage nouvelle génération dans le génome nucléaire et le génome mitochondrial. L’utilisation des Asellidae comme modèle biologique nous permet d’avoir, au sein du même groupe, des espèces ayant indépendamment effectuées une transition vers le milieu souterrain. Cette transition étant accompagnée de nombreux changements, tant biologiques (longévité, taux métabolique, temps de génération) qu’environnementaux, elle nous permet, au sein du même groupe, de pouvoir comparer des espèces contrastées en termes de longévité, de taille de populations, de rayonnements ionisants ou encore de productivité et de température. De plus, parce que ces organismes dispersent peu, ils persistent dans le même environnement durant de nombreuses générations, permettant de préciser et de quantifier les facteurs responsables de variations du taux d’évolution moléculaire entre les espèces.Cette approche nous a permis de mettre en évidence un effet du temps de génération sur le taux d’évolution du génome nucléaire mais pas sur le génome mitochondrial. Un effet de la radioactivité naturelle, d’une ampleur analogue à celle du temps de génération a également été mis en évidence. Enfin, l’étude des variations des taux d’évolution moléculaire à une échelle globale a révélée des biais dans les calculs des taux de substitutions qui devront être pris en compte dans les études cherchant a établir le lien entre le taux de mutations et la diversification

How do sex chromosomes and modes of reproduction evolve? In nematodes, many modes of reproduction exist ('regular' sexuality, hermaphroditism, parthenogenesis), but most species have a XX/X0 system: females have two X chromosomes and males have one. In rare cases, Y chromosomes have emerged in males, but without associated changes in reproductive mode. Here we demonstrate that, in Mesorhabditis nematodes, a new Y chromosome co-emerged with an unconventional mode of reproduction called autopseudogamy. In this system, females produce clonal females plus rare (~10%) males, needed for fertilisation only. These males do not contribute to the female genome and may thus be 'genetically useless' - except for their Y. Analysing the Y chromosomes of two autopseudogamous species, we found two conserved features: i) they accumulated male-beneficial genes, and ii) they display a strong fertilisation drive, in that mainly Y-bearing sperm fertilise female oocytes. Both features are, evolutionarily speaking, favourable in the context of autopseudogamy, making the Y chromosome a possible stabilisor of this mode of reproduction.

GC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favors the accumulation of deleterious AT to GC substitutions in proteins, moving them away from their fitness optimum. In many mammals, recombination hotspots have a rapid turnover, leading to episodic gBGC, with the accumulation of deleterious mutations stopping when the recombination hotspot dies. Selection is therefore expected to act to repair the damage caused by gBGC episodes through compensatory evolution. However, this process has never been studied or quantified so far. Here, we analyzed the nucleotide substitution pattern in coding sequences of a highly diversified group of Murinae rodents. Using phylogenetic analyses of about 70,000 coding exons, we identified numerous exon-specific, lineage-specific gBGC episodes, characterized by a clustering of synonymous AT to GC substitutions and by an increasing rate of nonsynonymous AT to GC substitutions, many of which are potentially deleterious. Analyzing the molecular evolution of the affected exons in downstream lineages, we found evidence for pervasive compensatory evolution after deleterious gBGC episodes. Compensation appears to occur rapidly after the end of the episode and to be driven by the standing genetic variation rather than new mutations. Our results demonstrate the impact of gBGC on the evolution of amino-acid sequences and underline the key role of epistasis in protein adaptation. This study contributes to a growing body of literature emphasizing that adaptive mutations, which arise in response to environmental changes, are just 1 subset of beneficial mutations, alongside mutations resulting from oscillations around the fitness optimum.

Problematic taxa, often referred to as species complexes, are common among freshwater organisms. Understanding their species composition, distribution and history is key to integrating these taxa into many ecological disciplines. We investigated the taxonomy and biogeography of the Proasellus coxalis species complex (PCC), a diversified and functionally important group of asellid isopods (Pancrustacea) in freshwaters of the Mediterranean Basin and central Europe. We used phylogenetic and phylogeographic analyses from specimens collected at 143 localities across the range of the PCC to document its diversity, phylogenetic position and historical biogeography. First, we used molecular species delimitation methods based on the mitochondrial cytochrome oxidase subunit I (COI) gene to identify molecular operational taxonomic units (MOTUs) representing putative species within that complex. Second, we used three additional genes—the 16S mitochondrial rDNA, FASTKD4 nuclear and 28S nuclear rDNA genes—to generate a four‐gene dated phylogeny of Asellidae to test the monophyly and phylogenetic position of the PCC. Third, we applied statistical ancestral reconstruction methods to the four‐gene dated phylogeny of the PCC to infer its biogeographic history. Fourth, we used Bayesian phylogeographic diffusion models based on the COI and 16S genes to reconstruct the range dynamics of the only widely distributed MOTU in this species complex. We identified ≥ 25 MOTUs within the PCC. The eastern Mediterranean Basin, including the Pontic‐Mediterranean and Italian peninsulas, contained numerous narrowly distributed MOTUs. In contrast, central Europe, northern Italy, the Dinarides, the Iberian peninsula and northwestern Africa were colonised by a single MOTU, which we term P. banyulensis. The four‐gene phylogeny of the Asellidae clustered all PCC MOTUs into a well‐supported monophyletic group, which we term the P. coxalis clade. Ancestral reconstruction methods indicated that the clade originated during the early Miocene in the southern Hellenides, at that time part of the Balkanian‐Anatolian landmass. From there, it dispersed and diverged mainly during the Miocene, through the eastern Mediterranean Basin, including the Italian peninsula. Bayesian phylogeographic diffusion models revealed that central Europe and the western Mediterranean Basin were recently colonised from Italian populations of P. banyulensis. During the Pleistocene, multiple waves of colonisation of that species followed each other from central Italy, the most northerly (Germany, Sweden) and southerly (southern Spain, Morocco and Algeria) regions being colonised last. We resolved major taxonomic, phylogenetic and biogeographic uncertainties that have marked more than a century of research on the PCC. Our updated understanding of this complex is that of a species‐rich clade that has long diversified in the eastern Mediterranean Basin, but of which a single species—P. banyulensis—has recently colonised central Europe and the western Mediterranean Basin from Italian refugia. In central Europe, this species adds to two other widespread species—Asellus aquaticus from Pannonian refugia and P. meridianus, most probably from Iberian refugia—to produce mixed asellid communities.

Inducible defences in response to predation risk are a well-known example of adaptive phenotypic plasticity. Although inducible defences have been studied mainly within a generation (within-generational plasticity), there is now clear evidence that ancestral exposure to predation risk can influence the defences expressed by offspring, even if they have not been exposed themselves (transgenerational plasticity). The molecular mechanisms allowing the transmission of environmental information across generations are not well understood. In this study, we combined measures of antipredator responses (behavioural and morphological) with transcriptomic investigations across two generations in the freshwater snail Physa acuta. We hypothesised that both within- and transgenerational plasticity would induce phenotypic changes associated with differential gene expression. Our results confirmed within- and transgenerational plasticity: F1 snails respond to predator-cue exposure by increasing escape behaviour, reducing shell length, and developing thicker and slenderer shells, whereas F2 snails from exposed parents have longer and thicker shells with narrower apertures. Within- and transgenerational plasticity were accompanied by the differential expression of 112 genes (101 up- and 11 downregulated) and 23 differentially expressed genes (17 up- and 6 downregulated), respectively. Within- and transgenerational plasticity did not share common differentially expressed genes, but the associated molecular functions, involving metabolism and transcription regulation, were similar. These results suggest that predator-induced within-generational plasticity and transgenerational plasticity may result from different genomic pathways and may evolve independently.

GC-biased gene conversion (gBGC) is a widespread evolutionary force associated with meiotic recombination that favours the accumulation of deleterious AT to GC substitutions in proteins, moving them away from their fitness optimum. In many mammals recombination hotspots have a rapid turnover, leading to episodic gBGC, with the accumulation of deleterious mutations stopping when the recombination hotspot dies. Selection is therefore expected to act to repair the damage caused by gBGC episodes through compensatory evolution. However, this process has never been studied or quantified so far. Here, we analysed the nucleotide substitution pattern in coding sequences of a highly diversified group of Murinae rodents. Using phylogenetic analyses of about 70,000 coding exons, we identified numerous exon-specific, lineage-specific gBGC episodes, characterised by a clustering of synonymous AT to GC substitutions and by an increasing rate of non-synonymous AT to GC substitutions, many of which are potentially deleterious. Analysing the molecular evolution of the affected exons in downstream lineages, we found evidence for pervasive compensatory evolution after deleterious gBGC episodes. Compensation appears to occur rapidly after the end of the episode, and to be driven by the standing genetic variation rather than new mutations. Our results demonstrate the impact of gBGC on the evolution of amino-acid sequences, and underline the key role of epistasis in protein adaptation. This study contributes to a growing body of literature emphasizing that adaptive mutations, which arise in response to environmental changes, are just one subset of beneficial mutations, alongside mutations resulting from oscillations around the fitness optimum.

Inducible defences in response to predation risk are a well-known example of adaptive phenotypic plasticity. Although inducible defences have been studied mainly within a generation (within-generational plasticity), there is now clear evidence that ancestral exposure to predation risk can influence the defences expressed by offspring, even if they have not been exposed themselves (transgenerational plasticity). The molecular mechanisms allowing the transmission of environmental information across generations are not well understood. In this study, we combined measures of antipredator responses (behavioural and morphological) with transcriptomic investigations across two generations in the freshwater snail Physa acuta . We hypothesised that both within- and transgenerational plasticity would induce phenotypic changes associated with differential gene expression. Our results confirmed within- and transgenerational plasticity: F1 snails respond to predator-cue exposure by increasing escape behaviour, reducing shell length, and developing thicker and slenderer shells, whereas F2 snails from exposed parents have longer and thicker shells with narrower apertures. Within- and transgenerational plasticity were accompanied by the differential expression of 112 genes (101 up- and 11 downregulated) and 23 differentially expressed genes (17 up- and 6 downregulated), respectively. Within- and transgenerational plasticity did not share common differentially expressed genes, but the associated molecular functions, involving metabolism and transcription regulation, were similar. These results suggest that predator-induced within-generational plasticity and transgenerational plasticity may result from different genomic pathways and may evolve independently.