Thomas Lenormand

Centre d'Écologie Fonctionnelle et Évolutive, French National Centre for Scientific Research | CEFE · Department of Evolutionary Ecology

Three major empirical patterns involving sex chromosomes have been observed in higher eukaryotes: Y (or W) chromosomes are often non-recombining and degenerate; when two species hybridize, but one sex is sterile or inviable among hybrid offspring, it is most often the heterogametic sex (XY or ZW)-the so-called Haldane's rule; and the X (or Z) plays...

Homologous recombination plays a fundamental role in the evolution of organisms. It serves as a DNA repair mechanism which, in sexual organisms, contributes to genetic diversity through the shuffling of alleles during meiosis. Here we investigate the two functions of homologous recombination in the bdelloid rotifer Adineta vaga, an ancient asexual...

How social organisation (number of queens and mating partners) and reproductive system (use of thelytoky vs sex) evolved in ants and how they interplay is still far from clear. The Cataglyphis desert ants represent a fascinating group as it harbours variation in both levels of polyandry and the use of thelytoky, with polyandry and sexual reproducti...

Obligate parthenogenesis (OP) is often thought to evolve by disruption of reductional meiosis and suppression of crossover recombination. In the crustacean Daphnia pulex, OP lineages, which have evolved from cyclical parthenogenetic (CP) ancestors, occasionally produce males that are capable of reductional meiosis. Here, by constructing high-densit...

How social organisation (number of queens and mating partners) and reproductive systems (use of thelytoky vs sex) evolved in ants and how they interplay is still far from clear. The Cataglyphis desert ants represent a fascinating group as it harbours variation in both levels of polyandry and the use of thelytoky, with polyandry and sexual reproduct...

Y and W chromosomes often stop recombining and degenerate. Different theories have been proposed to explain these observations. The classic theory supposes that recombination arrest is favored because it allows to permanently link sex-antagonistic alleles to the sex in which they are favorable. The regulatory theory supposes that recombination arre...

Local adaptation is pervasive. It occurs whenever selection favors different phenotypes in different environments, provided that there is genetic variation for the corresponding traits and that the effect of selection is greater than the effect of drift and migration. In many cases, ecologically relevant traits are quantitative and controlled by ma...

In some asexual species, parthenogenetic females occasionally produce males, which may strongly affect the evolution and maintenance of asexuality if they cross with related sexuals and transmit genes causing asexuality to their offspring ("contagious parthenogenesis"). How these males arise in the first place has remained enigmatic, especially in...

Local adaptation is pervasive. It occurs whenever selection favors different phenotypes in different environments, provided that there is genetic variation for the corresponding traits and that the effect of selection is greater than the effect of drift and migration. In many cases, ecologically relevant traits are quantitative and controlled by ma...

The climate is currently warming fast, threatening biodiversity all over the globe. Populations often adapt rapidly to environmental change, but for climate warming very little evidence is available. Here, we investigate the pattern of adaptation to an extreme +10°C climate change in the wild, following the introduction of brine shrimp Artemia fran...

In some asexual species, parthenogenetic females occasionally produce males, which may strongly affect the evolution and maintenance of asexuality if they cross with related sexuals and transmit genes causing asexuality to their offspring ('contagious parthenogenesis'). How these males arise in the first place has remained enigmatic, especially in...

Determining how and how often asexual lineages emerge within sexual species is central to our understanding of sex-asex transitions and the long-term maintenance of sex. Asexuality can arise “by transmission” from an existing asexual lineage to a new one, through different types of crosses. The occurrence of these crosses, cryptic sex, variation in...

In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or...

Current theory proposes that degenerated sex chromosomes-such as the mammalian Y-evolve through three steps: (i) recombination arrest, linking male-beneficial alleles to the Y chromosome; (ii) Y degeneration, resulting from the inefficacy of selection in the absence of recombination; and (iii) dosage compensation, correcting the resulting low expre...

It is often assumed that obligate parthenogenesis (OP) evolves by a disruption of meiosis and recombination. One emblematic example that appears to support this view is the crustacean Daphnia pulex . Here, by constructing high-density linkage maps, we estimate genome-wide recombination rates in males that are occasionally produced by OP lineages, a...

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-...

The Metabolic Scaling Theory (MST), hypothesizes limitations of resource-transport networks in organisms and predicts their optimization into fractal-like structures. As a result, the relationship between population growth rate and body size should follow a cross-species universal quarter-power scaling. However, the universality of metabolic scalin...

Determining how and how often asexual lineages emerge within sexual species is central to our understanding of sex-asex transitions and the long-term maintenance of sex. Asexuality can arise "by transmission" from an existing asexual lineage to a new one, through different types of crosses. The occurrence of these crosses, cryptic sex, variation in...

Current theory proposes degenerated sex chromosomes evolve via three successive steps: recombination arrest, which links male-beneficial alleles to the Y chromosome; degeneration of these regions due to the inefficacy of natural selection in the absence of recombination; and lastly, the evolution of dosage compensation to correct the resulting low...

The maintenance of sex is paradoxical as sexual species pay the “twofold cost of males” and should thus quickly be replaced by asexual mutants reproducing clonally. However, asexuals may not be strictly clonal and engage in “cryptic sex,” challenging this simple scenario. We study the cryptic sex life of the brine shrimp Artemia parthenogenetica, w...

The climate is currently warming fast, threatening biodiversity all over the globe. Adaptation is often rapid when the environment changes quickly, but for climate warming very little evidence is available. Here, we investigate the pattern of adaptation to an extreme +10°C climate change in the wild, following the introduction of brine shrimp Artem...

It is often difficult to determine why parasites do not evolve broader niches, especially when there are closely related and ecologically similar hosts available. We used an experimental evolution approach to test whether source–sink demography or trade‐offs drive specialization, and its underlying traits, in two microsporidian parasites infecting...

In many species, the Y (or W) sex chromosome is degenerate. Current theory proposes that this degeneration follows the arrest of recombination and results from the accumulation of deleterious mutations due to selective interference–the inefficacy of natural selection on non-recombining genomic regions. This theory requires very few assumptions, but...

Negative frequency‐dependent selection (NFDS) is an important mechanism for species coexistence and for the maintenance of genetic polymorphism. Long‐term coexistence nevertheless requires NFDS interactions to be resilient to further evolution of the interacting species or genotypes. For closely related genotypes, NFDS interactions have been shown...

The evolution of host specialization has been studied intensively, yet it is still often difficult to determine why parasites do not evolve broader niches - in particular when the available hosts are closely related and ecologically similar. Here, we used an experimental evolution approach to study the evolution of parasite specialization, and its...

In the study of multi-host parasites, it is often found that host species contribute asymmetrically to parasite transmission. Yet in natural populations, identifying which hosts contribute to parasite transmission and maintenance is a recurring challenge. Here, we approach this issue by taking advantage of natural variation in the composition of a...

The concept of “cost of resistance” has been very important for decades, for fundamental reasons (theory of adaptation), with a wide range of application for the genetics and genomics of resistance: resistance to antibiotics, insecticide, herbicide, fungicides; resistance to chemotherapy in cancer research; coevolution of all kinds of parasites to...

Resource allocation to offspring is the battleground for various intrafamilial conflicts. Understanding these conflicts requires knowledge of how the different actors (mother, siblings with different paternal genotypes) influence resource allocation. In angiosperms, allocation of resources to seeds happens postfertilization, and the paternally inhe...

The ecological specialization of parasites–whether they can obtain high fitness on very few or very many different host species–is a determining feature of their ecology. In order to properly assess specialization, it is imperative to measure parasite fitness across host species; to understand its origins, fitness must be decomposed into the underl...

Table S1. Host survival during the infectivity experiment. Table S2. Results of paired t‐tests comparing host growth before and after day 30 (all treatments combined). Table S3. Model comparison: link between survival and infection success. Table S4. Model comparison: link between reproduction and infection success. Figure S1. Spore production...

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology ( https://doi.org/10.24072/pci.evolbiol.100052 ). The cost of resistance, or the fitness effect of resistance mutation in absence of the drug, is a very widepsread concept in evolutionary genetics and beyond. It has represented an important addition to the sim...

Fig. S1. Selection coefficients of control lines evolved in the absence of antibiotic in competition against the non‐evolved wild‐type 10K‐YFP (or 10K‐CFP in the case of 0K‐YFP lines).

Fig. S2. Fitness change of the SRef lines during 400 generations of evolution in different evolution doses (colors) versus their fitness just after the screen of resistance in the different measure doses. Symbols indicate the gyrA mutations sequenced after evolution in each line while colors indicate the dose at which they were screened and evolved...

Fig. S3. Costs of resistance of the SRel lines evolved for 400 generations at five evolution doses of antibiotic. Symbols indicate the mutation detected in the gyrA sequence or the absence of mutation in the gyrA sequence while colors indicate the evolution dose. The dotted horizontal line at 0 corresponds to an equal fitness with the susceptible a...

A bstract The ecological specialization of parasites – whether they can obtain high fitness on very few or very many different host species – is a determining feature of their ecology. In order to properly assess specialization, it is imperative to measure parasite fitness across host species; to understand its origins, fitness must be decomposed i...

In the study of multi-host parasites, it is often found that host species contribute asymmetrically to parasite transmission, with cascading effects on parasite dynamics and overall community structure. Yet, identifying which of the host species contribute to parasite transmission and maintenance is a recurring challenge. Here, we approach this iss...

With the advent of new sequencing technologies, the evolution of gene expression is becoming a subject of intensive genomic research, with sparking debates upon the role played by these kinds of changes in adaptive evolution and speciation. In this paper, we model expression evolution in species differing by their reproductive systems. We consider...

Gynodioecy is a sexual dimorphism where females coexist with hermaphrodite individuals. In most cases, this dimorphism involves the interaction of cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Two scenarios can account for how these interactions maintain gynodioecy. Either CMS genes recurrently enter populations at low frequenc...

Antibiotic and pesticide resistance of pathogens are major and pressing worldwide issues. Resistance evolution is often considered in simplified ecological contexts: treated versus nontreated environments. In contrast, antibiotic usually present important dose gradients: from ecosystems to hospitals to polluted soils, in treated patients across tis...

In most sexual, diploid eukaryotes, at least one crossover occurs between each pair of homologous chromosomes during meiosis, presumably in order to ensure proper segregation. Well-known exceptions to this rule are species in which one sex does not recombine and specific chromosomes lacking crossover. We review other possible exceptions, including...

Resurrection Ecology (RE) is a very powerful approach to address a wide range of question in ecology and evolution. This approach rests on using appropriate model systems, and only few are known to be available. In this paper, we show that Artemia has multiple attractive features (short generation time, cyst bank and collections, well documented ph...

Gene duplications are widespread in genomes, but their role in contemporary adaptation is not fully understood. Although mostly deleterious, homogeneous duplications that associate identical repeats of a locus often increase the quantity of protein produced, which can be selected in certain environments. However, another type exists: heterogeneous...

Size is one of the most important biological traits influencing organismal ecology and evolution. However, we know little about the drivers of body size evolution in unicellulars. A long-term evolution experiment (Lenski's LTEE) in which Escherichia coli adapts to a simple glucose medium has shown that not only the growth rate and the fitness of th...

Fisher's geometrical model (FGM) has been widely used to depict the fitness effects of mutations. It is a general model with few underlying assumptions that gives a large and comprehensive view of adaptive processes. It is thus attractive in several situations, e.g. adaptation to antibiotics, but comes with limitations, so that more mechanistic app...

Quantifying links between ecological processes and adaptation dynamics in natura remains a crucial challenge. Many studies have documented the strength, form and direction of selection, and its variations in space and time, but only a few managed to link these variations to their proximal causes. This step is, however, crucial, if we are to underst...

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often ‘weird’ features. We discuss the origin of meios...

Stressful environments affect life‐history components of fitness through (i) instantaneous detrimental effects, (ii) historical (carry‐over) effects and (iii) history‐by‐environment interactions, including acclimation effects. The relative contributions of these different responses to environmental stress are likely to change along life, but such o...

Sex allocation theory is often hailed as the most successful area of evolutionary theory due to its striking success as a predictor of empirical observations [1]. Most naturally occurring sex ratios can be explained by the principle of equal investment in the sexes [2-4] or by cases of "extraordinary" sex allocation [5]. Deviations from the expecte...

Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often “weird” features. We discuss the origin of meios...

Parasites and pollutants can both affect any living organism, and their interactions can be very important. To date, repeated studies have found that parasites and heavy metals or metalloids both have important negative effects on the health of animals, often in a synergistic manner. Here, we show for the first time that parasites can increase host...

How species coexist is a central question in ecology. Niche differentiation can prevent two species from excluding each other by competition. However, this interaction can vary in space because of internal factors such as intraspecific genetic variation, or external ones such as the presence of a third species. While these effects have been repeate...

Potential for evolutionary responses to climate change - Evidence from tree populations

Sexual reproduction leads to an alternation between hap-loid and diploid phases, whose relative length varies widely across taxa. Previous genetical models showed that diploid or haploid life cycles may be favored, depending on dominance interactions and on effective recombination rates. By contrast, niche differentiation between haploids and diplo...

Much of our knowledge of the fitness effects of new mutations has been gained from mutation accumulation (MA) experiments. Yet the fitness effect of single mutations is rarely measured in MA experiments. This raises several issues, notably for inferring epistasis for fitness. The acceleration of fitness decline in MA lines has been taken as evidenc...

Evidence is mounting that the evolution of gene expression plays a major role in adaptation and speciation. Understanding the evolution of gene regulatory regions is indeed an essential step in linking genotypes and phenotypes and in understanding the molecular mechanisms underlying evolutionary change. The common view is that expression traits (pr...

Symbiosis generally causes an expansion of the niche of each partner along the axis for which a service is mutually provided. However, for other axes, the niche can be restricted to the intersection of each partner’s niche and can thus be constrained rather than expanded by mutualism.We explore this phenomenon using Artemia as a model system. This...

Parthenogenesis (reproduction through unfertilized eggs) encompasses a variety of reproduction modes with (automixis) or without (apomixis) meiosis. Different modes of automixis have very different genetic and evolutionary consequences but can be particularly difficult to tease apart. In this paper, we propose a new method to discriminate different...

The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species' ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from paren...

When are mutations beneficial in one environment and deleterious in another? More generally, what is the relationship between mutation effects across environments? These questions are crucial to predict adaptation in heterogeneous conditions in a broad sense. Empirical evidence documents various patterns of fitness effects across environments but w...

Gene duplications have long been advocated to contribute to the evolution of new functions. The role of selection in their early spread is more controversial. Unless duplications are favored for a direct benefit of increased expression, they are likely detrimental. In this paper, we investigated the case of duplications favored because they combine...

Abrupt environmental changes are of particular interest to understand how species can quickly evolve at the boundary of their current niche. In particular the 'sliding niche' model, wherein a niche shifts globally toward the new condition, has been utilized in understanding and modeling this process. Here, we investigate the dynamics of relative fi...

Niche dimensionality is suggested to be a key determinant of ecological speciation ('multifarious selection' hypothesis), but genetic aspects of this process have not been investigated theoretically. We use Fisher's geometrical model to study how niche dimensionality influences the mean fitness of hybrids formed upon secondary contact between popul...